Ex Parte Weinschenk et al

Patent Trial and Appeal Board

Dec 20, 2012

11000474 (P.T.A.B. Dec. 20, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte TONI WEINSCHENK and HANS GEORG RAMMENSEE
____________

Appeal 2011-000966
Application 11/000,474
Technology Center 1600
____________

Before DONALD E. ADAMS, STEPHEN WALSH, and ULRIKE W.
JENKS, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 17, 56-67, and 69
(App. Br. 3; Reply Br. 2; Ans. 3).1 We have jurisdiction under 35 U.S.C.
§ 6(b).
STATEMENT OF THE CASE
The claims are directed to a method for identifying an
immunoreactive peptide (claims 17, 56-61, and 69) and an in vitro method
for identifying an MHC-ligand (claims 62-68). Independent claims 56, 62,

1 Pending claims 22-26, 30-34, 39-50, and 68 stand withdrawn from
consideration (App. Br. 3).
Appeal 2011-000966
Application 11/000,474

2
and 66 are representative and are reproduced in the Claims Appendix of
Appellants’ Brief.
I. Claims 17, 56, 57, 59-61, 66, and 69 stand rejected under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Schultze,2 Young,3
Maecker,4 Schirle,5 Kaufman,6 and Rammensee.7
II. Claims 17, 56-67, and 69 stand rejected under 35 U.S.C. § 103(a)
as unpatentable over the combination of Flad,8 Schirle, Young, Kaufman,
and Schultze.
Rejection I is cumulative to rejection II. Therefore, we vacate
rejection I in favor of rejection II, which addresses all claims before us on

2 Joachim L. Schultze, et al., From cancer genomics to cancer
immunotherapy: toward second-generation tumor antigens, 22(9) TRENDS
in Immunology 516-523 (2001).
3 Andrew N. Young, et al., Expression Profiling of Renal Epithelial
Neoplasms: A Method for Tumor Classification and Discovery of Diagnostic
Molecular Markers, 158(5) American Journal of Pathology 1639-1651
(2001).
4 B. Maecker, et al., Linking Genomics to Immunotherapy by Reverse
Immunology - ‘Immunomics’ in the New Millennium, 1 Current Molecular
Medicine 609-619 (2001).
5 M. Schirle, et al., Identification of tumor-associated MHC class I ligands
by a novel T cell-independent approach, 30 Eur. J. Immunol. 2216-2225
(2000).
6 Kaufman et al., US 6,022,697, issued February 8, 2000.
7 Rammensee et al., US 5,747,269, issued May 5, 1998.
8 Thomas Flad, et al., Direct Identification of Major Histocompatibility
Complex Class I-bound Tumor-associated Peptide Antigens of a Renal
Carcinoma Cell Line by a Novel Mass Spectrometric Method, 58 Cancer
Research 5803-5811 (1998).
Appeal 2011-000966
Application 11/000,474

3
appeal. We affirm the rejection over the combination of Flad, Schirle,
Young, Kaufman, and Schultze (Rejection II).9
ISSUE
Does the preponderance of evidence on this record support a
conclusion of obviousness?
FACTUAL FINDINGS (FF)
FF 1. Flad suggests a method of “identifying HLA class I bound tumor
associated peptide antigens of a renal carcinoma cell line by [a] mass
spectrometric method” that comprises “directly isolate[ing] peptides bound
to HLA class I molecules … and identif[ing] the peptides by HPLC-mass
spectrometry and sequencing” (Ans. 12-13).
FF 2. Flad suggests “comparing gene expression with peptide extraction …
[to] identify[] immunogenic peptide[s]” (id. at 13).
FF 3. Flads’ methodology “does not include epitope prediction” (id.).
FF 4. Examiner finds that Flad does not suggest “isolation of HLA
peptides from tumor tissue” or determining gene expression levels in “tumor
cells and their normal counterparts” (id. at 14).
FF 5. Schirle suggests that “MHC1 peptides can be eluted and identified
from tumor cell lines, as well as from tumor tissue … and [that] the MHC1
peptides eluted from tumor tissue can be compared … [to] those eluted from
healthy tissue obtained from the same patient” (id.).

9 We recognize the dispute regarding the Restriction requirement and
objection of claim 56 (see generally Ans. 5 and 24; App. Br. 6-7 and 17).
These issues are petitionable rather than appealable issues. See, e.g., Manual
of Patent Examining Procedure § 1002.02(c). Accordingly, we have not
considered these issues in our deliberations.
Appeal 2011-000966
Application 11/000,474

4
FF 6. Young suggests “expression profiling of renal epithelial neoplasm by
microarray analysis of matched specimens of renal tumor and grossly non-
neoplastic kidney from the same patients” (id.).
FF 7. Schultze suggests “that overexpressed genes in cancer can be
identified by gene-expression profiling such as microarrays” (id.).
FF 8. Kaufman suggests “that the frequence of IFN-gamma, IL-4 and IL-5
secreting T cells that are specific for a particular antigen in a subject can be
determined” by ELISPOT assay, ELISA, and PCR analysis (id.).
ANALYSIS
Based on the combination of Flad, Schirle, Young, Kaufman, and
Schultze Examiner concludes that, at the time Appellants’ invention was
made, it would have been prima facie obvious to:
A. Use Flad’s method “to elute and identify … HLA class I peptides
from tumor tissues obtained from cancer patients because” Schirle suggests
that MHC1 peptides can be eluted and identified from tumor cell lines or
tumor tissue (Ans. 15; FF 1-5); and
B. modify Flad’s method “to detect gene expression in matched
specimens of tumor and normal tissue from the same patient for identifying
differentially expressed genes in tumor cells” because Young suggests “that
matched specimens of tumor and normal tissue from the same patient were
used … [to] identify genes that are differentially expressed in tumor cells”
(id. at 15-16; FF 1-4 and 6; see also FF 7).
Appellants present separate arguments for the following groups of
claims: (I) claims 17, 56-61, and 69; (II) claims 62-65 and 67; and (III)
claim 66. Claims 56, 62, and 66 are representative.
Appeal 2011-000966
Application 11/000,474

5
Claim 56:
We are not persuaded by Appellants contention that “Flad fails to
disclose [the] isolation of HLA peptides from tumor tissue”, which is
suggested by Schirle (App. Br. 13; Cf. FF 5).
With reference to the Weinschenk Declaration10, Appellants contend
that Schirle’s method steps differ from those of Flad (App. Br. 13-14). We
are not persuaded. As Examiner explains, “Schirle is merely cited by the
Examiner to show that it was known in the prior art that MHC peptides can
be isolated either from tumor cell lines, or from tumor tissue” (Ans. 23).
Appellants fail to provide persuasive reasoning or evidence to suggest that
the source of the sample would detract from Flad’s methodology.
We are not persuaded by Appellants’ contention that Schirle fails to
teach determining whether peptides identified from isolated MHC-class I
ligands match the gene-expression comparison data, which is suggested by
Young and Schultze (App. Br. 14; Reply Br. 10-11; Cf. FF 6-7).
Lastly, we are not persuaded by Appellants’ contention that their
Specification demonstrates unexpected results because it was “much easier
to identify” an immunoreactive peptide utilizing a methodology such as that
suggested by Flad, wherein an immunoreactive peptide is isolated directly
from the immune components of a tissue, rather than attempting to predict
whether a particular peptide would be immunoreactive (App. Br. 11 and 14).
Appellants’ reasoning is more a statement of what a person of ordinary skill
in this art at the time of Appellants’ claimed invention would have
considered prima facie obvious and reasonably expected, rather than an
unexpected result.

10 Weinschenk Declaration, executed April 27, 2009.
Appeal 2011-000966
Application 11/000,474

6
Claim 62:
Appellants fail to establish that Flad’s methodology that utilizes, inter
alia, HPLC-mass spectrometry and sequencing is not an in vitro method (FF
1). Accordingly, we are not persuaded by Appellants’ contention to the
contrary (App. Br. 15).
We are not persuaded by Appellants’ contention that Flad fails to
suggest a method that “does not employ epitope prediction” (id.; Cf. FF 3)
For the reasons set forth above, we are not persuaded by Appellants’
contentions regarding Schirle (id.).

Claim 66:
As discussed above Flad does not utilize epitope prediction, but
instead identifies MHC class I peptides directly (FF 1; Cf. FF 3). Therefore,
we are not persuaded by Appellants’ contention that “the Flad Combination
necessarily requires the use of epitope prediction” (App. Br. 16).

To be complete, we recognize, but are not persuaded by, Appellants’
reliance on the Emmerich Declaration11 to support a contention that their
claimed invention fulfilled “a long felt need by being able to identify a
tumor by the claimed method and only 22 months later be able [to]
commence vaccination of the first patients” (Reply Br. 15).
Notwithstanding Appellants’ contention to the contrary, once Flad supplied
the key to identifying immunogenic peptides, without epitope prediction, the
alleged long-felt need was overcome. See Newell Companies, Inc. v. Kenney
Mfg. Co., 864 F.2d 757, 768 (Fed. Cir. 1988). Stated differently, once

11 Emmerich Declaration, executed April 12, 2007.
Appeal 2011-000966
Application 11/000,474

7
Flad’s methodology was available to a person of ordinary skill in this art,
one only needed an interest or appreciation of the method’s potential to
move forward, rather than the technical know-how to do so. See Scully
Signal Co. v. Elecs. Corp. of Am., 570 F.2d 355, 361 (Fed. Cir. 1977).
CONCLUSION OF LAW
The preponderance of evidence on this record supports a conclusion
of obviousness. The rejection of claims 56, 62, and 66 under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Flad, Schirle, Young,
Kaufman, and Schultze is affirmed. Because they are not separately argued
claims 17, 57-61, and 69 fall together with claim 56; and claims 63-65 and
67 fall together with claim 62. 37 C.F.R. § 41.37(c)(1)(iv).

TIME PERIOD FOR RESPONSE
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

lp