Ex Parte Kee et al

Patent Trial and Appeal Board

Aug 22, 2017

13501998 (P.T.A.B. Aug. 22, 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.
13/501,998 05/25/2012 Keh Kooi Kee STAN-695 7897
77974 7590 08/24/2017
Stanford University Office of Technology Licensing
Bozicevic, Field & Francis LLP
201 REDWOOD SHORES PARKWAY
SUITE 200
REDWOOD CITY, CA 94065
EXAMINER
WILSON, MICHAEL C
ART UNIT PAPER NUMBER
1632
NOTIFICATION DATE DELIVERY MODE
08/24/2017 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@bozpat.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte KEH KOOI KEE and RENEE A. REIJO PERA
Appeal 2016-004979
Application 13/501,99s1
Technology Center 1600
Before ULRIKE W. JENKS, RICHARD J. SMITH, and
DEVON ZASTROW NEWMAN, Administrative Patent Judges.
NEWMAN, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims to methods of
producing and enriching compositions of human primordial germ cells. The
Examiner entered final rejections that the claims lack adequate written
description and are not enabled. We have jurisdiction under 35 U.S.C.
§ 6(b).
We REVERSE.
1 Appellants identify the Real Party in Interest as the Board of Trustees of
the Leland Stanford Junior University. Br. 3.
Appeal 2016-004979
Application 13/501,998
STATEMENT OF THE CASE
Background
Infertility is a common heath problem that affects 10-15%
of reproductive-age couples. A major cause of infertility is the
production of few or no germ cells. However, today’s treatments
for infertility are largely ineffective in cases in which infertility
is due to few or no germ cells. Little is known about the genes
that regulate the production of germ cells or the factors that
contribute to the block in differentiation of germ cells in infertile
individuals. The elucidation of pathways and factors involved in
germ cell differentiation, and the identification of agents that
promote germ cell development and differentiation, is therefore
of clinical and research interest.
Spec. ^ 3.
The Specification discloses methods “for producing germ cells from
pluripotent cells by contacting a population of pluripotent cells with an
effective dose of at least one agent that promotes germ cell differentiation”
and for “enriching for a composition of primordial germ cells.” Id. 4, 5.
The Claims
Claims 1,3, and 11-15 are on appeal. Br. 1. Independent claims 1
and 11 are illustrative and read as follows:
1. A method of producing human primordial germ
cells, the method comprising:
contacting a population of pluripotent human embryonic
stem cells (ES cells) or induced pluripotent stem cells (iPSs) with
a DAZL polypeptide or a nucleic acid that encodes a DAZL
polypeptide;
wherein cells of the contacted population of pluripotent
cells are induced to become primordial germ cells (PGCs).
Br. (Claims Appendix) 3.
2
Appeal 2016-004979
Application 13/501,998
11. A method of enriching for a composition of
primordial germ cells (PGCs), the method comprising:
contacting a population of pluripotent cells with a
polynucleotide comprising a detectable marker under the control
of a promoter that is selectively active in primordial germ cells;
contacting the polynucleotide-contacted pluripotent cells
with a DAZL polypeptide or a nucleic acid that encodes a DAZL
polypeptide under conditions sufficient to promote PGC
differentiation; and
selecting for cells that express the detectable marker to
provide a selected cell population;
wherein the cells of the selected cell population are PGCs.
Id.
The Issues
The following rejections are before us to review:
Claims 1, 3, and 11-15, stand rejected under 35 U.S.C. § 112(a) or 35
U.S.C. § 112 (pre-AIA), first paragraph, under enablement. Id. at 3.
Claims 3 and 15 stand rejected under 35 U.S.C. § 112(a) or 35 U.S.C.
§ 112 (pre- AIA), first paragraph, as failing to comply with the written
description requirement. Ans. 2.
ENABLEMENT
Issue
The Examiner has rejected claims 1, 3, and 11-15 as nonenabled.
Ans. 3. The Examiner finds that:
the specification, while being enabling for differentiating
pluripotent stem cells into PGCs using retinoic acid, does not
reasonably provide enablement for using DAZL or nucleic acid
sequence encoding DAZL to differentiate pluripotent stem cells
3
Appeal 2016-004979
Application 13/501,998
into PGCs and/or male or female late-stage germ cells (i.e. egg
or sperm progenitors, spermatid, spermatozoa, eggs).
Id.
The Examiner notes that:
Claims 1 and 11 encompass making a primordial germ cell
(PGC) which encompasses a multipotent stem cell capable of
becoming any cell of the germline, i.e. mature sperm, spermatids,
secondary spermatocyte, primary spermatocyte,
spermatogonium, mature ovum, ootid, secondary oocyte,
primary oocyte, oogonium as well as gonocytes, meiotic germ
cells, pre-meiotic germ cells, et al. Thus, the function of PGCs
is limited to making cells of the reproductive system, specifically
the germline.
Id. at 4.
The Examiner finds that the Specification lacks specificity regarding
whether
DAZL, BOULE, DAZ or a combination thereof was used to
obtain the results in Fig. 4A & B. Furthermore, the cells obtained
after differentiation express SCP3 (Fig. 4A&B); however, SCP3
is merely an indicator that the pluripotent cells have started
meiosis (Eg 13, ^ 57) and is not a marker for PGCs. Expression
of SCP3 fails to correlate to any specific structure or function of
PGCs. Likewise, yH2AX expression does not correlate to PGCs
because pg 13. ^ 57. teaches yH2AX is a marker for
svnaptonemal complex formation in meiotic prophase I.
Id. at 8.
The Examiner further finds that with regard to Figure 4C, which
“teaches DAZL overexpression alone or in combination with DAZ and/or
BOULE elicits SCP3 expression in a fraction of the cells [but] it cannot be
determined what types of cells were counted [in Figure 4C] or whether the
cells have any structure or function in common with PGCs.” Id. The
4
Appeal 2016-004979
Application 13/501,998
Examiner reiterates that “SPC3 is merely an indicator that the pluripotent
cells have started meiosis and is not a marker for PGCs.” Id. at 9.
The Examiner finds that the Specification 30 and Fig. 20) further
describes “differentiating XY pluripotent cells using the combination of
DAZL, BOULE and DAZ and obtaining cells expressing TEKT1 and ACR”
but disregards this finding because “TEKT1 and ACR are markers for
spermatid and spermatozoa (pg 13, ^ 57) which do not correlate with the
PGCs now claimed.2” Id. The Examiner further finds that the
Specification’s description of epigenetic reprogramming as ‘“diagnostic of
germ-cell differentiation’” is insufficient because “it relies on VASA and
OCT4 staining which do not correlate to the specific structure of PGCs.” Id.
The Examiner finds that the Specification’s disclosure of “culturing
GFP+ cells obtained by differentiating pluripotent cells on inactivated feeder
cells in media lacking bFGF” to obtain colonies resembling embryonic germ
cells insufficient because the Specification “does not teach [that the
colonies] had the same structure or function as PGCs.” Id. at 9-10.
With regard to the Specification’s disclosure at paragraph 134
regarding the use of siRNA and gene silencing of DAZL to examine genetic
requirements for formation and differentiation of human PGCs, the
Examiner finds the disclosure lacks teaching that the colonies “had the same
structure or function as PGCs.” Id. at 10. The Examiner similarly finds the
disclosure at Example 2 insufficient to “teach differentiating ES or iPS cells
using DAZL” and that it further does not disclose that the conditions
2 We understand the Examiner’s reference is in response to Appellants’
deletion of “late-stage germ cells” from claims 1 and 11. Advisory Action 2.
5
Appeal 2016-004979
Application 13/501,998
required to culture “cells expressing VASA, IFITM1 and PLAP . . . included
DAZL or that the resultant cells had the same structure and function as
PGCs.” Id.
The Examiner concludes that Appellants
have failed to enable those of skill to differentiate pluripotent
cells into PGCs as claimed by teaching pluripotent cells
contacted with DAZL or a nucleic acid sequence encoding
DAZL expressing SCP3 or yH2AX (or expressing TEKT1 and
ACR specific to spermatids or spermatozoa) have the same
structure and function as PGCs, and it would have required those
of skill undue experimentation to determine how to use DAZL to
differentiate pluripotent stem cells into a functional PGC as
claimed.
Id.
With specific regard to claims 3 and 15, which the Examiner finds
“using DAZL, BOULE and DAZ to obtain PGCs,” the Examiner finds the
Specification’s disclosure insufficient as “limited to obtaining cells
expressing TEKT1 and ACR using the combination of DAZL, BOULE and
DAZ in XY pluripotent cells” because TEKT1 and ACR are markers for
spermatid and spermatozoa, and are irrelevant as the language “late-stage
cells” was removed by amendment. Id. at 10-11. The Examiner concludes
the Specifications’ guidance is insufficient and “would have required those
of skill undue experimentation to determine how to use the combination of
DAZL, BOULE and DAZ (or nucleic acid sequence thereof) to differentiate
pluripotent stem cells into PGCs as required in claims 3 and 15.” Id. at 11.
Appellants argue no such undue experimentation is required. Br. 6.
Appellants argue:
The specification characterizes the landmark events along
the differentiation pathway of human ES cells to germ-cells.
Specifically, the specification describes the validation of a
6
Appeal 2016-004979
Application 13/501,998
VASA-GFP reporter using a well-known germ-cell
differentiation assay where induction to germ cell fate is
achieved through culturing the cells with BMP (see, e.g., para.
[00116], [00130] and Fig. 8). The reporter is confirmed to
identify primordial germ cells (PGCs) (see para. [00131]-
[00134] and [0015]) and used to isolate PGCs which were in turn
used to identify important genetic components in early germ cell
formation, i.e., DAZ gene family members (see, e.g., para.
[0015] and Fig. 5). Multiple functional and cellular assays
demonstrated that formation of the PGCs (i.e., GFP+ cells) was
modulated by DAZL (see para. [0015]).
Id.
Appellants argue the Specification describes testing of differentiation
of hESCs ‘“in the absence of BMPs (to test whether internal factors alone
can induce late germ-cell differentiation)’” using “vectors that
overexpressed DAZ sene family members [that] were introduced into XX
and XY human ES cells.” Id. With this testing, Appellants argue,
“overexpression of DAZL was sufficient to differentiate the ES cells to
meiotic germ-cells in both the XX and XY lines (e.g., as measured by a
marker of meiosis (i.e., SCP3 staining).” Id. at 6-7. Appellants argue these
and other data in the Specification show that “‘human germ cells can be
differentiated and isolated from pluripotent human ES’ and that the ‘human
DAZL and BOULE genes function in PGC formation. ’” Id. at 6-7 (citing
also parallel studies in fetal induced pluripotent cells in Example 2).
Appellants further argue the Specification discloses techniques for
constructing DAZL overexpression vectors and “provides actual reduction to
practice of contacting human ES cells with a nucleic acid encoding DAZL to
induce PGC differentiation and ... demonstrate[s] that the PGCs are capable
of progressing into meiosis,” all of which would arm the ordinarily skilled
7
Appeal 2016-004979
Application 13/501,998
artisan to practice the claimed methods without undue experimentation. Id.
at 7-8.
With regard to Figure 4 of the Specification, Appellants argue that
because overexpressed DAZ gene members were introduced into human ES
cells, and those cells differentiated in the absence of BMPs,
the fact that the cells of Fig. 4 are seen to have started meiosis,
in fact, does indicate that the cells have function in common with
PGCs, particularly as the specification describes that “functional
entry into meiosis, [is] a diagnostic property of germ cells.” (see
para. [00147]. Thus, that the cells of Fig. 4 were differentiated
from ES cells all the way into meiosis indicates that such cells
were not only differentiated into PGCs but also that such PGCs
were functionally capable of producing germ-cells. The ability
to generate germ cells is the defining characteristic of PGCs and
therefore, the cells produced by overexpression of DAZL alone,
as well as in combination with other DAZ family members,
clearly share common function with PGCs.
Id. at 9.
Appellants further argue that the Examiner incorrectly interpreted the
silencing experiments, which further demonstrated the “importance of
DAZL in inducing PCG formation and, in particular, regulating VASA
expression,” including that “overexpression of DAZL alone is sufficient to
induce human ES cells to differentiate into functional PGCs which progress
to meiosis.” Id. at 10-11.
With regard to claims 3 and 15, Appellants argue the Specification
“clearly describes how the additional use of other DAZ family members,
namely BOULE and DAZ may be used to further promote PGC formation
and/or the percentage of produced PGCs that are verifiably functionally
capable of producing germ cells.” Id. at 12. Appellants cite examples from
the Specification correlating overexpression of BOULE with increased PCG
8
Appeal 2016-004979
Application 13/501,998
formation and vice versa. Id. Appellants reiterate that the markers used in
the experiments “test the potential of the generated PGCs to form functional
germ cells” and permit correlation of use of DAZ family members with
formation of germ cells, providing the skilled artisan with sufficient tools to
perform the claims method. Id. at 13.
With regard to claims 11-13, Appellants argue the Specification
enables the claimed method because it
provides an actual example of the use of a PGC reporter (i.e.,
VASA-GFP) to identify, select and characterize PGCs derived
from hESCs. . . . describes other germ cell specific genes
expressed in PGCs besides VASA and DAZL, namely
PRDM1 /BLIMP 1 and DPPA3/STELLA (see para. [0056]), the
promoters of which could be readily used to drive expression of
a reporter . . . [and] describes how cells expressing a detectable
marker may be cultured, selected, monitored and isolated in
order to generate compositions enriched for PGCs.
Id. at 14.
With regard to claim 14, Appellants argue that:
the specification provides an actual example of the use of a
VASA-GFP reporter to detect and select PGCs based on GFP
expression and extensive characterization and validation of the
GFP+ cells based on well-known criteria of PGCs, e.g., including
gene expression profiling (see para. [00131]), meiotic
progression (see para. [00131]), epigenetic reprogramming (see
para [00132]), and embryonic germ cell formation (see para.
[00133]).
Id. at 15.
Appellants argue claim 14 is thus enabled. Id.
The Examiner responds that Appellants’ evidence that VASA was
expressed after differentiating pluripotent stem cells is unpersuasive, even if
DAZL was used, because “expression of VASA alone is inadequate to
9
Appeal 2016-004979
Application 13/501,998
conclude the cells obtained have the same structure or function as PGCs”
because VASA is generic to ‘“migratory primordial germ cells in the region
of the gonadal ridge..... [and] fetal and adult gonadal germ cells in both
males and females and is most abundant in spermatocytes and mature
oocytes.’” Ans. 12.
The Examiner further responds that the disclosure did not show
that any of the identified “‘colonies that resembled embryonic germ
cells’ were capable of becoming ANY cell of the germline including
various precursors, mature sperm, spermatids, secondary
spermatocyte, primary spermatocyte, spermatogonium, mature ovum,
ootid, secondary oocyte, primary oocyte, oogonium as well as
gonocytes, meiotic germ cells, pre-meiotic germ cells, et al.” Id. at
13.
The Examiner responds that Appellants’ cited experiments do
not make clear if “DAZL, BOULE, DAZ or a combination thereof
was used to obtain cells expressing ‘yH2AX’ ‘accompanied by more
than ten punctate SCP3 foci’” and notes that the vectors were not
disclosed in the Specification. Id. at 14.
The Examiner further finds that “SCP3 and yH2AX are not
specific markers for PGCs; therefore, they cannot be used to indicate
PGCs had specifically been obtained.” Id. at 16. The Examiner states
that at the time of the invention, “the markers associated with PGCs
were known to be unclear” and identifies markers that are currently
10
Appeal 2016-004979
Application 13/501,998
available for use in distinguishing between PGCs and embryonic
cells3 (ES). Id. at 16-17.
With regard to claims 11-13, the Examiner responds that the marker
pattern cited by Appellants as evidence of expression of markers confirming
development of PGCs is not persuasive because it is “contrary to both Wei
published in 2008 and DeFelici in 2013” and because not all of the markers
were confirmed to be expressed or capable of becoming “any cell of the
germline including various precursors, mature sperm, spermatids, secondary
spermatocyte [listing additional types].” Id. at 17.
With regard to claim 14, the Examiner repeats earlier arguments
regarding the lack of correlation between the evidence cited by Appellants
and proof that the obtained cells are PGCs. Id. at 17-18.
ISSUE
The issue in this rejection is whether a preponderance of the evidence
supports the Examiner’s conclusion that the Specification does not enable
the claimed invention.
ANALYSIS
Claims 1 and 3
We agree with Appellants that a preponderance of the evidence shows
that the claimed method is likely to induce contacted populations of
pluripotent cells to become PGCs. Because Appellants amended claim 1 to
remove the limitation requiring induction to become “late-stage cells,” to
enable these claims, the Specification need only enable putting pluripotent
3 The Examiner cites “DeFelici (Oogenesis, Springer-Verlag London, G.
Coticchio et al (eds.), 2013).” As discussed herein, we do not consider this
reference as it is not part of the record.
11
Appeal 2016-004979
Application 13/501,998
cells on the path to becoming PGCs. With regard to claims 1 and 3, we are
persuaded by Appellants’ arguments that Figure 4 of the Specification
demonstrates that overexpressed DAZ gene members introduced into human
ES cells differentiated in the absence of factors such as BMPs, and showed
the hallmarks of meiosis. Because meiosis is a process relegated to germ
cells, we further agree with Appellants that “functional entry into meiosis,
[is] a diagnostic property of germ cells [and that the germ cells] were
functionally capable of producing germ cells.” App. Br. 9. Accordingly, we
are not persuaded by the Examiner’s concerns that “SPC3 is merely an
indicator that the pluripotent cells have started meiosis and is not a marker
for PGCs” and that the Specification did not report that the colonies of cells
“had the same structure or function as PGCs.” Id. at 9-10. That the meiosis
process is occurring sufficiently demonstrates that differentiation has been
induced, as required by claims 1 and 3.
Claims 11—15
We agree with Appellants that a preponderance of the evidence shows
that the claimed method is likely to facilitate enriching a composition of
PGCs by selecting markers of associated cell populations. In particular, we
are persuaded by disclosure in the Specification confirming that haploid
formation has occurred and that markers for spermatid and spermatozoa,
TEDKT1 and ACR, were confirmed to be present. See Spec. ^ 57. Further,
as the Examiner acknowledges, VASA “is most abundant in spermatocytes
and mature oocytes.” Ans. 12. Therefore, the expression of VASA
confirms that the germ cells are differentiating into late-stage cells. Spec. ^
134. See also Figure 5, instructing integration of a reporter indicative of
12
Appeal 2016-004979
Application 13/501,998
PGCs, permitting identification and selection of expressed PGCs. That
markers of late-stage cells are not relevant to the PGCs now claimed does
not negate that they evidence that differentiation into late-stage cells has
occurred.
We are further persuaded by Appellants’ argument that the
Specification provides “actual examples of the production of PGCs from
pluripotent cells which are capable of progressing to meiosis but also
provides the tools to detect and isolate such cells.” App. Br. 8.
Accordingly, we find the disclosed methods for selecting for cells expressing
such markers would lead to enrichment of the correlating cell population,
which are those able to undergo meiosis - pluripotent germ cells.
We are not persuaded by the Examiner’s reliance on new evidence in
the Answer. Wei and DeFelici (see Ans. 17) do not persuade us that the
Specification is not enabled.
In summary, we conclude that a preponderance of the evidence does
not support the Examiner’s conclusion that the claimed methods of inducing
contacted populations of pluripotent cells to become PGCs and to facilitate
enriching a composition of such cells would require undue experimentation.
Conclusion of Law
We reverse the rejection.
13
Appeal 2016-004979
Application 13/501,998
WRITTEN DESCRIPTION
The Examiner finds that:
The concept of contacting ES or iPS cells (pluripotent
cells) with DAZL or a nucleic acid sequence encoding DAZL
such that the pluripotent cells differentiate into PGCs and/or late-
stage germ cells and further contacting the pluripotent cells with
BOULE, a nucleic acid sequence encoding BOULE, DAZ, or a
nucleic acid sequence encoding DAZ, as newly required in
claims 3 and 15 is new matter.
Ans. 2.
Representative claim 3 states:
3. The method according to claim 1, further
comprising contacting the population of pluripotent cells with at
least one of: a BOULE polypeptide, a nucleic acid that encodes
a BOULE polypeptide, a DAZ polypeptide, and a nucleic acid
that encodes a DAZ polypeptide.
Br. (Claims Appendix) 3.
Appellants do not advance any arguments on this issue, and state in their
Brief that “[a]s indicated in the Advisory Action of April 3, 2015 the new
matter rejection has been withdrawn.” Br. 3. Appellants, however, are
mistaken on this position. See Advisory Action of April 3, 2015.4
4 The new . . . matter rejection regarding the concept of
contacting pluripotent cells with DAZL or nucleic acid sequence
encoding DAZL to make PGCs and/or late-stage germ cells has
been withdrawn because “late-stage germ cells” has been deleted
from claims 1 and 11. The new matter rejection regarding claims
3 and 15 remains.
Advisory Action 2. Rather, Appellants’ amendment of independent claims 1
and 11 did not address the substance of the rejection regarding claims 3 and
15 because both claims use the expansive language “further comprising” and
require contacting either pluripotent cells (claim 3) or the polynucleotide-
contacted pluripotent cells (claim 15) with a BOULE polypeptide, a nucleic
14
Appeal 2016-004979
Application 13/501,998
A description adequate to satisfy 35 U.S.C. § 112, first paragraph,
must “clearly allow persons of ordinary skill in the art to
recognize that [the inventor] invented what is claimed.” In other
words, the test for sufficiency is whether the disclosure of the
application relied upon reasonably conveys to those skilled in the
art that the inventor had possession of the claimed subject matter
as of the filing date.
Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010)
(citation omitted, alteration in original). “The descriptive text needed to
meet these requirements varies with the nature and scope of the invention at
issue, and with the scientific and technologic knowledge already in
existence.” Capon v. Eshhar, 418 F.3d 1349, 1357 (Fed. Cir. 2005).
As discussed above, we agree with Appellants that the Specification
provides multiple examples of the inducement of pluripotent cells to become
PGCs and methods of enriching a PGC population by selecting for markers
of end stage cells. We find general support for the use of polypeptides and
nucleic acids to modulate germ cell differentiation in paragraphs 63-72 of
the Specification. Because the peptides and nucleic acids at issue are known
in the art, the skilled artisan would recognize that the teachings of the
disclosure, including the working examples, reasonably convey that the
inventors possessed the claimed subject matter at the filing date.
Accordingly, because the Specification describes the methods of
claims 3 and 15, we find that the Examiner has not met the burden of proof
acid that encodes a BOULE polypeptide, a DAZ polypeptide, or a nucleic
acid that encodes a DAZ polypeptide. Br. 3—4.
15
Appeal 2016-004979
Application 13/501,998
to show that the Specification fails to adequately describe the claimed
method. We reverse the rejection.
SUMMARY
We reverse both rejections.
REVERSED
16