DREXEL UNIVERSITY

Patent Trials and Appeals Board

Jul 29, 2020

2019006769 (P.T.A.B. Jul. 29, 2020)

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.
15/203,616 07/06/2016 TIMOTHY M. BLOCK 101919.000103 / 06-0708 3069
23377 7590 07/29/2020
BakerHostetler
Cira Centre 12th Floor
2929 Arch Street
Philadelphia, PA 19104-2891
EXAMINER
GODDARD, LAURA B
ART UNIT PAPER NUMBER
1642
NOTIFICATION DATE DELIVERY MODE
07/29/2020 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):
eofficemonitor@bakerlaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte TIMOTHY M. BLOCK, MARY ANN COMUNALE, and
ANAND MEHTA
Appeal 2019-006769
Application 15/203,616
Technology Center 1600
Before FRANCISCO C. PRATS, ULRIKE W. JENKS, and
CYNTHIA M. HARDMAN, Administrative Patent Judges.
JENKS, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from Examiner’s
decision to reject claims as lacking written descriptive support for a
deglycosylated capture reagent comprising an antibody. We have
jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 Appellant identifies the real party in interest as Drexel University. Appeal
Br. 1. We use the word Appellant to refer to “applicant” as defined in
37 C.F.R. § 1.42(a).
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Application 15/203,616

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STATEMENT OF THE CASE
The Specification is directed to methods and kits for rapid and
accurate diagnosis of liver diseases. Spec. ¶ 3. The methods comprise
contacting a sample with a lectin and detecting the lectin-glycosylated
protein complex. Id. ¶ 14.
CLAIMED SUBJECT MATTER
The claims are directed to diagnosing liver pathology by determining
protein glycosylation. Claim 1, reproduced below, is illustrative of the
claimed subject matter:
1. A method for assessing the pathological status of a liver in a
subject suspected of having a liver pathology comprising:
obtaining biological fluid from the subject;
capturing a protein in the biological fluid using a
deglycosylated capture reagent comprising an antibody that is
specific to said protein,
wherein said protein is selected from
GP73, haptoglobin, hepatitis B viral particle, . . .
contacting said biological fluid with a core fucose-binding
lectin and allowing said lectin to bind to the captured protein in
said biological fluid,
wherein the binding of said core fucose-binding lectin to
said protein is determinative as to the presence of core fucose on
said protein;
quantifiably detecting bound lectin in the biological fluid
to obtain a detected core fucosylation value; and
comparing the detected core fucosylation value with a
reference value for core fucosylation on said protein in a
comparable biological fluid of subjects without said liver
pathology, said detected core fucosylation value relative to the
reference value being indicative of the presence or absence of
said liver pathology, wherein a detected core fucosylation value
that deviates from said reference value to a statistically
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significant degree is indicative of the presence of said liver
pathology,
or
comparing the detected core fucosylation value with a
reference value for core fucosylation on said protein in a
comparable biological fluid of subjects in which said liver
pathology is known to be present, said detected core fucosylation
value relative to the reference value being indicative of the
presence or absence of said liver pathology, wherein a detected
core fucosylation value that deviates from said reference value to
a statistically significant degree is indicative of the absence of
said liver pathology.
Appeal Br. 9 (Claims Appendix) (emphasis added).
REJECTION
Appellant requests review of Examiner’s new matter rejection of
claims 1, 4, 6, 7, and 9 under 35 U.S.C. § 112, first paragraph.2
OPINION
Examiner finds that the Specification teaches “utilizing a periodate-
treated capture antibody immobilized to a solid surface for ELISA.” Ans. 4,
see id. at 8. “Periodate oxidation modifies carbohydrates on the antibody to
form an aldehyde that can be reacted with an amine group for
immobilization on solid substrates for use in assays such as ELISA.” Id. at 4.
Examiner’s positon is that the scope of the “periodate oxidized capture
antibodies does not support the broadly claimed deglycosylated capture

2 Paragraph 1 of 35 U.S.C. § 112 was replaced with newly designated
§ 112(a) when § 4(c) of the America Invents Act (AIA), Pub. L. No. 112–29,
took effect on September 16, 2012. Because the claimed priority
applications were filed before that date, we refer to the pre-AIA version of
§ 112.
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reagents comprising antibodies specific to proteins.” Id. at 6. According to
Examiner, “[t]he periodate oxidized antibody is an intermediary component
to be immobilized on a solid surface,” such as an ELISA plate surface. Id. at
9. Examiner contends that the deglycosylation “describe[s] excision of
glycosylation or complete removal of glycosylation” but that the disclosure
of immobilized periodate oxidized antibodies does not implicitly or
inherently support the presently claimed reagents. Id. Examiner’s position is
that the term “deglycosylated capture reagent” as recited in claim 1
encompasses structurally and functionally unrelated antibodies well outside
the scope of the original disclosure of immobilized periodate oxidized
antibodies. Id. at 10 (citing Kim,3 Mann,4 Santora,5 Edge,6 and Wright7). In
other words, Examiner’s position is that an antibody that has the sugar
removed is different from an antibody that has the sugar chemically altered
into a different chemical entity, and while the claims embrace both, the
Specification discloses only the latter.

3 Min-Sung Kim & Dan Leahy, Enzymatic Deglycosylation of
Glycoproteins, 533 Methods in Enzymology 259–63 (2013).
4 A. C. Mann et al., A general method for the complete deglycosylation of a
wide variety of serum glycoproteins using peptide-N-glycosidase-F, 1
Glycosylation & Disease 253–61 (1994).
5 L. C. Santora et al., Determination of Recombinant Monoclonal Antibodies
and Noncovalent Antigen TNFα Trimmer Using Q-TOF Mass Spectrometry,
17 Spectrometry 50–57 (2002).
6 Albert S. B. Edge, Deglycosylation of glycoproteins with
trifluoromethanesulphonic acid: elucidation of molecular structure and
function, 376 J. Biochem 339−50 (2003).
7 Ann Wright & Sherie L. Morrison, Antibody variable region glycosylation:
biochemical and clinical effects, 15 Springer Seminars in Immunopathology
259–73 (1993).
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Appellant contends that just because there are different methodologies
for deglycosylating a protein does not mean that the Specification as filed
did not describe a deglycosylated capture reagent. Appeal Br. 5 (citing
Amgen Inc. v. Hoechst Marion Roussel, Inc., 314 F.3d 1313 (Fed. Cir.
2003)). “[T]he term ‘deglycosylation’ is not limited to wholesale excision of
a sugar moiety, but also embraces conversion of a sugar to a different
functional group, such as by the use of periodate.” Reply Br. 1 (citing
Swindell Declaration8); see Appeal Br. 4 (also citing Swindell Dec.).
Appellant contends “that additional methods for producing a deglycosylated
reagent were ‘well known’ [and thereby] further supports the conclusion that
the written description requirement has been satisfied.” Id. at 6.
The issue is whether the preponderance of evidence of record supports
a finding that the Specification describes “a deglycosylated capture reagent
comprising an antibody” as claimed.
“Deglycosylated capture reagent” is not specifically defined in the
Specification. The word deglycosylation appears twice in the Specification,
at paragraph 49. The Specification describes glycosylations as post-
translationally attached moieties and lists several methods for removing such
modifications from a polypeptide:
Post-translationally attached moieties can be separated
from a polypeptide by any means suitable in the art, including
chemically, for example by treatment with hydrazine or acids
such as hydrofluoric acid or trifluoromethanesulfonic acid,
enzymatically, for example by [] treatment with N-glycosidase
such as PNGase F, O-glycosidase, endoglycosidases, or
exoglycosidases, or by physical means. Commercially available

8 Declaration by Charles S. Swindell, Ph.D. under 37 C.F.R. § 1.132 signed
Aug. 9, 2018 (“Swindell Dec.” or “Swindell Declaration”).
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kits are available for removing post-translational modifications,
including deglycosylation. Chemical bases such as hydrazine, or
chemical reagents that lead to beta-elination [sic] reactions can
also be used in deglysosylation [sic] reactions. Other techniques
and reagents will be appreciated by those of skill in the art, and
are contemplated to be within the scope of the present invention.
Spec. ¶ 49. Accordingly, we determine that “deglycosylated capture reagent”
reasonably encompasses polypeptides, including antibodies, that have post-
translationally attached moieties either removed or chemically altered.
The claim recites a “deglycosylated capture reagent comprising an
antibody.” A reasonable reading of this limitation is that the capture reagent
is an antibody that has post-translational modifications removed.
Examiner takes the position that a “deglycosylated capture reagent”
comprises proteins and antibodies that are structurally and functionally
different from the “immobilized periodate oxidized antibodies” exemplified
in the Specification. Ans. 10, 13. We are not persuaded.
“[T]he written description requirement does not demand either
examples or an actual reduction to practice; a constructive reduction to
practice that in a definite way identifies the claimed invention can satisfy the
written description.” Ariad Pharm., Inc. v Eli Lilly & Co., 598 F.3d 1336,
1352 (2010). The test for determining whether a specification is sufficient to
support a particular claim “is whether the disclosure of the application relied
upon ‘reasonably conveys to the artisan that the inventor had possession at
that time of the later claimed subject matter.”’ Ralston Purina Co. v. Far-
Mar-Co, Inc., 772 F.2d 1570, 1575 (Fed. Cir. 1985) (quoting In re
Kaslow, 707 F.2d 1366, 1375 (Fed. Cir. 1983)).
Thus, “[i]t is not necessary that the application describe the claim
limitations exactly . . . but only so clearly that persons of ordinary skill in the
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art will recognize from the disclosure that appellants invented processes
including those limitations.” In re Wertheim, 541 F.2d 257, 262 (CCPA
1976) (citation omitted); see also Purdue Pharma L.P. v. Faulding, Inc., 230
F.3d 1320, 1323 (Fed. Cir. 2000) (“In order to satisfy the written description
requirement, the disclosure as originally filed does not have to provide in
haec verba support for the claimed subject matter at issue.”).
Moreover,
A claim will not be invalidated on section 112 grounds simply
because the embodiments of the specification do not contain
examples explicitly covering the full scope of the claim
language. That is because the patent specification is written for a
person of skill in the art, and such a person comes to the patent
with the knowledge of what has come before. Placed in that
context, it is unnecessary to spell out every detail of the invention
in the specification; only enough must be included to convince a
person of skill in the art that the inventor possessed the invention
and to enable such a person to make and use the invention
without undue experimentation.
Falkner v. Inglis, 448 F.3d 1357, 1366 (Fed. Cir. 2006) (quoting LizardTech,
Inc. v. Earth Resource Mapping, PTY, Inc., 424 F.3d 1336, 1345 (Fed. Cir.
2005)). There is no requirement to teach that which is well known in the art.
See Hybritech Inc. v. Monoclonal Antibodies, Inc., 802 F.2d 1367, 1384
(Fed. Cir. 1986) (“[A] patent need not teach, and preferably omits, what is
well known in the art.” (Citation omitted.)).
The Specification, and the claims, describe detecting a fucosylated
glycoprotein by contacting the sample with a fucose-specific lectin. Spec.
¶¶ 14, 41; see claim 1 (“contacting said biological fluid with a core fucose-
binding lectin and allowing said lectin to bind to the captured protein in said
biological fluid.”). The bound lectin “can be directly coupled to a detectable
moiety, or detection can proceed via a secondary reagent that specifically
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binds to the lectin, such as an anti-lectin antibody.” Spec. ¶ 14, see id. ¶ 18
and Figure 3.
One of ordinary skill in the art the time of the invention would have
known that antibodies contain carbohydrate modifications. See Ans. 5
(“Carbohydrate modification [of an antibody] is particularly useful for
creating target site for conjugation on polyclonal antibodies because the
polysaccharides are located in the Fc region,” away from the antigen biding
site.); Wright 259 (“All antibodies are glycoproteins containing at least one
N-linked carbohydrate in their constant region.”). In addition, one of
ordinary skill in the art at the time of the invention would have known that
the carbohydrate on an antibody could also include fucose moieties. See
Santora 50 (“D2E7 is N-glycosylated at heavy-chain Asn (position 301) with
fucosylated biantennary oligosaccharides containing zero, one, or two
galactoses.”). Knowing that antibodies contain carbohydrates that could
contain fucose moieties, one of skill in the art would recognize the
importance of eliminating fucose moieties from any assay component that is
not the focus of the assay, such as the detection reagents used in the assay.
The Specification exemplifies the use of periodate oxidized antibodies
as a capture reagent. Spec. ¶¶ 18, 85. Dr. Swindell avers that “[i]t is
commonplace among those working in the field of chemistry to refer to
conversion of a first chemical moiety to a second chemical moiety as
removal of the first moiety.” Swindell Dec. ¶ 5; see Al-Ghouleh9 2

9 Abeer Al-Ghouleh et al., The Glycosylation Pattern of Common Allergens:
The Recognition and Uptake of Der p 1 by Epithelial and Dendritic Cells Is
Carbohydrate Dependent, 7 PLoS ONE 1–11 [e33929] (2012), submitted as
Exhibit C with the Swindell Declaration.
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(Periodate deglycosylation); see Pizarro-Bauerle10 (deglycosylation of
hemocyanin using sodium periodate oxidation). We credit Dr. Swindell’s
testimony and find that the cited references support the position that a skilled
artisan would understand that periodate oxidation deglycosylates a protein.
Because the periodate treatment changes the chemical structure of the
carbohydrate attached to the antibody (or protein) we agree with Appellant
that the capture antibodies after periodate treatment as disclosed in the
Specification no longer contain glycosylations.
The ordinarily skilled artisan would have recognized that the inclusion
of a carbohydrate, i.e. glycosylation, on a capture antibody would interfere
with a lectin-binding assay, motivating the removal of the carbohydrate. See
Spec. ¶¶ 49, 85, 86. The Specification lists several known methods for
removing post-translational modifications, such as glycosylations, from a
protein. See Spec. ¶ 49. There is no requirement that the Specification
disclose deglycosylations beyond the periodate oxidized antibody already
exemplified. See Hybritech Inc., 802 F.2d at 1384. (“[A] patent need not
teach, and preferably omits, what is well known in the art.” (Citation
omitted.)). Accordingly, we determine that the disclosure of periodate
oxidized antibodies in the Specification reasonably supports the claimed
limitation of a “deglycosylated capture reagent comprising an antibody.”
We are also not persuaded by Examiner’s position that the claims
encompass deglycosylated capture reagents that are not antibodies. See

10 Javier Pizarro-Bauerle et al., Molluskan Hemocyanins Activate the
Classical Pathway of the Human Complement System through Natural
Antibodies, 8 Frontiers in Immunology 1–10 (2017), submitted as Exhibit D
with the Swindell Declaration.
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Ans. 9 (“deglycosylated ‘capture reagents’ (not antibodies) that are outside
the scope of the original disclosure . . . the term ‘capture reagents encompass
ligands, peptides, glycoproteins outside the scope of periodate oxidized
antibodies.”). As discussed above, a reasonable reading of the limitation
“deglycosylated capture reagent comprising an antibody” is that the capture
reagent is an antibody that has post-translational modifications removed. On
this record, we do not find Examiner’s interpretation of the claim reasonable.
CONCLUSION
Examiner erred in finding that the disclosure of the Specification fails
to demonstrate possession and descriptive support for the claims.
Accordingly, we reverse the rejection.
DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1, 4, 6, 7, 9 112 first
paragraph
Written
Description
1, 4, 6, 7, 9

REVERSED