A-IMBN RESEARCH

Research Highlights Collection 2010

SUPPORTED BY
Editorial Board
Ken-ichi Arai University of Tokyo, Japan
Yoshito Kaziro Kyoto University Graduate School of Medicine, Japan
Peng Li Tsinghua University, China
John Mattick Institute for Molecular Bioscience,
University of Queensland, Australia
Amit Sharma International Centre for Genetic Engineering and
Biotechnology, India
James Shen Academia Sinica, Taiwan
Chris Tan Institute of Molecuar and Cell Biology, Singapore
Jeongbin Yim Seoul National University, Korea

Advisory Board
Shigetaka Asano Department of Chemistry and Biochemistry,
Waseda University, Japan
Virander Chauhan ICGEB New Delhi, India
Pham Thi Tran Chau Protein-Enzyme Laboratory,
Vietnam National University, Vietnam
Robert Gallo Institute of Human Virology, USA
Frank Gannon Queensland Institute of Medical Research, Australia
Benjamin Geiger Weizmann Institute of Science, Israel
Yoram Groner Weizmann Institute of Science, Israel
Yi Guan Department of Microbiology,
University of Hong Kong, China
Wanjin Hong Institute of Molecular and Cell Biology, Singapore
Robert Huber Max-Planck-Institut für Biochemie, Germany
Joh-E Ikeda Department of Molecular Life Sciences,
Tokai University School of Medicine, Japan
Nancy Ip School of Science, Hong Kong University of Science
& Technology, China
Yoshiaki Ito Department of Medicine,
National University of Singapore, Singapore
Kanyawim Kirtikara National Center for Genetic Engineering and
Biotechnology, Thailand
Kiyoshi Kita School of International Health/Global Health
Sciences, University of Tokyo, Japan
Kiyoshi Kurokawa National Graduate Institute for Policy Studies, Japan
Michael Lai Academia Sinica, Taiwan
Kong Peng Lam Institute of Molecular and Cell Biology, Singapore
Yong Jun Liu MD Anderson, USA
Peter Lobie Liggins Institute, New Zealand
Nor Muhammad Mahadi Malaysia Genome Institute, Malaysia
Barry Marshall University of Western Australia, Australia
Atsushi Miyajima Institute of Molecular and Cellular Biosciences,
University of Tokyo, Japan
Yoshikazu Nakamura Institute of Medical Science, University of Tokyo, Japan
Yusuke Nakamura Institute of Medical Science, University of Tokyo, Japan
Filipinas Natividad St Luke's Medical Center, Philippines
Nicos Nicola Walter and Eliza Hall Institute, Australia
Rofina Yasmin Othman University of Malaya, Malaysia
Gang Pei Shanghai Institute for Biological Sciences,
Institute of Biochemistry and Cell Biology, China
Sang Ki Rhee College of Medical Sciences,
Soon Chun Hyang University, Korea
Yijun Ruan Genome Institute of Singapore, A*STAR, Singapore
Jeongsun Seo College of Medicine, Seoul National University, Korea
Jinho Seo Department of Agricultural Biotechnology,
Seoul National University, Korea
Rho Hyun Seong College of Biological Sciences,
Seoul National University, Korea
Hee-Sup Shin Korea Institute of Science and Technology, Korea
Obaid Siddiqi National Centre for Biological Sciences, India
Richard Simpson Ludwig Institute for Cancer Research, Australia
Jisnuson Svasti Mahidol University, Thailand
Axel Ullrich Max-Planck-Institut für Biochemie, Germany
Andrew Wang Academia Sinica, Taiwan
Sumiko Watanabe Institute of Medical Science, University of Tokyo, Japan
John Wong National University Health System, Singapore
Zhi-cheng Xiao Innovative Research, GSK, China
Ook Joon Yoo Korea Advanced Institute of Science and
Technology, Korea

A-IMBN RESEARCH
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updated every two weeks with concise, high-
quality research highlights of papers published
by Asia-Pacific-based researchers in molecular
biology in leading international research journals.
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A-IMBN EDITORIAL
Asia Pacific International Molecular Biology
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Seoul National University
Bio-MAX Institute
BK3 Grad School Research Bldg (220) 6F
Seoul, Korea
Editor-in-Chief Jeongbin Yim
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Managing Editor Kevin Yoon
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Table of Contents
Cell biology
06 A T-ALL tale
6 Divide and conquer
07 Better feed at lower cost
7 Nutrition makes the cell cycle
08
go round
Confining cancer
8 Following new instructions
09 Stem cell short-cuts
9 Stem cells on steroids
10 When the time is right
10 Seeing i-to-I
11
11
Cell-cycle blockers
Fitting the profile
12 Lipids trapped within a SNARE
12 The acid advantage
13 Tracking cellular hunger pangs
13 Reciprocal connections
14 Profiling cell death perpetrators
14 The missing link
15 Pinpointing a missing link
15 Maintaining stem cell identity
16 AIDing our understanding of cancer
16 Identifying a cancer-spreading culprit
17 The accomplice to viral entry
17 Route of entry
18
18
Dissecting cellular crisis management
Front-line healer
Genetics
20 Knockout resource for yeast biologists
20 Looking out for number one
21 Exploring the genetic ‘generation gap’
21 Evolution through 40,000 generations
; ISTOCKPHOTO/Sebastian Kaulitzki; ISTOCKPHOTO/Martin McCa
Henrik Jonsson rthy; ISTOC
TOCKPHOTO/ KPHOTO/
ulitzki; IS Henrik
TO/Seb astian Ka Jonsso
© ISTO CKPHO n
40 Stopping the cancer spreading
40 Binding and gagging tumors
22 Thank you for not smoking 41 Tying up loose ends
22 Lung cancer link 41 Putting injured cells to sleep
23 Extremophiles: Cold complexity 42 Compatible partners
23
24
Mountains that make the people
Combining forces to combat cancer
42
43
All mixed up
Cellular stress protection
24 Filling the gaps of a genome map 43 Tracking transcriptional traffic
25 Pinpointing inflammatory 44 Unraveling the roles of
genomic changes multi-tasking enzymes
25 Keeping track of changes 44 Working with a silent partner
26 Pinpointing genetic susceptibility 45 Spotlighting single DNA molecules
to Parkinson’s disease 45 Making the right connections
26 Asian genomes point the way 46 Bacterial chaperonin
27 Different strokes, different genes — a trick of the tail
27 Casting wide yields aneurysm suspects
28
28
Plant fungi’s jump on pathogenicity
Sprouting information
Immunology
29 Transcending ethnic differences & Therapeutics
29 Linking more suspects to bowel disease
30 Getting at the roots of cancer risk 48 Taking a shot at pandemic flu
30 Diversity in the genome 48 Last line of defense
49 Curtailing cholera
Neuroscience & 49 Slow and steady
50 Fighting the flu virus
Developmental Biology 50 Flu fighter
51 The good without the bad
32 Muscling in on receptor clusters 51 Poisoning the well of cancer
32 A model of dementia 52 Collaborating with the enemy
33 Benefitting from mixed messages 52 Dialing up diabetes
33 Sniffing out the olfactory code 53 Unmasking bacterial saboteurs
34 Shaping blood vessel formation 53 Pathways of presentation
34 Accelerating synapse formation 54 Unlikely allies against infection
35 Keeping genes in their place 54 Infection-proofing by the gut
35 First instructions for male mice 55 When antibiotics backfire
36 A green light for growth 55 Fate director
56 Immune response linked to
Structural & early arrival
56 Building a better booster
Molecular biology 57 Single protein seeks mature partner
57 Protective markings
38 Getting in the blood
38 Making the cut
39 Maintaining the silence
39 Amplifying the silence
A-IMBN RESEARCH
Research Highlight Collection 2010
INTRODUCTION | A-IMBN RESEARCH

Welcome to the
A-IMBN Research Collection 2010

W e at NPG Nature Asia-Pacific in partnership with the Asia-Pacific

International Molecular Biology Network (A-IMBN) are delighted to
present this collection of research highlights published on the A-IMBN Research
website in 2010. A-IMBN Research covers some of the best research in molecular
biology and biotechnology from the Asia-Pacific region, and the ever-expanding
showcase of high-quality research that can be found on the website is a testament
to the growing strength of life science research in this part of the world. The
website provides a remarkable overview of the efforts being made by the top
scientists in the region and draws attention to many of the key Asia-Pacific
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NPG Nature Asia-Pacific would like to take this opportunity to thank the
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Network Asia (LSNA) supported by the Japanese government.

The research highlights presented in this collection are only a snapshot of what is
being published on the website every month. To read the very latest highlights of
top research published by Asia-Pacific scientists in the best international journals,
be sure to visit the A-IMBN Research website (www.natureasia.com/A-IMBN).
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David Swinbanks, PhD

Managing Director Asia and Australasia
& Medical and Scientific Communications
Nature Publishing Group

2 www.natureasia.com/A-IMBN
 A-IMBN RESEARCH | INTRODUCTION

I have great pride in welcoming you to this, the latest collection of research
highlights from A-IMBN Research, the web-based journal of the Asia-
Pacific International Molecular Biology Network (A-IMBN).

Since its founding in 1997, the mission of the A-IMBN has been to raise the
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Modern molecular, cell and computational biology along with bioinformatics

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A-IMBN Research is only made possible by the financial support of sponsors

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Research an effective means of introducing their research activities to the global
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Professor, Seoul National University
President, A-IMBN

RESEARCH HIGHLIGHT COLLECTION 2010 3

 Gold sponsor
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Sponsor Information Institute of Medical Science, The University of Tokyo
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Silver sponsors
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Biology Network (A-IMBN)
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© ISTOCKPHOTO/Sebastian Kaulitzki

Cell Biology
CELL BIOLOGY | A-IMBN RESEARCH
© ISTOCKPHOTO/ERAXION
Published in Proceedings of the National Academy of Sciences USA
Divide and conquer
Insights provided by a gene expression signature
signal the effects of a gene mutation on breast
cancer prognosis
Understanding how breast cancers
differ from each other at the mo-
lecular level can allow for targeted
therapy against these molecules and
lead to greater success at fighting the
cancer. Now, an international team
of researchers has identified a gene
expression profile in breast cancer
samples from human patients that
can flag whether the tumors contain
a mutation in the cell signaling
gene PIK3CA.
In cancer patients whose tumor
expressed the estrogen receptor
protein, the gene signature also
could identify patients who were
likely to have a better outcome. This
association of the mutant PIK3CA
gene expression profile with good
outcome was surprising, according
to lead author Sherene Loi from the
Peter MacCallum Cancer Centre,
Australia, because these mutations
6 www.natureasia.com/A-IMBN
Published in Science
A T-ALL tale
Cell fate mapping and genetic analysis reveals how a
T cell cancer-causing gene gives rise to leukemia
T cell acute lymphoblastic leukemia
(T-ALL) is marked by hyperprolifera-
tion of T cells in the blood system and
if left untreated results in rapid death.
The hyperproliferating T cells, which
are thought to induce tumor forma-
tion. However, the researchers found
that the mutant gene signature
actually demonstrated very low
activation of downstream signaling.
This means that drugs that are being
developed to block this signaling
cascade are unlikely to work in
patients with the mutant PIK3CA
gene expression profile.
While the mechanisms that
mediate the effects of the mutations
on tumor outcome remain to be de-
termined, parsing out the differences
in signaling between breast cancer
subtypes could pave the way for
therapy tailored for each individual
breast cancer patient in the future.
Loi, S. et al. PIK3CA mutations associated with
gene signature of low mTORC1 signaling and
better outcomes in estrogen receptor-positive
breast cancer. Proceedings of the National Academy of
Sciences USA 107, 10208–10213 (2010).
overrun normal T cells, arise from a
single leukemia-initiating cell (LIC)
that commonly harbors an activating
mutation in a cancer-causing gene
called an oncogene.
Now, Matthew McCormack from
Royal Melbourne Hospital, Australia,
and colleagues from the Walter
and Eliza Hall Institute of Medical
Research and other institutions in
Australia and the UK have provided
mechanistic insights on how the
activation of the oncogene Lmo2 — an
important transcription factor in blood
cell development — leads to T-ALL.
After genetically labeling cells in a
mouse model of T-ALL, the research-
ers found that the LIC appeared in the
thymus, the source of T cells, months
before the onset of disease. This indi-
cates that Lmo2 activation alone does
not cause leukemia per se. Rather, they
found that Lmo2 inhibits T cell matu-
ration while also initiating a genetic
program that induces a stem cell-like
behavior. Hence, the LIC undergoes
continuous self-renewal, which allows
secondary mutations to accumulate
that in turn cause T-ALL.
These new insights may lead to
therapeutics that target the LIC rather
than just the hyperproliferating leuke-
mia cells, thus preventing the relapse
that often occurs in the clinic.
McCormack, M. P. et al. The Lmo2 oncogene initiates
leukemia in mice by inducing thymocyte self-renewal.
Science 327, 879–883 (2010).

Published in FEMS Microbiology Letters
Better feed at lower cost
A yeast supplement that exploits a cell-surface
enzyme could provide a more cost-effective method for
producing animal feed
Genetically engineered yeast cells that
release nutrients from plant-based
foods could be used to produce
cheap and highly nutritious animal
feed, researchers at the National
Center for Genetic Engineering and
Biotechnology have shown.
Inorganic phosphorous in plant-
based feedstuff is stored largely in the
form of phytic acid. Most animals
cannot absorb this, so feed is normally
treated with phytase, an enzyme that
releases the phosphorous. However,
using phytase is costly and time-
consuming, as it involves collecting and
concentrating the enzyme from the
micro-organisms that produce it.
Piyanun Harnpicharnchai and her
colleagues engineered Pichia pastoris
yeast cells that express phytase and
display it on their surface.
The researchers found that their
cell-surface enzyme was stable at high
temperatures and under acidic and
alkaline conditions. It also released
phosphorous from feedstuff as efficiently
as commercially available phytase.
When added to feed, the modified yeast
provided biotin, niacin and proteins,
increasing its nutritional value.
The researchers are currently devel-
oping yeast cells that co-display phytase
with other enzymes that are often
added to animal feed.
Yeast engineered in this way could
be used as an animal feed supplement.
As well as being cheaper to produce,
feed containing such a supplement
would require fewer ingredients
but would also be more nutritious,
Harnpicharnchai notes.
RESEARCH HIGHLIGHT COLLECTION 2010
Harnpicharnchai, P., Sornlake, W., Tang, K.,
Eurwilaichitr, L. & Tanapongpipat, S. Cell-surface
phytase on Pichia pastoris cell wall offers great potential
as a feed supplement. FEMS Microbiology Letters
302, 8–14 (2010).
Published in Proceedings of the National Academy of Sciences USA
Nutrition makes the cell cycle
go round
A landscape model shows how cells remain stable
under changing chemical conditions
Jin Wang and colleagues from the
Chinese Academy of Sciences and the
State University of New York have
developed an energy-based, three-
dimensional landscape model of the
cycle of growth, development and
reproduction in budding yeast cells.
Their work helps explain how net-
works of chemical reactions give rise
to such a stable, functioning system.
The model revealed that the
progress of yeast around the cell
cycle is driven by increasing mass
and energy through nutrition. The
researchers found that changing the
rates and numbers of chemical inter-
actions does not necessarily weaken
the stability of the cycle.
The cell cycle is generally thought
to have four phases — G1 or first
gap where the cell grows, S or
A-IMBN RESEARCH | CELL BIOLOGY
© ISTOCKPHOTO/knorre
synthesis when it duplicates its
chromosomes, G2, another growth
phase to prepare for division, and M
or mitosis when it divides.
The landscape picture, predicted
from the modeling results, develops
as the mass of an individual cell
increases. The cell moves from one
phase of the cell cycle to the next
like a ball rolling between holes or
depressions of lower energy sepa-
rated by barriers of higher energy.
Its energy pathway, as it proceeds
around the cell cycle, eventually
traces a ring. The same methods
can be applied to other complicated
networks, the researchers say.
Wang, J., Li, C. & Wang, E. Potential and flux
landscapes quantify the stability and robustness of
budding yeast cell cycle network. Proceedings of the
National Academy of Sciences USA
107, 8195–8200 (2010).
7
CELL BIOLOGY | A-IMBN RESEARCH
© ISTOCKPHOTO/WILLSIE
Published in The Journal of Clinical Investigation
Following new instructions
Overexpression of a cellular protein helps clear the
way for lung cancer by switching off genes that
restrain cell growth
Enzymes such as DNA methyl-
transferase I (DNMT1) routinely
downregulate expression of genes by
masking specific stretches of DNA
with chemical modifications, but
some cancers exploit this activity
to block production of factors that
suppress tumor growth.
A new study from a team led by
Li-Jung Juan at Taiwan’s Academia
Sinica has revealed a cofactor that
facilitates this process in lung cancer.
Although previous data linking the
hNaa10p protein to tumorigenesis
have been somewhat ambiguous,
Juan and co-workers demonstrate
that hNaa10p helps to recruit
DNMT1 to specific sites in the
genome and facilitates the silencing
of cancer-related genes. E-cadherin,
a known tumor suppressor, is among
the targets inactivated by hNaa10p
and DNMT1, and the researchers
8 www.natureasia.com/A-IMBN
Published in Proceedings of the National Academy of Sciences USA
Confining cancer
Treatments that stop lung cancer cells from invading
other tissues could stem from the recent identification
of a critical signaling pathway
Researchers from the Chinese
Academy of Sciences, along with
colleagues from other institutes in
China and the US, have deciphered
found that the interaction of these
two factors significantly promoted
transformation and cell proliferation
in cultured lung cancer cells.
Clinical data showing elevated
hNaa10p expression in more than
half of all lung cancer specimens
examined further supported these
findings. This overexpression was
generally associated with downregu-
lation of E-cadherin and other tumor
suppressor genes, as well as poor
overall patient prognosis.
However, the researchers also
note that some previous studies have
found that hNaa10p may inhibit
growth in breast cancers, and con-
clude that this protein’s function may
vary considerably depending on the
tumor context.
Lee, C.-F. et al. hNaa10p contributes to
tumorigenesis by facilitating DNMT1-mediated
tumor suppressor gene silencing. The Journal of
Clinical Investigation 120, 2920–2930 (2010).
the molecular mechanism by which a
tumor suppressor gene called LKB1
inhibits lung cancer progression.
Mutations in the LKB1 gene are
observed in up to 30% of human
lung adenocarcinomas and contribute
significantly to cancer progression,
but little was known about the
underlying mechanisms.
Hongbin Ji, in collaboration
with Gaoxiang Ge and colleagues,
found that the enzyme called lysyl
oxidase (LOX) is inhibited by the
LKB1 protein through the signaling
pathway known as mTOR-HIF-1α,
which mediates metastasis of lung
tumors lacking the LKB1 gene. They
also found that the elevated LOX
expression in LKB1-deficient lung
tumors ultimately resulted in excessive
deposition of collagen, which in turn
activated signaling by β1 integrin and
promoted cancer cell invasion. Then,
in mice with Lkb1-deficient lung
tumors, they showed that treatment
with a pharmacological inhibitor
of LOX dramatically alleviated
malignancy progression.
The researchers’ work links the
microenvironment of cells to enhanced
lung cancer progression and metastasis
induced by the loss of LKB1. They
also identified LOX as a potential
therapeutic target for metastatic cancer
treatment, and observed that LOX
may serve as an important biomarker
for lung cancer prognosis.
Gao, Y. et al. LKB1 inhibits lung cancer progression
through lysyl oxidase and extracellular matrix
remodeling. Proceedings of the National Academy of
Sciences USA 107, 18892–18897 (2010).

Published in Nature
Stem cell short-cuts
Refinement of a powerful cellular reprogramming
technique could represent important progress in
the development of viable alternatives to embryonic
stem cells
Embryonic stem cells (ESCs) retain
the capacity to develop into any cell
type from the body, a property known
as pluripotency — but their tantalizing
clinical potential is countered by the
strict regulatory environment sur-
rounding work in this area. Adult cells
that have been ‘reprogrammed’ into a
pluripotent state by the activation of
selected genes could offer a practical
alternative, but these ‘induced pluripo-
tent stem cells’ (iPSCs) can vary widely
in their resemblance to true ESCs.
In an effort to identify factors that
could boost reprogramming, Genome
Institute of Singapore researcher Bing
Lim and colleagues looked for genes
whose activity is modulated by known
pluripotency regulators Nanog and
Tcf3, identifying transcription factor
Tbx3 as a promising candidate.
Lim and colleagues observed faster
and more efficient iPSC formation
when the Tbx3 gene was introduced
into mouse fibroblasts alongside a
combination of three other reprogram-
ming genes. Importantly, these cells
expressed other key pluripotency
genes at levels equivalent to ESCs,
and proved significantly more effective
than standard cell preparations for
the experimental generation of purely
iPSC-derived animals.
The authors note that cellular re-
programming is hypothesized to occur
via multiple developmental ‘routes’,
yielding cells with varying degrees of
pluripotency, and conclude that Tbx3
expression may help steer iPSC pro-
duction down a more efficient path.
RESEARCH HIGHLIGHT COLLECTION 2010
Han, J. et al. Tbx3 improves the germ-line competency
of induced pluripotent stem cells. Nature
463, 1096–1100 (2010).
Published in Nature
Stem cells on steroids
Estrogen and progesterone increase mammary
stem cell number and enhance their potential for
outgrowth in breast tissue
The risk for breast cancer increases
after prolonged exposure to the
ovarian steroid hormones estrogen
and progesterone, such as during
pregnancy. Now, researchers in
Australia and Japan have a plausible
explanation: exposure to these hor-
mones enhances the growth capacity
of mammary stem cells (MaSCs) —
potential ‘seeds’ of breast cancer.
When the researchers trans-
planted MaSCs from mice lacking
ovaries into breast tissue of normal
mice, they found that the cells could
not populate the tissue as well as
MaSCs from mice with ovaries. The
data indicated that MaSCs from
the mice lacking ovaries had trouble
completing the cell cycle normally.
After administering estrogen and
progesterone to mice, the researchers
noted that MaSC number increased.
MaSCs also increased during
A-IMBN RESEARCH | CELL BIOLOGY
PLoS Biology Vol. 3/7/2005, e234
pregnancy, when estrogen and pro-
gesterone levels are high. Drugs that
blocked these hormones reduced
MaSC counts, and mice lacking
the genes involved in the synthesis
of these hormones also had fewer
MaSCs than normal mice.
MaSCs do not express the
receptors for these hormones, so the
researchers realized that mature cells
in the breast responded to the hor-
mones, and these mature cells then
secreted a protein called RANKL
onto the MaSCs, which in turn
affected their growth potential.
These findings could explain why
ovary removal or anti-estrogens
reduce breast cancer risk, the
team suggests.
Asselin-Labat, M.-L. et al. Control of mammary
stem cell function by steroid hormone signalling.
Nature 465, 798-802 (2010).
9
CELL BIOLOGY | A-IMBN RESEARCH
© ISTOCKPHOTO/alxpin
Published in Blood
Seeing i-to-I
Different classes of blood cells use a common
mechanism to undergo changes associated
with maturation
Blood cells display diverse antigen
molecules on their surface, includ-
ing chains of N-acetyllactosamine
carbohydrates. These can manifest
in a linear ‘i’ form or branched ‘I’
form; the i variant is most prevalent
during early development in human
red blood cells, but by the age of 18
months these cells predominantly
display the I antigen.
Previous research from Lung-Chih
Yu of the National Taiwan University
has highlighted a key role for the
transcriptional regulator C/EBPα in
regulating genes that facilitate this
i-to-I transition in red blood cells.
However, C/EBPα also contributes
to development of white blood cells
known as granulocytes, and Yu and
co-workers have now determined that
these cells employ a similar mecha-
nism for I antigen production.
10
Published in Proceedings of the National Academy of Sciences USA
When the time is right
One protein acts as a gatekeeper that regulates the
activation of key genes involved in blood cell maturation
The development of red blood cells,
also known as erythrocytes, depends
on the properly timed activation
of a subset of genes involved in
C/EBPα activity is modulated
by the addition of phosphate mol-
ecules to specific amino acids, and
the researchers identified a single
phosphorylation site at serine-21
that appears to act as a direct switch
for triggering I antigen expression.
Working with cells that can dif-
ferentiate into either red blood cells
or granulocytes, they demonstrated
that I production is directly correlated
with removal of phosphorylation
from this C/EBPα residue in blood
cells from both lineages, suggesting
that this may represent a common
pathway for driving this antigenic
transition in diverse cell types.
Twu, Y.-C. et al. Phosphorylation status of
transcription factor C/EBP determines cell surface
poly-LacNAc branching (I antigen) formation in
erythropoiesis and granulopoiesis. Blood
115, 2491–2499 (2010).
differentiation. In undifferentiated
erythroid precursors, many of these
genes are maintained in an inactive
state by the inhibitory Bach1/Maf
protein complex, which associates
with a regulatory DNA sequence
known as the Maf recognition
element (MARE).
Activation in turn depends on
the substitution of Bach1 with p45,
although it has remained unclear how
cells maintain appropriate control
over this latter protein. However, new
research from a team led by Che-Kun
James Shen of the Academia Sinica
in Taiwan has provided insights into
the regulatory mechanisms that ensure
that p45 is only present at the right
time and place.
Shen and co-workers determined
that p45 is normally marked for
destruction through chemical
modifications introduced by the JNK
enzyme, but can be stabilized via the
inactivation of JNK in the earliest
stages of erythrocyte differentiation.
The resulting increase in p45 levels
initiates a chain of events that lead to
Bach1 release and degradation, so that
MARE elements are instead bound by
gene-activating p45/Maf complexes.
Based on these findings, the authors
conclude that JNK-mediated regula-
tion of p45 likely represents a vital,
top-level checkpoint governing the
onset of blood cell maturation.
Lee, T.-L. et al. JNK-mediated turnover and
stabilization of the transcription factor p45/NF-E2
during differentiation of murine erythroleukemia cells.
Proceedings of the National Academy of Sciences USA 107,
52–57 (2010).
www.natureasia.com/A-IMBN

Published in Science
Cell-cycle blockers
The mechanism used by two pathogenic bacterial
species to block the division of their host cells is no
longer a mystery
The bacteria Burkholderia pseudomallei
and Escherichia coli cause the human
condition melioidosis and diar-
rheal disease, respectively. By injecting
virulence factors called effectors, they
curtail the division of host cells, which
then fuse allowing the bacteria to
spread from cell to cell. Now, a team
led by Feng Shao of the Chinese
National Institute of Biological
Sciences in Beijing has revealed the
mechanism by which these effectors
block the cell cycle.
Escherichia coli produces an effector
called ‘cycle inhibiting factor’ (Cif ),
whereas B. pseudomallei produces the
related protein CHBP. Both Cif and
CHBP can block the normal cycle
of cell division, when injected into
host cells.
Shao and his collaborators showed
that Cif and CHBP directly interfere
with the ‘ubiquitin-proteasome system’,
which normally drives the cell cycle by
degrading key regulatory proteins at
the appropriate times. When no longer
needed, these cell-cycle regulators
are tagged with a small protein called
ubiquitin. This directs them to a struc-
ture called the proteasome where they
are broken down for recycling.
The researchers revealed that CHBP
and Cif interfere with ubiquitination
by chemically altering and thereby
inactivating ubiquitin and/or the
ubiquitin-like protein NEDD8.
Because ubiquitination is involved in
many cellular processes, they suggest
that these effectors probably play a
range of roles in bacterial pathogenesis.
RESEARCH HIGHLIGHT COLLECTION 2010
Cui, J. et al. Glutamine deamidation and dysfunction
of ubiquitin/NEDD8 induced by a bacterial effector
family. Science 329, 1215–1218 (2010).
Published in Proceedings of the National Academy of Sciences USA
Fitting the profile
Variations in surface proteins may help researchers
to reliably isolate and track cells with potential value
for studying blood cell development
Characterizing the differentiation
of hematopoietic stem cells (HSCs)
into mature blood cells in vivo poses
a serious challenge, and researchers
have begun to seek cell preparations
with HSC-like characteristics that
might prove more practical for
experimental use.
Recent work from a team led
by Donald Metcalf at Australia’s
Walter and Eliza Hall Institute of
Medical Research demonstrated
how mouse bone marrow cells could
be chemically induced to yield two
subtypes of so-called ‘blast colony-
forming cells’. These ‘multicentric’
and ‘dispersed’ blast cells differ in
their capacity for differentiation into
mature blood cells, but both could
represent useful HSC alternatives for
certain applications.
Metcalf and colleagues have since
investigated the composition of these
A-IMBN RESEARCH | CELL BIOLOGY
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two cell preparations in greater detail.
They found they could enrich either
type of blast cell from initial cultures
with reasonable efficiency based on
differential expression of cell-surface
proteins, although they noted con-
siderably more heterogeneity than
expected in these preparations.
The researchers observed clear
differences in the marker surface
proteins displayed by multicentric
and dispersed colonies, as well as
between the various blood cell
types these two colonies yield. They
conclude that these findings should
provide useful guidelines for more
effectively identifying and observing
maturation of these two blast cell
types in future work.
Metcalf, D. et al. Murine hematopoietic blast
colony-forming cells and their progeny have
distinctive membrane marker profiles. Proceedings of
the National Academy of Sciences USA
106, 19102–19107 (2009).
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Published in Proceedings of the National Academy of Sciences USA
The acid advantage
An acid-sensing receptor protein on the surface of
tumor cells enhances their ability to survive and grow
Cancerous cells often reside in an
acidic environment which would kill
normal cells. Now, a team of research-
ers in Japan describe how tumor cell
expression of a protein that signals in
response to acid can confer a selective
advantage to cancer cells.
The researchers expressed the
protein, T-cell death-associated gene
8 (TDAG8), in lung cancer cells that
are normally free of the protein, and
transplanted them into mice. These
TDAG8-expressing cells formed
more and larger tumors than normal
cells lacking TDAG8. Mutating the
portions of TDAG8 that allow it to
sense acid reduced the ability of the
protein to drive tumor formation in
the animals.
In tissue culture experiments, the
researchers found that lung cancer
cells expressing TDAG8 survived
12
Published in Molecular Cell
Lipids trapped within a SNARE
An unusual regulatory mechanism provides tight
control over intracellular transport of molecules
Within every eukaryotic cell is a
constant flow of molecular traffic, with
various cargos being ‘shipped’ from
one place to another in membrane-
based bubbles known as vesicles.
better and proliferated faster in acidic
conditions than did cells lacking
TDAG8. They also observed that
reducing expression of TDAG8 in
lung cancer cells, which normally
expressed the protein, reduced cell
survival in acidic conditions and
reduced tumor formation in animals.
TDAG8 seemed to activate signal-
ing molecules inside the cancer cell,
including various kinase enzymes
that add phosphate groups to other
proteins. Blocking these kinases
decreased the ability of TDAG8 to
drive proliferation in tissue culture.
The findings suggest that targeting
TDAG8 signaling could be a thera-
peutic approach to fight cancer.
Ihara, Y. et al. The G protein-coupled receptor T-cell
death-associated gene 8 (TDAG8) facilitates tumor
development by serving as an extracellular pH
sensor. Proceedings of the National Academy of Sciences
USA 107, 17309–17314 (2010).
Each is addressed to a particular
destination via membrane-anchored
N-ethylmaleimide-sensitive fac-
tor attachment protein receptors
(SNAREs), which allow vesicles
to recognize the membranes of
target organelles.
Most SNAREs are permanently
membrane-bound, but the essential
vesicle-targeting protein Ykt6 appears
to exist in an inactive soluble form
that can be induced to undergo rear-
rangements that enable membrane
insertion. A team led by Mingjie
Zhang of the Hong Kong University
of Science and Technology has
now provided direct experimental
confirmation for this atypical
activation model.
Ykt6 is typically modified with
a farnesyl lipid group, and Zhang
and co-workers determined that this
farnesyl group preferentially sequesters
itself within a ‘pocket’ formed by
various protein domains. As a result,
Ykt6 is stably maintained in a compact
soluble conformation, where it is
incapable of binding other SNAREs
or interacting with membranes.
The authors hypothesize that
subsequent addition of a palmitoyl
lipid group shifts Ykt6 into an ‘open’
arrangement that leaves the farnesyl
group exposed and capable of
membrane insertion. Importantly,
this palmitoylation is reversible, thus
providing cells with a useful means to
regulate Ykt6 activity.
Wen, W. et al. Lipid-induced conformation switch
controls fusion activity of longin domain SNARE
Ykt6. Molecular Cell 37, 383–395 (2010).
www.natureasia.com/A-IMBN

Published in Nature Structural and Molecular Biology
Tracking cellular hunger pangs
Animal cells have retained components of an
essential bacterial signaling mechanism for coping
with starvation
When external nutrient supplies run
dry, bacteria and plant cells produce a
warning signal that halts cell growth
while ramping up the activity of
cellular processes that might help to
rectify the shortage.
Levels of this ‘alarmone’, guanosine
3’,5’-diphosphate (ppGpp), are
governed by two enzymes: RelA,
which synthesizes ppGpp, and SpoT,
which breaks it down. Until recently,
neither enzyme had been observed
in animal cells, but new work from
a team led by Jongkyeong Chung at
Seoul National University in Korea
and Young Ho Jeon at the Korea
Basic Science Institute has now
identified homologs of SpoT in diverse
animal species.
Both the human and fruit fly ho-
mologs, which the researchers termed
metazoan SpoT homolog-1 (Mesh1),
showed remarkable structural similar-
ity to their bacterial counterparts and
proved equally capable of the specific
processing of ppGpp molecules.
Escherichia coli bacteria lacking the
gene encoding SpoT normally ac-
cumulate ppGpp under nutrient-poor
conditions and subsequently undergo
growth arrest, but this condition could
be effectively reversed by inducing
these cells to express human or fly
Mesh1. As this enzyme apparently
plays an equivalent role in flies, regu-
lating both cell growth and responses
to nutrient deprivation, these findings
shed light on a highly important
but previously uncharacterized
environmental-sensing pathway in
animal cells.
RESEARCH HIGHLIGHT COLLECTION 2010
Sun, D. et al. A metazoan ortholog of SpoT hydrolyzes
ppGpp and functions in starvation responses. Nature
Structural and Molecular Biology 17, 1188–1194 (2010).
Published in Neuron
Reciprocal connections
Odor responses in the fruit fly brain are modulated
by an exchange of excitatory signals between two
specific neuron populations
Researchers in China have found how
neuronal populations in the antennal
lobe of the fruit fly brain communi-
cate with each other to encode olfac-
tory information. The fly’s response
to olfactory information is critical,
particularly in the search for food. The
findings have been published in the
journal Neuron.
The researchers stimulated neurons
in flies that expressed a fluorescent
protein in a population of excitatory
interneurons in the antennal lobe of
the brain. They recorded the response
in projection neurons that send
olfactory information to higher brain
centers. Stimulating the excitatory
interneurons activated the projection
neurons, and stimulating projection
neurons activated the excitatory
interneurons. These two neuronal
populations seemed to be connected
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to each other through direct gap
junction coupling, allowing for rapid
communication between them.
Certain odors triggered stronger
responses than others in the excit-
atory interneurons, the researchers
observed. They also found that
switching an odor on or off in the
flies’ environment could preferentially
activate these neurons. The specific-
ity of these interneuron responses,
and their reciprocal excitation of
the projection neurons, suggested
to the researchers that these excit-
atory interneurons might amplify the
response of the olfactory neuronal
circuit to low concentrations of odors
in the environment.
Huang, J., Zhang, W., Qiao, W., Hu, A. & Wang, Z.
Functional connectivity and selective odor responses
of excitatory local interneurons in Drosophila
antennal lobe. Neuron 67, 1021–1033 (2010).
13
CELL BIOLOGY | A-IMBN RESEARCH
NIEHS/NIH
Published in The EMBO Journal
The missing link
A commonly used anticancer therapeutic helps to
preserve the activity of a protein that causes tumor
cells to commit ‘suicide’
Many cancer patients benefit from
treatment with cellular signaling
molecules known as interferons
(IFNs), which eliminate tumor cells
by triggering cellular ‘self-destruct’
mechanisms via their influence on
proteins such as death-associated
protein kinase (DAPK).
Until recently, the molecular
details of this response were poorly
understood, but a team led by Ruey-
Hwa Chen at Academia Sinica in
Taiwan has revealed valuable details
about how IFN helps promote the
activity of this cell death initiator.
Cellular pathways are often
switched off via a process known
as ubiquitination, which marks
specific proteins for destruction by a
complex known as the proteasome.
Accordingly, Chen and co-workers
discovered that the KLHL20 protein
acts as an adapter that selectively
14
Published in Cell Death and Differentiation
Profiling cell death perpetrators
Genetic deletion reveals the individual and overlapping
roles of two key instigators of programmed cell death in
various cell types
Safeguarding against tumor forma-
tion and other diseases hinges on
programmed cell death, or apoptosis,
for the removal of redundant and
defective cells. Two important factors
facilitates DAPK degradation by
tethering it to proteins that help
direct it to the proteasome.
However, they observed that cells
treated with IFN-α or -γ exhibit
dramatically altered localization of
KLHL20, with much of this protein
segregated within the nucleus as
opposed to its typical distribution
throughout the cytoplasm. This
nuclear segregation essentially elimi-
nates the bridge that links DAPK to
the ubiquitination pathway, thereby
extending the protein’s lifespan and
promoting the onset of cell death.
Chen and co-workers suggest that
malfunctions in this process could
underlie emergence of interferon
resistance in certain cancer patients.
Lee, Y. R. et al. The Cullin 3 substrate adaptor KLHL20
mediates DAPK ubiquitination to control interferon
responses. The EMBO Journal 29, 1748 - 1761 (2010).
in apoptosis induction are the proteins
Bim and Bad. By genetically engineer-
ing mice to lack one or both of these
proteins, Andreas Strasser and his
colleagues from the Walter and Eliza
Hall Institute of Medical Research
in Australia have characterized how
Bim and Bad work together to trigger
apoptosis in various cell types.
The researchers found that loss of
Bad extended the life span of platelets,
whereas loss of Bim reduced the
production of these cells, possibly
because a Bim-dependent, apoptosis-
like, process may be critical for platelet
shedding. In mice lacking both Bim
and Bad, they recorded a normal
number of platelets, likely because the
effects of these proteins on these cells
counterbalance each other.
Strasser and colleagues also found
that loss of Bim in thymocytes, and
of Bad in their support cells, helped
nurture their sustained survival upon
radiation treatment. Accordingly, they
observed an acceleration of radiation-
induced lymphoma development when
both factors were lacking.
Since Bim and Bad play interacting
roles in apoptosis the team suggests
that pharmacologically activating both
might assist with the treatment of
certain types of lymphomas.
Kelly, P. N. et al. Individual and overlapping roles
of BH3-only proteins Bim and Bad in apoptosis
of lymphocytes and platelets and in suppression
of thymic lymphoma development. Cell Death and
Differentiation 17, 1655–1664 (2010).
www.natureasia.com/A-IMBN

Published in Proceedings of the National Academy of Sciences USA
Pinpointing a missing link
The discovery of the protein Stk40 will help facilitate full
use of embryonic stem cells in regenerative medicine
A research team led by Ying Jin of
the Chinese Academy of Sciences
has identified a key protein, Stk40,
involved in embryonic stem cell
(ESC) differentiation.
ESCs derived from early-stage
embryos renew themselves through cell
division. Their capacity to differentiate
into a diverse range of specialized cells
makes them attractive candidates for
use in regenerative medicine. However,
factors controlling renewal and differ-
entiation need to be better understood
before the full therapeutic potential of
ESCs can be realized.
The researchers identified Stk40 as a
target gene of Oct4, the ‘master regula-
tor’ of gene expression maintaining
ESCs in an undifferentiated state.
They showed that Stk40 cooperates
with a calcium-binding protein, Rcn2,
to activate a previously characterized
Erk/MAPK signaling pathway already
known to be crucial for ESC differen-
tiation. However, the exact mechanism
by which these proteins activate signal-
ing remains to be established.
Experiments with mouse embryos
revealed that signaling triggered by
Stk40 induces ESC differentiation
specifically into extra-embryonic
endoderm. In mammals, cells from
this lineage form yolk sacs, which
nourish the developing embryo, and
also orchestrate patterning of later
developmental structures.
The researchers concluded that Oct4
maintains ESCs in an undifferentiated
state by suppressing Stk40 expression,
thereby blocking signals that would
otherwise lead to differentiation.
RESEARCH HIGHLIGHT COLLECTION 2010
Li, L. et al. Stk40 links the pluripotency factor Oct4 to
the Erk/MAPK pathway and controls extraembryonic
endoderm differentiation. Proceedings of the National
Academy of Sciences USA 107, 1402–1407 (2010).
Published in Nature
Maintaining stem cell identity
Identification of the genes that keep embryonic stem
cells in an undifferentiated state is an important
step forward
Researchers from the A*STAR
Genome Institute of Singapore have
identified the genes that make human
embryonic stem cells (ESCs) remain
in the pluripotent, undifferentiated
state, which enables them to generate
the multiple cell types in the body.
Huck-Hui Ng and his colleagues
performed a genome-wide screen
to pinpoint the genes that specify
ESC identity by regulating the self-
renewing and pluripotency properties
of the cells. They used genetic
engineering to fuse green fluorescent
protein to the regulatory region of the
POU5F1 gene, which is critical for
ESC self-renewal. This enabled them
to identify the genes that interact
with and control POU5F1 expression.
They established that one of the
genes identified, PRDM14, directly
controls the expression of the OCT4
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gene, which is a key regulator of
ESC pluripotency. Furthermore,
inserting PRDM14 into cultured
cells called fibroblasts pushed them
towards a pluripotent state by
activating these genes, enabling more
efficient reprogramming of the cells.
Conversely, reducing PRDM14 levels
led to a reduction in ESC-associated
genes in three different stem cell
lines, causing them to express cell-
type specific genes and to undergo
morphological changes characteristic
of differentiation.
“We are currently studying the
novel regulators identified in the
screen,” says Ng. “It is likely that
many will play unexpected roles in
human embryonic stem cells.”
Chia, N.-Y. et al. A genome-wide RNAi screen
reveals determinants of human embryonic stem cell
identity. Nature 468, 316–320 (2010).
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Published in Cell Stem Cell
Identifying a
cancer-spreading culprit
The protein CD26 defines a population of cancer
stem cells that can spread human colorectal cancer
to other organs
Cancer researchers believe that
tumors harbor a relatively small
number of long-lived cells, dubbed
cancer stem cells (CSCs), which are
the mutant cells that initially gave
rise to the tumor. CSCs have been
identified in human tumors and
shown to initiate tumor development
when injected into mice. Benjamin
Wong and his colleagues from the
University of Hong Kong have now
identified the cell surface protein
CD26 as a marker of a subpopula-
tion of CSCs that also give rise to
secondary tumors (metastases).
Using cells collected from human
colorectal cancers, the researchers
found that a population of CSCs ex-
pressing CD26 within these samples
can initiate cancer metastasis when
injected into mice. They also observed
16
Published in Leukemia
AIDing our understanding
of cancer
A different approach in modeling AID-induced immune-
cell cancers reveals new insights into their development
Mutations introduced in the DNA
of immune cells by the enzyme called
activation-induced cytidine deaminase
that these cells displayed enhanced
tissue invasiveness and resistance to
chemo­therapeutic agents.
Wong and colleagues noted that at
the beginning of a study of colorectal
cancer patients without metastasis —
but with CSCs not expressing CD26
— 19 of 27 individuals (~70%) did not
develop secondary tumors. However,
5 of 8 colorectal patients (62.5%)
with CD26-positive cells eventually
developed secondary tumors.
These results suggest that CD26-
expressing CSCs may be the source
of metastases in colorectal cancer and
may also have prognostic value in the
clinic for this disease.
Pang, R. et al. A subpopulation of CD26+ cancer
stem cells with metastatic capacity in human
colorectal cancer. Cell Stem Cell 6, 603–615 (2010).
(AID) lead to the diversification of
these cells. However, misregulation
of AID can inappropriately introduce
mutations in the genes that regulate
cancer, resulting in the hyperprolifera-
tion of B cells and consequently tu-
mors of the lymph — so-called B-cell
lymphomas. Surprisingly, modeling
this disease by genetic overexpression
of AID in mice had resulted only in
T-cell lymphomas. Toshio Kitamura
from the University of Tokyo and his
colleagues have now found that bone
marrow cells transduced with AID
and injected into normal mice can
cause T- and B-cell lymphomas and
B-cell leukemia.
None of the recipient mice, how-
ever, developed myeloid leukemias
— even when the team injected mice
with purified precursors of these blood
cells that were transduced with AID.
The team speculates that AID induces
leukemia/lymphoma in one subset of
immune cells but not another because
myeloid cells have a more efficient
DNA-repair process than T or B cells.
Kitamura and colleagues also iden-
tified mutations in several key genes
regulating T-cell and B-cell prolifera-
tion and differentiation in the mice
that developed cancer, thus offering
a possible molecular mechanism by
which AID can induce such cancers
in humans.
Komeno, Y. et al. AID-induced T-lymphoma or
B-leukemia/lymphoma in a mouse BMT model.
Leukemia 24, 1018–1024 (2010).
www.natureasia.com/A-IMBN

Published in Proceedings of the National Academy of Sciences USA
The accomplice to viral entry
Researchers identify the cell surface receptor that
effectively opens the door to the nervous system for
herpes virus infection
The molecular mechanism by which
varicella zoster and related viruses gain
entry into host cells has been revealed
by researchers in Japan.
Varicella zoster virus (VZV) is
a herpes virus that targets primary
sensory neurons, leading to chicken pox
in children and shingles in immuno-
compromised and elderly adults.
During infection, virus envelope gly-
coproteins bind to receptors on the host
cell surface, causing the envelope to fuse
with the cell membrane and enabling
the virus to gain entry into its host. The
cell surface receptor which mediates
this process was, however, unknown.
Tadahiro Suenaga of Osaka
University and colleagues in Japan
have identified the host receptor
as myelin-associated glycoprotein
(MAG), a cell-surface protein expressed
predominantly by glial cells in the
nervous system, which is known to be
important for axonal outgrowth during
neural development.
The researchers transfected a human
kidney cell line with MAG and then
co-cultured them with cells transfected
with VZV glycoproteins B, E, H or L.
In all but the co-cultures containing
gE, they observed many fused cells (see
image). They also found that human oli-
godendrocytes transfected with MAG
were susceptible to VZV infection.
These findings demonstrate that cell–
cell fusion is mediated by an interaction
between MAG and VZV glycoproteins
B, H and L, but not glycoprotein E.
Suenaga, T., Satoh, T., Somboonthum, P.,
Kawaguchi, Y. & Mori, Y. Myelin-associated
RESEARCH HIGHLIGHT COLLECTION 2010
glycoprotein mediates membrane fusion and entry of
neurotropic herpesviruses. Proceedings of the National
Academy of Sciences USA 107, 866–871 (2010).
Published in Nature
Route of entry
The herpes virus enters host cells by binding to a
myosin protein found on the cell surface
The point of entry of the herpes
virus to human host cells has been
identified by researchers in Japan
and the US. The herpes virus glyco-
protein B (gB) binds to a cell surface
protein called non-muscle myosin
heavy chain IIA (NMHC-IIA),
which allows it to invade host cells.
The researchers focused on
NMHC-IIA by isolating and
sequencing host cell surface proteins
that interacted with herpes virus ex-
pressing gB. They found that human
leukemia cells that were relatively
resistant to herpes virus infection
became highly susceptible to viral
infection when they overexpressed
NMHC-IIA. Kidney epithelial
cells that are usually susceptible to
herpes infection became resistant
when the researchers reduced their
expression of NMHC-IIA.
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© 2010 PNAS
Since a drug called ML-7 that
blocks the ability of NMHC-IIA to
reach the cell surface could prevent
herpes virus infection in kidney cells,
NMHC-IIA could represent a new
target for drug development against
herpes virus infections.
Infection with herpes virus can
cause death in mice. The researchers
found that ML-7 could enhance
the survival of mice exposed to the
herpes virus.
The team’s discovery could assist
development of drugs against human
herpes virus infection, which can
cause blistering of the skin, mouth
and genitalia, and, in some cases,
damage to nerves.
Arii, J. et al. Non-muscle myosin IIA is a functional
entry receptor for herpes simplex virus-1. Nature
467, 859–862 (2010).
17
CELL BIOLOGY | A-IMBN RESEARCH
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Published in Developmental Cell
Front-line healer
Repair of physical damage to body tissues is
coordinated by one of the protein that helps
epithelial cells stay in layers
Many tissues in the body are com-
posed of sheets of tightly connected
epithelial cells. When these tissues
suffer damage, epithelial cells respond
by migrating towards wounds in
order to initiate healing.
For this process to succeed,
epithelial cells need a good sense of
direction, which is established by
so-called ‘polarity complexes’ such
as Par3-aPKC and Par6-aPKC.
Zhengjun Chen and colleagues
at China’s Shanghai Institutes for
Biological Sciences have now re-
vealed that this orientation depends
on the participation of occludin, one
of the proteins that helps epithelial
sheets maintain their cohesion.
Working with kidney epithelial
cells, the researchers showed that
occludin rapidly localizes to the
leading edge of epithelial cells near
the wound — essentially the front
18
Published in Molecular Cell
Dissecting cellular
crisis management
Cells rely on a complex, multi-step signal transduction
pathway to coordinate their response to DNA damage
Serious DNA damage triggers cellular
survival responses mediated by tran-
scription factor NF-κB, which some
cancer cells exploit to evade destruction
line of the healing process. Occludin
subsequently recruits Par3-aPKC,
and thereby establishes directionality
for cell migration; on the other hand,
artificially induced downregulation
of occludin prevented the cells from
undergoing cytoskeletal rearrange-
ments that are an essential prelude
to migration.
Likewise, Chen’s team also
demonstrated that occludin is needed
to localize and activate PI3K, an
important cellular signaling factor,
at the leading edge, where it triggers
formation of cellular projections that
help pull epithelial cells into motion.
Depletion of occludin sabotages this
process, further highlighting the
apparently critical role of this protein
in wound healing.
Du, D. et al. The tight junction protein, occludin,
regulates the directional migration of epithelial
cells. Developmental Cell 18, 52–63 (2010).
by radiation or chemotherapy. The
ATM protein coordinates a parallel
response to these toxic stimuli, and
although there is evidence for an
intersection between these two path-
ways, the details remain murky.
Zhao-Hui Wu from the University
of Tennessee Health Science Center
and colleagues including Ee Tsin
Wong and Vinay Tergaonka of the
A*STAR Institute of Molecular and
Cell Biology have filled in some of
those blanks. They identified a key
role for the ELKS protein, which gets
modified via the addition of chains of
ubiquitin molecules. This modifica-
tion enables ELKS interaction with
downstream elements of the NF-κB
activation pathway.
Ubiquitination of ELKS is driven
in response to DNA damage by the
cooperative action of ATM and a
second protein, NEMO. Interestingly,
NEMO also participates in a late stage
of NF-κB activation, indicating a key
role for this factor at both ends of this
particular pathway.
Numerous other stimuli can activate
NF-κB, including cellular signaling
factors like cytokine TNFα. However,
Wu and colleagues found evidence that
the interaction between NEMO–ATM
and ELKS plays a minimal role in the
TNFα response, suggesting that the
mechanism they uncovered represents
a specific response to DNA damage.
Wu, Z.-H. et al. ATM- and NEMO-dependent ELKS
ubiquitination coordinates TAK1-mediated IKK
activation in response to genotoxic stress. Molecular
Cell 40, 75–86 (2010).
www.natureasia.com/A-IMBN
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Genetics
GENETICS | A-IMBN RESEARCH
© ISTOCKPHOTO/MKucova
Published in Proceedings of the National Academy of Sciences USA
Looking out for number one
A mathematical analysis suggests that parasitic
genetic elements need not perish from their
singular selfishness
Most genes contribute to the
survival of the organism within
whose genome they reside, but some
are less beneficial. For example,
homing endonuclease genes (HEGs)
act only to ensure their own
duplication. When one member
of a chromosome pair contains an
HEG but the other does not, the
enzyme it encodes selectively cleaves
the ‘empty’ chromosome at the
appropriate site; the cellular DNA
repair machinery then copies the
HEG-containing chromosome to fill
in the resulting break.
Scientists have assumed that
once HEGs are established in a
population, they must be transmitted
‘horizontally’ to another population
or species to avoid extinction due to
accumulation of inactivating muta-
tions over time.
However, new mathematical
models from University of Tokyo
20
Published in Nature Biotechnology
Knockout resource for
yeast biologists
A genome-wide deletion collection for fission yeast
provides an invaluable new tool for biotechnology and
biomedical research
Scientists led by Kwang-Lae Hoe
of the Korea Research Institute of
Bioscience and Biotechnology have
ascertained which genes are dispensable
researcher Ichizo Kobayashi and his
colleagues at Kurume University
and the Graduate University
for Advanced Studies, Japan,
suggest otherwise.
Mutation of the HEG locus to an
inactive — but also uncleavable —
‘pseudogene’ sometimes carries a cost
to the host organism’s reproductive
fitness, and they identified this as
a key consideration in determining
the mechanism of HEG persistence.
But regardless of whether or not
this cost becomes significant,
Kobayashi’s team could identify
multiple scenarios that would enable
these genes — and, potentially,
other ‘selfish’ genetic elements — to
survive over long periods of time
within isolated populations.
Yahara, K., Fukuyo, M., Sasaki, A. & Kobayashi, I.
Evolutionary maintenance of selfish homing
endonuclease genes in the absence of horizontal
transfer. Proceedings of the National Academy of
Sciences USA 106, 18861–18866 (2009).
and which are essential in fission yeast
(Schizosaccharomyces pombe), a model for
studying basic biological processes in
eukaryotes, a group of organisms that
includes humans.
The researchers systematically
knocked out some 5,000 genes cover-
ing more than 98% the fission yeast
genome, and replaced each one with
a marker gene flanked by unique
molecular bar codes. This allowed them
to assess experimentally which genes
were needed for viability, growth and
reproduction in the laboratory.
By comparing their results with
previous findings from budding yeast
(Saccharomyces cerevisiae) used in baking
and brewing, they found that fission
yeast has more essential genes than
budding yeast despite having fewer
genes in total.
They also found that essential genes
tend to be present as single-copy, evolu-
tionarily conserved genes, often inter-
rupted by non-coding DNA sequences
called introns, possibly reflecting aspects
of their regulation and/or ancient origin.
In contrast, non-essential genes are
more often duplicated in the genome,
and less likely to contain introns or to
be present in both species.
The researchers believe that their
genome-wide fission-yeast deletion
library will facilitate the identification
of eukaryotic molecular pathways and
networks, benefiting both biotechnol-
ogy and biomedical research.
Kim, D.-U. et al. Analysis of a genome-wide set of gene
deletions in the fission yeast Schizosaccharomyces
pombe. Nature Biotechnology 28, 617–623 (2010).
www.natureasia.com/A-IMBN

Published in PLoS Biology
Exploring the genetic
‘generation gap’
The emergence of functional ‘mismatches’ between
genes in the nucleus and the mitochondria accelerates
the evolutionary process
As new species emerge over the course
of evolution, they lose the capacity to
generate fertile progeny with members
of their parent species. In many cases,
such ‘reproductive isolation’ is presumed
to occur via accumulation of mutations
that disrupt interactions between each
species’ complement of genes.
Jun-Yi Leu and colleagues at
Academia Sinica have explored an
alternative mechanism for reproduc-
tive isolation in yeast, driven by the
emergence of incompatibilities between
the nuclear genome and mitochondria,
an essential metabolic organelle with its
own discrete set of genes.
The researchers established a multi-
stage breeding scheme for generating
crosses between yeast species and
identifying pairs for which this ‘cyto-
nuclear incompatibility’ was a primary
obstacle to offspring fertility. Leu and
colleagues were subsequently able
to identify genes responsible for this
incompatibility by screening genomic
libraries for sequences that restored the
mitochondrial function of the various
infertile hybrids.
Their data revealed two genes, MRS1
and AIM22, which appear to contribute
to cytonuclear incompatibility via
distinct biological mechanisms.
Strikingly, the patterns of emergence
for these mutations directly correlated
with known evolutionary history of the
various species, and the authors con-
clude that genomic changes associated
with cytonuclear incompatibility may
represent important early drivers of the
speciation process.
RESEARCH HIGHLIGHT COLLECTION 2010
Chou, J.-Y., Hung, Y.-S., Lin, K.-H., Lee, H.-Y. &
Leu, J.-Y. Multiple molecular mechanisms cause
reproductive isolation between three yeast species.
PLoS Biology 8, e1000432 (2010).
Published in the Journal of Molecular Biology
Evolution through
40,000 generations
Tracking long-term evolution in bacteria reveals that
genome change and adaptation are linked in highly
complex ways
In addition to showing that relation-
ships between genomic change and
adaptation are complex, the results of
an extensive analysis of the evolution
of a population of bacteria over 40,000
generations have revealed that the pace
of genome evolution is not directly
coupled to improvement in fitness.
The international study, involving the
Korea Research Institute of Bioscience
and Biotechnology (KRIBB), does,
however, clearly demonstrate the
validity of Darwin’s theory of evolu-
tion by natural selection. The research-
ers believe that their work can be
applied to bettering the performance
of industrial strains of bacteria, as well
as contributing to understanding the
tempo and mode of evolution.
In 1988, researchers from Michigan
State University led by Richard Lenski
A-IMBN RESEARCH | GENETICS
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began to grow Escherichia coli in the
laboratory at a constant rate of six or
more generations a day. Samples were
frozen for future analysis. A team led
by Jihyun F. Kim at KRIBB sequenced
and compared bacterial genomes from
samples taken at 2,000, 5,000, 10,000,
15,000, 20,000 and 40,000 genera-
tions, after determining the complete
genome sequence of the ancestral
strain. In addition, Dominique
Schneider’s group in Grenoble, France,
measured the fitness of each popula-
tion, in part by moving mutations back
to ancestral populations and observing
their impact.
Barrick, J. E. et al. Genome evolution and
adaptation in a long-term experiment with
Escherichia coli. Nature 461, 1243–1247 (2009);
Jeong, H. et al. Genome sequences of Escherichia
coli B strains REL606 and BL21(DE3). Journal of
Molecular Biology 394, 644–652 (2009).
21
GENETICS | A-IMBN RESEARCH
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Published in Nature Genetics
Lung cancer link
A newly identified genetic variant is associated with
increased lung cancer risk in East Asian
Lung cancer is a leading cause of
death worldwide, but little is known
about the genetic factors that confer
susceptibility to it. Yataro Daigo of
the University of Tokyo and Shiga
University of Medical Science, and
his colleagues have now identified
a gene variant in the Japanese and
Korean populations that is associated
with increased risk of the disease.
The researchers performed a
genome-wide association study
that compared the entire genomes
of 2,098 lung cancer patients with
those of 11,048 healthy controls.
They found that a variant of the
TP63 gene is strongly associated
with increased susceptibility for lung
adenocarcinoma, which accounts
for approximately 50% of all lung
cancer cases, and whose prevalence
is increasing among East Asians and
Western Europeans.
22
Published in Acta Pharmacologica Sinica
Thank you for not smoking
Gender differences in the frequency of a cancer-
associated mutation among Chinese patients may arise
from differences in smoking behavior
Patients diagnosed with lung adeno-
carcinoma, the most common of all
lung cancers, can often benefit from
treatment with drugs such as Iressa
TP63 belongs to a family of
genes whose members are involved
in development, differentiation
and cellular responses to stress,
and are known to function as
tumor suppressors.
The newly identified genetic
variation in TP63 may play a role
in regulating TP63 expression, but
further research is needed to estab-
lish exactly how it influences suscep-
tibility to lung adenocarcinoma.
“We are continuing further
functional studies to clarify the
mechanisms of TP63 on lung
adenocarcinoma susceptibility,” says
Daigo, “as well as additional studies
on other ethnic populations.”
Miki, D. et al. Variation in TP63 is associated
with lung adenocarcinoma susceptibility in
Japanese and Korean populations. Nature Genetics
42, 893–896 (2010).
and Tarceva, which inhibit certain
signaling enzymes known as kinases.
These compounds are most effective
in patients with mutations in the
gene encoding one particular kinase,
the epidermal growth factor receptor
(EGFR). Previous studies have
suggested that females in general, and
males and females who have never
smoked are especially likely to acquire
such EGFR mutations, but new find-
ings from a team led by Hong-bin Ji at
the Shanghai Institutes for Biological
Sciences suggest that for some popula-
tions, this gender effect may simply be
an artifact of lifestyle differences.
Chinese women are considerably
less likely to smoke than their male
counterparts, a trend that Ji and
co-workers clearly observed in their
analysis of adenocarcinoma tissue
samples from 224 Chinese patients.
When they independently considered
only those individuals who had never
smoked, they were surprised to note
that EGFR mutations occurred
with essentially the same frequency
among both women and men (76.85%
versus 70.97%).
These findings suggest that a history
of smoking is a more important con-
sideration than gender in determining
whether Chinese patients diagnosed
with adenocarcinoma are likely to ben-
efit from kinase inhibitor treatment.
Sun, Y. H. et al. Comparable rate of EGFR kinase
domain mutation in lung adenocarcinomas from
Chinese male and female never-smokers. Acta
Pharmacologica Sinica 31, 647–648 (2010).
www.natureasia.com/A-IMBN

Published in Proceedings of the National Academy of Sciences USA
Extremophiles: Cold complexity
An impressive variety of microbes can survive in the
polar deserts of Antarctica
The McMurdo Dry Valleys, an
extremely cold, dry desert region
representing the largest ice-free area
in Antarctica, support a higher variety
of life than scientists once believed.
During a recent study of permafrost
in the high inland McKelvey Valley,
Steve Pointing and colleagues at the
University of Hong Kong, along with
Roberta Farrell at the University
of Waikato, New Zealand, and
co-workers in the USA, discovered
previously unreported bacteria and
fungi existing in highly specialized
microbial communities.
The researchers used molecular
techniques to assess the relative abun-
dance of different microbes and iden-
tify variations in community structure.
They found so-called endolithic and
chasmolithic cyanobacteria, which
are capable of photosynthesis and
occupy ecological niches in the pores
and cracks in sandstone outcrops. The
surrounding soil, however, contained
very few organisms except on scattered
quartz rocks.
“Our data counters the view…that
cyanobacteria are restricted to wetter,
more productive polar locations,” the
researchers note in their publication.
The data also showed that the abun-
dance of microbes in some areas may
occasionally increase due to moisture
input from melting snow. However,
they found no significant difference
in the biodiversity of communities at
different locations — probably because
only a few resilient species can survive
in such an extreme environment.
RESEARCH HIGHLIGHT COLLECTION 2010
Pointing, S. B. et al. Highly specialized microbial
diversity in hyper-arid polar desert. Proceedings of the
National Academy of Sciences USA
106, 19964–19969 (2009).
Published in the Journal of Human Genetics
Mountains that make
the people
Culture is geographically defined by the Himalayas,
and DNA fingerprinting shows that these
mountains also impede gene flow
The genetic structure of the peoples
of Tibet is consistent with the
geographical barriers and the
languages they speak, a study led by
researchers from Fudan University in
Shanghai has shown. The researchers
found Tibetans are relatively similar
to north Asians, but the small
Deng minority in the Himalayan
Mountains of southeast Tibet
is unique.
The Deng people are most closely
related to a neighboring minority,
the Luoba/Adi. The two are geneti-
cally more similar to each other than
to any other ethnic group in East
Asia. And although the Deng and
Luoba/Adi live in isolated valleys on
the southern side of the Himalayas,
the researchers found no detectable
genetic link with Indian peoples.
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These assessments were made on
the basis of the analysis of 15 differ-
ent regions of short tandem repeats
(STRs) from 114 Deng, 101 central
Tibetans and 78 eastern Tibetans.
STRs are groups of repeated
sequences of DNA code between
two and 16 units long, often used in
DNA fingerprinting. The numbers of
repeats varies in different individu-
als; but the more closely people are
related, the more similar the pattern
of repeats.
There was not enough evidence
to reconstruct a more detailed his-
tory of the settlement of Tibet, the
researchers say.
Kang, L. et al. Genetic structures of the Tibetans
and the Deng people in the Himalayas viewed
from autosomal STRs. Journal of Human Genetics
55, 270–277 (2010).
23
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Published in Cell Research
Filling the gaps of a
genome map
Application of a proteomic technique allows better
annotation of the genome reported for the pathogenic
bacterium Leptospira interrogans
The Genomic Age has allowed
scientists to quickly sequence the
complete genomes of several species,
including important human patho-
gens. Rong Zeng and colleagues in
Shanghai have now used a proteomics
technique to provide the information
needed to more accurately map the
genome of Leptospira interrogans, a
free-living pathogenic spirochete
that causes leptospirosis, a dangerous
malady marked by sever fever and
muscle ache. The genome of this
bacterium was sequenced in 2003.
Fully annotating the sequenced
genome of a species involves identify-
ing all of its genes and the proteins
that they encode. Identifying all the
post-translational modifications of
these proteins is also useful as they
are important regulators.
24
Published in the British Journal of Cancer
Combining forces to
combat cancer
Research into colorectal cancer genetics gets a large-
scale boost from the establishment of a multinational
research consortium
The COGENT (COlorectal cancer
GENeTics) consortium, comprised of
some twenty research groups, including
the Human Genome Research Center
Zeng’s group used a computational
algorithm that predicts the existence
of genes from known sequence data
while also performing mass spec-
trometry on cell extracts to physically
identify expressed proteins. These
two approaches allowed the team to
identify novel genes in the bacterium’s
genome, better define the start site of
several other genes and identify the
post-translational modifications of a
large percentage of its proteome.
This annotation of L. interrogans
may eventually allow for the identifi-
cation of gene products needed for its
survival and thus the development of
new antibiotics.
Cao, X.-J. et al. High-coverage proteome analysis
reveals the first insight of protein modification
systems in the pathogenic spirochete Leptospira
interrogans. Cell Research 20, 197–210 (2010).
at the University of Tokyo, has been
established to study genetic predisposi-
tion to colorectal cancer.
Colorectal cancer is the fourth most
common form of cancer in the United
States, and causes more than 650,000
deaths worldwide annually. Although
inherited susceptibility underlies
approximately 35% of genetic variance
in colorectal cancer, high-risk muta-
tions account for less than 6% of cases.
The goal of the COGENT
consortium is therefore to identify and
characterize so-called ‘low-penetrance
genetic variants’. The risk of colorectal
cancer associated with each of these
is modest, but they occur with high
frequency in the population, and may
significantly affect an individual’s
risk when acting together. Very few
of these variants have been identified
to date, because of small sample sizes
and the limitations of early genetic
testing methods.
COGENT overcomes these
limitations by enrolling researchers
who are conducting studies involving
a minimum of 500 patients and 500
controls. Collectively, the studies
performed by researchers in the
consortium have included 48,000 cases
and 43,000 controls. Pooling these
data provides a cost-effective means of
performing powerful statistical analyses
that could not be achieved from an
individual study.
Tomlinson, I. P. M. et al. COGENT (Colorectal
cancer GENeTics): an international consortium
to study the role of polymorphic variation on the
risk of colorectal cancer. British Journal of Cancer
102, 447–454 (2010).
www.natureasia.com/A-IMBN

Published in Nature Genetics
Pinpointing inflammatory
genomic changes
The effects of a subtle sequence variation in an
immunity-related gene may predispose individuals to
rheumatoid arthritis and other inflammatory diseases
Over the course of rheumatoid
arthritis, the immune system mobilizes
T cells against tissues within the joints
to produce debilitating pain and
inflammation. Genetic factors contrib-
ute to the onset and severity of this
disorder. A team of researchers from
several Japanese research institutes
recently surveyed the genomes of
more than 25,000 Japanese patients
(and controls) and revealed a two-
nucleotide sequence variant that has
an apparently strong role in conferring
vulnerability to rheumatoid arthritis.
The research team, which was led by
Yuta Kochi and Kazuhiko Yamamoto
of the RIKEN Center for Genomic
Medicine in Yokohama, identified
these changes within the CCR6 gene,
which encodes a receptor for signals
that promote activation of the immune
system. Intriguingly, CCR6 expression
is generally associated with Th17
cells, a subclass of helper T cells that
is poorly understood but has been
tentatively linked with rheumatoid
arthritis pathology.
The investigators noted that these
sequence changes dramatically affected
CCR6 expression levels in patients,
and that individuals with the highest
CCR6 levels were also significantly
more likely to exhibit increased pro-
duction of certain pro-inflammatory
signals. Their data also offer compel-
ling evidence that the gene variant
may also predispose some individuals
to Graves’ disease and Crohn’s disease,
two other common autoimmune
inflammatory disorders.
RESEARCH HIGHLIGHT COLLECTION 2010
Kochi, Y. et al. A regulatory variant in CCR6 is
associated with rheumatoid arthritis susceptibility.
Nature Genetics 42, 515–519 (2010).
Published in Proceedings of the National Academy of Sciences USA
Keeping track of changes
Coordination between two important pathways for
the chemical modification of chromosomes leads to
fine-tuned regulation of gene expression
Gene activity levels depend heavily
on so-called ‘epigenetic’ modifica-
tions, such as the targeted addition
of methyl chemical groups to
individual cytosine nucleotides or to
the histone proteins around which
genomic DNA is wrapped.
Scientists have proposed that
these two processes are closely
linked, with the methylation state
of the ‘tail’ domain of histone H3
directly affecting cytosine methyla-
tion within individual genes, and a
new study from a team led by Jin-
Qiu Zhou and Guo-Liang Xu at the
Shanghai Institutes for Biological
Sciences offers strong support for
this model.
The researchers introduced mouse
genes encoding DNA methyltrans-
ferase enzymes into yeast, which lack
this pathway but retain an innate
capacity for histone methylation,
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and noted that the activity of these
enzymes was apparently blocked by
methylation of a key lysine residue
in the H3 tail, H3K4. In fact, DNA
methylation was consistently absent
at the actively transcribed gene
loci where H3K4 methylation was
markedly enriched; disruption of
the histone methylation pathway
in turn led to DNA methylation at
previously unmarked sites.
They found that DNA modifica-
tion is dependent on the capacity
of DNA methyltransferases to bind
directly to the H3 tail, and hypoth-
esize that H3K4 modification helps
activate genes by masking this bind-
ing site and thereby preventing DNA
methylation-mediated repression.
Hu, J.-L. et al. The N-terminus of histone H3
is required for de novo DNA methylation in
chromatin. Proceedings of the National Academy of
Sciences USA 106, 22187–22192 (2009).
25
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Published in Nature Genetics
Asian genomes point the way
Personalized medicine takes a step closer to
reality with a new technique for analyzing
genomic variation
An international team of molecular
geneticists has developed a highly
sensitive technique for detecting the
differences between human genomes
known as copy number variants
(CNVs). The researchers used their
new technique, which provides finer
resolution than previously possible,
on 10 individuals each of Korean,
Chinese and Japanese origin, and
found 5177 CNVs of which 3,547
were distinctively Asian.
Humans ordinarily have two copies
of each region of DNA, one from
each parent. The ability to sequence
whole genomes, however, has shown
widespread variation in the number of
copies between different individuals
and ethnic groups. The CNVs are
the result of rearrangements such as
deletions and duplications.
Led by Jeong-Sun Seo of Seoul
National University, the researchers
26
Published in Nature Genetics
Pinpointing genetic
susceptibility to
Parkinson’s disease
A large-scale genomic study reveals two previously
unidentified genetic risk factors for Parkinson’s disease
A consortium led by Wataru Satake
of Kobe University Graduate School
of Medicine, including researchers
from the RIKEN Center for Genomic
developed a strategy combining array
comparative genomic hybridization
(aCGH) with whole genome
sequencing data.
Initially, the researchers used
so-called ‘24-million-probe aCGH’
technology to assess the relative
differences in copy number between
test and reference genomes for
regions as short as 438 base pairs.
The sequencing data then allowed
the relative copy numbers to be
turned into absolute numbers.
“Our results provide guidance for
future studies in genomic medicine
in Asian populations, especially
those that identify ethnic differences
in predisposition to disease and drug
response,” the team says.
Park, H. et al. Discovery of common Asian copy
number variants using integrated high-resolution
array CGH and massively parallel DNA sequencing.
Nature Genetics 42, 400–405(2010).
Medicine and the RIKEN Brain
Science Institute, Japan, has identified
two previously unknown genetic vari-
ants associated with increased suscepti-
bility to Parkinson’s disease (PD).
PD is a progressive neurodegen-
erative disorder caused by death of
dopamine-producing midbrain neurons
and characterized by tremor, rigidity
and slow movements.
In a genome-wide association study
(GWAS), the researchers compared the
entire genomes of 2,011 Japanese PD
patients with those of 18,381 healthy
controls. One of the variants identified
lies within the PARK16 region and
encodes a magnesium transporter.
The other is in BST1, which encodes
an enzyme that catalyses formation
of cyclic ADP-ribose, which releases
calcium from intracellular stores.
Magnesium deficiency has been
implicated in PD and other neurode-
generative diseases; disrupted calcium
homeostasis is thought to compromise
dopaminergic neurons. The researchers
compared these results with those of a
European GWAS. They found the BST1
variant only in Japanese patients, whereas
a variant of the MAPT gene was found
only in Europeans. The PARK16 vari-
ants, and previously identified variants
in the SCNA and LRRK2 genes, were
common to both populations. Although
most cases of PD are sporadic, identifi-
cation of these variants and others will
improve understanding of PD.
Satake, W. et al. Genome-wide association study
identifies common variants at four loci as genetic risk
factors for Parkinson’s disease. Nature Genetics 41,
1303–1307 (2009).
www.natureasia.com/A-IMBN

Published in the Journal of Human Genetics
Different strokes,
different genes
Two genetic variants that predispose Caucasians to
stroke are also found in the Japanese population
Stroke affects millions of people
every year and is a leading cause of
death, but very little is known about
its genetic predisposition factors.
Comparing the entire genomes of
healthy and diseased individuals in
genome-wide association studies
(GWASs) is a powerful way of identi-
fying disease-related genes.
Last year, an international team
of researchers identified two genetic
variants on chromosome 12 that are
associated with increased risk of stroke
in Caucasians in a GWAS. Now,
Tomonaga Matsushita of the RIKEN
Center for Genomic Medicine, Japan,
and his colleagues have reported that
one of these variants is also associated
with susceptibility to stroke in the
Japanese population.
The researchers replicated the
earlier GWAS using Japanese instead
of Caucasian participants, and ana-
lyzed the genomes of 3,784 patients
who had suffered different types of
stroke and 3,102 healthy controls.
They found that the two previously
identified variants are also present
in the Japanese, and are most closely
associated with atherothrombitic
stroke, in which a large artery to the
brain or smaller blood vessel is blocked
by a clot.
“Stroke is a heterogeneous disease
that comprises several subtypes,” says
Matsushita, “and very few associated
genetic variants have been identi-
fied. We [now] know of five, three
of which appear to be specific to
Asian populations.
RESEARCH HIGHLIGHT COLLECTION 2010
Matsushita, T. et al. Association study of the
polymorphisms on chromosome 12p13 with
atherothrombotic stroke in the Japanese population.
Journal of Human Genetics 55, 473–476 (2010).
Published in Nature Genetics
Casting wide yields
aneurysm suspects
A large-scale genetic study identifies three genes
associated with increased risk of brain aneurysm
Balloon-like dilations of arteries in
the brain, called secular intracranial
aneurysms, can cause severe neu-
rological damage and death. They
are the most common type of brain
aneurysm, affecting approximately 2%
of the population.
Richard Lifton of Yale University
School of Medicine, USA, in
collaboration with a large team of
international researchers, includ-
ing three from the University of
Tokyo’s Institute of Sciences, have
identified three gene variants
associated with increased risk for
intra­cranial aneurysms.
The researchers performed a
genome-wide association study
(GWAS) comparing the genomes
of healthy and diseased individuals
from Europe and Japan. By combin-
ing the data with those from a
previous GWAS, they analyzed a
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total of 5,891 aneurysm patients
and 14,181 controls.
Their analysis not only confirmed
the three gene variants identified in
the previous study, but also identified
three more hitherto unidentified vari-
ants that are associated with increased
risk for intracranial aneurysm.
Based on their chromosomal posi-
tions, the researchers speculate that
the newly identified gene variants are
likely to play a role in cell division,
and in maintaining the stem cells that
are responsible for the formation and
repair of blood vessels.
The team writes that these data
could contribute to the preclinical
identification of individuals at high
risk of developing intra­cranial
aneurysms.
Yasuno, K. et al. Genome-wide association study of
intracranial aneurysm identifies three new risk loci.
Nature Genetics 42, 420–427 (2010).
27
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Published in DNA Research
Sprouting information
Comparisons of the mungbean chloroplast genome
reveal evolutionary relationships and will help
genetically improve crop species
Photosynthesis occurs in chloroplasts,
organ-like structures within the cells
of green plant tissues. Chloroplasts are
believed to have evolved from bacteria
and have their own genomes.
A team led by Sithichoke
Tangphatsornruang of the National
Center for Genetic Engineering
and Biotechnology in Thailand has
sequenced the chloroplast genome of
mungbean (Vigna radiata). Mungbean
belongs to the family Fabaceae, which
contains some 20,000 species, and is
an economically important legume
with protein-rich seeds.
As in other higher plants, the
mungbean chloroplast genome is a
circular molecule of double-stranded
DNA. The researchers found that it is
also of a similar size to those of other
flowering plants, and that it contains a
pair of inverted repeats of nucleotide
sequences separated by two single-
copy regions.
28
Published in Nature
Plant fungi’s jump
on pathogenicity
Genome study reveals horizontal gene transfer
as a driver of rapid adaptation in disease-causing
plant fungi
An international genome consortium
including researchers from Seoul
National University in Korea has
found evidence that so-called ‘jumping
DNA sequencing revealed 127
genes, including 19 genes duplicated
in the inverted repeat, while nearly
a half of the genome is non-coding,
as in other sequenced chloroplast
genomes. Although chloroplast
structure and gene content is gener-
ally conserved, the researchers did
find a relatively large amount of
genome rearrangement, as reported
for other legumes.
Comparison with the previously
sequenced chloroplast genomes of
other members of the Fabaceae and
other plants allowed the researchers
to reconstruct evolutionary relation-
ships. Future studies should facilitate
genetic engineering of agriculturally
important legume species.
Tangphatsornruang, S. et al. The chloroplast
genome sequence of mungbean (Vigna radiata)
determined by high-throughput pyrosequencing:
structural organization and phylogenetic
relationships. DNA Research 17, 11–22 (2010).
genes’ — segments of DNA that move
location in the genome — facilitate
rapid adaptation of important fungal
pathogens to new plant hosts.
Species of fungi belonging to the
genus Fusarium cause economically
significant damage to crops around
the world through blights, root rots
and wilts. Some Fusarium species are
host specific, while others have broad
host ranges. Fusarium oxysporum, for
example, infects a wide range of plants
as well as humans with compromised
immune systems.
The researchers sequenced the
genomes of the maize pathogen
F. verticillioides, the toxins of which
contaminate grain, and a strain of
F. oxysporum that causes tomato wilt.
By comparing these genomes and that
of the previously sequenced cereal
pathogen F. graminearum, they identi-
fied lineage-specific genomic regions
of F. oxysporum rich in jumping genes
and other evolutionarily distinct genes
encoding virulence factors.
By simple co-incubation, they were
able experimentally to transfer lineage-
specific chromosomes between strains,
conferring an otherwise non-pathogenic
strain with the ability to cause tomato
wilt. The researchers propose that
horizontal transfer of virulence genes
between strains may mediate the rapid
emergence of new pathogenic lineages,
with important implications for the
management of crop diseases.
Ma, L.-J. et al. Comparative genomics reveals mobile
pathogenicity chromosomes in Fusarium. Nature
464, 367–373 (2010).
www.natureasia.com/A-IMBN

Published in Nature Genetics
Transcending ethnic differences
A genome-wide analysis of the gene variants associated
with blood and enzyme traits reveals similarities and
differences between the Japanese and Europeans
Sixty single nucleotide polymorphisms
(SNPs), or DNA variations, associ-
ated with differing characteristics of
blood, and a further 29 associated
with biochemical traits, have been
uncovered in genome-wide studies of
some 14,700 individuals whose genetic
material is stored in Japan’s Biobank.
Of these associations, just over half
were reported for the first time. The
work was completed by researchers
from the University of Tokyo and
RIKEN in Japan.
When the researchers compared
their Japanese results with previous
studies in European populations, the
vast majority of the associations found
among Europeans were replicated. A
significant advantage of the Japanese
work is that the array of data available
on donor individuals allows for adjust-
ment for factors which can potentially
bias results.
The research reveals genetic associ-
ations with differences in hemoglobin
concentrations and platelet, white and
red blood cell counts, as well as levels
of lipids, proteins, albumin, blood urea
nitrogen and several enzymes.
Knowledge of the genes involved in
some of the blood-related associations
gives rise to plausible explanations for
the observed impacts of the SNPs.
Often these genes are related to cell
division. Most of the differences found
between ethnic groups involve SNPs
at low frequency in one or other of
the populations.
RESEARCH HIGHLIGHT COLLECTION 2010
Kamatani, Y. et al. Genome-wide association study
of hematological and biochemical traits in a Japanese
population. Nature Genetics 42, 210–215 (2010).
Published in Nature Genetics
Linking more suspects to
bowel disease
A large-scale genetic study identifies three genes
associated with increased risk of brain aneurysm
Across Asia, the prevalence of
ulcerative colitis, a type of inflam-
matory bowel disease, is rising. Now,
as reported in the journal Nature
Genetics, Japanese researchers have
identified two genes that are associ-
ated with this disease in the Japanese
population: SLC26A3 and FCGR2A.
The SLC26A3 protein is involved
in ion transport in intestinal cells,
and its expression is reduced
in individuals with ulcerative
colitis. Near, but not within, the
coding region for this protein, the
researchers discovered changes — or
polymorphisms — in the genomic
DNA that they had established is
linked to the disease. They therefore
propose that these polymorphisms
may act to regulate the levels of
SLC26A3 gene expression.
FCGR2A encodes a receptor that
binds to antibodies and drives the
A-IMBN RESEARCH | GENETICS
© ISTOCKPHOTO/TommL
immune response. In individuals
with ulcerative colitis, the researchers
found a polymorphism that enhances
the affinity of the receptor for anti-
bodies, making it easier for immune
cells to be activated. Interestingly, an
opposing polymorphism that reduces
the receptor’s affinity for antibodies
has previously been linked to autoim-
mune diseases like lupus.
Another area of the genome
that the scientists associated with
increased disease risk did not
contain any known genes. More
research must be done to determine
whether or not this region is involved
in regulating the expression of
other genes.
Asano, K. et al. A genome-wide association study
identifies three new susceptibility loci for ulcerative
colitis in the Japanese population. Nature Genetics
41, 1325–1329 (2009).
29
GENETICS | A-IMBN RESEARCH
AFIP/peir.net
Published in Nature Genetics
Diversity in the genome
The first Japanese genome reveals the extent of
human genetic variation
The first whole genome sequence of
a Japanese individual reveals that the
human genome contains considerable
and as yet undiscovered variation.
Tatsuhiko Tsunoda of the RIKEN
Center for Genomic Medicine and
his colleagues used sophisticated
DNA sequencing technology and
analysis methods to analyze rare
variations that are not normally
targeted by previous methods.
They sequenced the whole
genome of a Japanese male
comprehensively, covering 99.9%
of the entire sequence 40 times.
They then compared the sequence
with six other previously sequenced
human genomes from non-
Japanese populations.
Their analysis revealed numerous
variations in the Japanese individu-
al’s genome, many of which have not
been reported. These included more
than 3.1 million single nucleotide
30
Published in Nature Genetics
Getting at the roots of
cancer risk
Genomic analysis reveals novel risk factors for a throat
cancer with elevated prevalence throughout much
of Asia
Relative to the general population,
individuals in south China or Southeast
Asia are at considerably greater risk of
variations, over 5,300 deletions,
duplicated chromosomal regions and
variations in the number of copies of
certain genes. Functionally impor-
tant variations were more enriched
in rare ones than in common ones.
The results suggest that a
considerable number of rare
variations, particularly those
associated with disease, may still be
undiscovered. They also show that
whole-genome sequencing can be
used to identify such variations, and
that it will eventually be valuable for
personalized medicine.
“We want to expand our scope
to study diseases caused by multiple
variants,” says Tsunoda, “and high-
throughput sequencing technologies
will greatly help such analyses.”
Fujimoto, A. et al. Whole-genome sequencing
and comprehensive variant analysis of a Japanese
individual using massively parallel sequencing.
Nature Genetics 42, 931–936 (2010).
developing nasopharyngeal carcinoma
(pictured), a tumor of the upper throat.
Environmental factors are partly to
blame, including smoking or exposure
to infection by Epstein-Barr virus.
However, there is also clear evidence
for genetic risk factors. A recent study,
led by Yi-Xin Zeng of China’s Sun
Yat-Sen University Cancer Center and
Jianjun Liu of the Genome Institute
of Singapore, has uncovered several
such candidate loci based on their
analyses of large cohorts of southern
Chinese individuals.
Zeng, Liu and their colleagues
performed a genome-wide association
study that assessed the distribution of
tiny DNA sequence variations within
these individuals. Their goal was to
zoom in on variants with a statisti-
cally robust correlation with the onset
of nasopharyngeal carcinoma.
Some of these ‘hits’ provided strong
additional support for previous findings
suggesting a meaningful connection
with the HLA genes, which contribute
to immune system function. However,
Liu and Zeng also identified entirely
novel risk factors, including a trio of
genetic loci that have already been asso-
ciated with leukemia and lymphoma.
Such blood disorders are often associ-
ated with nasopharyngeal carcinoma,
and the researchers intend to investigate
the interconnections between these risk
factors in future studies.
Bei, J.-X. et al. A genome-wide association study
of nasopharyngeal carcinoma identifies three new
susceptibility loci. Nature Genetics 42, 599–603 (2010).
www.natureasia.com/A-IMBN
 Neuroscience &
Developmental Biology
© ISTOCKPHOTO/Sebastian Kaulitzki
NEUROSCIENCE & DEVELOPMENTAL BIOLOGY | A-IMBN RESEARCH
© 2010 Elsevier
Published in The Journal of Experimental Medicine
A model of dementia
Transgenic mice reveal the cause of a common
neurodegenerative disease
A common form of dementia called
frontotemporal lobar degeneration
with ubiquitin-positive inclusions
(FTLD-U) is associated with
insoluble protein clumps, contain-
ing TDP-43, which accumulate
within neurons.
Che-Kun James Shen from
Academia Sinica, Taiwan, and his
colleagues created genetically engi-
neered mice over-expressing TDP-43
in the forebrain and hippocampus,
and found that this protein ac-
cumulated within neurons, causing
severe learning and memory defects1.
The mice could not remember the
location of a hidden platform in a
water maze, and failed to associate
a location in their housing chamber
with electric shocks. Additional
behavioral tests showed that TDP-43
over-expression affected the animals’
motor functions, with coordination,
balance and grasping reflex severely
32
Published in Neuron
Muscling in on receptor clusters
A protein that organizes receptors at cell
membranes is essential for development of the
neuromuscular junction
Efficient signaling at the neuromuscular
junction — the interface between nerves
and muscles — requires precise align-
ment of synaptic vesicles at the nerve
impaired by six months of age.
The memory defects were caused
by altered levels of memory-associat-
ed proteins in the hippocampus. This
led to impaired long-term potentia-
tion, the process by which neuronal
connections are strengthened, and
which is widely believed to underlie
memory formation. The mice also
exhibited characteristic FTLD-U
neuropathologies, which developed as
in humans with the disease, and had
shorter lifespans than normal animals.
“We have used these mice to test
the therapeutic effects of a few drugs,”
says Shen, “and are now analyzing
the defects of neuronal development,
neuron structure, gene expression, and
protein metabolism misregulation in
this FTLD-U mouse model.”
Tsai, K.-J. et al. Elevated expression of TDP-43
in the forebrain of mice is sufficient to cause
neurological and pathological phenotypes
mimicking FTLD-U. The Journal of Experimental
Medicine 207, 1661–1673 (2010).
terminal with acetylcholine receptors
(AChRs) in the muscle cell membrane.
During development, AChR clusters
are transformed from a simple oval-
shaped structure to a complex pretzel-
shaped one that is perfectly aligned with
the motor neuron nerve terminal. This
involves disassembling certain regions of
the AChR clusters, but the underlying
molecular mechanisms are unknown.
A research team led by Nancy Ip of
Hong Kong University of Science and
Technology has now shown that the
protein ephexin1 is essential for AChR
cluster maturation.
Ephexin1 was previously known to
interact with EphA4, a receptor tyrosine
kinase involved in gene transcription at
the neuromuscular junction, but the role
of ephexin1 was unclear.
The researchers found that mice
lacking the ephexin1 gene exhibit
severe muscle weakness and impaired
nerve-muscle signaling, because the
neuromuscular junction does not mature
properly, and the pretzel-shaped struc-
ture fails to form.
Experiments in cultured muscle
cells revealed that ephexin1 regulates
AChR cluster stability by activating the
enzyme RhoA GTPase, which induces
reorganization of the actin cytoskeleton.
“This raises the possibility that intro-
ducing ephexin1 might be a potential
therapeutic approach for neuromuscular
diseases such as myasthenia gravis,”
says Ip.
Shi, L. et al. Ephexin1 is required for structural
maturation and neurotransmission at the
neuromuscular junction. Neuron 65, 204–216 (2010).
www.natureasia.com/A-IMBN

Published in Proceedings of the National Academy of Sciences USA
Benefitting from
mixed messages
Cross-talk between two signaling pathways ensures
proper development of the nervous system within a
developing embryo
The transition from a simple ball of
cells into a properly formed embryo
depends on the coordinated interplay
of numerous signal transduction
pathways. By modulating each
other’s activity, each signaling fac-
tor’s effects are constrained to ensure
appropriate body patterning of the
developing organism.
A team led by Naihe Jing of the
Shanghai Institutes for Biological
Sciences, China, has provided a novel
example of such regulatory cross-talk
during the formation of the central
nervous system. This process is directed
in part by bone morphogenetic protein
(BMP) signaling, which coordinates
dorsal–ventral patterning, and retinoic
acid (RA) signaling, which contributes
to anterior–posterior patterning.
Jing and colleagues demonstrated
that RA gradually inhibits BMP
activity in cultured mouse cells, an
effect mediated by the accelerated
degradation of Smad1, a key down-
stream effector of BMP signaling. The
same effect was also observed in vivo
in chicken embryos. BMP signaling is
typically observed in the dorsal region
of the neural tube, the precursor to
the mature central nervous system,
but this activity could be restricted by
RA signaling. Likewise, inappropriate
BMP activity in embryos can mark-
edly disrupt normal neural develop-
ment, but the researchers showed that
these perturbations could be mitigated
through the effects of RA, highlight-
ing the crucial interplay between these
two networks.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | NEUROSCIENCE & DEVELOPMENTAL BIOLOGY
Sheng, N. et al. Retinoic acid regulates bone morphogenic
protein signal duration by promoting the degradation
of phosphorylated Smad1. Proceedings of the National
Academy of Sciences USA 107, 18886–18891 (2010).
Published in Neuron
Sniffing out the olfactory code
Genetically engineered mice provide fresh insights
into how mammalian neuronal circuits process
odor information
Odors are detected by olfactory
sensory neurons (OSNs) that express
olfactory receptors and form connec-
tions with mitral/tufted (M/T) cells
in the main olfactory bulb, which
sends the information to the brain.
Understanding how odor informa-
tion is processed involves comparing
OSN responses with those of their
corresponding M/T cells. This is pos-
sible in fruit flies, but is technically
challenging in the more complex
olfactory system of mammals.
To overcome this, Minmin Luo
of China’s National Institute of
Biological Sciences and his col-
leagues examined genetically engi-
neered mice with OSNs expressing
a specific olfactory receptor labeled
with green fluorescent protein. This
enabled them to record the electrical
activity of specified OSNs and their
corresponding M/T cells in response
to various odors.
© ISTOCKPHOTO/herbap
Their analysis revealed that M/T
cells respond selectively to the odors
detected by their corresponding
OSNs, but also respond weakly to
additional, non-corresponding odors
at higher concentrations. In fruit
flies, olfactory information is encoded
differently, with projection neurons
responding broadly to odors detected
by many different OSNs.
Further experiments revealed an
important role for inhibitory neurons
in the olfactory bulb. Blocking inter-
neuron activity reduced the selectivity
of M/T cells at high odorant concen-
trations, suggesting that they nor-
mally fine-tune M/T cell responses
by suppressing the weak responses to
non-corresponding odors.
Tan, J., Savigner, A., Ma, M. & Luo, M. Odor
information processing by the olfactory bulb analyzed
in gene-targeted mice. Neuron 65, 912–926 (2010).
33
NEUROSCIENCE & DEVELOPMENTAL BIOLOGY | A-IMBN RESEARCH
© 2010 PNAS
Published in Nature Neuroscience
Accelerating synapse
formation
An interaction between a scaffold protein
and a membrane protein helps neurons form
communication junctions
Thrombospondin 1 (TSP1), a scaffold
protein critical for blood clotting,
also plays a role in the formation of
synapses between brain cells, accord-
ing to a new study by researchers
from the Hong Kong University of
Science and Technology.
TSP1, which is secreted by vari-
ous cell types including astrocytes
in the brain, was already known to
promote formation of synapses in
retinal ganglion cells, but whether
it does so in neurons from the brain
has been unclear.
Junyu Xu and Nan Xiao, led
by neuroscientist Jun Xia, studied
TSP1’s effect by applying TSP1 to
cultured rat hippocampal neurons.
By staining for synapsin 1 and PSD-
95, proteins enriched in the pre- and
post-synaptic membranes of
34
Published in Proceedings of the National Academy of Sciences USA
Shaping blood vessel formation
Early development of the circulatory system is
regulated by an enzyme that induces chemical
modification of chromosomes
Chromosomal DNA is wound around
scaffolds composed of histone proteins,
and gene expression levels are pro-
foundly affected by the extent to which
excitatory synapses, respectively, they
found that TSP1 increases the num-
ber of synapse in the earlier stages of
neurons, but not in late stage mature
neurons. This indicates that TSP1
accelerates the formation of synapses
in neurons from the brain.
The researchers also found
that TSP1 binds the membrane
protein neuroligin 1 (NL1), and
that reducing NL1 levels blocked
TSP1-induced synaptogenesis. This
indicates that the effect of TSP1
is mediated by an interaction with
NL1. The effect in retinal ganglion
cells is bigger, so may involve a
different mechanism.
Xu, J., Xiao, N. & Xia, J. Thrombospondin 1
accelerates synaptogenesis in hippocampal
neurons through neuroligin 1. Nature Neuroscience
13, 22–24 (2009).
specific DNA sequences are exposed to
or masked from regulatory factors.
Certain enzymes can modulate gene
expression by introducing chemical
modifications to histones that help
regulate the arrangement of these
proteins on chromosomal DNA. Now,
new work from a team led by Qiu-
Hua Huang, Sai-Juan Chen and Zhu
Chen at China’s Shanghai Jiao Tong
University School of Medicine has
revealed an important role for one such
enzyme, the histone methyltransferase
Hypb, in blood vessel development.
The authors observed that mice
lacking Hypb expression (see image)
perish during embryonic development,
with profound physical defects that
include a relatively primitive and
disorganized circulatory network.
Compared with wild-type embryos,
yolk sacs of Hypb-deficient mutants
showed limited capacity for formation
of both capillaries and larger blood ves-
sels, and gene expression data revealed
that loss of Hypb leads to misregula-
tion of dozens of genes involved in
vascular development.
Accordingly, targeted inactivation of
HYPB in cultured human endothelial
cells impaired their innate capacity
to self-organize and assemble into
tightly interconnected capillary-like
structures, further supporting a role for
this enzyme in the direct regulation of
genes that govern maturation of the
vascular network.
Hu, M. et al. Histone H3 lysine 36 methyltransferase
Hypb/Setd2 is required for embryonic vascular
remodeling. Proceedings of the National Academy of
Sciences USA 107, 2956–2961 (2010).
www.natureasia.com/A-IMBN

Published in Developmental Cell
Keeping genes in their place
Expression of key developmental genes is restricted
to certain embryonic regions via activity-modulating
chemical modifications to chromosomal proteins
Embryonic segmentation is a key
component of development, wherein
the body is divided into discrete ‘zones’
whose maturation informs appropriate
formation of the skeleton, nervous
system and other tissues. These seg-
ments are established by the action of
numerous Hox genes, whose activity
is believed to be partly regulated by
the chemical modification of histones
— proteins that provide a structural
scaffold for the chromosomal DNA
containing these genes.
New work from a team at
Australia’s Walter and Eliza Hall
Institute of Medical Research, led
by Anne Voss and Tim Thomas, has
provided experimental support for this
model, identifying histone-modifying
enzyme Moz as an important regulator
of anterior embryonic development in
mice. This protein directly contributes
to the introduction of acetyl groups at
key points on histones associated with
Hox gene clusters, and thereby helps
govern their activation.
In the absence of Moz, expression
of the majority of Hox genes are
shifted toward the posterior of the
embryo, resulting in marked develop-
mental defects in the spinal column
and nervous system. Importantly,
these developmental problems can
be rescued by treatment with retinoic
acid, a compound known to induce
Hox gene activation. The authors
conclude that Moz directly contrib-
utes to the segmentation process via
its regulation of spatially-appropriate
expression of key Hox genes.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | NEUROSCIENCE & DEVELOPMENTAL BIOLOGY
Voss, A. K., Collin, C., Dixon, M. P. & Thomas, R.
Moz and retinoic acid coordinately regulate H3K9
acetylation, Hox gene expression, and segment identity.
Developmental Cell 17, 674–686 (2009).
Published in Developmental Cell
First instructions for
male mice
The fate of male sex cells is determined by a molecule
produced in the fetal testis
A protein called fibroblast growth
factor (FGF) 9 directs germ cells to
differentiate into sperm, researchers
led by Peter Koopman from the
University of Queensland, Australia,
have found. The finding finally
explains how a germ cell becomes
either a sperm or an egg after being
generated by meiosis, a form of
cell division.
Koopman and his colleagues per-
formed cell culture experiments and
examined mutant mice lacking either
the Fgf9 gene or the gene encoding
the enzyme CYP26B1. This enzyme
is normally expressed in the testes
and breaks down a molecule called
retinoic acid (RA), which drives egg
specification by increasing expression
of the Stra8 gene.
The researchers found that germ
cells in the testes of mice lacking
© ISTOCKPHOTO/Henrik5000
CYP26B1 did not differentiate
into eggs, suggesting that a signal
other than RA controls male sex
cell determination. They then
showed that FGF receptors are
expressed on the surface of germ
cells in the testes, and that Fgf9 acts
directly on the cells to alter gene
expression patterns.
The team therefore concludes
that high FGF9 levels in the testes
promote male sex cell fate by reduc-
ing expression of Stra8 and inducing
expression of male sex cell genes;
and is investigating how these
findings relate to human infertil-
ity syndromes and testicular germ
cell cancers.
Bowles, J. et al. FGF9 suppresses meiosis and
promotes male germ cell fate in mice. Developmental
Cell 19, 440–449 (2010).
35
NEUROSCIENCE & DEVELOPMENTAL BIOLOGY | A-IMBN RESEARCH
Published in Cell
A green light for growth
A small RNA molecule helps to stimulate body growth
by removing obstacles to cell division
© ISTOCKPHOTO/janeff
Proper body development requires
careful regulation to ensure that the
mature animal is neither excessively
big nor small, as either outcome could
have serious negative consequences.
A-IMBN RESEARCH
Molecular biology from an Asian perspective
SUPPORTED BY
Bio-MAX Institute
National Taiwan University
School of Medicine
www.natureasia.com/A-IMBN
36
Signaling pathways triggered by
insulin play an important role in this
process, but many gaps remain in
the current understanding of growth
control mechanisms.
Seoul National University re-
searcher V. Narry Kim and colleagues
recently uncovered an important
component of this process while
looking for microRNAs — small RNA
molecules that inhibit expression of
selected target genes — that affect
human cell proliferation. Her team
observed strong effects from the vari-
ous miR-200 RNAs, and decided to
further investigate their function by
characterizing their fruit fly counter-
part, miR-8.
Flies with reduced miR-8 levels
were considerably smaller than normal
due to reduced levels of cell division,
but Kim’s team noted that proper
growth could be fully rescued by
selective expression of this microRNA
in the fat body, a structure associ-
ated with metabolic regulation. They
subsequently identified the Ush gene
as a key target for downregulation by
miR-8, and showed that both factors
directly participate in regulation of
insulin signaling.
Since both miR-8 and Ush have
highly conserved human counterparts,
the investigators hypothesize that this
pathway could contribute to growth
— and, if misregulated, tumorigenesis
— in higher organisms.
Hyun, S. et al. Conserved microRNA miR-8/miR-
200 and its target USH/FOG2 control growth by
regulating PI3K. Cell 139, 1096–1108 (2009).
www.natureasia.com/A-IMBN
 Structural &
Molecular Biology
© ISTOCKPHOTO/Martin McCarthy
STRUCTURAL & MOLECULAR BIOLOGY | A-IMBN RESEARCH
CDC/MELVIN
Published in Nature
Making the cut
The malarial enzyme plasmepsin V mediates the
entry of malarial proteins into host red blood cells
Symptoms of malaria, such as coma,
can occur when the Plasmodium
falciparum parasite infects red blood
cells and exports its proteins into the
host cell. This results in changing
some of the properties of red blood
cells — including how readily it
sticks to receptors on endothelial
cells and other blood cells — caus-
ing dysfunction in the body. Now,
researchers in Australia have
identified plasmepsin V (PMV ) as
the protease — the protein-cutting
enzyme — that is involved in this
export process.
Before being exported into red
blood cells, malaria proteins need
to be cleaved at an amino acid
sequence called the Plasmodium
export element (PEXEL). The
researchers honed in on PMV owing
to its expression at the right time
and place during the P. falciparum
38
Published in Proceedings of the National Academy of Sciences USA
Getting in the blood
Increased understanding of how malaria parasites gain
entry to red blood cells should aid vaccine development
A team led by Alan Cowman of the
Walter and Eliza Hall Institute of
Medical Research in Australia has
made a significant breakthrough
life cycle, and because the PEXEL
sequence showed similarities to
protein sequences cleaved by HIV
proteases, which are targeted by HIV
‘protease inhibitor’ drugs.
The researchers found that
incubating PMV with PEXEL-
containing peptides caused cleavage
of the peptides, but this could be
blocked by mutating the PEXEL.
In addition, parasites expressing
inactive PMV could not cleave these
substrates. Importantly, PMV binds
to exported proteins, and seems to
be involved in directing them to be
exported into the host blood cell.
Developing drugs against PMV
could become a novel therapeutic
strategy against malaria.
Boddey, J. A. et al. An aspartyl protease directs
malaria effector proteins to the host cell. Nature
463, 627–631 (2010).
in understanding how malaria
parasites invade human red blood
cells (erythrocytes).
Malaria is a major killer in the
tropics. Humans can become infected
when bitten by mosquitoes carrying the
malaria parasite. But to survive within
the human host, the parasite must suc-
cessfully invade erythrocytes (see image).
Cowman’s team studied erythrocyte
invasion by Plasmodium falciparum,
which is responsible for the most severe
form of human malaria.
Invasion involves the binding of mo-
lecular ‘ligands’ expressed by the parasite
to receptor proteins on the erythrocyte
surface. Some of these receptors contain
sialic acid, whereas others do not. By
expressing different ligands, P. falci-
parum can switch between sialic acid-
dependent and -independent invasion
pathways, helping it to evade the host’s
immune system.
Cowman and his collaborators
showed that a known protein called
Complement receptor 1 (CR1) is
the erythrocyte receptor for PfRh4, a
major P. falciparum ligand essential for
sialic acid-independent invasion. This
is especially important because only
ligand-receptor pairs involved in sialic
acid-dependent invasion had been
identified previously.
The researchers hope that their dis-
covery will lead to the development of a
vaccine capable of blocking erythrocyte
invasion by malaria parasites.
Tham, W.-H. et al. Complement receptor 1 is the
host erythrocyte receptor for Plasmodium falciparum
PfRh4 invasion ligand. Proceedings of the National
Academy of Sciences USA 107, 17327–17332 (2010).
www.natureasia.com/A-IMBN

Published in Nature
Maintaining the silence
The enzyme ESET prevents the expression of
endogenous retroviruses to preserve the integrity of the
mammalian genome
Uncontrolled dispersal of endogenous
retroviral (ERV ) sequences throughout
the mammalian genome during early
development can be harmful. The
protein ESET can effectively ‘silence’
ERV sequences in embryonic stem
(ES) cells, but not more mature cells,
researchers from Japan and Canada
have found.
ESET is a histone methyltransfer-
ase — an enzyme that transfers methyl
groups onto histone proteins around
which genomic DNA is wrapped.
Methylation of histone proteins or
of the DNA itself can repress gene
expression. Previous reports had shown
that DNA methylation plays a key role
in ERV silencing in some cell types,
including germ cells, but another
silencing pathway separate from DNA
methylation operates in ES cells.
The research team, including Yoichi
Shinkai from Kyoto University, found
the ESET protein localizes near ge-
nomic regions of DNA that contained
ERV sequences in ES cells. In ES cells
lacking ESET, the researchers found
that transcription of three different
ERVs was induced, and this was inde-
pendent of DNA methylation. Because
they did not see this same activation
of ERVs in more mature fibroblasts
lacking ESET, they concluded that
ESET was only able to inhibit ERV
expression in immature cells.
The findings suggest that ESET si-
lences ERVs during early development
when DNA methylation is dynami-
cally reprogrammed to maintain the
integrity of the genome.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | STRUCTURAL & MOLECULAR BIOLOGY
Matsui, T. et al. Proviral silencing in embryonic stem
cells requires the histone methyltransferase ESET.
Nature 464, 927-931 (2010).
Published in Proceedings of the National Academy of Sciences USA
Amplifying the silence
Gene silencing in plants is affected by the length of
RNA molecules
A plant’s development and defense
against pathogen attack depends
on its ability to silence certain
genes. Now, a research team from
Taiwan and the UK has confirmed
that the power of gene silencing
activity in plants is increased by
microRNA molecules that are one
nucleotide longer than the norm of
21 nucleotides.
MicroRNAs are small molecules
that interfere with gene expres-
sion by instigating RNA cleavage.
MicroRNAs can trigger the break-up
of target messenger RNA (mRNA)
into secondary, small interfering
RNA molecules (siRNAs), which
further obstructs gene expression. The
team’s research clarifies why most
microRNA–mRNA interactions fail
to produce secondary siRNAs.
Led by Shu-Hsing Wu, the
researchers found that both
natural and engineered microRNA
CCA-SA/ Zephyris
molecules containing 22 nucleotides
can direct cleavage of target mRNA
and trigger the formation of sec-
ondary siRNA in the model plant
Arabidopsis. They also confirmed
experimentally that the length, not
the composition of the nucleotide
sequence, is the primary feature of
microRNAs that initiates secondary
siRNA production.
In the future, the researchers will
examine how the subtle increase
in size affects microRNA–mRNA
interactions during RNA cleavage.
Amplification in gene silencing
could benefit scientists working not
only to develop technologies for
disease resistance in plants but also
to manipulate gene expression in
biotechnological applications.
Chen, H.-M. et al. 22-nucleotide RNAs trigger
secondary siRNA biogenesis in plants. Proceedings
of the National Academy of Sciences USA 34, 15269–
15274 (2010).
39
STRUCTURAL & MOLECULAR BIOLOGY | A-IMBN RESEARCH
Published in Cell Research
Binding and gagging tumors
A newly identified molecular mechanism prevents
cancerous cells from breaking off from tumors
and spreading
Researchers in China have found
that a transcription factor called
FOXA2 prevents tumors from
spreading by inhibiting a process
called the epithelial-to-mesenchymal
transition (EMT).
EMT is characterized by loss
of cell adhesion and increased cell
movement. It is therefore critical
for cancer progression, as it enables
cancerous cells to break off from a
tumor, enter the bloodstream and
invade other organs.
Jianguo Song and his colleagues
from the Shanghai Institutes of
Biological Sciences made the discov-
ery by examining FOXA2 expression
in several human lung cancer cell
lines. They found that reducing
FOXA2 levels induced EMT and
promoted cell migration, whereas
over-expressing the protein inhibited
EMT and migration.
40
Published in Cancer Cell
Stopping the cancer spreading
The identification of a new molecular player advances
the quest to stop cancer in its tracks
A team led by Qi Zeng of the A*STAR
Institute of Molecular and Cell Biology,
Singapore, has discovered that a
protein called PCPB1 helps protect
Further investigation revealed
that FOXA2 inhibits expression of a
protein called slug, which normally
promotes cell migration by reducing
the expression of cell adhesion mol-
ecules in lung cancer cells.
Others have previously shown
that FOXA2 regulates the spread
of colorectal cancer to the liver. This
study now implicates FOXA2 in
lung tumors, and suggests that it is
a possible new drug target for lung
cancer treatment.
“Our study also implies that cells
with high FOXA2 levels are less
malignant than cells with a low level,”
says Song, “suggesting that FOXA2 is
an important marker for judging the
stages of lung cancer.”
Tang, Y., Shu, G., Yuan, X., Jing, N. &
Song, J. FOXA2 functions as a suppressor of
tumor metastasis by inhibition of epithelial-to-
mesenchymal transition in human lung cancers.
Cell Research 21, 316–326 (2011)
against metastasis — the spread of
cancer around the body — by sup-
pressing translation of the metastasis-
associated protein PRL-3 phosphatase.
Abnormally high levels of PRL-3
phosphatase found in diverse human
tumors are associated with metastasis
and poor prognosis.
Zeng and her collaborators analyzed
over 1,000 human tumor samples and
found that that PRL-3 protein levels
were elevated in nearly a quarter of
them. PRL-3 protein levels were not di-
rectly related to PRL-3 gene expression,
suggesting regulation at the level of
messenger RNA (mRNA) translation.
The researchers identified sequence
motifs in the non-protein-coding
region of PRL-3 mRNA that are
important for regulating translation
efficiency in colon cancer cell lines.
Further experiments revealed that a
known RNA-binding protein, PCBP1,
suppressed PRL-3 translation by
specifically binding to these regulatory
motifs, and that low levels of PCBP1
were associated with high levels of
PRL-3 in primary human cancers.
In addition, experiments with
mice showed that PCBP1 could
suppress tumor development by
limiting PRL-3 protein levels and
down­stream signaling.
The researchers hope that the iden-
tification of PCBP1 as a translational
regulator of PRL-3 will eventually lead
to new anti-cancer drugs.
Wang, H. et al. PCBP1 suppresses the translation of
metastasis-associated PRL-3 phosphatase. Cancer Cell
18, 52–62 (2010).
www.natureasia.com/A-IMBN

Published in Nature Structural and Molecular Biology
Tying up loose ends
A component of the telomerase complex folds DNA into
a conformation that directly facilitates that enzyme’s
chromosome-protecting activity
Every time a chromosome is copied for
cell division, it ends up slightly shorter
due to a quirk in the replication process.
The risk of serious genetic damage from
this shortening is ameliorated by the
presence of telomeres: ‘caps’ composed
of repetitive DNA sequences that are
maintained at the ends of each chromo-
some (see image) by the telomerase en-
zyme complex.
The single-stranded ends of telo-
meres are believed to form structures
called ‘G-quadruplexes’, but their
functional importance was unclear.
New work from Jin-Qiu Zhou and col-
leagues at the Shanghai Institutes for
Biological Sciences in China has now
shown that G-quadruplex formation is
critical to telomere maintenance, and
establishes an important role for telom-
erase subunit Est1p in this process.
Est1p is known to facilitate telomer-
ase recruitment to telomeres, but Zhou’s
team was surprised to discover that
this protein can directly convert single-
stranded yeast telomeric DNA into
G-quadruplexes via a magnesium-de-
pendent mechanism. They subsequently
showed that mutations in a magnesium-
binding domain of Est1p essentially
cripple telomere growth, bringing yeast
cell division to a grinding halt.
Zhou and colleagues hypothesize
that Est1p-mediated quadruplex
formation helps position the telom-
erase catalytic domain and potentially
contributes to its translocation during
telomere extension — a mechanism
that seems likely to be evolutionarily
conserved in higher organisms as well.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | STRUCTURAL & MOLECULAR BIOLOGY
Zhang, M.-L. et al. Yeast telomerase subunit Est1p
has guanine quadruplex–promoting activity that is
required for telomere elongation. Nature Structural and
Molecular Biology 17, 202–209 (2010).
Published in Nature Cell Biology
Putting injured cells to sleep
A DNA damage response pathway brings cell
division to a halt by eliminating a protein that
maintains chromosomal integrity
Each time a cell divides, chromosome
ends shorten owing to a quirk in the
DNA replication process. Protein-
capped repetitive sequences called
telomeres provide an essential buffer
against degradation of the chromo-
some ends.
Telomeric uncapping causes cell
division to shut down via a process
known as senescence, which is medi-
ated at least in part by the protein
p53. However, new findings from a
team led by Curtis Harris at the US
National Cancer Institute in Bethesda,
Maryland have shown that p53 can
also actively trigger this uncapping
process in response to genetic damage.
Exposure to DNA-damaging
conditions stimulates production of
p53. Harris and colleagues found
that this ‘up-regulation’ is associated
with reduced levels of TRF2, a key
telomere-binding protein, in cultured
NIH/PADILLA-NASH AND RIED
cells. Under these conditions, p53 also
induces the expression of Siah1; this
enzyme, ubiquitin ligase, selectively
marks other proteins for rapid degra-
dation; TRF2 appears to be among its
targets. Pre-malignant adenoma cells
exhibiting p53-associated senescence
also showed increased Siah1 and
decreased TRF2 levels relative to
healthy cells, indicating that this
regulatory pathway is also active in the
human body.
The researchers conclude that this
represents a potentially important
feedback loop that drives rapid
telomere uncapping in damaged cells,
shunting them towards senescence as
a protective measure against uncon-
trolled cancerous growth.
Fujita, K. et al. Positive feedback between p53
and TRF2 during telomere-damage signalling
and cellular senescence. Nature Cell Biology
12, 1205–1212 (2010).
41
STRUCTURAL & MOLECULAR BIOLOGY | A-IMBN RESEARCH
CDC/GOLDSMITH AND ROLLIN
Published in Science
All mixed up
Genetic reassortment of influenza strains within
pigs could yield more virulent or vaccine-resistant
derivatives of the 2009 pandemic-causing strain
The rapid emergence of the
H1N1/2009 ‘swine flu’ pandemic
triggered global panic in 2009, raising
fears of a potential public health
crisis on the scale of the devastating
1918 outbreak.
The H1N1/2009 virus contains
gene variants derived from a number
of other influenza strains, and it
remains an open question whether
this strain might stably establish itself
in pig populations to an extent that
enables further inter-viral recom-
bination. To address this question,
Yi Guan and Malik Peiris at the
University of Hong Kong character-
ized influenza variants isolated from
swine at a Hong Kong abattoir in late
2009 and early 2010.
In January 2010, they isolated
one novel H1N1 variant termed
42
Published in Virus Research
Compatible partners
Optimal enzyme activity for viral replication of a
pandemic swine-flu virus hinges on the enzyme’s
subunit origins
To replicate successfully, influenza
viruses (pictured) require the activity
of an RNA polymerase that consists
of three subunits: PB1, PB2 and PA.
swine/HK/201/10, which appears to
be an amalgam of genes from three
other strains. Importantly, the gene
encoding one major viral surface pro-
tein, neuraminidase, appears to have
originated from H1N1/2009, while
the other, hemagglutinin, is derived
from a different strain; as a result,
the H1N1/2009 vaccine is ineffec-
tive at blocking swine/HK/201/10
infection. Based on these findings,
Guan and Peiris caution that further
viral genome reorganization could
give rise to a more virulent influenza
strain in the near future, and advocate
more aggressive swine surveillance to
identify and intercept these variants
as they emerge.
Vijaykrishna, D. et al. Reassortment of pandemic
H1N1/2009 influenza A virus in swine. Science 328,
1529 (2010).
Now, researchers at the National
Center for Genetic Engineering and
Biotechnology in Thailand have found
that mixing subunits from different
influenza viral strains reduces the
activity of this enzyme and renders
it less able to replicate virus in cell
culture experiments.
The PA protein of the pandemic
swine-origin influenza virus (S-OIV)
of 2009 contains the amino acid serine
at position 186. Older swine flu strains
and human and avian flu viruses, how-
ever, contain the amino acid glycine
at this position. When the researchers
switched this serine in S-OIV PA to
glycine, the function of the S-OIV
RNA polymerase was reduced. They
also found that switching the glycine
at position 186 in an older swine flu
strain to a serine enhanced the activity
of an RNA polymerase that was also
composed of PB1 and PB2 from the
S-OIV strain.
The findings suggest to the
researchers that S-IOV is unlikely to
mix, or re-assort, with other strains to
create new viral strains. The results also
provide insight into how the enzyme
subunits work together to drive RNA
polymerase activity. Further, targeting
amino acid 186 may be efficacious in
fighting viral growth.
Wanitchang, A., Jengarn, J. & Jongkaewwattana, A.
The N terminus of PA polymerase of swine-origin
influenza virus H1N1 determines its compatibility with
PB2 and PB1 subunits through a strain-specific amino
acid serine 186. Virus Research 155, 325-333 (2011).
www.natureasia.com/A-IMBN

Published in Human Molecular Genetics
Cellular stress protection
Insights into the physiological function of a membrane
transport protein may explain the mechanism
underpinning a human vascular disease
A research team based in Taiwan has
revealed the mechanism by which
mutations in a membrane-bound
protein called glucose transporter 10
(GLUT10), which actually transports
solutes, can lead to the vascular
disease called arterial tortuosity
syndrome (ATS). Lax skin and joints,
as well as twisting of the major
arteries, which can cause aneurysms
and strokes, are hallmarks of patients
with ATS.
Building on earlier work by other
researchers who identified GLUT10
deficiency as the cause of ATS, the
research team, led by Yan-Tsong Chen
of Taiwan’s Academia Sinica, showed
that GLUT10 is expressed in the
mitochondria of smooth muscle cells
of mice.
The team also showed that, in
contrast to similar forms of this
protein that transport glucose,
GLUT10 actually delivers dehydro-
ascorbic acid (DHA) — the oxidized
form of vitamin C. Once in the
mitochondria, DHA protects the cell
from the ravages of reactive oxygen
species, a common by-product of
mitochondrial function.
The researchers conclude that
when mutations stop GLUT10
from functioning, ATS results from
excessive oxidative stress in smooth
muscle cells, which leads to distorted
and misshapen arteries. They also
note that their findings underline the
importance of a derivative of vitamin
C and reactive oxygen species in
degenerative diseases.
Lee, Y.-C., Huang, H.-Y., Chang, C.-J., Cheng, C.-H.
& Chen, Y.-T. Mitochondrial GLUT10 facilitates
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | STRUCTURAL & MOLECULAR BIOLOGY
dehydroascorbic acid import and protects cells against
oxidative stress: mechanistic insight into arterial
tortuosity syndrome. Human Molecular Genetics
19, 3721-3733 (2010).
Published in Proceedings of the National Academy of Sciences USA
Tracking transcriptional traffic
Detailed maps capture the starts and stops of the
machinery at the core of gene expression
Although the RNA polymerase
complex (Pol II) hypotheti-
cally travels in a straight line as it
transcribes gene sequences into
messenger RNA, its actual journey
is less straightforward. Transcription
proceeds in fits and starts, and is
coupled to other complex processes
such as splicing, in which non-
protein-coding intron sequences are
neatly excised from the ‘rough draft’
RNA transcript.
To chart the dynamic behavior
of Pol II during transcription, a
team led by Tatsuhiko Kodama and
Sigeo Ihara of the University of
Tokyo, Japan, and Peter Cook at the
University of Oxford, UK, performed
an elaborate series of time-course
experiments to track RNA produc-
tion from five large genes. All five are
activated by a common factor, tumor
© ISTOCKPHOTO/kativ
necrosis factor-α, which enabled the
researchers to turn on and track each
gene simultaneously.
They observed that each rough
transcript is produced in a fast-
moving initial ‘wave’; during this
period, additional waves start but do
not progress, and late-arriving Pol
II complexes produce only short,
abortive transcripts. Pol II doesn’t
appear to brake for splicing, with
introns trimmed almost as quickly
as they can be transcribed. However,
the complex does stall at sites
where DNA-interacting proteins
RAD21 and CTCF are bound. The
authors speculate that these may
act as physical roadblocks to Pol
II-mediated elongation.
Wada, Y. et al. A wave of nascent transcription on
activated human genes. Proceedings of the National
Academy of Sciences USA 106, 18357–18361 (2009).
43
STRUCTURAL & MOLECULAR BIOLOGY | A-IMBN RESEARCH
© ISTOCKPHOTO/dra_schwartz
Published in The Plant Cell
Working with a silent partner
Proper functioning of a key plant enzyme depends
on collaboration between a biologically active
‘catalytic’ subunit and a passive ‘regulator’ subunit
Early stages in the production of the
diverse family of biologically active
molecules known as terpenes depend
on the coordinated activity of various
prenyltransferase (PTS) enzymes.
The best characterized of these
operate as ‘homomeric’ complexes
containing two copies of the same
protein subunit. However, new work
from a team led by Tao-Hsin Chang
and Andrew H.-J. Wang at the
Academia Sinica in Taiwan has now
revealed details of the workings of a
more engimatic ‘heteromeric’ PTS,
C10-GPP synthase (GPPS), from the
mint plant Mentha piperita (Mp).
Mp GPPS contains two copies
each of a large subunit (LSU) and a
small subunit (SSU). Although LSU
closely resembles the subunits of
homomeric PTS complexes, Chang
44
Published in Genes & Development
Unraveling the roles of multi-
tasking enzymes
Studies of genetically engineered mice are uncovering
subtle molecular mechanisms responsible for fine
tuning protein expression in mammalian cells
Over recent years, molecular biologists
have increasingly recognized the
functional importance of small RNA
molecules called microRNAs that
inhibit protein-coding messenger RNAs.
and Wang found that it lacks cata-
lytic activity on its own, and depends
on interactions with SSU to achieve a
stable, fully functional structure.
Mp GPPS can synthesize two
distinct terpene precursors of vary-
ing length, but synthesizes only the
shorter of the two in vivo. Based on
their crystal structure data — the
first ever obtained for a heteromeric
PTS — as well as a series of func-
tional experiments, the researchers
formulated a ‘two-chamber’ model in
which the non-catalytic SSU acts as
a regulator that physically constrains
the length of molecules synthesized
by the catalytic LSU.
Chang, T.-H. et al. Structure of a heterotetrameric
geranyl pyrophosphate synthase from mint (Mentha
piperita) reveals intersubunit regulation. The Plant
Cell 22, 454–467 (2010).
A microRNA biosynthesis
pathway — known as the canonical
pathway — that has been described in
fruit flies and nematodes requires two
RNA-processing enzymes: Drosha and
Dicer. A team led by Mark Chong of
the Walter and Eliza Hall Institute of
Medical Research in Australia has now
determined the roles of these enzymes
in mice.
Chong and his collaborators con-
firmed that both enzymes are required
for canonical microRNA biosynthesis
in mice. However, they found different
gene expression and protein profiles
of mice deficient in Drosha or Dicer,
suggesting their separate involvement in
other processes.
Further experiments revealed that
Drosha directly cleaves many messenger
RNAs in early-stage thymocytes, which
eventually mature into the functional T
cells of the immune system.
The researchers also identified a
number of unusual microRNAs gener-
ated by a Dicer-dependent but Drosha-
independent mechanism, demonstrating
that Dicer is involved in generating
different classes of microRNA in
mammalian cells. However, these
microRNAs were mostly distinct from
mirtrons, a previously identified class of
microRNAs in fruit flies and nematodes
that are generated by messenger RNA
splicing machinery.
They hope now to elucidate the com-
plex mechanistic details of microRNA
pathways in mammals.
Chong, M. M. W. et al. Canonical and alternate
functions of the microRNA biogenesis machinery.
Genes & Development 24, 1951–1960 (2010).
www.natureasia.com/A-IMBN

Published in Nature Materials
Spotlighting single
DNA molecules
Synthesis of light-active nanostructures paves the way
for detection of single DNA molecules
A new approach for synthesizing
light-active nanostructured probes to
detect single DNA molecules — using
the technique called surface-enhanced
Raman scattering (SERS) — has been
developed in Korea. Single-molecule
detection is expected to shed light on
the behavior of biomolecules in living
cells and clinical samples.
Because SERS-based single-mol-
ecule detection hinges on the probe’s
‘nano’-environment, reproducible
synthesis of well-defined nanostruc-
tures is essential. The researchers, led
by Jwa-Min Nam of Seoul National
University and Yung Doug Suh of
Korea Research Institute of Chemical
Technology, combined DNA hybrid-
ization and magnetic nanoparticle
separation to generate dumbbell-
shaped gold–silver nanostructures
with a light-active dye at the center
(pictured) in high yield.
First, the researchers synthesized
two sets of DNA–gold nanoparticle
conjugates and tethered the dye to
one of the DNA strands. After
magnetic separation, they bridged the
nanoparticles into dumbbells using a
complementary single-stranded DNA.
Finally, they deposited silver on the
gold, creating nanometer shells around
the gold nanoparticles.
By controlling the silver deposition,
the researchers could tune the nanome-
ter-size gap between the dye and metal
nanoparticles. This strategy significantly
enhanced the single-molecule sensitiv-
ity of the nanostructures, allowing
reproducible single-DNA detection.
The team is currently investigating
the potential implementation of their
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | STRUCTURAL & MOLECULAR BIOLOGY
nanostructures in fast, quantitative and
multiplexed assays to detect infections.
Lim, D.-K., Jeon, K.-S., Kim, H. M., Nam, J.-M.
& Suh, Y. D. Nanogap-engineerable Raman-active
nanodumbbells for single-molecule detection. Nature
Materials 9, 60–67 (2010).
Published in Proceedings of the National Academy of Sciences USA
Making the right connections
An unusual partnership between proteins appears to
underlie healthy development of the inner ear
Harmonin and Sans are among
the various proteins associated
with Usher syndrome, a hereditary
disorder characterized by congenital
impairments in hearing and balance
and a predisposition to blindness.
These proteins form a complex
that contributes directly to hair
cell development within the ear.
Now Mingjie Zhang’s team at the
Hong Kong University of Science
and Technology has revealed
important details about the basis for
this interaction.
Harmonin features multiple
evolutionarily conserved PDZ
domains, which mediate pro-
tein–protein interactions. Zhang
and co-workers observed that one
PDZ domain combines with a
nearby helical domain to form a
Sans-recognizing ‘supramodule’.
Although PDZ domains have
been extensively studied, they were
surprised to note that, in addition
to the canonical PDZ binding
behavior, the harmonin PDZ also
associates with the SAM domain of
Sans via a previously unidentified
interaction mechanism.
Many Usher syndrome patients
express variants of these two pro-
teins with mutations that directly
affect PDZ or SAM. Cell culture
experiments confirmed that these
alterations can severely impair Sans
and harmonin co-localization and
complex formation. The authors
conclude that their findings could
not only help illuminate the
molecular foundations of this debili-
tating disorder, but may also guide
discovery of previously overlooked
binding partners for some200 other
PDZ-containing proteins in the
human genome.
Yan, J., Pan, L., Chen, X., Wu, L. & Zhang, M. The
structure of the harmonin/sans complex reveals
an unexpected interaction mode of the two Usher
syndrome proteins. Proceedings of the National
Academy of Sciences USA 107, 4040–4045 (2010).
45
STRUCTURAL & MOLECULAR BIOLOGY | A-IMBN RESEARCH

Published in Proceedings of the National Academy of Sciences USA

Bacterial chaperonin
— a trick of the tail
Discovery of a way to disrupt the structure of a
key protein of the potentially pathogenic bacterium
Heliobacter pylori could lead to new therapeutics
© ISTOCKPHOTO/sgame

Shujian Cun and Hongzhe Sun of pylori (pictured), which can cause peptic
Hong Kong University may have dis- ulcers and stomach cancer.
covered an ‘Achilles heel’ of Heliobacter In most organisms, the ‘chaperonin’
proteins GroEL and GroES together
protect cells from heat shock, which
causes protein unfolding. GroES
forms the lid of a ‘molecular container’
composed of GroEL, inside which
encapsulated proteins rapidly refold.
Because GroES dysfunction is lethal,
natural selection should tolerate few
changes in the sequence of amino-acid
building blocks.
Cun and Sun studied HspA, a form
of GroES found in H. pylori that,
uniquely, has the amino acids histidine
and cysteine at particular positions
of its tail. Biochemical experiments
showed that these amino acids form an
oxidation-sensitive zinc-binding site.
On infection, the host’s immune
system releases zinc and reactive ‘oxy-
gen free radicals’ that damage bacteria.
Supporting the idea that the unusual
Founded in 1997, the Asia-Pacific International Molecular Biology properties of HspA help counter these
Network (A-IMBN) is an organization dedicated to bringing together defenses, the researchers found that
leading researchers and institutions in Asia and the Pacific Rim to bismuth antiulcer drugs displace zinc
promote the development of scientific and technical excellence in from the metal-binding site, disrupting
the protein’s structure.
molecular biology and genetic engineering research in the region.
Comparison with GroES proteins
from other organisms suggested that
The A-IMBN serves the scientific community through a range of the zinc-binding site of HspA may
activities including its fellowship program, technical workshops as well have evolved as a result of negative se-
as regular scientific conferences. lection against variation at neighboring
sites. This discovery may lead to new
drugs that can retard the emergence of
Further information about the work of the A-IMBN including details of drug resistance.
how to become a member can be found at www.a-imbn.org Cun, S. & Sun, H. A zinc-binding site by negative
selection induces metallodrug susceptibility in an
essential chaperonin. Proceedings of the National
Academy of Sciences USA 107, 4943–4948 (2010).

46 www.natureasia.com/A-IMBN
© ISTOCKPHOTO/Henrik Jonsson

Therapeutics
Immunology &
IMMUNOLOGY & THERAPEUTICS | A-IMBN RESEARCH
© ISTOCKPHOTO/Mike_Kiev
Published in The EMBO Journal
Last line of defense
Cellular enzymes keep influenza from running
rampant by putting the brakes on viral replication
For a virus, getting inside a cell is
only half the job; successful infec-
tion also requires the production of
new viral particles, a process that is
heavily dependent on factors found
within the environment of the host
cell. For example, recent studies have
indicated that cellular enzymes may
regulate the efficiency of influenza
A replication by selectively tagging
viral proteins with individual mol-
ecules of the small protein ubiquitin.
New findings from Michael Lai
and colleagues at Academia Sinica
in Taiwan have now confirmed the
importance of this modification.
Based on a series of screening
experiments, the researchers were
able to determine that USP11, a
ubiquitin-removing enzyme, acts
as an effective inhibitor of virus
production in cells infected by
influenza A.
48
Published in The Lancet
Taking a shot at pandemic flu
A large-scale clinical trial reveals the safest and most
effective vaccine formulation to provide immunity to the
2009 pandemic influenza A H1N1 virus
Seasonal influenza vaccines help
control the spread of specific influenza
viruses by preparing the body to mount
an immune response upon exposure
to those viruses. After the pandemic
Early in infection, the influenza
genome is transcribed to produce
proteins that include viral nucleo-
protein and the components of the
RNA-dependent RNA polymerase
complex, which subsequently
combine to drive replication of the
viral genome.
Lai and colleagues demonstrated
that nucleoprotein is a target of
ubiquitination, and that this modi-
fication plays an important role in
stabilizing its interaction with viral
RNA. They hypothesize that by
removing this individual ubiquitin
molecule, USP11 prevents the rep-
lication complex from forming and
thereby undermines the production
of new virus particles.
Liao, T.-L., Wu, C.-Y., Su, W.-C., Jeng, K.-S. &
Lai, M. M. C. Ubiquitination and deubiquitination
of NP protein regulates influenza A virus RNA
replication. The EMBO Journal 29, 3879-3890 (2010).
originating in Mexico in 2009, there
is a pressing need to develop safe and
effective vaccines against the H1N1
influenza viruses originating in swine.
Now, researchers from China report
a placebo-controlled clinical trial
on an H1N1 vaccine that has been
produced in China, and tested in over
12,000 individuals.
The researchers administered eight
different vaccine formulations to
determine which was the safest and
most effective. For example, different
antigen concentrations were included
in the vaccine to ascertain how little
antigen could be used to still obtain
an effective immune response. This is
an important question in the event of
a pandemic and the need to vaccinate
the population quickly with a limited
antigen supply.
The researchers also included for-
mulations with or without aluminium
adjuvant, a chemical that may boost
the immune response to the vaccine.
Interestingly, the formulations without
adjuvant promoted a higher level of
immunity, as assessed by antibody
measurements against a viral antigen.
The findings demonstrate the safety
and efficacy of this vaccine, and will
guide immunization parameters
for patients.
Liang, X.-F. et al. Safety and immunogenicity of 2009
pandemic influenza A H1N1 vaccines in China: a
multicentre, double-blind, randomised, placebo-
controlled trial. The Lancet 375, 56–66 (2010).
www.natureasia.com/A-IMBN

Published in Proceedings of the National Academy of Sciences USA
Curtailing cholera
Long-term immunity against cholera from a rice-based,
oral vaccine takes a step forward
A team led by Hiroshi Kiyono from
the University of Tokyo, Japan, has
developed a rice-based oral vaccine
(MucoRice-CTB) that effectively in-
duces neutralizing antibodies against the
acute, and often fatal, disease cholera.
MucoRice-CTB contains a compo-
nent of cholera toxin (CT) produced
by Vibrio cholerae, the bacterium
responsible for cholera. The researchers
previously showed that MucoRice-
CTB protects against CT-induced
diarrhea in mice and also induces CT-
neutralizing antibodies in monkeys.
They have now shown that intestinal
secretion of specific CT-neutralizing
IgA antibodies (or secretory IgA: SIgA)
following oral immunization with
MucoRice-CTB is critical for protec-
tion against CT-induced diarrhea in
mice. Immunized mice were protected
up to six months after primary immu-
nization and a further four months by a
single booster immunization.
MucoRice-CTB also protected mice
against enterotoxigenic Escherichia
coli (ETEC), another major cause
of human diarrheal disease, because
CT-neutralizing antibodies also rec-
ognize the heat-labile toxin of ETEC.
MucoRice-CTB remained effective
even after storage for three years at
room temperature, suggesting that it
could be distributed cheaply without
refrigeration. Moreover, oral admin-
istration of the vaccine eliminates the
need for needles and syringes.
The findings confirmed the potential
of MucoRice-CTB as a new-generation
oral vaccine. Clinical trials are now
needed to show whether it is effective in
preventing cholera and ETEC-induced
gastroenteritis in humans.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | IMMUNOLOGY & THERAPEUTICS
Tokuhara, D. et al. Secretory IgA-mediated protection
against V. cholerae and heat-labile enterotoxin-
producing enterotoxigenic Escherichia coli by rice-based
vaccine. Proceedings of the National Academy of Sciences
USA 107, 8794–8799 (2010).
Published in Proceedings of the National Academy of Sciences USA
Slow and steady
A single injection of a large insulin aggregate into
diabetic animals can allow for long-term regulation
of their blood glucose levels
A team of scientists from India has
found that one injection of a specially
formulated insulin aggregate into
diabetic animals can lead to steady
release of insulin into the blood for
over 100 days. If the findings can be
extended into humans, this insulin
aggregate formulation could revolu-
tionize diabetes treatment by drasti-
cally reducing the number of insulin
injections that diabetic patients need
to administer.
Current treatment calls for mul-
tiple daily injections of the hormone
insulin, which is a high burden for
patients to endure. The inability of
diabetes patients to regulate their
blood sugar levels can lead to compli-
cations such as nerve damage, kidney
failure and cataracts.
© ISTOCKPHOTO/youngvet
Insulin is responsible for pulling
glucose out of the blood and into all
of the body’s cells. The insulin that is
currently used for diabetes treatment
is made up of single insulin peptides
in solution. However, insulin peptides
can aggregate into larger structures.
The researchers thought that these
larger aggregates could allow for slow
and steady release of insulin peptides.
When they injected the insulin
aggregate into diabetic animals, this
allowed for long-term control of
blood glucose levels, and a decrease in
the incidence of cataracts and other
complications in the animals.
Gupta, S., Chattopadhyay, T., Singh, M. P. &
Surolia, S. Supramolecular insulin assembly II for
a sustained treatment of type 1 diabetes mellitus.
Proceedings of the National Academy of Sciences USA
107, 13246–13251 (2010).
49
IMMUNOLOGY & THERAPEUTICS | A-IMBN RESEARCH
CDC/MURPHY
Published in Nature Biotechnology
Flu fighter
A drug that induces clumping of an influenza virus
protein enhances the survival of mice that have been
exposed to the flu
A team of researchers from Hong
Kong and Canada may have found a
new treatment to combat influenza
infections. The findings are timely
because particular influenza virus
strains that infect humans are now
resistant to existing antiviral drugs.
Led by Kwok-Yung Yuen of
the University of Hong Kong, the
team revealed a molecule called
nucleozin that causes aggregation
of influenza virus nucleoprotein
and reduces viral replication in cell
culture experiments.
The researchers identified nu-
cleozin as a suitable drug candidate
by screening a large chemical library
of over 50,000 compounds. They
found that nucleozin could protect
a kidney cell line from viral toxicity.
Nucleozin induced nucleoprotein
aggregation in lung epithelial cells,
50
Published in Proceedings of the National Academy of Sciences USA
Fighting the flu virus
A campaign of very high-throughput screening for
anti-influenza compounds could lead to new treatments
for flu
Scientists in Taiwan have screened over
1.2 million chemicals to identify unique
compounds that inhibit the replication
of the influenza virus (pictured).
which prevented nucleoprotein
from moving into the nucleus and
playing a role in replication of the
virus. Nucleozin seemed to act
directly on viral nucleoprotein alone,
because of its nuclear-exclusion of
purified nucleoprotein protein, and
because a single point mutation in
nucleoprotein reduced the efficacy
of nucleozin.
Yuen and colleagues showed
that nucleozin also had efficacy in
animals: it was able to enhance the
survival of mice that were exposed
to the influenza virus. If nucleozin
has similar effects in humans, it may
expand the current treatments for
influenza infection.
Kao, R. Y. et al. Identification of influenza A
nucleoprotein as an antiviral target. Nature
Biotechnology 28, 600–605 (2010).
A few established pharmaceuticals
that target the influenza enzyme
neuraminidase are effective at inhibiting
viral replication once an individual is
infected. However, the rapid evolution
of drug-resistant influenza strains
reduced the effectiveness of these drugs,
highlighting the need to develop new
anti-influenza agents against different
viral targets.
Using very high-throughput screen-
ing methods, the researchers identified
several new classes of anti-influenza
compound, including inhibitors of the
viral RNA polymerase, which is es-
sential for viral replication. One of these
compounds, FA-2, is chemically similar
to a recently reported influenza inhibitor
called Nucleozin. They found that FA-2
targets the polymerase subunit nucleo-
protein, whereas a second chemical,
called compound 367, targets a different
polymerase subunit called PB1.
Further experiments revealed that
FA-2 potently inhibits the replication of
several virulent influenza strains in cul-
tured cells, and that it protects against
lethal influenza infection in mice.
The researchers used specific
mutations in nucleoprotein and PB1
to confirm the selective targeting of
compounds FA-2 and 367. They believe
that these new anti-influenza com-
pounds against different influenza RNA
polymerase subunits could lead to new
anti-influenza drugs.
Su, C.-Y. et al. High-throughput identification of
compounds targeting influenza RNA-dependent RNA
polymerase activity. Proceedings of the National Academy
of Sciences USA 107, 19151–19156 (2010).
www.natureasia.com/A-IMBN

Published in Leukemia
The good without the bad
Stem cell transplants that fight leukemia could cause
fewer side effects if patients are on the drug imatinib
Some blood cancers can be cured with
stem cell transplantation, but this
can lead to graft-versus-host disease
(GVHD) — a side effect where
the grafted cells mount an immune
response against host organs, causing
symptoms such as diarrhea, dry eyes
and mouth, and skin rashes.
Now, researchers collaborating
across multiple institutions, hospitals
and medical centers across Japan have
discovered that the drug called imatinib
could be used to prevent the onset
of GVHD.
Imatinib can be used to treat
GVHD after onset, and is also used to
prevent cancer recurrence. It inhibits
signaling pathways that drive the
pathological changes in organs that
characterize GVHD, such as the
formation of fibrous connective tissue
where it does not belong.
The researchers compared the medi-
cal records of patients who had been
treated with imatinib after receiving
their stem cell transplant, but before
the development of GVHD, with those
not treated with imatinib. They found
that the imatinib-treated patients had
decreased incidence and severity of
GVHD, particularly of the gastroin-
testinal tract-related symptoms such as
diarrhea and dry mouth.
Because the researchers based their
analysis on existing medical records,
they suggest that a clinical trial be
initiated in leukemia patients after stem
cell transplantation to test whether or
not the beneficial effects of imatinib
stand true in a large population.
Nakasone, H. et al. Prophylactic impact of
imatinib administration after allogeneic stem cell
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | IMMUNOLOGY & THERAPEUTICS
transplantation on the incidence of chronic graft
versus host disease in patients with Philadelphia
chromosome-positive leukemia. Leukemia
24, 1236–1239 (2010).
Published in Science
Poisoning the well of cancer
Biochemical and biophysical analyses explain
the ability of arsenic to promote the remission
of leukemia
Chromosomal abnormalities, such
as those that stem from ionizing
radiation or exposure to chemical
mutagens, can lead to a fusion of
genes that results in the expression of
a novel, cancer-causing protein. This
often occurs in leukemias, including
acute promyelocytic leukemia (APL).
Therapeutically targeting these
unique fusion proteins is of high
interest as they represent a way to
specifically target cancer cells without
harming genetically normal, healthy
cells. The drug arsenic trioxide has
already proved effective in inducing
durable remission of APL. Zhu Chen
and his colleagues in Shanghai and
elsewhere in China and France have
now revealed the molecular mecha-
nism that underlies this therapeutic
effect of arsenic.
© ISTOCKPHOTO/thelinke
Using biochemical, genetic and
biophysical techniques the team
showed that arsenic binds to the cys-
teine residues of one portion of the
fusion protein that causes APL. This
binding induces a conformational
change in the protein such that it
forms aggregates, which increases its
recognition by the components of
the cellular machinery that lead to
protein degradation. Reduction in
the levels of the cancer-promoting
fusion protein explains the ability
of arsenic to promote remission
of APL. With the molecular
mechanism now identified, further
refinement of arsenic therapy can
now be developed.
Zhang, X.-W. et al. Arsenic trioxide controls the fate
of the PML-RARα oncoprotein by directly binding
PML. Science 328, 240–243 (2010).
51
IMMUNOLOGY & THERAPEUTICS | A-IMBN RESEARCH
© ISTOCKPHOTO/Eraxion
Published in Nature Immunology
Dialing up diabetes
Discovery of a mechanism that triggers
inflammation in patients with type 2 diabetes could
lead to a new type of treatment
An international team of researchers
from Ireland, the US and Japan has
identified the protein islet amyloid
polypeptide (IAPP), which is found
in abnormal clumps in the pancreas
of diabetic patients, as the cause
of an increase of a regulator of the
immune system that plays an impor-
tant role in inducing diabetes. The
regulator, proinflammatory cytokine
interleukin-1β (IL-1β), increased
when the team stimulated pancreatic
immune cells with IAPP.
The team found that mice that
were expressing high levels of IAPP
and on a high-fat diet — a signifi-
cant risk factor for the development
of diabetes in humans — also exhib-
ited elevated levels of IL-1β.
The researchers showed that the
clumps of IAPP are engulfed by
52
Published in Proceedings of the National Academy of Sciences USA
Collaborating with the enemy
An inflammatory signaling protein switches off
essential immune surveillance systems that help keep
tumor growth in check
Cellular signaling factor interleukin-23
(IL-23) induces an inflammatory re-
sponse that is believed to be conducive
to accelerated tumor growth. IL-23
the immune cells of the pancreas.
This led to activation of a protein
complex called the inflammasome,
which was already known to be
involved in the generation of IL-1β.
In cells lacking portions of the
inflammasome complex, they found
that IAPP was unable to alter IL-1β
protein levels.
Interestingly, a drug currently
used to treat diabetes also inhibited
IL-1β production that was induced
by IAPP in the immune cells. The
research team argues that reducing
IAPP-induced activation of the
inflammasome may be a new way to
treat diabetes.
Masters, S. L. et al. Activation of the NLRP3
inflammasome by islet amyloid polypeptide
provides a mechanism for enhanced IL-1β in type 2
diabetes. Nature Immunology 11, 897–904 (2010).
also drives the proliferation of a specific
subset of helper T cells (Th17) that se-
crete another pro-inflammatory factor,
interleukin-17A (IL-17A), although it
remains controversial whether IL-17A
is also involved in cancer progression.
A research team led by Mark Smyth
at the Peter MacCallum Cancer
Centre in Australia has helped to
clarify this situation, using a variety of
mouse tumor models to characterize
the growth-promoting or inhibitory
effects of these two interleukins. In
virtually every case examined, produc-
tion of IL-23 was directly associated
with tumor growth and metastatic
spread, and even undermined the
effectiveness of treatment strate-
gies known to reduce formation of
lung metastases. In comparison, the
researchers observed no significant
contribution from IL-17A to IL-23-
mediated acceleration of progression
in any of these cancer models.
The researchers note that IL-23 ap-
pears to act by thwarting the activation
of natural killer cells, which aggres-
sively target cancer cells for destruc-
tion, although the detailed mechanism
of this immunosuppression remains
unclear. Nevertheless, Smyth and
colleagues hypothesize that antibodies
or other drugs that selectively target
IL-23 have the potential to boost the
effectiveness of existing cancer thera-
peutic strategies.
Teng, M. W. L. et al. IL-23 suppresses innate
immune response independently of IL-17A
during carcinogenesis and metastasis. Proceedings
of the National Academy of the Sciences USA
107, 8328–8333 (2010).
www.natureasia.com/A-IMBN

Published in Nature Cell Biology
Unmasking bacterial saboteurs
A bacterial protein helps eliminate a key component of
the body’s defense mechanisms against infection
Bacteria produce molecules that set
off immune system alarms, but many
have also developed strategies that
enable them to directly counter the
body’s defensive response by blocking
immune signaling cascades.
A team led by University of Tokyo
researcher Chihiro Sasakawa has now
revealed how one of these factors, the
protein IpaH9.8 in the Shigella bacte-
rium (pictured), achieves its sabotage
of the host inflammatory response.
IpaH9.8 acts as an E3 ubiquitin ligase,
an enzyme that marks other proteins
for rapid destruction by tagging them
with ubiquitin molecules, although its
specific targets have remained a mystery.
Sasakawa’s team found that this
protein inhibits the activity of NF-κB,
a transcription factor that activates
numerous genes involved in triggering
inflammation. Screening experiments
subsequently confirmed that IpaH9.8
binds to NEMO, an upstream activator
of NF-κB, and ABIN-1, a protein
that normally inhibits this activation.
Interestingly, ABIN-1 appears to di-
rectly facilitate the action of IpaH9.8,
enhancing binding to and subsequent
ubiquitination of NEMO.
Mice infected with Shigella lacking
functional IpaH9.8 exhibited more
protracted inflammatory responses and
reduced numbers of bacteria in their
lung tissue.
The authors conclude that the accel-
erated degradation of NEMO induced
by this effector keeps the inflammatory
response in check and thereby clears
the way for infection.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | IMMUNOLOGY & THERAPEUTICS
Ashida, H. et al. A bacterial E3 ubiquitin ligase
IpaH9.8 targets NEMO/IKKγ to dampen the host
NF-κB-mediated inflammatory response. Nature Cell
Biology 12, 66–73 (2010).
Published in Proceedings of the National Academy of Sciences USA
Pathways of presentation
Specialized subsets of immune cells use separate
cellular pathways to display antigen on their
cell surface
When fighting infection, T cell
response is driven by antigens
presented on the surface of im-
mune cells called dendritic cells
(DCs). Typically, before being
presented at the cell surface, DCs
must degrade the antigen and load
the processed version of it onto
specialized molecules.
Now, a team of researchers
from Australia and France report
different mechanisms by which
different kinds of DCs in the spleen
present antigens.
When the researchers obtained
DCs from the spleen of animals
that had abdominal inflammation,
they found that these inflamma-
tory DCs use the mannose receptor
protein to send antigen to a cellular
compartment called the endosome.
There, the inflammatory DCs use
an enzyme called insulin-regulated
CDC
aminopeptidase (IRAP) to cleave the
antigen and load it onto the special-
ized antigen presentation machinery.
The researchers observed that
inflammatory DCs lacking the
mannose receptor or IRAP exhibited
decreased antigen presentation.
However, CD8+ DCs derived from
the spleen of healthy animals did not
use these proteins to present antigen.
Additional studies are needed to
characterize how CD8+ DCs process
antigen for display on their surface.
Nevertheless, the findings have
important implications for vaccine
development, since targeting antigen
to specific types of DCs can elicit
a more efficacious T cell response
to antigen.
Segura, E., Albiston, A. L., Wicks, I. P., Chai, S. Y.
& Villadangos, J. A. Different cross-presentation
pathways in steady-state and inflammatory
dendritic cells. Proceedings of the National Academy
of Sciences USA 106, 20377–20381 (2009).
53
IMMUNOLOGY & THERAPEUTICS | A-IMBN RESEARCH
CDC
Published in Nature
Infection-proofing by the gut
Clarification of the details of the molecular
mechanism of the intestinal immune system may
lead to new oral vaccines
An international research team has
unraveled the molecular details
of a key mechanism of the largest
segment of the immune system, the
lining of the gut. The work opens the
way to developing versatile, inexpen-
sive vaccines that are imbibed, rather
than injected.
In an investigation that employed
the latest techniques of micro-dis-
section, microarray analysis, staining,
microscopy and molecular genetics,
Hiroshi Ohno and colleagues from
the RIKEN Research Center for
Allergy and Immunology, Yokohama,
working with biologists from several
Japanese universities and Stanford
University in the US, have uncovered
a receptor molecule, glycoprotein 2
(GP2), on specialized microfold or
M cells of the gut lining. M cells are
54
Published in Proceedings of the National Academy of Sciences USA
Unlikely allies
against infection
Intestinal bacteria help out their hosts by
strengthening immune protection against other, less
benevolent microbes
Multitudes of bacteria make themselves
a happy home within the mammalian
small intestine. However, these resi-
dents are not merely freeloaders, but
involved in moving antigens from
the gut cavity to immune system
cells beneath. GP2 stimulates this
immune response by binding to a
protein on the hair-like projections or
pili of bacteria such as Escherichia coli
and Salmonella.
Ohno and colleagues experiment-
ed with mixing GP2 with E. coli, and
found that it linked to the protein
FimH on the type 1 pili of bacteria.
In fact, GP2 binds only to bacteria
that carry FimH, and not to those
without. The researchers found the
immune process was severely ham-
pered in Salmonella lacking FimH
and in mice lacking GP2.
Hase, K. et al. Uptake through glycoprotein 2
of FimH+ bacteria by M cells initiates mucosal
immune response. Nature 462, 226–230 (2009).
instead ‘earn their keep’ by facilitating
host digestion and metabolism, among
other functions.
New findings from a research team
led by Hiroshi Kiyono of the University
of Tokyo, Japan, now offer important
insights into another important func-
tion of these gut flora (pictured), reveal-
ing how the bacteria residing within
clumps of immune cells known as
Peyer’s patches (PPs) contribute to host
defense against pathogenic microbes.
Kiyono and colleagues determined
that the interior of mouse PPs is largely
populated by Alcaligenes, a common
opportunistic bacterium. Its presence
appears to trigger a highly localized
immune response, characterized by
elevated levels of IgA antibodies within
the gut, without inducing a strong
systemic reaction.
These antibodies appear to directly
contribute to stable internalization of
Alcaligenes within PPs. They also found
that this bacterium is in turn important
to proper development and function of
the mucosal immune system; without
Alcaligenes, mice generate considerably
fewer mature IgA-secreting cells.
This bacterium also resides within
primate and human PPs, and the au-
thors conclude that these and other
findings from their study may hint at
contributions of other bacterial species
to immune system development at the
whole-body level.
Obata, T. et al. Indigenous opportunistic bacteria
inhabit mammalian gut-associated lymphoid tissues
and share a mucosal antibody-mediated symbiosis.
Proceedings of the National Academy of Sciences USA
107, 7419–7424 (2010).
www.natureasia.com/A-IMBN

Published in Proceedings of the National Academy of Sciences USA
When antibiotics backfire
Antibiotic compounds directly initiate a defense
mechanism in certain highly pathogenic bacteria that
greatly undermines their effectiveness as drugs
Staphylococcal bacteria represent a
serious health concern, in part because
of their remarkable capacity to protect
themselves. For example, individual
Staphylococcus epidermidis cells can
respond to treatment with antibiotics
by banding together to form biofilms
that are resistant to both pharmaceuti-
cals and host immune cells. Initiation of
biofilm formation depends on produc-
tion of polysaccharide intercellular
adhesin (PIA) molecules.
New research from a team led by
Andrew Wang at the Academia Sinica
in Taiwan has revealed a mechanism
by which commonly used antibiotics
actually promote drug resistance by
activating the Ica genes that govern
PIA synthesis.
The S. epidermidis protein TcaR
is a known regulator of the Ica gene
cluster, and the researchers were able
to determine how interacting pairs of
TcaR molecules bind to specific DNA
sequence elements, physically obstruct-
ing gene expression and thus repressing
PIA production. However, TcaR is also
capable of binding to a diverse array of
antibiotics, including penicillin, kana-
mycin and chloramphenicol.
The researchers revealed that these
various molecules introduce structural
alterations in TcaR that interfere with its
capacity to bind DNA. As a result, these
drugs effectively alleviate Ica repression
and actively promote biofilm formation.
Wang and co-workers conclude that the
discovery of molecules that target this
regulatory pathway could help thwart
staphylococcal drug resistance.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | IMMUNOLOGY & THERAPEUTICS
Chang, Y.-M. et al. Structural study of TcaR and its
complexes with multiple antibiotics from Staphylococcus
epidermidis. Proceedings of the National Academy of
Sciences USA 107, 8617–8622 (2010).
Published in Nature Immunology
Fate director
Understanding the development of allergic
inflammation advances from the identification of a
crucial protein
Allergic responses can be triggered
by the inflammatory cytokine inter-
leukin-9 (IL-9), which is secreted
by a recently identified subset of
T cells called TH9 cells. Now, a
team of researchs from the US
and Australia, led by Mark Kaplan
from the Indiana University School
of Medicine, has identified that a
transcription factor protein called
PU.1 is needed for the development
of these cells.
The researchers found that T cells
from PU.1-deficient mice secreted
less IL-9 than T cells from normal
mice. When they forced expression
of PU.1 in T cells in cell culture,
they noted an increase in IL-9
expression. PU.1 seemed to act by
binding directly to the IL-9 gene in
the genomic DNA, and inducing the
expression of IL-9.
© ISTOCKPHOTO/ VisualField
In PU.1-deficient mice, the
researchers observed less allergic
airway inflammation in response
to antigen exposure, and this cor-
related with less IL-9 expression
in their T cells. Alterations in
levels of IL-9 also seemed to affect
allergic responses in humans: in
young children with allergies, the
researchers found increased expres-
sion of IL-9, which may have come
from TH9 cells. Moreover, blocking
PU.1 expression in human T cells
decreased IL-9 production.
Blocking production of PU.1
and IL-9 may provide therapies to
prevent or treat allergic responses,
the team suggests.
Chang, H. et al. The transcription factor PU.1 is
required for the development of IL-9-producing T
cells and allergic inflammation. Nature Immunology
11, 527–534 (2010).
55
IMMUNOLOGY & THERAPEUTICS | A-IMBN RESEARCH
© ISTOCKPHOTO/AndyL
Published in Proceedings of the National Academy of Sciences USA
Building a better booster
Stronger protective immune responses from vaccines
could now be possible from a modification made to a
modulator of immune cells
Vaccine efficacy can be improved by
adding chemicals called ‘adjuvants’
that boost the immune system, but
finding the right molecule for the job
can require iterations of modification.
In phase I clinical trials using
the molecule α-galactosylceramide
(α-GalCer) to activate immune cells
and modulate the immune response
to a foreign antigen, researchers
recorded limited biological activity.
Now, a team of researchers from
the US and Taiwan has designed a
molecule called 7DW8-5, a modifi-
cation of α-GalCer, which can serve
as a powerful adjuvant in mouse
models, and so could be promising
in humans.
The team found that 7DW8-5
was more effective than α-GalCer
at inducing inflammatory cytokine
secretion from human immune cells.
56
Published in Modern Pathology
Immune response linked to
early arrival
Chronic inflammation of the placental membranes
surrounding the fetus is linked to spontaneous preterm
birth in humans
Babies born prematurely have an
increased risk for developing cerebral
palsy and other chronic illnesses.
Understanding why preterm birth
7DW8-5 also bound more tightly
than α-GalCer to protein receptors
on both mouse and human immune
cells that are critical for modulating
immune responses.
The immune systems of mice
seemed to react more strongly to
malaria and HIV vaccines when
7DW8-5 was co-administered as
the immune-boosting adjuvant than
when α-GalCer was co-administered,
and the mice were better able to fight
infection if they had received vaccine
with the 7DW8-5 adjuvant. The
researchers contend that 7DW8-5
may be a new and efficacious adju-
vant to use in human vaccine clinical
trials in the future.
Li, X. et al. Design of a potent CD1d-binding
NKT cell ligand as a vaccine adjuvant. Proceedings
of the National Academy of Sciences USA
107, 13010–13015 (2010).
occurs is the first step toward devel-
oping appropriate interventions to
prevent it. Now, researchers in the US
and Korea have found that chronic
inflammation of the membranes
around the fetus — called chronic
chorioamnionitis — is prevalent in
patients who experienced spontaneous
preterm birth.
The researchers examined micro-
scopic sections of placental tissue —
including the fetal membranes — from
700 women who had given birth. They
found that the women who went into
labor spontaneously before their due
date had a much higher rate of chronic
chorioamnionitis than women who
delivered full-term babies.
The team found that expression of
inflammatory chemokines that induce
immune cell recruitment was increased
in the fetal membranes in patients
with chronic chorioamnionitis. They
therefore think that chronic chorio-
amnionitis may be caused by inflam-
matory processes that occur because
of a reaction of the mother’s immune
system against the fetus.
The preterm births that were associ-
ated with chronic chorioamnionitis oc-
curred later in pregnancy than preterm
births linked to acute chorioam-
nionitis, which is caused by bacterial
infections. The research team therefore
suggests that chronic chorioamnionitis
may explain near-term preterm births.
Kim, C. J. et al. The frequency, clinical significance,
and pathological features of chronic chorioamnionitis:
a lesion associated with spontaneous preterm birth.
Modern Pathology 23, 1000-1011 (2010).
www.natureasia.com/A-IMBN

Published in Nature
Single protein seeks
mature partner
Structural analysis reveals details of an important
safeguard mechanism for proper immune
system development
Within the mammalian thymus, a
sophisticated DNA recombination
process ensures the production of a
diverse array of T cell receptor (TCR)
protein complexes. This heterogeneity
is essential, as TCRs play a pivotal role
in recognizing potential threats from
foreign molecules within the body.
The pre-TCR, which consists of an
α-chain (pre-Tα) and a successfully
recombined TCR β-chain, helps drive
maturation of TCR-expressing cells.
Now, new findings from a team led by
James McCluskey at the University
of Melbourne and Jamie Rossjohn at
Monash University, Australia, have
revealed how pre-Tα molecules selec-
tively associate with mature β-chains to
move this process forward.
Both proteins are membrane-bound
(see image), and the researchers began
by collecting structural data for the
segments that project from the cell
membrane. They found that when these
two molecules are bound together, the
recombined ‘variable’ region of the
β-chain remains unpaired. Based on the
chemical composition of the exposed
regions, one might predict this to be an
unstable arrangement.
Rossjohn and McCluskey
determined, however, that these com-
plexes actually pair-off in dimers, with
a head-to-tail arrangement that shields
the exposed residues. This mode of
interaction can only occur with mature,
processed β-chains, such that this
highly stable arrangement also serves
as a ‘sensor’ for the production of fully
functional TCR components.
RESEARCH HIGHLIGHT COLLECTION 2010
A-IMBN RESEARCH | IMMUNOLOGY & THERAPEUTICS
Pang, S. S. et al. The structural basis for autonomous
dimerization of the pre-T-cell antigen receptor. Nature
467, 844–848 (2010).
Published in Proceedings of the National Academy of Sciences USA
Protective markings
Rapid antiviral response depends on enzymatic
modification of a protein that helps activate the
immune system
For many proteins, getting tagged
with molecules of ubiquitin is a
sentence of death via enzymatic
destruction, while other proteins
depend on ubiquitination to suc-
cessfully execute their functions in
the cell.
A recent study from a team led
by Kunitada Shimotohno at Japan’s
Chiba Institute of Technology has
added the NEMO protein to this
latter list. NEMO is known to be an
important ‘middle man’ in the innate
immune response, which represents
the first line of defense against viral
infection, although the details of its
involvement have been unclear.
Shimotohno and colleagues
demonstrated that NEMO interacts
with enzyme TRIM23, which modi-
fies at least five different sites on
the protein by appending multiple
molecules of ubiquitin arranged in a
© 2010 NPG
highly atypical chain configuration.
A number of genes that are typically
activated in response to viral infec-
tion showed reduced activity in cells
subjected to TRIM23 depletion, and
these cells also showed an impaired
capacity to produce signaling
factors that promote the innate
immune response.
These various antiviral responses
appear to be directly dependent
on TRIM23-mediated multi-site
ubiquitination of NEMO. As this
pathway is triggered in response
to a broad variety of viruses, the
authors suggest that it may prove
worthwhile to develop therapeutic
strategies that specifically stimulate
TRIM23 activity.
Ariomoto, K. et al. Polyubiquitin conjugation to
NEMO by triparite motif protein 23 (TRIM23) is
critical in antiviral defense. Proceedings of the National
Academy of Sciences USA 107, 15856–15861 (2010).
57
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