Ex Parte Vail

Patent Trials and Appeals Board

Mar 21, 2019

13786067 - (D) (P.T.A.B. Mar. 21, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/786,067 03/05/2013
84398 7590 03/25/2019
McCarter & English / KCI
265 Franklin St.
Boston, MA 02110
FIRST NAMED INVENTOR
Neal Vail
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
123436-09501 5910
EXAMINER
AUDET, MAURY A
ART UNIT PAPER NUMBER
1654
NOTIFICATION DATE DELIVERY MODE
03/25/2019 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):
docket@mccarter.com
mvaneman@McCarter.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte NEAL VAIL 1
Appeal2018-004434
Application 13/786,067
Technology Center 1600
Before ULRIKE W. JENKS, TIMOTHY G. MAJORS, and
MICHAEL A. VALEK, Administrative Patent Judges.
VALEK, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a
composition for promoting cell interaction, which have been rejected as
directed to patent-ineligible subject matter and as obvious. We have
jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
STATEMENT OF THE CASE
Claims 1, 13, 15, 17-25, 27-29, 31, 33, and 34 are on appeal, and can
be found in the Claims Appendix of the Appeal Brief. The only independent
claim is claim 1. It reads as follows:
1. A composition for promoting cell interaction comprising
a polycation and a polyanion, wherein at least one of the
1 Appellant identifies the real party in interest as KCI Licensing, Inc. App.
Br. 1.
Appeal2018-004434
Application 13/786,067
polycation and the polyanion comprises an engineered protein,
wherein the engineered protein comprises one or more sequences
each independently selected from the group consisting of SEQ
ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ
ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ
ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12,
SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO:
16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID
NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ
ID NO: 24, SEQ ID NO: 25, and SEQ ID NO: 26.
App. Br. 17. According to the Specification, "[i]n various embodiments, the
engineered protein is a collagen" and the claimed SEQ IDs are "biological
functioning motifs" found in collagen and described in Russell, 2 which the
Specification incorporates by reference. Spec. ,r,r 62, 87.
Appellant seeks review of the following grounds of rejection3 made
by Examiner:
I. Claims 1, 13, 15, 17-25, 27-29, 31, 33, and 34 under 35 U.S.C.
§ 101 as directed to patent-ineligible subject matter.
II. Claims 1, 13, 15, 17-25, 27-29, 31, 33, and 34 under 35 U.S.C.
§ I03(a) as obvious over Stewart4 and Russell.
As Appellant does not argue any of the dependent claims separately for
either rejection, we focus our analysis on claim 1, and claims 13, 15, 17-25,
27-29, 31, 33, and 34 stand or fall with claim 1. 37 C.F.R. § 4I.37(c)(l)(iv).
2 Brooke H. Russell et al., US 2011/0288274 Al, published Nov. 24, 2011
("Russell").
3 Examiner has withdrawn the section 112 rejections. Ans. 18. Thus, only
the patent eligibility and obviousness rejections remain before us.
4 Russell J. Stewart et al., US 2010/0120923 Al, published May 13, 2010
("Stewart").
2
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Application 13/786,067
ANALYSIS
I. Subject Matter Eligibility
An invention is patent-eligible if it claims a "new and useful process,
machine, manufacture, or composition of matter." 35 U.S.C. § 101.
However, the Supreme Court has long interpreted 35 U.S.C. § 101 to include
implicit judicial exceptions: "[l]aws of nature, natural phenomena, and
abstract ideas" are not patentable. E.g., Alice Corp. v. CLS Bankint'l, 573
U.S. 208,216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Supreme Court's two-step framework, described in Mayo
and Alice. Id. at 217-18 ( citing Mayo Collaborative Servs. v. Prometheus
Labs., Inc., 566 U.S. 66, 75-77 (2012)). In step one, we ask whether the
claims are directed to an exception to patent eligibility, such as an abstract
idea or law of nature. Alice Corp. Pty. V. CLS Bankint'l, 134 S.Ct. 2347,
2355 (2014). In step two, we examine the elements of the claims to
determine whether they contain an inventive concept sufficient to transform
the claimed judicial exception into a patent-eligible application. Mayo
Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66, 71-
72 (2012) (quoting Alice, 134 S.Ct. at 2355).
"When a law of nature or natural phenomenon is claimed as a physical
product," as Examiner determined here, "the courts have often referred to
the exception as a 'product of nature."' MPEP § 2106.04(b ); see, e.g., Ass 'n
for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2116-17
(2013) ("Myriad'') (analyzing whether isolated DNA was a patent ineligible
"product of nature"). The product of nature exception to patent eligibility
includes both naturally occurring products and "naturally occurring products
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that lack markedly different characteristics" from their natural counterpart.
Id. If it is determined that the claim is drawn, in whole or in part, to a
nature-based product that lacks markedly different characteristics from its
natural counterpart then the product of nature exception applies and we
move on to step two of the analysis. MPEP § 2106.04(c).
Examiner's analysis follows the Supreme Court's two-step framework
as well as the guidance concerning the product of nature exception in MPEP
§ 2106.04(b )-( c ). Examiner starts by determining that the product of nature
exception is implicated because the claims recite a composition comprising a
polycation and polyanion "wherein either ... is simply a derivative/fragment
of a natural peptide [ and] is not found to be significant/markedly different in
structure from naturally occurring products." Non-Final Act. 4. In doing so,
Examiner explains that the term "engineered" does not distinguish the
claimed proteins from their natural counterparts because "[a] protein can be
'engineered' that has not resulted in a markedly/significant difference from
that of a naturally occurring protein." Id. at 5. Then, analogizing
Appellant's claims to claim 1 of Nature-Based Product Example 6 in the
USPTO's Subject Matter Eligibility Guidance, 5 Examiner determines that
the claimed combination of a polycation and polyanion was not eligible
because "the mixture does not have markedly different characteristics from
what occurs in nature" and the claims do not recite "additional features that
could add significantly more to the exception." Id. at 7-9; Ans. 8.
5 This example, originally published in December 2014, has been
renumbered as Example 14 in current index of subject matter eligibility
examples. Index of Eligibility Examples, available at
https://www.usnto.gov/sites/default/:files/documents/ieg-exam,12le-index.ndf.
4
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Application 13/786,067
Appellant disputes Examiner's subject matter eligibility rejection in
three respects. First, Appellant contends that the product of nature exception
does not apply because claim 1 requires an "engineered" protein. App. Br.
6-7. Second, Appellant argues that the composition as a whole, which
comprises a polycation and a polyanion, is significantly different than what
is found in nature because it is "the combination of the two components that
forms the coacervate and promotes cell interaction." Id. at 7. Third,
Appellant urges that even if the judicial exception does apply, the claimed
compositions "amount to significantly more than the judicial exception"
because the "polycation and the polyanion by themselves do not possess the
beneficial properties of being able to form a coacervate ... to promote cell
interaction." Id. at 8; see also Reply 3.
USPTO Guidance Step 2A, Prong 1
We are unpersuaded by Appellant's arguments and agree with
Examiner that claim 1 is directed to the product of nature exception.
Claim 1 is broadly directed to a "composition ... comprising a polycation
and a polyanion, wherein at least one of the polycation and the polyanion
comprises an engineered protein" comprising one or more of the peptide
sequences in SEQ ID NO: 1 to SEQ ID NO: 26. Appellant does not dispute,
and Examiner cites evidence demonstrating, that several of the recited
sequences in SEQ ID NO: 1 to SEQ ID NO: 26 are present in naturally-
occurring collagen proteins. Non-Final Act. 8 (quoting Haynie ~111, 6 which
teaches that SEQ ID NOS: 1-3 are "recognition sequences in collagen for
collagen-binding integrins."); see also Russell~ 7 (teaching that SEQ ID
6 Donald T. Haynie, US 2007/0077276 Al, published Apr. 5, 2007
("Haynie").
5
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NO: 1 and 2 are "type I collagen derived sequences"). Thus, as written, the
"polycation" and "polyanion" in claim 1 encompass proteins with the same
amino sequence as their naturally-occurring counterparts, that is, naturally-
occurring collagen proteins and fragments thereof.
We are not persuaded by Appellant's argument that the product of
nature exception does not apply because the term "engineered protein" limits
the claims to "proteins that comprise engineered sequences (i.e., not
naturally occurring)." Id. at 7. Examiner determined otherwise, explaining
that "engineered ... also encompasses making any naturally occurring
protein, rather than isolating such from nature." Non-Final Act. 6. The
Specification supports Examiner's interpretation, not Appellant's. It states
that an "engineered protein" can be produced by "chemical synthesis" or by
"recombination biology, directed evolution, or combination thereof." Spec
,r 60. This suggests that the term encompasses proteins "engineered" by
chemically synthesizing an otherwise naturally-occurring protein. Indeed,
the Specification teaches that "[i]n various embodiments, the engineered
protein is a collagen, including a recombinant collagen." Spec ,r,r 62, 87
( emphasis added). Thus, while the term certainly includes proteins whose
amino acid sequence has been altered by recombinant techniques, the
broadest reasonable interpretation of "engineered protein" is not so limited.
Moreover, even if we agreed with Appellant's claim construction, the
test is not whether the claim is directed to a product that is structurally
identical to one found in nature. To avoid the product of nature exception,
the claimed product must exhibit characteristics that are "markedly
different" from its natural counterpart. MPEP § 2106.04( c ). This is true
even if the structure of the claimed product differs somewhat from its natural
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Application 13/786,067
counterpart. See, e.g., Myriad, 133 S. Ct. at 2116-17 (isolated gene not
patent eligible even though it differed from the structure of the gene in the
natural chromosome because it lacked connective covalent bonds at the
ends). Appellant does not contend that the "engineered sequences" it says
are required by claim 1 result in a polycation or polyanion protein with
markedly different characteristics from their natural counterparts. See App.
Br. 7.
To the contrary, the only characteristic recited in claim I-that these
proteins comprise one or more sequences at least some of which are
naturally-occurring-suggests that the claimed proteins need not have
markedly different characteristics from their natural counterparts.
According to Russell, which Appellant's Specification incorporates by
reference, the "collagen derived sequences" in SEQ ID NO: 1 and SEQ ID
NO: 2 are significant because they "bind with high affinity" to particular
integrins (i.e., cell surface receptors) "involved in cell-cell and cell-substrate
adhesion." Russell ,r,r 6-7. In other words, they are pre-existing sequences
that have been identified because they have the same function as naturally-
occurring collagen, i.e., promoting cell interaction, as that recited for the
claimed composition. In this sense, claim 1 is similar to the composition
claims for DNA primers, which our reviewing court has repeatedly held to
be patent ineligible. See Roche Molecular Sys. Inc. v. CEPHEID, 905 F.3d
1363, 1370-71 (Fed. Cir. 2018) (DNA primers identified because they bind
to certain naturally-occurring "position-specific signature nucleotides" held
ineligible because patentee only identified the "pre-existing" sequence; "it
did not create them."); In re BRCAJ- and BRCA2-Based Hereditary Cancer
Test Patent Litigation, 774 F.3d 755, (Fed. Cir. 2014) ("A DNA structure
7
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with a function similar to that found in nature can only be patent eligible as a
composition of matter if it has a unique structure, different from anything
found in nature."). It may be the case that a protein containing one of the
claimed peptide sequences, but possessing markedly different characteristics
can be engineered. Claim 1, however, is not limited to such proteins.
USPTO Guidance Step 2A, Prong 2
We are also unpersuaded by Appellant's argument that the claimed
composition as a whole avoids the product of nature exception because it
requires both a polycation and a polyanion. As explained above, claim 1 is
broadly drafted such that either or both of the claimed composition's
components may be a naturally-occurring collagen protein or protein
fragment. In the absence of some markedly different characteristic resulting
from their combination, a mixture comprising two products of nature is not
patent eligible. Funk Bros. Seed Co. v. Kala Inoculant Co., 333 U.S. 127,
131 (1948) (claims to a combination of different naturally-occurring bacteria
held ineligible where the combination "produces no new bacteria, no change
in the ... bacteria, and no enlargement of the range of their utility.").
Appellant contends that "the presently claimed compositions are
distinguishable from the mixture of bacteria in Funk Brothers" because the
claimed combination of a polycation and polyanion "forms the coacervate
and promotes cell interaction." Reply Br. 3. That argument is not
persuasive for two reasons. First, Appellant's claims do not require the
formation of a coacervate. Nor is such a requirement inherent in claim 1 's
recitation of a "composition for promoting cell interaction comprising a
polycation and a polyanion." To the contrary, the Specification
distinguishes between "polyionic compositions," like that in claim 1, and the
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"coacervates" such compositions may or may not form "depending" on
various other unclaimed parameters. Spec. ,r 1. Second, Appellant offers no
evidence that the mixture of a naturally-occurring polycation and polyanion
in the claimed composition functions differently with respect to promoting
cell interaction than do those components individually. Rather, the
Specification states that in various embodiments it is polycation or
polyanion alone as opposed to the composition of the two that promotes cell
interaction. Spec. ,r 4 7.
Accordingly, given their broadest reasonable interpretation, there is
nothing in the claims that demonstrates that either the claimed
"composition" or its individual polycation and polyanion components have
any markedly different property from their naturally-occurring counterparts.
See In re Roslin Institute (Edingurgh), 750 F.3d 1333, 1338 (Fed. Cir. 2014)
(holding that alleged differences in mitochondrial DNA of cloned sheep did
not distinguish them from natural sheep for patent eligibility analysis
because those differences were not claimed); see also MPEP § 2106.04( c ).
For this reason, we determine that claim 1 does not integrate the judicial
exception into a practical application. See USPTO's January 7, 2019
Memorandum, 2019 Revised Patent Subject Matter Eligibility Guidance, 84
Fed. Reg. 50-57, 54 n. 20 (2019) (noting that MPEP 2106.04(b) and (c)
continue to guide the analysis for the product of nature exception).
USPTO Guidance Step 2B
Proceeding to the second step of the Supreme Court's analysis (and
the related Step 2B as provided in the Office's Guidance), we determine that
claim 1 does not add significantly more beyond the claimed products of
nature themselves. As explained above, claim 1 is directed to a composition
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that comprises a polycation and a polyanion both of which may be naturally-
occurring proteins or protein fragments. There are no other requirements,
much less additional limitations requiring the composition's components to
be complexed or combined with other components that distinguish them
from their naturally-occurring counterparts. To the contrary, the only
structural requirement is that claimed proteins must contain peptide
sequences at least some of which Examiner has shown are identical to those
in naturally-occurring collagen proteins. Non-Final Act. 8 (quoting Haynie
,r 111 ); see also Russell ,r 7. As such, claim 1 does not add anything beyond
the product of nature itself. Appellant's argument regarding the coacervate
and its allegedly beneficial properties fails because, as explained above,
claim 1 does not recite a coacervate and is not limited to the formation of
such.
Appellant has not argued any of the dependent claims separately, nor
otherwise suggested that any limitation in those claims is pertinent to the
subject matter eligibility analysis. Accordingly, we conclude that claims 1,
13, 15, 17-25, 27-29, 31, 33, and 34 are directed to patent-ineligible subject
matter.
II. Obviousness
Claims 1, 13, 15, 17-25, 27-29, 31, 33, and 34 were rejected as
obvious over the combination of Stewart and Russell. Examiner finds that
Stewart teaches all of the claim limitations, including that the engineered
protein may be a known collagen. Non-Final Act. 11-12; 13-16. Examiner
points to Russell "as evidence that presently elected collagen peptide SEQ
ID NO: 1 was a known collagen peptide to a person having ordinary skill in
the art." Ans. 18. According to Examiner, the skilled artisan would
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"appreciate[] that the known collagen peptide of ... SEQ ID NO: 1 taught
by Russell was open for selection ... and in fact was one of three (3)
preferred peptides guided to in Russell." Id. (citing Russell ,r 44).
Appellant argues that Stewart teaches collagen hydrosolate, rather
than collagen. App. Br. 9-10. Thus, urges Appellant, "there [is] no teaching
or suggestion in Stewart that would motivate persons of ordinary skill in the
art to employ a collagen, such as that disclosed in Russell, as either a
polycation or polyanion in its adhesive complex coacervates." Id. at 10.
Appellant further contends that Stewart teaches away from the use of
collagens in its coacervates because "Stewart teaches that collagens need to
be chemically modified in order to be able to form coacervates." Id.
The issue with respect to this rejection is: Does the preponderance of
evidence of record support Examiner's conclusion that the cited prior art
renders obvious the claimed compositions?
We begin our analysis with findings of fact regarding the teachings in
Stewart and Russell.
FF 1. Stewart teaches "adhesive complex coacervates" that are "composed
of a mixture of one or more polycations and one or more polyanions."
Stewart, Abstract. These "adhesive complex coacervates have numerous
biological applications" including as "bioadhesives." Id.
FF2. In one embodiment, Stewart teaches a coacervate "created using a low
MW (3-5 kda) non-gelling collagen hydrosolate as the polycation." Stewart
,r 105. Stewart teaches that the collagen hydrosolate was aminated with
ethylenediamine, which "shifted the pl from 5.4 to 10.4" and allowed the
"aminated collagen [to] form[] dense coacervates at 25°C over a broad range
of compositions." Id.
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FF3. Russell teaches collagen proteins containing certain peptide
sequences, including the "type I collagen derived sequences" GFOGER,
GLOGER and GAS GER. Russell ,r 7. GFOGER, GLOGER and GASGER
are the amino acid sequences in SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID
NO: 3 of Appellant's claims.
FF4. Russell teaches that "[p]ost-translational modification of collagen to
include hydroxyproline residues is important to stabilize the triple helical
conformation of collagen." Russell ,r 43. In addition, Russell teaches other
"biologically active sequences" in SEQ ID NO: 4 to 12 that include
unhydroxylated pro line and "support adherence ... regardless of the lack of
hydroxyproline." Id. ,r 44. Russell's SEQ ID NO: 4 to 12 are the same
sequences as those in SEQ ID NO: 4 to 12 of Appellant's claims.
We are unpersuaded by Appellant's arguments and agree that the
obviousness rejection is supported by a preponderance of the evidence. Short
of describing the particular collagen-derived peptide sequences in SEQ ID
NO: 1 or others of the claimed SEQ IDs, Stewart teaches all of the limitations
of claim 1. Stewart teaches collagen hydrolysate as a preferred polycation
embodiment to form its coacervates. As Appellant acknowledges, "collagen
hydrolysate" is a form of collagen "produced from the hydrolysis of
collagen." App. Br. 10. A skilled artisan would recognize that the
hydrolysate is another common form of the same thing. Indeed, after
aminating collagen hydrolysate with ethylenediamine, Stewart refers to the
product as an "aminated collagen." FF2.
We disagree with Appellant's argument that Stewart's teaching that
its collagen needed to be aminated before a coacervate could be formed
constitutes a teaching away from using collagen as a polycation. To teach
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away, a reference generally must "criticize, discredit, or otherwise discourage
the solution claimed." In re Fulton, 391 F.3d 1195, 1201 (Fed. Cir. 2004).
Stewart does none of this. Rather, it provides a specific procedure for using a
collagen protein as a polycation in conjunction with a polyanion to form a
coacervate complex and teaches that it works "over a broad range of
compositions." Id.
We also find that Examiner has articulated a sufficient rationale to
combine Stewart with collagen proteins that include the biologically active
sequences, i.e., the claimed SEQ ID NOs, taught in Russell. As explained
above, Stewart teaches collagen as a preferred embodiment for forming a
coacervate. Russell teaches that SEQ ID NO: 1 and SEQ ID NO: 2 is derived
from naturally-occurring collagen and discloses collagen proteins comprising
the other claimed SEQ ID NOs. It would be obvious for the skilled artisan to
select a collagen protein comprising those sequences to form a coacervate as
taught in Stewart, particularly in light of Russell's teaching that the
hydroxyproline in SEQ ID NO: 1 and SEQ ID NO: 2 is "important" to
stabilize the protein's structure. FF4. Appellant points out that Russell
teaches that the proline residues in SEQ ID NO: 4 to SEQ ID NO: 12 are
sufficient to support adherence even when they do not undergo
posttranslational modification to hydroxyproline. App. Br. 11. But that
teaching merely provides additional support for Examiner's rationale to
combine the references because Appellant's claims encompass SEQ ID
NO: 4 to SEQ ID NO: 12 just as they do SEQ ID NO: 1. 7
7 Examiner's rejection focuses on SEQ ID NO: 1 because Appellant elected
that sequence earlier in prosecution. See Non-Final Act 2. However,
claim 1 encompasses proteins comprising any of the peptide sequences in
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Examiner also finds that Stewart teaches each of the limitations added
by the appealed dependent claims. Non-Final Act. 14--16. We agree with
Examiner's findings in that regard and incorporate them here. Appellant
does not dispute any of those findings on appeal. Accordingly, the
obviousness rejection is affirmed as to all of the appealed claims.
SUMMARY
We affirm the rejection of claims 1, 13, 15, 17-25, 27-29, 31, 33, and
34 under 35 U.S.C. § 101 as being directed to patent ineligible subject
matter.
We affirm the rejection of claims 1, 13, 15, 17-25, 27-29, 31, 33, and
34 under 35 U.S.C. § 103 over Stewart and Russell.
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
SEQ ID NO: 1 to SEQ ID NO: 26. As the Specification explains (Spec
~~ 62, 87) those sequences are incorporated from Russell, which teaches the
same SEQ ID NOs. See Russell 12-18 (listing sequences).
14