Ex Parte Zernicka-Goetz et al

Patent Trial and Appeal Board

Aug 28, 2014

11933153 (P.T.A.B. Aug. 28, 2014)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
11/933,153 10/31/2007 Magdalena Zernicka-Goetz KILBURN1100-5 3318
7590 08/28/2014
Lisa A. Haile, J.D., Ph.D.
DLA PIPER US LLP
Suite 1100
4365 Executive Drive
San Diego, CA 92121-2133
EXAMINER
GIBBS, TERRA C
ART UNIT PAPER NUMBER
1674
MAIL DATE DELIVERY MODE
08/28/2014 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte MAGDALENA ZERNICKA-GOETZ, FLORENCE WIANNY,
MARTIN JOHN EVANS, and DAVID MOORE GLOVER
__________

Appeal 2012-010432
Application 11/933,153
Technology Center 1600
__________

Before DEMETRA J. MILLS, ERIC B. GRIMES, and
ROBERT A. POLLOCK, Administrative Patent Judges.

MILLS, Administrative Patent Judge.

DECISION ON APPEAL

This is an appeal under 35 U.S.C. § 134. The Examiner has rejected
the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b).

STATEMENT OF CASE
According to the Specification, page 1 ¶ [0002], “[t]he present
invention relates to inhibiting gene expression. In particular, it relates to
inhibiting gene expression in mammals using double stranded RNA
(dsRNA).”

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The following claim is representative.
1. An in vivo RNA interference method for inhibiting the expression
of a target gene in a mammalian cell, the method comprising:
introducing into the cell an RNA interference molecule comprising a
double stranded structure having a nucleotide sequence which is substantially
identical to at least a part of the target gene and which is derived from an
endogenous template, wherein the cell is an oocyte, or a cell of an early
embryo, and
verifying inhibition of expression of the target gene in the cells to
which the RNA interference molecule was introduced, wherein inhibition can
be observed at least four days after introduction of the RNA interference
molecule.

Examiner Cited References

(“Fire PCT”) WO 99/32619 July 1, 1999

Barlow et al., Interferon synthesis in the early post-implantation mouse
embryo, 27 DIFFERENTIATION 229-235 (1984).

Haggarty et al., An embryonic DNA-binding protein specific for a region of
the human IFNβ1 promoter, 16 NUCLEIC ACIDS RESEARCH 10575-10592
(1988).

Mary Kay Francis & John M. Lehman, Control of β-Interferon Expression in
Murine Embryonal Carcinoma F9 Cells, 9 MOL. CELL. BIOL. 3553-3556
(1989).

Harada et al., Absence of the Type I IFN System in EC Cells: Transcriptional
Activator (IRF-1) and Repressor (IRF-2) Genes Are Developmentally
Regulated, 63 CELL 303-312 (1990).

Asangla Ao & Robert P. Erickson, Injection of Antisense RNA Specific for
E-Cadherin Demonstrates That E-Cadherin Facilitates Compaction, the
First Differentiative Step of the Mammalian Embryo, 2 ANTISENSE
RESEARCH AND DEVELOPMENT 153-163 (1992).

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Fire, RNA-triggered gene silencing, 15 TRENDS IN GENETICS 358-363
(1999).

Appellants’ Cited Art

Sharp, RNAi and double-strand RNA, 13 GENES & DEVELOPMENT 139-141
(1999).

Caplen et al., dsRNA-mediated gene silencing in cultured Drosophila cells:
a tissue culture model for the analysis of RNA interference, 252 GENE 95-
105 (2000).

Silva et al., RNA interference: a promising approach to antiviral therapy? 8
TRENDS IN MOLEC. MED. 505-508 (2002).

Grounds of Rejection
Claims 1–11, 13, 14, 18–20, 22, and 23 are rejected under 35 U.S.C.
§ 103(a) as being unpatentable over WO 99/32619 (Fire PCT) in view of
Fire and Ao.

FINDINGS OF FACT
The Examiner’s findings of fact are set forth in the Answer at pages
3–14. The following facts are highlighted.
1. The Examiner finds that
With regard to claim 1, WO 99/32619 teaches the use
of dsRNA to inhibit expression of a target gene in a cell.
It exemplifies RNA-mediated inhibition of target genes
in C. elegans. It further discloses the use of dsRNA to
inhibit expression of a target gene in a mammalian cell
such as a mouse, rat and human (page 12, lines 3-8 and
20).

(Ans. 5.)
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2. The Examiner finds that

Fire explicitly teaches:

“Even if the underlying mechanisms are absent in
mammals, it is possible that RNA-triggered silencing will
have clinical applications”.

“Any gene-specific dsRNA response in mammals would
need to exist in cells or conditions where PKR is less
effective, or would need to work in the shadow of the
PKR-induced global response”

(Ans. 6.)

3. Table 1 of Barlow is reproduced below.

“Table 1 shows both constitutive and induced interferon synthesis in
separate tissues of the embryo and the maternal tissues enclosing the
developing embryo at the early 7th, late 7th and 8th day of development.”
(Page 231, col. 2.)

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4. According to Barlow,
1. Induced synthesis [of interferon] is initially absent
in most tissues of the early 7th-day embryo, with the
exception of the trophoblast, which shows a low level
(33%) of inducible synthesis. It should also be noted that
control virus-induced maternal tissues early in the 7th
day showed a reduced level of induced synthesis [of
interferon] compared to the late 7th and early 8th day of
development (approximately 35%, compared to greater
than 70% at later stages.) These results were seen in two
separate assays of early 7th-day material obtained from
different matings.

2. Induced synthesis is developmentally regulated,
reaching high levels in late 7th-day and early 8th day
embryos in tissues which initially showed nil or low
levels of induction . . . . By the early 8th day, all tissues,
with the exception of the visceral extra-embryonic
endoderm . . . and the embryonic ectoderm . . ., could be
induced to produce interferon.

(Page 231, col. 2.)
5. According to the Specification, page 3 ¶ [0006], “[p]art of the interferon
response is the activation of a dsRNA responsive protein kinase (PKR)
(Clemens, Int J Biochem Cell Biol 29, 945-949 (1997)).”
6. According to the Specification, page 15 ¶ [0038], “[t]he cell may be any
individual cell of the early embryo, and may be a blastocyte. Alternatively,
it may be an oocyte.”
7. Example 4 of the Specification, page 30 ¶ [0083], states that, “dsRNA to
E-cadherin was microinjected into one cell of a two cell stage mouse
embryo . . . .”

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Discussion
ISSUE
The Examiner concludes from the cited evidence that
It would have been prima facie obvious to one of
ordinary skill in the art, at the time the invention was made to
devise an in vivo RNA interference method for inhibiting the
expression of a target gene in a mammalian cell using the
teachings of WO 99/32619. It would have been prima facie
obvious to one of ordinary skill in the art, at the time the
invention was made to have the mammalian cell be an oocyte or
cells of an early embryo using the teachings and motivation of
WO 99/32619 and Fire.
One of ordinary skill in the art would have been
motivated to devise an in vivo RNA interference method for
inhibiting the expression of a target gene in a mammalian cell
since WO 99/32619 and Fire taught that such a method could
have clinical applications. One of ordinary skill in the art would
have been motivated to have the mammalian cell be an oocyte
or cells of an early embryo since Fire taught that in cells void of
the interferon response, RNAi would be successful, and at the
time of invention, these two cell types were known to be
incapable of the PKR response. See the evidence of Haggarty
et al., Harada et al., Barlow et al., and/or Francis and Lehman.
One of ordinary skill in the art would have had a
reasonable expectation of success of devising an in vivo RNA
interference method for inhibiting the expression of a target
gene in a mammalian cell since WO 99/32619 generally taught
such a method and Fire taught that RNAi would successfully
work in cells where the interferon response is less effective.
One of ordinary skill in the art would have been well aware that
oocytes and cells of the early embryo are examples of such cells
since it was known that these cells are void of the interferon or
PKR response.
One of ordinary skill in the art would have had a
reasonable expectation of success of observing inhibition of the
expression of the target gene at least four days after
introduction of the dsRNA since Ao et al. taught inhibition of
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the expression of the target gene at least four days after
introduction of an antisense RNA and KSR forecloses that the
simple substitution of one known element for another would
have yielded predictable results at the time of the invention.

(Ans. 8–9.)
Appellants assert that the perception at the time of the
filing of the present application was that RNAi cannot be made
to work in mammals. As such, one of ordinary skill in the art
would have no reasonable expectation of success in practicing
the claimed method of inhibiting the expression of a target gene
in a mammalian cell using a double stranded RNAi molecule.

(Br. 6.)

Appellants contend that, “Exhibits A-C[1], as well as the Fire Article
itself, clearly show that it is unequivocal that … skepticism existed in the art
for some years after its publication and such skepticism pervaded the art.”
(Br. 7.) Appellants conclude that
Based on the art-accepted skepticism as to the workability of
RNAi in mammals both at the time of the Fire references and in
recollections of Fire himself, clearly there could be no
reasonable expectation for one ordinarily skilled in the art of
successfully practicing RNA interference in mammalian cells as
claimed.

(Br. 9.) Finally, Appellants argue that the claimed subject matter is the
product of unexpected results and that the Examiner has engaged in
hindsight reconstruction of Appellants’ invention. (Br. 12.)

1 The references by Silva, Sharp, and Caplen, cited previously.
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The issue is: Does the Examiner’s cited evidence establish a prima
facie case of obviousness? If so, have Appellants rebutted the Examiner’s
prima facie case of obviousness by a preponderance of the evidence?

PRINCIPLES OF LAW
In making our determination, we apply the preponderance of the
evidence standard. See, e.g., Ethicon, Inc. v. Quigg, 849 F.2d 1422, 1427
(Fed. Cir. 1988) (explaining the general evidentiary standard for proceedings
before the Office). The Board “determines the scope of claims in patent
applications not solely on the basis of the claim language, but upon giving
claims their broadest reasonable construction ‘in light of the specification as
it would be interpreted by one of ordinary skill in the art.’” Phillips v. AWH
Corp., 415 F.3d 1303, 1316 (Fed. Cir. 2005) (quoting In re Am. Acad. of Sci.
Tech. Ctr., 367 F.3d 1359, 1364 (Fed. Cir. 2004).
“In rejecting claims under 35 U.S.C. § 103, the examiner bears the
initial burden of presenting a prima facie case of obviousness. Only if that
burden is met, does the burden of coming forward with evidence or
argument shift to the applicant.” In re Rijckaert, 9 F.3d 1531, 1532 (Fed.
Cir. 1993) (citations omitted). In order to determine whether a prima facie
case of obviousness has been established, we consider the factors set forth in
Graham v. John Deere Co., 383 U.S. 1, 17 (1966): (1) the scope and content
of the prior art; (2) the differences between the prior art and the claims at
issue; (3) the level of ordinary skill in the relevant art; and (4) objective
evidence of nonobviousness, if present.
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“The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).

ANALYSIS
We find that the Examiner has provided evidence to support a prima
facie case of obviousness. In particular, Fire PCT generally teaches “the use
of dsRNA to inhibit expression of a target gene in a cell. It exemplifies
RNA-mediated inhibition of target genes in C. elegans. It further discloses
the use of dsRNA to inhibit expression of a target gene in a mammalian cell
such as a mouse, rat and human (page 12, lines 3-8 and 20).” (Ans. 5.)
Fire suggests that due to the vehement response of mammals to
dsRNA “[a]ny gene-specific dsRNA response in mammals would need to
exist in cells or conditions where PKR is less effective, or would need to
work in the shadow of the PKR-induced global response.” (Fire, page 363,
col. 1.) According to the Specification, page 3, it is known that “[p]art of the
interferon response is the activation of a dsRNA responsive protein kinase
(PKR) (Clemens, Int J Biochem Cell Biol 29, 945-949 (1997)).” Thus, Fire
would reasonably appear to suggest that to avoid the vehement response of
mammals to dsRNA one of ordinary skill in the art should select a cell
where the PKR response and interferon response is less effective.
The Examiner asserts that, “the lack of a PKR response in
undifferentiated cells was known well before the priority date of the instant
application,” citing Haggarty, Harada, Barlow, and Francis to support this
position. (Ans. 6.)
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Barlow, in particular, “tested the competence of early embryonic and
associated maternal tissues to synthesise interferon” (page 229, col. 1) and
evidences that
Induced synthesis [of interferon] is initially absent in
most tissues of the early 7th-day embryo, with the exception of
the trophoblast, which shows a low level (33%) of inducible
synthesis. It should be also noted that control virus-induced
maternal tissues in the 7th day showed a reduced level of
induced synthesis [of interferon] compared to the late 7th and
early 8th day of development . . . .

(Page 231, col. 2.) For a dsRNA introduced at day 1 or day 2 of
development, four days after introduction of the dsRNA (as claimed) would
be approximately day 6 of embryonic development.
Barlow suggests that induced synthesis of interferon is initially absent
in most tissues of the early 7th day mouse embryo and that induced synthesis
of interferon is developmentally regulated. (Page 231, col. 2.) From this,
one of ordinary skill in the art would understand that on day 6 of embryonic
development, the induced synthesis of interferon would be at least reduced
compared to older embryos, if not completely absent. One of ordinary skill
in the art would also have understood that because the interferon response is
reduced or absent there would be little or no PKR response (FF5), and no
vehement response to dsRNA, and therefore an introduced dsRNA would
not be prevented from inhibiting a target gene.
Thus, consistent with the suggestion in Fire and Barlow, a day six
embryo would have been recognized by those of ordinary skill in the art as a
cell “or conditions where PKR is less effective.” (FF2.) Therefore, we find
that the Examiner has presented a prima facie case of obviousness.
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“[W]hen a prima facie case is made, the burden shifts to the applicant
to come forward with evidence and/or argument supporting patentability.”
In re Glaug, 283 F.3d 1335, 1338 (Fed. Cir. 2002). Rebuttal evidence is
“merely ‘a showing of facts supporting the opposite conclusion.’” In re
Piasecki, 745 F.2d 1468, 1472 (Fed. Cir. 1984).
In rebuttal, Appellants assert that the perception at the time of the
filing of the present application was that RNAi cannot be made to work in
mammals. As such, one of ordinary skill in the art would have no
reasonable expectation of success in practicing the claimed method of
inhibiting the expression of a target gene in a mammalian cell using a double
stranded RNAi molecule. (Br. 6.) Appellants contend that “Exhibits A-C[2],
as well as the Fire Article itself, clearly show that it is unequivocal that this
skepticism existed in the art for some years after its publication and such
skepticism pervaded the art.” (Br. 7.)
We are not persuaded. Appellants have requested consideration of
three references as evidence that skepticism existed for several years after
the Fire publication. (Br. 7.) Appellants characterize the references as
follows:
1) Silva et al. . . . state that “[T]he use of RNAi as an
experimental or therapeutic tool in mammalian systems was
initially problematic owing, ironically, to the presence of an
endogenous antiviral response”. See column 1, page 506.

2) Sharp . . . state that “[I]n vertebrate systems, dsRNA
was long ago recognized as a potent signaling molecule in the

2 The references by Silva, Sharp and Caplen, cited previously.
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induction of interferons and execution of the antiviral state.”
See column 1, page 141.

3) Caplen et al. . . . introduced dsRNA molecules into
mammalian tissue culture cells from three different species:
human, hamster, and mouse but failed to produce any evidence
for RNAi. Instead, they found that the dsRNAs produced either
no effect, or a non-specific decrease in gene expression. See id
at 102, section 3.6 and Fig. 7.

(Br. 7.) While Silva agrees with Fire that “dsRNA activates Protein Kinase
R (PKR) and RNase L pathways, leading to . . . apoptosis” (Silva, page 506,
col. 1), for the reasons discussed above, a skilled artisan would not expect an
early (pre-day 7) embryo to synthesize interferon or produce a PKR
reaponse. Sharp further acknowledges the teachings of Fire that “[i]n
vertebrate systems, dsRNA was long ago recognized as a potent signaling
molecule in the induction of interferons and execution of the antiviral state.”
(Sharp 141, col. 1) Caplen also recognizes a response to dsRNA in
mammalian cells is mediated by PKR. (Page 96, col. 1.) However, none of
the cited references evidences that there would be a dsRNA interferon
response in cells which do not present a PKR response. In other words,
acknowledgement of the known PKR response to dsRNA in the cited
references would not lead those skilled in the art to doubt the success of
obtaining a dsRNA response in cells without a PKR response, as suggested
by Fire.
In KSR, the Supreme Court addressed the “obvious to try” issue:
When there is a design need or market pressure to solve a
problem and there are a finite number of identified, predictable
solutions, a person of ordinary skill has good reason to pursue
the known options within his or her technical grasp. If this
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leads to the anticipated success, it is likely the product not of
innovation but of ordinary skill and common sense. In that
instance the fact that a combination was obvious to try might
show that it was obvious under § 103.

KSR, 550 U.S. at 421.

In the present case, the finite, predictable solution is that it is known
that early embryo cells do not evidence a PKR/interferon response (Barlow).
Since Fire suggests that a gene-specific dsRNA response in mammals would
need to exist in cells or conditions where PKR is less effective, one of
ordinary skill in the art would have had a good reason to pursue the known
option of selecting an early embryo cell which exhibit a lessened (or absent)
PKR response to obtain effective dsRNA gene silencing. In the present
case, the use of early embryo cells with little or no PKR response, led to the
anticipated success. For this reason, we do not agree that Appellants have
presented evidence of an unexpected result (see Br. 12).
Appellants further argue that the Examiner has engaged in hindsight
and has used Appellants’ Specification as a blueprint to assemble the prior
art publications to arrive at the claimed method. (Br. 12.) Again we are not
persuaded. The suggestion to combine the cited references has come from
the disclosure of Fire, which would reasonably appear to suggest that one of
ordinary skill in the art select a cell where the PKR response and interferon
response is less effective. We find no evidence of hindsight here.
We acknowledge Appellants’ other arguments concerning Ao that
antisense oligonucleotides and dsRNA are not functional equivalents (Br.
10) and that Haggarty used embryonic carcinoma cells which vary
significantly from early embryo cells (Reply Br. 3–4) but do not find them
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convincing. We find that Haggarty is not necessary to support the rejection
of the Examiner, notwithstanding its disclosure that both embryonic
carcinoma cells and early embryos share the inability to produce interferon
(Haggarty, page 10576). Ao discloses that antisense DNA, RNA, or
oligonucleotides inhibit gene expression in mouse oocytes and
preimplantation embryos. (Ao, page 159.)
The Examiner primarily relied upon Ao et al. to teach
that after administration of an antisense oligonucleotide in the
preimplantation mouse embryo, expression of a target gene is
inhibited after four days when compared to control embryos.
This teaching provides one of skill in the art with a reasonable
expectation of success of observing inhibition of target gene
expression in a mammalian cell at least 4 days after
introduction of a nucleic acid inhibitor of gene expression as
instantly claimed. Therefore, all the functional elements of
Appellant’s claimed method are accounted for in the prior art
relied upon on the record.

(Ans. 13.)

The Examiner goes on to show that the induced interferon response is
absent in most tissues of the early 7th day mouse embryo (Barlow) and by
deduction, the embryo of Ao. While there are acknowledged differences
between antisense DNA, RNA or oligonucleotides, Ao groups them together
with respect to their ability to inhibit gene expression in mouse oocytes and
preimplantation embryos (e.g., those with no PKR/interferon response).
In view of the above, we conclude that Appellants have failed to rebut
the Examiner’s prima facie case of obviousness by a preponderance of the
evidence, and the obviousness rejection is affirmed.

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CONCLUSION OF LAW
The cited references support the Examiner’s obviousness rejection
which has not been rebutted by Appellants by a preponderance of the
evidence.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED

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