DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
The present application, filed on March 2, 2023, is a 371 of PCT/US2021/047506, filed on August 25, 2021 and claims priority to U.S. Provisional Patent Application 63/074101, filed on September 3, 2020.
Election/Restrictions
Applicant’s election without traverse of Group I (claims 1-7 and 10-14) in the reply filed on October 24, 2025 is acknowledged.
Claim Status/Action Summary
This action is in response to the papers filed on March 31, 2026.
Claims 8-9 and 15-20 were withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claim 10, now amended as dependent upon withdrawn claim 8, has likewise been withdrawn as directed to a nonelected invention.
Claims 5-7 and 11 were canceled in the response.
Claims 1-4, 8-10 and 12-20 are currently pending in the present application. Claims 8-10 and 15-20 are withdrawn. Claims 1-4 and 12-14 are under examination.
Any objections and rejections not reiterated below are hereby withdrawn.
The objections to the specification have been withdrawn in view of the substitute specification filed with the response.
The 112(b) rejections of record have been withdrawn in view of the amendments to the claims.
All rejections and arguments regarding only claims 5-7 and 11 are moot in view of the cancellation of these claims.
The 102 rejection of record over Too et al. has been withdrawn in view of the amendments to the claims now requiring extracting DNA or mRNA from the breast milk sample.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1-4 and 12-14 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
This is a new grounds of rejection necessitated by the amendments to the claims.
Claim 1 as amended recites steps of “extracting DNA or mRNA from the breast milk sample…analyzing the DNA or the mRNA in the breast milk sample for gene expression and breast cancer enriched gene aberrations, quantifying the gene expression level and breast cancer enriched gene aberrations of a cancer marker, and detecting the cancer marker based on quantification of the gene expression and breast cancer enriched gene aberrations.”
The claim encompasses embodiments having the following required steps: DNA is extracted from the sample (i.e. DNA or mRNA), the DNA is analyzed for gene expression and breast cancer enriched gene aberrations… quantifying gene expression level and… gene aberrations… and detecting… based on… gene expression and… aberrations.
In the art, “gene expression” refers to the process of producing, or the presence or abundance of, products of transcription from DNA (e.g. RNA species produced by transcribing genes encoded in DNA or proteins produced by a subsequent translation step).
It is therefore unclear how “gene expression” is intended to be analyzed and quantified in embodiments of the claim wherein DNA, but not mRNA (i.e. as recited “DNA or mRNA”) is extracted from the sample.
Claims 2-4 and 12-14 are rejected as indefinite because they depend from and thus include the indefinite limitation(s) of the claims rejected above.
Claim Interpretation
The claim term “breast cancer enriched gene aberrations” has been interpreted herein as encompassing a very broad genus of differences between nucleic acid molecules obtained from a breast milk sample comprising breast cancer-derived nucleic acids and nucleic acid molecules obtained from a breast milk sample that does not comprise breast cancer-derived nucleic acids. Therefore, “a gene aberration” encompasses, for example, any mutation, difference in methylation or other covalent modification, or DNA damage that are “enriched” in the breast cancer derived sample relative to the control sample.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2 are rejected under 35 U.S.C. 103 as being unpatentable over Too et al., US 2018/0230544 A1, published August 16, 2018.
This is a new grounds of rejection necessitated by the amendments to the claims.
Regarding claim 1, Too et al. teach methods for detecting markers of breast cancer in bodily fluid samples (Too et al., Abstract), wherein the bodily fluid is a breast milk sample (Too et al., paragraph 0065).
Too et al. teach extracting nucleic acids from the sample, quantifying and analyzing the expression levels of breast-cancer associated genes (Too et al., Abstract and Figure 2; see below) as well as breast cancer enriched gene aberrations used to establish breast cancer subtypes (i.e. HER2, ER, PR, and HR) (Too et al., paragraphs 0027-0029).
Too et al. further teach detecting the cancer markers based on quantification of the gene expression (the expression levels of the various markers taught by Too et al.) and breast cancer enriched gene aberrations (i.e. the breast cancer enriched gene aberrations used to establish breast cancer subtypes HER2, ER, PR, and HR) (Too et al., Figure 2 and paragraphs 0027-0029).
Too et al. teach extracting total RNA from bodily fluid samples prior to cDNA synthesis, analysis of expression, quantification of expression, and detection of a miRNA cancer marker by quantitative reverse transcriptase PCR (Too et al., paragraph 0085 and paragraph 2).
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Too et al. further teach that miRNAs (microRNAs) are small non-coding RNA molecules that regulate the expression of genes by binding to the 3’-untranslated region of specific mRNAs (Too et al., paragraph 0024).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Too et al. to additionally comprise quantifying the expression of mRNAs known to be regulated by the differentially expressed miRNAs because of the teachings of Too et al. that the differentially regulated miRNAs associated with the presence of breast cancer have the known and predictable function of regulating the expression of mRNAs in the tissues in which they are present.
Regarding claim 2, Too et al. teach amplifying the extracted polynucleotides before the quantification step (Too et al., Figure 2).
Claims 1-4 and 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over Too et al., US 2018/0230544 A1, published August 16, 2018 in view of Thomas et al., “14-3-3 (sigma) regulates proliferation and differentiation of multipotent p63-positive cells isolated from human breastmilk” Cell cycle 10:2, 278-284; January 15, 2011, Hassiotou et al., “Expression of the pluripotency transcription factor OCT4 in the normal and aberrant mammary gland” Frontiers in Oncology April 2013; Volume 3; article 79, and Koker et al., “p63 expression in breast cancer; A Highly Sensitive and Specific Marker of Metaplastic Carcinoma” Am J Surg Pathol 2004; 28:1506-1512.
This rejection has been updated as necessitated by the amendments to the claims.
Regarding claim 1, Too et al. teach methods for detecting markers of breast cancer in bodily fluid samples (Too et al., Abstract), wherein the bodily fluid is a breast milk sample (Too et al., paragraph 0065).
Too et al. teach extracting nucleic acids from the sample, quantifying and analyzing the expression levels of breast-cancer associated genes (Too et al., Abstract and Figure 2; see below) as well as breast cancer enriched gene aberrations used to establish breast cancer subtypes (i.e. HER2, ER, PR, and HR) (Too et al., paragraphs 0027-0029).
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Too et al. further teach detecting the cancer markers based on quantification of the gene expression (the expression levels of the various markers taught by Too et al.) and breast cancer enriched gene aberrations (i.e. the breast cancer enriched gene aberrations used to establish breast cancer subtypes HER2, ER, PR, and HR) (Too et al., Figure 2 and paragraphs 0027-0029).
Too et al. teach extracting total RNA from bodily fluid samples prior to cDNA synthesis, analysis of expression, quantification of expression, and detection of a miRNA cancer marker by quantitative reverse transcriptase PCR (Too et al., paragraph 0085 and paragraph 2).
Additionally, Too et al. teach that miRNAs (microRNAs) are small non-coding RNA molecules that regulate the expression of genes by binding to the 3’-untranslated region of specific mRNAs (Too et al., paragraph 0024).
While Too et al. explicitly teach methods for analyzing, quantifying, and detecting miRNA molecules extracted from breast milk samples, Too et al. do not explicitly teach analyzing, quantifying, and detecting mRNA or DNA molecules extracted from a breast milk sample.
However, Thomas et al. teach that p63-positive cells (i.e. expressing a cancer marker) are present in human breastmilk (Thomas et al., page 279, column 1, paragraph 2 and figure 4).
Thomas et al. teach extracting mRNA from cells isolated from human breast milk, analyzing, quantifying, and detecting the expression of the cancer marker p63 (Thomas et al., figure 1c, see below).
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Additionally, Hassiotou et al. teach that cancer stem cells (CSCs) with elevated expression of stem cell markers OCT4, SOX2, and NANOG are present in lactating breast cancers (Hassiotou et al., page 7, column 2, paragraph 2-page 9, column 1, paragraph 2).
Furthermore, Koker et al. teach that aberrant expression of p63 is a specific and sensitive marker for metaplastic carcinomas of the breast (i.e. is a breast cancer marker) (Koker et al., page 1511, column 1, paragraph 1).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Too et al. for detecting cancer markers in breast milk comprising extracting nucleic acids from human breastmilk, amplifying said nucleic acids, quantifying and analyzing the expression of cancer markers in the extracted nucleic acids to further comprise quantitation of expression of the breast cancer marker p63. The ordinary artisan would have been motivated to detect aberrant expression of p63 in breastmilk in the assay taught by Too et al. because of the teachings of Koker et al. that aberrant p63 expression is a sensitive and specific marker for breast cancer. The ordinary artisan would have had a reasonable expectation of success in detecting aberrant p63 expression in breastmilk because of the teachings of Thomas et al. that a population of multipotent, p63-positive cells is readily isolated from human breastmilk collected from healthy lactating mothers and because of the teachings of Hassiotou et al. that cancer stem cells are present in breastmilk samples from breast cancer patients.
Regarding claim 2, Too et al. teach amplifying the extracted polynucleotides before the quantification step (Too et al., Figure 2).
Regarding claim 3, Hassiotou et al. teach that measurement of the gene expression of the cancer markers OCT4 and NANOG varies by lactation stage, wherein peak expression of these markers in breast milk is detectable at 6 months postpartum (i.e. at the end of the fifth month after delivery; between 1 to 5 months after delivery), and decrease in expression in later lactation (Hassiotou et al., page 7-8 bridging paragraph).
Even more, Hassiotou et al. teach measuring expression of these mRNA cancer markers in breast milk during pregnancy and post-partum (Hassiotou et al., figure 7).
Regarding claim 4, Thomas et al. teach that p63-positive cells are present in human breastmilk (Thomas et al., page 279, column 1, paragraph 2 and figure 4) and further teach measuring expression of p63 mRNA in breast milk by qPCR (Thomas et al., figure 1c).
Additionally, Hassiotou et al. teach that cancer stem cells (CSCs) with elevated expression of stem cell markers OCT4, SOX2, and NANOG are present in lactating breast cancers (Hassiotou et al., page 7, column 2, paragraph 2-page 9, column 1, paragraph 2).
Furthermore, Koker et al. teach that aberrant expression of p63 is a specific and sensitive marker for metaplastic carcinomas of the breast (i.e. is a breast cancer marker) (Koker et al., page 1511, column 1, paragraph 1).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Too et al. for detecting cancer markers in breast milk comprising extracting nucleic acids from human breastmilk, amplifying said nucleic acids, quantifying and analyzing the expression of cancer markers in the extracted nucleic acids to further comprise quantitation of expression of the breast cancer marker p63. The ordinary artisan would have been motivated to detect aberrant expression of p63 in breastmilk in the assay taught by Too et al. because of the teachings of Koker et al. that aberrant p63 expression is a sensitive and specific marker for breast cancer and by the teachings of Thomas et al. that p63 mRNA expression is detectable in cells isolated from breast milk. The ordinary artisan would have had a reasonable expectation of success in detecting aberrant p63 expression in breastmilk because of the teachings of Thomas et al. that a population of multipotent, p63-positive cells is readily isolated from human breastmilk collected from healthy lactating mothers and because of the teachings of Hassiotou et al. that cancer stem cells are present in breastmilk samples from breast cancer patients.
Regarding claims 12-13, Too et al. teach quantifying the absolute copy number of various miRNA cancer markers (i.e. the copy number of a gene in the nucleotides) (Too et al., paragraph 0009 and 0082) per mL of sample (Too et al., paragraph 0107). Similarly, Thomas et al. teach quantifying the amount (i.e. the copy number) of p63 in cells isolated from breast milk normalized to the quantity of an internal control gene (GAPDH, i.e. per cell) (Thomas et al., figure 1c).
Response to arguments
The response asserts that the combined teachings of Too, Thomas, Hassiotou, and Koker fail to teach or suggest all of the limitations of claim 1 as amended, specifically the newly added limitation “detecting expression levels of DNA or mRNA in breast milk”.
This assertion has been thoroughly reviewed and is not persuasive. As one example of the teachings of the cited prior art discussed in detail in the rejection above that is relevant to this particular limitation, Thomas et al. expressly teach detecting expression levels of p63 mRNA by qPCR in cells from breast milk (Thomas et al., figure 1c).
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Too et al., Thomas et al., Hassiotou et al., and Koker et al. as applied to claims 1-4 and 12-13 above, and further in view of Zhang et al., “A genetic variant in p63 (rs17506395) is associated with breast cancer susceptibility and prognosis” Gene 535 (2014) 170-176, published December 4, 2013.
Regarding claim 14, the method taught by Too et al., Thomas et al., Hassiotou et al., and Koker et al. do not teach that detecting the cancer marker comprises detecting a mutation.
However, Zhang et al. teach a single nucleotide polymorphism (SNP) in p63 that is associated with higher aberrant expression of p63 in breast cancers (Zhang et al., Figure 1).
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Furthermore, Zhang et al. teach the presence of the SNP is a biomarker for poor prognosis in breast cancer, with SNP homozygotes exhibiting poorer overall survival relative to both heterozygotes and reference allele homozygotes (Zhang et al., figure 2).
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Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the method taught by Too et al., Thomas et al., Hassiotou et al., and Koker et al. for detecting cancer markers in breast milk comprising extracting nucleic acids comprising mRNA from human breastmilk, amplifying said nucleic acids, quantifying and analyzing the expression of the breast cancer marker p63 to further comprise detecting the presence of the mutation rs17506395 in p63. The ordinary artisan would have been motivated to include detection of this mutation in p63 into the assay taught by Too et al., Thomas et al., Hassiotou et al., and Koker et al., because of the teaching of Zhang et al. that hetero- or homozygotes for the T/T allele at rs17506395 display higher expression of p63 in breast cancer samples, and further exhibit poorer prognosis relative to the population of breast cancer patients with the G/G reference genotype.
Response to arguments
The response asserts that claim 14 is not obvious over Too, Thomas, Hassiotou, Koker, and Zhang because the claim depends from claim 1, which is asserted to be nonobvious over Too, Thomas, Hassiotou, and Koker.
This assertion has been reviewed and is not persuasive in view of the updated 103 rejection and response to arguments regarding claim 1 above.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ZACHARY MARK TURPIN whose telephone number is (703)756-5917. The examiner can normally be reached Monday-Friday 8:00 am - 5:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Z.M.T./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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