IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`Applicants:
`
`Gregory J. Hannon et al.
`
`Confirmation No.:
`
`5718
`
`Application No:
`
`12/152,837
`
`Art Unit:
`
`1635
`
`Filed:
`
`Title:
`
`May 16,2008
`
`Examiner:
`
`K. CHONG
`
`METHODS AND COMPOSITIONS FOR RNA INTERFERENCE
`
`Commissioner for Patents
`P.O. Box 1450
`Alexandria, VA 22313-1450
`
`AMENDMENT AND RESPONSE TO FINAL OFFICE ACTION
`
`This Amendment is filed in response to the March 18, 2011 Office Action for which a
`
`response was due June 18, 2011. Applicants hereby request a three-month extension of time to
`
`September 18, 2011. Accordingly, this paper is being timely filed. A Request for Continued
`
`Examination accompanies this paper. The Commissioner is authorized to charge any fees due, or
`
`to credit any overpayment in fees, to Deposit Account No. 08-0219.
`
`Amendments to the Specification begin on page 2.
`
`Amendments to the Claims begin on page 3.
`
`Amendments to the Drawings begin on page 6.
`
`Remarks begin on page 7.
`
`ACTIVEUS 90555450vl
`
`1
`
`Benitec - Exhibit 1022 -page 1
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`In the Specification
`
`AMENDMENT
`
`Please amend the paragraph beginning at page 1, line 3, of the specification as filed as
`
`follows:
`
`-- This application is a continuation of U.S. Ser. No. 10/055,797, filed on Jan. 22, 2002,
`
`the specification of which is a continuation in part of PCT application PCT/USOI/08435, filed
`
`on Mar. 16, 2001, vthich claims the benefit of U.S. Provisional applications U.S. Ser. No.
`
`60/189,739, filed on Mar. 16, 2000, and U.S. Ser. No. 60/243,097, filed on Oct. 24, 2000. The
`
`specifications of the above referenced applications are incorporated by reference herein.
`
`International i\pplication PCT/USOI/08435 \Vas published under PCT i\rticle 21(2) in English.--
`
`ACTIVEUS 90555450vl
`
`2
`
`Benitec - Exhibit 1022 -page 2
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`In the Claims
`
`Please amend the claims as follows, without prejudice. This listing of the claims will
`
`replace all prior versions and listings of claims in the application:
`
`1-47.
`
`(Cancelled)
`
`48.
`
`(Currently amended) A population of mammalian cells stably transfected or stably
`
`transduced with a library of expression constructs, wherein each expression construct encodes a
`
`short hairpin RNA, each expression construct comprising:
`
`(i)
`
`(ii)
`
`an RNA polymerase promoter, and
`
`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,
`
`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 cells,
`
`wherein the double-stranded region of the short hairpin RNA molecule comprises a
`
`sequence that is complementary to a portion of a target gene in the mammalian cells, wherein the
`
`target gene is an endogenous gene of the mammalian cells, and
`
`wherein said population of mammalian cells comprises cells in which the short hairpin
`
`RNA molecule is stably expressed in an amount sufficient to attenuate expression of the target
`
`gene in a sequence specific manner, and is expressed in the cells without use of a PKR inhibitor.
`
`49.
`
`(Previously presented) The population of mammalian cells of claim 48, wherein
`
`the expression construct further comprises L TR sequences located 5' and 3' of the sequence
`
`encoding the short hairpin RNA molecule.
`
`50.
`
`(Previously presented) The population of mammalian cells of claim 48, wherein
`
`the short hairpin RNA molecule comprises a double-stranded region consisting of at least 21
`
`nucleotides.
`
`51.
`
`(Previously presented) The population of mammalian cells of claim 48, wherein
`
`the short hairpin RNA molecule comprises a double-stranded region consisting of at least 22
`
`nucleotides.
`
`52.
`
`(Previously presented) The population of mammalian cells of claim 48, wherein
`
`the short hairpin RNA molecule comprises a double-stranded region consisting of at least 25
`
`nucleotides.
`
`ACTIVEUS 90555450vl
`
`3
`
`Benitec - Exhibit 1022 -page 3
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`53.
`
`(Previously presented) The population of mammalian cells of claim 48, wherein
`
`the short hairpin RNA molecule comprises a double-stranded region consisting of 29
`
`nucleotides.
`
`54.
`
`(Previously presented) The population of mammalian cells of claim 48, wherein
`
`the short hairpin RNA molecule has a total length of about 70 nucleotides.
`
`55.
`
`(Previously presented) The population of mammalian cells of claim 48, wherein
`
`the RNA polymerase promoter comprises a pol II promoter or a pol III promoter.
`
`56.
`
`(Previously presented) The population of mammalian cells of claim 55, wherein
`
`the pol III promoter comprises a U6, an HI, or an SRP promoter.
`
`57.
`
`(Previously presented) The population of mammalian cells of claim 55, wherein
`
`the pol II promoter comprises a Ul or a CMV promoter.
`
`58.
`
`59.
`
`60.
`
`(Cancelled)
`
`(Cancelled)
`
`(Currently amended) A mammalian cell stably transfected or stably transduced
`
`with an expression construct encoding a short hairpin RNA molecule, the expression construct
`
`compnsmg:
`
`(i)
`
`(ii)
`
`an RNA polymerase promoter, and
`
`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,
`
`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,
`
`wherein the double-stranded region of the short hairpin RNA molecule comprises a
`
`sequence that is complementary to a portion of a target gene in the mammalian cell, wherein the
`
`target gene is an endogenous gene of the mammalian cell, and
`
`wherein the short hairpin RNA is stably expressed in an amount sufficient to attenuate
`
`expression of the target gene in a sequence specific manner, an:d is ORJ9ressed iR the eell without
`
`use of a PKR inhibitor.
`
`61.
`
`(Previously presented) The mammalian cell of claim 60, wherein the expression
`
`construct further comprises L TR sequences located 5' and 3' of the sequence encoding the short
`
`hairpin RNA molecule.
`
`ACTIVEUS 90555450vl
`
`4
`
`Benitec - Exhibit 1022 -page 4
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`62.
`
`(Previously presented) The mammalian cell of claim 60, wherein the short hairpin
`
`RNA molecule comprises a double-stranded region consisting of at least 21 nucleotides.
`
`63.
`
`(Previously presented) The mammalian cell of claim 60, wherein the short hairpin
`
`RNA molecule comprises a double-stranded region consisting of at least 22 nucleotides.
`
`64.
`
`(Previously presented) The mammalian cell of claim 60, wherein the short hairpin
`
`RNA molecule comprises a double-stranded region consisting of at least 25 nucleotides.
`
`65.
`
`(Previously presented) The mammalian cell of claim 60, wherein the short hairpin
`
`RNA molecule comprises a double-stranded region consisting of 29 nucleotides.
`
`66.
`
`(Previously presented) The mammalian cell of claim 60, wherein the short hairpin
`
`RNA molecule has a total length of about 70 nucleotides.
`
`67.
`
`(Previously presented) The mammalian cell of claim 60, wherein the RNA
`
`polymerase promoter comprises a pol II promoter or a pol III promoter.
`
`68.
`
`(Previously presented) The mammalian cell of claim 67, wherein the pol III
`
`promoter comprises a U6, an HI, or an SRP promoter.
`
`69.
`
`(Previously presented) The mammalian cell of claim 67, wherein the pol II
`
`promoter comprises a Ul or a CMV promoter.
`
`70.
`
`71.
`
`(Cancelled)
`
`(Cancelled)
`
`ACTIVEUS 90555450vl
`
`5
`
`Benitec - Exhibit 1022 -page 5
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`In the Drawings
`
`Please replace Figures 2A-2D with the accompanying figures 2A-2C, which are marked
`
`"Replacement Sheet" in accordance with 37 C.F.R. § 1.121(d).
`
`ACTIVEUS 90555450vl
`
`6
`
`Benitec - Exhibit 1022 -page 6
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`REMARKS
`
`I.
`
`STATUS OF CLAIMS AND FORMAL MATTERS
`
`A.
`
`Amendments
`
`Claims 48-57 and 60-69 are pending and under examination. Claims 58, 59, 70, and 71
`
`are cancelled, and claims 48 and 60 are amended. Support for the target gene being an
`
`endogenous gene, as recited in claims 48 and 60, can be found at page 3, line 27, of the
`
`specification as filed. The amendment to claims 48 and 60, reciting that the shRNA is "stably"
`
`expressed, is supported at least by the preambles of claims 48 and 60.
`
`The specification is amended to delete the priority claim to International Application No.
`
`PCT/USOI/08435 and U.S. provisional application Serial Nos. 60/189,739 and 60/243,097. An
`
`amended Application Data Sheet accompanies this paper.
`
`Upon review of Figure 2, it has come to Applicant's attention that the transcripts depicted
`
`in Figure 2D were erroneously separated from Figures 2B and 2C. See, for example, the
`
`description of Figure 2B at page 10, lines 18-23, which refers to the "cross hatched box, below."
`
`The attached Replacement Sheet for Figure 2 includes the transcripts as originally intended, as
`
`part of Figures 2B and 2C.
`
`No new matter is added.
`
`B.
`
`Inventorship
`
`On June 16, 2011, Applicants filed a Request to Correct Inventorship Under 37 C.F.R.
`
`1.48(a) to add Douglas Conklin and Patrick J. Paddison, along with the documents required by
`
`37 C.F.R. 1.48(a). Applicants also filed on June 16, 2011 a Request to Amend Inventorship
`
`Under 37 C.F.R. 1.48(b)(l) to delete David H. Beach. Applicants request confirmation that these
`
`Requests have been granted.
`
`II.
`
`PRIORITY
`
`The Examiner states "the effective filing date for purposes of prior art to be 05/16/2008,
`
`which is the filing date of the instant application." The present application is a continuation of
`
`U.S. application Serial No. 10/055,797 ("the '797 application), with which it shares an identical
`
`ACTIVEUS 90555450vl
`
`7
`
`Benitec - Exhibit 1022 -page 7
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`disclosure. Priority to the '797 application under 35 U.S.C. § 120 was properly claimed in the
`
`present application. (See Utility Patent Application Transmittal, Section 18, filed on May 16,
`
`2008; page 1, line 3, of specification as filed on May 16, 2008; Oath or Declaration and
`
`Application Data Sheet filed on January 28, 2009 in response to Missing Parts.) As the
`
`disclosure of the present application is identical to that of the '797 application, Applicants are
`
`entitled to an effective filing date of January 22, 2002, the filing date of the '797 application.
`
`Acknowledgement of an effective filing date of January 22, 2002 is requested.
`
`III. WRITTEN DESCRIPTION REJECTION
`
`Claims 48-71 were rejected under 35 U.S.C. § 112, first paragraph, as allegedly lacking
`
`adequate written description. The Examiner asserted that the recitations "is a substrate for Dicer(cid:173)
`
`dependent cleavage" and "is expressed in the cells without the use of a PKR inhibitor" are new
`
`matter. The rejection is traversed.
`
`During an interview on March 22, 2011 with the Examiner, SPE Calamita, SPE Celsa,
`
`and SPE Woitach, Professor Nouria Hernandez, a Rule 132 Declarant on behalf of the
`
`Applicants, indicated that as one of ordinary skill in the art, the '797 application provides explicit
`
`and implicit written description support for the rejected recitations. A copy of the Interview
`
`Summary filed by Applicants on March 31, 2011 is attached. In view of the evidence set forth
`
`by Dr. Hernandez, this Examiner, in related U.S. application Serial No. 11/894,676 ("the '676
`
`application"), allowed claims that include the same two recitations.
`
`Reconsideration and withdrawal of the written description rejection are requested.
`
`IV.
`
`REJECTION UNDER 35 U.S.C. § 103 OVER SYMONDS, LIEBER, FIRE, GOOD,
`N OONBERG, AND ELBASHIR
`
`Claims 48-71 were rejected as allegedly being obvious over Symonds et al., Lieber et al.,
`
`Fire et al., Good et al., Noonberg et al., and Elbashir et al., as evidenced by McManus et al.
`
`Applicants traverse the rejection. This combination ofreferences would not make the claimed
`
`invention obvious to one of ordinary skill in the art at the time of the invention. And in fact,
`
`Elbashir et al. teaches away from the claimed invention, as discussed below and in Dr.
`
`Hernandez's 132 Declaration dated October 29, 2009 ("First Hernandez Declaration"), which
`
`was filed in U.S.S.N. 10/997,086 ("the '086 application") on February 26, 2010, and submitted
`
`ACTIVEUS 90555450vl
`
`8
`
`Benitec - Exhibit 1022 -page 8
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`in this application on December 23, 2010, and which the Examiner chose not to address. 3/18/11
`
`Office Action at 2. The cited references are not sufficient to make a prima facie case of
`
`obviousness for the reasons set out below.
`
`A.
`
`The State of the Art Prior to January 22, 20021
`
`In order to provide background to the views of a person of ordinary skill in the art, and
`
`background against which the present invention was made, Applicants provide below a brief
`
`summary of the state of the art regarding gene silencing using RNA molecules. This summary is
`
`not to be considered an admission that any reference set out below is proper prior art as to the
`
`presently claimed invention.
`
`1.
`
`Dr. Hannon 's Goal: Exploiting RNAi to Study Gene Function in
`Mammalian Cells
`
`By the invention of the short hairpin technology described in the Hannon application, Dr.
`
`Hannon and his co-inventors successfully achieved an ambitious goal of exploiting RNAi as a
`
`powerful and widely applicable genetic tool to study gene function in mammalian cells. In
`
`particular, this novel approach allowed one to use RNAi to stably attenuate expression of the
`
`target gene in a sequence specific manner in a mammalian cell, without activating a non(cid:173)
`
`sequence specific PK response. To achieve this goal, Dr. Hannon and his co-inventors focused
`
`on identifying and understanding the cellular machinery that mediated RNAi in the cell. A key
`
`part of their work involved identifying and characterizing the components of the RNAi pathway.
`
`Among other things, Dr. Hannon and his co-inventors isolated and described two critical
`
`components of the RNAi machinery: the enzyme Dicer, which the inventors named and
`
`demonstrated as mediating the processing of double-stranded RNA ( dsRNA) (Bernstein et al.
`
`Nature, 2001), and "RISC", the nuclease complex responsible for degradation of target mRNAs.
`
`Dr. Hannon concisely summarized his overall strategy in a grant proposal for the work he
`
`subsequently carried out:
`
`My laboratory has devoted a number of years to creating improved
`tools for probing gene function in cultured mammalian cells;
`however, our experience indicates that a facile loss-of-function
`tool is lacking. Unfortunately, dsRNA induces somewhat generic
`
`1 As discussed in Section II, January 22, 2002 is the filing date of the parent '797 application, of which the present
`application is a continuation.
`
`ACTIVEUS 90555450vl
`
`9
`
`Benitec - Exhibit 1022 -page 9
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`responses in mammalian cells. It is our hope that by understanding
`the mechanistic basis of dsRNA-induced silencing, we may not
`only unravel a mysterious and important piece of biology but also
`provide the means to create improved tools for analyzing gene
`function in diverse organisms in which traditional genetic methods
`are either cumbersome or unavailable. This notion that has
`contributed to the decision to focus substantial effort in my
`laboratory toward elucidating the mechanism of RNA
`interference ...
`
`. . .In this application, we propose a biochemical approach to
`deciphering the mechanisms that underlie dsRNA-induced gene
`silencing. RNA-interference allows an adaptive defense against
`both exogenous and endogenous dsRNAs, providing something
`akin to a dsRNA immune response. The primary goal of the work
`proposed in this application is to understand the mechanisms by
`which a cell can raise this response. We have presented evidence
`that RNA interference is accomplished, at least in part, through the
`action of a sequence-specific nuclease that is generated in response
`to dsRNA. Our data, and that of others (Hamilton and Baulcombe,
`1999), is consistent with a model in which dsRNAs present in a
`cell are converted, in a manner analogous to antigen processing,
`into discrete, small RNAs that guide the nuclease in the choice of
`substrate. We propose to purify and characterize the nuclease and
`to clone the protein and RNA components of the enzyme. In
`addition, we propose to develop approaches that may allow the use
`of cultured Drosophila cells as a general tool for probing gene
`function. The combination of these studies may lead eventually to
`an ability to harness RNA interference as a genetic tool in other
`organisms, particularly mammals, in which analogous tools are
`presently lacking.
`
`2.
`
`Dicer Cleaves Long dsRNA to Make Guide RNAs or siRNAs
`
`Hannon and his co-inventors demonstrated that Dicer processes long dsRNAs into short
`
`(approximately 21-25 nt) RNAs, which are referred to as short interfering RNAs (siRNAs) or
`
`"guide" RNAs, the term coined by Dr. Hannon. Bernstein et al. Nature 409: 363-366 (2001).
`
`The siRNAs are then incorporated into a protein (nuclease) complex called the RNA-induced
`
`silencing complex (RISC) Hammond et al., Nature 404:293-296 (2000). The siRNAs function
`
`to guide the RISC/siRNA complex to specific mRNAs, which are recognized through base
`
`pairing interactions by having a complementary sequence to the siRNA, and are then destroyed
`
`by RISC. Through this process, guide RNAs or siRNAs can inhibit gene expression by
`
`ACTIVEUS 90555450vl
`
`10
`
`Benitec - Exhibit 1022 -page 10
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`targeting destruction of specific mRNAs in the cell. Notably, the ability of long dsRNAs to
`
`trigger RNAi, therefore, requires Dicer to first cleave or process the long dsRNA into guide or
`
`siRNAs. Bernstein et al. Nature 409: 363-366 (2001); Hammond et al., Nature Rev. Genetics
`
`2:110-119.
`
`3.
`
`Pre-Dicer and Post-Dicer Strategies to Achieve RNAi
`
`Dr. Hannon's work in discovering Dicer and the mechanism of Dicer processing
`
`demonstrated that one could potentially intervene in the RNAi pathway in two places.
`
`I Pre-Dicer
`Long dsRNA
`
`I Post-Dicer I
`siRNA
`
`(I) A Pre-Dicer strategy (see Pre-Dicer Pathway in above diagram) starts with long
`
`dsRNA triggers (see "Long dsRNA" in diagram above). Fire et al. demonstrated that long
`
`dsRNAs (for example, 300-500 bp) could effect gene silencing. Once introduced into a cell,
`
`these long dsRNA triggers are cleaved into siRNAs by Dicer. The siRNAs then combine with
`
`RISC to mediate specific gene silencing.
`
`ACTIVEUS 90555450vl
`
`11
`
`Benitec - Exhibit 1022 -page 11
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`(II) A Post-Dicer strategy (see Post-Dicer Pathway above) uses short RNAs that mimic
`
`the siRNA products of Dicer cleavage (i.e., 21-25 nucleotide long short RNAs with 3'
`
`overhangs). Once introduced into a cell, the siRNAs bypass the Dicer enzyme altogether. The
`
`siRNAs directly combine with RISC to effect gene silencing. Elbashir SM, Lendeckel W,
`
`Tuschl T (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev
`
`15(2):188-200. Elbashir et al. has been discussed in the First Hernandez Declaration filed in this
`
`case on December 23, 2010. In this regard, Elbashir et al. included data showing that dsRNAs of
`
`30 nucleotides in length or shorter were ineffective in mediating RNAi and would not work as
`
`Pre-Dicer triggers. Short RNAs would work only if they were designed to bypass Dicer
`
`processmg.
`
`4.
`
`Fire and Elbashir Fail to Show Stable, Long Term Silencing
`
`Fire's approach of using long dsRNA as a pre-Dicer trigger failed to show how one could
`
`use this strategy in mammalian cells. 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.
`
`(Williams, B. R. Role of the double-stranded RNA-activated protein kinase (PKR) in cell
`
`regulation. Biochem. Soc. Trans. 25, 509-513 (1997).) This innate anti-viral pathway would
`
`have taught away from using dsRNA for silencing expression of a particular gene in a
`
`mammalian cell.
`
`Another approach was taken by Elbashir-using post-Dicer triggers, that is, siRNAs to
`
`achieve inhibition of gene expression. One primary drawback of this approach is that the effect
`
`is only transient. The application of siRNAs (see the post-Dicer pathway in the above diagram)
`
`is transitory. Once the siRNAs are applied exogenously into the cell, processed by Dicer and
`
`then complexed with RISC, there is no additional effect. This Post-Dicer approach using
`
`siRNAs will only temporarily silence genes.
`
`These two approaches (Pre-Dicer and Post-Dicer) did not provide for stable, long term
`
`silencing in mammalian cells. Therefore, the pre-Dicer and post-Dicer approaches were of
`
`limited benefit in mammalian cells. Stable, long term silencing was necessary to carry out
`
`studies in mammalian cells to understand the genetic basis of human disease that Dr. Hannon
`
`envisioned. Before RNAi could be harnessed as a tool for silencing specific genes in
`
`mammalian systems, such as in methods claimed in the present invention, a considerable hurdle
`
`ACTIVEUS 90555450vl
`
`12
`
`Benitec - Exhibit 1022 -page 12
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`had to be overcome. The problem was how to trigger RNAi in a gene-specific manner in
`
`mammalian cells without invoking non-specific anti-viral responses to the RNAi trigger.
`
`B.
`
`Invention of Hannon et al. Using Expressed shRNA in Mammalian Cells
`
`1.
`
`Explanation of the Invention
`
`Hannon demonstrated that one could actually engineer a pre-Dicer trigger that would not
`
`activate the anti-viral/PKR response, that could be stably expressed in the mammalian cell and
`
`surprisingly, would function as a potent trigger to specifically silence gene expression in
`
`mammalian cells. The presently claimed invention solves the problems of stable expression,
`
`avoidance of the PKR response and sequence-specific inhibition of gene expression in
`
`mammalian cells. The diagram below illustrates the shRNA expression vector approach, which
`
`is claimed by the applicants.
`
`ACTIVEUS 90555450vl
`
`13
`
`Benitec - Exhibit 1022 -page 13
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`The above diagram shows the introduction of shRNA expression vectors into the
`
`mammalian cell. These vectors can be stably expressed in a mammalian cell and don't activate
`
`the PKR response. The vectors express a short hairpin RNA molecule which is a substrate for
`
`Dicer-dependent cleavage and does not activate the PKR response. The double-stranded region
`
`of the short hairpin RNA molecule comprises a sequence that is complementary to a portion of
`
`the target gene.
`
`Thus, the entirely different approach of Elbashir-that of using post-Dicer triggers which
`
`could act to silence gene expression without being processed by Dicer taught away from
`
`Hannon's invention of using stable expression of short hairpin RNAs as pre-Dicer triggers to
`
`suppress mammalian gene expression.
`
`2.
`
`Industry Acclaim for the Invention
`
`As evidenced by numerous awards and by the adoption of his short hairpin technology as
`
`a fundamental biomedical research tool, Dr. Hannon's pioneering work in the RNAi field has
`
`received widespread acclaim. In 2005, Dr. Hannon received the Award for Outstanding
`
`Achievement in Cancer Research from the American Association for Cancer Research (AACR),
`
`which honored Dr. Hannon " ... for his work uncovering the biochemical mechanism of RNA
`
`interference of gene expression (RNAi) and his contributions to the discovery and development
`
`of short hairpin RNAs as tools for genetic manipulation of mammalian cells." (See Declaration
`
`Under 37 C.F.R. §1.131, Exhibit 0). In 2007, Dr. Hannon received two more prestigious
`
`awards, the Award in Molecular Biology from the National Academy of Sciences, and the Paul
`
`Marks prize for the valuable contribution his RNAi work to cancer research from Memorial
`
`Sloan-Kettering Cancer Center (See Declaration Under 37 C.F.R. §1.131, Exhibit Q). In
`
`granting that award, MSKCC noted how Dr. Hannon had applied his research in understanding
`
`the RNAi pathway to develop this valuable new technology, and his recognition as a leader in
`
`the field:
`
`Dr. Hannon is a leader in the relatively new field of RNA
`interference (RNAi). RNAi is a naturally occurring mechanism for
`regulating the expression of genes (controlling which genes are
`turned on and turned off in cells). In the laboratory, it is used as a
`tool to study the function of specific genes, and it's being
`investigated as a therapeutic approach for treating many different
`diseases, including cancer.
`
`ACTIVEUS 90555450vl
`
`14
`
`Benitec - Exhibit 1022 -page 14
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`Dr. Hannon's laboratory has elucidated key biochemical details of
`the components of the pathways involved in RNAi and is using
`these findings to develop molecular tools that can be used for gene
`discovery, the evaluation of gene function, and the generation of
`animal models. He has developed new techniques for using RNAi
`to study cancer development and is investigating possible cancer
`therapies that make use of small interfering RNAs (siRNAs).
`
`Dr. Hannon discovered several proteins and enzymes that are an
`essential part of the RNAi mechanism, including Dicer, which
`cleaves double-stranded RNA into siRNAs; the RISC complex,
`which helps regulate protein translation and is involved in the
`body's defense against viral infections; and Argonaute2, which
`cleaves messenger RNA.
`
`He also has been at the forefront of adapting RNAi techniques to
`study genes in mammals, and using these techniques to understand
`the variety of pathways that can lead to the formation of tumors.
`
`The presently claimed invention described in the Hannon application was the basis for
`
`various shRNA libraries, which have become widely used tools for genetic analysis in
`
`mammalian cells. Reflecting the valuable contribution of this technology to biomedical research,
`
`during 2002-2006, Dr. Hannon was among the top five most highly cited scientists with the
`
`highest number of high impact papers in the field of molecular biology and genetics. The 2002
`
`Genes & Development paper, "Short hairpin RNAs (shRNAs) induce sequence-specific
`
`silencing in mammalian cells," in which Dr. Hannon reported much of the work underlying the
`
`presently claimed invention, was cited more than 500 times, including more than 100 papers in
`
`the biotechnology field (See Declaration Under 37 C.F.R. §1.131, Exhibits K, Mand N).
`
`C.
`
`Second Declaration of Professor Hernandez Under 37 C.F.R. §1.132
`
`The First Hernandez Declaration provides evidence that a person of ordinary skill in the
`
`art would not have had a reasonable expectation of success at using a shRNA with a double
`
`stranded region of between 20 and 29 nucleotides in length. The art ofrecord would not make
`
`obvious the claimed invention and would not provide any basis for a person of ordinary skill in
`
`the art at the time (note that Prof. Hernandez was such a person of ordinary skill in this art at that
`
`time) to believe the claimed invention would have been obvious. The Second Declaration of
`
`Professor Hernandez Under 35 U.S.C. § 1.132 ("Second Hernandez Declaration), filed in the
`
`'676 application on January 31, 2011 and submitted herewith, provides further evidence of the
`
`ACTIVEUS 90555450vl
`
`15
`
`Benitec - Exhibit 1022 -page 15
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`non-obviousness of the claimed invention. Dr. Hernandez's Curriculum vitae (CV) is also
`
`submitted herewith.
`
`As Applicants have stated previously, Professor Hernandez is providing the opinion of a
`
`person of ordinary skill in the art, which is different than an expert opinion. The opinion of a
`
`person of ordinary skill in the art at the critical time is a fact to be considered in an obviousness
`
`analysis. Prof. Hernandez was an Investigator at the Howard Hughes Medical Institute at the
`time working in the area of RNA and studying RNA polymerase III. (See at least iJ 3 of the
`Second Hernandez Declaration and Prof. Hernandez's CV.) She was aware ofElbashir et al. at
`
`the time. Unlike a retrospective expert opinion, the Declarations are based on the personal
`
`knowledge of Prof. Hernandez testifying as a person of ordinary skill in the art at that time. The
`
`statements of Professor Hernandez are therefore factual evidence that must be taken into account,
`
`and not expert opinion as discussed in MPEP 716.0l(c).
`
`As a person of ordinary skill in the art, Prof. Hernandez has testified that the Elbashir
`
`paper teaches away by discouraging one of skill from pursuing the claimed invention. The
`
`evidence is overwhelming that Elbashir et al. teaches away from the claimed invention. See
`iii! 9-15 of Second Hernandez Declaration. Figure 1 b of Elbashir reports that dsRNAs of 29bp
`and 30bp in length failed to mediate RNAi (bars indicating that the effect of both 29bp and 30bp
`
`was equivalent to controls). Further, there is no evidence whatsoever in Elbashir that dsRNAs
`
`shorter than 29bp were effective as pre-Dicer triggers. Such an inference has no scientific
`
`support. Moreover, the expectation of one of ordinary skill in the art at the time, for example, in
`
`view of the conservation across species of the RNAi machinery (see Bernstein et al, Nature 409,
`
`363-366 (2001)), was that the negative results provided by Elbashir et al. in insect cells would
`
`also apply to the use of short hairpin RNA in mammalian cells. It would have been backwards
`
`and contrary to the Elbashir paper's text for a person of ordinary skill in the art to interpret the
`
`negative results in Elbashir as providing any reasonable expectation that one could have
`
`achieved gene silencing by stably expressing a short hairpin RNA in mammalian cells. (See
`Second Hernandez Declaration, iJ 15.) Instead, the Elbashir et al. paper and the state of the art
`"would have taught away from using short hairpin RNAs in mammalian cell types." (Id.)
`
`Rebuttal evidence can be submitted by way of a declaration and the entire situation
`
`regarding patentability must be reviewed in view of the new evidence. (See 37 C.F.R. §1.132
`
`ACTIVEUS 90555450vl
`
`16
`
`Benitec - Exhibit 1022 -page 16
`
`

`
`Application No. 12/152,837
`Attorney Docket No. 0287000-127.US2
`
`and M.P.E.P. § 2141.) In particular, whenever an applicant submits additional evidence, the
`
`Examiner must reconsider patentability of the claimed invention, and any decision to maintain a
`
`rejection must show it was based on the totality of the evidence. (Id.) "Facts established by the
`
`rebuttal evidence must be evaluated along with the facts on which the conclusion of obviousness
`
`was reached, not against the conclusion itself." M.P.E.P. 2142 (citing In re Eli Lilly & Co., 902
`
`F.2d 943 (Fed. Cir. 1990))(emphasis added). "Consideration ofrebuttal evidence and arguments
`
`requires Office personnel to weigh the proffered evidence and arguments. Office personnel
`
`should avoid giving evidence no weight, except in rare circumstances." (See In re Alton, 76 F.3d
`
`1168, 1174-75, 37 USPQ2d 1578, 1582-83 (Fed. Cir. 1996).)
`
`Here, applicants have met their burden by providing rebuttal evidence via the First and
`
`Second Hernandez Declarations, a person of ordinary skill in the art at the time, including her
`
`testimony on how a person of ordinary skill in the art would have viewed the state of the art and
`
`the non-obviousness of the claimed invention. Applicants reiterate that Prof. Hernandez is not
`
`offering an expert opinion, but is offering the opinion of a person who was a person of ordinary
`
`skill in the art, and thus the opinion of Prof. Hernandez is a fact that must be considered in
`
`carrying out a paten