Ex Parte Trono et al

Patent Trial and Appeal Board

Nov 7, 2013

11680414 (P.T.A.B. Nov. 7, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte DIDIER TRONO and MACIEJ WIZNEROWICZ1
__________

Appeal 2012-004323
Application 11/680,414
Technology Center 1600
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Before DEMETRA J. MILLS, ERIC GRIMES, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a viral
vector, which have been rejected for obviousness. We have jurisdiction
under 35 U.S.C. § 6(b).
We affirm-in-part.

1 Appellants identify the Real Party in Interest as Institut Clayton de la
Recherche (Appeal Br. 2).
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STATEMENT OF THE CASE
“Lentiviruses are a subgroup of retroviruses that can infect non-
dividing cells” (Spec. 3:4-5). “[L]entiviral vectors derived from human
immunodeficiency virus type 1 (HIV-1) can mediate the efficient delivery,
integration and long-term expression of transgenes into non-mitotic cells
both in vitro and in vivo” (id. at 3:6-9). The Specification discloses
“increased transduction efficiency through the inclusion of a central
polypurine tract (cPPT) in the vector” (id. at 7:24-25).
Claims 1-9, 12-15, 17, 18, 22, 24-27, 29-36, 39, 41, 42, 47-56, 69, and
70 are on appeal. Claim 1 is illustrative and reads as follows:
1. A recombinant lentiviral vector comprising:
(a) an expression cassette comprising a transgene positioned
under the control of a promoter that is active to promote
detectable transcription of the transgene in a human cell;
(b) a central polypurine tract (cPPT) positioned upstream of
the expression cassette;
and
(c) multiple unique cloning sites positioned adjacent,
upstream or downstream or both upstream and
downstream of the cPPT.

The claims stand rejected under 35 U.S.C. § 103(a) as follows:
• Claims 1, 6-9, 35, 47, 49-54, 69, and 70 based on Zennou2 and
Zufferey (1999)3 (Answer 5);

2 Zennou et al., HIV-1 Genome Nuclear Import Is Mediated by a Central
DNA Flap, 101 CELL 173-185 (2000).
3 Zufferey et al., Woodchuck Hepatitis Virus Posttranscriptional Regulatory
Element Enhances Expression of Transgenes Delivered by Retroviral
Vectors, 73 J. VIROL. 2886-2892 (1999).
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• Claim 2 based on Zennou, Zufferey (1999), and Charneau4 (Answer
8);
• Claims 3-9, 55, and 56 based on Zennou, Zufferey (1999), and
Sirven5 (Answer 8);
• Claims 12-15 based on Zennou, Zufferey (1999), and Zufferey
(1998)6 (Answer 9);
• Claims 17, 18, 22, 24-27, 41, and 42 based on Zennou, Zufferey
(1999), Cannon,7 and Lien8 (Answer 10);
• Claims 29-31 based on Zennou, Zufferey (1999), and Kafri9
(Answer 11);
• Claims 32-34 based on Zennou, Zufferey (1999), and Eklund10
(Answer 13);
• Claims 36 and 39 based on Zennou, Zufferey (1999), and
Chinnasamy11 (Answer 14); and

4 Charneau et al., US 6,682,907 B1, issued Jan. 27, 2004.
5 Sirven, The human immunodeficiency virus type-1 central DNA flap is a
crucial determinant for lentiviral vector import and gene transduction of
human hematopoietic stem cells, 96 BLOOD 4103-4110 (2000).
6 Zufferey et al., Self-Inactivating Lentivirus Vector for Safe and Efficient In
Vivo Gene Delivery, 72 J. VIROL. 9873-9880 (1998).
7 Cannon et al., US 2002/0042136 A1, published Apr. 11, 2002.
8 Lien et al., Regulation of the Myeloid-Cell-Expressed Human gp91-phox
Gene As Studied by Transfer of Yeast Artificial Chromosome Clones into
Embryonic Stem Cells: Suppression of a Variegated Cellular Pattern of
Expression Requires a Full Complement of Distant cis Elements, 17
MOLECULAR AND CELLULAR BIOLOGY 2279-2290 (1997).
9 Kafri et al., Lentiviral Vectors: Regulated Gene Expression, 1 MOLECULAR
THERAPY 516-521 (2000).
10 Eklund et al., PU.1, Interferon Regulatory Factor 1, and Interferon
Consensus Sequence-binding Protein Cooperate to Increase gp91phox
Expression, 273 J. BIOLOGICAL CHEM. 13957-13965 (1998).
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• Claim 48 based on Zennou, Zufferey (1999), and Trono12 (Answer
14).
DISCUSSION
Each of the rejections on appeal is based on the combination of
Zennou and Zufferey (1999). The Examiner finds that Zennou discloses a
lentiviral vector meeting all of the limitations of claim 1: an expression
cassette with a transgene (EGFP) under the control of an appropriate
promoter (CMV), a cPPT, and multiple unique cloning sites (Answer 6,
citing Zennou’s Figure 6).13 More specifically, the Examiner reasons that
“Figure 6a clearly shows additional restrictions sites, Eco NI, Ava II and
Xho I. . . . The Examiner is interpreting multiple cloning site as any region
containing more than one restriction site.” (Answer 16.)
Appellants argue that “[a]s noted in the specification of the present
invention, multiple unique cloning sites are clusters of several unique
cloning sites (page 8, lines 1-4). . . . Thus, to qualify as a MCS [multiple
cloning site], several restriction sites need to cluster together within a short
segment of nucleic acid.” (Appeal Br. 6.)
We agree with the Examiner that the broadest reasonable
interpretation of “multiple unique cloning sites,” as recited in claim 1, reads
on the restriction sites of Zennou’s vector. The Specification describes

11 Chinnasamy et al., Efficient Gene Transfer to Human Peripheral Blood
Monocyte-Derived Dendritic Cells Using Human Immunodeficiency Virus
Type 1-Based Lentiviral Vectors, 11 HUMAN GENE THERAPY 1901-1909
(2000).
12 Trono et al., US 7,629,153 B2, issued Dec. 8, 2009.
13 The Examiner relies on Zufferey (1999) for its disclosure of a
posttranscriptional regulatory element, as recited in claim 69 (Answer 6).
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“multiple unique cloning sites” as follows: “Further preferred aspects of the
invention include multiple unique cloning sites. Unique cloning sites are
sites of restriction enzyme recognition sequences that are unique within the
vector sequence. Several such sites clustered together provide for multiple
unique cloning sites.” (Spec. 8:1-4.)
As noted by the Examiner (Answer 16), however, this description
does not require any specific number of unique restriction enzyme
recognition sites to be located within any specific number of nucleotides
from each other. In addition, as Appellants themselves have noted (Appeal
Br. 6), the Specification describes “multiple cloning sites” in a separate
passage from the description of “multiple unique cloning sites.” The
Specification states that “[v]ectors of the present invention can include a
multiple cloning site (MCS), which is a nucleic acid region that contains
multiple restriction enzyme sites” (Spec. 45:12-13).
Although Appellants have argued that Zennou does not show any
MCS in its vector (Appeal Br. 5), claim 1 does not recite “a multiple cloning
site” but “multiple unique cloning sites.” We agree with the Examiner that,
under the broadest reasonable interpretation, the claim language requires
only a plurality of (“multiple”) restriction enzyme recognition sites (“cloning
sites”) that occur only once in the vector (“unique”).
Zennou’s Figure 6A shows that its vector comprises three restriction
enzyme recognition sites (for the enzymes Eco NI, Ava II, and Xho I) that
are shown to occur only at a single location in the vector (Zennou 180, Fig.
6A). The Eco NI and Ava II sites are located upstream of the cPPT (id.).
Zennou’s vector therefore includes “multiple unique cloning sites positioned
. . . upstream . . . of the cPPT,” as required by claim 1.
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Claims 35, 47, and 49-54 were not argued separately and therefore
fall with claim 1. 37 C.F.R. § 41.37(c)(1)(vii).
With regard to claims 6-9 and 70, Appellants argue that the cited
references do not teach an MCS or MCSs positioned as required by the
claims (Appeal Br. 8-11).
We agree with Appellants that the Examiner has not shown that the
limitations of claims 8, 9, and 70 would have been obvious based on the
cited references. These claims require multiple unique cloning sites
positioned downstream of the cPPT (claim 8), both upstream and
downstream of the cPPT (claim 9), or between the cPPT and the promoter of
claim 1 (claim 70).
As discussed above, the vector shown in Zennou’s Figure 6A has
three identified unique cloning sites, two of which are upstream and one of
which is downstream from the cPPT. None of the sites is between the cPPT
and the promoter (CMV) in Zennou’s vector, and since only one is
downstream from the cPPT, the vector lacks multiple unique cloning sites
downstream of the cPPT.
The Examiner reasoned that “[s]ince cPPT is inserted into a region
containing multiple restrictions sites, the mcs is upstream, downstream,
adjacent and upstream and downstream of the cPPT” (Answer 6). The
Examiner also reasoned that “a restriction site can be placed anywhere on a
plasmid. Positioning the MCS between the cPPT and the promoter is merely
a design choice that does not make the invention nonobvious.” (Id.)
We do not agree that this reasoning supports a prima facie case of
obviousness. The Examiner has not provided evidence that the vector
described by Zennou has unique cloning sites other than those shown in its
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Figure 6A. As discussed above, those sites do not include multiple sites
downstream from the cPPT or between the cPPT and the promoter.
In addition, while it may be true that a restriction site could be
inserted into Zennou’s vector at any position, including between the cPPT
and the promoter, the Examiner has not provided any reasoning that would
show that this modification to Zennou’s vector would have been obvious.
The Examiner therefore has not made a prima facie case that claim 70 would
have been obvious based on the cited prior art. See KSR Int’l Co. v. Teleflex
Inc., 550 U.S. 398, 418 (2007) (“[I]t can be important to identify a reason
that would have prompted a person of ordinary skill in the relevant field to
combine the elements in the way the claimed new invention does.”); In re
Fritch, 972 F.2d 1260, 1266 (Fed. Cir. 1992) (“The mere fact that the prior
art may be modified in the manner suggested by the Examiner does not
make the modification obvious unless the prior art suggested the desirability
of the modification.”).
With respect to claims 6 and 7, however, Appellants’ argument is not
persuasive. Claim 7 requires that the “multiple unique cloning sites are
positioned upstream of the cPPT” and, as discussed above, Zennou’s Figure
6A shows a vector with two unique cloning sites upstream of the cPPT.
Claim 6 requires that the “multiple unique cloning sites are positioned
adjacent to the cPPT.” The Specification defines “adjacent” to mean that
“the subject element . . . is the first functionally important element
encountered when scanning the vector sequence from the boundaries of the
reference element” (Spec. 9:4-6). Zennou’s Figure 6A does not show any
functionally important elements between the Eco NI/Ava II restriction sites
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and the cPPT.14 Thus, the upstream multiple unique cloning sites of
Zennou’s vector are “adjacent” to the cPPT according to the Specification’s
definition.
With regard to claim 69, Appellants argue that a person of ordinary
skill in the art would have no reason to combine the posttranscriptional
regulatory element taught by Zufferey (1999) with Zennou’s vector because
“Zufferey does not teach or suggest a cPPT positioned upstream of the
expression cassette or a MCS . . . [and] cPPT is a key element of a lentiviral
vector” (Appeal Br. 10-11).
This argument is not persuasive. Claim 69 is directed to the “vector
of claim 1, further comprising a posttranscriptional regulatory sequence
positioned to promote the expression of the transgene.” The Examiner
concludes that it would have been obvious to modify the vector disclosed by
Zennou to include a posttranscriptional regulatory element (WPRE) because
Zufferey (1999) “teaches that lentiviral vectors containing WPRE
substantially increased their levels of expression in a transgene-, promoter-
and vector-independent manner” (Answer 7).
The Examiner’s reasoning and conclusion are supported by the
evidence of record. Zufferey (1999) states that expression of transgenes on
retroviral vectors “is often inefficient, a potential obstacle for their

14 Zennou’s figure shows a region labeled “probe” that extends into the
region between the Eco NI site and the Ava II site (Zennou 180, Fig. 6A).
However, that notation simply marks the region to which a separate probe,
used in Southern blotting experiments, hybridizes (cf. id. at 178, legend to
Fig. 4). Appellants have not provided a reasoned basis for concluding that a
probe hybridization site is a “functionally important element,” as required by
the Specification’s definition of “adjacent.”
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widespread use in human gene therapy” (Zufferey (1999) 2886, abstract) .
Zufferey (1999) discloses that insertion of the posttranscriptional regulatory
element from woodchuck hepatitis virus (WPRE) “in the 3' untranslated
region of coding sequences carried by either oncoretroviral or lentiviral
vectors substantially increased their levels of expression in a transgene-,
promoter- and vector-independent manner” (id.) (emphasis added).
Based on the disclosure of Zufferey (1999), we agree with the
Examiner that it would have been obvious to a person of ordinary skill in the
art to include a posttranscriptional regulatory element such as WPRE in
Zennou’s vector, in order to increase expression of coding sequences carried
by the vector and make it more useful for gene therapy. Appellants’
argument that the combination would not have been obvious because
Zufferey (1999) does not disclose a vector containing a cPPT is
unpersuasive because Zufferey (1999) expressly states that WPRE increases
expression in a vector-independent manner.
The Examiner has rejected claims 2-9, 12-15, 17, 18, 22, 24-27, 29-
34, 36, 39, 41, 42, 48, 55, and 56 based on Zennou, Zufferey (1999), and
additional prior art (Answer 8-15). Appellants have waived arguments
based on the other references cited by the Examiner (Appeal Br. 11-13). We
therefore affirm the rejections of claims 2-9, 12-15, 17, 18, 22, 24-27, 29-34,
36, 39, 41, 42, 48, 55, and 56 for the reasons set out in the Answer.
SUMMARY
We reverse the rejection of claims 8, 9, and 70 as obvious based on
Zennou and Zufferey (1999). We affirm the rejection of the other claims on
appeal.
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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-IN-PART

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