Ex Parte Glaab et al

Board of Patent Appeals and Interferences

Dec 9, 2010

10554433 (B.P.A.I. Dec. 9, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
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United States Patent and Trademark Office
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
10/554,433 10/24/2005 Warren E. Glaab 21287P 5786
210 7590 12/10/2010
MERCK
P O BOX 2000
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EXAMINER
EPPS -SMITH, JANET L
ART UNIT PAPER NUMBER
1633
MAIL DATE DELIVERY MODE
12/10/2010 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 BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte WARREN E. GLAAB, THOMAS SKOPEK,
KATERINA VLASAKOVA, and JUDITH E. MILLER
__________

Appeal 2010-005665
Application 10/554,433
Technology Center 1600
__________

Before DEMETRA J. MILLS, ERIC GRIMES, and MELANIE L.
McCOLLUM, Administrative Patent Judges.

McCOLLUM, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134 involving claims to a method
for evaluating a compound’s genotoxic activity. The Examiner has rejected

1 The two-month time period for filing an appeal or commencing a civil
action, as recited in 37 C.F.R. § 1.304, or for filing a request for rehearing,
as recited in 37 C.F.R. § 41.52, begins to run from the “MAIL DATE”
(paper delivery mode) or the “NOTIFICATION DATE” (electronic delivery
mode) shown on the PTOL-90A cover letter attached to this decision.
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the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We
reverse.
STATEMENT OF THE CASE
Claims 1-18 are pending and on appeal (App. Br. 5). We will focus
on claim 1, which reads as follows:
1. A method for evaluating the genotoxic activity of a test compound
comprising the steps of:
a) providing microbial indicator cells that are 5-fluorouridine
resistant (5-FURR) at a desired cell density;
b) preparing a test compound for evaluation which may optionally
include exposing the test compound to a metabolic activation system;
c) preparing a test sample comprising the test compound of b) and
the microbial indicator cells;
d) incubating the test sample under conditions that promote the
growth of the indicator strain;
e) evaluating the toxicity of the test compound;
f) incubating the test sample overnight under conditions that
promote the growth of the indicator strain and expression of FUR
phenotypes;
g) exposing the test sample to a selective concentration of
5-Fluorouracil (5-FU); and
h) determining the presence and number of 5-FU-resistant mutant
indicator cells present in the test sample wherein the presence of 5-FU-
resistant indicator cells indicates that the test compound has genotoxic
activity.
Claims 1-12 and 15-18 stand rejected under 35 U.S.C. § 103(a) as
obvious over Skopek,2 McCann,3 Landis,4 and Tiraby5 (Ans. 3).

2 Skopek and Thilly, Rate of induced forward mutation at 3 genetic loci in
Salmonella typhimurium, 108 MUTATION RESEARCH 45-56 (1983).
3 McCann et al., Detection of Carcinogens as Mutagens: Bacterial Tester
Strains with R Factor Plasmids, 72 PNAS 979-983 (1975).
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Claim 13 stands rejected under 35 U.S.C. § 103(a) as obvious over
Skopek, McCann, Landis, Tiraby, and Skory6 (Ans. 10-11).
Claim 14 stands rejected under 35 U.S.C. § 103(a) as obvious over
Skopek, McCann, Landis, Tiraby,7 and Kazarinova8 (Ans. 12-13).
The Examiner relies on Skopek for teaching “a method of forward
mutation assays in Salmonella typhimurium” (id. at 4). The Examiner finds:
Skopek uses the S. typhimurium strain TM677. . . . [A]liquots
of the . . . cells were thawed from frozen aliquots, and test
compounds requiring metabolic activation and those not
requiring metabolic activation were prepared, and then added to
the . . . cells. After a 4 hour incubation in conditions that
promote growth of the TM677 cells to determine the survival of
the cells (evaluation of the toxicity of the test compound) the
cells were subjected to a selective concentration of 5-FU, at
0.5 ug/mL, and the number of surviving clones were counted
after a 36 hour (overnight) incubation (page 48).
(Ans. 4-5.) In addition, the Examiner finds: “In essence, Skopek’s method
employs one mutant cell line derived from Ames TA100 cells that are His+
and ampicillin resistant, and uses them in a forward mutation assay to
develop a second resistance to 5-fluorouracil.” (Id. at 5.) However, the

4 Landis et al., Tolerance of 5-fluorodeoxyuridine resistant human
thymidylate synthases to alterations in active site residues, 27 NUCLEIC
ACIDS RESEARCH 3702-3711 (1999).
5 Tiraby et al., Concomitant expression of E. coli cytosine deaminase and
uracil phosphoribosyltransferase improves the cytotoxicity of
5-fluorocytosine, 167 FEMS MICROBIOLOGY LETTERS 41-49 (1998).
6 Skory, US 6,268,189 B1, Jul. 31, 2001.
7 The Examiner fails to list Tiraby in the statement of this rejection (Ans. 12-
13: ¶ 22). However, it is clear from the discussion of the rejection that this
reference should have been included (id. at 13: ¶ 23).
8 Kazarinova et al., US 6,344,344 B1, Feb. 5, 2002.
Appeal 2010-005665
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Examiner acknowledges that “Skopek does not teach that the indicator cells
are 5-fluorouridine [5-FUR] resistant prior to performing the forward
mutation assay to develop 5-FU resistance” (id. at 5-6).
The Examiner relies on McCann for teaching a cell line having many
of the features recited in the claims (id. at 6). However, the Examiner
acknowledges that, like Skopek, “McCann does not teach that the indicator
cells are 5-fluorouridine resistant prior to performing the forward mutation
assay to develop 5-FU resistance” (id.).
The Examiner relies on Landis for disclosing “5-fluorouridine
resistant microbial cell lines” (id. at 7). The Examiner finds that “Landis
teaches that different concentrations of 5-FUR were used in the assay to
develop the resistant clones” (id.). The Examiner relies on Tiraby for
teaching “that 5-Fluorouracil and 5-Fluorouridine both are capable of
formation of 5-FuMP” (id.). Based on the teachings in Landis and Tiraby,
the Examiner concludes that it would have been obvious “to modify the
teachings of Skopek . . . [to] use 5-fluorouracil [sic, 5-fluorouridine]
resistant cells as the initial indicator cell lines” (id. at 8).
With regard to claims 13 and 14, the Examiner additionally relies on
Skory and Kazarinova, respectively, for features disclosed in these
dependent claims (id. at 10-15). The Examiner does not rely on these
additional references for providing a reason to use 5-fluorouridine resistant
cells in Skopek’s method (id.).
Appellants contend:
There is no disclosure in any of the cited references that wild
type cells could poison upp mutant cells by leaking FUR into
the surrounding medium. Without such an appreciation, one
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skilled in the art would not have looked to any art concerning
FUR resistance or metabolism in connection with the forward
mutation assay.
(App. Br. 11.)
ISSUE
Has the Examiner set forth a prima facie case that it would have been
obvious to modify Skopek’s forward-mutation assay to use 5-fluorouridine
resistant indicator cells?
FINDINGS OF FACT
1. Skopek discloses a forward-mutation assay comprising thawing
a frozen aliquot of TM677 cells, incubating the culture for 30 minutes at
37°C, delivering compounds to samples of the cell culture, plating cultures
to determine survival, allowing the cultures “to grow at 37°C for 4 h . . . to
insure full phenotypic expression of FUR mutants and gene segregation,”
resuspending the cultures in PBS, adding an aliquot of the suspension to
molten top agar containing FU, plating the cells, and counting the cells
“after a 36-h incubation at 37°C” (Skopek 48).
2. Landis relates to the use of fluoropyrimidines, such as
5-fluorouracil (5-FU), in cancer therapy (Landis, Abstract).
3. Landis discloses that “5-FU is metabolized to
5-fluorodeoxyuridylate (5-FdUMP), a tight binding covalent inhibitor of
thymidylate synthase (TS),” the inactivation of which “results in decreased
production of TMP, cessation of DNA synthesis and ultimately thymineless
death” (id. at 3702).
4. Landis also discloses that, “[i]n order to select for library
members that are resistant to killing with 5-FdUR, transfectants were plated
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on minimal medium containing increasing amounts of 5-FdUR . . . and
incubated at 37°C for 36-48 h” (id. at 3704).
5. Tiraby relates to the use of 5-fluorocytosine (5-FC) in cancer
chemotherapy (Tiraby, Abstract).
6. Tiraby discloses combining “the E. coli upp gene encoding
uracil phosphoribosyltransferase (UPRT) with codA gene to create . . . a
bacterium very efficient in metabolizing 5-FC” (id.).
7. Tiraby Fig. 1 is reproduced below:

Tiraby Fig. 1 depicts the “metabolism of cytosine and uracil in Escherichia
coli and mammalian cells. Enzymatic steps missing in E. coli and in animal
cells are indicated by a bold × or a plain ×, respectively. . . . The bold arrow
indicates the preferential step in E. coli.” (Id. at 42.)
PRINCIPLES OF LAW
“In rejecting claims under 35 U.S.C. § 103, the examiner bears the
initial burden of presenting a prima facie case of obviousness. Only if that
burden is met, does the burden of coming forward with evidence or
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argument shift to the applicant.” In re Rijckaert, 9 F.3d 1531, 1532 (Fed.
Cir. 1993) (citation omitted).
ANALYSIS
The Examiner concludes that it would have been obvious “to modify
the teachings of Skopek . . . [to] use 5-fluorouracil [sic, 5-fluorouridine]
resistant cells as the initial indicator cell lines” (Ans. 8). In particular, the
Examiner concludes:
It would be obvious to do so because, as Landis and Tiraby
teach, . . . F-UMP can be made via multiple pathways in E.coil
[sic]. So even if Skopek identifies mutations that affect 5-FU
resistance with his screen, there is still an alternate pathway for
the generation of 5-FUMP in bacterial cells. However, if one
creates 5-Fluoruridine resistant indicator cells first, then uses
them in the methodology of Skopek, one would be able to
identity [sic] cells that were completely resistant to 5-FU and
5-FUR, and the only 5-FUMP in these cells would only occur
through de novo synthesis as evidenced by Tiraby’s figure 1).
Such a modification of Skopek’s cells would garner a greater
specificity for the identification of mutagens in the genotoxic
screens.
(Id. at 8-9.)
We do not agree that the Examiner has set forth a prima facie case of
obviousness. As we understand it, the Examiner’s reasoning is that
Skopek’s assay could be made more accurate (“garner a greater specificity,”
Ans. 8) if the cells used were 5-FUR resistant because of inactivation of the
udk gene, because Tiraby discloses that 5-FU can be converted into the toxic
metabolite 5-FUMP via 5-FUR. However, the Examiner has not provided
evidence that those skilled in the art recognized or would have expected that
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the conversion of 5-FU to 5-FUMP via 5-FUR affected the accuracy of
Skopek’s assay.
In particular, the Examiner has not shown that it was known in the art
that mutation in the upp gene was the basis of Skopek’s 5-FU resistance. In
the absence of such a teaching, we do not agree that it would have been
obvious to render the indicator cells 5-FUR resistant in an effort to reduce
the production of 5-FUMP via the alternate pathway depicted in Tiraby
Fig. 1.
CONCLUSION
The Examiner has not set forth a prima facie case that it would have
been obvious to modify Skopek’s forward-mutation assay to use
5-fluorouridine resistant indicator cells. We therefore reverse the
obviousness rejections of claims 1-18.

REVERSED

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