Ex Parte Barros Olmedo et al

Patent Trials and Appeals Board

Apr 12, 2019

14394018 - (D) (P.T.A.B. Apr. 12, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
14/394,018 10/10/2014 Luis Felipe Barros Olmedo
23552 7590 04/16/2019
MERCHANT & GOULD P.C.
P.O. BOX 2903
MINNEAPOLIS, MN 55402-0903
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.
15807.0097FPWO 5394
EXAMINER
BROWN, MINDY G
ART UNIT PAPER NUMBER
1636
NOTIFICATION DATE DELIVERY MODE
04/16/2019 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):
USPT023552@merchantgould.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte LUIS FELIPE BARROS OLMEDO,
ALEJANDRO SAN MARTIN, SEBASTIAN CEBALLO CHARPENTIER,
and WOLF B. FROMMER
Appeal2018-000441
Application 14/394,018 1
Technology Center 1600
Before FRANCISCO C. PRATS, JOHN E. SCHNEIDER, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
TOWNSEND, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of measuring lactate transport, which have been rejected as obvious. We
have jurisdiction under 35 U.S.C. § 6(b ).
We reverse.
STATEMENT OF THE CASE
"Lactate is an organic chemical compound that participates in the
metabolism of eukaryotic and prokaryotic cells." (Spec. 1.) "Lactate is in
dynamic flux between subcellular compartments, between the cell and the
1 Appellants identify the real party in interest as Centro De Estudios
Cientificos De Valdivia. (Appeal Br. 3.)
Appeal2018-000441
Application 14/394,018
extracellular space and between cells." (Id. at 2.) Methods to measure
lactate include enzymatic reactions, including by using enzyme-based
electrodes, as well as high performance liquid chromatography. (Id.)
However, the Specification states that these methods require extraction of
samples or consume lactate, and they cannot "detect the minute amount of
lactate present in a single cell or a single subcellular organelle." (Id.) The
present invention is directed to the use of a genetically-encoded Forster
resonance energy transfer (FRET)-based nanosensor that can measure lactate
in a cell sample. (Id. at 5.)
Claims 6-17 are on appeal. Claim 6 is representative and reads as
follows:
6. A method for the measurement of lactate transport wherein
the method comprises the steps of:
a) expressing a FRET-based lactate nanosensor in a
cytosol of a desired host selected from single cells or cell
populations, adherent cells or cells in suspension, cells in a cell
culture, a tissue culture, a mixed cell culture, a tissue explant, or
cells in animal tissues in vivo, wherein the nanosensor
comprises a bacterial LldR transcription factor between donor
and acceptor fluorescent protein moieties, wherein the
nanosensor remains in the cytosol;
b) calibrating the host with predetermined values of
intracellular, extracellular, subcellular lactate concentrations,
recording lactate concentrations in time;
c) disrupting the steady-state of lactate in the cell; and
d) recording the output from the nanosensor calculating
the lactate concentration at different time points and
determining the rates of transport.
(Appeal Br. 27.)
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Application 14/394,018
The following grounds of rejection by the Examiner are before us on
review:
Claims 6, 9, and 12 under 35 U.S.C. § 103 as unpatentable over
Deuschle2 and Aguilera. 3
Claims 7, 8, 10, 11, and 13-17 under 35 U.S.C. § 103 as unpatentable
over Deuschle, Aguilera, and Kennedy. 4
DISCUSSION
The Examiner finds that Deuschle teaches a FRET nanosensor for
detecting metabolites in a cell, where the sensor is expressed in mammalian
cell culture and the cytosolic level of the metabolite is monitored based on
the relative emission ratio from the sensor. (Final Action 3--4.) The
Examiner also finds that Deuschle teaches calibrating the sensor. (Id. at 4.)
The Examiner recognizes that Deuschle does not specifically teach a FRET
nanosensor that can recognize lactate, but finds that it does "state" that
"redesign of the binding sites can recognize different metabolites including
lactate (page 8)." (Id.)
The Examiner finds that Aguilera discloses a bacterial LldR
transcription factor that comprises a lactate binding domain and that lactate
binds LldR. (Id.) The Examiner further finds that "LldR has a dual function
2 Karen Deuschle et al., Genetically Encoded Sensors for Metabolites,
Cytometry Part A 64A:3-9 (2005).
3 Laura Aguilera et al., Dual Role of LldR in Regulation of the lldPRD
Operon, Involved in !-Lactate Metabolism in Escherichia coli, 190(8) J.
Bacteriology 2997-3005 (2008).
4 Kelly M. Kennedy and Mark W. Dewhirst, Tumor metabolism of lactate:
the influence and therapeutic potential for MCT and CD 147 regulation, 6( 1)
Future Oncol. 127 (2010).
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Application 14/394,018
as a repressor and activator based on the presence of L-lactate." (Id.) The
Examiner concludes that it would have been obvious to one of ordinary skill
in the art to use the method and platform taught Deuschle to detect lactate by
"replacing the metabolite binding protein in the FRET-based metabolite
nanosensor taught by Deuschle et al. with the bacterial LldR transcription
factor taught by Aguilera et al. for detecting lactate level because Deuschle
et al. states that the nanosensor can be reconfigured to detect other
metabolites." (Id.)
We disagree with the Examiner's conclusion that claims 6, 9, and 12
would have been obvious from the teachings of Deuschle and Aguilera.
Deuschle describes a FRET-based sensor for the detection of maltose,
glucose, and ribose. (Deuschle at 5-6.) Those sensors involved fusion of a
specific periplasmic binding protein between enhanced cyan fluorescent
protein (ECFP) and enhanced yellow fluorescent protein (EYFP). (Id. at 5-
6.) In the case of maltose detection, periplasmic maltose binding protein
(MBP) was used. (Id. at 6.) For glucose detection, periplasmic
glucose/ galactose binding protein was used. (Id.) And for ribose,
periplasmic ribose binding protein (RBP) was used. (Id.) These binding
proteins when bound to ligand were found to undergo a conformational
change large enough to transduce metabolite binding into a FRET change.
(Id.)
Deuschle explains that computational "redesign" of the binding sites
"of several of these binding proteins," i.e., the PBPs that were examined in
Deuschle, resulted in a redesign that "recognize[s]" lactate. (Id. at 8.) Thus,
we agree with the Examiner that lactate is a metabolite of interest for
detection with a FRET-based sensor.
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Application 14/394,018
However, as Appellants note, Deuschle teaches the feasibility of PBPs
with particular characteristics as the binding partner for detecting a
compound of interest using FRET sensors. (Deuschle 4.) Deuschle explains
that "it is essential" that "a sensor domain is able to undergo a
conformational change large enough to transduce metabolite binding into a
FRET change" and that the conformational change "must be tightly coupled
to substrate binding." (Id. at 5.) The FRET change being the relative
position of the two fused FRET binding pairs so as to alter the fluorescence
energy transfer (i.e., the "FRET"). Deuschle also explains that "FRET
requires a number of prerequisites such as suitable distance (typically in the
range up to 10 nm), a suitable geometry of donor and acceptor molecules,
and an overlap between the donor emission and the acceptor excitation
spectra." (Id. at 4.)
Deuschle further points out that "despite the ingenious concept of
conformation-dependent FRET sensors, until recently, sensors for primary
metabolites were unavailable because suitable domains that might be used to
transduce a conformational change into an altered FRET signal were not
developed." (Id. at 5.) Deuschle explains that periplasmic binding proteins
were found to meet the criteria. (Id. at 5---6.)
In particular, according to Deuschle, "[m]ost importantly, PBPs
undergo a significant conformational change when binding to their target
ligands." (Id. at 5.) Deuschle explains "most PBPs consist of two similar
globular domains. The binding site is created by specific residues in the
cleft between the domains, which engulfs the ligand through a Venus
flytrap-like hinge-twist motion." (Id. at 6.) Deuschle explains that "[t]he
overall diameter (longitudinal elliptic axis) of PBPs is in the range of 5 to 7
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Application 14/394,018
nm" and that "[t]he distance between the N- and C-termini ... is
approximately 4 to 5 nm for MBP and RBP." (Id. at 7.) Upon binding, the
termini "move closer together ... by about 0.7 nm in [the] case of MBP and
farther apart by 0.2 nm in the case of RBP." (Id.)
The Examiner has not provided sufficient evidence to support a
reasonable expectation of success in substituting the LldR transcription
factor for the PBPs described for use in the ribose, maltose, and
glucose/galactose FRET sensors described by Deuschle. All that the
Examiner has established is that Aguilera teaches that the LldR undergoes a
conformational change when binding lactate. (Ans. 7 .)
It is true that Aguilera teaches a conformational change of the LldR on
binding lactate (Aguilera 3002), but the Examiner has not established with
any evidence what the size of the LldR protein is, that the binding site is
similar to PBP, or that the conformational change is one that "engulfs the
ligand through a Venus flytrap-like hinge-twist motion" sufficient to
transduce binding into a change in relative position of the two fused FRET
binding pairs so as to alter the fluorescence energy transfer of them. In
short, there is insufficient evidence of record to establish that LldR
transcription factor would behave similarly to PBP so as to be a suitable
domain that would reasonably be likely to transduce a conformational
change into an altered FRET signal when lactate bound to it in the modified
FRET sensor of Deuschle.
"[T]he examiner bears the initial burden, on review of the prior art or
on any other ground, of presenting aprimafacie case ofunpatentability." In
re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992). The Examiner has failed
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Application 14/394,018
to meet that burden here for the reasons just discussed. Consequently, we do
not sustain the Examiner's obviousness rejection of claims 6, 9, and 12.
We also note that the Examiner has also failed to establish with
sufficient evidence that the prior art teaches or suggests steps b through d of
claims 6, 9, and 12. According to the Examiner, steps band d would have
been obvious "to accurately record data from a system." (Ans. 7.) First, the
Examiner does not point to what in Deuschle is the teaching of step c. We
do not discern any such step. While Deuschle teaches measuring free
glucose in cytosol (Deuschle 6), and determining a metabolite range over
which certain FRET sensors could be used for quantification of the
metabolite in cytosol (Id. Table 1 ), it does not teach disrupting steady-state
of the metabolite. Furthermore, while it is true that calibrating a sensor for
use is standard procedure, we do not discern any teaching in Deuschle as to
calibrating intracellular, extracellular, and subcellular lactate concentrations.
Nor do we discern any reason that such would have been necessary to
accurately record the metabolite in the cytosol of the Deuschle system.
Furthermore, we do not discern any teaching or suggestion in Deuschle of
determining a rate of transport of the metabolite, or that such would have
been necessary to accurately record the metabolite in the cytosol of the
Deuschle system. The Examiner does not rely on Aguilar for any of these
teachings or for a suggestion of taking these steps, and we do not discern any
relevant teaching in Aguilar related to these steps. Thus, for this additional
reason we do not sustain the Examiner's obviousness rejection of claims 6,
9, and 12.
Regarding the Examiner's obviousness rejection of claims 7, 8, 10,
11, and 13-1 7 adding the Kennedy reference, we note that Kennedy is not
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relied upon to cure the deficiencies of the rejection noted above. Thus, for
the reasons just discussed, we also do not sustain the Examiner's
obviousness rejection of claims 7, 8, 10, 11, and 13-17.
SUMMARY
We reverse the rejection of claims 6, 9, and 12 under 35 U.S.C. § 103
as unpatentable over Deuschle and Aguilera.
We reverse the rejection of claims 7, 8, 10, 11, and 13-17 under
35 U.S.C. § 103 as unpatentable over Deuschle, Aguilera, and Kennedy.
REVERSED
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