Ex Parte Giritch et al

Patent Trial and Appeal Board

May 16, 2017

10545665 (P.T.A.B. May. 16, 2017)

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.
10/545,665 10/13/2005 Anatoly Giritch 070313.0002 1406
45309 7590 05/18/2017
Williams; Mullen
EXAMINER
8300 Greensboro Drive DEVEAU ROSEN, JASON
#1100
Tysons, VA 22102-3664 ART UNIT PAPER NUMBER
1662
NOTIFICATION DATE DELIVERY MODE
05/18/2017 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
following e-mail address(es):
ip @ williamsmullen. com
kmoore @ williamsmullen. com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ANATOLY GIRITCH, SYLVESTRE MARILLONNET,
VICTOR KLIMYUK, and YURI GLEBA1
Appeal 2016-001290
Application 10/545,665
Technology Center 1600
Before DEMETRA J. MILLS, JOHN E. SCHNEIDER,
and TIMOTHY G. MAJORS, Administrative Patent Judges.
MAJORS, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to
processes for genetically modifying plants. The claims have been rejected
as obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.
STATEMENT OF THE CASE
Appellants’ “invention relates to a process of endowing a plant or plant
cells with a trait of interest.” (Spec. 1.) According to the Specification, the
invention is based on the surprising finding that efficient
assembly of transcribed sequences, notably of a coding sequence
1 Appellants identify the Real Party in Interest as Bayer Crop Science NV.
(Br. 1.)
Appeal 2016-001290
Application 10/545,665
that encodes or results in a trait of interest, can be achieved by
transforming plant cells with two or more vectors each carrying
a segment coding for a part of a transcribed sequence or a part of
said coding sequence.
(Id. at 4.)
Claims 1—3, 6—14, 16, 19, 22, and 23 are on appeal. Claim 1, the only
independent claim, is illustrative and reads as follows:
1. A process of endowing a plant or plant cells with a trait of
interest by expressing an RNA sequence of interest, said process
comprising:
providing by co-transformation plant cells or cells of said
plant with a first vector and a second vector and selecting cells
endowed with said trait of interest, wherein
said first vector contains a first nucleotide sequence with
a first segment coding in 5' to 3' direction, for
- a 5' part of said RNA sequence of interest and
- a 5' part of an intron; and
said second vector contains a second nucleotide sequence
with a second segment coding, in 5' to 3' direction, for
- a 3' part of an intron and
- a 3' part of said RNA sequence of interest;
wherein said 5' part of an intron and said 3' part of an intron form
said RNA sequence of interest by splicing of a primary transcript
containing said 5' part of said RNA sequence of interest, said 5'
part of an intron, said 3' part of an intron, and said 3' part of said
RNA sequence of interest, thereby forming said RNA sequence
of interest as a secondary transcript, wherein said primary
transcript is transcribed from a functional transcription unit
comprising said first nucleotide sequence and said second
nucleotide sequence, and wherein said second vector is devoid of
a transcriptional promoter for transcribing said 3' part of an intron
and said 3' part of said RNA sequence of interest.
(Br. A-l (Claims App’x).)
2
Appeal 2016-001290
Application 10/545,665
The claims stand rejected as follows:
I. Claims 1—3, 6—14, 16, 19, and 22 under 35 U.S.C. § 103(a) over
Patten2 and De Block3 (“Rejection I”).
II. Claims 1—3, 6—14, 16, 22, and 23 under 35 U.S.C. § 103(a) over
Patten, De Block, and Smith4 (“Rejection II”).
DISCUSSION
We address Rejection I and Rejection II together. As Appellants note,
it appears the Examiner’s reliance on Smith is limited to its teachings related
to certain limitations of dependent claim 23. (Br. 22; see also Ans. 13.) The
Examiner does not assert that Smith makes up for any of the deficiencies
alleged by Appellants concerning the combination of Patten and De Block
with respect to claim 1, from which claim 23 depends. Also, in arguing
Rejection II, Appellants essentially repeat their arguments about Rejection I.
(Br. 21—24.) Accordingly, Rejections I and II rise or fall together depending
on whether claim 1 would have been obvious over the combination of Patten
and De Block. 37 C.F.R. § 41.37(c)(l)(iv).
The Examiner finds that Patten teaches “a method of unencrypting a
trait encrypted gene sequence to provide at least one unencrypted RNA or
polypeptide.” (Ans. 3.) As noted by the Examiner, Patten teaches this
method is done by mating first and second parental organisms, each of
2 Patten et al., US 6,531,316 Bl, issued Mar. 11, 2003.
3 De Block et al., Two T-DNA ’s co-transformed into Brassica napus by a
double Agrobacterium tumefaciens infection are mainly integrated at the
same locus, 82 Theoretical and Applied Genetics 257-63 (1991).
4 Smith et al., Total silencing by intron-spliced hairpin RNAs, 407 Nature
319-20 (2000).
3
Appeal 2016-001290
Application 10/545,665
which have a portion of a split gene sequence. (Id.) According to the
Examiner, this mating “produce[s] progeny comprising the first and second
split gene sequences which are transcribed to provide a plurality of RNA
segments, and trans-splicing at least two of the plurality of RNA segments []
to provide at least one unencrypted RNA.” (Id.) As the Examiner notes,
Patten also teaches an embodiment where an organism having a first genetic
element is infected with a vector that includes a second genetic element to
produce an organism with the full genetic sequence capable of expressing a
functional polypeptide or trait of interest. (Id. at 3 4.)5
The Examiner finds that Patten does not disclose all the limitations of
claim 1 and turns to De Block. More specifically, the Examiner finds:
Patten et al does not teach a co-transformation method to produce
a RNA sequence of interest using a first vector and a second
devoid of a transcriptional promoter to form a primary transcript
that is transcribed from a functional transcriptional unit to
produce a protein of interest, wherein said RNA sequence of
interest can cause degradation or suppression of a message RNA,
or wherein said first and second vectors contain site-specific
recombination sites for recombining with each other to produce
said RNA sequence of interest.
(Id. at 4.) The Examiner finds De Block teaches “Brassica napus co­
transformed with two Agrobacterium carrying T-DNA containing distinct
selectable markers led to high co-transformation efficiencies.” (Id. at 5.)
5 (See Patten 17:27—38; see also id. at Abstract (“Methods of unencrypting
trait encrypted gene sequences to provide unencrypted RNAs or
polypeptides. The invention also relates to methods of encrypting traits
including splitting genes between two parental organisms or between a host
organism and a vector.”).)
4
Appeal 2016-001290
Application 10/545,665
Also, according to the Examiner, De Block teaches that in 57% of the co­
transformations, the plants contained the two T-DNAs as linked copies and,
in 19% of the cases, the copies were in tandem (as opposed to inverted)
orientation. (Id. at 5.) Citing De Block, the Examiner further finds “[c]o-
transformation is known to be more efficient than two independent
transformation events . . . and leads to stable integration of foreign genes
into the plant genome.” (Id. at 5.)
The Examiner concludes it would have been obvious “to unencrypt an
encrypted gene sequence using two vectors as taught by Patten et al by co­
transforming said vectors for stable integration in the plant genome, for
example, as taught by De Block et al.'” (Id.) The Examiner reasons the
skilled person would have been motivated to modify the prior art “because
the gene of interest would be stably and efficiently integrated into the plant
genome, produce the gene of interest, and would obviate the need to re­
transform a plant.” (Id.) The Examiner further reasons that using co­
transformation as described in De Block with split sequences of a gene as
described in Patten would produce “a single primary transcriptional unit []
such that splicing [of introns] will lead to a secondary transcript and the
RNA sequence of interest.” (Id.) Finally, the Examiner finds, based on “the
frequency of tandem insertion events” disclosed in De Block, it would have
been obvious “to make a second vector devoid of a transcriptional promoter
because said promoter would not be required.” (Id.; see also id. at 10
(“because the first vector contains a promoter and would drive expression of
the second vector . . . inserted in the same orientation, and in close
proximity, to the first insertion event.”)
5
Appeal 2016-001290
Application 10/545,665
Appellants raise two arguments. First, Appellants contend the
combination of prior art fails to teach all the limitations of claim 1. (Br. 5—
12.) And second, Appellants argue, there is no sufficient reason to combine
and modify the art in the manner proposed by the Examiner to arrive at the
method of claim 1. (Id. at 12—20.)
With respect to Appellants’ first argument, Appellants contend
“several elements or features o[f] Appellant’s claimed invention are neither
taught nor suggested by the cited combination of documents.” (Id. at 6.) In
support, Appellants explain, inter alia, that claim 1 involves a process
“known in the art as ds-splicing because the splicing involves the
elimination or removal [of] an intron from a single primary transcript” and
this “is in contrast to the fundamentally different process of trans-splicing of
RNA [as taught in Patten] which comprises the splicing of two or more
independently transcribed, primary transcripts.” (Id. at 6-7.) Further,
Appellants cite the Examiner’s assertion that “Patten teaches a first vector
and a second vector that when expressed form an RNA sequence of interest
from a functional transcription unit comprising said first nucleotide sequence
and said second nucleotide.” (Id. at 8 (quoting Final Act. 7) (emphasis
omitted).) Appellants point out that the Examiner provides no citation for
this alleged teaching in Patten, which Appellants contend is actually “not
consistent” with Patten. (Id.)
Appellants contend De Block “does not teach or even suggest that a
first vector containing a first nucleotide sequence and a second vector
containing a second nucleotide sequence, when expressed in an organism,
form an RNA sequence of interest from a functional transcription unit.” (Id.
6
Appeal 2016-001290
Application 10/545,665
at 10.) To the contrary, Appellants contend, De Block describes co­
transformation “with two different T-DNA vectors . . . with each of these T-
DNA vectors containing a different selectable marker gene under the control
of the constitutive promoter.” {Id. at 10.)
Thus, Appellants argue, the combination of art does not teach or
suggest at least the limitations of claim 1 reciting: (i) “a primary transcript
that is transcribed from a functional transcription unit comprising said first
nucleotide sequence and said second nucleotide sequence,” (ii) “splicing of a
primary transcript containing said 5' part of said RNA sequence of interest,
said 5' part of an intron, said 3' part of an intron, and said 3' part of said
RNA sequence of interest” and (iii) “a second vector . . . which is devoid of
a transcriptional promoter for transcribing said 3' part of an intron and said 3'
part of said RNA sequence of interest.” {Id. at 12.)
Turning to Appellants’ second argument, Appellants contend there
was “no credible reason” to combine Patten and De Block and modify
Patten’s method as proposed “because such a modification would have
changed the principle of operation” of Patten. {Id. at 13.) Appellants
contend “the Examiner has misunderstood the teachings of Patten” related to
encrypting/unencrypting genes. (Id. at 14.) More specifically, Appellants
contend “the advantages of the method of Patten et al.[,] depends on
encryption wherein the two portions of a gene are split between two parental
organisms or between one host organism and a vector” and “these
advantages would be destroyed if the two portions of the split gene were
unencrypted by being co-transformed into a single organism.” {Id. at 18.)
7
Appeal 2016-001290
Application 10/545,665
Based on the preponderance of the evidence on the present record,
Appellants have the better position.
As an initial matter, it appears that modifying the prior art in the
manner proposed would result in the method of claim 1. If, as the Examiner
proposes, the split genetic sequences (portions of an intron and RNA
sequence encoding a gene/trait of interest) described in Patten were used in
two vectors and a plant was co-transformed with those vectors as described
in De Block, that would reasonably appear to produce (at least some of the
time) a functional transcription unit and primary transcript, and ultimately
(upon splicing of the intron) a secondary transcript as recited in claim 1.6
The decisive question in this appeal is, however, why would the
skilled person modify Patten and De Block as proposed? On the present
record, the only apparent reason for splitting the genetic sequences that
encode a polypeptide or trait of interest relied on by the Examiner is to
facilitate encryption of genes as described in Patten. (Patten 7:49-50
(“Traits are encrypted using ‘split gene sequences.’ Split gene sequences are
subsequences of a genetic element.”) Ans. 5. Patten describes splitting the
genetic sequences — between two parental organisms or between an
organism and vector — to encrypt and thus avoid expression of the
polypeptide or trait except when desired. (See, e.g., Patten 1:33—42.)7 When
expression is desired, the genetic material is then unencrypted by mating two
6 As to the limitation that the “second vector is devoid of a transcriptional
promoter,” the Examiner provided a reasoned explanation why a promoter in
the second vector would be unnecessary. (Ans. 9-10, 18.)
7 As described in Patten, the full-length sequence may, for example, encode
a polypeptide that produces sterility in plants. (Patten 8:31—35.)
8
Appeal 2016-001290
Application 10/545,665
organisms or transfecting an organism including a portion of the genetic
sequence with a vector including the other portion of the sequence. (Id.)
Put differently, Patten teaches a particular lock (encryption) and key
(unencryption) method for controlling gene expression.
Absent hindsight provided by Appellants’ application, we are not
persuaded the skilled person would split a genetic sequence for a particular
polypeptide or trait between two vectors and then perform co-transformation
of a host with those two vectors. The Examiner asserts the skilled person
would predictably modify the art to “obviate the need to re-transform a plant
to produce the gene of interest.” (Ans. 5.) But, if the skilled person simply
desired to transform a plant to express a trait of interest, why split the
sequence at all — why not just infect the host in a single transformation
event with a vector encoding the full RNA sequence for the desired trait?
The only reason for splitting the sequence on the present record is to enable
encryption as described in Patten. And, as Appellants persuasively argued,
modifying Patten as proposed by the Examiner “would provide a result that
is contrary to the teachings of Patten . . . and that would eliminate the
advantage provided by encrypting the split genes.” (Br. 16; see also id. at
18.) In reFritch, 972 F.2d 1260, 1266 n.12 (Fed. Cir. 1992) (“This court
has previously found a proposed modification inappropriate for an
obviousness inquiry when the modification rendered the prior art reference
inoperable for its intended purpose”) (citation omitted).
De Block does not teach splitting individual genes or suggest a reason
to do so. De Block teaches “co-transformation of two distinct T-DNA’s
each delivered by a different [bacterial] strain.” (De Block 261 (emphasis
9
Appeal 2016-001290
Application 10/545,665
added).) And, although De Block does teach that co-transformation is an
efficient process with high co-transformation frequencies, De Block is
describing co-transformation compared to multiple-independent
transformation events. {Id. at 257, 261.) As noted above, if not for the
particular encryption described in Patten, the Examiner has provided no
persuasive reason why the skilled artisan would split the gene in the first
place, much less modify Patten’s method in the way proposed. “[Rejections
on obviousness grounds cannot be sustained by mere conclusory statements;
instead, there must be some articulated reasoning with some rational
underpinning to support the legal conclusion of obviousness.” KSR Int’l Co.
v. Teleflex Inc., 550 U.S. 398, 418 (2007) (quoting In re Kahn, 441 F.3d
977, 988 (Fed. Cir. 2006).
Accordingly, for the reasons above, we are unpersuaded the Examiner
established by a preponderance of the evidence that claim 1 (and its
dependent claims) would have been obvious over Patten and De Block. We
thus reverse Rejections I and II.
SUMMARY
We reverse the rejection of claims 1—3, 6—14, 16, 19, and 22 under
35 U.S.C. § 103(a) over Patten and De Block.
We reverse the rejection of claims 1—3, 6—14, 16, 19, 22, and 23 under
35 U.S.C. § 103(a) over Patten, De Block, and Smith.
REVERSED
10