Ex Parte Fahrenkrug et al

Patent Trial and Appeal Board

Mar 2, 2017

12504286 (P.T.A.B. Mar. 2, 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.
12/504,286 07/16/2009 Scott C. Fahrenkrug 5054.02US02 9819
62274 7590 03/02/2017
DARDI & HERBERT, PLLC
Moore Lake Plaza, Suite 205
1250 East Moore Lake Drive
Fridley, MN 55432
EXAMINER
NGUYEN, QUANG
ART UNIT PAPER NUMBER
1633
MAIL DATE DELIVERY MODE
03/02/2017 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 SCOTT C. FAHRENKRUG, KARL J. CLARK,
DANIEL F. CARLSON, and MICHAEL J. LEAVER
Appeal 2016-002238
Application 12/504,286
Technology Center 1600
Before DONALD E. ADAMS, JEFFREY N. FREDMAN, and
RYAN H. FLAX, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134(a) involving claims to
transposase, a transposon, vectors, cells, a gene transfer system, and methods
of using a transposase. The Examiner rejected the claims as obvious. We
have jurisdiction under 35 U.S.C. § 6(b). We affirm.
Statement of the Case
Background
“A transposase is an enzyme that is capable of binding to inverted
repeats of a transposon and catalyzes the incorporation of the transposon into
1 Appellants identify the Real Party in Interest as Recombinetics (see App.
Br. 3).
Appeal 2016-002238
Application 12/504,286
DNA” (Spec. 8:27—29). “Transposons are mobile, in that they can move
from one position on DNA to a second position on DNA in the presence of a
transposase” (Spec. 7:12—13). “Passport transposons are a viable way of
introducing DNA into a cell and can be used to modify germline and somatic
cells for the production of transgenic animals, germline mutagenesis, or for
somatic modification like gene therapy” (Spec. 7:13—16).
The Claims
Claims 1, 3—18, and 20-39 are on appeal.2 Independent claim 1 is
representative and reads as follows:
1. A transposase comprising:
a polypeptide that has an amino acid sequence that has
at least 85% identity to SEQ ID NO: 29, with the
polypeptide specifically binding to a nucleic acid fragment
that comprises an inverted terminal repeat sequence of at
least one of SEQ ID NO: 34 and SEQ ID NO: 35, with the
polypeptide being capable of catalyzing the integration of a
target nucleic acid into a vertebrate cell, with the
polypeptide further comprising a signal peptide that directs
the transposase to a particular cellular location, with the
amino acid sequence and the signal peptide being a non-
naturally occurring combination.
The Issues
A. The Examiner rejected claims 7—18, 20-30, 32, and 36—39 under
35 U.S.C. § 103(a) as obvious over Leaver3 and Hackett4 (Final Act. 3—8).
2 Claims 2 and 19 were cancelled (see App. Br. 16, 18).
3 Leaver, M., A family of Tel-like transposons from the genomes of fishes
and frogs: evidence for horizontal transmission, 111 Gene 203—14 (2001)
(“Leaver”).
4 Hackett et al., US 6,489,458 B2, issued Dec. 3, 2002 (“Hackett”).
2
Appeal 2016-002238
Application 12/504,286
B. The Examiner rejected claims 1—6, 31, and 33—35 under 35 U.S.C.
§ 103(a) as obvious over Leaver, Hackett, and Hasebe5 (Final Act. 14—15).
Because the same issue is dispositive for both rejections, we will
consider both rejections together.
The issue with respect to these rejections is: Does the evidence of
record support the Examiner’s conclusion that the consensus transposase
sequence of Leaver would have been enabled for use in catalyzing
integration of a target nucleic acid into a vertebrate cell?
Findings of Fact
1. The Specification teaches: “[t]he term‘transposase
polypeptide’ as used herein refers to any amino acid sequence that is at least
70 percent (e.g., at least 75, 80, 85, 90, 95, 99, or 100 percent) identical to
the PPTsl sequence set forth in Figure 8” (Spec. 10:2-4).
2. The Specification teaches: “Nucleic acid molecules can be
obtained using any method including, without limitation, common molecular
cloning and chemical nucleic acid synthesis techniques” (Spec. 12:15—16).
3. The Specification teaches: “Transposase polypeptides can be
produced using any method. For example, transposase polypeptides can be
produced by chemical synthesis. Alternatively, transposase polypeptides
described herein can be produced by standard recombinant technology using
heterologous expression vectors encoding transposase polypeptides” (Spec.
17:13-16).
4. The Specification teaches: “Any type of promoter can be
operably linked to a target nucleic acid sequence. Examples of promoters
5 Hasebe et al., US 6,492,510 B2, issued Dec. 10, 2002 (“Hasebe”).
3
Appeal 2016-002238
Application 12/504,286
include, without limitation, tissue-specific promoters, constitutive
promoters, and promoters responsive or unresponsive to a particular
stimulus” (Spec. 13:30 to 14:1).
5. The Specification teaches that “Figure 10A-10F contains
sequence of the Passport transposon. The first sequence is PPTN4 (SEQ ID
NO: 33), published by Leaver in 2001 (Gene, 271(2):203-214). Figure 10B
is PTsl (SEQ ID NO: 29) and is the amino acid sequence of the native
Passport transposase as found in PPTN4” (Spec. 7:3—6).
6. Leaver teaches: “This paper describes the distributions and
sequences of a subfamily of related 727-like transposons in fishes and frogs.
It also defines an apparently intact transposon from plaice and is the first
report of a complete and thus potentially active 727-like transposon from a
vertebrate genome” (Leaver 204, col. 1).
7. Leaver teaches “products were cloned from plaice, Atlantic
salmon, and frog . . . two of these plaice sequences appeared to contain full-
length, uninterrupted reading frames encoding a Tcl-like transposase (Fig. 1)
... By constructing consensus sequences for these elements it was possible
to minimize the level of degeneracy” (Leaver 209, col. 2).
8. Leaver teaches:
Significantly, two of the plaice transposons described here
contain complete, uninterrupted reading frames encoding
transposases with all of the structural elements required for
function, and these reading frames are flanked by conserved IRs
each containing perfect DRs. This would suggest that PPTN is
potentially functional and if this were the case it would be the
first active 72'/-like element isolated from a vertebrate genome.
(Leaver 212, col. 1).
4
Appeal 2016-002238
Application 12/504,286
9. Figure 1 of Leaver is reproduced below:
GATA X••at-.;' €H- :hk....4 KbOiOS
A AJ'-TNft rT 'w > ,.—.mmr i 1$ 2.7 top
Pt>TJJ3 FT™“ 344 5.bp
S'PO'KO ► ► ~mMmmMrnmmmm 4 IftftXbp
sOPOKS L...i... ..“1 1027bp
3-£-:TN5 FJ_ :L44Lbp
“J2i3C:H 5
Asj2450Si5
Av: 2420 20
OW.JOOOOS
&:5'.;0'j363
B ✓ ■Mzrrrspj^
f ' % ' * \\T£2ftACCA^<^
A '"T v Vs""*
TATataTkCAi^TOTTCSaGTGftCXiG^^
& K T ft E L T ft G ft R 0 ft V V S K V S A G
m&TraX&AftftAMraTC£tt3A3CT!’2^
L S Y K K I 5 ft A ft t$ X A L £ T I ft 3 X X A
AAATra^AAaAATAfOCCAeXWXXrA^^^
A W ft A Y G T T A N ft P F A 0 & P P ft L A A
A Y E R A ft I B E A T S A ? M V T L £ 2 X.
Q A ft T A ft V G E .‘5 V c£ A '? TIER ft ft :i X
YCY?AAXrrrA3X£;AAGNXN>CftAAG(G^
A G ft V G A V A A R A * ft ft K G 5 H ft K 3 R
3TxAAXA\A^rTACXAGAAf>rrCAT^TC^XIACACAC^AC’C\AAACXNX'J:'?^AAv R ft ft V G •? A' A A S ft X V ft G ft
AiX,’ALXADX.VvAATXv;-AijCTTTA^OX'Ov:‘iA:PA2XA^XAAAoXX>XTATAX^3X’C^A/XoAAA^A’CA\A¥X.At;',X
ft £ T K X S L S’ G ft G A X A V V G ft X 1? !Y T
GSCCATCACOT^GCGkC^
A H H ft ft ft T : ft T A K ft. A A G A I G ft G A
C: A A X A G T A ft. ft V AXE G A St 'A G A ft
AftAAGGAAAGGCTXVftftSmAAAK^
Y P. 5 X x. £ £ G: ft M ft> -:. A ft ft ft. A ft G ft ft ft
ATXTGCCAwACGACsNftX'GGCCGtAAACA^^^^^^
I i' Q Q D N £■ ft X ft - ' ft. ■'■ S’ c: ft A
GAA;T*7rr/v\^rCXJTAA^^
N V W v ft X G P 3 Q A A A ft A ft X £ X t. v;
AAG&ra£3tt^Ttt3CC£!TI^^
O & ft JC X A V K ft. ft ;■ .6 3 M 5. X' ft ft- ft. L F C
Q E E Vi T M 5, X. ! ft ft ft' ft. ft. L ft'’ ft T Y ft K ft
ACf'i.^:ACXT?JTXvftrr:>;>3G^
ft. ft A V t ft ft X G G ft T ■■: :.: <
M^v^CCJAAAXftGft^^ArftCTTrTTTOTTC-^
CK'.«'X^:OJvV.CiTAC?A®CATOTTTTGT?;-A'JX;A.OACCSKm«A^iXrrTAT^
AJVt*J