Ex Parte Shimada et al

Patent Trial and Appeal Board

Mar 31, 2017

12516790 (P.T.A.B. Mar. 31, 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.
12/516,790 05/28/2009 Takashi Shimada OKA-0311 1049
74384 7590
Cheng Law Group, PLLC
1133 13th St. N.W.
Suite C2
Washington, DC 20005
EXAMINER
LYONS, MARY M
ART UNIT PAPER NUMBER
1645
MAIL DATE DELIVERY MODE
03/31/2017 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 TAKASHI SHIMADA, ATSUHIKO TOYAMA,
and TAKA-AKI SATO1
Appeal 2015-006087
Application 12/516,790
Technology Center 1600
Before MELANIE L. McCOLLUM, JOHN G. NEW, and
TAWEN CHANG, Administrative Patent Judges.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
appellants state the real party-in-interest is the Shimadzu Corporation of
Kyoto, Japan. App. Br. 2.
Appeal 2015-006087
Application 12/561,790
SUMMARY
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of claims 1—20. Specifically, claims 1—8, 10—16,
and 18—20 stand rejected as unpatentable under 35 U.S.C. § 102(b) as being
anticipated by McFadden et al. (US 2003/0170722 Al, September 11, 2003)
“McFadden”).
Claims 1, 6—9, and 14—19 stand rejected as unpatentable under
35 U.S.C. § 102(b) as being anticipated by C.E. Parker et al., MALDI/MS-
Based Epitope Mapping of Antigens Bound to Immobilized Antibodies, 20
Mol. Biotechnol. 49-62 (2002) (“Parker”).
Claims 1—20 also stand rejected as unpatentable under 35 U.S.C.
§ 103(a) as being obvious over the combination of Kropshofer et al. (US
2004/0086521 Al, May 6, 2004) (“Kropshofer”) and Parker.
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
NATURE OF THE CFAIMED INVENTION
Appellants’ invention is directed to a method for analyzing a
“biological sample with clinical significance.” In particular, the invention is
directed to “[mjass spectrometry of a biological sample using
immunoprecipitation.” Abstract.
REPRESENTATIVE CLAIM
Claim 1 is representative of the claims on appeal and recites:
1. A method for mass spectrometry of a biological
sample using immunoprecipitation, comprising the steps of:
2
Appeal 2015-006087
Application 12/561,790
preparing a sample containing an objective biological
molecule;
concentrating the biological molecule in the sample by
immunoprecipitation using an antibody-bound carrier for
precipitation or a carrier for precipitation to which a molecule
capable of specifically binding to an antibody is bound, thereby
obtaining an immunoprecipitate comprising a complex of the
biological molecule and the antibody;
washing the immunoprecipitate comprising the complex
of the biological molecule and the antibody, without dissociation
of binding between the biological molecule and the antibody,
using an aqueous solution containing a charge neutralizing agent
as a washing liquid, wherein the charge neutralizing agent is an
agent that maintains binding capacity between the biological
molecule and the antibody; and
detecting the biological molecule by subjecting the
washed immunoprecipitate comprising the complex of the
biological molecule and the antibody to mass spectrometry,
without dissociating the carrier from the immunoprecipitate.
App. Br. 20.
ISSUES AND ANALYSES
We agree with, and adopt, the Examiner’s findings and conclusions
that the claims on appeal are either anticipated or obvious over the cited
prior art references. We address the arguments raised on appeal by
Appellants below.
3
Appeal 2015-006087
Application 12/561,790
A. Rejection of claims 1—8, 10-16, and 18—20 as anticipated by McFadden
Issue
Appellants argue the Examiner erred in finding McFadden discloses
the limitations of claim 1 reciting “detecting the biological molecule by
subjecting the washed immunoprecipitate comprising the complex of the
biological molecule and the antibody to mass spectrometry, without
dissociating the carrier from the immunoprecipitate.” App. Br. 5 (emphasis
omitted).
Analysis
Appellants argue McFadden discloses that “the targeted proteins
(Flag-Ml IF IP and control HEK293T IP) [are] dissociated, excised, and
prepared for mass spectrometer analysis.” App. Br. 7 (citing McFadden ||
27, 98, 230—235). According to Appellants, this means that “the proteins are
reduced, subjected to digestion by trypsin, purified by Cis reverse-phase
chromatography, and resuspended prior to analysis by mass spectrometry.”
Id. Therefore, argue Appellants, the “‘Flag-tagged proteins’ (i.e., the
immunoprecipitate) of McFadden are not a complex of the biological
molecule and the antibody, as required by the present claims. Id. Rather,
Appellants assert, only the target protein (i.e., the biological molecule) is
analyzed by mass spectrometry in McFadden. Id.
Appellants assert further that McFadden discloses that the supernatant
is incubated with M2-agarose, which is washed twice with kinase lysate
buffer, and washed one time with ammonium bicarbonate to elute the Flag-
tagged protein. App. Br. 7—8. Appellants contend that although McFadden
discloses that an antigen-antibody complex bound to a support is washed
4
Appeal 2015-006087
Application 12/561,790
with ammonium bicarbonate; the mass spectrometry was performed after
eluting the Flag-tagged protein. Id. at 8. In other words, Appellants argue,
McFadden discloses the mass spectrometry is performed only after
dissociating the antigen-antibody complex from the support by eluting the
Flag-tagged protein. Id.
Appellants argue further that the washing in McFadden “is performed
for the purpose of adjusting pH in order to weaken a binding force between
the support and the antigen-antibody complex, as a pre-treatment for eluting
the antigen-antibody complex by the Flag-tagged polypeptide from the
support, after removing impurities by ... washing [twice] with buffer.” App.
Br. 8 (citing McFadden 198). Therefore, argue Appellants, “the washing
disclosed by McFadden ... is performed for the purpose of dissociating the
antigen-antibody complex from the support.” Id.
The Examiner points out that paragraph [0098] of McFadden
discloses: “Following incubation, the beads are washed to remove any
unbound label, and the matrix immobilized and labeled target polypeptide
retained on the matrix determined directly, or in the supernatant after the
complexes are subsequently dissociated.” McFadden 198; Ans. 4—5, 18.
Appellants dispute the Examiner’s finding that “the matrix immobilized and
labeled target polypeptide retained on the matrix determined directly” means
that the labeled target polypeptide (i.e., the complex of the biological
molecule and the antibody) is subjected to mass spectrometry without
dissociation from the matrix (i.e., without dissociating the carrier from the
immunoprecipitate). App. Br. 8 (citing Final Act. 7—8). Appellants argue
instead that McFadden “clearly discloses dissociating the complex of the
biological molecule and the antibody from the carrier prior to analysis by
5
Appeal 2015-006087
Application 12/561,790
mass spectrometry,” given the other disclosures in McFadden recited in the
Appeal Brief and discussed above. Id. at 7—9.
The Examiner responds that McFadden discloses that the “labeled
target polypeptide retained on the matrix [is] determined directly, or in the
supernatant after the complexes are dissociated from the matrix.” Ans. 18
(quoting McFadden 198) (internal quotation marks omitted and emphasis
original in Answer). The Examiner therefore finds McFadden teaches direct
detection for antigen-antibody complexes that are dissociated as well as for
those that are not dissociated. Id. Accordingly, the Examiner finds that,
despite the exemplary embodiment disclosed by McFadden of an alternate
method (i.e., detection following dissociation), McFadden also discloses
both embodiments (i.e., detecting with or without dissociation). Id.
The Examiner also finds McFadden discloses washing the
immunoprecipitate with ammonium bicarbonate (i.e., a charge neutralizing
agent and an aqueous solution of ammonium salt). Ans. 18 (citing
McFadden 1231). With respect to Appellants’ argument that McFadden
discloses a different motivation for washing the immunoprecipitate, the
Examiner notes that the fact that Appellants have recognized another
advantage which would flow naturally from following the suggestion of the
prior art cannot be the basis for patentability when the differences would
otherwise be obvious. Id. at 19 (citing Ex parte Obiaya, 227 USPQ 58, 60
(BPAI 1985)).
Appellants reply that paragraph [0098] of McFadden should properly
be interpreted as teaching “[f] olio wing incubation, the beads are washed to
remove any unbound label, and the matrix immobilized and labeled target
polypeptide which was retained on the matrix is determined after the
6
Appeal 2015-006087
Application 12/561,790
complexes are dissociated either (1) directly or (2) in the supernatant [sic].”
Reply Br. 3. Appellants contend that this interpretation is consistent with
the disclosures in McFadden’s paragraphs [0027] and [0230]—[0235], which
Appellants argue discloses that disassociating is necessary prior to
determination. Id.
Appellants respond further that the washing step disclosed by
McFadden results in dissociation of the carrier and immunoprecipitate, and
therefore does not disclose the limitation, “without dissociating the carrier
from the immunoprecipitate.” Reply Br. 4 (citing McFadden 198).
Appellants assert paragraph [0098] of McFadden does not teach an
embodiment where disassociation does not occur, and therefore McFadden
does not disclose a washing step that does not involve dissociation. Id.
We are not persuaded by Appellants’ arguments. McFadden
discloses:
Typically, it will be desirable to immobilize either the
BAK [protein] or the target polypeptide to facilitate separation
of complexes from uncomplexed forms of one or both of the
proteins, as well as to accommodate automation of the assay.
Binding of a BAK polypeptide to the target polypeptide, in the
presence and absence of a candidate agent, can be accomplished
in any vessel suitable for containing the reactants .... Following
incubation, the beads are washed to remove any unbound label,
and the matrix immobilized and labeled target polypeptide
retained on the matrix determined directly, or in the supernatant
after the complexes are subsequently dissociated. Alternatively,
the complexes can be dissociated from the matrix, separated by
SDS-PAGE, and the level of target polypeptide found in the bead
fraction quantitated from the gel using standard electrophoretic
techniques.
7
Appeal 2015-006087
Application 12/561,790
McFadden 198 (emphasis added). We interpret the plain language of this
passage to mean that the target polypeptide-antibody-carrier complex can be
measured directly (i.e., while the antigen-antibody-carrier complex is
immobilized on the matrix) or after the complex has been disassociated.
Moreover, the language “labeled target polypeptide retained on the matrix
determined directly” contradicts Appellants’ assertion that the passage
quoted above should be interpreted as meaning “determined after ... the
complexes are dissociated.” See Reply Br. 4 (emphasis added). Nor are we
persuaded by Appellants’ arguments with respect to the exemplary
embodiment disclosed in paragraphs [0230]—[0235] of McFadden. We find
no language in that disclosure, or elsewhere in McFadden, that excludes the
alternative method disclosed by McFadden in which “the matrix [is]
immobilized and labeled target polypeptide retained on the matrix
determined directly.” McFadden 198.
Similarly, we are not persuaded, for the same reason, that the washing
step recited in paragraph 98 requires, or is for the purpose of, dissociation of
the polypeptide-antibody from the carrier (see Reply Br. 4), because
McFadden is explicit in the same paragraph that the polypeptide-antibody-
carrier complex can be measured directly while still affixed to the matrix.
We consequently affirm the Examiner’s rejection on this ground.
B. Rejection of claims 1, 6—9, and 14—19 as anticipated by Parker
Issue
Appellants argue the Examiner erred in finding Parker discloses the
limitation of claim 1 reciting:
8
Appeal 2015-006087
Application 12/561,790
[W]ashing the immunoprecipitate comprising the complex of the
biological molecule and the antibody, without dissociation of
binding between the biological molecule and the antibody, using
an aqueous solution containing a charge neutralizing agent as a
washing liquid, wherein the change neutralizing agent is an
agent that maintains binding capacity between the biological
molecule and the antibody.
App. Br. 10 (emphasis original).
Analysis
Appellants argue Parker does not disclose the washing step of the
present invention, which provides for weak capping of charges of molecules
such as fatty acids or salts that would otherwise inhibit ionization in mass
spectrometry. App. Br. 10 (citing Spec. 12, 25). According to Appellants,
ions derived from salts, and other charged molecules coexisting with the
immunoprecipitate, would suppress ionization if they remain present in the
subsequent mass spectrometry step. Id. Appellants assert that, by washing
the immunoprecipitate with a charge-neutralizing agent, such ionization
suppression in mass spectrometry can be neutralized by capping. Id. (citing
Spec. 24). Therefore, Appellants argue, the washing step of their claimed
invention provides for superior and unexpected results, viz., making it
possible to accomplish mass spectrometry with high sensitivity while
conducting a simple washing step. Id.
Furthermore, argue Appellants, when using compact reaction columns
(CRCs), as disclosed by Parker, “it is necessary to immobilize the substrate
... to a CRC matrix via covalent bonding by a hydrophobic linker group.”
App. Br. 10—11 (citing Mo Bi Tec, Immobilized Enzymes in Compact
Reaction Columns, Product Information and Instructions (May 2002)).
9
Appeal 2015-006087
Application 12/561,790
Appellants assert the covalent bonding by the hydrophobic linker group
degrades antibody activity with regard to specific bonding between the
antibody and the target antigen, and allows non-specific bonding between
the antibody and impurities other than target antigen. Id. at 11; Reply Br. 6.
Appellants argue that “the use of CRCs complicates a method for mass
spectrometry of a biological sample,” and renders Parker disadvantageous as
compared to the present invention. App. Br. 11.
The Examiner responds that Parker discloses buffers to be used as
washing agents, including ammonium acetate, ammonium carbonate, and
ammonium sulfate (i.e., charge neutralizing agents). Ans. 20 (citing Parker
52, 58). The Examiner finds that any and all washing steps must be
completed prior to detection via mass spectrometry, otherwise the results are
obscured by contaminants. Id. The Examiner finds the mass spectrometry
disclosed in Parker indicates the complexes were not dissociated by any
washing steps because the laser is specifically aimed during mass
spectrometry at or near the affinity beads comprising the target. Id. (citing
Parker 52).
The Examiner further notes that secondary considerations, such as
unexpected results, are not relevant to rejections based on anticipation under
Section 102. Ans. 21 (citing MPEP § 2131.04; In re Wiggins, 488 F.2d 538,
543 (C.C.P.A. 1973)).
We are not persuaded by Appellants’ arguments. Parker discloses the
use of ammonium acetate, ammonium carbonate, and ammonium sulfate
buffers. Parker 52, 58. Appellants’ Specification discloses, by way of
example: “The mass spectrometry of a biological sample using
immunoprecipitation according to any one of (1) to (6), wherein the aqueous
10
Appeal 2015-006087
Application 12/561,790
solution containing the charge neutralizing agent is selected from the group
consisting of ammonia water and aqueous solution of ammonium salt.”
Spec. 9. We agree with the Examiner that Parker’s disclosure of the use of
buffers of ammonium acetate, ammonium carbonate, and ammonium sulfate,
correspond to the Specification’s exemplary description of a charge
neutralizing agent. Parker thus disclose the claimed washing step.
Similarly, while Appellants emphasize the Parker’s method involves
covalent bonding between the substrate and the matrix, Appellants have not
shown that the claims exclude such linkage. We also note but are not
persuaded by Appellants’ argument that Parker’s method degrades specific
bonding between the antibody and the target antigen and allows non-specific
bonding between the antibody and impurities other than target antigen. As
an initial matter, Appellants do not suggest any claim limitation that is not
met in light of the alleged degradation of antibody activity. In any event,
Appellants’ “[attorneys’ argument is no substitute for evidence.” Johnston
v. IVAC Corp., 885 F.2d 1574, 1581 (Fed. Cir. 1989). Finally, as the
Examiner notes, Appellants’ apparent argument regarding unexpected
results do not apply in an anticipation analysis. Cf. Celeritas Techs. Ltd. v.
RockwellInt’l Corp., 150 F.3d 1354, 1361 (Fed. Cir. 1998) (citation
omitted) (teaching away inapplicable to anticipation). We consequently
affirm the Examiner’s rejection on this ground.
C. Rejection of claims 1—20 as obvious over Kropshofer and Parker
Issue
Appellants argue the Examiner erred because Kropshofer neither
teaches nor suggests the limitation of claim 1 reciting: “detecting the
11
Appeal 2015-006087
Application 12/561,790
biological molecule by subjecting the washed immunoprecipitate comprising
the complex of the biological molecule and the antibody to mass
spectrometry, without dissociating the carrier from the immunoprecipitate.”
App. Br. 13.
Analysis
Appellants argue that Kropshofer is directed to
a method for isolating antigenic peptides in femtomolar amounts,
which method comprises: (a) providing immature dendritic cells in a
number providing 0.1 to 5 pg MHC II molecules; (b) contacting the
cells of (a) with a source of potential antigen and inducing maturation
of the dendritic cells by adding TNFalpha; (c) isolating MHC II
molecule-antigenic peptide complexes from the cells with methods
comprising solubilization of the cells with the detergent TX-100 and
sequestration of the complexes of MHC II molecules with antigenic
peptides by immunoprecipitation or immunoaffmity chromatography;
(d) washing the sequestered complexes of MHC II molecules with
antigenic peptides with water in an ultrafiltration tube; (e) eluting the
associated antigenic peptides from the MHC II molecules at 37°C with
diluted trifluoro acetic acid; and (f) sequencing and identifying the
isolated peptides by liquid chromatography and mass spectrometry.
App. Br. 12—13 (citing Kropshofer claim 27). Appellants therefore argue
Kropshofer neither teaches nor suggests the disputed limitation but instead
“discloses eluting the associated antigenic peptides from the MHC II
molecules and identifying the isolated peptides by liquid chromatography
and mass spectrometry.” Id. at 13.
Appellants further argue that Parker fails to cure the deficiencies of
Kropshofer. App. Br. 13. Appellants repeat their argument, presented
supra, that Parker fails to teach or suggest the claimed washing step that
provides for weak capping of the charges of molecules such as fatty acids or
12
Appeal 2015-006087
Application 12/561,790
salts that would otherwise inhibit ionization in mass spectrometry. Id.
(citing Spec. 12, 25).
Appellants also contend the washing step of the present invention
provides for superior and unexpected results, that is, the step “makes it
possible to accomplish mass spectrometry with high sensitivity while
conducting the simple steps,” due to suppression of ionization by capping
effect of this washing step. App. Br. 13 (citing Spec. 24).
The Examiner responds that Kropshofer teaches methods for immune
isolation of target molecules comprising incubating antibody-bound beads
with cell lysates followed by washing with low salt buffers (i.e., a charge
neutralizing agent as a washing agent. Ans. 22 (citing Kropshofer || 44, 46,
50). The Examiner also finds Kropshofer teaches that the peptide-antibody-
bead complexes may be washed either before or after centrifugation; and
that the efficiency of the immunoprecipitation using antibody-beads may be
analyzed after washing. Id. (citing Kropshofer || 44 125, 128).
The Examiner further finds Parker teaches the advantages of mass
spectroscopy utilizing direct detection, i.e., without dissociating the peptide-
antibody complex and the bead carrier. Ans. 22 (citing Parker 52). The
Examiner therefore concludes it would have been prima facie obvious to a
person of ordinary skill in the art to modify the method for mass
spectrometry of a biological sample using immunoprecipitation and
MALDI-mass spectroscopy as taught by Kropshofer, by using antibodies
that remain bound to the sepharose beads, as taught by Parker, because
Parker teaches using immobilized antibodies greatly simplifies the procedure
by eliminating additional steps for sample preparation. Id.
13
Appeal 2015-006087
Application 12/561,790
The Examiner also finds that, contrary to Appellants’ arguments with
respect to the weak capping of charges of molecules such as fatty acids or
salts that would otherwise inhibit ionization in mass spectrometry, no such
limitation is present in the claims, and Appellants may not read additional
limitations from their Specification into the claims. App. Br. 22—23.
However, the Examiner finds, because the references explicitly teach
washing agents that meet this step, the limitation is interpreted as a
functional feature that flows naturally from the washing steps, using the
same charge neutralizing agents that are taught in the cited prior art. Id. at
23.
Finally, with respect to Appellants’ alleged showing of unexpected
results, the Examiner finds that washing steps for preparing samples for
analysis via mass spectroscopy are routine in the art for improving the
corresponding results, as taught by all of the cited prior art references. Ans.
23. The Examiner therefore finds that a person of ordinary skill in the art
would reasonably expect improved results and Appellants’ results are
consequently not unexpected. Id.
We agree with the Examiner. As we explained supra, we are not
persuaded by Appellants’ arguments that Parker fails to teach the recited
washing steps. Furthermore, Kropshofer also teaches washing steps using,
inter alia, ammonium sulfate, as recited in Appellants’ Specification. See
Kropshofer || 44, 46, 125. Furthermore, for Appellants to demonstrate
unexpected or surprising results as evidence of nonobviousness, the results
must be shown to be unexpected compared with the closest prior art. In re
Baxter TravenolLabs., 952 F.2d 388, 392 (Fed. Cir. 1991). Appellants
adduce no evidence that their results are unexpected or surprising compared
14
Appeal 2015-006087
Application 12/561,790
to a reference of the closest prior art, they merely assert that this is so. That
is insufficient to overcome the Examiner’sprima facie conclusion of
obviousness. “[I]t is well settled that unexpected results must be established
by factual evidence. ‘Mere argument or conclusory statements in the
specification does not suffice.’” In re Geisler, 116 F.3d 1465, 1470 (Fed.
Cir. 1997) (quoting In re De Blauwe, 736 F.2d 699, 705 (Fed. Cir. 1984)).
We consequently affirm the rejection of claims 1—20.
DECISION
The Examiner’s rejection of claims 1—8, 10—16, and 18—20 as
anticipated by McFadden under 35 U.S.C. § 102(b) is affirmed.
The Examiner’s rejection of claims 1, 6—9, and 14—19 as anticipated
by Parker under 35 U.S.C. § 102(b) is affirmed.
The Examiner’s rejection of claims 1—20 as unpatentable under
35 U.S.C. § 103(a) 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). See 37 C.F.R.
§ 1.136(a)(l)(iv).
AFFIRMED
15