UNITED STATES PATENT AND TRADEMARK OFFICE
`
`____________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`____________
`
`BENITEC BIOPHARMA LIMITED
`
`Petitioner,
`
`v.
`
`COLD SPRING HARBOR LABORATORY
`
`Patent Owner.
`
`
`
`Case IPR Unassigned
`
`Patent No. 8,153,776
`
`____________
`
`PETITION FOR INTER PARTES REVIEW OF
`U.S. PATENT NO. 8,153,776 UNDER 37 C.F.R. § 42.100
`
`
`
`
`Mail Stop "Patent Board"
`Patent Trial and Appeal Board
`U.S. Patent and Trademark Office
`P.O. Box 1450
`Alexandria, VA 22313-1450
`
`
`
`
`
`

`
`I.
`
`TABLE OF CONTENTS
`
`COMPLIANCE WITH FORMAL REQUIREMENTS ................................. 1
`A. Mandatory Notices Under 37 C.F.R. § § 42.8(b)(1)-(4) ...................... 1
`1.
`Real Party-in-Interest ................................................................. 1
`2.
`Related Matters .......................................................................... 1
`3.
`Lead And Back-Up Counsel and Service Information .............. 2
`4.
`Powers of Attorney and Service Information ............................ 2
`Proof of Service on the Patent Owner .................................................. 2
`B.
`Fees ....................................................................................................... 2
`C.
`II. GROUNDS FOR STANDING ....................................................................... 3
`III. STATEMENT OF PRECISE RELIEF REQUESTED .................................. 3
`IV.
`IDENTIFICATION OF CHALLENGE ......................................................... 3
`V.
`LEVEL OF ORDINARY SKILL IN THE ART ............................................ 4
`VI. SUMMARY OF THE ‘776 PATENT ............................................................ 4
`A.
`Brief Description of the ‘776 Patent .................................................... 4
`B.
`Summary of the Prosecution History of the ‘776 Patent ..................... 4
`VII. CLAIM CONSTRUCTION ........................................................................... 5
`VIII. THERE IS A REASONABLE LIKELIHOOD THAT AT LEAST
`ONE CLAIM OF THE ‘776 PATENT IS UNPATENTABLE ..................... 5
`A.
`State of the Prior Art ............................................................................ 5
`B.
`Summary of Invalidity Arguments ....................................................... 8
`IX. CLAIM-BY-CLAIM EXPLANATION OF GROUNDS FOR
`UNPATENTABILITY ................................................................................... 9
`A. Ground 1: Detailed Explanation Under 37 C.F.R. § 42.104(b) of
`How Graham (Ex. 1005) Anticipates Claims 1–10 ............................. 9
`B. Ground 2: Detailed Explanation Under 37 C.F.R. § 42.104(b) of
`How Zamore (Ex. 1003) Anticipates Claims 1-10 ............................ 23
`
`
`
`i
`
`

`
`C. Ground 3: Detailed Explanation Under 37 C.F.R. § 42.104(b) of
`How Claims 1-10 are Obvious under 35 U.S.C. § 103(a) over a
`combination of Graham and/or Zamore, in view of a
`combination of Tuschl, Fire, Harborth, Parrish, Sijen, Green,
`Tian, Waterhouse, and/or Symonds, and in View of the
`Ordinary Skill in the Art ..................................................................... 41
`CONCLUSION ............................................................................................. 60
`
`
`
`X.
`
`
`
`ii
`
`

`
`
`EXHIBIT
`
`1001
`
`1002
`
`1003
`
`1004
`
`1005
`
`1006
`
`1007
`
`1008
`
`1009
`
`1010
`
`1011
`
`1012
`
`1013
`
`1014
`
`1015
`
`1016
`
`
`
`TABLE OF EXHIBITS
`
`DESCRIPTION
`
`U.S. Patent No. 8,153,776 to Hannon et al.
`
`Prosecution History of U.S. Patent No. 8,153,776
`
`U.S. Patent No. 7,691,995 to Zamore et al.
`
`U.S. Provisional Patent Application 60/305,185 to Zamore et al.
`
`U.S. Patent No. 6,573,099 to Graham et al.
`
`U.S. Patent No. 6,506,559 to Fire et al.
`
`U.S. Patent. Pub. No. 2002/0086356 to Tuschl et al.
`
`Green et al., Genes Dev. 6: 2478-2490 (1992).
`
`Tian et al., RNA, 6:79-87 (2000).
`
`Parrish et al., Molecular Cell, 6:1077-1087 (Nov. 2000).
`
`Sijen et al., Cell, 107:465-476 (Nov. 2001).
`
`Harborth et al., J. Cell Science 114, 4557-4565 (2001).
`
`Waterhouse et al., Nature, Vol. 411:834-842 (June 2001).
`
`[RESERVED]
`
`U.S. Patent No. 7,345,025 to Symonds et al.
`
`Elbashir et al., Nature, Vol. 411 (May 2011).
`
`iii
`
`

`
`EXHIBIT
`
`DESCRIPTION
`
`Paddison, et al., Genes and Dev., 16:948-958 (Apr. 2002). 1
`
`[RESERVED]
`
`[RESERVED]
`
`[RESERVED]
`
`[RESERVED]
`
`Excerpt from U.S. Patent No. 8,383,599 prosecution history
`(Sept. 19, 2011 Remarks by Patentee)
`Excerpts from U.S. Patent No. 8,202,846 prosecution history
`(January 3, 2011 and March 14, 2012 Remarks by Patentee)
`
`1017
`
`1018
`
`1019
`
`1020
`
`1021
`
`1022
`
`1023
`
`
`
`
`
`
`
`
`
`1 As indicated in Section I.2, this Petition is being filed concurrently with
`three related Petitions. Several of the exhibits are being submitted with multiple
`petitions. The documents submitted with each petition are numbered sequentially
`as exhibits, and each submitted exhibit is given the same exhibit number if used in
`the related petitions. Ex. 1002 in each petition, however, is the prosecution history
`for that petition and will differ across petitions. Petitioner respectfully submits that
`its sequential exhibit numbering system complies with the requirements of the
`Patent Review Processing System and further minimizes any confusion to the
`parties and the Board in any instituted reviews.
`iv
`
`
`
`

`
`Benitec Biopharma Limited ("Petitioner") in accordance with 35 U.S.C.
`
`§§ 311-319 and 37 C.F.R. § 42.100 et seq., requests that the United States Patent
`
`and Trademark Office ("USPTO") proceed with an inter partes review of claims 1-
`
`10 of U.S. Patent No. 8,153,776 (the "‘776 patent") (Ex. 1001). The sole
`
`independent claim of the ‘776 patent recites methods of attenuating gene
`
`expression in mammalian cells, by expressing libraries of RNA constructs, that
`
`trigger inherent cellular gene-silencing mechanisms. The limitations of these
`
`claims are largely directed to structural features in the expression product that
`
`trigger inherent cellular gene-silencing mechanisms, while avoiding triggering
`
`unwanted immune responses. These cellular mechanisms and structural triggers
`
`were well-known, as evidenced by the prior art identified below. The dependent
`
`claims add nothing more than known limitations abundantly disclosed in the prior
`
`art. Accordingly, claims 1-10 of the ‘776 patent are invalid.
`
`I.
`
`COMPLIANCE WITH FORMAL REQUIREMENTS
`A. Mandatory Notices Under 37 C.F.R. § § 42.8(b)(1)-(4)
`1.
`Real Party-in-Interest
`Benitec Biopharma Limited (“Petitioner”) is the real party-in-interest.
`2.
`Petitioner advises that it has also requested inter partes review of the
`
`Related Matters
`
`following related patents, U.S. Patent Nos. 8,829,264; 8,383,599; and 8,202,846,
`
`but to its knowledge there are no related matters.
`
`
`
`1
`
`

`
`Lead And Back-Up Counsel and Service Information
`
`3.
`Pursuant to 37 C.F.R. § 42.8(b)(3) and 42.10(a), Petitioner provides the
`
`
`
`following designation of counsel: Lead counsel is Lisa A. Haile (Reg. No. 38,347),
`
`backup counsel is John M. Garvey (Reg. No. 37,833), both at email address:
`
`Benitec-IPR@dlapiper.com. Postal and hand delivery for both is DLA Piper LLP
`
`(US), 4365 Executive Drive, Suite 1100, San Diego, California 92101-4297.
`
`Telephone for Dr. Haile is (858) 677-1456; telephone for Dr. Garvey is (617) 406-
`
`1456; the fax for both is (858) 677-1465.
`
`Powers of Attorney and Service Information
`
`4.
`Pursuant to 37 C.F.R. § 42.10(b), a Power of Attorney accompanies this
`
`Petition. Petitioner consents to service by email at Benitec-IPR@dlapiper.com.
`
`
`
`Proof of Service on the Patent Owner
`
`B.
`As identified in the attached Certificate of Service, a copy of this Petition in
`
`its entirety is being served to Patent Owner (“Patentee”) at the address listed in the
`
`USPTO's records by overnight courier pursuant to 37 C.F.R. § 42.6.
`
`Fees
`
`C.
`A fee of $23,000 has been paid for this Petition. Ten (10) claims are being
`
`reviewed. The undersigned further authorizes the USPTO, including the Patent
`
`Trial and Appeal Board to charge any additional fee that might be due or required
`
`to Deposit Account No. 07-1896.
`
`
`
`2
`
`

`
`II. GROUNDS FOR STANDING
`
`In accordance with 37 C.F.R. § 42.104(a), Petitioner certifies that the ‘776
`
`patent is available for inter partes review and that Petitioner is not barred or
`
`estopped from requesting an inter partes review challenging the patent claims on
`
`the grounds identified in this Petition.
`
`III. STATEMENT OF PRECISE RELIEF REQUESTED
`In accordance with 37 C.F.R. § 42.22, Petitioner respectfully requests that
`
`claims 1-10 of the ‘776 patent be found invalid for the reasons set forth below.
`
`IV.
`
`IDENTIFICATION OF CHALLENGE
`
`In accordance with 35 U.S.C. § 311 and 37 C.F.R. § 42.104(b), inter partes
`
`review of claims 1-10 of the ‘776 patent is requested. Each of the patents and
`
`printed publications set forth below is prior art to the ‘776 patent:
`
`Ground
`1
`
`Proposed Statutory Rejections for the ‘776 Patent
`Claims 1-10 are anticipated by Graham (Ex. 1005) pursuant to 35
`
`U.S.C. §102(b).
`
`2
`
`3
`
`Claims 1-10 are anticipated by Zamore (Ex. 1003) pursuant to 35
`
`U.S.C. §102(e).
`
`Claims 1-10 are rendered obvious by a combination of Graham
`
`(Ex. 1005) and/or Zamore (Ex. 1003), in view of a combination of
`
`Tuschl (Ex. 1007), Fire (Ex. 1006), Harborth (Ex. 1012), Parrish
`
`
`
`3
`
`

`
`Ground
`
`Proposed Statutory Rejections for the ‘776 Patent
`(Ex. 1010), Sijen (Ex. 1011), Green (Ex. 1008), Tian (Ex. 1009),
`
`Waterhouse (Ex. 1013) and/or Symonds (Ex. 1015), in view of the
`
`knowledge of one skilled in the art pursuant to 35 U.S.C. §103.
`
`
`V. LEVEL OF ORDINARY SKILL IN THE ART
`A person of ordinary skill in the area of post-translational gene silencing at
`
`the time of the alleged invention would have a graduate or post-graduate degree in
`
`the life sciences field, or have a Master's degree or Ph.D. in molecular biology,
`
`microbiology, biochemistry, immunology, chemistry or a related discipline.
`
`VI. SUMMARY OF THE ‘776 PATENT
`A. Brief Description of the ‘776 Patent
`The ‘776 patent is entitled “Methods and Compositions for RNA
`
`Interference”. It discloses mammalian cells having libraries stably expressing
`
`constructs for inhibiting gene expression in a mammalian cell using post-
`
`transcriptional gene silencing methods, based on the properties of double-stranded
`
`RNA (“dsRNA”) and the innate responses mammalian cells display towards
`
`dsRNA. It contains one independent and nine dependent claims.
`
`Summary of the Prosecution History of the ‘776 Patent
`
`B.
`The ‘776 patent issued Apr. 10, 1012 from application No. 11/894,676 filed
`
`Aug. 20, 2007, which was a continuation of App. No. 10/997,086 filed Nov. 23,
`
`
`
`4
`
`

`
`2004, and a continuation-in part 10/055,797 (now abandoned), originally filed on
`
`January 22, 2002, the priority date of the ‘776 patent. The ‘776 patent is subject to
`
`a terminal disclaimer over U.S. Patent No. 8,202,846.
`
`VII. CLAIM CONSTRUCTION
`In accordance with 37 C.F.R. § 42.104(b)(3), claims in an inter partes
`
`
`review of an unexpired patent are to be given their “broadest reasonable
`
`interpretation in light of the specification”. 37 C.F.R. § 42.100(b). Petitioner
`
`asserts that each claim term carries its ordinary and customary meaning.
`
`VIII. THERE IS A REASONABLE LIKELIHOOD THAT AT LEAST ONE
`CLAIM OF THE ‘776 PATENT IS UNPATENTABLE
`A.
`The ‘776 patent is directed to methods of gene silencing by RNA
`
`State of the Prior Art
`
`interference (“RNAi”). RNAi is an innate sequence-specific response to the
`
`presence of double stranded RNA (“dsRNA”) within a cell, which destroys gene
`
`expression products and thereby “silences” the gene. However, in mammalian
`
`cells, a potent response against dsRNA is observed as well, referred to as the PK
`
`response (“PKR”). The range of lengths of dsRNA that would successfully trigger
`
`RNAi without triggering PKR were described specifically in the art before January
`
`22, 2002, the priority date of the ‘776 patent. Accordingly, the ‘776 patent merely
`
`recites methods that were already known in the art.
`
`
`
`5
`
`

`
`As disclosed in numerous prior art references, discussed below, the process
`
`of RNAi was well-established long before January 22, 2002, as several researchers
`
`observed RNAi in a variety of organisms, including mammalian cells in 1998
`
`(Graham, Ex. 1005), and C. elegans in 1999 (Fire, Ex. 1006). Other researchers
`
`observed components of RNAi activity and their gene silencing effects. For
`
`example, Tuschl (Ex. 1007) discovered that dsRNA fragments, i.e. short interfering
`
`RNA (“siRNA”), directly mediated gene silencing, as these fragments arose from
`
`processing of longer duplex RNA by cell-free extracts. In 2001, Zamore and
`
`colleagues engineered small temporal RNA (“stRNA”) precursors that caused
`
`RNAi in mammalian cells. (Exs. 1003 & 1004). In addition to the foregoing,
`
`Petitioner provides additional unconsidered references (Ex. 1010-1012) that
`
`evidence RNAi effects with constructs inclusive of the critical range of lengths
`
`specified by Patentee (e.g., long enough to trigger gene silencing but short enough
`
`to avoid triggering PKR). These references further evidence that RNAi was a well-
`
`characterized sequence specific gene silencing technology, and Patentee’s claims
`
`merely reflect elements known in the art prior to January 22, 2002.
`
`As stated above, numerous responses of mammalian cells to the presence of
`
`cytoplasmic dsRNA are mediated by the enzyme PK. PK binds dsRNA and
`
`initiates a type of post-transcriptional gene silencing different from RNAi.
`
`However, PK triggers interferon synthesis, initiates interferon-related cellular
`
`
`
`6
`
`

`
`immune responses and causes cellular death through apoptotic pathways (i.e.,
`
`“PKR”). PKR is an inherent response to dsRNA, and was well-appreciated and
`
`described in the prior art before January 22, 2002. Indeed, as disclosed in the art,
`
`one can avoid PKR by utilizing RNA constructs that are short. For example, by at
`
`least 1993, it was known that the enzyme PK will only bind dsRNA longer than 30
`
`bases in length (Green, Ex. 1008). In 2000, the same approximate critical length
`
`was observed for hairpin dsRNA structures as well (Tian, Ex. 1009). Accordingly,
`
`to avoid PKR, the prior art fully disclosed that fragment length must be kept
`
`shorter than 30 bases in length. Accordingly, Patentee’s alleged “invention”
`
`amounts to nothing more than incorporation of well-known features relative to
`
`RNA length and PKR, already disclosed before January 22, 2002. Indeed,
`
`Patentee’s own statements during prosecution of related U.S. Patent No. 8,383,599
`
`reflect its awareness of these known features, providing, “Of course it was known
`
`that introducing or expressing long dsRNA in most mammalian cells would kill
`
`them by activating the anti-viral/PKR response…This innate anti-viral pathway
`
`would have taught away from using dsRNA for silencing expression of a particular
`
`gene in a mammalian cell.” (Ex. 1022, 9/19/11 Remarks, p. 12, lines 12-17).
`
`(emphasis added). However, Patentee’s statement is contradicted by numerous
`
`prior art references (e.g., Exs. 1010-1012), which disclose the successful use of
`
`dsRNA as gene silencing constructs, which due to their size, avoid triggering PKR.
`
`
`
`7
`
`

`
`As noted above, the claims of the ‘776 patent are largely directed to
`
`structural features (lengths) of dsRNA expression constructs that will initiate gene
`
`silencing mechanisms, while avoiding triggering PKR. These features were known
`
`before the January 22, 2002 priority date of the ‘776 patent, and successfully used
`
`by others in connection with mammalian gene silencing studies. Accordingly, the
`
`instant claims are invalid.
`
`B.
`
`Summary of Invalidity Arguments
`
`First, claims 1-10 are invalid as being anticipated under §102(b) and as
`
`obvious under §103(a) by Graham. (Ex. 1005). This reference was not used as a
`
`basis for rejection by Examiner during prosecution and anticipates and renders
`
`obvious, directly and inherently all claims of the ‘776 patent.
`
`Second, claims 1-10 are invalid as being anticipated under §102(e) and as
`
`obvious under §103(a) by Zamore (Ex. 1003). These grounds of rejection were
`
`asserted and overcome during prosecution. However, “critical elements” (as
`
`alleged by Patentee in the prosecution history (Ex. 1002) distinguishing over
`
`Zamore) reflect innate and natural phenomena in mammalian cells, inherent in the
`
`Zamore prior art, widely known prior to January 22, 2002.
`
`Third, claims 1-10 are invalid as being obvious under §103(a) in view of
`
`Graham and/or Zamore (Exs. 1003 – 1005) and in further view of combinations of
`
`Tuschl, Fire, Harborth, Parrish, Sijen, Green, Tian, Waterhouse and/or Symonds
`
`
`
`8
`
`

`
`(Exs. 1007, 1006, 1012, 1010, 1011, 1008, 1009, 1013, and 1015). These
`
`combinations establish that all of the elements of claims 1-10 were well
`
`represented in the prior art before January 22, 2002. A person of ordinary skill of
`
`the art, therefore, would have been motivated to combine these references because
`
`these innate biological systems were known, as discussed above, the references
`
`evidence a strong motivation to utilize short hairpin dsRNA mediated gene
`
`silencing in human therapies, with the desire and knowledge to avoid triggering
`
`PKR, as will be discussed.
`
`IX. CLAIM-BY-CLAIM EXPLANATION OF GROUNDS FOR
`UNPATENTABILITY
`
`Claims 1-10 are unpatentable as demonstrated by the following grounds.
`
`A. Ground 1: Detailed Explanation Under 37 C.F.R. § 42.104(b) of
`How Graham (Ex. 1005) Anticipates Claims 1–10.
`
`Graham (Ex. 1005) is §102(b) prior art to the ‘776 patent. Graham
`
`anticipates claims 1-10 as set forth in further detail below.
`
`CLAIM 1
`
`
`
`‘776 Patent Claim Element
`
`1. A method for attenuating expression
`of a target gene in a mammalian cell, the
`method comprising
`introducing into mammalian cells a
`library of RNA expression constructs,
`each expression construct comprising:
`
`
`Prior Art Disclosure
`
`Ex. 1005 [Graham] (Abstract, 2:24-55,
`4:1-13)
`
`Ex. 1005 [Graham] (4:1-13, 4:19-24,
`10:22-32, 13:57-67, 21:45-52).
`
`
`
`
`9
`
`

`
`Graham attenuates expression of a target gene in a mammalian cell. The
`
`relevant quotes are provided below. Graham provides “synthetic genes for
`
`modifying endogenous [target] gene expression in a cell, tissue or organ of a
`
`transgenic organism, in particular a transgenic animal or plant…” (Ex. 1005, 2:24-
`
`55) and “novel synthetic genes and genetic constructs which are capable of
`
`repressing delaying or otherwise reducing the expression of an endogenous gene or
`
`a target gene in an organism when introduced thereto.” (Ex. 1005, Abstract).
`
`Graham goes on to specify a “gene”, which includes “mRNA… corresponding to
`
`coding regions, (i.e., “exons”) optionally comprising 5’ or 3’ untranslated
`
`sequences linked thereto.” (Ex. 1005, 4:1-13). Graham further notes “synthetic
`
`gene refers to a non-naturally occurring gene… which preferably comprises at least
`
`one or more transcriptional and/or translational regulatory sequences operably
`
`linked to a structural gene sequence.” (Ex. 1005, 4:19-24). Accordingly, Graham
`
`discloses this element.
`
`Graham further teaches libraries of these RNA expression constructs.
`
`Graham discloses e.g., using libraries of the tyrosinase enzyme, stating, “gene
`
`fragments are produced, for example, by sonication or mechanical shearing and
`
`end-repair using T4 DNA polymerase. Accordingly, the structural gene insert in
`
`plasmid pCMV.TYRLIB
`
`is variable, and a
`
`representative
`
`library of
`
`pCMV.TYRLIB plasmids covering the complete tyrosinase gene sequence, may be
`
`
`
`10
`
`

`
`produced using such procedures. The present invention clearly encompasses such
`
`representative libraries.” (Ex. 1005, 21:45-52). Graham notes that transcriptional
`
`and/or translational regulatory sequences operably linked to a structural gene
`
`sequence regulates expression (Ex. 1005, 4:19-24).
`
`Graham introduces a library of RNA expression constructs into mammalian
`
`cells. Graham provides “the synthetic genes may be introduced into a suitable cell,
`
`tissue or organ without modification as linear DNA in the form of a genetic
`
`construct…” and that “to produce a genetic construct, the synthetic gene of the
`
`invention is inserted into a suitable vector or episome molecule… which is capable
`
`of being maintained and/or replicated and/or expressed in the host cell, tissue or
`
`organ into which it is subsequently introduced.” (Ex. 1005, 13:57-67). Graham
`
`discloses attenuating expression of a target gene in a mammalian cell by
`
`introducing into mammalian cells a library of RNA expression constructs.
`
`‘776 Patent Claim Element
`
`(i) an RNA polymerase promoter, and
`
`Graham discloses RNA polymerase promoter sequences. Promoter
`
`Ex. 1005 [Graham] (8:4-34).
`
`Prior Art Disclosure
`
`sequences are necessary to drive expression of constructs carried on transgenes,
`
`and reflect routine technology. The inclusion of this known element by Patentee is
`
`neither remarkable nor novel.
`
`
`
`11
`
`

`
`Graham details “examples of promoters suitable for use in the synthetic
`
`genes of the present invention include viral, fungal, bacterial, animal and plant
`
`derived promoters capable of functioning in plant, animal, insect, fungal, yeast or
`
`bacterial cells. The promoter may regulate the expression of the structural gene
`
`component constitutively, or differentially with respect to cell, the tissue or organ
`
`in which expression occurs or, with respect to the developmental stage at which
`
`expression occurs, or in response to external stimuli such as physiological stresses,
`
`or pathogens, or metal ions, amongst others. Preferably, the promoter is capable of
`
`regulating expression of a nucleic acid molecule in a[n] eukaryotic cell, tissue or
`
`organ, at least during the period of time over which the target gene is expressed
`
`therein and more preferably also immediately preceding the commencement of
`
`detectable expression of the target gene in said cell, tissue or organ. Accordingly,
`
`strong constitutive promoters are particularly preferred for the purposes of the
`
`present invention or promoters which may be induced by virus infection or the
`
`commencement of target gene expression. Examples of preferred promoters
`
`include the bacteriophage T7 promoter, bacteriophage T3 promoter, SP6 promoter,
`
`lac operator-promoter, tac promoter, SV40 late promoter, SV40 early promoter,
`
`RSV-LTR promoter, CMV IE promoter and the like. Particularly preferred
`
`promoters contemplated herein include promoters operable in eukaryotic cells, for
`
`example the SV40 early promoter, SV40 late promoter or the CMV IE promoter
`
`
`
`12
`
`

`
`sequence. Those skilled in the art will readily be aware of additional promoter
`
`sequences other
`
`than
`
`those specifically described.” (Ex. 1005, 8:4-34).
`
`Accordingly, Graham discloses this element of claim 1.
`
`Prior Art Disclosure
`
`‘776 Patent Claim Element
`
` (ii) a sequence encoding a short hairpin
`RNA molecule comprising a double-
`stranded region wherein the double-
`stranded region consists of at least 20
`nucleotides but not more than 29
`nucleotides,
`
`Graham discloses a silencing construct having short hairpin RNA, with
`
`Ex. 1005 [Graham] (6:25-40, 10:22-32,
`10:38-44).
`
`
`duplex regions at least 20 nts and not more than 29 in length. This is the range of
`
`nucleotide lengths that are sufficient to trigger gene silencing but short enough to
`
`avoid triggering PKR.
`
`Graham states “preferred structural gene components of the synthetic gene
`
`of the invention comprise at least about 20-30 nucleotides in length” (Ex. 1005,
`
`6:25-40). Graham’s “at least about 20-30 nucleotides” includes, therefore, at least
`
`20 but not more than 29 nucleotides. Graham teaches hairpin sequences in the
`
`synthetic construct, stating “the optimum number of structural gene sequences
`
`which may be involved in the synthetic gene of the present invention will vary
`
`considerably, depending upon the length of each of said structural gene sequences,
`
`their orientation and degree of identity to each other. For example, those skilled in
`
`the art will be aware of the inherent instability of palindromic nucleotide sequences
`13
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`

`
`in vivo and the difficulties associated with constructing long synthetic genes
`
`comprising inverted repeated nucleotide sequences, because of the tendency for
`
`such sequences to form hairpin loops and to recombine in vivo.” (Ex. 1005, 10:22-
`
`32). Graham teaches “reducing the number of repeated sequences to a level which
`
`eliminates or minimizes recombination events and by keeping the total length of
`
`multiple structural gene sequences to an acceptable limit… even more preferably
`
`no more than 0.5-2.0 kb in length.” (Ex. 1005, 10:38-44). Thus, Graham evidences
`
`short hairpin RNA with 20-29 nt lengths as well as the undesirability of longer
`
`sequences with hairpin structures.
`
`Prior Art Disclosure
`
`Ex. 1005 [Graham] (1:51-55, 6:25-40).
`
`
`‘776 Patent Claim Element
`
`wherein the short hairpin RNA molecule
`is a substrate for Dicer-dependent
`cleavage and does not trigger a protein
`kinase RNA-activated (PKR) response
`in the mammalian cell,
`
`Graham discloses constructs that are substrates for Dicer-dependent
`
`
`
`cleavage, that are short enough not to trigger PKR, for example the constructs
`
`described in the paragraph above.
`
`While the identity of the Dicer enzyme was unknown at the time of Graham,
`
`it was known that an innate cellular RNAse processed longer dsRNA into shorter
`
`fragments (e.g., Tuschl’s siRNA, Ex. 1007). Graham states “in work leading up to
`
`the present invention, the inventors sought to elucidate the mechanisms involved in
`
`
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`14
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`down-regulating gene expression in an attempt to provide improved methods
`
`therefor. In so doing the inventors have developed a wide range of synthetic genes
`
`capable of modulating gene expression in both prokaryotic and eukaryotic cells
`
`and genetic constructs comprising same.” (Ex. 1005, 1:51-55).
`
`Conversely, Patentee secured its patent based on claim features addressing
`
`an inherent property of dsRNA, its cleavage by Dicer into siRNA, which is
`
`impermissible. See Schering Corp. v. Geneva Pharms., Inc., 339 F.3d 1373 (Fed.
`
`Cir. 2003) (a patent is invalid for anticipation if a single prior art reference
`
`discloses each and every limitation of the claimed invention). Moreover, 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. The Dicer enzyme is inherently present in mammalian cells
`
`and is intrinsic to processing of dsRNA into siRNA to mediate gene silencing. In
`
`the instant case, Graham’s gene silencing constructs and their use, necessarily and
`
`inherently disclose the function Dicer plays in vivo, even without identifying the
`
`enzyme by name.
`
`Similarly, Patentee claims an inherent property of PK as a limitation. It was
`
`known that PK could only bind to dsRNA about 30 bp or longer. (Exs. 1008-1009)
`
`Thus shorter fragments inherently avoid triggering PKR. This is not a patentable
`
`invention of Patentee, it reflects a property that is “necessarily present” in the short
`
`
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`15
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`

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`sequences of Graham, and the “preferred structural gene components… at least
`
`about 20-30 nucleotides in length.” (Ex. 1005, 6:25-40). That short sequences do
`
`not bind PK and therefore cannot initiate the interferon response and cellular
`
`apoptosis was disclosed extensively in the prior art. Patentee implies it was his
`
`discovery (e.g., Paddison et al., Ex. 1017) but this property of PK was known since
`
`at least 1993, as was its binding site and structure. Moreover, PKR was not a minor
`
`problem with RNAi in mammalian cells--PKR caused cellular death.
`
`Prior Art Disclosure
`
`‘776 Patent Claim Element
`
`wherein the double-stranded region of
`the short hairpin RNA molecule
`comprises a sequence that is
`complementary to a portion of the target
`gene, and
`
`Graham teaches that shRNA has a sequence complementary to the target
`
`Ex. 1005 [Graham] (5:7-15, 6:25-40,
`10:22-32, and 10:38-44).
`
`gene. Graham teaches the use of short hairpin RNA as described above (Ex. 1005,
`
`6:25-40, 10:22-32, and 10:38-44). Graham describes complementarity of the
`
`sequence, stating “[t]he synthetic genes of the present invention may be derived
`
`from naturally-occurring genes by standard recombinant techniques, the only
`
`requirement being that the synthetic gene is substantially identical at the nucleotide
`
`sequence level to at least a part of the target gene, the expression of which is to be
`
`modified. By ‘substantially identical’ is meant that the structural gene sequence of
`
`
`
`16
`
`

`
`the synthetic gene is at least about 80%-90% identical to 30 or more contiguous
`
`nucleotides of the target gene...” (Ex. 1005, 5:7-15).
`
`Prior Art Disclosure
`
`Ex. 1005 [Graham] (Abstract, 4:40-42,
`6:25-40, 10:22-32, 10:38-44, 14:43-48).
`
`‘776 Patent Claim Element
`
`wherein the short hairpin RNA molecule
`is stably expressed in the mammalian
`cell in an amount sufficient to attenuate
`expression of the target gene in a
`sequence specific manner, and is
`expressed in the cell without use of a
`PK inhibitor, whereby expression of the
`target gene is inhibited.
`
`Graham teaches stable expression of shRNA in mammalian cells. Graham
`
`teaches integration of the silencing construct into the genome, and attenuation of
`
`expression of target genes as a result, without the use of PK inhibitors.
`
`Graham provides “genetic sequences intended for the maintenance and/or
`
`replication of said genetic construct in prokaryotes and/or the integration of said
`
`genetic construct or a part thereof into the genome of a eukaryotic cell or
`
`organism.” (Ex. 1005, 14:43-48). Graham teaches sequence specific inhibition of
`
`the target gene. Graham states “[T]he term “target gene” shall be taken to refer to
`
`any gene, the expression of which is to be modified using the synthetic gene of the
`
`invention.” (Ex. 1005, 4:40-42). Graham teaches “synthetic genes for modifying
`
`endogenous gene expression in a cell, tissue or organ of a transgenic organism, in
`
`particular a transgenic animal or plant…” as well as “novel synthetic genes and
`
`genetic constructs which are capable of repressing delaying or otherwise reducing
`17
`
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`

`
`the expression of an endogenous gene or a target gene in an organism when
`
`introduced thereto.” (Ex. 1005, Abstract).
`
`Patentee claims gene silencing “without use of a PK inhibitor.” Graham
`
`appreciates the problem of PKR, and discloses constructs having physical
`
`properties that would inherently avoid PKR as described (6:25-40, 10:22-32,
`
`10:38-44). However, as to this negative claim limitation, at no point in the Graham
`
`reference is a PK inhibitor employed. Moreover, it would be impossible to detail
`
`all of the agents that were not incorporated into Graham’s gene silencing studies,
`
`or those of any other researchers. For the above reasons, Petitioner asserts that all
`
`elements of claim 1 are described and inherently present in Graham (Ex. 1005).
`
`Accordingly, Graham anticipates claim 1.
`
`
`
`CLAIM 2
`
`Prior Art Disclosure
`
`‘776 Patent Claim Element
`
`2. The method of claim 1, wherein the
`expression construct further comprises
`LTR sequences located 5′ and 3′ of the
`sequence encoding the short hairpin
`RNA molecule.
`
`Graham teaches that the expression vector further comprises LTR sequences
`
`Ex. 1005 [Graham] (4:7-9, 7:34-39,
`8:24-28).
`
`located 5′ and 3′ of the sequence encoding the short hairpin RNA molecule. Long
`
`Terminal Repeat sequences are well-characterized regions of genetic material,
`
`containing promoter and enhancer elements, discovered in the 1980s in many
`
`
`
`18
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`
`species of viruses. Viral genomes are compact, and so LTRs contain elements
`
`positioned 5’ and 3’ to the coding sequences, driving expression of sense and
`
`antisense constructs. The use of LTR sequences to drive expression of constructs
`
`carried on transgenes in the claimed expression vector of Patentee is neither
`
`remarkable nor novel, and represents routine technology, reflected in Graham.
`
`Graham states
`
`that “examples of preferred promoters
`
`include
`
`the
`
`bacteriophage T7 promoter, bacteriophage T3 promoter, SP6 promoter, lac
`
`operator-promoter, tac promoter, SV40 late promoter, SV4