`
`
`
`APPENDIX B
`
`
`Precision BioSciences, Inc. v. Institut Pasteur &
`Universite Pierre et Marie Curie,
` Appeal 2011-012285, Control 95/000,490, 2012 WL
`1050572 (B.P.A.I. March 14, 2012) 
`
`IPR 2013-00154
`Patent No. 7,335,996
`
`TSMC Request for Reconsideration
`Under 37 C.F.R. 42.71(c) - Appendix B
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`Page 1
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`2012 WL 1050572 (Bd.Pat.App. & Interf.)
`
`
`Board of Patent Appeals and Interferences
`Patent and Trademark Office (P.T.O.)
`
`
`
`
`
`
`
`*1 Precision BioSciences, Inc. Requester & Respondent
`v.
`Institut Pasteur & Universite Pierre et Marie Curie Patent Owner & Appellant
`
`Appeal 2011-012285
` Reexamination
` 95/000,490
`Patent 7,309,605 B2 Technology Center 3900
`
`March 14, 2012
`
`
`For Patent Owner:
`Kenneth J. Meyers, Esq.
`Finnegan, Henderson, Farabow, Garrett & Dunner LLP
`901 New York Avenue, NW
`Washington, DC 20001-4413
`For Third Party Requester
`
`Michael J. Twomey, Esq.
`Wilmer Cutler Pickering Hale and Dorr LLP
`60 State Street
`Boston, MA 02109
`
`Before SALLY G. LANE, RICHARD M. LEBOVITZ, and JEFFREY B. ROBERTSON
`Administrative Patent Judges
`LEBOVITZ
`Administrative Patent Judge
`
`
`
`This is a decision on appeal by the Patent Owner from the Patent Examiner's rejections of claims in an inter partes
`
`DECISION ON APPEAL
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
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`IPR 2013-00154
`Patent No. 7,335,996
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`reexamination of U.S. Patent No. 7,309,605 B1. The Board's jurisdiction for this appeal is under 35 U.S.C. §§ 6(b),
`134, and 315. We affirm all rejections.
`
`
`STATEMENT OF THE CASE
`
`
`The patent in dispute in this appeal is U.S. Patent No. 7,309,605 B1 (hereinafter, “the '605 patent”), which issued
`December 18, 2007. The named inventors are Bernard Dujon, Andre Choulika, Arnaud Perrin, and Jean-Francois
`Nicolas.
`
`The claims in the '605 patent are directed to a method for introducing a double-stranded break into chromosomal DNA
`of a viable cell of an organism. The method is accomplished using a Group I intron encoded endonuclease (“GIIEE” or
`“GIIE endonuclease”). GIIE endonucleases are endonucleases which are encoded in the intron of certain genes and are
`responsible for intron mobility ('605 patent, col. 2, ll. 6-60). More background on this process is described in the
`Decision on the reexamination of the related U.S. Patent No. 7,214,536 B2 ( Reexamination 95/000,427, Appeal
`2011-010572).
`
` A
`
` request for inter partes reexamination under 35 U.S.C. §§ 311-318 and 37 C.F.R. §§ 1.902-1.997 for the '605
`patent was filed on July 31, 2009 by a Third-Party Requester (Request for Inter Partes Reexamination Transmittal
`Form). The Third-Party Requester is Precision BioSciences, Inc., who is the Respondent in this appeal (Respondent
`Br. iii, dated February 22, 2011). The Patent Owners and Appellants in this appeal are the Institut Pasteur and Uni-
`versité Pierre et Marie Curie (Appellant App. Br. 1, dated January 19, 2011). The patent has been licensed to Cellectis
`SA, of Paris, France (id.).
`
`*2 There are three additional pending reexamination proceedings involving the same parties and related patents:
`
`1. Reexamination Control No. 95/000,443 for U.S. Patent No. 6,833,252 B1;
`
`2. Reexamination Control No. 95/000,427 for U.S. Patent No. 7,214,536 B2; and
`
`3. Reexamination Control No. 95/000,491 for U.S. Patent No. 6,610,545 B2.
`
`All three reexaminations are on appeal before the Board.
`
`In addition, there is a pending litigation in a district court asserting U.S. Pat. Nos. 7,309,605 B1 and 6,610,545
`B2(Cellectis SA v. Precision Biosciences, Inc., No. 5:08-cv-119 (E.D.N.C.)) (Respondent Br. R-1; Appellant App. Br.,
`Appendix D.)
`
`Claims 1-18 are pending and stand finally rejected by the Examiner. There are 32 rejections, each of which is appealed
`by the Patent Owner (Appellant App. Br., Appendix E).
`
`Grounds 1 and 2 are anticipation rejections under 35 U.S.C. § 102(b) over Bell-Pedersen[FN1] and Quirk,[FN2] respec-
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
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`IPR 2013-00154
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`tively.
`
`Grounds 5 and 6 are obviousness rejections 35 U.S.C. § 103(a) over Schiestl[FN3] in combination with “admissions” or
`Frey.[FN4]
`
`The remaining rejections are for obviousness involving either Bell-Pedersen or Quirk, and additionally cited sec-
`ondary publications. In these rejections, the Examiner made a rejection over Bell-Pedersen and a secondary publica-
`tion, and then the exact same rejection using Quirk instead of Bell-Pedersen. For example Ground 7 rejects claim 2
`over Bell-Pedersen and Seraphin,[FN5] and Ground 8 rejects claim 2 over Quirk and Seraphin. Bell-Pedersen and Quirk
`were relied upon by the Examiner for same teachings. Consequently, we limit our discussion largely to Bell-Pederson,
`as the rejections based on Quirk are cumulative.
`
` A
`
` number of different declarations by experts were cited as evidence by both parties in this proceeding and in the
`related three reexamination proceedings. For consistency and ease of reference, we have renumbered the declarations
`as Exhibits 1001 to 1015, and attached them to Reexamination 95/000,427 of U.S. Patent No. 7,214,536 B2, which is
`Appeal 2011-010572.
`
`Claims 1 and 18 are representative and read as follows (underlining and brackets indicate amendments relative to the
`issued patent claim):
`1. A method for inducing at least one site directed double-stranded break in the chromosomal DNA of an or-
`ganism comprising: (a) providing an isolated, viable cell of said organism containing at least one Group I intron
`encoded endonuclease recognition site at a location in the chromosomal DNA of the cell, (b) providing said
`Group I intron encoded endonuclease to said cell by genetically modifying the cell with a nucleic acid comprising
`said Group I intron encoded endonuclease or by introducing said Group I intron encoded endonuclease protein
`into the cell such that the Group I intron encoded endonuclease cleaves said Group I intron encoded endonuclease
`site at the location in the chromosomal DNA of the cell.
`*3 18. The method of any one of claims 1 to 17, wherein the isolated, viable cell of the organism is a eukaryotic
`cell.
`
`
`Claim 1
`Claim 1 is directed to a method of inducing a double-stranded break in the chromosome of an organism. The method
`comprises two recited steps:
`
`a) providing a viable cell with a chromosome containing a GIIE endonuclease recognition site; and
`
`b) providing a GIIE endonuclease to the cell “such that the Group I intron encoded endonuclease cleaves said Group I
`intron encoded endonuclease site at the location in the chromosomal DNA of the cell.”
`
`The claims in this appeal are similar to those in the related reexamination of U.S. Patent No. 7,214,536 B2 (
`Reexamination Control No. 95/000,427; Appeal 2011-010572). However, the latter claims were limited to plant and
`animal cells, where the claims in this appeal are broader and are drawn to the cells of an organism, with dependent
`claims drawn to eukaryotic cells.
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
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`IPR 2013-00154
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`
`Claim interpretation
`Claim 1 was amended during the reexamination proceeding by adding the term “viable” to the step of providing a
`viable cell of an organism with a GIIE endonuclease recognition site to the chromosomal DNA of the cell. The term
`“chromosomal” was also added to the claim at the same time. (Patent Owner Response 5, dated Nov. 17, 2009.) The
`term “viable” means that the cell is a living cell (id.).
`
`The claim requires that endonuclease is provided to the viable cell “such that the endonuclease cleaves the endonu-
`clease site in the target nucleic acid sequence” which resides in the chromosome of the viable cell. We interpret the
`“viable” requirement to mean that the cell is alive, and not dying, upon introduction of the endonuclease and after
`cleavage of the chromosomal DNA by the endonuclease.
`
`
`ANTICIPATION REJECTIONS
`
`
`
`
`The Examiner rejected claim 1, and dependent claim 15, as anticipated by Quirk, and claims 1, 10, 11, 14, and 15 as
`anticipated by Bell-Pedersen (Grounds 1 & 2). The issue in each rejection is the same: whether a GIIEE recognition
`site was necessarily cleaved in the chromosome of a viable cell of a bacterial cell in the experiments described in Quirk
`and Bell-Pedersen.
`
`
`Issue
`
`Legal Principles
`
` A
`
` “prior art reference may anticipate without disclosing a feature of the claimed invention if that missing characteristic
`is necessarily present, or inherent, in the single anticipating reference.”SmithKline Beecham Corp. v. Apotex Corp.,
`403 F.3d 1331, 1343 (Fed. Cir. 2005). Inherency asks whether a subject matter is “necessarily” present in the prior art
`reference, “not merely probably or possibly present, in the prior art.”Trintec Indus., Inc. v. Top-U.S.A., Corp., 295
`F.3d 1292, 1295 (Fed. Cir. 2002). It is the Examiner's burden to provide “reason to believe that … the claimed subject
`matter may, in fact, be an inherent characteristic of the prior art.”In re Schreiber, 128 F. 3d 1473, 1478 (Fed. Cir.
`1997). Once the Examiner has satisfied this duty, the burden shifts to Appellant to provide evidence to the contrary. In
`re Spada, 911 F.2d 705, 708 (Fed. Cir. 1990) (once “the PTO shows sound basis for believing that the products of the
`applicant and the prior art are the same, the applicant has the burden of showing that they are not.”).
`
`
`Quirk publication
`
`
`*4 Quirk described experiments in E. coli designed to study intron mobility of the td and sunY introns, introns con-
`tained in the td and sunY genes which are present in a class of phage know as T-even bacteriophages (Quirk 455)
`[FF1].[FN6] The “td” refers to the thymidylate synthase gene and “sunY” refers to a gene having an unknown function at
`the time the publication was published (Quirk 455) [FF2]. Both the td and sunY genes include introns containing open
`reading frames (ORFs), which is a sequence of nucleotides encoding a protein (Quirk 455) [FF3]. The ORF of the td
`intron encodes I-TevI, and the ORF of the sunY intron encodes I-TevII (Bell-Pedersen Decl. of May 19, 2010, ¶ 17,
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
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`IPR 2013-00154
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`Exhibit 1001) [FF4], both which are Group I intron encoded endonucleases.
`
`Quirk demonstrated that the td and sunY introns could be transferred to the corresponding intronless gene, and that
`such transfer (“mobility”) required the intact ORF encoding the GIIE endonuclease (Quirk 461) [FF5]. The intronless
`gene contains a site-specific recognition site for the GIIE endonuclease (Quirk 458-459, 463, col. 2 (section titled
`“Phages,” T2L and T2H); Bell-Pedersen Decl. of May 19, 2010, ¶ 27, Exhibit 1001) [FF6]. The GIIE endonuclease
`recognition site is a sequence of DNA nucleotides that must be present in the DNA (i.e., gene) for it to be cleaved by
`the endonuclease (Quirk 458-459, 463, col. 2 (section titled “Phages,” T2L and T2H); Bell-Pedersen Decl. of May 19,
`2010, ¶ 27, Exhibit 1001) [FF7].
`
`During the course of the experiments, Quirk observed that E. coli containing the td and sunY genes with an intact ORF
`(i.e., the intact and functional endonuclease) grew poorly because the ORF product was apparently toxic to the cells
`(Quirk 456, col. 2) [FF8].
`
`To address the toxicity issue, td fragments were cloned into a plasmid and placed under control of the “more tightly
`regulated phage <<lambda>> pL promoter.”(Quirk 457, col. 1) [FF9]. The pL promoter (also referred to as a “tem-
`perature inducible” or “temperature sensitive” promoter) is controlled by the temperature repressor cI857 “which
`allows low level expression at permissive temperatures (30°-32°C) and high level expression at elevated temperature
`(37°-42°C).” (Quirk 457, col. 1) [FF10] The expression of the GIIE endonuclease from this plasmid “did not result in
`significantly poor growth” of the E. coli cells, suggesting that lower expression levels of the endonuclease were less or
`not toxic to the cells (Bell-Pedersen Decl. of May 19, 2010, ¶ 23, Exhibit 1001; Quirk 457, col. 2) [FF11].
`
`To determine whether the intron had inserted into the site-specific recognition site, Quirk harvested phage from the E.
`coli after temperature induction (Quirk 458-59) [FF12]. The harvested phage were examined to determine whether the
`intron had inserted into the phage in the vicinity of the site-specific GIIEE recognition site (Quirk 458-59); at the
`“cognate site[]”). Quirk found that the intron had inserted into the cognate site (Quirk 458-59) [FF13].
`
`
`Bell-Pedersen publication
`
`
`*5 The experiments described in the Bell-Pedersen publication were performed in the same laboratory as those in the
`Quirk publication, the laboratory directed by Dr. Marlene Belfort, who is one of the experts for the Patent Owner. Drs.
`Deborah Bell-Pedersen, Susan Quirk, and Marlene Belfort were listed as coauthors of both Quirk and Bell-Pedersen.
`Quirk was published in 1989. Bell-Pedersen was published in 1990. Dr. Bell-Pedersen is also an expert for the Re-
`quester.
`
`Bell-Pedersen performed experiments in E. coli using similar systems to those described in the Quirk publication. The
`experiments described in Bell-Pedersen showed that an intron comprising a marker gene was mobilized from a
`plasmid and inserted into a recipient phage containing a recognition site for a GIIE endonuclease (Bell-Pedersen 3763)
`[FF14], the site in the DNA where the endonuclease cleaves (FF7, Quirk 458-459, 463, col. 2 (section titled “Phages,”
`T2L and T2H); Bell-Pedersen Decl. of May 19, 2010, ¶ 27, Exhibit 1001). As explained below, the recognition site is
`provided by a phage; the endonuclease is provided by a plasmid. Once the site is recognized by the endonuclease, the
`endonuclease cleaves the DNA into two pieces, creating a site where the intron can be inserted into it [FF15]. As stated
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
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`above, the issue is whether the cleavage occurred when the recognition site was present in the bacterial chromosome.
`
`In one set of experiments performed by Bell-Pedersen, the following DNA constructs were made (Bell-Pedersen
`3764-3765; Bell-Pedersen Decl. of May 19, 2010, ¶¶ 32-44, Exhibit 1001).
`
` •
`
` a plasmid containing a GIIEE intron into which a gene conferring antibiotic resistance (a marker gene) had been
`inserted. The antibiotic-resistance gene was inserted into the intron as a marker to determine when the intron had been
`inserted into the phage (Bell-Pedersen 3764-3765; Bell-Pedersen Decl. of May 19, 2010, ¶¶ 32-44, Exhibit 1001)
`[FF16];
`
` •
`
` a plasmid containing a GIIE endonuclease under control of a temperature inducible promoter (pL) (Bell-Pedersen
`3764-3765; Bell-Pedersen Decl. of May 19, 2010, ¶¶ 32-44, Exhibit 1001) [FF17]; and
`
` •
`
` a phage containing the recognition site for the GIIE endonuclease. The phage genes are under control of the same
`temperature inducible promoter present in the plasmid containing the GIIE endonuclease (Bell-Pedersen 3764-3765;
`Bell-Pedersen Decl. of May 19, 2010, ¶¶ 32-44, Exhibit 1001) [FF18].
`
`The plasmids and phage were introduced into E. coli hosts. When the GIIE endonuclease was expressed by the
`plasmid and manufactured in the host E. coli cell, the endonuclease would cleave the recognition site in the phage and
`then the antibiotic resistance gene would integrate into the phage Bell-Pedersen 3764-3765; Bell-Pedersen Decl. of
`May 19, 2010, ¶¶ 32-44, Exhibit 1001) [FF19]. As one of the steps in the experiment, the phage first integrates into the
`E. coli chromosome Bell-Pedersen 3764-3765; Bell-Pedersen Decl. of May 19, 2010, ¶ ¶ 32-44, Exhibit 1001) [FF20].
`
`*6 After integration into the bacterial chromosomal DNA, the temperature of the cells is raised - turning on the
`temperature inducible promoter. As a result, the endonuclease is manufactured from the plasmid and the phage is
`excised from the bacterial chromosome, beginning the cycle of phage reproduction. (Bell-Pedersen 3765 [FF21].)
`
`As with Quirk, to determine whether the intron had inserted into the site-specific recognition site, phage are harvested
`from the E. coli after temperature induction and the harvested phage were examined to determine the presence of the
`inserted intron comprising the marker gene (Bell-Pedersen 3765, col. 1; Bell-Pedersen Decl. of May 19, 2010, ¶ 54,
`Exhibit 1001) [FF22].
`
`
`Expert testimony
`
`
`Dr. Bell-Pedersen
`The Requester filed three written declarations by Deborah Bell-Pedersen, Ph.D. Dr. Bell-Pedersen performed her
`doctoral research in the laboratory of Dr. Marlene Belfort and is a co-author of the Quirk and Bell-Pedersen publica-
`tions. In her declarations, Dr. Pedersen testified that cleavage of the DNA and insertion of the marker gene into the
`phage took place when the phage was resident in the E. coli bacterial chromosome. According to Dr. Bell-Pedersen:
`
` •
`
` Although the temperature inducible pL promoter is induced as 42°C, the GIIE endonuclease would be expressed at a
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
`
`IPR 2013-00154
`Patent No. 7,335,996
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`Under 37 C.F.R. 42.71(c) - Appendix B
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`low level from the pL promoter when the E. coli cells were grown at 30°C (the “leaky” promoter; Bell-Pedersen Decl.
`of Dec. 16, 2009, ¶ 38, Exhibit 1002 [FF23]).
`
` •
`
` During this growth period at 30°C, Dr. Bell-Pedersen stated that the endonuclease would be manufactured, and
`would cleave the endonuclease recognition site carried by the E. coli chromosome (Bell-Pedersen Decl. of Dec. 16,
`2009, ¶¶ 39 & 40, Exhibit 1002) [FF24].
`
`Dr. Bell-Pedersen supported her conclusion with evidence from her own publications and research, as well as from the
`scientific literature. We summarize some of the additional points discussed in the Bell-Pedersen declarations:
`
` •
`
` Quirk taught that the pL promoter is controlled by the temperature repressor cI857 “which allows low level ex-
`pression at permissive temperatures (30°-32°C) and high level expression at elevated temperatures (37°-43°C)”
`(Quirk 457; Bell-Pedersen Decl. of Dec. 16, 2009, ¶ 14. Exhibit 1002) [FF25]. Thus, Dr. Bell-Pedersen concluded,
`some GIIE endonuclease would be produced at all times during the experiment (Bell-Pedersen Decl. of May 19, 2010,
`¶¶ 29, 42, & 47, Exhibit 1001) [FF26].
`
` •
`
` Her own experiments demonstrating that cleavage of double-stranded DNA required only a GIIE endonuclease,
`making cleavage of the chromosome “inevitable at some level” when the endonuclease is expressed in the cell
`(Bell-Pedersen Decl. of Aug. 4, 2010, ¶ 13, Exhibit 1003) [FF27].
`
` •
`
` Her thesis in which she “suggested that the toxicity associated with expression of I-TevI could be due to endonu-
`clease cleavage sites on the E. coli chromosome.”(Bell-Pedersen Decl. of Aug. 4, 2010, ¶ 23, Exhibit 1003) [FF28].
`This suggestion was based on evidence from the Quirk publication, as well as additional experiments involving the
`SOS response (Bell-Pedersen Decl. of May 19, 2010, ¶¶ 73-78, Exhibit 1001) [FF29].
`
`*7 • Scientific literature showing that E. coli “possesses a set of recombination and repair proteins that repair DSBs
`that are known to substitute for <<lambda>>'s proteins.” (Bell-Pedersen Decl. of Aug. 4, 2010, ¶ 20, Exhibit 1003)
`[FF30]. Based on this evidence, Dr. Bell Pedersen concluded that the E. coli would have been able to repair DSBs
`made by the GIIE endonuclease (Bell-Pedersen Decl. of Aug. 4, 2010, ¶ 20, Exhibit 1003) [FF31].
`
` •
`
` Testimony that she believed at the time of the publication that insertion of the intron (with the antibiotic resistance
`gene) into the phage occurred while the phage was integrated into the E. coli chromosome (Bell-Pedersen Decl. of
`Dec. 16, 2009, ¶¶ 44-46), Exhibit 1002 [FF32].)
`
` •
`
` Testimony that the intent of the Bell-Pedersen experiments was “to determine whether 1-TevI could function in trans
`to promote insertion of a gene of interest (foreign DNA sequences) into an I-TevI recognition site in a << lambda>>
`prophage integrated into the E. coli chromosome, independent of the DNA sequences that encode the in-
`tron.”(Bell-Pedersen Decl. of May 19, 2010, ¶ 45. Exhibit 1001) [FF33].)
`
` •
`
` Testimony that:
`The expression of I-TevI from the low copy number pKC30 plasmid in the RRI (<<lambda>>c+) lysogen or the
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
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`IPR 2013-00154
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`N99(<<lambda>>cI857) lysogen at 30°C did not result in significantly poor growth of the E. coli lysogens. This
`suggested that the lower levels of 1-TevI were not toxic (or less toxic) because they resulted in cleavage of the
`naturally-occurring I-TevI recognition sites at rates sufficiently low to allow for successful repair by the natural E.
`coli repair mechanisms.
`(Bell-Pedersen Decl. of May 19, 2010, ¶ 23, Exhibit 1001 [FF34].)
`
`Dr. Victoria Derbyshire
`Victoria Derbyshire, Ph.D., provided expert testimony on behalf on the Requester. Dr. Derbyshire was a post-doctoral
`research affiliate in the laboratory directed by Dr. Marlene Belfort from 1992 to 1998. Dr. Derbyshire testified that
`“one of ordinary skill in the art at the relevant time would have understood the Bell-Pedersen et al. (1990) reference to
`show cleavage of the I-TevI recognition site of the E. coli lysogen occurring primarily, if not exclusively, before
`excision of the prophage DNA from the E. coli chromosome.”(Derbyshire Decl. of Dec. 17, 2009, ¶ 27, Exhibit 1004
`[FF35].) Dr. Derbyshire also testified that the majority of cleavage and integration of the antibiotic resistance gene
`occurred before excision of the phage from the bacterial chromosome (Derbyshire Decl. of Dec. 17, 2009, ¶ 28, Ex-
`hibit 1004) [FF36]. Derbyshire based her opinion primarily on the knowledge that the pL promoter used to control the
`endonuclease expression was “leaky” and would have been expressed at 30°C, during the growth phase, prior to
`intentional induction of the promoter (Derbyshire Decl. of Dec. 17, 2009, ¶ 31, Exhibit 1004 [FF37]).
`
`*8 Additional points include:
`
` •
`
` “even if repression of pL at 30°C were ‘leaky,’ it does not follow that induction of the <<lambda>> prophage will
`result.”(Derbyshire Decl. of May 19, 2010, ¶ 14. Exhibit 1005 [FF38].)
`
` •
`
` Citing six pre-filing date publications, Dr. Derbyshire stated one of ordinary skill in the art in 1992 would have in the
`art would have known that E. coli had the capacity to repair double-strand breaks in and DNA and conduct homolo-
`gous recombination without phage proteins (Derbyshire Decl. of August 4, 2010, ¶¶ 19-21, Exhibit 1006 [FF39].)
`
`Dr. Marlene Belfort
`During the course of the reexamination proceeding, the Patent Owner provided series of declarations by Dr. Marlene
`Belfort, a scientist with more than twenty years of experience in the field of molecular biology as it relates to endo-
`nucleases. Dr. Belfort was the senior author of both the Quirk and Bell-Pedersen publications. She was the director of
`the laboratory in which the research reported in Quirk and Bell-Pedersen was performed. Dr. Bell-Pedersen was
`working under Dr. Belfort's supervision as a Ph.D. graduate student. Dr. Derbyshire was a postdoctoral affiliate in her
`lab. We have considered all the testimony in the Belfort declarations. Below we summarize some of the main points
`made by Dr. Belfort.
`
` •
`
` Bell-Pedersen did not show cleavage of chromosomal DNA by a GIIE endonuclease or evidence that a GIIE en-
`donuclease could cleave chromosomal DNA (Belfort Decl. of Nov. 17, 2009, ¶¶ 10 & 16, Exhibit 1007) [FF40]).
`
` •
`
` The pL temperature inducible promoter controlled both endonuclease production and phage excision from the
`chromosome. Consequently, Dr. Belfort declared that when there was a low activity of the pL promoter at 30°C, the
`phage would have been excised from the chromosome where it could serve as a target for endonuclease cleavage and
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
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`IPR 2013-00154
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`intron insertion (Belfort Decl. of Nov. 17, 2009, ¶ 33, Exhibit 1007 [FF41]).
`
` •
`
` Belfort acknowledged that “[s]ome baseline integration of the [antibiotic resistance gene or marker gene] may have
`occurred prior to induction, but this was neither the intent of the experiment nor the bulk of what was measured in the
`experiment” (Belfort Decl. of Nov. 17, 2009, ¶ 37, Exhibit 1007). However, Dr. Belfort clarified that it was “theo-
`retically possible” that the gene integrated into the chromosomal DNA, but “this is not what Bell-Pedersen and Quirk
`show, nor is it what a skilled artisan would conclude from reading these references.”(Belfort Decl. of June 30, 2010, ¶
`30, Exhibit 1008) [FF42]).
`
` •
`
` “Since the time of the research, experiments and publications, none of the authors of either the Bell-Pedersen ref-
`erence or the Quirk reference have discussed with me their belief that the research and experiments described in the
`two references demonstrated the introduction of a site-specific double-strand break at a group I intron encoded en-
`donuclease recognition site in chromosomal DNA.”(Belfort Decl. of March 8, 2010, ¶ 21, Exhibit 1009) [FF43].)
`
`*9 • “Nowhere in Bell-Pedersen or Quirk is it shown or suggested that cleavage of the I-TevI recognition site occurred
`while the recognition' site was present in chromosomal DNA. In fact, the intent of the experiments described in
`Bell-Pedersen and Quirk was for I-TevI to cleave its recognition site in bacteriophage that was replicating inde-
`pendently of the chromosome.” (Belfort Decl. of March 8, 2010, ¶ 23, Exhibit 1009) [FF44].
`
` •
`
` Dr. Derbyshire's conclusion that intron insertion would not have occurred in excised phage because they were rep-
`licating too rapidly is flawed since in other experiments, using phage that were not capable of integrating into the E.
`coli chromosome, intron insertion rates were similar (Belfort Decl. of March 8, 2010, ¶¶ 29 & 30, Exhibit 1009)
`[FF45].
`
` •
`
` “the only explanation for the productive cleavages that are reported in Bell-Pedersen and Quirk is that repair and
`recombination are taking place in developing phage (i.e., phage that are in the lytic phase and expressing phage pro-
`teins) … Since phage proteins that are required for recombination are not present in lysogens [when phage is inserted
`into the chromosomal DNA], and since E. coli cells are not able to repair the double-strand break without the assis-
`tance of phage proteins, one must conclude that a productive cleavage occurred after induction (i.e., after expression of
`phage proteins and excision). If cleavage had occurred prior to induction, the cell would have died, and there would
`have been no progeny phage to report intron acquisition.”(Belfort Decl. of June 30, 2010, ¶ 26, Exhibit 1008) [FF46].
`
` •
`
` “As the person who designed these experiments [reported in the Bell-Pedersen publication], and directed laboratory
`members to conduct the experiments, I can say with certainty that it was not our intent to determine whether I-TevI
`could function on a chromosome.”(Belfort Decl. of June 30, 2010, ¶ 36, Exhibit 1008) [FF47].
`
`
`Rejection
`
`
`The method of claim 1 comprises two recited steps: 1) providing a GIIE endonuclease recognition site to the chro-
`mosome of a cell; and 2) providing a GIIE endonuclease to a cell such that the endonuclease cleaves the chromosome
`at the recognition site.
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
`
`IPR 2013-00154
`Patent No. 7,335,996
`
`TSMC Request for Reconsideration
`Under 37 C.F.R. 42.71(c) - Appendix B
`
`

`

`
`
`
`Page 10
`
`
`The Examiner found (Right of Appeal Notice (“RAN”) 12-14) that each of Quirk and Bell-Pedersen described: 1)
`providing a GIIE endonuclease recognition site to the chromosome of an E. coli cell, where the site is present in a
`phage DNA which integrates into the E. coli chromosome. The Examiner also found (RAN 12-14) that both publi-
`cations described 2) providing a GIIE endonuclease to the cell such that it cleaved the chromosomal DNA. As both
`steps were found to be described in Quirk and Bell-Pedersen, the Examiner concluded that claim 1 was anticipated by
`the publications (RAN 12-14).
`
`The Patent Owner contends that the Examiner erred in finding that Bell-Pedersen produced a double-stranded break in
`a chromosome. The Patent Owner contends that the Examiner did not establish that cleavage of the DNA took place
`when the phage was integrated into the bacterial chromosome (Appellant App. Br. 15).
`
`*10 The Patent Owner reasoned, based on expert testimony, that when the temperature inducible promoter (pL) was
`expressed, excision of the phage from the bacterial chromosome and the manufacture of the endonuclease would
`happen simultaneously. Consequently, the endonuclease would be made as the phage is excised from the bacterial
`chromosome, and in this excised form, would be available for the endonuclease to cleave it. Cleavage and insertion of
`the antibiotic resistance, according to the Patent Owner, would thus have occurred when the phage is no longer part of
`the E. coli chromosomal DNA.
`
`The Examiner and Requester challenged the Patent Owner's interpretation of the Quirk and Bell-Pedersen publica-
`tions. The cells are shifted to a high temperature to activate the promoter which, in turns, directs manufacture of the
`endonuclease (FF9-FF10, Quirk 457, col. 1). In agreement with the Examiner, the Requester contends that a low level
`of endonuclease was made during the growth phase of the E. coli (due to “leakiness” of the promoter), prior to the shift
`to a higher temperature. During this time, the Requester argued that cleavage would have occurred while the GIIEE
`recognition site was still resident in the E. coli chromosome. (Requester Brief 7.)
`
`The Examiner also stated “the prior art only needs to teach that at least some integration of the kanamycin resistance
`gene occurred in the bacterial chromosome in the experiments described in Bell-Pedersen. It need not teach that every
`single incident of integration occurred while the recognition site was integrated in the chromosome of the lyso-
`gen.”(RAN 56.)
`
`In addressing this issue it is important to recognize that neither the Patent Owner nor Requester disputed the fact that
`Bell-Pedersen did not disclose whether cleavage of the DNA and insertion of the marker gene into the intron occurred
`while the phage was still residing in the bacterial chromosome or after the phage had been excised from the chro-
`mosome. It was silent on where this event took place. Thus, the position of the Examiner, the Patent Owner, and
`Requester is based on opinion and evidence of what the skilled worker would have understood, based on their
`knowledge, the level of ordinary skill in the art, and their reading of the Quirk and Bell-Pedersen publications.
`
`
`Analysis
`
`
`Quirk and Bell-Pedersen are silent on where cleavage of the recognition site takes place. The recognition site is in-
`troduced into the E. coli cell on a phage (FF6, Quirk 458-459, 463, col. 2 (section titled “Phages,” T2L and T2H);
`
`© 2013 Thomson Reuters. No Claim to Orig. US Gov. Works.
`
`IPR 2013-00154
`Patent No. 7,335,996
`
`TSMC Request for Reconsideration
`Under 37 C.F.R. 42.71(c) - Appendix B
`
`

`

`
`
`
`Page 11
`
`Bell-Pedersen Decl. of May 19, 2010, ¶ 27, Exhibit 1001; FF7; FF14, Bell-Pedersen 3763; & FF18, Bell-Pedersen
`3764-3765; Bell-Pedersen Decl. of May 19, 2010, ¶¶ 32-44, Exhibit 1001). The phage integrates into the bacterial
`chromosome as part of its replication cycle, and then, when the temperature inducible promoter is activated by an
`increase in temperature, the phage is excised from the chromosome (FF21, Bell-Pedersen 3765 & FF22, Bell-Pedersen
`3765, col. 1; Bell-Pedersen Decl. of May 19, 2010, ¶ 54, Exhibit 1001). The GIIE endonuclease is contro