Ex Parte 7462489 et al

Patent Trial and Appeal Board

Jan 9, 2015

90011666 (P.T.A.B. Jan. 9, 2015)

UNITED STATES PATENT AND TRADEMARKOFFICE
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.
90/011,666 05/02/2011 7462489 MPL-001-US 9737
27326 7590 01/09/2015
VANCE INTELLECTUAL PROPERTY, PC
5467 HILL TOP STREET
CROZET, VA 22932-3167
EXAMINER
CAMPELL, BRUCE R
ART UNIT PAPER NUMBER
3991
MAIL DATE DELIVERY MODE
01/09/2015 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 MICROPARTICLES PROTEOMICS, LLC 1
APPELLANT
__________

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Patent US 7,462,489 B2
Technology Center 3900
__________

Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and
ROBERT A. POLLOCK, Administrative Patent Judges.

POLLOCK, Administrative Patent Judge.

DECISION ON APPEAL
Appellants appeal under 35 U.S.C. §§ 134(b) and 306 from the
Examiner’s rejections of claims 1–20. We have jurisdiction under 35 U.S.C.
§§ 6(b)(2) and 306.
We affirm.
STATEMENT OF THE CASE
A request for ex parte reexamination of the Ley Patent2 was filed on
May 2, 2011. The request for ex parte reexamination was assigned

1 Appellant asserts that Microparticles Proteomics, LLC is the Real Party in
Interest and assignee of the patent under reexamination. (App. Br. 3.)
2 Ley et al., US 7,462,489 B2, entitled “METHODS FOR IDENTIFYING AND
ANALYZING BIOMARKERS FROM PLASMA-DERIVED MICROPARTICLES,” issued
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Reexamination Control No. 90/011,666 on July 1, 2011. Claims 1–20 are on
Appeal and can be found in the Claims Appendix of Appellant’s brief.
The detection of proteins in human blood plasma is an important tool
for evaluating the predisposition, presence, and progression of numerous
clinical conditions. (Spec. 1:14–18.) However, common plasma proteins,
such as albumin, fibrinogen, immunoglobulins, and transferrin, interfere
with the detection of less abundant proteins and “[r]emoval of the ten most
abundant proteins only increases the sensitivity by one order of magnitude,
still leaving most proteins undetected.” (Id. at 1:32–42). Thus, although
there may be 40,000 different proteins present in normal plasma, and another
500,000 proteins which may be present under a variety of clinical
conditions, current methodology, based on 2D gels, liquid chromatography,
and /or mass spectroscopy, has led to the detection of only about 500
different plasma proteins. (Id. at 1:18–32.) This “appears to be the limit of
detection for the analysis of unfractionated plasma due to the dynamic range
of these analytical methods.” (Id. at 1:29–34.)
“The present invention provides methods for isolating, identifying,
and analyzing microparticles derived from plasma, particularly platelet-poor
plasma.” (Id. at 2:32–35). “Microparticles (MPs) are small subcellular
membranous vesicles released by essentially all cell types, especially when
activated or under stress.” (Id. at 1:43–45). “[S]ignificant evidence has
accumulated to indicate that MPs contain a unique set of proteins and
inflammatory factors that have important biological functions.” (Id. at 2:1–

December 9, 2008, to Klaus F. Ley and David M. Smalley, based on
Application No. 11/935,048, filed November 5, 2007.
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3). “Many microparticles in plasma are derived from platelets, but it is
believed that valuable information resides in plasma microparticles derived
from other cells as well.” (Id. at 2:23–25.) “It is therefore desirable to find
methods of identifying biomarkers in plasma microparticles that can be
useful for diagnosing various diseases, disorders, and conditions.” (Id. at
2:26–28).
Representative claim 1, the sole independent claim on appeal, reads as
follows:
1. A method of identifying candidate biomarkers in the plasma
microparticle sub-proteome, comprising:
(a) isolating proteins from blood plasma microparticles
obtained from at least one blood sample from a case and at least
one blood sample from a control;
(b) identifying the proteins;
(c) applying a statistical test to measure the abundance of each
protein identified; and,
(d) determining the presence of positive and negative
biomarkers by comparing the abundance of each protein
identified in at least one case blood sample with the abundance
of the same protein in at least one control blood sample.
The following grounds of rejection are before us for review:
The Examiner rejects claims 1–4, 6, 7, 9, 10, and 13–17 under
35 U.S.C. § 103(a) as unpatentable over the combination of Jin3 and Simak.4

3 Ming Jin, et al. Distinct Proteome Features of Plasma Microparticles,
5 PROTEOMICS 1940–1952 (2005).
4 Jan Simak, et al., Elevated Circulating Endothelial Membrane
Microparticles in Paroxysmal Nocturnal Haemoglobinuria, 125 BR. J.
HAEMATOL. 804–813 (2004).
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The Examiner rejects claims 5, 8, 11, 12, and 18–20 under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Jin and Simak as applied to
claims 1–4, 6, 7, 9, 10, and 13–17 above, and further in view of Garcia,5
Liu,6 and Kim.7
FINDINGS OF FACT
We have reviewed Appellant’s contentions that the Examiner erred in
rejecting claims 1–20 as obvious in view of the art of record. (App. Br. 6–
20; Reply 5–14.) We disagree with Appellant’s conclusions and adopt as
our own the factual findings and well-reasoned analysis set forth in the
Examiner’s Answer. For emphasis, we highlight and address the following.
FF1. The Examiner finds the claims on appeal drawn to “a method of
identifying potentially useful biomarkers by quantitatively comparing
the proteins found in plasma microparticles (MPs) of ‘case’ and
‘control’ subjects.” (Ans. 2; see also App. Br. 5.) “Claim 1 sets forth
the basic method and dependent claims 2-20 detail specific steps in
the isolation, identification and quantitation of the MP proteins
(collectively referred to as the MP proteome).” (Ans. 2.)
FF2. With regard to the method set forth in independent claim 1, the
Examiner finds that “Jin performs all the recited steps except for

5 Benjamin A. Garcia, et al., The Platelet Microparticle Proteome, 4 J.
PROTEOME RES. 1516–1521 (2005).
6 Hongbin Liu, et al., A Model for Random Sampling and Estimation of
Relative Protein Abundance in Shotgun Proteomics, 76(14) ANAL. CHEM.
4193–4201 (2004).
7 Jeong Whun Kim, et al., Fas Ligand-Positive Membranous Vesicles
Isolated from Sera of Patients with Oral Cancer Induce Apoptosis of
Activated T Lymphocytes, 11 CLIN. CANCER RES. 1010–1020 (2005).
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comparing ‘case’ samples with those obtained from control subjects.”
(Id.)
Jin isolated plasma MPs from healthy human subjects.
The MPs were isolated from an MP-enriched plasma
fraction obtained by centrifugation, then proteins were
extracted from the MPs, separated by 2-D gel
electrophoresis (one dimension being SDS-PAGE),
quantified, and the most abundant plasma MP proteins
identified by mass spectrometry (MS). Jin suggests that
plasma MP proteins might include disease markers (p.
1940, col. 2).
(Id.)
FF3. Jin states that “The number of observed protein spots from the
three MP 2-D gels (1021-1055) was consistently higher than that in
each of the three plasma 2-D gels (296-360). Six 2-D gels of three
MPs and three plasma were matched to the MP reference 2-D map
and the relative densities of all protein spots quantified using
ImageMaster software.” (Jin 1942–43.) “For each spot on the 2-D
gel, the mean density was obtained along with a standard deviation for
calculation of protein quantity.” (Id. at 1943.) The relative amounts
of plasma MP proteins (normalized volume of each 2D gel spot by
percent and standard deviation) are shown in Jin Figure 2. (Id. at
1944, see also Addendum Table 2.)
FF4. Jin suggests the step of comparing “case” samples with those
obtained from control subjects. (See id. at Figs. 2, 5.) Accordingly,
Jin teaches that “the importance of plasma MPs in the regulation of
many physiological processes and their potential values as a source of
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disease markers are well-appreciated.” (Id. at 1946). Jin further states
that:
Proteomics provides a means to globally examine
protein features and their changes in different
pathophysiological conditions . . . However, the proteome
of plasma MPs has yet to be described. Knowledge of
basic protein constituents and their characteristics in
healthy donors will create a basis for future investigation
of MPs’ biology and clinical utility in disease diagnosis
and disease prediction. The present study establishes
groundwork for analysis of the plasma MP proteome.
(Id. at 1941.)
In disease states, MPs derived from the injured organ
likely contain valuable markers for determining the site,
type, and extent of disease pathology.
(Id. at Abstract)
Attempts to explore the blood plasma proteome and to
discover new disease markers were initiated almost 30
years ago . . . Constant improvements in technology have
allowed recent studies to resolve unprecedented numbers
of plasma and serum proteins by applying various
combinations of protein fractionation and analysis
strategies
(Id. at 1943.)
With respect to protein detection sensitivity, 2-D gel
analysis of MPs displayed greater than 1000 distinct
protein spots, three times the number of protein spots
obtained in 2-D gel analysis of whole plasma under
analogous conditions. Therefore, it offers a novel method
to detect many low-abundant proteins and examine their
changes under various pathophysiological conditions.
(Id. at 1946.)
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It remains, however, undefined yet about the amount and
cell origins of MPs in various disease states. Future
proteomic analysis of plasma MPs in the patient
population will provide significant insight into disease
pathophysiology and potentially new diagnostic utilities.
(Id.)
Under pathological conditions, part of the MP
population are cell membrane fragments that may be
created by activated, apoptotic, or otherwise damaged cells
from the site of injury . . . This exciting fact provides
much promise for the clinical application of MP
proteomics in the prediction and early diagnosis of
diseases. Currently, our laboratories are engaged in
establishing the biological variation of major MP proteins
in the general population. A future project will be to
translate knowledge of the MP proteome into clinical
application and practice.
(Id. at 1946–1947.)
FF5. Simak teaches that MPs contain protein biomarkers for disease
states and that “[a]n increasing number of recent studies have
analyzed circulating blood cell, platelet, and endothelial cell MP
[ECMP] in different vascular pathologies.” (Simak 808.) “MP of
endothelial origin are of particular interest because of their possible
diagnostic importance as increased counts of these MP could signal
endothelial cell injury.” (Id.)
FF6. Simak uses flow cytometry and antibodies against specific MP
proteins to analyze “endothelial cell membrane microparticles
(ECMP) in the peripheral blood of patients with paroxysmal nocturnal
haemoglobinuria (PNH) (n = 9), aplastic anaemia (AA) (n = 10),
sickle cell disease (SCD) (n = 8), and healthy donors (HD) (n = 11).”
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(Id. at Summary.) Applying a “Kruskal-Wallis One Way Analysis of
Variance on Ranks” for group comparisons (id. 806), Simak reports
that “[t]he population of CD105+AVB+ ECMP was significantly (P
< 0.05) higher” in SCD and PNH patients when compared to the
healthy donors group (id. at Summary). “Even more pronounced
differences were observed in ECMP exhibiting a marker of
inflammatory stimulation CD54 (CD105+CD54+). Similarly, ECMP
that exhibited endothelial specific and proteolysis-sensitive antigen
CD144 were increased in SCD and PNH, but not in AA.” (Id.)
FF7. “Simak explicitly compares plasma MPs from case (diseased)
and control (healthy) subjects.” (See Ans. 11.) In particular, Simak
discloses
isolated endothelial cell MPs from healthy donors and
donors suffering from various disease states. Endothelial
cell MPs are a subset of plasma MPs identified by labeling
MPs with antibodies against cellular antigens and
quantified by flow cytometry. Several antigens were
identified which appear to be markers for certain diseases.
While different analytical methods were used, Simak’s
results show that disease biomarkers can be found by
comparing the proteins found in plasma MPs of healthy
and diseased individuals. Specifically, MPs isolated from
patients with paroxysmal nocturnal haemoglobinuria were
found to contain elevated amounts of AVB and CD54
(p. 812).
(Id. at 3) The Examiner concludes that:
It would have been obvious to one of ordinary skill in the
art to study the plasma MP proteome by the method of Jin
in order to identify biomarkers for clinical conditions. It
would have been obvious to compare control and “case”
samples, given Jin’s explicit suggestion to do so. There
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would have been a reasonable expectation of success
given the knowledge that plasma MPs do contain proteins
that can be used as biomarkers for certain disease states, as
shown by Simak. Thus the invention as a whole was
clearly prima facie obvious to one of ordinary skill in the
art at the time the invention was made.
(Id.)
ANALYSIS
Appellant’s arguments are directed to the combination of Jin and
Simak as applied to claim 1. (See, e.g., App. Br. 5.) Claims 1–4, 6, 7, 9, 10,
and 13–17 are argued together. (Id. at 6.) Appellant relies on the same
arguments with respect to the rejection of claims 5, 8, 11–12, and 18–20.
(Id. at 19–20.)
Appellant contends that Jin is “not related to finding biomarkers, but
instead is a paper that reported the results of surveying proteins from a
pooled plasma sample from healthy donors.” (Id. at 8.) We do not find
Appellant’s argument persuasive. “[I]n considering the disclosure of a
reference, it is proper to take into account not only specific teachings of the
reference but also the inferences which one skilled in the art would
reasonably be expected to draw therefrom.” In re Preda, 401 F.2d 825, 826
(CCPA 1968). Properly considered, Jin suggests far more than a mere
survey of biomarkers in healthy donors.
As set forth in FF2–4, and further detailed at pages 4 and 5 of the
Examiner’s Answer, Jin emphasizes the importance of MPs “as a source of
disease markers,” teaches that “Proteomics provides a means to globally
examine protein features and their changes in different pathophysiological
conditions,” and that states that “[i]n disease states, MPs derived from the
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injured organ likely contain valuable markers for determining the site, type,
and extent of disease pathology.” Considering the reference as a whole, we
agree with the Examiner that not only does Jin suggest comparing MP
protein biomarkers from case and control subjects, but “shows that those
skilled in the art expected that disease markers would be found. In fact, the
study reported in Jin was intended as the first step in this process.” (Ans. 5.)
Moreover, that Simak expressly compares MP protein antigens in the plasma
of diseased patients and healthy donors underscores the obviousness
identifying candidate biomarkers in the plasma microparticle sub-proteome.
(See FF5–7.)8
Appellants contend that “the technology of Jin was crude and
extremely limited” as it could only identify 169 of the 260 most abundant
MP protein spots on a 2D gel, and this represents only about 17% of the 2D
spots from a “pooled sample.” (App. Br. 8–9.) These arguments do not
persuade us that the Examiner erred in rejecting the claims on appeal.
As an initial matter, we do not read the claims at issue to exclude the
use of pooled samples. To the contrary, the language of independent claim 1
(“isolating proteins . . . from at least one blood sample from a case and at
least one blood sample from a control”) appear to expressly contemplate
such pooling. Nor do the claims require any particular level of sensitivity.

8 Simak assays known proteins in case and control MP populations to
determine which, if any, provide biomarkers for diseases of interest, finding,
for example, that the abundance of CD105 and AVB antigens were
significantly higher in those from SCD and PNH patients as compared to
healthy donors. We therefore reject Appellant’s argument that Simak “is
entirely unrelated to looking for biomarkers in a case/control method.” (See
App. Br. 16–17.)
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(See Ans. 6–7.) Indeed, given the Examiner’s finding that the Ley Patent
“also excluded unidentified and/or low abundance peptides (col. 11, lines 1–
9) . . . . and only identified 209 gene products (col. 15, lines 14–16)” (Ans.
6) out of more than 40,000 (or 500,000) potential target proteins (Spec.
1:18–23), it is not immediately apparent whether Appellant’s Specification
would support an increased sensitivity as compared to the cited art. Finally,
with respect to Appellant’s argument that Jin’s 2D gel system is somehow
inapplicable because “Jin could only identify 17% of the reported spots”
(Reply 7, see also Reply 18), we note that nothing in the claims requires the
ability to identify every possible MP protein.
Appellant contends that Jin does not “apply a statistical analysis to
measure the abundance of each protein identified” as required by claim 1.
(App. Br. 9–10; Reply 6–9.) Appellant first argues that the ImageMaster2D
software used by Jin is not a statistical analysis at all, but “a straightforward
algorithm that converts density of a 2-D gel into protein weight.” (App. Br.
9, 18.)
In accord with the Examiner’s findings, we note that the Ley Patent
broadly teaches the quantitation of protein abundance (claim step (c)) from
mass spectrometer ion currents by “integrating the area under the curve for
cases and controls.” (Spec. 6:4–6; Ans. 6–7.) Applying the broadest
reasonable interpretation in light of the Specification, we agree with the
Examiner that a mean and standard deviation implies a statistical test, such
that claim step (c) is satisfied by Jin’s use of “optical density data from
multiple gels to determine a mean and standard deviation (statistical
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analysis) of the % normalized gel volume for each selected protein spot (see
p. 1943, col. 2; pp. 1948–1952, far right column of Table 2).” (Ans. 7.)
In the alternative, Appellant argues that, contrary to the language of
claim 1, any statistical analysis taught by Jin is used on “unidentified
proteins.” (App. Br. 9.) In other words, Appellant contends that the claims
require that the identification and statistical quantitation steps be performed
in a particular order, “which cannot be reversed.” (Reply 6.) “[T]o apply
step (c), the statistical analysis to calculate abundance, the identities of the
proteins in the case and control samples must be known.” (Id. at 8.)
Moreover, “step (c), a statistical measurement of abundance of each
identified protein, requires a comparison. This comparison must be between
the case and control proteins in order for one to practice step (d), the
determining of a positive or negative biomarker.” (Id.) We do not find
Appellant’s arguments persuasive.
First, step (c) does not require a comparison between case and control
samples. Such a requirement would in fact be duplicative of the express
language of step (d): “comparing the abundance of each protein identified in
at least one case blood sample with the abundance of the same protein in at
least one control blood sample.” Accordingly, the “abundance” of each
protein in step (c) need not be measured relative to a case (or control)
sample.
Moreover, we agree with the Examiner that Appellant has not
explained why one of ordinary skill in the art would not consider it obvious
to apply a statistical test to measure the abundance of each protein before, as
opposed to after, identifying it. (See Ans. 7–8 (“In this case, it does not
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appear that the order of steps (quantitation and identification) would affect
the results obtained.”).)
Appellant fails to provide sufficient evidence or argument that the
steps (c) and (d) – in either order–leads to anything other than predictable
results. See KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398, 401 (2007) (the
“combination of familiar elements according to known methods is likely to
be obvious when it does no more than yield predictable results.”) We
therefore find that the reasoning in Burhans applies. In Burhans, the
Appellant identified four process steps, where each of the steps was
disclosed in the prior art, differing only order of the steps. In re Burhans,
154 F.2d 690, 692 (CCPA 1946). The court was unpersuaded of
patentability, finding that “[t]here is no merit in the point here in the absence
of any proof in the record that the order of performing the steps produces
any new and unexpected results.” Id. We conclude that the same reasoning
applies in the instant case, where Jin teaches the application of a statistical
test to measure the abundance of each protein prior to determining its
identity. (See Ans 7–8; FF2–3.)
In sum, the Examiner’s explanation provides sufficient factual basis
and technical reasoning to support a determination that Jin, alone or in
combination with Simak, renders obvious claims 1–4, 6, 7, 9, 10, and 13–17.
Appellant has not rebutted the Examiner’s prima facie showing. Because
Appellant provides no additional arguments with respect to claims 5, 8, 11–
12, and 18–20, which directly or indirectly depend from claim 1, those
claims also fall with claim 1.
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SUMMARY
We affirm the rejection of claims 1–4, 6, 7, 9, 10, and 13–17 under
35 U.S.C. § 103(a) as unpatentable over the combination of Jin and Simak.
We affirm the rejection of claims 5, 8, 11, 12, and 18–20 under
35 U.S.C. § 103(a) as unpatentable over the combination of Jin and Simak as
applied to claims 1–4, 6, 7, 9, 10, and 13–17 above, and further in view of
Garcia, Liu, and Kim.

TIME PERIOD FOR RESPONSE
Requests for extensions of time in this ex parte reexamination
proceeding are governed by 37 C.F.R. § 1.550(c). See 37 C.F.R. § 41.50(f).

AFFIRMED

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