Ex Parte Kato et al

Patent Trial and Appeal Board

Mar 23, 2017

12310258 (P.T.A.B. Mar. 23, 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.
12/310,258 07/06/2009 Shigeo Kato 392.1006 7352
23280 7590 03/27/2017
Davidson, Davidson & Kappel, LLC
589 8th Avenue
16th Floor
New York, NY 10018
EXAMINER
TREPTOW, NANCY ANN
ART UNIT PAPER NUMBER
1636
NOTIFICATION DATE DELIVERY MODE
03/27/2017 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):
ddk @ ddkpatent .com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte SHIGEO KATO, YOICHI KUMADA, TOMOMI KAWASAKI,
and YASUFUMI KIKUCHI
Appeal 2016-003542
Application 12/310,25s1
Technology Center 1600
Before JEFFREY N. FREDMAN, TIMOTHY G. MAJORS and
DAVID COTTA, Administrative Patent Judges.
COTTA, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a process
for producing an intracellular soluble fraction of an antibody fragment, and a
related vector allowing for this production. The Examiner rejected the
claims on appeal as obvious under 35 U.S.C. § 103(a).
We affirm.
1 According to Appellants, the real parties in interest are National University
Corporation Kobe University and Chugai Seiyaku Kabushiki Kaisha. App.
Br. 2.
Appeal 2016-003542
Application 12/310,258
STATEMENT OF THE CASE
Claims 16, 18, 19, 23—27, and 29 are on appeal. Claim 16 is
illustrative and reads as follows:
16. A process for producing an intracellular soluble fraction
of an antibody fragment comprising two or more polypeptide
domains and a polypeptide linker joining the domains,
comprising culturing a prokaryotic host cell transformed by a
vector comprising a polynucleotide inserted into the vector to
allow the polynucleotide to be expressed in the host cell,
wherein the polynucleotide encodes the antibody fragment, and
wherein the sequence of the polynucleotide encoding the
polypeptide linker is such that the nucleotide encoding the
polypeptide linker contains one or more rare codons in the host
cell; and recovering the antibody fragment thus produced.
The Examiner rejected claims 16, 18, 19, 23—27, and 29 under 35
U.S.C. § 103(a) as unpatentable over the combination of Smallshaw,2
Huston,3 Komar,4 Purvis5 and Khan.6
2 Smallshaw et al., Synthesis, Cloning and Expression of the Single-Chain
Fv Gene of the HPr-Specific Monoclonal Antibody, Jel42, 12(7) Protein
Engineering 623-630 (1999) (“Smallshaw”).
3 Huston et al., Protein Engineering of Antibody Binding Sites: Recovery of
Specific Activity in an Anti-Digoxin Single-Chain Fv Analogue Produced in
Escherichia Coli, 85 Proc.Natl. Acad. Sci. USA, 5879-83 (1988)
(“Huston”).
4 Komar et al., Kinetics of Translation of yB Crystallin and its Circularly
Permutated Variant in an in Vitro Cell-Free System: Possible Relations to
Codon Distribution and Protein Folding, 376 Federation of European
Biochemical Societies Letters 195-98 (1995) (“Komar”).
5 Purvis et al, The Efficiency of Folding of Some Proteins is Increased by
Controlled Rates of Translation in Vivo, 193 J. Mol. Biol. 413—417 (1987)
(“Purvis”).
6 Khan et al., US Patent No. 6,680,182 Bl, issued Jan. 20, 2004 (“Khan”).
2
Appeal 2016-003542
Application 12/310,258
FINDINGS OF FACT
1. The Examiner finds, and Appellants do not dispute, that:
Smallshaw et al. and Huston et al. disclose a method of
producing a large amount of single chain Fv fragments by
creating a DNA encoding a single chain Fv fragment, in which
a heavy chain and a light chain of an antibody [are] connected
by a peptide linker, and expressing the DNA using E. coli
transformed with a vector comprising a polynucleotide
encoding said antibody (see abstract, page 626 of Smallshaw;
see abstract and pages 5881—5882 [of Huston]).
Ans. 2—3.
2. Komar discloses:
As a consequence of the irregular distribution of rare codons
along the polypeptide chain of yB-crystallin, translation of the
two-domain protein is a non-uniform process characterized by
specific pauses. ... In this connection, the pause in the linker
region between the domains provides a delay allowing the
correct folding of the N-terminal domain and its subsequent
assistance in the stabilization of the C-terminal one.
Komar Abstract (emphasis added).
3. Purvis discloses:
It is possible that some genes have evolved translation pauses
through the development of strings of infrequently used codons,
or sequences that are capable of forming strong secondary
structures, or both. Selective advantages might have been
gained by the introduction of specific translational pauses in
mRNAs that encode proteins with potential problems in their
folding pathway (for example, polypeptides with alternative,
kinetically feasible folding pathways that lead to aberrant, but
stable conformations).
Purvis 414 (emphasis added).
3
Appeal 2016-003542
Application 12/310,258
4. Khan discloses:
Codons which are infrequently utilised in E. coli [H. Grosjean
et al, Gene 18, 199-209, 1982] and Salmonella are selected to
encode for the hinge, as such rare codons are thought to cause
ribosomal pausing during translation of the mess[e]nger RNA
and allow for the correct folding of polypeptide domains.
Khan col. 4,11. 35—40 (emphasis added).
5. Khan discloses: “The hinge region is a region designed to
promote the independent folding of both the first and second proteins by
providing both spatial and temporal separation between the domains.” Id. at
col. 3,11. 57-60.
6. Khan discloses:
The fusion protein was stably expressed in a number of
different genetic backgrounds including E. coli (TG2) and S.
typhimurium (SLB338,SL3261) as judged by SDS-PAGE and
Western blotting. Of interest was a minor band of 50 kDal
which co-migrates with the TetC-Hinge protein alone and
cross-reacts exclusively with the anti-TetC sera is visible in a
Western blot. As the codon selection in the hinge region has
been designed to be suboptimal, the rare codons may cause
pauses during translation which may occasionally lead to the
premature termination of translation, thus accounting for this
band.
Id. at col. 9,11. 17-27.
7. Khan discloses: “In summary the antibody responses against
the repitopes improved dramatically with increasing copy number, with the
tetrameric and octameric repitope fusions being the most potent.” Id. at col.
11,11. 19-24.
8. Khan discloses: “Improved constructs consisting of codon
optimised hinge regions, codon optimized P28, and multiple copies of full
length P28, are currently in preparation.” Id. at col. 12,11. 25—29.
4
Appeal 2016-003542
Application 12/310,258
9. Kane7 discloses:
Within Escherichia coli and other species, a clear codon bias
exists among the 61 amino acid codons found within the
population of mRNA molecules, and the level of cognate tRNA
appears directly proportional to the frequency of codon usage.
Given this situation, one would predict translational problems
with an abundant mRNA species containing an excess of rare
low tRNA codons. Such a situation might arise after the
initiation of transcription of a cloned heterologous gene in the
E. coli host. Recent studies suggest clusters of AGG/AGA,
CUA, AUA, CGA or CCC codons can reduce both the quantity
and quality of the synthesized protein. In addition, it is likely
that an excess of any of these codons, even without clusters,
could create translational problems.
Kane Abstract.
10. Smallshaw discloses:
Once the amino acid sequence of the gene product had been
determined by translation of the corrected DNA sequence (see
Results), a DNA sequence using the codons found in highly
expressed E.coli genes (Sharp and Li, 1987) was made,
incorporating codon redundancy where appropriate. The
sequence was then searched for potential restriction
endonuclease sites, and changes were made that did not
introduce unfavourable codons.
Smallshaw 624.
11. Huston discloses: “Design of the 744-base sequence for the
synthetic sFv gene was derived from the sFv protein sequence by choosing
codons preferred by E. coli.'” Huston 5879.
7 Kane, Effects of Rare Codon Clusters on High-Level Expression of
Heterologous Proteins in Escheria Coli, 6 Current Opinion in
Biotechnology 494—500 (1995). Kane was cited by Appellants as
evidence that “at the time of filing of the present application it was
recognized that rare codons reduce the quantity and quality of synthesized
proteins and could create translational problems.” App. Br. 10.
5
Appeal 2016-003542
Application 12/310,258
ANALYSIS
Claims 16, 18, 19, 23, 24, 26, 27, and29
Appellants argue claims 16, 18, 19, 23, 24, 26, 27, and 29 as a group.
We designate claim 16 as representative for the group.
The Examiner found that Smallshaw and Huston disclosed a method
of producing a large amount of single chain Fv fragments by creating a DNA
encoding a single chain Fv fragment, in which a heavy chain and a light
chain of an antibody are connected by a peptide linker, and expressing the
DNA using E. coli transformed with a vector comprising a polynucleotide
encoding said antibody. FF1. Neither Smallshaw nor Huston, however,
discloses that the nucleotide encoding the polypeptide linker contains one or
more rare codons. Ans. 3.
The Examiner found that it was well known in the art that “rare
codons in the DNA encoding [the] interdomain region of polypeptides
cause[] pausing in translation, which allows proper folding of the domains.”
Id. As evidence, the Examiner cited Komar, Purvis, and Khan. Id. The
Examiner concluded:
it would have been obvious to one of ordinary skill in the
art to provide a rare codon in the DNA encoding the
polypeptide linker region and adjust the translation speed
of any domain located downstream of another domain,
including two portions of a fusion protein or antibody, so
as to become slower in the linker region, compared to
that of a domain located upstream thereof, in order to
produce a protein being correctly folded and stable, as
described by the references.
Id.
6
Appeal 2016-003542
Application 12/310,258
We adopt the Examiner’s findings of fact and reasoning regarding the
scope and content of the prior art (Ans. 2—11; Final Act. 2—8) and agree that
the claims would have been obvious over Smallshaw, Huston, Komar,
Purvis and Khan. We address Appellants’ arguments below.
Appellants argue that Huston teaches to choose “codons preferred by
E. coir rather than rare codons and that Smallshaw teaches ‘“not to
introduce unfavorable codons’ during gene design.” App. Br. 9 (citing
material quoted at FF10 and FF11). Appellants assert that “[a]t the time of
filing of the present application, rare codons were recognized to be
‘unfavorable’, because it was recognized that rare codons reduce the
quantity and quality of synthesized proteins and could create translational
problems.” Id. (citing Kane (see FF 9)). Appellants thus contend that
because “the cited references teach[] not to utilize rare codons in a process
for producing an intracellular soluble fraction of an antibody fragment in a
prokaryotic host cell,” the references cannot be combined to achieve the
claimed invention. Id. at 8. We are not persuaded.
Smallshaw and Huston disclose all of the elements of claim 16 except
for “the nucleotide encoding the polypeptide linker contains one or more
rare codons.” See FF1; Ans. 2—3. Komar and Khan disclose that the use of
rare codons in the linker (or “hinge”) region provides translational “pauses”
that allow the “correct folding” of the encoded protein. FF2 and FF4.
Consistent with this teaching, Purvis discloses that “infrequently used
codons” may provide “[selective advantages ... by the introduction of
specific translational pauses . . . .” FF3. In view of these teachings, we
agree with the Examiner that it would have been obvious to “provide a rare
7
Appeal 2016-003542
Application 12/310,258
codon in the DNA encoding the polypeptide linker region ... in order to
produce a protein being correctly folded and stable.” Ans. 4.
[A] given course of action often has simultaneous advantages
and disadvantages, and this does not necessarily obviate
motivation to combine. See [Winner Inti Royalty Corp. v.
Wang, 202 F.3d 1340, 1349 n.8 (Fed. Cir. 2000)] (“The fact
that the motivating benefit comes at the expense of another
benefit, however, should not nullify its use as a basis to modify
the disclosure of one reference with the teachings of another.
Instead, the benefits, both lost and gained, should be weighed
against one another.”). Where the prior art contains “apparently
conflicting” teachings (i.e., where some references teach the
combination and others teach away from it) each reference must
be considered “for its power to suggest solutions to an artisan of
ordinary skill. . . . considering] the degree to which one
reference might accurately discredit another.” In re Young, 927
F.2d 588, 591 (Fed. Cir. 1991).
Medichem, S.A. v. Rolabo, S.L., 437 F.3d 1157, 1165 (Fed. Cir. 2006).
We acknowledge Appellants’ argument that Huston and Smallshaw
suggest a preference for commonly used codons in designing a gene
sequence for a synthetic protein. See FF10 and FF11. We similarly
acknowledge Appellants’ argument that Kane teaches that rare codons can
create translational problems. See FF9. In the obviousness analysis
however, these references are not considered alone. Considering Huston and
Smallshaw together with the clear teaching of Komar, Khan and Purvis that
using rare codons in the linking region ensures proper protein folding, the
ordinary artisan would have had reason to include some rare codons in order
to obtain the advantage of improved protein folding, without adding large
clusters of rare codons that could reduce protein quantity and quality as
taught by Kane. FF9. Because claim 16 is open to “one or more rare
codons”, we find that a preponderance of the evidence supports the
8
Appeal 2016-003542
Application 12/310,258
Examiner’s conclusion that the claimed process would have been obvious
over the cited references.
Appellants dispute the Examiner’s finding that Khan teaches to
include rare codons at the linking region. Appellants contend that Khan
teaches the opposite — i.e. to “avoid” rare codons because “the use of rare
codons in the region[s] between domains is suboptimal.” App. Br. 11. We
disagree. As the Examiner explains, Khan uses the term “suboptimal” to
indicate that translation in the linking/hinge region occurs at less than
maximum possible speed due to the use of rare codons. FF6; Ans. 7. This
causes a “pause,” which, as the Examiner also points out, “is the desired
effect.” FF5 and FF6 (“the hinge region has been designed to be
suboptimal”) (emphasis added); Ans. 7. Accordingly, Khan does not teach
to “avoid” rare codons. To the contrary, Khan teaches that the use of rare
codons “ allow [s] for the correct folding of polypeptide domains.” FF4.
Appellants argue that Komar and Purvis are silent on the expression
of an antibody fragment in a prokaryotic cell and thus cannot overcome
Smallshaw’s and Huston’s preference for not using rare codons in a
prokaryotic host. Appellants assert:
At the priority date of the claimed invention, it was recognized
that proper folding in a cell-free system does not necessarily
translate to proper folding in E. Coli, and that folding in E. Coli
is affected by many factors. There is nothing in Komar that
indicates that the technique described in Komar can be used to
make functional antibodies in E. Coli as described in
Smallshaw and Huston
App. Br. 12. We are not persuaded.
As an initial matter, Khan discloses the use of rare codons in
prokaryotic cells. FF6. Komar’s disclosure regarding rare codons is
9
Appeal 2016-003542
Application 12/310,258
cumulative of and consistent with Khan. Moreover, as explained in the
Examiner’s Answer, Komar makes general statements about protein folding
and translation without any limiting language suggesting that the statements
apply only in the context of in vitro translation methods. See, Ans. 9—10.
Finally, Appellants do not provide persuasive evidence to support their
position that folding in a cell-free system would not translate to folding in E.
coli. See Johnston v. IVAC Corp., 885 F.2d 1574, 1581 (Fed. Cir. 1989)
(“Attorneys’ argument is no substitute for evidence.”); In re Pearson, 494
F.2d 1399, 1405 (CCPA 1974).
Accordingly, we affirm the Examiner’s decision to reject claim 16.
Because they were not argued separately, claims 18, 19, 23, 24, 26, 27, and
29 fall with claim 16.
Claim 25
Claim 25 depends from claim 16 and adds the requirement “wherein
the nucleotide encoding the polypeptide linker has a sequence set forth in
SEQ ID NO: 6, 8, 10, 12, or 24.” In the Appeal Brief, Appellants argued
that the Examiner did not provide “any evidence or explanation of how and
why the combination of the cited references teaches or suggests SEQ ID
NO: 6, 8, 10, 12, or 24.” App. Br. 13. In the Examiner’s Answer, the
Examiner asserted that Huston disclosed “using the linker region comprising
(Gly-Gly-Gly-Gly-Ser)3” and that “[t]his is the same polypeptide as the
polypeptide sequence encoded by SEQ ID NO: 24 of the instant claim.”
Ans. 10. Appellants’ Reply Brief does not contest that Huston discloses
SEQ ID NO: 24, instead arguing that claim 25 is patentable for the same
reasons discussed with respect to claim 16. Accordingly, we affirm the
10
Appeal 2016-003542
Application 12/310,258
Examiner’s decision to reject claim 25 under 35 U.S.C. § 103(a) for the
reasons provided in connection with claim 16.
SUMMARY
For these reasons and those set forth in the Examiner's Answer, and
the Final Office Action, the Examiner’s decision to reject claims 16, 18, 19,
23—27, and 29 is affirmed.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1).
AFFIRMED
11