Ex Parte Reed et al

Patent Trial and Appeal Board

Nov 26, 2013

11836563 (P.T.A.B. Nov. 26, 2013)

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.
11/836,563 08/09/2007 Thomas D. Reed 2584.0390001/RWE/GER 3434
80011 7590 11/27/2013
Sterne, Kessler, Goldstein & Fox P.L.L.C.
1100 New York Avene
N.W.
Washington, DC 20005
EXAMINER
LEAVITT, MARIA GOMEZ
ART UNIT PAPER NUMBER
1633
MAIL DATE DELIVERY MODE
11/27/2013 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 THOMAS D. REED and AMY H. ATZEL
____________

Appeal 2012-0055201
Application 11/836,563
Technology Center 1600
____________

Before DONALD E. ADAMS, ANNETTE R. REIMERS, and SUSAN L. C.
MITCHELL, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL2
This appeal under 35 U.S.C. § 134 involves claims 125-129 and 133-
135 (App. Br. 7).3 Examiner entered rejections under the written description
and enablement provisions of 35 U.S.C. § 112, first paragraph. We have
jurisdiction under 35 U.S.C. § 6(b).
We affirm.

1 This Appeal is related to Appeal No. 2012-005519, Application No.
11/834,897 (see App. Br. 5).
2 The Real Party in Interest is Intrexon Corporation (App. Br. 4).
3 Pending claims 130-132 stand “withdrawn from consideration” (App. Br.
7). Examiner found the subject matter of claim 136 allowable if rewritten in
independent form (Ans. 5).
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STATEMENT OF THE CASE
The claims are directed to an isolated polynucleotide. Claims 125 and
135 are representative and are reproduced in the Claims Appendix of
Appellants’ Brief.
Claims 125-129 and 133-135 stand rejected under the written
description and enablement provisions of 35 U.S.C. § 112, first paragraph.
ISSUES
Does the preponderance of evidence on this record support
Examiner’s:
1. finding that Appellants’ Specification fails to provide written
descriptive support for the full scope of Appellants’ claimed invention; and
2. conclusion that undue experimentation would be required to
practice the full scope of claimed invention?
FACTUAL FINDINGS (FF)
FF 1. “Protein Kinase C … also known as PKC … can phosphorylate
serine and threonine residues in protein or peptide substrates” (Spec. 1:
¶ [0004]).
FF 2. “Protein kinase C,” as that term is used in Appellants’ claimed
invention, represents a genus of isoforms. The polypeptides encoded by the
polynucleotides of Appellants’ claimed invention “are designed to modulate
the endogenous effects of one or more isoforms of PKC” (Spec. 7:
¶ [0032]; Ans. 12 (“Protein kinase C (PKC) represents a family of
homologous subtypic kinases”)).
FF 3. Appellants’ “invention intends to capture all combinations of
homopolyligands and heteropolyligands without limitation to the examples”
provided in Appellants’ Specification (id. at 4: ¶ [0009]; see also id. at 7:
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¶ [0031] (“The instant invention is directed to all possible combinations of
homopolyligands and heteropolyligands . . . without limitation”); id. at 12-
13: ¶ [0050]).
FF 4. Appellants disclose that “ligands of the invention are optionally
linked to additional molecules or amino acids that provide an epitope tag, a
reporter, and/or a cellular localization signal,” wherein each may represent
the same or “different molecules” (id. at 4-5: ¶ [0014]; see also id. at 13:
[0052]).
FF 5. Appellants disclose that “[p]olyligands may comprise any two or
more [monomers] of SEQ ID NOS:43-123, wherein Xaa is any amino acid”
(id. at 7: ¶ [0031]).
FF 6. Appellants disclose that “SEQ ID NOS:43-105 are subsequences of
SEQ ID NOS:13-42, where . . . the locations of the PKC phosphorylatable
residues are represented by Xaa,” wherein “Xaa can be any amino acid,”
including naturally and non-naturally occurring amino acids (id. at ¶ [0032]).
FF 7. Appellants disclose that “[t]here are numerous ways to combine SEQ
ID NOS:43-123 into homopolymeric or heteropolymeric ligands” (id. at
¶ [0031]).
FF 8. Appellants disclose that “[t]he length and composition of the spacer
may vary” (id. at 12: ¶ [0050]).
FF 9. Appellants exemplify the structure of three heteropolyligands,
wherein:
[T]he PKC polyligand of SEQ ID NO:1 is encoded by
SEQ ID NO:2, SEQ ID NO:3 and by SEQ ID NO:4, wherein
the codons of SEQ ID NO:3 and SEQ ID NO:4 have been
optimized for vector insertion. SEQ ID NO:4 includes flanking
restriction sites . . . . SEQ ID NO:1 is an embodiment of a
polyligand of the structure A-S1-B-S2-C-S1-D, wherein A is
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SEQ ID NO:43, B is SEQ ID NO:44, C is SEQ ID NO:45, and
D is SEQ ID NO:46, and wherein S1 is a spacer of the amino
acid sequence GAGA, S2 is a spacer of amino acid sequence
AGAG. A polyligand of structure A-S1-B-S2-C-S1-D is also
called herein a heteropolyligand . . . .
SEQ ID NO:5 is an embodiment of a polyligand of the
structure X-S4-Y-S4-Z-S4-Y, wherein X is SEQ ID NO:47, Y
is SEQ ID NO:48, and Z is SEQ ID NO:49, wherein Xaa is
alanine, and wherein S4 is a spacer of amino acid sequence
AAGPGAA. The PKC polyligand of SEQ ID NO:5 is encoded
by SEQ ID NO:6, SEQ ID NO:7 and by SEQ ID NO:8, wherein
the . . . codons of SEQ ID NOS:7 and 8 have been optimized
for vector insertion. SEQ ID NO:8 includes flanking restriction
sites. A polyligand of structure X-S4-Y-S4-Z-S4-Y is also
called herein a heteropolyligand . . . .
SEQ ID NO:9 is an embodiment of a polyligand of the
structure X-S5-Y-S6-Z-S7-A, wherein X is SEQ ID NO:50, Y
is SEQ ID NO:51, Z is SEQ ID NO:52, A is SEQ ID NO:53,
wherein Xaa is alanine, and wherein S5 is a six amino acid
spacer with the sequence AAGGAA, S6 is a[] six amino acid
spacer with the sequence GGAAGG, and S7 is a seven amino
acid spacer with sequence PGAGAGA. The PKC polyligand of
SEQ ID NO:9 is encoded by SEQ ID NO:10, SEQ ID NO:11,
and by SEQ ID NO:12, wherein the . . . codons of SEQ ID
NOS:11 and 12 have been optimized for vector insertion. SEQ
ID NO:12 includes flanking restriction sites. A polyligand of
structure X-S5-Y-S6-Z-S7-A is also called herein a
heteropolyligand.

(Id. at 22-23: ¶¶ [0087]-[0089].)
FF 10. Examiner finds that Appellants’ Specification fails to provide written
descriptive support for, or provide an enabling description of,
[A] genus of isolated nucleic acid sequences encoding a PKC
polyligand comprising a structure selected from the group
consisting of X-S-X and X-S-Y, wherein X and Y are different
polypeptide monomers, wherein X and Y are monomers
selected from an amino acid sequence having at least 85%
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(claim 125), 90% (claim 133), 95% (claim 134)[,] and 98%
(claim 135) sequence identity to any of the polypeptides of
SEQ ID NOS: 43-123 . . . , able to inhibit PKC activity.
(Ans. 7.)
FF 11. Examiner finds that Appellants fail to disclose a “core structure” that
is representative of the “full scope of the claimed genera” (id. at 12).
FF 12. Examiner finds that
While one of skill in the art can readily envision numerable
species of nucleic acid sequences that are at least a give %
identity to a reference nucleotide sequence and . . . encode a
polypeptide monomer at least of a given % identify to a recited
reference amino acid sequence i.e., SEQ ID NOS: 47, 48[,] and
49, one cannot envision which of these also encode a
polypeptide with a specified activity in the context of the
polyligand structure X-S-X or X-S-Y.
(Id. at 16.)
FF 13. Examiner finds that Appellants’ Specification fails to disclose “how
the linker segments in the context of a polyligand comprising the claimed
variants of inhibitory peptides interact with particular PKC isozyme[] active
sites” (id. at 17).
FF 14. Examiner finds that “excessive trial and error experimentation would
have been required to identify” a polynucleotide that encodes a polypeptide
that inhibits protein kinase C activity as set forth in Appellants’ claimed
invention (id.).
FF 15. Appellants disclose that “[i]hibition of PKC activity is demonstrated
by measuring phosphorylation of endogenous substrates against controls”
(Spec. 21: ¶ [0078]).
FF 16. Kimchi-Sarfaty discloses that
The amino acid sequence of proteins is generally
believed to determine protein expression, folding, and function;
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mutations that alter the primary structure of a protein can affect
these properties. The important question addressed by this
study is the role of silent mutations (i.e., those that do not affect
amino acid sequence) in protein folding and function. Recent
theoretical studies have suggested that codon usage is not
random, and experimental studies in prokaryotes suggest that
this may be so. Here we show that a silent mutation in a
complex, mammalian membrane transport protein alters the
substrate specificity. We hypothesize that when frequent
codons are changed to rare codons in a cluster of infrequently
used codons, the timing of cotranslational folding is affected
and may result in altered function.
(Kimchi-Sarfaty4 527: col. 3, ll. 36-53 (endnotes omitted); see generally
Ans. 12-15.)
ANALYSIS
Initially, we note that there is some confusion on this record as to the
exact scope of the claims before this Panel for review (see, e.g., Ans. 6
(While the claims before this Panel for review are drawn to polynucleotides,
Examiner states that “[t]he claims are examined to the extent that they read
on the elected species: the polypeptide of SEQ ID NO: 5 encoded by the
nucleotides of SEQ ID NOS: 6, 7[,] and 8”); Cf. App. Br. 14). Nevertheless,
during the November 14, 2013 Oral Hearing, Appellants’ representative
confirmed that the full scope of Appellants’ claimed invention is before this
Panel for review.5

4 Chava Kimchi-Sarfaty, et al., “A ‘Silent’ Polymorphism in the MDR1
Gene Changes Substrate Specificity,” 315 SCIENCE 525-528 (2007).
5 Appellants addressed Appeal Nos. 2012-005519 and 2012-005520
collectively during the November 14, 2013 Oral Hearing, using 2012-
005519 as representative of the issues in both Appeals and confirmed that
the comments made toward Appeal No. 2012-005519 also apply to the
2012-005520 Appeal.
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Claim Interpretation:
Appellants’ claims 125 and 135 are directed to: (1) a polynucleotide
of any sequence and length; (2) that encodes a polypeptide of any length; (3)
wherein the polypeptide includes within its sequence; (4) at least one region
represented by the formula X-S-X or X-S-Y; and (5) any number of
additional molecules (e.g., an epitope tag, reporter, cellular localization
signal, X or Y monomers, and spacers (S)) attached to the polypeptide in
some manner (FF 4-6; Claims 125 and 135).
Appellants define the components of the X-S-X and X-S-Y formula as
a polypeptide monomer (a) of any length that (b) contains an amino acid
sequence at least 85% (claim 125) or 98% (claim 135) identical to any one
of SEQ ID NOS: 43-123, wherein (c) “Y” is a different polypeptide
monomer than “X,” and (d) the Xaa recited in SEQ ID NOS: 43-123
represents a naturally or non-naturally occurring amino acid (FF 5 and 6;
Claims 125 and 135).
The “S” component of Appellants’ formula is (i) optionally present
and (ii) may be of any length and composition (FF 8; Claims 125 and 135).
According to Appellants’ Specification, variants of SEQ ID NOS: 43-
123 may be combined in any number of ways and with any number of
additional molecules of any length to realize the intended scope of
Appellants’ claimed invention, which is “to capture all combinations of
homopolyligands and heteropolyligands without limitation” (FF 3 and 7;
Claims 125 and 135).
The remaining limitation of Appellants’ claimed invention requires
the foregoing highly variable polynucleotide to encode a polypeptide that
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inhibits at least one isoform of protein kinase C activity (FF 2; Claims 125
and 135).

Representative Species:
Appellants disclose three heteropolyligands that fall within the scope
of Appellants’ claimed invention and comprise a structure having the
formula, A-S1-B-S2-C-S1-D; X-S4-Y-S4-Z-S4-Y; and X-S5-Y-S6-Z-S7-A
(FF 9). Appellants fail to identify which protein kinase C isoform is
inhibited by the representative heteropolyligands (see FF 9; Cf. FF 2 and
15). Instead, Appellants discloses that “[i]hibition of PKC activity is
demonstrated by measuring phosphorylation of endogenous substrates
against controls” (FF 15).

Written Description:
Examiner finds that Appellants’ Specification fails to provide written
descriptive support for the genus of isolated nucleic acid sequences,
encompassed by Appellants’ claims 125 and 135, that encode a polypeptide
that inhibits the activity of at least one isoform of protein kinase C (FF 10;
see also FF 2). According to Examiner, “one cannot envision which of the
[highly variable polynucleotides encompassed by Appellants’ claimed
invention] encode[s] a polypeptide with a specified activity in the context of
the polyligand structure X-S-X or X-S-Y (FF 12 (emphasis added)). In this
regard, Examiner finds that variability in both nucleic acid and amino acid
sequence contribute to the unpredictability associated with protein function
and Appellants failed to disclose a “core structure” that is representative of
the “full scope of the claimed genera” (FF 11, 13, and 16).
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Claim 125:
Appellants contend that because it would have been obvious to make
and test a polynucleotide within the genus of Appellants’ claimed invention,
Appellants had possession of every polynucleotide sequence contained
therein that is capable of inhibiting the activity of at least one protein kinase
C isoforms (App. Br. 15-16; FF 2). We are not persuaded. “[A] description
that merely renders the invention obvious does not satisfy the requirement.”
Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co., 598 F.3d 1336, 1352 (Fed.
Cir. 2010) (en banc).
Appellants contend that the law does not require a correlation between
structure and function (App. Br. 25). While we agree with Appellants that
the written description requirement of 35 U.S.C. § 112, first paragraph, may
be satisfied in a number of ways, the Specification must “itself …
demonstrate[s] possession” of the claimed invention. Ariad, 598 F.3d at
1352. For the reasons set forth above, Appellants’ Specification fails to
demonstrate possession of the entire claimed genus of polynucleotides that
encode a protein that is capable of inhibiting the activity of at least one
isoform of protein kinase C. For the same reasons we are not persuaded by
Appellants’ contention that “one need not disclose what amino acid
modifications are permissible” (App. Br. 25; Cf. FF 16).
We recognize, but are not persuaded by, Appellants’ reliance on
Example 14 of the “REVISED INTERIM WRITTEN DESCRIPTION
GUIDELINES TRAINING MATERIALS” (see e.g. App. Br. 16-19 and 25-
26; see also Appellants’ Exhibit A). Appellants’ contentions fail to account
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for the revised “TRAINING MATERIALS”6 dated prior to the filing date of
Appellants’ Briefs.
We recognize, but are not persuaded by, Appellants’ contention that
Examiner’s written description rejection is contrary to Federal Circuit Case
Law (App. Br. 19-22). See e.g., Ariad; see also University of Rochester v.
G.D. Searle & Co., Inc., 358 F.3d 916, 925 (Fed. Cir. 2004) (“[e]ven with
the three-dimensional structures of enzymes such as COX-1 and COX-2 in
hand, it may even now not be within the ordinary skill in the art to predict
what compounds might bind to and inhibit them”). Simply stated, contrary
to the disclosure set forth in Appellants’ Specification and Appellants’
contentions, the written description requirement “requires a description of an
invention, not an indication of a result that one might achieve if one made
that invention.” Regents of the University of California v. Eli Lilly & Co.,
119 F.3d 1559, 1568 (Fed. Cir. 1997); see also Novozymes A/S v. DuPont
Nutrition Biosciences APS, 723 F.3d 1336, 1350 (Fed. Cir. 2013) (“A patent
. . . ‘is not a reward for the search, but compensation for its successful
conclusion.’ . . . For that reason, the written description requirement
prohibits a patentee from ‘leaving it to the . . . industry to complete an
unfinished invention.’” (citations omitted)).

Claim 135:
We recognize Appellants’ contention that Appellants’ Specification
provides written descriptive support for the genus encompassed by

6 “WRITTEN DESCRIPTION TRAINING MATERIALS,” 33-35,
(Revision 1, March 25, 2008) (see http://www.uspto.gov/web/menu/
written.pdf).
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Appellants’ claim 135, because the recited monomers “are at least 98%
identical to SEQ ID NOS: 43-123” (App. Br. 27-28). We are not persuaded
for the reasons set forth above. To be clear, as discussed above, the claimed
polynucleotide comprises any number of different components that vary,
inter alia, in size, composition, and sequence, in addition to at least two
monomer units that vary to some degree relative to the recited SEQ ID NOS.

Enablement:
Examiner finds that Appellants’ Specification fails to provide an
enabling description of the genus of isolated nucleic acid sequences, as set
forth in Appellants’ claims 125 and 135, that encode a polypeptide able to
inhibit the activity of at least one isoform of protein kinase C (FF 11; see
also FF 2). Examiner finds that “excessive trial and error experimentation
would have been required to identify” a polynucleotide that encodes a
polypeptide that inhibits protein kinase C activity as set forth in Appellants’
claimed invention (FF 14).

Claim 125:
“Appellants submit that one of ordinary skill in the art would be able
to make and derive the claimed isolated polynucleotide of claim 125 based
on the specification as filed” (App. Br. 33). Appellants’ claims are not,
however, limited to a polynucleotide that encodes a protein. Instead,
Appellants’ claims require the polynucleotide to encode a protein that
inhibits the activity of at least one protein kinase C isoform (see, e.g., FF 2
and 13).
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Appellants’ Specification fails to disclose which polypeptides
encoded by a polynucleotide, within the scope of Appellants’ claimed
invention, would be capable of inhibiting the activity of at least one protein
kinase C isoform or, if not all isoforms, which particular isoform such an
encoded polypeptide would inhibit. At best, Appellants’ Specification
directs one to make polynucleotides that fall within the extremely large
scope of Appellants’ claim and then figure out, through trial and error
testing, which of these polynucleotides encode a polypeptide capable of
inhibiting the activity of at least one protein kinase C isoform (see FF 15).
As Examiner explains, this activity would require “excessive trial and error
experimentation” (FF 14). See In re ʼ318 Patent Infringement Litigation,
583 F.3d 1317, 1327 (Fed. Cir. 2009) (“[A]t the end of the day, the
specification, even read in light of the knowledge of those skilled in the art,
does no more than state a hypothesis and propose testing to determine the
accuracy of that hypothesis. That is not sufficient.”).
We acknowledge Appellants’ concession that “it would . . . require[]
experimentation in order to modify the claimed polynucleotide to encode a
PKC ligand across the full scope of the claims” (Reply Br. 18). See In re
Vaeck, 947 F.2d 488, 495 (Fed. Cir. 1991) (“That some experimentation may
be required is not fatal; the issue is whether the amount of experimentation
required is ‘undue.’”) However, notwithstanding Appellants’ contention to
the contrary, we agree with Examiner’s conclusion that making and testing
every possible species that falls within the scope of Appellants’ claimed
invention to identify those polynucleotides that encode a polypeptide
exhibiting the claimed activity would require undue experimentation (See
Ans. 20 and 28-29; Cf. Reply Br. 18). “[T]o be enabling, the specification of
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a patent must teach those skilled in the art how to make and use the full
scope of the claimed invention without ‘undue experimentation.’”
Genentech, Inc. v. Novo Nordisk, A/S, 108 F.3d 1361, 1365 (Fed. Cir. 1997)
(quoting In re Wright, 999 F.2d 1557, 1561 (Fed. Cir. 1993)).

Claim 135:
We recognize Appellants’ contention that Appellants’ Specification
provides written descriptive support for the genus encompassed by
Appellants’ claim 135, because the recited monomers “are at least 98%
identical to SEQ ID NOS: 43-123” (App. Br. 33-34). We are not persuaded
for the reasons set forth above.

CONCLUSION OF LAW
The preponderance of evidence on this record supports Examiner’s:
1. finding that Appellants’ Specification fails to provide written
descriptive support for the full scope of Appellants’ claimed invention; and
2. conclusion that undue experimentation would be required to
practice the full scope of claimed invention.
The rejection of claims 125 and 135 under the written description and
enablement provisions of 35 U.S.C. § 112, first paragraph is affirmed.
Claims 126-129, 133, and 134 fall together with claim 125.

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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

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