Filed: July 17, 2018
`
`
`Filed on behalf of: Benson Hill Biosystems, Inc.
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`
`
`
`
`
`
`
`
`
`
`__________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`__________________
`
`BENSON HILL BIOSYSTEMS, INC.,
`Petitioner,
`
`v.
`
`
`THE BROAD INSTITUTE INC.,
`PRESIDENTS AND FELLOWS OF HARVARD COLLEGE &
`MASSACHUSETTS INSTITUTE OF TECHNOLOGY
`Patent Owners.
`
`__________________
`
`
`U.S. Patent No. 9,790,490
`
`__________________
`
`
`
`PETITION FOR POST GRANT REVIEW
`
`

`

`
`
`TABLE OF CONTENTS
`
`Page(s)
`INTRODUCTION ........................................................................................... 1
`I.
`BACKGROUND AND STATE OF THE ART .............................................. 2
`II.
`III. SUMMARY OF THE ’490 PATENT ............................................................. 5
`A.
`The Challenged Claims ......................................................................... 5
`B.
`The Specification ................................................................................... 6
`C.
`The Prosecution History ........................................................................ 8
`IV. LEVEL OF ORDINARY SKILL IN THE ART ............................................. 9
`V.
`CLAIM CONSTRUCTION ..........................................................................10
`VI.
`IDENTIFICATION OF CHALLENGES ......................................................14
`A. Ground 1: Failure to Comply with the Written Description
`Requirement for the Recited Genus of “Cpf1 effector
`protein[s]” ............................................................................................15
`1.
`The Specification Does Not Describe a Sufficient
`Number of Representative Species or Provide a
`Structure/Function Correlation Sufficient to Adequately
`Describe the Full Scope of the Subject Matter Recited in
`Claims 1-60 ...............................................................................15
`Claims 12-14 Fail to Sufficiently Narrow the Scope of
`the Genus ...................................................................................24
`B. Ground 2: Claims 1-60 Fail to Comply with the Enablement
`Requirement for the Recited Genus of “Cpf1 effector
`protein[s]” ............................................................................................25
`1.
`The Amount of Direction or Guidance Presented and The
`Presence or Absence of Working Examples .............................27
`
`2.
`
`i
`
`
`
`

`

`2.
`
`3.
`
`4.
`
`E.
`
`The Predictability or Unpredictability of the Art and The
`Quantity of Experimentation Necessary ...................................31
`Claims 12-14 Fail to Sufficiently Narrow the Scope of
`the Genus ...................................................................................37
`Conclusion that the Claimed Invention Lacks
`Enablement ................................................................................39
`C. Ground 3: Claims 1-60 Fail to Inform with Reasonable
`Certainty the Scope of “a Cpf1 effector protein” ................................39
`D. Ground 4: Claims 1-60 Fail to Comply with the Enablement
`Requirement for the Recited Genus of Systems “lack[ing] a
`tracr sequence” ....................................................................................46
`Ground 5: Claims 1-60 Fail to Comply with the Written
`Description Requirement for the Recited Genus of Systems
`“lack[ing] a tracr sequence” ................................................................49
`Ground 6: Claims 1-60 Lack Practical Utility ...................................51
`F.
`G. Ground 7: Claims 1-60 Would Have Been Obvious Over
`Schunder in View of the General Knowledge in the Art and
`Secondary References .........................................................................53
`VII. STATEMENT OF PRECISE RELIEF REQUESTED .................................69
`VIII. GROUNDS FOR STANDING ......................................................................69
`IX. MANDATORY NOTICES UNDER 37 C.F.R. § 42.8 .................................70
`X.
`CERTIFICATION UNDER 37 C.F.R. § 42.24(d) ........................................71
`XI. CONCLUSION ..............................................................................................71
`
`
`
`
`
`
`
`ii
`
`
`
`

`

`
`
`TABLE OF AUTHORITIES
`
` Page(s)
`
`Federal Cases
`In re ’318 Patent Infringement Litigation,
`583 F.3d 1317 (Fed. Cir. 2009) .......................................................................... 52
`AbbVie Deutschland GmbH & Co. v. Janssen Biotech, Inc.,
`759 F.3d 1285 (Fed. Cir. 2014) .............................................................. 15, 16, 23
`ALZA Corp. v. Andrx Pharmaceuticals, LLC,
`603 F.3d 935 (Fed. Cir. 2010) ...................................................................... 26, 48
`Amgen Inc. v. Sanofi,
`872 F.3d 1367 (Fed. Cir. 2017) .................................................................... 18, 37
`Ariad Pharms., Inc. v. Eli Lilly and Co.,
`598 F.3d 1336 (Fed. Cir. 2010) (en banc) .............................................. 15, 16, 23
`Atlas Powder Co. v. E.I. duPont de Nemours & Co.,
`750 F.2d 1569 (Fed. Cir. 1984) .......................................................................... 28
`Biogen Idec, Inc. v. GlaxoSmithKline LLC,
`713 F.3d 1090 (Fed. Cir. 2013) .......................................................................... 13
`Broad Inst., Inc. et al. v. Regents of the Univ. of California,
`2017 WL 657415 (PTAB 2017) ....................................................... 18, 19, 30, 33
`Dow Chem. Co. v. Nova Chems. Corp.,
`803 F.3d 620 (Fed. Cir. 2015) ............................................................................ 40
`Enzo Biochem, Inc. v. Calgene, Inc.,
`188 F.3d 1362 (Fed. Cir. 1999) .......................................................................... 26
`Geneva Pharms., Inc. v. GlaxoSmithKline PLC,
`349 F.3d 1373 (Fed. Cir. 2003) .................................................................... 40, 51
`Nat’l Recovery Techs., Inc. v. Magnetic Separation Sys., Inc.,
`166 F.3d 1190 (Fed. Cir. 1999) .......................................................................... 26
`
`iii
`
`
`
`

`

`Nautilus, Inc. v. Biosig. Instruments Inc.,
`134 S. Ct. 2120 (2014) ........................................................................................ 39
`PAR Pharmaceutical, Inc. v. TWI Pharmaceuticals, Inc.,
`773 F.3d 1186 (Fed. Cir. 2014) .................................................................... 54, 55
`In re Paulsen,
`30 F.3d 1475 (Fed. Cir. 1994) ............................................................................ 42
`Phillips v. AWH Corp.,
`415 F.3d 1303 (Fed. Cir. 2005) .......................................................................... 11
`Plant Genetic Sys., N.V. v. DeKalb Genetics Corp.,
`315 F.3d 1335 (Fed. Cir. 2003) .......................................................................... 37
`PPG Indus., Inc. v. Guardian Indus. Corp.,
`75 F.3d 1558 (Fed. Cir. 1996) ............................................................................ 27
`SciMed Life Sys., Inc. v. Advanced Cardiovascular Sys., Inc.,
`242 F.3d 1337 (Fed. Cir. 2001) .......................................................................... 44
`In re Vaeck,
`947 F.2d 488 (Fed. Cir. 1991) ...................................................................... 28, 29
`In re Wands,
`858 F.2d 731 (Fed. Cir. 1988) ............................................................................ 27
`In re Wright,
`999 F.2d 1557 (Fed. Cir. 1993) .................................................................... 25, 26
`Wyeth & Cordis Corp. v. Abbott Labs.,
`720 F.3d 1380 (Fed. Cir. 2013) ...................................................................passim
`Federal Statutes
`35 U.S.C. § 101 .................................................................................................passim
`35 U.S.C. § 103 ............................................................................................ 15, 54, 69
`35 U.S.C. § 112 .................................................................................................passim
`35 U.S.C. § 112(b) ................................................................................................... 45
`
`iv
`
`
`
`

`

`Regulations
`Regulations
`37 C.F.R. § 1.821(d) .......................................................................................... 24, 25
`37 C.F.R. § 1.821(d) .......................................................................................... 24, 25
`37 C.F.R. § 42.8 ................................................................................................. 70, 71
`37 C.F.R. § 42.8 ................................................................................................. 70, 71
`37 C.F.R. § 42.24(d) ................................................................................................ 71
`37 C.F.R. § 42.24(d) ................................................................................................ 71
`37 C.F.R. § 42.100(b) .............................................................................................. 11
`37 C.F.R. § 42.100(b) .............................................................................................. 11
`
`v
`
`
`
`

`

`
`
`
`
`EXHIBIT
`1001
`1002
`1003
`
`1004
`
`1005
`
`1006
`
`1007
`
`1008
`
`1009
`
`1010
`
`1011
`
`1012
`
`1013
`
`PETITIONER’S EXHIBIT LIST
`
`DESCRIPTION
`United States Patent No. 9,790,490
`Prosecution History of the ’490 patent
`Declaration of Dr. Chase L. Beisel and accompanying
`Appendices A-C
`Schunder et al., “First indication for a functional CRISPR/Cas
`system in Francisella tularensis,” International Journal of
`Medical Microbiology, 303:51-60 (2013)
`Zetsche et al., “Cpf1 Is a Single RNA-Guided Endonuclease of a
`Class 2 CRISPR-Cas System,” Cell, 163:759-71 (2015)
`Zetsche et al., “A Survey of Genome Editing Activity for 16
`Cpf1 orthologs,” bioRxiv, doi: https://doi.org/10.1101/134015
`(2017)
`Hsu et al., “Development and Applications of CRISPR-Cas9 for
`Genome Engineering,” Cell, 157:1262-78 (2014)
`Shmakov et al., “Discovery and Functional Characterization of
`Diverse Class 2 CRISPR-Cas Systems,” Molecular Cell, 60:385-
`97 (2015)
`Koonin et al., “Diversity, classification and evolution of
`CRISPR-Cas systems,” Current Opinion in Microbiology, 37:67-
`78 (2017)
`Karvelis et al., “Rapid characterization of CRISPR-Cas9
`protospacer adjacent motif sequence elements,” Genome Biology,
`16:253, 1-13 (2015)
`Lowder et al., “Rapid Evolution of Manifold CRISPR Systems
`for Plant Genome Editing,” Frontiers in Plant Science,
`7(1683):1-12 (2016)
`Leenay et al., “Identifying and visualizing functional PAM
`diversity across CRISPR-Cas systems,” Mol Cell, 62(1):137-47
`(2016)
`Makarova & Koonin, “Annotation and Classification of CRISPR-
`Cas Systems,” Chapter 4 in CRISPR: Methods and Protocols,
`Methods in Molecular Biology, 1311:47-75 (2015)
`
`vi
`
`
`
`

`

`EXHIBIT
`
`1014
`
`1015
`
`1016
`
`1017
`
`1018
`
`1019
`
`1020
`
`1021
`
`1022
`1023
`
`1024
`
`1025
`1026
`1027
`
`1028
`
`1029
`1030
`
`DESCRIPTION
`HMM Summary Page: TIGR04330 (http://tigrfams.jcvi.org/cgi-
`bin/HmmReportPage.cgi?acc=TIGR04330) last visited June 27,
`2018
`Begemann et al., “Characterization and Validation of a Novel
`Group of Type V, Class 2 Nucleases for in vivo Genome
`Editing,” bioRxiv, doi: http://dx.doi.org/10.1101/192799 (2017)
`Ran et al., “In vivo genome editing using Staphylococcus aureus
`Cas 9,” Nature, 520(7546):186-91 (2015)
`Kleinstiver et al., “Engineered CRISPR-Cas9 nucleases with
`altered PAM specificities,” Nature, 523(7561):481-85 (2015)
`Gao et al., “Engineered Cpf1 variants with altered PAM
`specificities increase genome targeting range,” Nature
`Biotechnology, 35(8):789-92 (2017)
`Stella et al., “Structure of the Cpf1 endonuclease R-loop complex
`after target DNA cleavage,” Nature, 546(7659):559-63 (2017)
`Hirano et al., “Structure and Engineering of Francisella novicida
`Cas9,” Cell, 164(5):950-61 (2016)
`Fieck et al., “Modifications of the E. coli Lac repressor for
`expression in eukaryotic cells: effects of nuclear signal
`sequences on protein activity and nuclear accumulation,” Nucleic
`Acids Research, 20(7):1785-91 (1992)
`United States Patent No. 8,697,359
`Chiu et al., “Engineered GFP as a vital reporter in plants,”
`Current Biology, 6(3):325-30 (1996)
`Mali et al., “RNA-Guided Human Genome Engineering via
`Cas9,” Science, 339(6121):823-26 (2013)
`Sandy et al., “Mammalian RNAi: a practical guide,”
`BioTechniques, 39:215-24 (2005)
`United States Patent Application Publication No. 2013/0302401
`International Publication No. WO 2014/118272
`Nair et al., “Multivalent N-Acetylgalactosamine-Conjugated
`siRNA Localizes in Hepatocytes and Elicits Robust RNAi-
`Mediated Gene Silencing,” JACS, 136:16958-63 (2014)
`Ludlum et al., “Alkylation of Synthetic Polynucleotides,”
`Science, 145(3630):397-99 (1964).
`Glen Research, The Glen Report, 19(1):1-16 (2007)
`
`vii
`
`
`
`

`

`EXHIBIT
`1031
`
`1032
`
`1033
`
`1034
`
`1035
`
`1036
`
`1037
`
`1038
`
`1039
`
`1040
`
`1041
`
`1042
`
`DESCRIPTION
`El-Andaloussi et al., “Exosome-mediated delivery of siRNA in
`vitro and in vivo,” Nat Protoc, 7(12):2112-26 (2012)
`Choulika et al., “Transfer of single gene-containing long terminal
`repeats into the genome of mammalian cells by a retroviral vector
`carrying the cre gene and the loxP site,” J Virol., 70(3):1792-98
`(1996)
`Bergemann et al., “Excision of specific DNA-sequences from
`integrated retroviral vectors via site-specific recombination,”
`Nucleic Acids Research, 23(21):4451-56 (1995)
`Dahlman et al., “In vivo endothelial siRNA delivery using
`polymeric nanoparticles with low molecular weight,” Nat
`Nanotechnol., 9(8):648-55 (2014)
`Senís et al., “CRISPR/Cas9-mediated genome engineering: an
`adeno-associated viral (AAV) vector toolbox,” Biotechnol J.,
`9(11):1402-12 (2014)
`Shukla et al., “Precise genome modification in the crop species
`Zea mays using zinc-finger nucleases,” Nature, 459(7245):437-
`41 (2009)
`Jinek et al., “A programmable dual-RNA-guided DNA
`endonuclease in adaptive bacterial immunity,” Science,
`337(6069):816-21 (2012).
`Mojica et al., “Biological significance of a family of regularly
`spaced repeats in the genomes of Archaea, Bacteria and
`mitochondria,” Mol Microbiol, 36(1):244-46 (2000)
`Ishino et al., “Nucleotide Sequence of the iap Gene, Responsible
`for Alkaline Phosphatase Isozyme Conversion in Escherichia
`coli, and Identification of the Gene Product,” Journal of
`Bacteriology, 169(12):5429-33 (1987)
`Jansen et al., “Identification of genes that are associated with
`DNA repeats in prokaryotes,” Molecular Microbiology,
`43(6):1565-75 (2002)
`Bolotin et al., “Clustered regularly interspaced short palindrome
`repeats (CRISPRs) have spacers of extrachromosomal origin,”
`Microbiology, 151(Pt 8):2551-61 (2005)
`Mojica et al., “Intervening sequences of regularly spaced
`prokaryotic repeats derive from foreign genetic elements,” J Mol
`Evol, 60(2):174-82 (2005)
`
`viii
`
`
`
`

`

`EXHIBIT
`1043
`
`1044
`
`1045
`
`1046
`
`1047
`
`1048
`
`1049
`
`1050
`
`1051
`
`1052
`
`1053
`
`1054
`
`1055
`
`DESCRIPTION
`Pourcel, “CRISPR elements in Yersinia pestis acquire new
`repeats by preferential uptake of bacteriophage DNA, and
`provide additional tools for evolutionary studies,” Microbiology,
`151(Pt 3):653-3 (2005)
`Barrangou et al., “CRISPR provides acquired resistance against
`viruses in prokaryotes,” Science, 315(5819):1709-12 (2007)
`Haft et al., “A Guild of 45 CRISPR-Associated (Cas) Protein
`Families and Multiple CRISPR/Cas Subtypes Exist in
`Prokaryotic Genomes,” PLOS Computational Biology, 1(6):474-
`83 (2005)
`Brouns et al., “Small CRISPR RNAs Guide Antiviral Defense in
`Prokaryotes,” Science, 321(5891):960-64 (2008)
`Garneau et al., “The CRISPR/Cas bacterial immune system
`cleaves bacteriophage and plasmid DNA,” Nature, 468(7320):67-
`71 (2010)
`Deveau et al., “Phage Response to CRISPR-Encoded Resistance
`in Streptococcus thermophilus,” Journal of Bacteriology,
`190(4):1390-1400 (2008)
`Mojica et al., “Short motif sequences determine the targets of the
`prokaryotic CRISPR defence system,” Microbiology, 155(Pt
`3):733-40 (2009)
`Anders et al., “Structural basis of PAM-dependent target DNA
`recognition by the Cas9 endonuclease,” Nature, 215(7219):569-
`73 (2014)
`Nishimasu et al., “Crystal Structure of Cas9 in Complex with
`Guide RNA and Target RNA,” Cell, 156(5):935-49 (2014)
`Deltcheva et al., “CRISPR RNA maturation by trans-encoded
`small RNA and host factor RNase III,” Nature, 471(7341):602-
`07 (2011)
`Makarova et al., “Unification of Cas protein families and a
`simple scenario for the origin and evolution of CRISPR-Cas
`systems,” Biology Direct, 6:38, pp. 1-27 (2011)
`Nam et al., “Cas5d protein process pre-crRNA and assembles
`into a Cascade-like interference complex in Subtype I-C/Dvulg
`CRISPR-Cas system,” Structure, 20(9):1574-84 (2012)
`Haurwitz et al., “Sequence- and structure-specific RNA
`processing by a CRISPR endonuclease,” Science,
`329(5997):1355-58 (2010)
`ix
`
`
`
`

`

`EXHIBIT
`1056
`
`1057
`
`1058
`
`1059
`
`1060
`
`1061
`
`1062
`
`1063
`
`1064
`
`1065
`
`1066
`
`1067
`
`1068
`
`DESCRIPTION
`Hatoum-Aslan et al., “Mature clustered, regularly interspaced,
`short palindromic repeats RNA (crRNA) length is measured by a
`ruler mechanism anchored at the precursor processing site,”
`PNAS, 108(52):21218-222 (2011)
`Rouillon et al., “Structure of the CRISPR Interference Complex
`CSM Reveals Key Similarities with Cascade,” Molecular Cell,
`52:124-34 (2013)
`Hale et al., “RNA-Guided RNA Cleavage by a CRISPR RNA-
`Cas Protein,” Cell, 139(5):945-56 (2009)
`Vestergaard et al., “CRISPR adaptive immune systems of
`Archaea,” RNA Biology, 11(2):156-67 (2014)
`Voskarides & Deltas, “Screening for Mutations in Kidney-
`Related Genes Using SURVEYOR Nuclease for Cleavage at
`Heteroduplex Mismatches,” Journal of Molecular Diagnostics,
`11(4):311-18 (2009)
`Findlay et al., “A Digital PCR-Based Method for Efficient and
`Highly Specific Screening of Genome Edited Cells,” PLoS One,
`11(4):e0153901 (2016)
`Kim et al., “Genotyping with CRISPR-Cas-derived RNA-guided
`endonucleases,” Nat Commun, 5:3157 (2014)
`Minton, “How can biochemical reactions within cells differ from
`those in test tubes?,” Journal of Cell Science, 119:2863-69
`(2006)
`Ellis, “Macromolecular crowding: obvious but
`underappreciated,” Trends Biochem Sci, 26(10):597-604 (2001)
`Nishimasu et al., “Structural Basis for the Altered PAM
`Recognition by Engineered CRISPR-Cpf1,” Mol Cell, 67(1):139-
`47 (2017)
`Shmakov et al., “Diversity and evolution of class 2 CRISPR-Cas
`systems,” Nat Rev Microbiol., 15(3):169-82 (2017)
`Aravind et al., “Holliday junction resolvases and related
`nucleases: identification of new families, phyletic distribution
`and evolutionary trajectories,” Nucleic Acids Research,
`28(18):3417-32 (2000)
`Chen et al., “Structural asymmetry in the Thermus thermophilus
`RuvC dimer suggests a basis for sequential strand cleavages
`during Holiday junction resolution,” Nucleic Acids Research,
`41(1):648-59 (2013)
`
`x
`
`
`
`

`

`EXHIBIT
`1069
`
`1070
`
`1071
`
`DESCRIPTION
`Leenay & Beisel, “Deciphering, communicating, and engineering
`the CRISPR PAM,” J Mol Biol., 429(2):177-91 (2017)
`Pul et al., “Identification and characterization of E. coli CRISPR-
`cas promoters and their silencing by H-NS,” Mol Microbiol,
`75(6):1495-512 (2010)
`Kim et al., “Highly efficient RNA-guided genome editing in
`human cells via delivery of purified Cas9 ribonucleoproteins,”
`Genome Res., 24(6):1012-9 (2014)
`
`xi
`
`
`
`

`

`I.
`
`INTRODUCTION
`Benson Hill Biosystems, Inc. (“Petitioner”) requests post grant review of U.S.
`
`Patent No. 9,790,490 (“the ’490 patent”), which is assigned to The Broad Institute
`
`Inc., Presidents and Fellows of Harvard College, and Massachusetts Institute of
`
`Technology (“Patent Owners”). The ’490 patent broadly claims systems for genetic
`
`engineering of eukaryotic cells using a Cpf1 CRISPR effector protein and at least
`
`one targeting nucleic acid component (i.e., guide RNA).
`
`As shown in this Petition and supported by the declaration of Dr. Chase
`
`Beisel, the claims of the ’490 patent cover an incredibly broad and vast genus1 of
`
`Cpf1 effector proteins that are required to be functional in eukaryotic cells, in that
`
`they cleave DNA. This genus of proteins encompasses a virtually unknowable
`
`number of molecules. Yet, out of the several different Cpf1 proteins disclosed in the
`
`specification only a few actually functioned in eukaryotic cells, and the specification
`
`fails to explain how or why these particular proteins were effective while others were
`
`not. Similarly, the specification fails to provide any correlation between the
`
`structure of the Cpf1 proteins and their claimed function of successfully cleaving
`
`DNA in eukaryotic cells. As such, the well-established precedent of the Federal
`
`
`1 The accompanying declaration of Dr. Chase Beisel refers to a “family” of
`
`Cpf1 proteins encompassed by the claims, instead of the more legal term “genus.”
`
`1
`
`

`

`Circuit dictates that the challenged claims fail to satisfy the written description
`
`requirement of 35 U.S.C. § 112, particularly given the manifest unpredictability in
`
`the field. And for essentially the same reasons, the full scope of the claims is not
`
`enabled by the limited teachings in the specification. It would take complex iterative
`
`testing, of precisely the sort found by the Federal Circuit to constitute undue
`
`experimentation, to identify the genus of Cpf1 proteins that are functional within the
`
`meaning of the claims. Accordingly, because the scope of claims 1-60 of the ’490
`
`patent vastly exceeds what is described and enabled in the specification, those claims
`
`are not patentable. Each of claims 1-60 is also unpatentable for indefiniteness, as
`
`the specification provides ambiguous and often contradictory descriptions of what
`
`constitutes a “Cpf1 effector protein.” Additionally, if the Board determines that the
`
`claims require no functional activity and/or that the art was sufficiently predictable
`
`to enable and describe the full scope of the claimed genus, then claims 1-60 are
`
`unpatentable for lack of practical utility and/or obviousness. Petitioner, therefore,
`
`requests cancellation of the challenged claims.
`
`II. BACKGROUND AND STATE OF THE ART
`CRISPR (clustered regularly interspaced short palindromic repeats) systems
`
`were first discovered in bacteria and archaea, where they play a role in adaptive
`
`immune responses by specifically cleaving DNA or RNA of invading foreign
`
`nucleic acids (e.g., phages). Ex. 1003, ¶¶ 17-18, 22; Ex. 1007, 8-12. A key
`
`2
`
`

`

`component of CRISPR systems is the “effector protein” (also called a CRISPR-
`
`associated, or Cas protein), which cleaves target nucleic acids in a sequence-specific
`
`manner. Ex. 1003, ¶ 19; Ex. 1008, 6-7, 13-15. In most CRISPR systems, sequence
`
`specificity is provided by a “guide RNA” (gRNA; also called a CRISPR RNA or
`
`crRNA), which forms a complex with the effector protein and base-pairs with the
`
`target nucleic acid. Ex. 1003, ¶¶ 19, 21; Ex. 1009, 4, 7-9. To effect cleavage,
`
`effector proteins discovered to date require the presence of a “protospacer adjacent
`
`motif” or “PAM” sequence in the target DNA, which enables the effector
`
`protein/gRNA complex to pin-point the specific cleavage site in the target genome.
`
`Ex. 1003, ¶ 20; Ex. 1010, 1-2, 8-9.
`
`Once the cleavage site is identified, the target DNA unwinds and base pairs
`
`with the guide RNA, and the effector protein cleaves the target DNA within the base-
`
`paired region. Ex. 1003, ¶¶ 25-26. The cleaved genomic DNA then undergoes one
`
`of two fates. The vast majority of CRISPR-induced cleavages are repaired by non-
`
`homologous end joining, which introduces small insertions, deletions, or
`
`substitution mutations at the cleavage site. Ex. 1001, 107:29-63; Ex. 1003, ¶ 27.
`
`But if a source of homologous DNA is available, the genomic DNA can undergo
`
`homology-directed repair to include the homologous DNA. Ex. 1003, ¶ 27; Ex.
`
`1011, 1-2.
`
`3
`
`

`

`CRISPR systems are remarkably diverse, despite their common role in
`
`adaptive immunity, and show extreme variability in their effector protein
`
`compositions, as well as their genomic loci architecture. Ex. 1003, ¶ 24; Ex. 1008,
`
`6-7, 9, 13-15; Ex. 1012, 7. Current CRISPR classification systems define two
`
`classes, six main types, and nineteen subtypes. Ex. 1003, ¶¶ 23, 28; Ex. 1013, 8-11,
`
`15; Ex. 1008, 6-7, 13-15; Ex. 1069, 9. Each grouping is distinguished by its effector
`
`proteins and by the mechanisms of RNA processing, target recognition, and target
`
`destruction. Class 2/type II systems have received the most attention because their
`
`machinery can be packaged
`
`into a portable
`
`two-component system for
`
`biotechnological applications involving genetic manipulations. Ex. 1003, ¶ 24; Ex.
`
`1007, 9-12; Ex. 1013, 14-19. The hallmark effector protein of class 2/type II systems
`
`is Cas9 (particularly, SpCas9 derived from Streptococcus pyogenes), which has
`
`become the most commonly utilized effector protein for genome editing
`
`applications. Nevertheless, despite intense efforts to characterize different CRISPR
`
`systems, by the end of 2015, major aspects of their basic biology, diversity, and
`
`evolution remained unknown. Ex. 1003, ¶ 23; Ex. 1008, 13.
`
`The ’490 patent relates to a class 2 CRISPR system containing an effector
`
`protein called “Cpf1,” and its use in genome editing applications. The Cpf1 system
`
`was identified informatically in several bacterial genomes in 2012. Ex. 1014; see
`
`also Ex. 1004, 6-7, 14; Ex. 1003, ¶ 28. By the end of 2015, however, no functional
`
`4
`
`

`

`activity had yet been demonstrated for Cpf1, and it was unknown whether the
`
`genomic regions encoding Cpf1 proteins represented functional CRISPR systems.
`
`Ex. 1003, ¶ 28; Ex. 1013, 23; Ex. 1005, 7-8. Thus, the technology involved in
`
`harvesting Cpf1 proteins for genetic manipulation of eukaryotic cells was still
`
`nascent when the ’490 patent was filed in 2015.
`
`III. SUMMARY OF THE ’490 PATENT
`A. The Challenged Claims
`The ’490 patent contains four independent claims, each drawn to an
`
`engineered, non-naturally occurring system comprising: (a) a Cpf1 effector protein
`
`(claims 1 and 42) or a nucleotide sequence encoding a Cpf1 effector protein (claims
`
`2-4); and (b) an engineered guide polynucleotide designed to form a complex with
`
`the Cpf1 effector protein and hybridize with a target sequence in a eukaryotic cell
`
`(claims 1 and 4) or a nucleotide sequence encoding such a guide polynucleotide
`
`(claims 2-4). Ex. 1001, 547:49-549:26.
`
`
`2 Claim 4 is an improper duplicate of claims 1 and 2, since claim 4 merely
`
`combines the elements of claims 1 and 2 in the alternative. For similar reasons,
`
`claims 5 and 7 (which depend from claim 4 and specify elements from claim 1) are
`
`improper duplicates of claim 1, while claims 6 and 8 (which depend from claim 4
`
`and specify elements from claim 2) are improper duplicates of claim 2.
`
`5
`
`

`

`Each of claims 1-4 recites that the system lacks a tracr sequence. Claim 1 is
`
`representative of the challenged claims, and recites:
`
`An engineered, non-naturally occurring system
`comprising
`a) a Cpf1 effector protein, and
`b) at least one engineered guide polynucleotide designed
`to form a complex with the Cpf1 effector protein and
`comprising a guide sequence, wherein the guide
`sequence is designed to hybridize with a target sequence
`in a eukaryotic cell; and
`wherein the system lacks a tracr sequence, the engineered
`guide polynucleotide and Cpf1 effector protein do not
`naturally occur together, and a complex of the engineered
`guide polynucleotide and Cpf1 effector protein does not
`naturally occur.
`Ex. 1001, 547:49-61. All of the dependent claims fall within the scope of claims 1-
`
`4 and either recite additional aspects of the system (claims 5-24), delivery particles
`
`comprising the system (claims 25-28), methods of genetic modification using the
`
`system (claims 29-55), or eukaryotic cells comprising the system (claims 56-60).
`
`Ex. 1001, 549:27-552:26.
`
`The Specification
`B.
`The ’490 patent investigates the diversity of Cpf1-family proteins that had
`
`been deposited in public sequence databases by performing a BLAST search of the
`
`WGS database at the NCBI (presumably using one or more previously-identified
`
`6
`
`

`

`Cpf1 sequences as a starting point), which “revealed 46 non-redundant Cpf1 family
`
`proteins (FIG. 64).”3 Ex. 1001, 444:1-3; Ex. 1003, ¶¶ 29, 33. The patent provides
`
`a sequence alignment of putative Cas-Cpf1 proteins in Fig. 38, along with a
`
`“consensus sequence” (SEQ ID NO:1033) based on that alignment. Ex. 1001, 14:1-
`
`3, 388:62-64, Fig. 38, Sequence Listing at 1408-17. An overview of Cpf1 loci
`
`alignment with the consensus sequence is shown in Fig. 39. Ex. 1001, 388:64-65.
`
`The sequence alignment reveals very little sequence conservation among the
`
`putative Cpf1 proteins. Ex. 1003, ¶ 34. While the specification explains that a
`
`protein may be considered a Cpf1 effector protein if it has “sequence homology or
`
`identity of at least 80%” (presumably to SEQ ID NO:1033; Ex. 1001, 35:37-39; Ex.
`
`1003, ¶ 35), BLASTP alignments of SEQ ID NO:1033 with the 17 putative Cpf1
`
`proteins that were tested in the examples show sequence identity as low as 25%. Ex.
`
`1003, ¶¶ 34-35.
`
`The ’490 patent explains that 16 of the identified Cpf1 proteins were chosen
`
`for testing. Ex. 1001, 444:3-5.4 At least six of the enzymes failed to show any
`
`
`3 Fig. 64 actually identifies 51 non-redundant putative Cpf1 proteins. Ex.
`
`1003, ¶ 33.
`
`4 A careful review of the Examples and Figures indicates that 17 enzymes
`
`were actually tested. Ex. 1003, ¶¶ 42-46.
`
`7
`
`

`

`activity in vitro or in vivo. Ex. 1003, ¶¶ 47-54. In vitro activity (in lysate or purified
`
`protein assays) was demonstrated for only eleven of the enzymes. Ex. 1001,
`
`Examples 6, 13, 14, Figs. 89, 90, 100A-B, 100F, 101C, 106; Ex. 1003, ¶ 51. In vivo
`
`activity in eukaryotic cells was demonstrated for merely three of the enzymes. Ex.
`
`1001, Examples 4, 6, 14, Figs. 88, 93, 101C, 108A-C; Ex. 1003, ¶ 54. One of those
`
`enzymes (FnCpf1), along with another enzyme that did not exhibit in vivo activity
`
`in eukaryotic cells (PaCpf1), presumably did exhibit in vivo activity in prokaryotes
`
`(E. coli) based on reported PAM sequences for those species. Ex. 1001, Examples
`
`3, 4, 5, 8, Figs. 45A-E, 62A-E, 95C-E, 102D; Ex. 1003, ¶ 47. PAM sequences were
`
`determined for a total of 9 of the enzymes. Ex. 1003, ¶ 49.
`
`C. The Prosecution History
`The ’490 patent was filed on December 18, 2015, claiming priority to five
`
`U.S. provisional applications. A non-final Office Action was issued rejecting all of
`
`the elected claims for indefiniteness, lack of subject matter eligibility, and
`
`anticipation in view of the Schunder et al. paper (Ex. 1004 (“Schunder”)) that
`
`originally identified Cpf1 systems in several bacterial genomes. Ex. 1002, 6148-55.
`
`In response, Patent Owners amended the claims to overcome the
`
`indefiniteness and subject-matter eligibility rejections. Ex. 1002, 6173-83.
`
`Regarding the anticipation rejection, Patent Owners argued that Schunder “fails to
`
`demonstrate that any of the putative [CRISPR-Cpf] components were functional,”
`
`8
`
`

`

`and “fails to teach or suggest elements needed to engineer an operable F. tulerenis
`
`[sic] CRISPR-Cas system,” such as the “Protospacer Adjacent Motif (PAM), which
`
`would be required to design a functional guide.” Ex. 1002, 6184 (emphasis added).
`
`Patent Owners concluded that “Schunder does not teach or suggest all of the
`
`limitations of the instant claims” or “teach one of ordinary skill in the art how to
`
`make and use the instantly claimed invention.” Id.
`
`An Examiner-Initiated Interview was conducted, during which the Examiner
`
`and Patent Owners discussed proposed new claims to overcome the rejections of the
`
`previous Office Action. Ex. 1002, 7664. The Examiner noted that the lack of tracr
`
`sequence in the system was a substantive and non-obvious functional and structural
`
`difference from prior art systems that required a tracr sequence, and required Patent
`
`Owners to include such language in the claims. Id. The agreed-upon claims were
`
`set forth in the Examiner’s Amendment that was appended to the Notice of