Ex Parte Runge et al

Board of Patent Appeals and Interferences

Apr 23, 2007

09832069 (B.P.A.I. Apr. 23, 2007)

The opinion in support of the decision being entered today was not written
for publication and is not binding precedent of the Board.

UNITED STATES PATENT AND TRADEMARK OFFICE
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BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
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Ex parte MARSCHALL S. RUNGE,
BENNETT VAN HOUTEN, and SCOTT W. BALLINGER
__________

Appeal 2007-0582
Application 09/832,069
Technology Center 1600
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Decided: April 23, 2007
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Before DONALD E. ADAMS, ERIC GRIMES, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of predicting atherosclerotic heart disease based on mitochondrial DNA
damage. The Examiner has rejected the claims as nonenabled and indefinite.
We have jurisdiction under 35 U.S.C. § 6(b). We reverse.
BACKGROUND
The Specification states that “there is growing evidence that
atherosclerotic lesions result from factors mediated by reactive oxygen
Appeal 2007-0582
Application 09/832,069

species” (Specification 4: 1-2). “Numerous studies have implicated the
mitochondria as a vulnerable target for reactive oxygen species” (id. at 5: 1-
2).
The Specification states that because “mitochondrial DNA is more
susceptible to reactive oxygen species-mediated damage, and because
increased oxidative stress is believed to play a role in the early events of
atherogenesis, . . . the mitochondrial DNA in aortic tissues destined to
become atherosclerotic has increased damage” (id. at 7: 1-6). The
Specification discloses
methods of predicting coronary atherosclerotic heart disease . . .
based upon the extent of mitochondrial DNA damage or upon
related measurement of mitochondrial dysfunction that is the
result of mitochondrial DNA damage including changes in
mitochondrial protein production, changes in mitochondrial
oxidative phosphorylation or changes in mitochondrial ATP
production.
(Id. at 8: 20 to 9: 5.)
DISCUSSION
1. CLAIMS
Claims 6, 8, 9, and 14-23 are pending and on appeal. Claims 6 and 16
are representative and read as follows:
6. A method of measuring the amount of oxidative stress
in a human individual, comprising the steps of:

(a) collecting a blood sample from said individual;

(b) assessing the amount of mitochondrial DNA damage
in cells from said sample wherein such amount of damage is
indicative of oxidative stress in said individual.
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16. The method of claim 6, wherein said mitochondrial DNA
damage is assessed by measuring mitochondrial mRNA production.

2. PRIOR ART
The Examiner relies on the following references:
Corral-Debrinski et al., “Association of mitochondrial DNA damage
with aging and coronary atherosclerotic heart damage,” Mutation Research,
Vol. 275, pp. 169-180 (1992).

Lenaz, “Role of mitochondria in oxidative stress and ageing,”
Biochimica Biophysica Acta, Vol. 1366, pp. 53-67 (1998).

Williams et al., “Increased oxidative damage is correlated to altered
mitochondrial function in heterozygous manganese superoxide dismutase
knockout mice,” Journal of Biological Chemistry, Vol. 273, pp. 28510-
28515 (1998).

Hudson et al., “Age-associated change in mitochondrial DNA
damage,” Free Rad. Res., Vol. 29, pp. 573-579 (1998).

3. INDEFINITENESS
Claims 6, 8, 9, and 14-23 stand rejected under 35 U.S.C. § 112,
second paragraph, as indefinite
because it is unclear whether the final clause of the method is
directed to detecting amount of damage or mere presence of
damage. The claim states, “wherein such damage is indicative
of oxidative stress in said individual.” Thus, the claim does not
particularly appear to require establishing a correlation based
upon any amount or ratio or other measurement of quantity of
damage.
(Answer 8.)
We will reverse this rejection. The Answer does not accurately quote
the claim language. Claim 6 states the “amount of damage is indicative of
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oxidative stress.” The claim language makes clear that oxidative stress is
determined based on the amount of mitochondrial DNA damage, not the
mere presence of damage.
4. ENABLEMENT
Claims 6 and 16-20 stand rejected under 35 U.S.C. § 112, first
paragraph, on the basis that the specification,
while being enabling for a method for measuring the amount of
oxidative stress in an individual by detecting the amount of
DNA damage per length of DNA using QPCR, does not
reasonably provide enablement for detecting mtDNA damage
by measuring mitochondrial mRNA production, mitochondrial
protein production, mitochondrial oxidative phosphorylation,
mitochondrial ATP production or mitochondrial redox state.
(Answer 3.)
Thus, the Examiner does not dispute that atherosclerotic heart disease
can be predicted by measuring mitochondrial DNA (mtDNA) damage; the
issue is whether mtDNA damage can be measured indirectly. Appellants
identify this as the real issue in the case (Br. 5-6) and the Examiner agrees
(Answer 11: “‘whether the assay is reasonably predictive of mtDNA
damage’ . . . [is] the true question of enablement in the instant application”).
The Examiner argues that the
specification provides no evidence teachings regarding the
relationship between mtDNA damage and mitochondrial
mRNA production, mitochondrial protein production,
mitochondrial oxidative phosphorylation, mitochondrial ATP
production or mitochondrial redox state. The specification does
not teach how these measurements are associated.
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(Answer 5.) The Examiner also states that the “specification has no working
examples of measuring the amount of mtDNA damage in tissue using
mitochondrial mRNA production,” etc. (id. at 6).
Appellants disagree with the “Examiner’s position that there is no
exemplary support in the specification” (Br. 8). Appellants point to
Examples 5-7 in the Specification, which they characterize as showing that
oxidative damage causes changes in mitochondrial mRNA production,
protein production, oxidative phosphorylation, ATP production, and redox
state (id.). Appellants argue that the Examiner’s reasoning in support of the
rejection is based on the effects of single mutations, while the claimed
method measures the cumulative effect of mutations in a population of
mitochondria (id. at 9).
We agree with Appellants that the Examiner has not provided an
adequate basis for concluding that the measurements recited in claims 16-20
would not be reasonably predictive of the amount of mitochondrial DNA
damage.
The Specification provides several relevant working examples,
describing experiments in which human umbilical vein endothelial cells
(HUVEC) and human aortic smooth muscle cells (HASMC) were treated in
vitro with the reactive oxygen species hydrogen peroxide (H2O2) and
peroxynitrite (ONOO–) (Specification 27-39).
The Specification reports that “[h]ydrogen peroxide treatment resulted
in increased mitochondrial DNA damage in both cell lines” (id. at 41: 6-7),
and “[p]eroxynitrite treatment resulted in preferential damage to the
mitochondrial DNA [compared to nuclear DNA] in HUVEC and HASMC”
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(id. at 42: 9-10). The damage was reported to be significant in both cell
types, treated with either reactive oxygen species (id. at 64: 22-29).
The Specification also reports that:
• “Treatment of HUVEC and HASMC with peroxynitrite resulted in
substantially decreased transcript levels in the mitochondrial encoded genes,
NADH dehydrogenase 2 (ND2) and cytochrome b (Cyt b), but not the 16S
rRNA” (id. at 43: 20 to 44: 2);
• “Reactive oxygen species treatment also resulted in a decrease in
mitochondrial protein synthesis in both cell lines” (id. at 45: 13-14), with
decreases of 12% to 70% depending on the concentration of reactive oxygen
species (id. at 46: 10-15); and
• “Peroxynitrite treatment also resulted in an overall decrease in ATP
levels and mitochondrial respiration (complex II) in HUVEC and HASMC”
(id. at 46: 17 to 47: 1), with “significant decreases in ATP” and “a
significant decrease of complex II reduction of MTT (mitochondrial
respiration)” (id. at 47: 4-7).
Thus, the Examiner is correct in stating that the Specification does not
provide “working examples of measuring the amount of mtDNA damage in
tissue using mitochondrial mRNA production,” etc. (Answer 6); i.e., the
examples do not provide formulas to convert a specific amount of, e.g.,
mitochondrial mRNA production to a specific amount of mtDNA damage.
However, the Specification provides convincing evidence of a
correlation between increased mitochondrial DNA damage and decreased
mitochondrial mRNA production, protein production, ATP levels, and
respiration. The claims do not require precise, quantitative determination of
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the amount of mitochondrial DNA damage: the Specification states that
increased mitochondrial DNA damage indicates increased oxidative stress.
The Examiner has not adequately explained why the correlations shown in
the working examples do not allow those skilled in the art to the make type
of qualitative determination (normal range vs. abnormal) that is required to
practice the claimed method.
The Examiner also argues that the effect of a given mutation is
unpredictable: depending on its type and location, a mutation can
completely abolish the function of a gene product or it can have no effect at
all (Answer 5). Because a given mutation can have a range of effects on
mRNA production, protein production, etc., the Examiner concludes that
measuring such “downstream” effects cannot be relied on to measure the
amount of DNA damage (id. at 5-6).
We agree with Appellants that the Examiner’s concern is misplaced.
As Appellants have pointed out,
[w]here there is a population of mitochondria being tested
(which there certainly would be if one were testing a blood
sample or blood products as stated by the claim), there would
necessarily be a vast range of mutations occurring in the
mitochondria, some within coding regions and some outside of
a particular coding region. Nevertheless, the distribution would
be expected to be random and thus demonstrate a readily
identifiable correlation between the amount of damage in any
one gene, as measured by expression of that gene, and the
amount of damage overall.
(Br. 9.) We agree with Appellants’ analysis, and note that it is supported by
the correlations demonstrated in the Specification’s working examples.
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SUMMARY
The Examiner has not established that the claims are indefinite or that
undue experimentation would have been required to practice the claimed
method. We reverse the rejections under 35 U.S.C. § 112, first and second
paragraphs.

REVERSED

dm
David L. Parker
FULBRIGHT & JAWORSKI LLP
600 Congress Avenue Suite 2400
Austin TX 78701
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