Ex Parte Ren et al

Patent Trial and Appeal Board

Dec 23, 2016

11992332 (P.T.A.B. Dec. 23, 2016)

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.
11/992,332 03/20/2008 Peifeng Ren 074021-0089-US (286725) 8303
123223 7590 12/28/2016
Drinker Biddle & Reath LLP (WM)
222 Delaware Avenue, Ste. 1410
Wilmington, DE 19801-1621
EXAMINER
DEVEAU ROSEN, JASON
ART UNIT PAPER NUMBER
1662
NOTIFICATION DATE DELIVERY MODE
12/28/2016 ELECTRONIC
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.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
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PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte PEIFENG REN, HEE-SOOK SONG,
YUWEN WANG, and JOHN McMILLAN
Appeal 2015-004371
Application 11/992,332
Technology Center 1600
Before JEFFREY N. FREDMAN, JOHN G. NEW, and
JOHN E. SCHNEIDER, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35U.S.C. § 134 involving claims to a method
for silencing or attenuating expression of at least one target gene in a plant.
The Examiner rejected the claims as drawn to an improper Markush group
and as failing to comply with the enablement and written description
requirements. We have jurisdiction under 35 U.S.C. § 6(b). We reverse.
Statement of the Case
Background
“Recently, small RNAs, 21—26 nucleotides, have emerged as
important regulators of eukaryotic gene expression. The known small
1 Appellants identify the Real Party in Interest as BASF Plant Science
GmbH (see App. Br. 1).
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Application 11/992,332
regulatory RNAs fall into two basic classes. One class of small RNAs is the
short interfering RNAs (siRNAs). These play essential roles in RNA
silencing” (Spec. 1:19-23). “One recently identified group of small RNAs
are known generically as short temporal RNAs (stRNAs) and more broadly
as micro-RNAs (miRNAs)” (Spec. 1:28—29). “In plants, miRNAs and trans­
acting (ta) siRNAs form through distinct biogenesis pathways, although they
both interact with target transcripts and guide cleavage” (Spec. 4:15—17).
The Specification teaches “an unfulfilled need for efficient methods
and compositions to achieve gene silencing in plants, especially for two and
more target genes. This goal is achieved by the present invention” (Spec.
7:30-32).
The Claims
Claims 1, 4, 6—12, 15—20, 23—34, 38, and 39 are on appeal. Claim 1 is
representative and reads as follows:
1. A method for silencing or attenuating expression of at
least one target gene comprising introducing or expressing in a
plant or a part thereof a chimeric ribonucleotide sequence
comprising a modified ta-siRNA sequence, wherein said
modified ta-siRNA sequence is modified from a natural ta-
siRNA sequence which comprises at least one microRNA
binding site and at least one phase region by:
a) replacing the at least one phase region of said natural
ta-siRNA sequence with a sequence which is substantially
complementary to said at least one target gene and is
heterologous to said natural ta-siRNA sequence; and
b) replacing the at least one micro RNA binding site of
said natural ta-siRNA sequence with the sequence of a
microRNA binding site which is substantially complementary
to the sequence of a microRNA present in a plant.
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The Issues
A. The Examiner rejected claims 4—7, 12, 25, 38 on the judicially-created
basis that they contain improper Markush grouping of alternatives (Ans. 2—
3).
B. The Examiner rejected claims 1, 4, 6-12, 15—20, 23—34, 38, and 39
under 35 U.S.C. § 112, first paragraph, scope of enablement (Ans. 3—11).
C. The Examiner rejected claims 1, 4, 6—12, 15—20, 23—34, 38, and 39
under 35 U.S.C. § 112, first paragraph, as failing to comply with the written
description requirement (Ans. 11—17).
A. Improper Markush grouping
The Examiner finds the “claims are drawn to different trans-acting
small interfering RNA (ta-siRNA) sequences or subsequences thereof
having different structures, and thus, are presumed to have different
functions” (Ans. 2).
Appellants contend:
Upon expression in a plant, ta-siRNAs interact with target
mRNAs and guide cleavage by the same mechanism as plant
microRNAs. Thus, it is evident that all ta-siRNAs, including
those recited in the present claims, when considered as wholes,
share a common utility, i.e. regulating accumulation of the
respective targeting mRNAs.
(App. Br. 11).
The issue with respect to this rejection is: Does the evidence of
record support the Examiner’s conclusion that claims 4—7, 12, 25, and 38
contain improper Markush groupings?
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Findings of Fact
1. The Specification teaches “by choice of the sequence
corresponding to a small RNA (e.g., microRNA sequence) for replacement
of the natural microRNA binding site the profile of silencing can be
modulated e.g., in a tissue or developmental specific way” (Spec. 12:31—33).
2. The Specification teaches:
For the specific ta-siRNA molecules disclosed herein the
microRNA binding site to be replaced is selected from the
group consisting of a) the binding site described by nucleotide
698 to 718 of SEQ ID NO: 1 ... t) the binding site described by
nucleotide 1022 to 1043 of SEQ ID NO: 20 ... A broad variety
of target genes can be modulated (e.g., silenced or attenuated)
by using the method of the invention, including genes in a plant
but also genes or plant infecting or eating pathogens, animals,
or even human.
(Spec. 11:28 to 12:19).
Principles of Law
A Markush claim contains an “improper Markush
grouping” if: (1) the species of the Markush group do not share
a “single structural similarity,” or (2) the species do not share a
common use. Members of a Markush group share a “single
structural similarity” when they belong to the same recognized
physical or chemical class or to the same art-recognized class.
Members of a Markush group share a common use when they
are disclosed in the specification or known in the art to be
functionally equivalent.
Supplementary Examination Guidelines for Determining Compliance With
35 U.S.C. 112 and for Treatment of Related Issues In Patent Applications,
76 Fed. Reg. 7162, 7166 (2011) (“Guidelines”).
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Analysis
We find that Appellants have the better position. The nucleic acid
sequences recited in the rejected claims are reasonably understood to belong
to the same recognized chemical class of ta-siRNA sequences that share a
nucleic acid backbone (FF 1). While the individual sequences differ because
they are drawn to different genes or different plants, all of the sequences
share the common use of modulating or silencing plant genes (FF 1—2). Our
reasoning is consistent with the Guidelines and with Harnisch, where the
CCPA reversed a rejection over compounds that shared a common function
as dyes and a common coumarin backbone. See In re Harnisch, 631 F.2d
716, 722 (CCPA 1980).
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that claims 4—7, 12, 25, and 38 contain improper Markush groupings.
B. 35 U.S.C. § 112, scope of enablement
The Examiner finds
the specification, while being enabling for a method for
silencing a target gene comprising introducing a modified ta-
siRNA sequence having SEQ ID NO: 20, does not reasonably
provide enablement for said method by introducing a modified
ta-siRNA sequence comprised of at least one miRNA binding
site and at least one phase region, or wherein the miRNA has
SEQ ID NO: 78.
(Ans. 3). The Examiner specifically finds
based on the breadth of the claims, the lack of appropriate
guidance, the nature of the invention, and the lack of working
examples, the skilled practitioner would be subject to undue
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trial and error experimentation in order to determine whether, in
fact, a modified ta-siRNA as broadly claimed could be used to
predictably silence at least one target gene.
(Ans. 8).
The issue with respect to this rejection is: Does the evidence of
record support the Examiner’s conclusion that the Specification does not
enable the full scope of the claimed invention?
Findings of Fact
Breadth of Claims
3. Claim 1 is drawn to silencing or attenuating the expression of a
target gene in a plant through expression of a modified ta-siRNA sequence
(see Claim 1).
Presence of Working Examples
4. The Specification teaches, in Example 2, a working example for
identification of plant ta-siRNA primary transcripts through datamining,
specifically identifying a
list of ta-siRNA primary transcripts identified through
datamining: Maize (SEQ ID NO: 1 ), Wheat (SEQ ID NO: 2),
Rice (SEQ ID NO: 3), Cotton (SEQ ID NO: 4), Soybean (SEQ
ID NO: 5), Canola (SEQ ID NO: 6), Sunflower (SEQ ID NO:
7), Barley (SEQ ID NO: 8), Tomato (SEQ ID NO: 9), Sorghum
(SEQ ID NO: 10), Spruce (SEQ ID NO: 11), Cocoa (SEQ ID
NO: 12), Grape (SEQ ID NO: 13), Lotus (SEQ ID NO: 14) and
Populus (SEQ ID NO: 15), Arabidopsis TASla (SEQ ID NO:
16), Arabidopsis TASlb (SEQ ID NO: 10 17), Arabidopsis
TASlc (SEQ ID NO: 18), Arabidopsis TAS2 (SEQ ID NO: 19)
and Arabidopsis TAS3 (SEQ ID NO: 20).
(Spec. 110:4—11).
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5. The Specification teaches, in Example 5, expression of a ta-
siRNA to downregulate phytoene desaturase gene expression in Arabidopsis,
specifically teaching that “all four engineered ta-siRNA/PDS constructs
targeting different regions of PDS mRNA were able to cause photo-
bleaching phenotypes” (Spec. 122:8—9).
6. Example 5 of the Specification further notes that “transgenic
plants expressing engineered ta-siRNA (TASla/PDSl) had a significantly
reduced PDS mRNA level compared to the wild-type Col-0 plants and the
transgenic plants expressing wild-type ta-siRNA (TASla)” (Spec. 124:3—5).
7. The Specification teaches, in Example 8, the ability of a ta-
siRNA to prevent regeneration in maize, where “miR390-directed ta-PDS
siRNA production inhibits plant regeneration. This is contributed by
endogenous miR390 because transgenic calli carrying RLM423 alone were
unable to regenerate” (Spec. 141:9-11).
Amount of Direction or Guidance Presented
8. The Specification teaches:
In general a ta-siRNAs can be identified by computer algorithm
based on scoring criteria. Preferably, said scoring criteria may
include the following eight criteria used:
1. 30%-52% GC content - Add 1 point for satisfying this
criterion.
2. Three or more A/Us at positions 15-19 (sense) - Add 1
point for each AIU for a total up to 5 points. At least 3 points
are required to be scored as positive (“+”) in the final output.
3. The absence of internal repeats or hairpins as
measured by a Tm< 20 degrees C. — Add 1 point for satisfying
this criterion.
4. A at position 19 (sense) - Add 1 point for satisfying
this criterion.
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5. A at position 3 (sense) - Add 1 point for satisfying this
criterion.
6. U at position 10 (sense) - Add 1 point for satisfying
this criterion.
7. No G/C at position 19 (sense) - Subtract 1 point for not
satisfying this criterion.
8. No G at position 13 (sense) - Subtract 1 point for not
satisfying this criterion.
(Spec. 47:28 to 48:5).
9. The Specification teaches:
The term “phase region” means a region of about 21
nucleotides, which is processed by Dicer from a ta-siRNA
primary transcript, and which preferably resembles substantial
complementarity to at least one plant endogenous gene. These
phases can be identified in general as follows (in
exemplification for a miR173 ta-siRNA): For ta-siRNA
formation by 5’ initiation such as miR173-guided ta-siRNA,
miR173 binds to its complementary site in the primary
transcript and mediates the cleavage of the transcript between
position 10 and 11 from 5’ end of miRI 73. From this cleavage
site, a series of about 21 nt phases of ta-siRNA are generated
via 5 ’ to 3 ’ direction involving a group of key enzymes such as
RDR6, SGS3 and Dicer. For ta-siRNA formation by 3 ’
initiation such as miR390-guided ta-siRNA, a similar process
applies except that the formation of ta-siRNA is via 3 ’ to 5 ’
direction starting from miR390 cleavage site.
(Spec. 49:21-31).
10. The Specification teaches that:
[Phase region] replacement can be done by various techniques
of cloning known to the person skilled in the art and for
examples described in in Maniatis . . . Preferably, said
replacement is done by a PCR-mediated mutation approach.
The sequence replacing the natural phase region shall be
substantially complementary to a target gene of interest, ft has
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been found that an absolute complementarity to the target gene
is not absolutely required to achieve efficient gene silencing or
attenuation.
(Spec. 52:11-22).
11. The Specification teaches that:
The method according to the invention is preferably employed
for the purposes of plant biotechnology for generating plants
with advantageous properties. Thus, the suitability of the plants
or their seeds as foodstuff or feeding stuff can be improved, for
example via a modification of the compositions and/or the
content of metabolites, in particular proteins, oils, vitamins
and/or starch. Also, growth rate, yield or resistance to biotic or
abiotic stress factors can be increased.
(Spec. 89:16-21).
State of the Prior Art and Unpredictability of the Art
12. Yoshikawa2 teaches “[tjrans-acting small interfering RNAs
(tasiRNAs) are plant-specific endogenous siRNAs that control non-identical
mRNAs via cleavage. . . . tasiRNA production is a model system of
secondary siRNA production in plants. This review focuses on the
production of tasiRNAs that are endogenous secondary siRNAs”
(Yoshikawa, abstract).
13. Yoshikawa teaches that “[wjhile TAS3 and miR390 are well
conserved in moss and higher plants, the other TAS loci and their trigger
miRNAs are unique in Arabidopsis” (Yoshikawa 79, col. 1).
2 Yoshikawa, M., Biogenesis of trans-acting siRNAs, endogenous secondary
siRNAs in plants, 88 Genes Genet. Syst. 77-84 (2013).
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14. Allen3 teaches “new Arabidopsis miRNA and ta-siRNA targets
were identified through an integrated strategy that included computational,
genome-wide expression profiling and experimental validation components”
(Allen 208, col. 1).
15. Allen teaches “[u]sing the rules developed for miRNA target
prediction, four genes (ARF1, ARF2, ARF3, and ARF4) were predicted as
targets of these conserved, putative tasiRNAs from the 5'07(+) and 5'08(+)
positions of TAS3. ARF3 andARF4 genes were upregulated in dc/1-7, henl-
1, and rdr6-15 mutant plants” (Allen 215, col. 1).
16. Allen teaches:
Mutations affecting the TASlb target site or miR173 resulted in
the loss of siR255 biogenesis ... In contrast, siR2SS
accumulation was restored when the TASlb mutant was
coexpressed with the miR173resl construct. . . These data
clearly show that a functional miRNA target site in the ta-
siRNA primary transcript is required to trigger ta-siRNA
formation.
(Allen 217, col. 1).
17. Wu4 teaches:
It is well known that miRNAs and ta-siRNAs associate with
AGOl and contribute to target gene silencing in an mRNA
cleavage manner. Recently, however, we demonstrated that a
class of 24-nucleotide-long miRNAs in rice (Oryza sativa) that
are generated by DCL3 can be recruited into AG04 complexes
3 Allen et al., microRNA-Directed Phasing during Trans-Acting siRNA
Biogenesis in Plants, 121 Cell 207—221 (2005).
4 Wu et al., Roles of DICER-LIKE and ARGONAUTE Proteins in
TAS-Derived Small Interfering RNA-Triggered DNA Methylation,
160 Plant Physiology 990-999 (2012).
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Application 11/992,332
and perform transcriptional regulation of target gene expression
by DNA methylation in addition to mRNA cleavage.
(Wu 991, col. 1).
Quantity of Experimentation
18. The Specification teaches the “person skilled in the art is aware
of various ta-siRNAs, which may be utilized for the present invention. The
term ‘Ta-siRNA’ or ‘trans-acting siRNA’ as used herein means a
ribonucleotide sequence with trans[ac]ting silencing properties” (Spec.
46:1-3).
19. The Specification teaches “various target genes can by
advantageously silenced by the method of the invention. . . . All these
sequences are well known to the person skilled in the art an[d] can be easily
obtained from DNA data bases (e.g., GenBank)” (Spec. 13:31 to 14:6).
20. The Specification teaches the degree of silencing or “reduction
can be determined by methods with which the skilled worker is familiar”
(Spec. 18:12-13).
21. The Specification teaches the “skilled worker is familiar with a
variety of ways to obtain one of a DNA construct. Constructs can be
prepared by means of customary recombination and cloning techniques”
(Spec. 35:21-23).
22. The Specification teaches a “chimeric RNA molecule can be
produced and applied to the host cell or organism by various means, familiar
to the person skilled in the art. The chimeric RNA molecules of the
invention can be produced or synthesized by any method known in the art”
(Spec. 60:7-9).
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Skill in the Art
23. The Examiner makes no finding regarding the level of skill in
the art, but Appellants contend there is a “high level of skill” (Br. 13).
Principles of Law
Factors to be considered in determining whether a disclosure
would require undue experimentation . . . include (1) the
quantity of experimentation necessary, (2) the amount of
direction or guidance presented, (3) the presence or absence of
working examples, (4) the nature of the invention, (5) the state
of the prior art, (6) the relative skill of those in the art, (7) the
predictability or unpredictability of the art, and (8) the breadth
of the claims.
In re Wands, 858 F.2d 731, 737 (Fed. Cir. 1988).
Analysis
As we balance the Wands factors, we find that Appellants have the
better position. The Specification provides several working examples (FF
4—7). The Specification provides detailed discussions regarding the
methodology necessary to identify ta-siRNA sequences (FF 8), to identify
phase sequences (FF 9), and to replace phase sequences with modified
sequences (FF 10) for a variety of beneficial improvements (FF 11). The
Specification also indicates that the various method steps are routine for the
skilled artisan and do not require a large quantity of experimentation (FF
18-22).
Allen demonstrates the ability to predict ta-siRNA sequences (FF 14—
15). Yoshikawa teaches that ta-siRNA sequences are present in plants other
than Arahidopsis (FF 13) and Wu teaches that as of 2012, four years post-
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filing, ta-siRNAs were well known (FF 17). None of these references
identifies significant unpredictability in identifying or applying ta-siRNA
sequences for use in silencing or attenuating gene expression.
Therefore, we agree with Appellants that “the present claims recite a
scope of subject matter which a skilled artisan could clearly make and use
according to the teaching in the specification” (Br. 15).
We recognize, but find unpersuasive, the Examiner’s contention that
because “TAS1 a corresponding to SEQ ID NO: 16, for down-regulating
GUS gene expression in Arabidopsis plants did not result in downregulation
of the GUS transgene”, we should conclude that “modified ta-siRNA cannot
be used to predictably silence expression of at least one target gene” (Ans.
20).
However, the existence of a non-working embodiment alone is not
fatal to enablement, as long as the experimentation involved in identifying
working embodiments is not undue. Even if a specific sequence in Example
3 does not work, the Examiner has not established that undue
experimentation would have been required to identify other ta-siRNA
sequences that are functional. Indeed, Amgen found
that for those skilled in the art it was a relatively simple matter
to determine whether a certain promoter would work within a
specific . . . cell, whether a particular . . . cell would produce
[the desired product], and whether a particular promoter could
be operatively linked to control the transcription of the . . .
DNA.
Amgen, Inc., v. Hoechst Marion Roussel, Inc., 314 F.3d 1313, 13351—336
(Fed. Cir. 2003). If screening for efficacy was routine as of the filing date of
Amgen, a fortiori such screening of plant cells for ta-siRNA induced
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repression as expressly suggested by the Specification (FF 8—10 and 18—22)
several years after Amgen represents routine, not undue, experimentation.
We recognize, but find unpersuasive, the Examiner’s contention that
“guidance is insufficient for determining ta-siRNAs from other plants
species, fails to provide the skilled artisan the requisite information to
identify miRNA binding and target sites in a ta-siRNA from any other plant
species by using public databases” (Ans. 22). The Examiner also contends
that Allen “does not teach the skilled artisan how to extrapolate this
position-dependent coding system for uncovering other ta-siRNAs targeted
by microRNAs” (Ans. 24).
The Examiner does not provide evidence that such screening would be
anything other than routine, and does not explain why the use of the specific
scoring criteria taught by the Specification (FF 8) or Allen (FF 14—15) for
use in screening known genomic databases (FF 19) would result in a degree
of unpredictability that is undue.
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that the Specification does not enable the full scope of the claimed invention.
C. 35 U.S.C. § 112, written description
The Examiner finds “the specification fails to describe ta-siRNAs,
other than TAS1, TAS2 and TAS3, and fails to describe miRNAs, other than
miR173 and miR390, which are capable of processing a ta-siRNA to silence
expression of a target gene” (Ans. 14). The Examiner finds “there are only
four known ta-siRNA loci in Arabidopsis and three miRNA binding sites
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that trigger processing of the ta-siRNA to silence expression of
pentatricopeptide repeat proteins, ARF transcription factors, and MYB
transcription factors” (Ans. 14).
The Examiner concludes that:
in the absence of art describing the particular structure of a
representative number of microRNA binding sites that are
required to process ta-siRNAs, the skilled artisan would not be
led to believe that Applicant possess a modified ta-siRNA
comprised of a modified miRNA binding site and a modified
phase region that will silence the expression of a desired target
gene.
(Ans. 16).
The issue with respect to this rejection is: Does the evidence of
record support the Examiner’s conclusion that the Specification fails to
provide descriptive support for the claims?
Principles of Law
Falko-Gunter teaches that “we hold that where, as in this case,
accessible literature sources clearly provided, as of the relevant date, genes
and their nucleotide sequences (here ‘essential genes’), satisfaction of the
written description requirement does not require either the recitation or
incorporation by reference (where permitted) of such genes and sequences.”
Falko-Gunter Falkner v. Inglis, 448 F.3d 1357, 1368 (Fed. Cir. 2006).
“[T]he determination of what is needed to support generic claims to
biological subject matter depends on a variety of factors, such as the existing
knowledge in the particular field, the extent and content of the prior art, the
maturity of the science or technology, the predictability of the aspect at
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issue, and other considerations appropriate to the subject matter.” Capon v.
Eshhar, 418 F.3d 1349, 1359 (Fed. Cir. 2005).
Analysis
The Specification identifies twenty different ta-siRNA sequences
from a variety of plant species including wheat, rice, cotton, tomato, grape,
and others (FF 4) as well as a general algorithm to identify such sequences
(FF 8). Allen, a prior art reference, teaches that rules were known for
miRNA identification (FF 15).
“We held that a sufficient description of a genus instead requires the
disclosure of either a representative number of species falling within the
scope of the genus or structural features common to the members of the
genus so that one of skill in the art can ‘visualize or recognize’ the members
of the genus.” Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co., 598 F.3d
1336, 1350 (Fed. Cir. 2010). Applying Ariad to the instant facts, the
evidence here of twenty different ta-siRNAs from a variety of different plant
species along with general algorithms showing common structural features
reasonably supports a finding that the claims satisfy the written description
requirement. Moreover, unlike the facts in Ariad where there was a single
example of a natural inhibitor, not supported by the Specification, the instant
case shows a variety of different ta-siRNA sequences, a variety of miRNA
sequences, and clear guidance on simple computer based methods for
identifying any additional sequences that are desired and specific details for
utilizing identified sequences in the claimed method (FF 8—10 and 18—22).
See Ariad, 598 F.3d at 1356—1357.
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We therefore agree with Appellants that “[bjecause the specification
describes an actual reduction to practice and provides sufficient disclosure of
relevant identifying characteristics to distinguish the claimed subject matter
from other materials . . . the written description requirement is satisfied” (Br.
17).
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that the Specification fails to provide descriptive support for the claims.
SUMMARY
In summary, we reverse the rejection of claims 4—7, 12, 25, 38 on the
judicially-created basis that they contain improper Markush grouping of
alternatives
We reverse the rejection of claims 1, 4, 6—12, 15—20, 23—34, 38, and
39 under 35 U.S.C. § 112, first paragraph, scope of enablement (Ans. 3—11).
We reverse the rejection of claims 1, 4, 6—12, 15—20, 23—34, 38, and
39 under 35 U.S.C. § 112, first paragraph, as failing to comply with the
written description requirement.
REVERSED
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