Broad Opp. No. 3

Filed on behalf of: Junior Party, Broad
By:
Steven R. Trybus
Harry J. Roper
Paul D. Margolis
Jenner & Block LLP
353 North Clark Street, Chicago, IL 60654
Telephone: 312-222-9350
Facsimile: 312-527-0484
strybus@jenner.com
Paper No. ____
UNITED STATES PATENT AND TRADEMARK OFFICE

____________________
BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________________
THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF
TECHNOLOGY, and PRESIDENT AND FELLOWS OF HARVARD COLLEGE,
(Patents 8,697,359; 8,771,945; 8,795,965; 8,865,406; 8,871,445; 8,889,356; 8,895,308;
8,906,616; 8,932,814; 8,945,839; 8,993,233; 8,999,641 and Application 14/704,551),
Junior Party,
v.
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, UNIVERSITY
OF VIENNA, and EMMANUELLE CHARPENTIER
(Application 13/842,859),
Senior Party.
Patent Interference No. 106,048 (DK)
BROAD et al. OPPOSITION 4
TABLE OF CONTENTS
I.
PRECISE RELIEF REQUESTED.......................................................................................1
II.
DESCRIPTION OF APPENDICES ....................................................................................1
III.
REASONS WHY THE MOTION SHOULD BE DENIED ................................................1

A.
Summary Of The Argument ....................................................................................1

1.
Doudna P1s Failure to Discuss Any Role of PAM Sequences

Would Have Conveyed a Lack of Possession for Non-Natural
Targets..........................................................................................................1
2.
Doudna P1 and P2 Do Not Reasonably Convey Possession of a

CRISPR-Cas9 System Adapted to Function in Eukaryotic Cells ................2
3.
The Guidance Set Forth in Doudna P1 and P2 Did Not Enable

Ordinarily Skilled Persons to Practice the Methods of Count 1 ..................3
4.
Doudna P3 Fails to Show Possession of the Invention of Count 1..............4
B.
Legal Standards ........................................................................................................4
C.
Senior Party Mischaracterizes The Factual Background Relating To

Allegedly Successful CRISPR Systems for Eukaryotic Cells To
Compensate for the Lack of Sufficient Disclosure in Its Provisional
Applications .............................................................................................................5
D.
1.
The Junior Partys Scientists Commenced CRISPR-Cas9 Work in

Eukaryotic Cells in 2011 and Achieved Success Prior to Jinek
2012..............................................................................................................6
2.
The Senior Party Inventors Approach Led to Many Frustrations

When Adapting Their System to a Eukaryotic Environment ......................8
3.
The Industry Recognized Dr. Zhangs Eukaryotic Contribution ...............10
Senior Party is Not Entitled to the Benefit of its Doudna P1, Doudna P2,
or Doudna P3 Applications ....................................................................................11
1.
Persons Of Ordinary Skill Would Have Concluded That Doudna

P1 Lacks Written Description Support For A CRISPR-Cas9
System For Use With Non-Natural Targets, Including Eukaryotic
DNA ...........................................................................................................11
2.
IV.
Persons Of Ordinary Skill Would Have Concluded That Doudna

P1 And P2 Do Not Reasonably Convey Possession Of A CRISPRCas9 System Adapted to Function In Eukaryotic Cells .............................14
a.
The Combination of Example 1, Paragraph 00165 and

Various Claims With Eukaryotic Limitations From Doudna
P1 and Doudna P2 Did Not Convey Possession ............................14
b.
Contemporaneous And Pre-Interference Statements

Confirm The Lack of Possession Based on In Vitro Tests ............17
c.
Persons of Ordinary Skill Would Not Have Known

Whether A CRISPR-Cas9 System That Functioned In Vitro
Would Function in a Eukaryotic Cell ............................................20
d.
Prior Difficulties Experienced in Attempting to Adapt

Other Prokaryotic Systems to Function in Eukaryotic Cells .........23
e.
The Later Work of Other Laboratories Does Not Support

Senior Partys Written Description Argument ...............................24
3.
The Doudna P1 And P2 Applications Do Not Enable A Skilled

Artisan To Practice An Embodiment Of Count 1 ......................................26
4.
The Doudna P3 Application Does not Provide Written Description

Support For An Embodiment Of Count 1 ..................................................28
CONCLUSION ..................................................................................................................30
APPENDIX 1: LIST OF EXHIBITS ..............................................................................................1

APPENDIX 2: STATEMENT OF MATERIAL FACTS................................................................1
ii
TABLE OF AUTHORITIES
Page(s)
CASES
Ariad Pharm., Inc. v. Eli Lilly & Co.,
598 F.3d 1336 (Fed. Cir. 2010)......................................................................................5, 15, 16
Chiron Corp. v. Genentech, Inc.,
363 F.3d 1247 (Fed. Cir. 2004)..................................................................................................5
Genentech Inc. v. Novo Nordisk AS,
108 F.3d 1361 (Fed. Cir. 1997)............................................................................................5, 27
Hunt v. Treppschuh,
523 F.2d 1386 (C.C.P.A. 1975) .................................................................................................5
In re Kaslow,
707 F.2d 1366 (Fed. Cir. 1983)..................................................................................................5
In re Wands,
858 F.2d 731 (Fed. Cir. 1988)..............................................................................................5, 27
Manning v. Paradis,
296 F.3d 1098 (Fed. Cir. 2002)................................................................................................21
Univ. of Rochester v. G.D. Searle & Co.,
358 F.3d 916 (Fed. Cir. 2004)....................................................................................................5
STATUTES
35 U.S.C. 112(a) ...........................................................................................................................5
OTHER AUTHORITIES
37 C.F.R. 41.202 ...........................................................................................................................5
MPEP 2163 ...................................................................................................................................5
iii
I.
PRECISE RELIEF REQUESTED

Junior Party Broad requests that the Board deny Senior Party Motion 4, which requests
that it be accorded the benefit of the filing date of each of its three Provisional Applications
(Doudna P1, P2 and P3). Senior Party should be denied the benefit of each of those applications.
II.
DESCRIPTION OF APPENDICES
Appendix 1 is a list of Exhibits cited in this motion. Appendix 2 is the Statement of
Material Facts, including a listing of UCs statement of facts, which are admitted, denied or
which cannot be admitted or denied, and Broads statement of facts in support of the opposition.
III.
REASONS WHY THE MOTION SHOULD BE DENIED
10
A.
11
Senior Party does not dispute that neither Doudna P1 nor Doudna P2 includes an
12
experiment that falls within the scope of Count 1, which is directed to a method of using
13
CRISPR-Cas9 systems to target DNA in eukaryotic cells. Instead, Senior Party relies on an in
14
vitro experiment in combination with the general disclosure that the system could be used in any
15
cells of interest, including eukaryotic cells. However, given the nascent state of the art, and
16
the uncertainties and unknowns associated with adapting the prokaryotic CRISPR-Cas9 system
17
to eukaryotic cells, as well as the failure to describe eukaryotic-specific considerations such as
18
use of a target sequence comprising a protospacer adjacent motif (PAM), the disclosures of
19
Doudna P1 and P2 fail to provide adequate written description and are non-enabling. Doudna P3
20
includes eukaryotic experiments, but the results are inconclusive at best and do not demonstrate
21
possession.
22
23
24
Summary Of The Argument
1.
Doudna P1s Failure to Discuss Any Role of PAM Sequences Would

Have Conveyed a Lack of Possession for Non-Natural Targets
Based on Doudna P1s lack of any discussion of the role, if any, of PAM sequences for
1
non-natural targets, persons of ordinary skill would not have understood that the inventors were
in possession of an invention within the scope of Count 1. Count 1 is directed to a method, in a
eukaryotic cell, of cleaving or editing a target DNA molecule or modulating transcription of at
least one gene encoded thereon. Thus, the method of Count 1 is directed to a target DNA
molecule in a eukaryotic cell, which would not be a natural target of the prokaryotic CRIPSR-
Cas9 system.
By Doudna P1s May 2012 filing date, publications had already disclosed that PAM
sequences played a role in the ability of a CRISPR system in bacteria to recognize natural DNA
targets. The complete lack of any discussion of PAM would have indicated to persons of
10
ordinary skill that the inventors failed to describe an invention configured for use against non-
11
natural targets in a eukaryotic cell. In other words, the inventors failed to describe information
12
that persons of ordinary skill would have expected and required for making and using a CRISPR-
13
Cas9 system capable of functioning against non-natural DNA targets, such as in eukaryotic cells.
14
Thus, from an objective point of view, the failure to mention any role of PAM would have led
15
one of ordinary skill in the art to conclude that the inventors did not have possession of an
16
invention that falls within the scope of Count 1.
17
18
19
2.
Doudna P1 and P2 Do Not Reasonably Convey Possession of a

CRISPR-Cas9 System Adapted to Function in Eukaryotic Cells
Doudna P1 lacks sufficient written disclosure for the additional reason that it fails to
20
show objectively that the inventors had overcome the other unknowns and uncertainties relating
21
to transferring the prokaryotic CRISPR-Cas9 system to eukaryotic cells. Doudna P2 fails for the
22
same reason. Given the nascent state of the art and the unpredictable nature of this field, persons
23
skilled in the art in 2012 would have required actual experiments in eukaryotic cells to
24
demonstrate possession. In fact, contemporaneous statements of Senior Party UCs expert Dr.
2
Carroll in 2012 confirm that skilled persons would not have considered in vitro tests and the
general disclosure of eukaryotic cells sufficient to demonstrate possession. In a September 2012
article, Dr. Carroll commented on the Jinek 2012 paper, noting the in vitro experiments and
expressing doubt about whether the system would work in eukaryotic cells. Dr. Carroll stated
that [o]nly attempts to apply the system in eukaryotes i.e., actual eukaryotic testswould
address his concerns. Ex. 1152, Carroll 2012 at 1660. Dr. Carrolls statements confirm what
skilled persons would have concluded upon reading Doudna P1 and P2that the inventors were
not yet in possession of an invention of a CRISPR-Cas system adapted to function in eukaryotes.
Senior Party attempts to compensate for the deficiencies in Doudna P1 and P2 by
10
focusing on the timing of alleged success by others and linking that to publication of its Jinek
11
2012 paper, which included the same in vitro tests as Doudna P1 and P2. However, the test for
12
possession depends on what skilled persons would have understood based on a reading of the
13
application as of its filing date, not later publications or whether a system later turned out to be
14
easy to implement in the hands of others. As Dr. Carrolls article confirms, skilled persons
15
reading Jinek 2012 (and thus Doudna P1 and P2) would not have concluded that the inventors
16
possessed an invention of a CRISPR-Cas9 embodiment of Count 1.
17
Moreover, Senior Partys attempt to attribute the later alleged success of other groups to
18
Jinek 2012 is also wrong on the facts. For example, Senior Party asserts that Jinek 2012
19
triggered and guided the work of the Junior Party at the Broad. However, the Broad scientists
20
commenced their eukaryotic work in 2011 and were successful prior to Jinek 2012s publication.
21
Senior Partys reliance on other groups is also flawed.
22
23
24
3.
The Guidance Set Forth in Doudna P1 and P2 Did Not Enable

Ordinarily Skilled Persons to Practice the Methods of Count 1
Doudna P1 and P2 also do not enable embodiments within Count 1. Senior Party asserts
3
that skilled persons could have adapted the chimeric RNA system disclosed in Example 1 to
eukaryotic cells using only routine techniques. Senior Party relies on its own alleged success in
eukaryotic cells as reported in Doudna P3, asserting that Doudna P3 simply followed the
teachings of Doudna P1 and P2 using routine techniques. The actual facts, however, show that
after its in vitro tests, Senior Party experienced many frustrations in eukaryotic cells.
Moreover, the Senior Party inventors received unpublished data from another group, as detailed
below, and then published their own results in eukaryotic cells, further evidencing both a lack of
possession and enablement in Doudna P1 and P2.

4.
9
10
Doudna P3 Fails to Show Possession of the Invention of Count 1
Finally, while Doudna P3 reports experiments involving CRISPR-Cas9 systems in
11
eukaryotic cells, the results are inconclusive at best. Ordinarily skilled persons reading Doudna
12
P3 would have concluded that the inventors still did not describe information sufficient to
13
objectively show possession of the invention of Count 1.
14
Moreover, the disclosure present in Doudna P3, but missing in Doudna P1 and P2, such
15
as actual eukaryotic testing (albeit failed in P3) and specific techniques for CRISPR-Cas systems
16
for eukaryotic cells, illustrate the type of information that would have been expected in Doudna
17
P1 and P2 to demonstrate actual possession of a CRISPR-Cas9 system for eukaryotic cells.
18
B.
Legal Standards
19
A party seeking the benefit of an earlier application in an interference must establish that
20
the earlier application provided a constructive reduction to practice of an embodiment within
21
the scope of the count, which must satisfy both the written description and the enablement
22
requirements. 37 C.F.R. 41.202; Hunt v. Treppschuh, 523 F.2d 1386, 1389 (C.C.P.A. 1975).
23
24
The test for determining compliance with the written description requirement is whether
the disclosure of the application as originally filed reasonably conveys to the artisan that the
4
inventor had possession at that time of the later claimed subject matter, rather than the presence
or absence of literal support in the specification for the claim language. In re Kaslow, 707 F.2d
1366, 1375 (Fed. Cir. 1983). The application must show more than a wish or plan for
obtaining the claimed invention. Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927
(Fed. Cir. 2004). Rather, the description must clearly allow persons of ordinary skill in the art
to recognize that the inventor invented what is claimed. Ariad Pharm., Inc. v. Eli Lilly & Co.,
598 F.3d 1336, 1351 (Fed. Cir. 2010). When a technology is in an early stage of development,
the application typically must disclose more information to provide written description support.
Id. at 1358; see also MPEP 2163 ([F]or inventions in emerging and unpredictable
10
technologies, or for inventions characterized by factors not reasonably predictable which are
11
known to one of ordinary skill in the art, more evidence is required to show possession.).
12
A specification also must provide an enabling disclosure. 35 U.S.C. 112(a). A claim
13
can be sufficiently enabled even if experimentation is necessary, so long as the experimentation
14
is merely routine. If undue experimentation is needed, however, the claims are not enabled.
15
In re Wands, 858 F.2d 731, 737 (Fed. Cir. 1988). Moreover, when the invention arises out of
16
nascent technology, enablement requires a specific and useful teaching of how to practice the
17
invention. Genentech Inc. v. Novo Nordisk AS, 108 F.3d 1361, 1367-68 (Fed. Cir. 1997); see
18
also Chiron Corp. v. Genentech, Inc., 363 F.3d 1247, (Fed. Cir. 2004).
19
20
21
C.
Senior Party Mischaracterizes The Factual Background Relating To

Allegedly Successful CRISPR Systems for Eukaryotic Cells To Compensate
for the Lack of Sufficient Disclosure in Its Provisional Applications
22
Senior Partys Motion 4 is based on a flawed characterization of the factual background
23
of events leading to the development of CRISPR-Cas9 systems for eukaryotic cells. It is
24
indisputable that CRISPR-Cas9 was a nascent technology in an unpredictable field when Senior
25
Partys provisional applications were filed; yet, Senior Party has no eukaryotic experiments to
5
demonstrate possession or provide an enabling disclosure in Doudna P1 or P2. Facts 81, 85; Ex.
2009 11.117. Senior Party attempts to compensate for this lack of specific teachings by
focusing on the alleged impact of Jinek 2012 and timing of alleged success by others. According
to Senior Party at page 18, lines 17-19 and page 19, lines 15-24 of its Motion 4, the Jinek 2012
paper taught the necessary and sufficient components for a CRISPR-Cas9 complex, which
triggered four other independent groups to successfully use CRISPR-Cas9 systems in
eukaryotic cells. Senior Party states at page 18, lines 4-6, that the rapid success by other
groups after Jinek 2012 constitutes independent, empirical evidence that the First Provisional
describes and enables embodiments within the scope of Count 1. See also UC Motion 4 at
10
1:24-2:3 (arguing that success of others after Jinek 2012 evidences the sufficiency of the
11
guidance provided by the First Provisional as well as the ease and predictability of applying the
12
methods to eukaryotic cells.).
13
Junior Partys response is that Senior Partys characterization is flawed in three important
14
respects: (1) it assumes that Jinek 2012 triggered and guided the work of the other groups; (2) it
15
suggests that CRISPR-Cas9 work in eukaryotic cells did not occur prior to Jinek 2012 because
16
such work could not even proceed, or certainly be successful, until Jinek 2012 identified the
17
three minimal components of the CRISPR-Cas9 interference complex; and (3) it asserts that the
18
other groups implemented the Jinek system to achieve success.
19
Junior Party provides a more complete and accurate factual background below. The facts
20
show that the Junior Partys scientists work using CRISPR-Cas9 systems in eukaryotic cells
21
commenced long before the June 2012 publication of the Jinek 2012 paper.
22
23
24
1.
The Junior Partys Scientists Commenced CRISPR-Cas9 Work in

Eukaryotic Cells in 2011 and Achieved Success Prior to Jinek 2012
By early 2011, Junior Partys scientist Feng Zhang had conceived of the idea of, and
6
began experiments, adapting CRISPR-Cas9 systems to function in eukaryotic cells. See Ex.
2412; Paper 53; Ex. 2009 11.102. Fact 88. Prior publications had identified components as
playing a potential role in the natural CRISPR-Cas9 system. Fact 89; Ex. 1032; Ex. 1153; Ex.
1227; Ex. 2009 11.98. Dr. Zhangs group used those components for their eukaryotic
experiments, understanding that they were sufficient, without first determining the minimum
components that were necessary.
Consistent with that approach, Dr. Zhang filed a grant proposal with the NIH on January
12, 2012 showing his development of single vector delivery of a multiplexed system with dual
molecule guide RNAs and Cas9. Fact 90; Ex. 2411; Ex. 2009 11.97. Dr. Zhang identified the
10
design of a mammalian CRISPR expression system, using four componentsCas9 nuclease
11
and bacterial RNase III genes from Streptococcus thermophilus LMD-9, a tracrRNA element to
12
facilitate the processing of guide RNAs, and the guide RNA array. Ex. 2411 at 16 (caption for
13
Figure 4)(emphasis added). With those components, Dr. Zhang adapted a CRISPR-Cas9 system
14
to function in eukaryotic cells using a dual molecule guide RNA. Fact 91.
15
The Cong et al. 2013 article reported Dr. Zhangs success with a dual molecule guide
16
RNA, stating that Cotransfection of all four required CRISPR components resulted in efficient
17
cleavage of the protospacer in eukaryotic cells. Ex. 1055 at 2; Fact 92. Thus, Senior Partys
18
contentions that Jinek 2012 spurred DNA cleavage and gene editing eukaryotes using the
19
CRISPR/Cas9 system by the Junior Party and that knowledge of the minimal basic
20
components was required for success in eukaryotes are false. UC Motion 4 at 19:10-14.
21
Dr. Zhangs group at the Broad also later conducted tests relating to a single molecule
22
chimeric RNA, using a modified version of the Chimera A disclosed in Jinek 2012. Fact 96; Ex.
23
1055 at 2; Ex. 2009 11.11.106. The Broad scientists used special techniques that they
7
developed in their earlier eukaryotic work to adapt a modified Chimera A to function in
eukaryotic cells, including the use of two NLSs to target the Cas9 protein to the nucleus, a vector
to drive expression of the Cas9 and the chimeric guide, and a slightly longer tracrRNA segment
that included four extra nucleotides as compared to Chimera A. Fact 97; Ex. 1055 at 2; Ex. 2009
11.107. Even with those improvements, eight of the 14 modified Chimera A-type samples
tested by the Broad scientists did not work at all in a eukaryotic cell. Fact 98; Ex. 1055 at 20;
Ex. 2009 11.130. The tests showed that Chimera A with its short tracrRNA component was
inferior to the previously developed system with a longer tracrRNA component. Id.; Fact 163.
Other research groups also used a longer tracrRNA component in the eukaryotic
10
environment, as the Broad had. For example, the Church group at Harvard published the Mali
11
2013 article using a longer tracrRNA component. Fact 99; Ex. 1056 at 824 ; Ex. 2009 11.109.
12
The Junior Party includes both Harvard and the Broad. Fact 100. Harvard is affiliated with the
13
Broad and some Broad scientists have advisors at both institutions. Fact 100. Dr. George
14
Church was co-advisor to Dr. Cong, who conducted the tests at the Broad showing that the
15
longer tracrRNA functioned better in the eukaryotic environment than Chimera A. Fact 101;
16
Simons Tr. 89:4-15. Dr. Hwangs Harvard group thanked Church for sharing unpublished
17
results. Ex. 1058 at 6; Ex. 2009 11.109; Fact 102. None of these groups indicated Jinek 2012
18
triggered their initial work. Ex. 1055; Ex. 1056; Ex. 1058; Ex. 1059.
19
20
21
2.
The Senior Party Inventors Approach Led to Many Frustrations

When Adapting Their System to a Eukaryotic Environment
While Dr. Zhangs laboratory at the Broad worked at adapting CRISPR for eukaryotes
22
starting in 2011, the Senior Partys inventors took a different approach that led to many
23
frustrations in a eukaryotic environment. Ex. 2230, Ex. 2009 11.100. The Senior Partys UC
24
and University of Vienna inventors assert a conception date for Count 1, including the eukaryotic
8
cell claim limitations, no later than October 18, 2011. Fact 121; Senior Party Priority Statement
at 1. Senior Party Dr. Charpentier asserts an even earlier conception date of July 30, 2010. Fact
122; id. Yet, Senior Party does not assert that there was any actual reduction to practice until
October 29, 2012. Fact 103. Thus, Senior Party failed to make the claimed invention for over a
year (over two years for Dr. Charpentier), despite its contention that one would have been
immediately motivated to develop gene-editing tools for eukaryotic cells. Facts 121-122.
And, as described below, they did not report any success until after receiving unpublished data.
8
9
In 2011, the Senior Partys inventors took the approach of conducting in vitro
experiments to determine the minimal necessary and sufficient components, including a
10
minimal tracrRNA component length. Ex. 2009 11.99. The Senior Partys inventors created
11
two versions of a chimeric RNA with a covalent linker between the crRNA component and the
12
tracrRNA component, both with substantially shorter tracrRNA components than wild-type
13
tracrRNA. Ex. 1155, Jinek 2012 at 818, 820; Ex. 1003 at 2, 0006; Fact 93. The Jinek 2012
14
paper reported that Chimera A version worked efficiently in vitro, while the even shorter
15
Chimera B version did not. Fact 94; Ex. 1155 at 820. The Jinek 2012 paper did not teach any
16
longer tracrRNA components for use as a part of a chimeric RNA, but instead suggested to those
17
of ordinary skill the use of Chimera A. Ex. 1155; Ex. 2009 11.66; Fact 95.
18
However, Chimera A did not translate well to the eukaryotic environment. Fact 105.
19
Senior Party asserts in its Motion 4 at page 5:21-6:23 that one could adapt Chimera A for
20
eukaryotes using routine techniques. Junior Partys response is that Dr. Doudnas groupthose
21
who were best positioned to do what Senior Party now arguesactually experienced many
22
frustrations trying to make it work in eukaryotes, as Dr. Doudna publicly acknowledged:
23
24
Doudna experienced many frustrations getting CRISPR to work in human

cells. But she knew if she succeeded, CRISPR would be a profound discovery
9
1
2
3
and maybe even a powerful gene therapy technique.

Ex. 2230 (emphasis added); Fact 87.
The timeline of events corroborates Dr. Doudnas many frustrations. The Doudna P1
application, which was filed on May 25, 2012, set forth in vitro experiments with Chimera A and
expressed the hope that the system could be applied to eukaryotic cells. As Senior Party stated,
after publication of those results, persons of ordinary skill would have been immediately
motivated to apply the Type II CRISPR-Cas system to Eukaryotic cells. UC Motion 3 at 9
(emphasis added). Yet, the Doudna P2 application, filed four months later on October 19, 2012,
reported no such eukaryotic experiments despite such immediate motivation. Ex. 1004.
10
Indeed, consistent with Dr. Doudnas frustrations trying to adapt the Jinek system to
11
eukaryotes, Dr. Doudnas laboratory was surprised when they learned that Dr. Churchs
12
laboratory had achieved success in eukaryotes. Ex. 2230; Fact 106. It was only after the Church
13
laboratory shared unpublished data that Dr. Doudnas laboratory reported they were able to adapt
14
a CRISPR-Cas9 system for eukaryotic cells in the Jinek 2013 paper. Fact 107; Ex. 2009
15
11.141. The Senior Party inventors then filed a third provisional patent application (Doudna
16
P3) containing the same eukaryotic test results as in Jinek 2013. Ex. 1005 at Figures 36-38; Ex.
17
1055 at Figures 3-5; Fact 108. Those tests included the use of a chimeric RNA with longer
18
tracrRNA components than what was used in Chimera A. Fact 108. However, as discussed in
19
more detail below in Section III.D.4, the eukaryotic test results in the Jinek 2013 paper and
20
Doudna P3 are inconclusive at best, consistent with their many frustrations.
21
22
3.
The Industry Recognized Dr. Zhangs Eukaryotic Contribution
Thus, the Senior Party inventors focus on in vitro experiments led them to develop
23
Chimera A, but appears to have misguided their efforts to adapt a CRISPR-Cas9 system for use
24
in eukaryotic cells. The short tracrRNA component of Chimera A worked well in in vitro
10
environments, but not in the more complex eukaryotic environment. In contrast, Dr. Zhangs
approach resulted in the first CRISPR-Cas9 system adapted to function in eukaryotic cells.
The industry has recognized the pioneering nature of Dr. Zhangs work, differentiating it
from the biochemical work and in vitro data by the Senior Partys inventors. Recently, Drs.
Zhang, Horvath, Doudna, Charpentier and Barrangou jointly received the 2016 Gairdner Award
for their work with CRISPR-Cas systems. Ex. 2419; Fact 110. The Gairdner Foundations
announcement identified the respective contributions of each of the award recipients. For Dr.
Zhang, they noted that he pioneered the development of the microbial CRISPR-Cas system as a
[sic] genome editing tools for function in eukaryotic cells. See Fact 111; Ex. 2419 at 2. This
10
award counters Senior Partys pre-interference claim of the alleged ease and predictability of
11
applying the methods [of Jinek 2012] to eukaryotic cells. UC Motion 4 at 1:24-2:3. Indeed, the
12
actual timeline of events belies the entirety of Senior Partys benefit arguments.
13
14
D.
Senior Party is Not Entitled to the Benefit of its Doudna P1, Doudna P2, or
Doudna P3 Applications
15
Senior Party asserts that it is entitled to the benefit of each of its earlier applications,
16
Doudna P1, Doudna P2, and/or Doudna P3. To obtain benefit, Senior Party must show that those
17
earlier applications meet two requirements: (a) that each application conveyed to one of ordinary
18
skill in the art as of its filing date that the inventors were in possession of at least one
19
embodiment within the scope of Count 1, and (b) that each application enabled one of ordinary
20
skill in the art to practice that embodiment of Count 1 without undue experimentation. Senior
21
Party has not met either the written description or enablement requirements for Doudna P1 and
22
P2, and has not established written description in Doudna P3.
23
24
25
1.
Persons Of Ordinary Skill Would Have Concluded That Doudna P1

Lacks Written Description Support For A CRISPR-Cas9 System For
Use With Non-Natural Targets, Including Eukaryotic DNA
11
Persons of ordinary skill reviewing the Doudna P1 application in May 2012 would have
concluded that the Senior Party inventors were not in possession of an invention of a CRISPR-
Cas9 System that falls within the scope of Count 1 for multiple reasons. First, Doudna P1
includes no discussion of the role of PAM sequences for non-natural targets. Fact 82; Ex. 2009
11.43.
DNA molecule or modulating transcription of at least one gene encoded thereon. Thus, Count 1
is directed to a target DNA molecule in a eukaryotic cell, not a natural target of the prokaryotic
CRIPSR-Cas9 system. Fact 112; Ex. 2009 11.17. Based on the lack of any PAM discussion,
skilled persons would have concluded that the inventors had not begun to provide the
10
Count 1 is directed to a method, in a eukaryotic cell, of cleaving or editing a target
information needed to use CRISPR systems with non-natural targets. Ex. 2009 11.43.
11
Prior to Doudna P1s May 2012 filing date, persons of ordinary skill would have been
12
aware of publications disclosing that PAM sequences played a role in the ability of a CRISPR
13
system in bacteria to target natural DNA targets. Fact 84; Ex. 2246 (Deveau); Ex. 1298
14
(Mojica); Ex. 2009 11.12-11.13. In light of these disclosures, persons of ordinary skill would
15
have expected that if an application described a CRISPR-Cas9 invention directed to work on
16
non-natural targets, that it would address whether or not PAM played a role with respect to non-
17
natural targets, or at least mentioned PAM sequences. Fact 84; Ex. 2009 11.43.
18
Doudna P1, however, says nothing about PAM sequences. Ex. 2009 11.43. Indeed,
19
Figure 5 of Doudna P1 is particularly telling, showing cleavage assay results conducted using six
20
Cas9 orthologs from different species of bacteria, of which three did not show any cleavage.
21
Fact 113; Ex. 1003 at 95; Ex. 2009 11.49. To persons of ordinary skill, these poor results
22
would have indicated that the Doudna inventors did not appreciate the need to match the
23
different Cas9 proteins for the different species to different PAM sequences. Fact 114. The
12
absence of information on PAM sequences in P1, and the failure to appreciate the significance of
PAM in the experiments in Figure 5, would have indicated to skilled persons that the inventors
had not yet begun to provide the type of information required for possession of a CRISPR-Cas9
invention applied to non-natural targets. Ex. 2009 11.52-53.
If the Doudna inventors had understood the significance of PAM when the Doudna P1
application was filed in May 2012, then they chose to conceal that information for some reason.
It is notable that one of the Senior Party inventors, Dr. Charpentier, was a co-author on
Makarova 2010, which stated that the CRISPR-Cas9 system probably involves a process that
requires the PAM, and was aware of the relationship between PAM sequences and CRISPR for
10
natural targets. Ex. 2009 11.45. It also notable that Figure 1A from Doudna P1 appears to
11
have deleted a marker indicating the PAM sequence on the DNA target. A comparison of Figure
12
1A from Doudna P1 and Figure 5A from the Jinek 2012 article is telling on this point:
13
14
Figure 5A from Jinek identifies PAM as part of the CRISPR system, with a diagonal
15
line extending from the upper right portion of the figure. Figure 1A from Doudna P1 includes a
16
similar line extending up and to the right, shown in the red box, but with no label identifying
13
PAM. Figure 1A of Doudna evidently had been scrubbed to remove any reference to PAM
sequences. Ex. 2009 11.45. It is unclear why reference to PAM was not included in Figure 1A
of Doudna P1, but it is clear that without it, Doudna P1 would have conveyed to persons of
ordinary skill in the art at the time it was filed that the inventors were not in possession of a
CRISPR-Cas embodiment adapted to function on non-natural targets.
Moreover, as discussed below, separate and apart from the PAM issue, skilled persons
would have concluded that the inventors had done nothing to overcome the other unknowns and
uncertainties relating to transferring a protein/RNA-based prokaryotic system to eukaryotic cells.
9
10
11
12
2.
Persons Of Ordinary Skill Would Have Concluded That Doudna P1

And P2 Do Not Reasonably Convey Possession Of A CRISPR-Cas9
System Adapted to Function In Eukaryotic Cells
Senior Party asserts at page 13, lines 2-7 of Motion 4 that Doudna P1 and Doudna P2
13
each provide written description support for an embodiment of Count 1 that functions in a
14
eukaryotic cell. Junior partys response is that persons skilled in the art reading Doudna P1 and
15
P2 would not have recognized that the inventors possessed as their invention an embodiment of a
16
CRISPR-Cas9 system adapted to function in eukaryotic cells. The evidence shows that skilled
17
persons would not predict a CRISPR-Cas system would work in a eukaryotic cell based on in
18
vitro tests. Fact 119; Ex. 2009 11.6, 11.92. Rather, skilled persons in 2012 would have
19
required positive eukaryotic tests results to recognize that the inventor invented what is
20
claimed in Count 1, a CRISPR-Cas system for eukaryotic cells. Fact 120; Ex. 2009 11.32.
21
22
23
a.
The Combination of Example 1, Paragraph 00165 and Various

Claims With Eukaryotic Limitations From Doudna P1 and
Doudna P2 Did Not Convey Possession
24
For written description with respect to Doudna P1 and Doudna P2, the Senior Party relies
25
primarily on the combination of two disclosures: Example 1 and Paragraph 00165. UC Motion 4
26
at 4 line 11-12. Junior Partys response is that those portions of the applications would not have
14
conveyed to persons of ordinary skill that the inventors had invented a CRISPR-Cas9 system
capable of functioning in eukaryotic cells. Example 1 describes only in vitro testing in a cell-
free environment, not testing in eukaryotic cells. Fact 115; Ex. 1003 at 248-253; Ex. 1004; Ex.
2009 11.5. Paragraph 00165 broadly states that cells of interest include cells of any
organism, including eukaryotic cells. Ex. 1003 at 00165. However, the mere recitation of
eukaryotic cells is not sufficient for written description. Ariad, 598 F.3d at 1350 (Generic
claim language appearing in ipsis verbis in the original specification does not satisfy the written
description requirement if it fails to support the scope of the genus claimed.).
Example 1 and Paragraph 00165 do not provide any testing or other evidence that a
10
CRISPR-Cas9 system actually works in eukaryotic cells. Fact 117; Ex. 1003 at 165, 248-253;
11
Ex. 1004; Ex. 2009 11.22. Nor do Example 1 and Paragraph 00165 identify any structural
12
aspect of the CRISPR-Cas9 system of Example 1 that purportedly makes it adapted to function
13
in eukaryotic cells. Id. Thus, Paragraph 00165 is nothing more than a wish or a plan for future
14
experiments, which legally does not provide written description support. Eli Lilly, 119 F.3d at
15
1566.
16
Senior Party also points to other portions of Doudna P1 and P2, including claims and
17
other portions of the specification, which it says provide written description support. From
18
Doudna P1, Senior Partys Motion 4 (at 13:20-14:18, 15:22-16:4,) cites paragraphs 121, 129,
19
167, 177, 178, 201, 215, and 216, as well as claims 54, 58, 61, 66 and 72-75 as allegedly
20
providing written description support. In Doudna P2, Senior Partys Motion 4 (at 21:15-22:2)
21
relies on paragraphs 00114, 00116, and 00120 as well as claims 60, 65, 66, 69-72, and 98-100.
22
Junior Partys response is that none of these excerpts cure the deficiencies in Doudna P1
23
and P2. Fact 118. Paragraph 00216 of Doudna P1 is duplicative of paragraph 00165. Ex. 1003;
15
Ex. 2004; Ex. 2009 11.25. The other paragraphs Senior Party cites state broadly the hope of
genetically modifying cells, of expressing nucleotides or polypeptides in cells or of injecting
nucleotides or polypeptides into cells. Id. Likewise, the claims only recite some aspect of a
eukaryotic cell. Ex. 1003; Ex. 2004; Ex. 2009 11.25. None of these disclosures provide
evidence that the CRISPR system would actually work in eukaryotes, and none of them identify
a structural aspect that would make the system adapted for eukaryotic cells. Ex. 2009 11.25.
Senior Partys reliance on a 2009 patent application by Sontheimer supports the lack of
written description in the Doudna P1 and P2 applications. See UC Motion 3 at 10. The
Sontheimer inventors, like the Senior Party inventors, stated that their CRISPR system could be
10
used in eukaryotic cells and also taught routine techniques for eukaryotic experiments. Fact 123;
11
Ex. 1161 at 0054-0060; Ex. 2009 11.33. The Sontheimer inventors conducted experiments in
12
prokaryotic cells using the Type III CRISPR system. Their application discussed possible
13
techniques and tests for potentially establishing that the CRISPR system functioned in eukaryotic
14
cells, but they included no actual eukaryotic experiments. Fact 124; Ex. 2009 11.33
15
The Sontheimer inventors nevertheless presented claims to the use of the CRISPR system
16
in eukaryotic cells. Ex. 2413 at 9. The Patent Office, however, rejected those claims for lack of
17
written description and for non-enablement, stating for example:
18
19
20
21
22
23
24
25
26
27
Further, the disclosure of the instant specification is entirely prophetic such that
"CRISPR RNA-directed DNA targeting is tested for efficacy in animals by
exploiting the genetic and phenotypic tools that are available for the Drosophila
melanogaster." ... There is not a single working example that demonstrates even a
slightest possibility that such method steps would inhibit a broad spectrum of
eukaryotic DNA sequences in a subject, nor is there sufficient guidance that
would lead one of ordinary skill in the art to perform the claimed methods without
undue experimentation at the time of filing.
Ex. 2413 at 9 (emphasis added); Fact 125.
Similarly, the Doudna P1 and P2 applications are entirely prophetic and they do not
16
contain a single working example that demonstrates to persons of ordinary skill that such an
embodiment would function in eukaryotic cells. Ex. 2009 11.117; Fact 126. Due to the
uncertainties and unknowns in adapting prokaryotic CRISPR systems to eukaryotic cells, persons
of ordinary skill in the art would not have recognized that the Senior Party inventors possessed
the claimed invention in the absence of actual eukaryotic test results demonstrating successful
adaptation of the system. Id.
Moreover, skilled persons reviewing Doudna P2 would have had an additional reason to
conclude that the Senior Party inventors lacked possession. 1 According to Senior Party, after the
publication of Jinek 2012, persons of ordinary skill would have been immediately motivated to
10
apply the Type II CRISPR-Cas system to eukaryotic cells. UC Motion 3 at 9:1-3. Based on
11
that motivation, skilled persons who read Jinek 2012 in June 2012 would have expected to see
12
eukaryotic experiments in Doudna P2 if the inventors could adapt the system for eukaryotic cells
13
using routine techniques. Ex. 2009 11.74. The absence of such tests four months later would
14
have confirmed that Doudna P2 did not convey the information needed to show possession of an
15
invention of a CRISPR-Cas9 system adapted to function in a eukaryotic cell. Ex. 2009 11.74.
16
17
18
b.
Contemporaneous And Pre-Interference Statements Confirm

The Lack of Possession Based on In Vitro Tests
This interference presents the unusual situation where there is pre-interference evidence
1 A person of ordinary skill would also note that the results in Doudna P2, Figure 5, are
inconsistent and that the inventors did not explain whether it was due to a lack of a PAM
sequence, inappropriate tracr length, or some other factor. From that, persons of ordinary
skill would have concluded that the inventors lacked possession of an embodiment of Count
1, which is directed to non-natural targets in eukaryotic cells. Ex. 2009 11.76.
17
on whether skilled persons reading a patent application would have concluded that the inventors
possessed the claimed invention. The test for written description relates to how persons of
ordinary skill would have read the disclosure of a patent application at the time it was filed. This
is a hypothetical inquiry because skilled persons typically cannot access and read the application
until its publication months later. Here, however, the Senior Party asserts that the Jinek 2012
paper is a proxy for Doudna P1 and P2, because it contains the same in vitro tests set forth in
Doudna P1 and P2 with the same general disclosure of eukaryotic cells. Fact 104; UC Motion 4
at 18:14-19:5. Senior Party relies on the alleged ability of skilled workers to practice the Jinek
2012 system in eukaryotic cells as evidence that the Doudna P1 and P2 applications provide a
10
11
sufficient disclosure.
In fact, Senior Party UCs expert, Dr. Carroll, admitted that all of the information in
12
Doudna P1 and P2 either appears in Jinek 2012 or were well-known routine techniques, thereby
13
making Jinek 2012 an appropriate proxy for how persons of ordinary skill would have read
14
Doudna P1 and Doudna P2. Fact 127; Carroll Tr. at 255:4-258:17; 305:6-338:10; Ex. 2009
15
11.86-87. Accordingly, contemporaneous statements regarding Jinek 2012 address the
16
hypothetical inquiry of whether Doudna P1 or P2 would have conveyed possession of the
17
invention of an embodiment of a CRISPR-Cas9 system that functioned in a eukaryotic cell.
18
Dr. Carrolls 2012 statements show that skilled persons would not have believed that the
19
inventors possessed such an invention. Ex. 2009 11.92. In his September 2012 article,
20
Molecular Therapy 20(9): 1659-60 (September 2012) (Ex. 1152), Dr. Carroll observed that [a]ll
21
the experiments described in Jinek 2012 were performed in vitro with purified components
22
and expressed doubt about whether the CRISPR-Cas system would function in eukaryotic cells:
23
24
What about activity of the system in eukaryotic cells? Both zinc fingers and TALE
modules come from natural transcription factors that bind their targets in a
18
1
2
3
4
chromatin context. This is not true of the CRISPR components. There is no

guarantee that Cas9 will work effectively on a chromatin target or that the
required DNARNA hybrid can be stabilized in that context Only attempts to
apply the system in eukaryotes will address these concerns.
Ex. 1152 at 1660 (with emphasis added); Fact 128. Dr. Carroll purports to have the knowledge
of one of ordinary skill in the art. Fact 129; Ex. 1024 at 19 (my knowledge as one of
ordinary skill in the art and as an expert in the relevant field). Dr. Carrolls statement confirms
that skilled persons, even with expert knowledge, reading the in vitro experiments and with
knowledge of the existing techniques in the art, questioned whether the inventors provided
10
sufficient information to demonstrate possession of a eukaryotic invention. Ex. 2009 11.85.
11
Dr. Carroll insisted at this deposition that it was actually his strong expectation at the
12
time that the CRISPR-Cas9 system would work in eukaryotic cells. Carroll Tr. at 117:5-118:2.
13
Dr. Carroll, however, did not dispute that his 2012 article does not state any expectation of
14
success. Id.; Fact 130. Instead, he stated that if he had 20 pages instead of two-and-a-half
15
pages to talk about the subject, he would have explained that other prokaryotic systems had
16
been found to work in a eukaryotic context. Carroll Tr. at 117:5-118:2. But, Dr. Carroll could
17
have said that in one sentence. Instead, he only expressed concerns, stating that [o]nly attempts
18
to apply the system in eukaryote will address these concerns. Ex. 1152 at 1660; Fact 131. Dr.
19
Carrolls attempt now to revise his 2012 opinion only highlights the extent to which his 2012
20
article is dispositive on a central issue in this interference: how skilled persons actually would
21
have interpreted Jinek 2012 and, by extension, the disclosure in Doudna P1 and P2.
22
Dr. Doudna also made statements confirming that the information in Doudna P1 and P2
23
did not convince her that they possessed an invention that would work in eukaryotic cells. Fact
24
86. In a July 2014 article, Dr. Doudna confirmed her view that even after the publication of
25
Jinek 2012, they did not know if the CRISPR-Cas9 system would work in eukaryotic cells:
19
1
2
3
4
Says Doudna, Our 2012 paper was a big success, but there was a problem. We
werent sure if CRISPR/Cas9 would work in eukaryotesplant and animal
cells. Unlike bacteria, plant and animal cells have a cell nucleus, and inside, DNA
is stored in a tightly wound form, bound in a structure called chromatin.
Ex. 2207; Fact 132; Fact 86. Likewise, an article from July 28, 2012, reported the views of Drs.
Charpentier and Doudna that even after Jinek 2012, they did not know whether the CRISPR
system would work in eukaryotes: [t]he next steps, Charpentier and Doudna say, are to test the
single-RNA construct along with Cas9 to find out whether the RNA-programmed enzyme works
in eukaryotic organisms. Ex. 2290; Ex. 2009 11.89; Fact 133.
10
For the same reasons of uncertainty that Drs. Carroll, Doudna, and Charpentier expressed
11
with respect to whether a CRISPR-Cas9 system would work in eukaryotic cells based on in vitro
12
tests in Jinek 2012, skilled persons reading Doudna P1 and P2 would have likewise concluded that
13
the Senior Party inventors did not yet provide sufficient information to show possession of a
14
CRISPR-Cas9 system adapted to function in eukaryotes. Ex. 2009 11.92; see Manning v. Paradis,
15
296 F.3d 1098, 1104 (Fed. Cir. 2002) (contemporaneous statements by inventor outweigh later
16
statements made for purposes of interference).
17
18
19
c.
20
Persons of Ordinary Skill Would Not Have Known Whether A

CRISPR-Cas9 System That Functioned In Vitro Would
Function in a Eukaryotic Cell
Senior Party asserts at page 20, lines 18-19 of Motion 4 that using the CRISPR-Cas9 of
21
Example 1 in eukaryotic cells required only well-known, routine experiments with a new
22
technology that had been fully described in the First Provisional. Junior Partys response is
23
that, just as Dr. Carroll stated, skilled persons would have recognized an in vitro environment is
24
very different from the environment of eukaryotic cells. Fact 134; Ex. 2009 11.114. The in
25
vitro testing in Example 1 was conducted with a limited set of synthetic components in a test
26
tube under artificial conditions. Ex. 2009 11.28. In contrast, it was known that the contents of
20
eukaryotic cells cause molecular crowding which can impact the folding of proteins like Cas9.
Fact 135; Ex. 2009 11.29. In addition, temperature, ion concentration, pH, and cellular milieu
in a eukaryotic cell differ from that of a cell-free in vitro test. Fact 135; Ex. 2009 11.30. It
would have been known in the art that those differences could have unpredictable effects on
Cas9 and RNA expression, Cas9 folding, and CRISPR-Cas9 formation and function, which
could prevent a CRISPR-Cas9 system from functioning even if it worked in an in vitro
environment. Id.
8
9
In addition, as of May 2012, persons of ordinary skill recognized that other features of a
eukaryotic environment made it so that an in vitro test did not convey that the CRISPR-Cas9
10
would work in eukaryotic cells. Persons of ordinary skill knew: (1) that it may not be possible to
11
deliver the necessary components of adapted CRISPR-Cas9 systems to eukaryotic cells so they
12
would be properly transcribed and translated in eukaryotic cells, (Fact 136; Ex. 2009 11.31); (2)
13
that proteins or nucleic acids in eukaryotic cells could interfere with the various components of
14
CRISPR-Cas9 and eukaryotic cells, (Fact 137; id.); and (3) that systems in eukaryotic cells
15
developed to attack foreign invaders may degrade the RNA of the CRISPR-Cas9 system (Fact
16
138 id.). Doudna P1 and P2 did not account for any of the unique features of eukaryotic cells,
17
which might prevent CRISPR-Cas9 from functioning in eukaryotic cells. Fact 139.
18
Furthermore, it was known that CRISPR-Cas9 evolved in nature in prokaryotic cells,
19
which differ greatly from eukaryotic cells. Fact 140; Ex. 2009 11.88. Thus, Count 1 requires
20
engineering a CRISPR-Cas9 system to function in a manner that is antithetical to its natural
21
function in prokaryotic cells, and to function in a vastly more complex and different
22
environment. Fact 141; Ex. 2009 10.5. In particular, skilled persons understood that the size of
23
the human genome is at least about a thousand-fold greater than that of bacteria. Fact 142; Ex.
21
2009 10.7. Indeed, it was also understood that while CRISPR was found naturally in many
prokaryotic cells, it had never been found (and still has not been found) in any eukaryotic cells in
nature. Fact 143; id. Thus, persons of ordinary skill would have concluded that the Doudna
inventors actually lacked possession in the absence of successful testing in eukaryotic cells. Id.
It was also known that the proteins and/or RNA molecules of a CRISP-Cas9 system,
which originated in prokaryotic cells, may have toxic effects on eukaryotic cells that must be
overcome in order for CRISPR-Cas9 to function properly. Fact 144; Ex. 2009 11.31. Toxic
effects include genome editing in locations other than the target DNA, which are called off-
target effects. Fact 145; id. UCs expert, Dr. Carroll, agreed that off-target effects are an
10
important concern for genome editing and that off-target effects could, in fact, be lethal.
11
Carroll Tr. at 227:3-6, 229:2-12; Fact 146. UCs expert, Dr. Greider, testified that skilled
12
persons would have had no expectation regarding possible off-target effects from using CRISPR-
13
Cas9 in eukaryotic cells without doing experiments. Greider Tr. at 405:14-22; Fact 147.
14
In addition, it was known that it may not be possible to localize the CRISPR-Cas9 system
15
with target DNA at the same time and place in the crowded and compartmentalized environment
16
of eukaryotic cells. Fact 148. It was known at the times that Doudna P1 and P2 were filed that a
17
nuclear localization signal (NLS) can sometimes be used to direct components to the nucleus
18
of a eukaryotic cell. Ex. 2009 11.31. Doudna P1 and Doudna P2 do not teach to use an NLS in
19
eukaryotic cells, much less how many NLSs to use or in what locations. Fact 149; id.
20
Based on deposition questioning, it appears that Senior Party might argue that some
21
obstacles in dealing with eukaryotic cells are irrelevant because they relate to the nucleus. At her
22
deposition, UCs expert Dr. Greider testified that the DNA target of interest resides in the
23
nucleus. Greider Tr. 285:20-286:1; Fact 150. But, when questioned by UCs counsel on
22
redirect, she testified that eukaryotic cells contain other DNA targets of interest outside the
nucleus, including mitochondrial DNA and chloroplast DNA. Greider Tr. 422:4-18. However,
other than a conclusory statement that it was possible to inject CRISPR-Cas9 into mitochondria
and chloroplast, (id.), Dr. Greider provided no opinion that Doudna P1 or P2 provide sufficient
information to show possession an embodiment of Count 1 for delivering a functioning CRISPR-
Cas9 system into a mitochondria or chloroplast. Fact 151; Ex. 2009 11.31.
Moreover, arguments relating to DNA targets outside the nucleus do not deal with the
numerous other scientific uncertainties stated above that do not relate to the nucleus. Thus,
persons of ordinary skill would have required actual test results in eukaryotic cells to conclude
10
that the inventors had overcome the uncertainties relating to a CRISPR-Cas9 system adapted to
11
function anywhere in eukaryotic cells. Ex. 2009 11.31.
12
13
d.
Prior Difficulties Experienced in Attempting to Adapt Other

Prokaryotic Systems to Function in Eukaryotic Cells
14
Persons of ordinary skill reading Doudna P1 and Doudna P2 also would have been aware
15
of prior difficulties adapting systems that originated in prokaryotic cells to eukaryotic cells. Fact
16
152. The well-known history of targetrons, which are gene-editing tools based on group II
17
self-splicing ribozymes, served as the most reasonable comparator for CRISPR researchers
18
because targetrons originated in prokaryotes and include both protein and RNA components, like
19
the CRISPR system. Facts 153-155; Ex. 2010 1.45-1.48. Group II self-splicing ribozymes
20
were initially described in 1986, and targetrons were developed that acted on prokaryotic genes
21
by 2003. Fact 156; Ex. 2010 1.46. But even after nine more years of research by multiple
22
laboratories, researchers had achieved little or no targetron functioning in eukaryotic cells. Fact
23
157; Ex. 2010 1.47-1.54. Persons of ordinary skill reading the Doudna P1 and P2 applications
24
would have understood that similar challenges could face researchers attempting to adapt the
23
1
2
CRISPR-Cas9 system to function in eukaryotic cells. Fact 158; Ex. 2010 1.54.
The targetron experience taught that simply because a prokaryotic system could edit
genes in other environments did not mean that it could be adapted to function in eukaryotic cells.
Fact 159. Indeed, skilled persons would have known that one problem that frustrated research on
targetrons, the level of Mg2+ ions, might also pose a problem for CRISPR, which also evolved
to function in the Mg2+ rich environment of prokaryotic cells. Fact 160; Ex. 2010 1.51-1.53.
The history of prior failed attempts to transfer prokaryotic systems to eukaryotes would
have increased the insistence of persons of ordinary skill to see actual experimental results in
eukaryotic cells to show possession of a CRISPR-Cas9 invention for eukaryotic cells. Fact 161.
10
Indeed, statements from other researchers confirm the unpredictability and difficulty of
11
transferring the bacterial CRISPR-Cas system to eukaryotes. Dr. Luciano Marraffini, who
12
studies CRISPR/Cas systems at Rockefeller University, stated that Its not trivial to make
13
CRISPR/Cas systems work in eukaryotic cells, and that [o]ne thing is to have them in silico
14
and have a sequence and realize theyre smaller, and another thing is to do the [eukaryotic]
15
experiments and make it work. Fact 109; Ex. 2213. Similarly, Dr. Churchwho provided
16
unpublished data to the Doudna groupcharacterized the move of CRISPR-Cas from bacteria to
17
eukaryotic cells as a huge jump. Fact 116; Ex. 2423.
18
19
20
e.
The Later Work of Other Laboratories Does Not Support

Senior Partys Written Description Argument
Senior Party contends that the rapid success of numerous other research groups
21
in applying the [CRISPR-Cas9 system of Doudna P1 and Doudna P2] to eukaryotic cells
22
immediately after the invention was published is evidence that Doudna P1 describes and
23
enables embodiments within the scope of Count 1. UC Motion 4 at 18. Senior Party contends
24
that, after Jinek 2012 published information from Doudna P1 and P2, four other laboratories
24
published articles showing the use of the CRISPR-Cas9 systems in eukaryotic cells. The
response is that this does not support Senior Partys argument for multiple reasons.
First, the publications by the four other research groups occurred after the filing dates of
Doudna P1 and P2. Therefore, these publications are legally irrelevant because a person of
ordinary skill in the art could not be aware of them as of the filing dates of the applications.
Second, Senior Party is also wrong when it suggests that Jinek 2012 inspired Dr. Zhang
to start his eukaryotic work. As shown in Section III.C.1 above, Dr. Zhang started his work on
eukaryotic targets in 2011 and succeeded prior to the publication of Jinek 2012. Fact 162.
Third, Senior Party cites no support for its assertion that the articles came from
10
independent research groups. Fact 164; Ex. 1024 at 151. Dr. Carroll indicated that by
11
independent he included groups sharing data. Carroll Tr. 102:1-7. As noted above, Dr.
12
Church, the senior author of the Mali 2013 article at Harvard, was co-advisor to Dr. Zhangs
13
colleague Dr. Cong. Fact 101; Ex. 2009, Simons.3d at 11.111. Dr. Church and Keith Joung
14
(the senior author on the Hwang article) are reported to be members of the Broad, which is a
15
community including scientists from Harvard, Harvard Hospitals and MIT founded to accelerate
16
breakthroughs and to impact human health by encouraging collaboration. Dr. Church
17
acknowledged that his graduate student Dr. Cong worked with Dr. Zhang on the eukaryotic
18
experiments at the Broad. Fact 170; Ex. 2423. Moreover, the Hwang 2013 paper acknowledges
19
the assistance of George Church. Ex. 1058 at 6. These are hardly what most would consider
20
entirely independent research groups.
21
Fourth, the actions of these research groups do not indicate the understanding of persons
22
of ordinary skill. Many of these research groups include individuals with significantly more than
23
the ordinary level of skill, including Drs. Church and Joung and Jin-Soo Kim of the Cho 2013
25
paper, who have significant history working with mammalian cells using both zinc fingers and
TALENs. Fact 165; Ex. 2009 11.112. Dr. Carroll confirmed that Dr. Kim and Dr. Doudna had
higher than the ordinary level of skill. Carroll Tr. 263:18-264:20; Fact 166.
4
5
6
3.
The Doudna P1 And P2 Applications Do Not Enable A Skilled Artisan

To Practice An Embodiment Of Count 1
Senior Party asserts in Motion 4 that Doudna P1 and P2 enable embodiments falling
within Count 1. UC Motion 4 at 14:19, 22:3. Junior Partys response is that nothing in Doudna
P1 and P2 enable a person of ordinary skill to use a CRISPR-Cas9 system of Count 1 in
eukaryotic cells. Fact 167. Senior Party relies on the alleged ability of skilled persons to use
10
Chimera A of Example 1 in eukaryotic cells. However, Doudna P1 and P2 do not teach a person
11
of ordinary skill how to adapt a CRISPR-Cas9 system with Chimera A or any guide RNA to
12
function in eukaryotic cells. Those applications certainly do not provide the specific and useful
13
teaching of how to practice the invention required for technology like CRISPR, which was in a
14
nascent stage of development when the applications were filed. Genentech, 108 F.3d at 1367-68.
15
Consideration of the Wands factors emphasizes that practicing the method of Count 1
16
based on Doudna P1 or P2 would have required undue experimentation. Wands, 858 F.2d at
17
737. For Factor 1, Doudna P1 and P2 each provide essentially no useful guidance for practicing
18
the method of the count in eukaryotic cells. Ex. 2009 11.117. For Factor 2, adapting Chimera
19
A to function in eukaryotic cells required extensive experimentation, as shown by Dr. Doudnas
20
own many frustrations. Id. For Factor 3, the applications contained no working examples of
21
CRISPR-Cas9 functioning in eukaryotic cells. Id. For Factors 4, 5, and 6, the nature of the
22
technology requires more disclosure than may be needed in other instances, given the nascent
23
state of CRISPR-Cas9 art. Id. For Factor 7, the technology here is highly unpredictable, with
24
multiple examples where others tried and failed to use prokaryotic systems in eukaryotic cells.
26
Ex. 2009 11.32; Ex. 2010 1.45-1.54. As Dr. Carroll observed in 2012, the only way to
establish what would happen if one used CRISPR-Cas9 in eukaryotic cells was to conduct the
experiment. Ex. 1152 at 1660; Ex. 2009 11.32. In the absence of such tests, the result was
completely unpredictable. Id.
The lack of enablement is also demonstrated by the failures of other researchers using the
CRISPR-Cas9 system with Chimera A using routine techniques. Fact 105. The Chen US
application No. 61/734,256, filed December 6, 2012 (Chen P1), included unsuccessful testing
of Chimera A and a modified Chimera A. Fact 168; Ex. 2125 at 32, 34; Carroll Tr. at 178:6-18.
Chen P1 presents evidence from three tests in eukaryotic cells with Chimera A or modified
10
Chimera A type RNA, all three of which of generated negative results, indicating that Chimera A
11
did not function in eukaryotic cells. Fact 168; Ex. 2009 11.123-11.129. Altogether, the results
12
in Chen P1 are at best inconclusive, if not outright failures. Fact 169; Ex. 2009 11.123-11.129.
13
On the other hand, Dr. Zhangs group at the Broad used non-routine techniques to adapt
14
CRISPR-Cas9 with a modified Chimera A-type RNA for eukaryotic cells. They used two NLS
15
groups (one on each end) on the Cas9 protein, expressed the Chimera A using a vector, and
16
added four nucleotides to the end of the tracr component that were not present in Jinek 2012s
17
Chimera A. Ex. 1055 at 2; Ex. 2009 11.130. Even with those improvements, eight of the 14
18
samples tested reported no activity at all. Ex. 1055 at 21; Ex. 2009 11.130.
19
Senior Party relies on Dr. Kims work with Chimera A (Cho 2013), where CRISPR-
20
Cas9 systems with Chimera A were introduced to eukaryotic cells using a technique called
21
nucleofection. Ex. 1059 at 6; Ex. 2009 11.132. Rather than routine research, those researchers
22
added 2-15 times more plasmids and RNA to the eukaryotic cells than was recommended by the
23
manufacturer of their nucleofection equipment. Fact 172; id. Overloading cells in that manner
27
was not routine and would not work for real world applications. Fact 93; Ex. 2009 11.133. This
confirms that persons of ordinary skill would have needed undue experimentation to make the
Chimera A function in eukaryotic cells. Facts 173, 176. Indeed, in subsequent papers from the
same laboratory, the researchers abandoned Chimera A and used a longer tracr. Fact 174; Ex.
1509; Ex. 1508; Carroll Tr. at 279:20-281:8, 288:10-289:12, 289:13-291:7; Ex. 2009 11.134.
Also, the Kim group did not attribute their alleged success in eukaryotic cells to Jinek
2012 or the Senior Party. To the contrary, the Kim group filed a patent application and recently
submitted arguments, and a supporting declaration of Bryan Cullen, stating that their eukaryotic
work was not obvious over Jinek 2012. Fact 171; Ex. 2422 at 11, 20-24.
10
It is also significant to note that the journal SCIENCE has a large reach in the scientific
11
community, with 570,400 readers each week and over five million monthly visits to the Science
12
website. Fact 175; Ex. 2420 at 5; Ex. 2009 11.113. Given this reach, the fact that only one
13
highly specialized group, using non-routine techniques, was able to use a CRISPR-Cas9 system
14
with unmodified Chimera A in eukaryotic cells, highlights the shortcomings of the description in
15
Jinek 2012 and the Doudna applications. Fact 176; Ex. 2009 11.113.
16
17
18
19
20
Thus, the record demonstrates that Doudna P1 and P2 did not enable a person of ordinary
skill to practice an embodiment of Count 1 without undue experimentation.
4.
The Doudna P3 Application Does not Provide Written Description

Support For An Embodiment Of Count 1
Senior Party asserts in Motion 4 that Doudna P3 contains a working example of the
21
methods of Count 1. UC Motion 4 at 23:3. Junior Partys response is that the working
22
example in Doudna P3 was in fact a failure it did not show that the CRISPR-Cas9 systems of
23
Doudna P3 were adapted to function in eukaryotic cells. The Doudna P3 application, filed
24
January 29, 2013 (Fact 177), includes for the first time testing in eukaryotic cells, and also adds a
28
description of new CRISPR-Cas9 systems with tracrRNA components that differ from Chimera
A. Fact 178; Ex. 2009 11.137. While Doudna P3 asserts that its tests in eukaryotic cells were
successful, the results in the application show otherwise. Persons skilled in the art reading
Doudna P3 in January 2013 would have concluded that the eukaryotic test results reported in
Doudna P3 are inconclusive at best. Thus, persons of ordinary skill would have concluded from
reading Doudna P3 that the inventors did not provide information showing possession of an
invention of a CRISPR-Cas9 system that functioned in eukaryotic cells.
8
9
Only two experiments in Doudna P3 purport to show cleavage in living eukaryotic cells.
Fact 179. According to the methods section in Doudna P3, the experiment reported in Figure
10
38B of Doudna P3 should show bands of 360 bp for PCR product with no cleavage. Ex. 1005 at
11
412; Fact 180; Ex. 2009 11.140. The gel should show bands between 160 and 200 bp if the
12
CRISPR-Cas9 successfully cleaved the target DNA. Fact 181; Ex. 2009 11.140. But the
13
samples containing Cas9 and sgRNA do not show any bands between 160 and 200 bp. Fact 182;
14
Ex. 1005 at 38B; Ex. 2009 11.140. Persons skilled in the art would have concluded that the
15
named inventors failed to obtain cleavage in eukaryotic cells. Fact 183; Ex. 2009 11.140.
16
The only data in Doudna P3 from a eukaryotic cells experiment is in Figure 36E, which
17
shows a single lane suggested to show cleavage. The authors claim that a very faint band in lane
18
5 from the left represents cleavage of the target sequence resulting in editing of the sequence.
19
Ex. 1005 at 418, Figure 36E. Persons of ordinary skill reviewing Fig. 36E would have
20
concluded that the data was inconclusive. Fact 184; Ex. 2009 11.151-11.159. It is clear from
21
the figure that the authors did not purify their PCR product as evidenced by the additional bands
22
visible in lanes 2 and 4. Fact 185; Ex. 2009 11.151-11.159
23
In addition, experiments in Figure 36B of Doudna P3 would have confirmed that the P3
29
experiments in eukaryotic cells were unsuccessful. Figure 36B according to Doudna P3,
revealed abundant Cas9 expression and nuclear localization. Fact 186; Ex. 1005 at 416. To
persons of ordinary skill, however, the test results did not indicate nuclear localization. Fact 187;
Ex. 2009 11.154. The failure of the Senior Party inventors to localize the Cas9 protein in the
nucleus could account for the poor results shown in Figures 36E and 38B. Fact 188; Ex. 2009
11.162.
In view of the poor experimental results in Doudna P3, Doudna P3 did not provide
sufficient information to demonstrate possession. Moreover, Senior Party contends that Jinek
2013, a proxy for Doudna P3, is pertinent to written description because it allegedly showed that
10
the system published in Jinek 2012 (disclosed in the First Provisional) worked in eukaryotic
11
cells. UC Motion 4 at 19:15-19. Junior Partys response is that because the eukaryotic tests in
12
Doudna P3 were unsuccessful, if anything, they would demonstrate that the inventors also did
13
not possess a CRISPR-Cas9 system that could function in eukaryotic cells the time of filing of
14
Doudna P1 and P2. In addition, to the extent that Doudna P3 discloses information such as such
15
as actual eukaryotic testing (albeit failed in P3) and specific techniques for CRISPR-Cas systems
16
for eukaryotic cells, it only highlights the absence of that information in Doudna P1 and P2.
17
IV.
18
19
CONCLUSION
For the reasons set forth herein, Senior Partys Motion 4 should be denied.
Dated: August 15, 2016
Respectfully submitted,
20
21
22
23
24
25
26
27
/s/Steven R. Trybus
Steven R. Trybus
Reg. No. 32,760
Counsel for Broad
Jenner & Block LLP
353 North Clark Street
Chicago, IL 60654
Telephone: (312) 222-9350
strybus@jenner.com
30
APPENDIX 1: LIST OF EXHIBITS
EXHIBIT
NUMBER
DESCRIPTION
1003
U.S. Provisional Patent Application No. 61/652,086, filed on

May 25, 2012 (Doudna P1 or P1).
1004

October 19, 2012 (Doudna P2 or P2)
1005

January 28, 2013 (Doudna P1 or P1).
1024
Declaration of Dr. Dana Carroll.
1055
Cong et al., Multiplex Genome Engineering Using

CRISPR/Cas Systems, 339 Science 819-823 (2013).
1056
Mali, et al., RNA-Guided Human Genome Engineering via

Cas9, 339 Science 823-826 (2013).
1058
Hwang et al., Efficient genome editing in zebrafish using a

CRISPR-Cas system, 31 Nature Biotechnology 227-29 (2013).
1059
Cho et al., Targeted genome engineering in human cells with

the Cas9 RNA-guided endonuclease, 31 Nature Biotechnology
230-232 (2013).
1152
Carroll, A CRISPR Approach to Gene Targeting, 20 Molecular

Therapy 1659-1660 (2012).
1155
Jinek et al., A programmable dual-RNA-guided DNA

endonuclease in adaptive bacterial immunity, 337 Science 816821 (2012).
1161
Sontheimer et al., U.S. Patent Publication No. 2010/0076057,

published on March 25, 2010.
1508
Kim et al., Highly efficient RNA-guided genome editing in

human cells via delivery of purified Cas9 ribonucleoproteins,
24 Genome Research 1012-1019 (2014) with Supplemental
Information.
A1-1
1509
Cho et al., Heritable Gene Knockout in Caenorhabditis elegans

by Direct Injection of Cas9-sgRNA Ribonucleoproteins, 195
Genetics 1177-1180 (2013) with Supplemental Materials and
Methods.
2009
Third Declaration of Dr. Paul Simons, executed August 15,

2016.
2010
Declaration of Dr. Ronald Breaker, executed August 15, 2016.
2125
U.S. Patent Application No. 61/734,256, filed December 18,

2013.
2207
Chen et al., U.S. Patent Application No. 61/734,256, filed

December 18, 2013.
2230
Pandika, Rising Stars: Jennifer Doudna, CRISPR Code Killer,

OZY (Jan. 7, 2014), http://www.ozy.com/rising-stars/jenniferdoudna-crispr-code-killer/4690.
2246
Deveau et al., Phage Response to CRISPR-Encoded Resistance

in Streptococcus thermophiles, 190 J. Bacteriology 1390-1400
(2008).
2290
Max E. Perutz Laboratories, Programmable RNA Complex

Could Speed Genome Editing in the Lab (June 28, 2012),
https://www.mfpl.ac.at/about-us/news/article/newsdetail/programmable-rna-complex-could-speed-genomeediting-in-the-lab.html.
2411
SN 14/704,551 Excerpt, NIH grant application.
2413
SN 12/565,589 Excerpt.
APPENDIX 2: STATEMENT OF MATERIAL FACTS
UCs Alleged Facts with Broads Responses
1. The U.S. Provisional Application No. 61/652,086 (the First Provisional) titled
Methods and Compositions for RNA-Directed Site-Specific DNA Modification, was filed on
May 25, 2012, and lists Martin Jinek, Jennifer Doudna, Emmanuelle Charpentier, and Krzysztof
Chylinski as co-inventors. See Ex. 1003.
7
8
Broads response: ADMIT
9
10
2. U.S. Provisional Application No. 61/716,256 (the Second Provisional), titled,
11
Methods and Compositions for RNA-Directed Site-Specific DNA Modification, was filed on
12
October 19, 2012, and lists Martin Jinek, Jennifer Doudna, Emmanuelle Charpentier, Krzysztof
13
Chylinski, and James Harrison Doudna Cate as co-inventors. See Ex. 1004.
14
15
16
17
3. U.S. Provisional Application No. 61/757,640 (the Third Provisional), titled, Methods
18
and Compositions for RNA-Directed Site-Specific DNA Modification, was filed on January 28,
19
2013, and lists Martin Jinek, Jennifer Doudna, Emmanuelle Charpentier, Krzysztof Chylinski,
20
and James Harrison Doudna Cate as co-inventors. See Ex. 1005.
21
22
23
24
4. The technology behind Count 1 is explained in the Declarations of Drs. Carroll and
A2-1
Greider. See Ex. 1022, 36-67, 332-337, Ex. 1024, 30-61, 323-328 (both citing Exs. 1007,
1020, 1032, 1033, 1125, 1126, 1153, 1154, 1155, 1156, 1199, 1208, 1211, 1214, 1225, 1227,
1254, 1255, 1261, 1262, 1270, 1271, 1288, 1298, 1299, 1301, 1304, 1322, 1370).
4
5
Broads response: DENY
6
7
5. Each of the First Provisional, Second Provisional, and Third Provisional describes and
enables an anticipation of Count 1. See Exs. 1003-1005; see also Ex. 1022, 35, 329, 332-363,
373-448, Ex. 1024, 29, 320, 323-354, 3640439.
10
11
12
13
6. The First Provisional describes and enables methods within the scope of Count 1. See
14
Ex. 1003; see also Ex. 1022, 341-363, 373-431, Ex. 1024, 332-354, 364-422.
15
16
17
18
7. Example 1 of the First Provisional sets forth all elements of Count 1 other than the
19
eukaryotic cell element. See Ex. 1003, 00248-00252, Figures 3, 5; see also Ex. 1022, 341-
20
349, Ex. 1024, 332-340.
21
22
23
A2-2
8. The eukaryotic cell element of Count 1 is described and enabled throughout the First
Provisional, including at Paragraph 00165. See Ex. 1003, 00165; see also 00167, 00177,
00178, 00201, 00215, 00216; see also Ex. 1022, 341-363, 373-431, Ex. 1024, 332-354,
364-422.
5
6
7
8
9. Example 1 in combination with Paragraph 00165 describes and enables an anticipation of
Count 1 because one of ordinary skill in the art as of May 25, 2012, would have recognized that
10
the listed inventors were in possession of the methods of Count 1 and could have performed
11
those methods using only routine and predictable techniques. See Ex. 1003, 00165, 00248-
12
00252; see also Ex. 1022, 350-351, Ex. 1024, 341-342.
13
14
15
16
10. Example 1 in the First Provisional is an actual working example of a method of cleaving
17
target DNA, albeit not in a eukaryotic cell. See Ex. 1003, 00248-00252, Figs. 3, 5; see also
18
see also Ex. 1022, 350-352, Ex. 1024, 341-343.
19
20
21
22
11. Example 1 of the First Provisional satisfies all aspects of the second element of Count 1,
23
except for contacting in a eukaryotic cell, because it employs Cas9, which is necessarily a Type
A2-3
II CRISPR-associated Cas protein, and specifies that the [t]arget DNAs were obtained by
chemical synthesis and that the target DNA was contacted with a Type II CRISPR-Cas system:
[t]he DNA-targeting RNA/polypeptide complexes were assembled . . . . [and] the assembled
complex was added to target DNA and incubated. See Ex. 1003, 00248-00249; see also Ex.
1156, pp. 4-6; see also Ex. 1022, 350-353, Ex. 1024, 341-344.
6
7
8
9
10
12. Included in the Type II CRISPR-Cas system of Example 1 of the First Provisional were
11
engineered and non-naturally-occurring single-molecule DNA-targeting RNAs. See Ex. 1003,
12
00248; see also Ex. 1022, 353, Ex. 1024, 344.
13
14
15
16
13. Contacting a target DNA with the system of Example 1 of the First Provisional in
17
eukaryotic cells is taught throughout the First Provisional. See Ex. 1003, 00165; see also Ex.
18
1003, 00167, 00177, 00178, 00201, 00215, 00216; see also Ex. 1022, 352-353, 376, Ex.
19
1024, 343-344, 367.
20
21
22
23
14. Example 1 of the First Provisional satisfies all aspects of the third, fourth, fifth, and sixth
A2-4
elements of Count 1 because it uses the required system and specifies that the DNA-targeting
polypeptide was based on the sequence of Streptococcus pyogenes Cas9 and that a complex
was assembled from [t]he DNA-targeting RNA and the [Cas9] polypeptide. See Ex. 1003,
00248-00249; see also Appendix 3; see also Ex. 1022, 354, Ex. 1024, 345.
5
6
7
8
15. Figure 3B of the First Provisional illustrates the structure of the engineered and non-naturally
occurring single-molecule DNA-targeting RNAs, which combined the targeter-RNA
10
and activator-RNA into a single molecule. See Ex. 1003, 00251, Figs. 1, 3B; see also
11
Appendix 3; see also Ex. 1022, 354, Ex. 1024, 345.
12
13
14
15
16. Example 1 of the First Provisional satisfies all aspects of element 7 of Count 1 because
16
the DNA-targeting RNA formed a complex with the Cas9 protein during incubation [with each
17
other] in the cleavage buffer for 15 min[utes] at room temperature. See Ex. 1003, 00249; see
18
also Ex. 1022, 355, Ex. 1024, 346.
19
20
21
22
17. Example 1 of the First Provisional explains how the Cas9 protein was targeted to the
23
target DNA by adding the assembled DNA-targeting RNA/Cas9 complex to target DNA and
A2-5
incubated for 1 h[ou]r at 37C. See Ex. 1003, 00249; see also Ex. 1022, 355, Ex. 1024,
346.
3
4
5
6
18. Figure 1 of the First Provisional supports the seventh element of Count 1 because it
depicts the DNA-targeting RNA forming a complex with the site-directed modifying polypeptide
(such as Cas9) and that cleavage (depicted by scissors) occurs because the Cas9 protein was
targeted to the target DNA. See Ex. 1003, Fig. 1; see also Appendix 3; see also Ex. 1022, 355,
10
Ex. 1024, 346.
11
12
13
14
19. Figures 3A and 5A of the First Provisional show that cleavage of the target DNA
15
molecules did occur, i.e., the methods worked. See Ex. 1003, 00248-00252, Figs. 3A, 5A; see
16
also Ex. 1022, 355, Ex. 1024, 346.
17
18
19
20
20. The First Provisional states the tested single-molecule DNA-targeting RNAs (RNA
21
chimera A) supported efficient target DNA cleavage. See Ex. 1003, 00251, Fig. 3B.
22
23
A2-6
1
2
21. Example 1 of the First Provisional demonstrates the necessary and sufficient components
of the CRISPR-Cas9 system. See Ex. 1003, 00248-00252; see also Ex. 1022, 342-349, Ex.
1024, 333-340.
5
6
7
8
22. Extensive guidance in the First Provisional, such as that provided in Paragraph 00165,
explained that the methods of Example 1 could be used in host cells, including eukaryotic cells.
10
See Ex. 1003; see also Ex. 1022, 341-358, 373-407, Ex. 1024, 332-349, 364-398.
11
12
13
14
23. Claims 54, 58, 61, 66, and 72-75 of the First Provisional describe and enable all elements
15
of Count 1, including the eukaryotic limitation. See Ex. 1003, pp. 76-78; see also Ex. 1022,
16
359-363, 380-381, Ex. 1024, 350-354, 371-372.
17
18
19
20
24. Claim 54, whose DNA-targeting RNA can be a single-molecule DNA-targeting RNA as
21
illustrated in Figure 1B, provides the framework of Count 1s second, third, fourth, and fifth
22
elements of relying upon a DNA-targeting RNA comprising i) a targeter-RNA or guide
23
sequence that hybridizes with the target sequence, and ii) an activator-RNA, or a trans-activating
A2-7
CRISPR RNA (tracrRNA), that hybridizes with the targeter-RNA to form a double-stranded
RNA duplex of a protein binding segment. See Ex. 1003, p. 76, Fig. 1B; see also Ex. 1022,
360, Ex. 1024, 351.
4
5
6
7
25. Claims 58, 61, and 66 of the First Provisional make clear that the methods for cleaving
target DNA set forth in Example 1 may take place in a eukaryotic cell, such as in animal cells.
See Ex. 1003, pp. 76-77; see also Ex. 1022, 361, Ex. 1024, 352.
10
11
12
13
26. Claim 72 of the First Provisional satisfies the second element of Count 1 because it
14
specifies that the DNA-modifying polypeptide used in the method of Claim 54 comprises an
15
amino acid sequence having at least about 75% amino acid sequence identity to amino acids 7-
16
166 or 731-1003 of the Cas9/Csn1 amino acid sequence depicted in Figure 2, or to the
17
corresponding domains in any of the amino acid sequences depicted in Figure 12. See Ex.
18
1003, p. 78; see also Ex. 1022, 362, Ex. 1024, 353.
19
20
21
22
27. Because Cas9 proteins are necessarily part of a Type II CRISPR system and because the
23
Cas9 protein may be mutated up to 25% from a naturally-occurring Cas9, the second and sixth
A2-8
elements of Count 1 are satisfied by Claim 72 of the First Provisional. See Ex. 1003, pp. 76-78;
see Ex. 1156, pp. 4-6; see also Ex. 1022, 362, Ex. 1024, 353.
3
4
5
6
28. As used in Claim 75 of the First Provisional, nuclease activity is synonymous with
cleavage. See Ex. 1003, p. 78; see also Ex. 1022, 363, Ex. 1024, 354.
8
9
10
11
29. Claims 54 and 73-75 of the First Provisional, especially in view of Figure 1, satisfy
12
element seven of Count 1. See Ex. 1003, p.78; see also Ex. 1022, 363, Ex. 1024, 354.
13
14
15
16
30. From at least Claims 54, 58, 61, 66, and 72-75 of the First Provisional, one of ordinary
17
skill in the art would have recognized that the inventors were in possession of the methods of
18
Count 1 and would have been able to perform those methods from the enabling disclosures
19
throughout the First Provisional. Ex. 1003, pp. 76-78; see also Appendix 3; see also Ex. 1022,
20
380, Ex. 1024, 371.
21
22
23
A2-9
31. Many disclosures in the First Provisional other than Example 1 in combination with
Paragraph 00165 and Claims 54, 58, 61, 66, and 72-75 demonstrate that by May 25, 2012, the
inventors were in possession of methods that include each and every element of Count 1. See
Ex. 1003; see also Ex. 1022, 356-358, Ex. 1024, 347-349.
5
6
7
8
32. The First Provisional uses Cas9, formerly known as Csn1, as an example of a site-directed
modifying polypeptide. See Ex. 1003, 0006, 0096; see also Ex. 1022, 356, Ex.
10
1024, 347.
11
12
13
14
33. The First Provisional explains that the target DNA used in the disclosed methods may
15
include a cell from any organism and specifically identifies, among others, a cell of a single-
16
cell eukaryotic organism. See Ex. 1003, 0165; see also Ex. 1022, 356, Ex. 1024, 347.
17
18
19
20
34. Figure 1B of the First Provisional illustrates a single-molecule DNA-targeting RNA,
21
demonstrating that the inventors were in possession of an engineered and non-naturally occurring
22
Type II CRISPR-Cas system, because the natural system uses a DNA-targeting RNA comprising
23
two RNA molecules (illustrated in Figure 1A). See Ex. 1003, 0004, Fig. 1; see also Ex. 1022,
A2-10
357, Ex. 1024, 348.
2
3
4
5
35. The First Provisional makes clear that the inventors possessed the methods of Count 1 by
explaining that crRNA, tracrRNA, and the Cas9 protein were both necessary and sufficient for
Cas9 cleavage of target DNA and that such cleavage would occur in a eukaryotic cell. See Ex.
1003, 0002-0004, 0006, 0096, 0165, Fig. 1A; see also Ex. 1022, 358, Ex. 1024, 349.
9
10
11
12
36. Guidance provided in Example 1 and Paragraph 00165 of the First Provisional, Claims
13
54, 58, 61, 66, and 72-75, and numerous passages in the Specification demonstrate that one of
14
ordinary skill in the art as of May 25, 2012, would have readily performed the methods of Count
15
1 without undue experimentation. See Ex. 1003, 00248-00252; see also Ex. 1022, 373-
16
407, Ex. 1024, 364-398.
17
18
19
20
37. The First Provisional teaches that the Cas9 protein and/or the DNA-targeting RNAs can
21
be provided in the form of a nucleic acid containing a nucleotide sequence encoding those
22
components, and further explains that the nucleotide sequences can be contained on an
23
expression vector, such as a viral vector, as would be commonly done when performing the
A2-11
method in a eukaryotic cell. See Ex. 1003, 00120-00123; see also Ex. 1022, 387, Ex. 1024,
378.
3
4
5
6
38. Suitable expression vectors are specifically identified in the First Provisional and it was
known as of May 25, 2012, that vectors, such as viral vectors, were used to deliver prokaryotic
polynucleotides into eukaryotic cells. See Ex. 1003, 00120-00123; see Exs. 1031, 1039,
1194, 1203, 1218, 1283, 1285, 1334, 1353; see also Ex. 1022, 388-389, Ex. 1024, 379-
10
380.
11
12
13
14
39. The First Provisional explains that [i]n some embodiments, a nucleotide sequence
15
encoding a DNA-targeting RNA and/or a site-directed modifying polypeptide is operably linked
16
to a control element, e.g., a transcriptional control element, such as a promoter, and that the
17
transcriptional control element may be functional in [] a eukaryotic cell. See Ex. 1003,
18
00126; see also Ex. 1022, 390, Ex. 1024, 381.
19
20
21
22
40. The First Provisional provides numerous examples of promoters that were known by May
23
25, 2012, to be functional in eukaryotic cells. See Ex. 1003, 00127; see also Exs. 1229, 1237,
A2-12
1310, 1332, 1337; see also Ex. 1003, 00127; see also Ex. 1022, 390-392, Ex. 1024, 381-
383.
3
4
5
6
41. The First Provisional guides one to carry out the methods in eukaryotic cells by stating
that the methods can involve introducing into a cell (or a population of cells) one or more
nucleic acids comprising nucleotide sequences encoding a DNA-targeting RNA and/or a site-
directed modifying polypeptide, and explains that there are numerous well-known methods that
10
can be used to accomplish this introduction. See Ex. 1003, 00121, 00129; see also Ex. 1022,
11
393, Ex. 1024, 384.
12
13
14
15
42. Methods for introducing a nucleic acid into a eukaryotic cell were known in the art for
16
over 30 years before the First Provisional was filed. See Exs. 1040, 1200, 1248, 1260, 1307; see
17
also Ex. 1022, 393-394, Ex. 1024, 384-385.
18
19
20
21
43. The First Provisional explains the use of elements to target the Cas9 protein to a desired
22
cellular compartment, such as Protein Transduction Domains (PTDs) or nuclear localization
23
signals (NLSs). See Ex. 1528; see also Ex. 1022, 395, Ex. 1024, 386.
A2-13
1
2
3
4
44. PTDs and NLSs are helpful, but not always necessary, to target eukaryotic genomic DNA
(residing in the nucleus of eukaryotic cells). See Ex. 1022, 395, Ex. 1024, 386.
6
7
8
9
45. The First Provisional discloses that the Cas9 protein can include a conjugate to facilitate
10
traversing a cell or organelle membrane (a PTD). See Ex. 1003, 00115; see also Ex. 1022,
11
395, Ex. 1024, 386.
12
13
14
15
46. Some of the PTDs discussed in the First Provisional were well known NLSs, including
16
the sequence RKKRRQRRR. See Ex. 1003, 00115, 00179; see also Ex. 1022, 395, Ex.
17
1024, 386.
18
19
20
21
47. The First Provisional also provides examples of expression vectors that contain an NLS,
22
such as the vector pSVK3. See Ex. 1003, 00124; see also Ex. 1022, 395, Ex. 1024, 386.
23
A2-14
2
3
48. For decades prior to the filing of the First Provisional, researchers had used nuclear
localization signals to target prokaryotic peptides expressed in eukaryotic cells. See Ex. 1528;
see also Ex. 1022, 395, Ex. 1024, 386.
6
7
8
9
49. The First Provisional explains that standard recombinant nucleic acid manipulation
10
techniques, such as codon optimization, can be used to practice the methods in eukaryotic cells.
11
See Ex. 1003, 0033; see also Exs. 1029, 1030, 1035, 1213, 1217, 1235, 1236, 1293, 1302,
12
1319, 1327, 1329, 1335, 1336, 1502; see also Ex. 1003, 0033; see also Ex. 1022, 396-404,
13
Ex. 1024, 387-395.
14
15
16
17
50. For many years prior to the filing of the First Provisional, researchers had used codon
18
optimization to enhance expression of prokaryotic polypeptides in eukaryotic cells. See Ex.
19
1003, 0033; see also Ex. 1022, 397, Ex. 1024, 388.
20
21
22
23
51. The First Provisional would have allowed persons of ordinary skill in the art to carry out
A2-15
the methods of Count 1 without undue experimentation. See Ex. 1003; see also Ex. 1022,
405-407, 431, Ex. 1024, 396-398, 422.
3
4
5
6
52. In terms of adapting in vitro results to a eukaryotic environment, the relative skill of those
in the art as of May 25, 2012, was high and the art associated with biotechnology was vast and
highly developed. See Ex. 1022, 406, Ex. 1024, 397.
9
10
11
12
53. Numerous passages throughout the First Provisional set forth each and every element of
13
Count 1 and the application explains how to perform the methods. See Ex. 1003; see also Ex.
14
1022, 406, Ex. 1024, 397.
15
16
17
18
54. Because the First Provisional provides detailed descriptions and the reagents and
19
techniques necessary to perform the methods were well-known, minimal experimentation was
20
needed to perform the methods of Count 1. See Ex. 1003; see also Ex. 1022, 406, Ex. 1024,
21
397.
22
23
A2-16
1
2
55. That the First Provisional describes and enables embodiments within the scope of Count
1 is further evidenced by the U.S. Patent and Trademark Office rejecting Junior Partys claims as
anticipated by the First Provisional. See Exs. 1003, 1512-1527; see also Ex. 1022, 430a-430f,
Ex. 1024, 421a-421f.
6
7
8
9
56. Example 1 in the First Provisional is an actual, working example of all but the eukaryotic
10
element of Count 1, and one of ordinary skill in the art could readily and predictably have
11
transitioned Example 1 to eukaryotic cells based upon the guidance provided in the application.
12
See Ex. 1003; see also Ex. 1022, 406, Ex. 1024, 397.
13
14
15
16
57. The rapid success of numerous other research groups in applying the system of Example
17
1 of the First Provisional to eukaryotic cells immediately after the invention was published is
18
empirical evidence that the First Provisional describes and enables embodiments within the
19
scope of Count 1. See Exs. 1003, 1055, 1056, 1058, 1059, 1508-1510; see also Ex. 1022,
20
408-430, Ex. 1024, 399-421.
21
22
23
A2-17
58. Jinek 2012 publicly disclosed the components that are necessary and sufficient for
cleavage by a Type-II CRISPR-Cas system (crRNA, tracrRNA, and Cas9) and demonstrated
successful reconstitution of the system outside of its natural bacterial environment. See Ex.
1155; see also Ex. 1022, 410, Ex. 1024, 401.
5
6
7
8
9
59. Jinek 2012 explained the basic components required for the CRISPR system to operate,
10
demonstrated its effectiveness outside of a cell, and discussed its usefulness within a eukaryotic
11
cell. See Ex. 1155; see also Ex. 1022, 413, Ex. 1024, 404.
12
13
14
15
60. Within just seven months after Jinek 2012 published, the Cong (Ex. 1055), Mali (Ex.
16
1056), Cho (Ex. 1059), and Hwang (Ex. 1058) groups had successfully performed experiments,
17
prepared and submitted manuscripts for review, and published papers on their results showing
18
that the system published in Jinek 2012 (disclosed in the First Provisional) worked in eukaryotic
19
cells. See, e.g., Ex. 1055, p. 819, middle col.; Ex. 1056, p. 1, Ex. 1059, p. 230, left col, and Ex.
20
1058, pp. 1-2; see Exs. 1002, 1011-1013, 1057, 1371, 1372; see also Ex. 1022, 414-423, Ex.
21
1024, 405-414.
22
23
A2-18
1
2
61. Cong, Mali, Cho, and Hwang used the single molecule DNA-targeting RNA from the
First Provisional and Jinek 2012 and attribute Jinek 2012 as the inspiration that led to the rapid
and successful demonstration of DNA cleavage and gene editing in eukaryotes. See Ex. 1155,
Fig. 5; Ex. 1055, p. 819 and Fig. 2; Ex. 1056, p. 1, and Fig. 1; Ex. 1059, p. 230, left col, and Ex.
1058, pp. 1-2; see also Ex. 1022, 416-418, Ex. 1024, 407-409.
7
8
9
10
62. The ordinary, well-known, and routine techniques (including particular promoters,
11
codon-optimization, and nuclear localization signals) employed by Cong, Mali, Cho, and Hwang
12
to successfully move the system of Jinek 2012 into eukaryotic cells are disclosed in the First
13
Provisional. See Exs. 1003, 1055, 1056, 1058, 1059; see also Ex. 1022, 423, Ex. 1024, 414.
14
15
16
17
63. Less than two years after Jinek 2012 published, at least three more groups Kim (Ex.
18
1508), Cho (Ex. 1509), and Sung (Ex. 1510) successfully transitioned the methods of the First
19
Provisional to eukaryotic cells. See Exs. 1508-1510, 1531, 1532; see also Ex. 1022, 424-430,
20
Ex. 1024, 415-421.
21
22
23
A2-19
64. The Cong, Mali, Cho, Hwang, Kim, Cho, and Sung groups were not conducting
extensive research, nor were they engaged in undue experimentation but were instead performing
well-known, routine experiments with a new technology that had been fully described in the First
Provisional. See Exs. 1003, 1055, 1056, 1058, 1059, 1508-1510; see also Ex. 1022, 430, Ex.
1024, 421.
6
7
8
9
10
65. The Second Provisional provides at least one constructive reduction to practice of Count
1. See Ex. 1004; see also Ex. 1022, 432-439, Ex. 1024, 423-430.
11
12
13
14
66. The Second Provisional includes all relevant content from the First Provisional to show at
15
least one constructive reduction to practice of Count 1. See Ex. 1004; see also Ex. 1022, 434-
16
436, Ex. 1024, 425-427.
17
18
19
20
67. Claims 60, 65, 66, 69-72, and 98-100 of the Second Provisional disclose embodiments
21
within the scope of Count 1. See Ex. 1004, pp. 111, 112, 115-117; see also Appendices 6-8; see
22
also Ex. 1022, 435, Ex. 1024, 426.
23
A2-20
2
3
68. All of the pertinent disclosure found to describe and enable an embodiment within the
scope of Count 1 in the First Provisional is carried through and included in the Second
Provisional. Compare Ex. 1003 with Ex. 1004; see also Ex. 1022, 437-439, Ex. 1024,
428-430.
7
8
9
10
69. That in vitro working Example 1 of the First Provisional could have readily been
11
transitioned to a eukaryotic cell is evidenced by Cho, Mali, Cong, and Hwang and their reliance
12
on Jinek 2012. See Exs. 1003, 1004, 1055, 1056, 1058, 1059; see also Ex. 1022, 437, Ex.
13
1024, 428.
14
15
16
17
70. The information in the Second Provisional that is not in the First Provisional provides
18
more guidance to one of ordinary skill in the art for carrying out the methods of Count 1. See Ex.
19
1004, 0016-0018, 0053-0061, 0084-0089, 00178, 00255-00256, 00289-00359, Figs. 13-35;
20
see also Ex. 1022, 437-439, Ex. 1024, 428-430.
21
22
23
A2-21
71. The Third Provisional contains a working example of the methods of Count 1, which is
one of several constructive reductions to practice of Count 1 in that application. See Ex. 1005;
see also Ex. 1022, 440-448, Ex. 1024, 431-439.
4
5
6
7
72. The Third Provisional includes all relevant content from the First Provisional to describe
and enable an embodiment within the scope of Count 1. Compare Ex. 1003 to Ex. 1005; see also
Ex. 1022, 442, Ex. 1024, 433.
10
11
12
13
73. Claims 64, 69, 70, 73-76, and 102-104 of the Third Provisional disclose embodiments
14
within the scope of Count 1. See Ex. 1005, pp. 152, 153, 155-160; see also Ex. 1022, 443, Ex.
15
1024, 434.
16
17
Broads response: ADENY
18
19
74. All of the pertinent disclosure found in the First Provisional and the Second Provisional
20
to describe and enable an embodiment within the scope of Count 1 is carried through and
21
included in the Third Provisional. Compare Ex. 1003 with Ex. 1004 and Ex. 1005; see also Ex.
22
1022, 445-448, Ex. 1024, 436-439.
23
A2-22
2
3
75. Example 1 of the First Provisional could have readily been trasitioned to a eukaryotic
cell even as early as May 25, 2012, and certainly by the Third Provisionals filing date of
January 28, 2013. See Exs. 1003, 1005; see also Ex. 1022, 445, Ex. 1024, 436.
6
7
8
9
76. The rapid successes at performing the methods of Example 1 in eukaryotic cells by Mali,
10
Cho, Cong, Hwang, Kim, Cho, and Sung further evidence that one of ordinary skill in the art was
11
readily and predictably able to transition those methods to eukaryotic cells. See Exs. 1055, 1056,
12
1058, 1059, 1508-1510; see also Ex. 1022, 445, Ex. 1024, 436.
13
14
15
16
77. Additional information included in the Third Provisional not included in the First
17
Provisional provides guidance to one of ordinary skill in the art for carrying out the methods of
18
Count 1. See Ex. 1005, 0005-0028, 0064-0074, 00119-00120, 00240-00244, Figs. 36-46; see
19
also Ex. 1022, 445, Ex. 1024, 436.
20
21
22
23
78. The Third Provisional includes working Examples 2 and 3. See Ex. 1005, 00408-
A2-23
00450; see also Ex. 1022, 446, Ex. 1024, 437.
2
3
4
5
79. Not only does Example 2 of the Third Provisional describe and enable embodiments
within Count 1, it further demonstrates that one of ordinary skill in the art would have applied
the methods disclosed in the First Provisional in eukaryotic cells without undue experimentation.
See Ex. 1005, 00408-00423; see also Ex. 1022, 447, Ex. 1024, 438.
9
10
11
12
80. U.S. Patent Application Serial No. 13/842,859 currently shares four inventors from each
13
of the Provisional Applications, i.e., Martin Jinek, Jennifer Doudna, Emmanuelle Charpentier,
14
and Krzysztof Chylinski. See Ex. 1001, pp. 346-347; see also Exs. 1003-1005, 1533.
15
A2-24
Broads Additional Facts:
81. Neither Doudna P1 nor P2 includes an experiment that falls within the scope of Count 1. Ex.
1003; Ex. 1004; Ex. 2009 11.22.
82.
P1 lacks any discussion of PAM sequences. Ex. 1003; Ex. 2009 11.43.
83.
Prior to P1s May 2012 filing date, the role of PAM sequences in CRISPR system
targeting of natural DNA targets in bacteria was known. Ex. 2009 11.12-11.13.
84.
be addressed when adapting a CRISPR-Cas9 system for non-natural target DNA. Ex. 2009
11.43.
Persons of ordinary skill (POSITA) in 2012 would have expected the role of PAM to
10
85.
The state of the art in May 2012 relating to CRISPR-Cas9 systems was nascent and
11
unpredictable. Ex. 2009 11.117.
12
86.
13
would work in a eukaryotic cell. Ex. 2230.
14
87.
15
Ex. 2009 11.100.
16
88.
17
Cas9 systems to function in eukaryotic cells. See Ex. 2412; Paper 53; Ex. 2009 11.102.
18
89.
19
CRISPR-Cas9 system in prokaryotes. Ex. 1032; Ex. 1153; Ex. 1227; Ex. 2009 11.98-11.99.
20
90.
21
development of a CRISPR-Cas9 system showing his development of a single vector delivery of a
22
multiplexed system with dual molecule guide RNA and Cas9. Ex. 2411 at 16; Ex. 2009 11.97.
23
91.
Dr. Doudna conceded that even after Jinek 2012, she did not know if the Jinek system
After its in vitro tests, Senior Party experienced many frustrations in eukaryotic cells.
By early 2011, Junior Partys Feng Zhang had begun experiments adapting CRISPR-
By 2011, publications had identified certain components that potentially played role in
Dr. Zhang filed a grant application with the NIH on January 12, 2012, relating to his
Using four componentsCas9 nuclease and bacterial RNase III genes, a tracrRNA
A2-25
element, and the guide RNA arrayDr. Zhangs group successfully adapted a CRISPR-Cas9
system to function in eukaryotic cells using a dual molecule guide RNA. Ex. 1055 at 2.
92.
system to function in eukaryotic cells. Ex. 1055 at 2.
93.
B), with shorter tracrRNA components than the wild-type tracrRNA. Ex. 1003 at 2, 0006.
94.
Chimera B did not. Ex. 1155 at 820.
95.
The Cong et al. 2013 article reported Dr. Zhangs groups work adapting a CRISPR-Cas
Senior Partys inventors created two versions of chimeric RNA (Chimera A and Chimera
Jinek 2012 reported that Chimera A worked efficiently in vitro but the even shorter
The Jinek 2012 paper did not teach any longer tracrRNA components for their chimeric
10
RNA, but instead suggested to those of ordinary skill the use of Chimera A with its relatively
11
short tracrRNA component as compared to wild-type tracrRNA. Ex. 1155; Ex. 2009 11.66.
12
96.
13
to the CRISPR-Cas9 system previously developed in their laboratory. Ex. 1155 at 20;
14
97.
15
function in eukaryotic cells, using non-routine techniques, adding two NLSs to target the Cas9
16
protein to the nucleus, and a vector to express Cas9 and crRNA, with four nucleotides not
17
present on Chimera A. Ex. 1055 at 2.
18
98.
19
eukaryotic cell. Ex. 1055 at 20; Ex. 2009 11.130.
20
99.
21
longer tracrRNA. Ex. 1056 at 824; Ex. 2009 11.109.
22
100.
23
and some Broad scientists have advisors at both institutions. Ex. 2423; Ex. 2009 11.90.
Dr. Zhangs group at the Broad compared a modified version of Chimera A of Jinek 2012
Dr. Zhangs group at the Broad adapted CRISPR-Cas9 with Chimera A-type RNA to
Eight of the 14 Chimera A-type samples tested by the Broad scientists did not work in a
Dr. Churchs group at Harvard published the Mali 2013 article in January 2013 using
The Junior Party includes both the Broad and Harvard, which is affiliated with the Broad,
A2-26
101.
Dr. Zhangs group at the Broad included Dr. Cong and Dr. Church at Harvard was the co-
advisor to Dr. Cong. Simons Tr. 89:4-15.
102.
Dr. Hwangs group thanked Dr. Church for sharing unpublished results. Ex. 1058 at 6.
103.
Senior Party does not assert actual reduction to practice until October 29, 2012. Paper 58.
104.
The Senior Partys in vitro work published in Jinek 2012. UC Motion 4 at 18:14-19:5
105.
The Jinek system with Chimera A did not work in eukaryotic cells using routine
techniques. Ex. 2009 11.74.
106.
Harvard had achieved success in eukaryotes. Ex. 2230.
Dr. Doudnas laboratory was surprised when they learned that Dr. Churchs laboratory at
10
107.
After Dr. Churchs laboratory shared unpublished results, Dr. Doudnas laboratory
11
published Jinek 2013 paper with attempt to adapt CRISPR-Cas9 system to function in
12
eukaryotic cells. Ex. 2009 11.141.
13
108.
14
2013 using a chimeric RNA with longer tracrRNA components than Chimera A. Ex. 1005 at
15
Figures 36-38; Ex. 1055 at Figures 3-5.
16
109.
17
stated that Its not trivial to make CRISPR/Cas systems work in eukaryotic cells, and that
18
[o]ne thing is to have them in silico and have a sequence and realize theyre smaller, and
19
another thing is to do the [eukaryotic] experiments and make it work. Ex. 2213.
20
110.
21
Gairdner Award for their work with CRISPR-Cas systems. Ex. 2419.
22
111.
23
CRISPR-Cas system as a genome editing tools for function in eukaryotic cells. Ex. 2419 at 2.
Senior Partys inventors filed P3 containing the same eukaryotic test results as in Jinek
Dr. Luciano Marraffini, who studies CRISPR/Cas systems at Rockefeller University,
Drs. Zhang, Horvath, Doudna, Charpentier and Barrangou jointly received the 2016
The Gairdner Foundation noted Dr. Zhangs work in the development of the microbial
A2-27
112.
Count 1 recites a target DNA molecule in a eukaryotic cell that is not a natural target of
the prokaryotic CRIPSR-Cas9 system. Ex. 2009 11.17.
113.
bacteria, of which three did not show any cleavage. Ex. 1003 at 95; Ex. 2009 11.49.
114.
the correct PAM for all six orthologs in Figure 5 of Doudna P1. Ex. 2009 11.49.
115.
eukaryotic cells. Ex. 1003 at 248-253; Carroll Tr. 156:20-157:8; Ex. 2009 11.5.
116.
Figure 5 of Doudna P1 shows results using six Cas9 orthologs from different species of
Persons of ordinary skill would have understood that the Doudna P1 inventors did not use
Example 1 of Doudna P1 and P2 describes only in vitro testing and not testing in
Dr. Church characterized the move of CRISPR-Cas from bacteria to eukaryotic cells as a
10
huge jump. Ex. 2423.
11
117.
12
CRISPR-Cas9 system of Example 1 actually works in eukaryotic cells. Ex. 2009 11.22.
13
118.
14
CRISPR-Cas9 actually worked in eukaryotic cells, or identify a structural aspect of a CRISPR-
15
Cas9 system that would make it adapted for eukaryotic cells. Ex. 2009 11.25.
16
119.
17
CRISPR-Cas system in a eukaryotic cell based on in vitro experiments. Ex.2009 11.6, 11.92.
18
120.
19
that the Doudna inventors provided sufficient information to show possession of an invention of
20
an embodiment of a CRISPR-Cas system functioning in eukaryotic cells. Ex.2009 11.6, 11.92.
21
121.
22
Senior Partys UC and University of Vienna inventors asserted conception date for Count 1 of
23
October 18, 2011. Paper 58 at 1.
Example 1 and Paragraph 00165 of P1 and P2 do not provide any evidence that the
None of the portions of P1 or P2 cited by Senior Party provide evidence that the
Persons of ordinary skill in the art in 2012 would not predict the operability of a
Skilled persons in 2012 would have required positive eukaryotic tests results conclude
Senior Party did not make an embodiment of Count 1 until more than a year after the
A2-28
122.
Senior Party did not make an embodiment of Count 1 until more than two years after Dr.
Charpentiers asserted conception date for Count 1 of July 30, 2010. Paper 58 at 1.
123.
taught techniques for eukaryotic experiments. Ex. 1161 at 0054-0060; Ex. 2009 11.33.
124.
The Sontheimer application did not include actual eukaryotic experiments. Ex. 1161.
125.
The claims in the Sontheimer application to Type III CRISPR system for use in
eukaryotic cells were rejected by the USPTO. Ex. 2413 at 23.
126.
have conveyed to persons of ordinary skill lack of possession of an invention of a CRISPR-Cas9
Sontheimer application stated that its CRISPR system could be used in eukaryotes and
The lack of tests in eukaryotic cells in Doudna P2 four months after Jinek 2012 would
10
system adapted to function in a eukaryotic cell. Ex. 2009 11.74.
11
127.
12
or was known. Carroll Tr. at 255:4-258:17; 305:6-338:10; Ex. 2009 11.86-87.
13
128.
14
Jinek 2012 were performed in vitro with purified components and expressed doubt about
15
whether the CRISPR-Cas system would function in eukaryotic cells. Ex. 1152 at 1660.
16
129.
Dr. Carroll claims to have knowledge of one of ordinary skill in the art. Ex. 1024 at 19.
17
130.
Dr. Carroll did not dispute that his 2012 article does not state any expectation of success
18
for CRISPR-Cas9 systems in eukaryotic cells. Carroll Tr. at 117:5-118:2.
19
131.
20
system in eukaryotes will address concerns he had raised. Ex. 1152 at 1660.
21
132.
22
not know if the CRISPR-Cas9 system would work in eukaryotic cells. Ex. 2207.
23
133.
Dr. Carroll admitted that all of the information in P1 and P2 either appears in Jinek 2012
Dr. Carroll observed in a September 2012 article that [a]ll the experiments described in
In 2012, Dr. Carroll stated in reference to Jinek 2012 that [o]nly attempts to apply the
In a July 2014 article, Dr. Doudna confirmed that after publication of Jinek 2012, she did
An article from July 28, 2012 stated that [t]he next steps according to Dr. Charpentier
A2-29
and Dr. Doudna were to test the single-RNA construct with Cas9 to find out whether it works in
eukaryotic organisms. Ex. 2290.
134.
different from the environment of eukaryotic cells. Ex. 2009 11.114.
135.
Cas9 and RNA expression, Cas9 folding, and CRISPR-Cas9 complex formation and function,
even if it worked in an in vitro environment. Ex. 2009 11.30.
136.
systems to eukaryotic cells so as to be properly transcribed and translated. Ex. 2009 11.31.
A POSITA in May 2012 would have recognized that an in vitro environment is very
Differences between eukaryotic and prokaryotic cells could have unpredictable effects on
It was known in May 2012 that it may not be possible to deliver components of CRISPR
10
137.
It was known in May 2012 that proteins or nucleic acids present in eukaryotic cells could
11
interfere with interactions of components of CRISPR-Cas9. Ex. 2009 11.31.
12
138.
13
of CRISPR-Cas9 system. Ex. 2009 11.31.
14
139.
15
prevent CRISPR-Cas9 from functioning in eukaryotic cells. Ex. 2009 11.31.
16
140.
It was known in May 2012 that CRISPR-Cas9 evolved in prokaryotes. Ex. 2009 11.88.
17
141.
Count 1 requires engineering a CRISPR-Cas9 system to function in a manner that is
18
antithetical to its natural function in prokaryotic cells. Ex. 2009 10.5.
19
142.
20
larger than that of bacteria. Ex. 2009 10.7.
21
143.
22
nature. Ex. 2009 10.7.
23
144.
It was known in May 2012 that systems in eukaryotic cells developed may degrade RNA
P1 and P2 did not discuss any of the unique features of eukaryotic cells that might
A POSITA in May 2012 understood that the human genome is at least a thousand-fold
It was understood in May 2012 that CRISPR had never been found in eukaryotes in
It was known in May 2012 that the proteins and RNA molecules of a CRISPR-Cas9
A2-30
system may be toxic to eukaryotic cells. Ex. 2009 11.31.
145.
which are called off-target effects. Ex. 2009 11.31.
146.
and that off-target effects could, in fact, be lethal. Carroll Tr. at 227:3-6, 229:2-12.
147.
effects from CRISPR-Cas9 in eukaryotes without doing experiments. Greider Tr. at 405:14-22.
148.
CRISPR-Cas9 system to target DNA in the environment of a eukaryotic cell. Ex. 2009 11.31.
Toxic effects include the effect of genome editing in locations other than the target DNA,
Dr. Carroll testified that off-target effects are an important concern for genome editing
Dr. Greider testified that POSITA would have had no expectation regarding off-target
It was known in May 2012 that it may not be possible to localize the components of the
10
149.
P1 and P2 do not teach using an NLS in eukaryotic cells. Ex. 2009 11.31; Ex. 1003.
11
150.
Dr. Greider testified DNA target of interest is in nucleus. Greider Tr. at 285:20-286:1.
12
151.
Dr. Greider provided no opinion that the Senior Party inventors possessed an
13
embodiment of Count 1 for delivering a functioning CRISPR-Cas9 system, with the requisite
14
RNA, into a mitochondria or chloroplast. Greider Tr. (7/20/16) 422:4-18.
15
152.
16
difficulties adapting a prokaryotic system to eukaryotic cells. Ex. 2010 1.45-1.54.
17
153.
18
targetrons, gene editing tools based on group II self-splicing ribozymes. Ex. 2010 1.54
19
154.
20
to adapt them to function in eukaryotic cells. Ex. 2010 1.45-1.48
21
155.
Targetrons include protein and RNA components, like CRISPR systems. Ex. 2010 1.45.
22
156.
Group II self-splicing ribozymes were initially described in 1986, and targetrons were
23
developed that could act on bacterial genes by 2003. Ex. 2010 1.46.
A POSITA reading P1 and P2 at the times they were filed would have known of prior
A POSITA in May 2012 would have also been aware of the history of research relating to
Like CRISPR-Cas9, targetrons originated in prokaryotic cells, and researchers attempted
A2-31
157.
After nine more years of research, researchers had not been able to adapt targetrons to
function effectively in eukaryotic cells. Ex. 2010 1.47-1.54
158.
similar challenges could face researchers attempting to adapt the CRISPR-Cas9 system described
in Example 1 to function in eukaryotic cells. Ex. 2010 1.54.
159.
environments did not show adaptation to function in eukaryotic cells. Ex. 2010 1.45-1.54.
160.
problem for CRISPR-Cas9 as with targetrons, since both systems evolved to function in
A POSITA in May 2012 reading the P1 and P2 applications would have understood that
History of targetrons taught that ability of prokaryotic system to edit genes in other
A POSITA in May 2012 would have known that the level of Mg2+ ions could be a
10
prokaryotic cells. Ex. 2010 1.51-1.53.
11
161.
12
POSITA would have needed experimental results in eukaryotic cells to show possession of a
13
CRISPR-Cas9 invention for eukaryotic cells. Ex. 2009 11.35.
14
162.
15
publication of Jinek 2012. Ex. 1055 at 2; Ex. 2411; Ex. 2009 11.97.
16
163.
17
than modified Chimera A-type system for eukaryotic cells. Ex. 1055 at 20; Ex. 2009 11.130.
18
164.
19
2013, Cho 2013 and Hwang 2013 articles were inspired by Jinek 2012 or that those groups were
20
independent with respect to CRISPR research. Ex. 2009 11.6.
21
165.
22
2013 articles include individuals with more than the ordinary level of skill, including Drs.
23
George Church, Keith Joung and, Jin-Soo Kim. Ex. 2009 11.112.
Given the history of prior failed attempts to transfer prokaryotic systems to eukaryotes,
Dr. Zhang achieved success with a CRISPR-Cas9 system in eukaryotic cells prior to the
Dr. Zhang showed that his CRISPR-Cas9 system with longer tracrRNA worked better
Senior Party has not shown that the research groups responsible for the Cong 2013, Mali
The research groups responsible for the Cong 2013, Mali 2013, Cho 2013 and Hwang
A2-32
166.
Dr. Carroll confirmed that Dr. Kim and Dr. Doudna, one of the authors on Jinek 2013,
had higher than the ordinary level of skill. Carroll Tr. 263:18-264:20.
167.
P1 and P2 provide no guidance for practicing Count 1 in eukaryotes. Ex. 2009 11.114.
168.
Chen P1 reported testing of Chimera A and modified Chimera A, all of which generated
negative results. Ex. 2125 at 32, 34; Carroll Tr. at 178:6-18.
169.
Ex. 2009 11.123-11.129.
170.
the eukaryotic experiments at the Broad. Ex. 2423.
The testing in Chen P1 of Chimera A or modified Chimera A was inconclusive or failed.
Dr. Church acknowledged that his graduate student Dr. Cong worked with Dr. Zhang on
10
171.
The Kim group filed a patent application and recently submitted arguments, and a
11
supporting declaration of Bryan Cullen, stating that their eukaryotic work was not obvious over
12
Jinek 2012. Ex. 2422 at 11, 20-24.
13
172.
14
manufacturer of their nucleofection equipment, which was not routine. Ex. 2009 11.132.
15
173.
16
experimentation to make unmodified Chimera A function in eukaryotic cells. Ex. 2009 11.133.
17
174.
18
tracr. Ex. 1509; Ex. 1508; Carroll Tr. at 279:20-291:7; Ex. 2009 11.134.
19
175.
20
each week and over five million monthly visits to Science website. Ex. 2420; Ex. 2009 11.113.
21
176.
22
with unmodified chimera A could function in eukaryotic cells. Ex. 2009 11.113.
23
177.
Cho 2013 added more plasmids and RNA to eukaryotic cells than recommended by
The testing in Cho 2013 confirms that a POSITA would have needed extensive
In later papers from Cho laboratory, researchers abandoned Chimera A and used a longer
The journal SCIENCE has large reach in scientific community, with 570,400 readers
Only Dr. Chos group using non-routine techniques showed that a CRISPR-Cas9 system
The Doudna P3 application was filed January 29, 2013. Ex. 1005.
A2-33
178.
P3 includes testing in eukaryotic cells, and also adds a description of new CRISPR-Cas9
systems with tracrRNA components that differ from Chimera A. Ex. 1005.
179.
Two experiments in P3 purport to show cleavage in living eukaryotic cells. Ex. 1005.
180.
According to the methods section in P3, the experiment reported in Figure 38B of P3
should show bands of 360 bp for the PCR product in all samples. Ex. 1005 at 412.
181.
Cas9 successfully cleaved the target DNA. Ex. 2009 11.140.
182.
between 160 and 200 bp. Ex. 1005 at 36E; Ex. 2009 11.140.
In P3, Figure 38B, the gel should show bands between 160 and 200 bp if the CRISPR-
The samples in P3 containing Cas9 and sgRNA do not show any diagnostic bands
10
183.
A POSITA would have concluded from Figure 38B of P3 that there was no successful
11
cleavage in eukaryotic cells. Ex. 2009 11.140.
12
184.
13
details are missing. Ex. 2009 11.151-11.159.
14
185.
15
purify their PCR product as evidenced by the additional bands visible in lanes 2 and 4 and that
16
the test results were inconclusive at best. Ex. 2009 11.151-11.159.
17
186.
18
Cas9 expression and nuclear localization. Ex. 1005 at 416.
19
187.
20
Partys inventors obtained nuclear localization. Ex. 2009 11.154.
21
188.
22
the poor results shown in Figures 36E and 38B. Ex. 2009 11.162.
A POSITA reviewing Fig. 36E of P3 would have concluded that necessary experimental
A POSITA reviewing Fig. 36E of P3 would have concluded that the authors did not
Figure 36B reports results of an experiment that according to P3, revealed abundant
To a POSITA, the results in Fig. 36B of P3 would not have indicated that the Senior
The failure in Fig. 36B of P3 to localize the Cas9 protein in the nucleus could account for
A2-34
CERTIFICATE OF FILING AND SERVICE

I hereby certify that on the 15th day of August, 2016, a true and complete copy of the
foregoing BROAD et al. OPPOSITION 4 is being filed by 5:00 pm EST via the Interference
Web Portal. Pursuant to agreement of the parties, service copies are being sent by e-mail by 8:00
pm EST, to counsel for Senior Party as follows:
Todd R. Walters, Esq.
Erin M. Dunston, Esq.
Travis W. Bliss, Ph.D., Esq.
BUCHANNAN INGERSOLL & ROONEY PC
1737 King Street, Suite 500
Alexandria, Virginia 22314-2727
(703) 836-6620
todd.walters@bipc.com
erin.dunston@bipc.com
travis.bliss@bipc.com
Date: August 15, 2016
Li-Hsien Rin-Laures, M.D., Esq.

Sandip H. Patel, Esq.
Greta Noland
MARSHALL GERSTEIN & BORUN LLP
6300 Willis Tower
233 South Wacker Drive
Chicago, Illinois 60606
(312) 474-6300
lrinlaures@marshallip.com
spatel@marshallip.com
gnoland@marshallip.com
/s/ Steven R. Trybus

Steven R. Trybus
Reg. No. 32,760
Lead Counsel for Broad
Jenner & Block LLP
353 North Clark Street
Chicago, IL 60654
Telephone: (312) 222-9350
Facsimile: (312) 527-0484
strybus@jenner.com

Broad Opp. No. 3

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Broad Opp. No. 3

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Filed on behalf of: Junior Party, Broad

Paper No. ____

UNITED STATES PATENT AND TRADEMARK OFFICE

Patent Interference No. 106,048 (DK)

BROAD et al. OPPOSITION 4

PRECISE RELIEF REQUESTED.......................................................................................1

DESCRIPTION OF APPENDICES ....................................................................................1

REASONS WHY THE MOTION SHOULD BE DENIED ................................................1

Summary Of The Argument ....................................................................................1

Doudna P1s Failure to Discuss Any Role of PAM Sequences

Doudna P1 and P2 Do Not Reasonably Convey Possession of a

The Guidance Set Forth in Doudna P1 and P2 Did Not Enable

Doudna P3 Fails to Show Possession of the Invention of Count 1..............4

Legal Standards ........................................................................................................4

Senior Party Mischaracterizes The Factual Background Relating To

The Junior Partys Scientists Commenced CRISPR-Cas9 Work in

The Senior Party Inventors Approach Led to Many Frustrations

The Industry Recognized Dr. Zhangs Eukaryotic Contribution ...............10

Persons Of Ordinary Skill Would Have Concluded That Doudna

Persons Of Ordinary Skill Would Have Concluded That Doudna

The Combination of Example 1, Paragraph 00165 and

Contemporaneous And Pre-Interference Statements

Persons of Ordinary Skill Would Not Have Known

Prior Difficulties Experienced in Attempting to Adapt

The Later Work of Other Laboratories Does Not Support

The Doudna P1 And P2 Applications Do Not Enable A Skilled

The Doudna P3 Application Does not Provide Written Description

APPENDIX 1: LIST OF EXHIBITS ..............................................................................................1

PRECISE RELIEF REQUESTED

Appendix 1 is a list of Exhibits cited in this motion. Appendix 2 is the Statement of

REASONS WHY THE MOTION SHOULD BE DENIED

to eukaryotic cells, as well as the failure to describe eukaryotic-specific considerations such as

Summary Of The Argument

Doudna P1s Failure to Discuss Any Role of PAM Sequences Would

BROAD et al. OPPOSITION 4

in possession of an invention within the scope of Count 1. Count 1 is directed to a method, in a

eukaryotic cell, of cleaving or editing a target DNA molecule or modulating transcription of at

invention that falls within the scope of Count 1.

Doudna P1 and P2 Do Not Reasonably Convey Possession of a

BROAD et al. OPPOSITION 4

general disclosure of eukaryotic cells sufficient to demonstrate possession. In a September 2012

not yet in possession of an invention of a CRISPR-Cas system adapted to function in eukaryotes.

Senior Party attempts to compensate for the deficiencies in Doudna P1 and P2 by

possessed an invention of a CRISPR-Cas9 embodiment of Count 1.

Senior Partys reliance on other groups is also flawed.

The Guidance Set Forth in Doudna P1 and P2 Did Not Enable

BROAD et al. OPPOSITION 4

possession and enablement in Doudna P1 and P2.

Doudna P3 Fails to Show Possession of the Invention of Count 1

Finally, while Doudna P3 reports experiments involving CRISPR-Cas9 systems in

objectively show possession of the invention of Count 1.

P1 and P2 to demonstrate actual possession of a CRISPR-Cas9 system for eukaryotic cells.

the earlier application provided a constructive reduction to practice of an embodiment within

BROAD et al. OPPOSITION 4

A specification also must provide an enabling disclosure. 35 U.S.C. 112(a). A claim

can be sufficiently enabled even if experimentation is necessary, so long as the experimentation

Senior Party Mischaracterizes The Factual Background Relating To

Senior Partys Motion 4 is based on a flawed characterization of the factual background

of events leading to the development of CRISPR-Cas9 systems for eukaryotic cells. It is

triggered four other independent groups to successfully use CRISPR-Cas9 systems in

methods to eukaryotic cells.).

other groups implemented the Jinek system to achieve success.

The Junior Partys Scientists Commenced CRISPR-Cas9 Work in

BROAD et al. OPPOSITION 4