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 .
Claim Status/Action Summary
This action is in response to the papers filed on February 26, 2026.
Claims 5, 8, 23-27, and 29-34 were canceled in the response. Claim 25 was newly added in the response. Claims 1-4, 6-7, 9-22, 28, and 35 are currently pending and under examination. No other claims are currently pending in the present application
Any objections and rejections not reiterated below are hereby withdrawn.
The 102 rejection of record over Sakamoto et al. has been withdrawn in view of the claim amendments narrowing “performing an ambient ionization MS” to “performing 2D DESI-MSI”.
Effective Filing Date
The present application, filed on December 9, 2022 is a 371 of PCT/US2021/036108, filed on June 7, 2021, which claims priority to U.S. Provisional application no: 63/038,593, filed on June 12, 2020. Therefore, the effective filing date of the present application is determined to be June 12, 2020.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
In the response, reference to color drawings was removed from the text of the specification. However, the replacement drawings and photographs “Drawings-black and white line and/or other drawings, DRW.SUPP” are now rendered in color. It is noted no petition has been filed under 37 CFR 1.84(a)(2) in this application.
The replacement drawings are objected to because the conditions for accepting color drawings and black and white photographs have not been satisfied. See 37 CFR 1.84(b)(2).
Claim Objections
Claim 6 is objected to because of the following informalities: claim 6 contains duplicate claim language at lines 4 and 5 “kidney cancer… kidney cancer”. Appropriate correction is required.
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.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 1-4, 6-7, 9-22, 28, and 35 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.
Claims 1-3 and 10, as amended, recite the limitation "mCTC". There is insufficient antecedent basis for this limitation in the claim because the claim phrase “circulating tumor cell (CTC)” has been deleted from the claim.
Furthermore, the terms “metastatic” before “circulating tumor cell” and “mCTC” in place of “CTC” in claim 1 appear to have been inserted and deleted (i.e. are underlined and stricken) in the amended claims.
The specification provides no limiting definition for the abbreviation “mCTC”. It is noted that, in the prior art, the abbreviation “mCTC” may refer to several distinct terms in addition to “metastatic circulating tumor cell” including at least: “micro-CT colonography” (Durkee et al., “Small animal micro-CT colonography” Methods. 2010 Jan;50(1):36-41), “MCTC (a subtype of mast cells) (Oskeritzian et al., “Surface CD88 functionally distinguishes the MCTC from the MCT type of human lung mast cell” J Allergy Clin Immunol. 2005 Jun;115(6):1162-1168), “model CTCs” (Campton et al., “High-recovery visual identification and single-cell retrieval of circulating tumor cells for genomic analysis using a dual-technology platform integrated with automated immunofluorescence staining” BMC Cancer 2015 May 6:15:360), or “mixed epithelial/mesenchymal phenotype CTC” (Martini et al., “Circulating Tumor Cells in Pancreatic Cancer: Current Perspectives” Cancers(Basel). 2019 Oct 26;11(11):1659.).
Because there is no limiting definition of the claim term “mCTC” in the specification, the claim phrase “circulating tumor cell (CTC)” has been deleted, and the term “mCTC” has multiple definitions in the prior art, it is unclear from the claim language whether the claim is intended to require “thereby detecting the presence of”: “a metastatic circulating tumor cell”, a “MCTC”, a “model CTC”, a “mixed epithelial/mesenchymal phenotype CTC”, or something else.
Claim 1 as amended recites the claim term “wherein the mCTC is from a socancer that gives rise to blood borne metastases”. It is unclear whether the claim term “socancer” is a typographical error for “cancer”, or is intended to refer to something else.
Claim 2 as amended recites the limitation "said sample" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 1, from which claim 2 depends, recites “a cell-containing fluid sample” and “said fluid sample is buffy coat portion of a blood sample” in step (a). It is unclear whether claim 2 requires that “said sample” is the “fluid sample” recited by claim 1, or is/encompasses something else.
Claim 3 is 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 rejection has been updated as necessitated by the claim amendments.
Claim 3 as amended, revises “hybridizing the detected abnormal cells in said sample with labeled nucleic acid probes” to “hybridizing the detected mCTC with labeled nucleic acid probes… and detecting the mCTC based on pattern of hybridization to…said detected abnormal cells”. There is insufficient antecedent basis for the claim term “said detected abnormal cells” in the claim as amended.
Claim 3 was previously rejected because it recited the limitation “the detected abnormal cells” in line 2, now replaced with “the detected mCTC” (see above).
Claim 6 is 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 6 recites the broad recitation “a sarcoma”, and the claim also recites “gastro-intestinal cancer” (encompassing gastro-intestinal sarcomas), “lung cancer” (encompassing lung sarcomas), “breast cancer” (encompassing breast sarcomas), “colorectal cancer” (encompassing colorectal sarcomas), “prostate cancer” (encompassing prostate sarcomas), “pancreas cancer” (encompassing pancreas sarcomas), “esophageal cancer” (encompassing esophageal sarcomas), “renal cancer” (encompassing renal sarcomas), “urogenital cancer” (encompassing urogenital sarcomas), “endocrine cancer” (encompassing at least uterine or adrenal sarcomas) which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 10 is rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
This is a new grounds of rejection necessitated by the amendments to the claims.
In the instant case, claim 10 recites “The method of claim 1, further comprising obtaining a reference profile and detecting the presence of the mCTC by comparing the profile from the sample to a reference profile.” Claim 1 recites “comparing the test profile” (i.e. the profile from the sample) “to one or more reference profiles, thereby detecting the presence of a mCTC”. Because claim 1 requires comparing a test profile to a reference profile, claim 1 necessarily requires “obtaining a reference profile” in order to perform the recited comparison step. The claims and the specification do not require a particular method for, or limit, the “obtaining” in any way. Therefore, “obtaining a reference profile” appears to encompass simply receiving a printed report, downloading a reference profile from a database, or any other means for “obtaining” the information in “a reference profile”.
Therefore, claim 10 does not recite any further limitations or method steps in addition to those recited by claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Newly added Claim 35 is 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 addition of claim 35.
Claim 35 requires “the one or more nucleic acid probe is [chosen from alternative probe sets recited as (i)-(viii) in the claim]”. However, the recited probe sets include “(vii) a surface” or “ (viii) a cytoplasmic biomarker probe”
It is unclear whether group (vii) is intended to require “a surface biomarker probe” or something else.
It is unclear what nucleic acid probe(s) are required by the claim term, as written, “(vii) a surface” as “a surface” does not define any particular nucleic acid probe(s).
It is unclear what, if anything, is required by “biomarker probe” that is not encompassed by “nucleic acid probe”. If “biomarker probes” are meant to be limited to a subset of possible nucleic acid ligands, it is not clear what ligands belong in this genus as the specification does not provide any special definition for “biomarker” and the art, for example, the NCI Dictionary of Cancer Terms, defines a biomarker is “a biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease”. Because “biomarker” encompasses molecules that are signs of normal or abnormal processes, a “biomarker probe” encompasses a probe that detects any biological molecule that participates in any normal process, for example, DNA replication or transcription (i.e. encompassing all nucleic acids present in the cell).
It is unclear whether “the one or more nucleic acid probe” is intended to be limited to nucleic acids that bind to “a surface” or “a surface biomarker”. Furthermore, it is unclear whether this limitation is intended to encompass only nucleic acid probes that bind to biological molecules present on the surface (i.e. the outer surface of the plasma membrane) of a cell (e.g. encompassing aptamers that bind to cell surface proteins. It is noted that the claim language “the one or more nucleic acid probe is…” excludes “probes” that are biological molecules other than nucleic acids (e.g. antibodies).
The list of alternate “one or more nucleic acid probe” that recite particular chromosome regions and/or genes to which the probes correspond recited by claim 35 “is a”: (i) centromeric 7/7p12 Epidermal Growth Factor (EGFR) probe, (ii) cep7/7p22.1, cep 17, and 9p21.3 probes, (iii) EGFR/cep and 10/cep10q probes, (iv) pTEN, cep10 and cep10q probes, (v) an EML4-ALK probe set…”
The recitation of “centromeric 7/7p12 [EGFR] probe” is indefinite because it is unclear whether the “/” character is intended to mean “or”, “and” or to imply that the probe binds to both of the two distinct targets centromere 7 and 7p12. Furthermore, it is unclear whether the claim requires that the 7p12 probe is specific to the EGFR gene (i.e. an approximately 191,000 base pair long subset of the 8.6 million base pair long chromosome band 7p12), or whether the recitation of EGFR is merely exemplary of one gene within 7p12.
The recitations of “cep7/7p22.1”, “EGFR/cep”, “10/cep10q”, and cep10 and cep10q” are indefinite for the same reasons as described above for the “centromeric 7/7p12 EGFR” probe
Claims 2-4, 6-7, 9-22, 28, and 35 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 because they depend from, and therefore include the indefinite limitation(s) of the claim(s) rejected as indefinite above.
Claim Interpretation
In the interest of compact prosecution, for the purposes of the following rejections, claim 1 has been treated as requiring “a metastatic circulating tumor cell (mCTC)”.
Claim 28, now dependent upon claim 3 as amended, recites “detecting comprises assessing all abnormalities or gains only”. Claim 3 requires “detecting… based on pattern of hybridization” and claim 1, upon which claim 3 depends, requires “comparing the test profile to one or more reference profiles, thereby detecting…”.
For the purposes of compact prosecution, the claim term “all abnormalities”, recited by claim 28, has been interpreted as encompassing all differences detected between the 2D DESI-MSI profile of the sample and the reference and all differences detected between the “pattern of hybridization” of the recited nucleic acid probes and an expected pattern of hybridization in a reference. Similarly, the claim term “gains only” has been interpreted as encompassing only DESI-MSI signals or hybridization signals that are present in the sample and are not present in the reference.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4, 6, 7, 9-22, 28 and 35 remain/are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
This rejection has been updated as necessitated by the amendments to the claims.
35 U.S.C. 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 209 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
Based on consideration of the claims as a whole, as well as consideration of elements/steps recited in addition to the judicial exception, the present claims fail to meet the elements required for patent eligibility.
Step 1
The claimed invention is directed to a process that involves a natural principle and judicial exceptions.
Step 2A Prong 1
The claims are taken to be directed to a natural phenomenon and abstract ideas.
Claim 1 is directed to a method of detecting circulating tumor cells in blood comprising performing 2D DESI-MSI on a buffy coat portion of a blood sample from a subject to obtain “a test profile” for the sample and “comparing the test profile to one or more reference profile, thereby detecting the presence of an mCTC” (i.e. a comparison to a control). Claim 1 is therefore directed to observing the natural correlation between the presence of certain biomarkers in blood and the presence of tumor cells in blood.
Claims 10-12 require obtaining reference profile(s) for comparison to the profile of the sample containing CTCs. (i.e. comparison to a control).
Claim 28 recites assessing abnormalities or gains [in the MS profiles recited by claim 1 compared to some unspecified control, reference, or standard] (i.e. a comparison to a control).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions for the reasons that follow.
A correlation that preexists in the human is an unpatentable phenomenon. The association between the presence of fatty acids or metabolites (detected by MS; claims 1-2, 6, 9-22, 28) and/or copy number variation (detected by FISH; claims 3-4, 7, 28, 35) and circulating tumor cells in blood is a law of nature/natural phenomenon. The “detecting the presence” steps recited by claims 1, 3, 10-12, and 28 which tells users of the process to determine that a circulating tumor cell is present in a blood sample, amount to no more than an “instruction to apply the natural law”. These detecting steps amount to no more than mental steps. Even if the step requires something more such as to verbalize the discovery of the natural law, this mere verbalization is not an application of the law of nature to a new and useful end. The “detecting” steps do not require the process user to do anything in light of the correlation. These steps fail to provide the “practical assurance” sought by the Prometheus Court that the “process is more than a drafting effort designed to monopolize the law of nature itself.”
Step 2A Prong II
The exception is not integrated into a practical application of the exception. While the claims recite further treating the subject with chemotherapy, hormonal therapy, or immunotherapy, “wherein the mCTC is from a socancer that gives rise to blood borne metastases” this is not an integration of the exceptions into a practical application. There is no particularity between the application of any chemotherapy, hormonal therapy, or immunotherapy to the natural correlation between the presence of mCTC biomarkers that are different between a test sample and a reference (observed by MS or FISH) and the presence of mCTCs in blood (i.e. cancer in a subject). Rather, these elements amount to a mere invitation to the skilled artisan to apply the judicial exception (i.e. the natural correlation between the presence of biomarkers in blood and the presence of cancer) to a general field of use (oncology).
Accordingly, the claims are directed to judicial exceptions.
Step 2B
The second step of Alice involves determining whether the remaining elements, either in isolation or combination with the other non-patent eligible elements, are sufficient to “transform the nature of the claims into a patent eligible application” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
The claims are not sufficiently defined to provide a method which is significantly more than a statement of a natural principle for at least these reasons:
The claims do not add a specific limitation other than what is well-understood, routine and conventional in the field.
The claims require the detection of specific biomarkers of circulating tumor cells in the buffy coat portion of a blood sample by 2D DESI-MSI. The claims do not recite a new, innovative method for such determination. Analyzing cancerous and healthy biological tissues by DESI-MS imaging was well known in the art prior to, and at the time the invention was made. The prior art, for example the Review published by Feider et al., “Ambient Ionization Mass Spectrometry: Recent Developments and Applications” Analytical Chem. 2019, 91, 4266-4290, published February 21, 2019 (more than one year prior to the effective filing date of the claimed invention) teaches “Ambient ionization MS methods have been widely used for ex vivo analysis of cancerous and healthy biological tissues. DESI-MS imaging, in particular, has been extensively used in cancer research to investigate lipid and metabolite profiles of a variety of cancer and normal tissues including prostate, brain, skin, ovarian, thyroid, and breast” (Feider et al., page 4276, column 2) Further, Feider et al. teach “DESI utilizes a voltage to generate an electrospray to extract and ionize analytes from the sample surface (Feider et al., page 4267, column 2, paragraph 2). Even more, Sakamoto et al., “Ambient mass spectrometry-based detection system for tumor cells in human blood” Translational Cancer Research 2018; 7(3):758-764 teach detecting circulating tumor cells in the buffy coat layer of blood samples by ambient ionization MS (Sakamoto et al., Abstract and figure 1).
As amended, the FISH probes recited by the claims no longer recite the use of commercially available kits of FISH probes (i.e. LaVysion DNA probe sets). However, as amended, the claims recite the use of a set of labeled nucleic acid probes comprising 3p22.1, 10q22.3, chromosome 10 centromeric, and chromosome 3 centromeric that are well-known, routine, and conventional in the art.
For example, Yendamuri et al., “3p22.1 and 10q22.3 Deletions Detected by Fluorescence In Situ Hybridization (FISH): A Potential New Tool For Early Detection of Non-small Cell Lung Cancer (NSCLC)” Journal of Thoracic Oncology Vol 3, Iss 9, September 2008, 979-984 AND Katz et al., “Genetically Abnormal Circulating Cells in Lung Cancer Patients: An Antigen-Independent Fluorescence In situ Hybridization-Based Case-Control Study” Clin Cancer Res (2010) 16(15):3976-3987 teach detecting lung cancer cells using the 3p22.1, CEP3, 10q22.3, and CEP10 probes (and in the case of Katz et al., specifically in the context of detecting “circulating cytogenetically abnormal cells containing similar genetic abnormalities to the primary tumor” (i.e. metastatic circulating tumor cells).
Similarly, the probes recited by new claim 35 are also well-known, routine, and conventional in the art. For example, Kim et al., “Identification of circulating tumor cells with EML4-ALK translocation using fluorescence in situ hybridization in advanced ALK-positive patients with lung cancer” Oncol Lett. 2018 April 12; 15(6):8959-8964 teach such probes for identifying precisely the same natural correlation recited in the present claims.
Therefore, the claims do not require the use of any particular non-conventional reagents and the claims are recited at a high level of generality. When recited at this high level of generality, there is no meaningful limitation that distinguishes this step from well understood, routine, and conventional activities prior to applicant’s invention and at the time the invention was filed.
For these reasons, the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to arguments
The response asserts that the claims have been “amended to focus on the presence of metastatic circulating tumor cells from cancers that produce the same” and “the therapies listed – chemotherapy, hormonal therapy and immunotherapy – are ones that could be delivered systematically and contact mCTCs, which other therapies could not. This is a specific application of the allegedly natural phenomenon, and therefore would be outside the concerns of §101.
These arguments/assertions have been thoroughly considered and are not persuasive. The rejection under 35 USC 101 has been updated as necessitated by the amendments to the claims. As described above, the treatment step comprising “treating said subject with chemotherapy, hormonal therapy or immunotherapy” wherein the subject has “a cancer that gives rise to blood borne metastases” does not integrate the recited judicial exceptions into a practical application. There is no particularity between the application of any chemotherapy, hormonal therapy, or immunotherapy to the natural correlation between the presence of mCTC biomarkers that are different between a test sample derived from any subject having any cancer that happens to have released any number of cancer cells into circulation and a reference (observed by MS or FISH) and the presence of mCTCs in blood (i.e. cancer in a subject). Rather, these elements amount to a mere invitation to the skilled artisan to apply the judicial exception (i.e. the natural correlation between the presence of biomarkers in blood and the presence of cancer) to a general field of use (oncology) (see MPEP 2106.04(d)(2)).
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, 6, 9-11, 13-20, and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Sakamoto et al., “Ambient mass spectrometry-based detection system for tumor cells in human blood”, Translational Cancer Research 2018;7(3):758-764, published June 27, 2018 in view of Eberlin et al., “Nondestructive, Histologically Compatible Tissue Imaging by Desorption Electrospray Ionization Mass Spectrometry”, ChemBioChem 2011, 12, 2129-2132, published July 26, 2011, Feider et al., “Ambient Ionization Mass Spectrometry: Recent Developments and Applications”, Analytical Chemistry 2019, 91, 4266-4290, published February 21, 2019, and Kawada et al., “Circulating tumor cells in patients with head and neck squamous cell carcinoma: Feasibility of detection and quantitation”, Head & Neck. 2017;39:2180-2186.
This rejection has been updated as necessitated by the amendments to the claims.
Regarding amended claim 1, Sakamoto et al. teach a method comprising detecting circulating tumor cells (CTCs) in human blood (i.e. detecting cancer) using ambient ionization mass spectrometry (MS) (Sakamoto et al., abstract and figure 1). Sakamoto et al. teach a “proof-of-concept experiment” demonstrating oral squamous cell carcinoma cells “SAS cells” are detectable by ambient ionization MS and conventional immunohistochemistry when artificially spiked into a sample of blood collected from a healthy donor. Sakamoto et al. teach purifying PBMC from the buffy coat layer obtained by centrifuging donor blood +/- SAS cells (i.e. comparing between a test sample and a reference sample) on a Ficoll-Paque gradient, wherein the spiked SAS cells (i.e. simulated CTCs) co-purify with PBMC on the buffy coat (Sakamoto et al., page 763, column 2 and page 759, column 2, paragraphs 2-4).
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Sakamoto et al. do not teach “disposing said buffy coat portion on a surface” and the ambient ionization MS is “2D DESI-MSI” as required by the amended claim 1.
However, Eberlin et al. teach methods of detecting tumor cells within tissue sections disposed on a surface using ambient ionization mass spectrometry imaging, “DESI-MS imaging” wherein the morphology of the sample is preserved such that the MS-detection step is compatible with subsequent conventional histological techniques such as H&E staining and immunohistochemistry (Eberlin et al., page 2129, column 1-2, and figure 2).
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Eberlin et al. further teach high-quality 2D MS images can be directly compared and overlaid with the histology stain images for better correlation between the spatial distribution of the lipid species (detected by MS) and tissue substructures (detected by histology, see Eberlin et al., Figure 2 above). Eberlin et al. continue: The ability to perform MS imaging and histochemical analysis of the same tissue section (i.e. the same cells) is important for accurate correlation between molecular signatures (i.e. lipid species detected by MS) and disease state (i.e. histologic tumor markers). “Because the information from the two methods is orthogonal, it is expected to greatly improve discrimination and diagnosis of the disease state” (Eberlin et al., page 2130, column 2).
Furthermore, Feider et al. teach a review of a range of ambient ionization mass spectrometry techniques including PESI-MS (used by Sakamoto et al.) and DESI-MS (used by Eberlin et al.) (i.e. PESI-MS and DESI-MS are known alternative ambient ionization mass spectrometry techniques).
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 subjected the blood samples comprising circulating tumor cells taught by Sakamoto et al. to the orthogonal non-destructive MS and histology profiling techniques taught by Eberlin et al. The ordinary artisan would have been motivated to apply the orthogonal, sequential tumor cell detection techniques by ambient ionization MS and histology, taught by Eberlin et al., to the diagnostic system taught by Sakamoto et al. comprising parallel ambient ionization MS and histology because of the teaching of Eberlin et al. that “The ability to perform DESI-MS imaging and histochemical analysis of the same tissue section is important for accurate correlation between molecular signatures and disease state. Because the information from the two methods is orthogonal, it is expected to greatly improve discrimination and diagnosis of the disease state. This is especially true in the analysis of cancerous tissue sections, which are very often highly heterogeneous…” (Eberlin et al., page 2130, column 2). The ordinary artisan would have had a reasonable expectation that exchanging the (presumably) destructive ambient ionization MS technique and parallel histology techniques taught by Sakamoto et al. with the non-destructive ambient ionization followed by histology on the same cells, as taught by Eberlin et al. would have successfully improved the identification of single circulating tumor cells because of the teaching of Eberlin et al. that orthogonal characterization of the same tissue sample (the same cells) predictably improves discrimination and diagnosis of disease state.
Sakamoto et al. teach detection of CTCs by ambient ionization MS is clinically useful for monitoring therapeutic efficacy, screening for metastatic relapse and identification of therapeutic targets (i.e. methods comprising monitoring therapeutic efficacy necessarily comprise administering at least a first anticancer therapy).
Sakamoto et al. do not teach treating a subject with circulating tumor cells with chemotherapy, hormonal therapy, or immunotherapy as required by the amended claim 1.
However, Kawada et al. teach detecting CTCs in patients with head and neck squamous cell carcinoma prior to administration of any anticancer treatment (Kawada et al., page 2181, column 1, paragraph 3). Anticancer therapies were then administered to the patients and subsequent blood samples were taken after treatment for detection of changes in number of CTCs (Kawada et al., page 2181, column 1, paragraph 3). Kawada teaches that patients underwent surgery, with or without adjuvant chemoradiotherapy after surgery or concurrent with surgery (Kawada et al., page 2182, column 2). (i.e. treating the subject with an anticancer therapy, comprising radiation, surgery, or chemotherapy, or a combination therapy thereof), and that the number of CTCs present in the peripheral blood of the patients significantly decreased after the administration of anticancer therapies to the subjects (Kawada et al., figure 4).
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 Sakamoto et al. comprising detecting CTCs in subjects by ambient ionization mass spectrometry of CTCs isolated from a buffy coat fraction of blood from the subject to further comprise administering an anticancer therapy comprising surgery and or chemoradiotherapy or adjuvant chemoradiotherapy, as taught by Kawada et al.
The ordinary artisan would have been motivated to administer a treatment, as taught by Kawada et al. to a subject having CTCs, because of the teaching of Kawada et al that none of the healthy control subjects have CTCs (Kawada et al., page 2182, column 1), and that detection of CTCs in peripheral blood is associated with a worse prognosis of cancer (Kawada et al., page 2180, column 2).
Regarding claim 2, Eberlin et al. teach methods of detecting tumor cells within tissue sections disposed on a surface using ambient ionization mass spectrometry imaging, “DESI-MS imaging” wherein the morphology of the sample is preserved such that the MS-detection step is compatible with subsequent conventional histological techniques such as H&E staining and immunohistochemistry (Eberlin et al., page 2129, column 1-2, and figure 2).
Eberlin et al. further teach high-quality 2D MS images can be directly compared and overlaid with the histology stain images for better correlation between the spatial distribution of the lipid species (detected by MS) and tissue substructures (detected by histology, see Eberlin et al., Figure 2 above). Eberlin et al. continue: The ability to perform MS imaging and histochemical analysis of the same tissue section (i.e. the same cells) is important for accurate correlation between molecular signatures (i.e. lipid species detected by MS) and disease state (i.e. histologic tumor markers). “Because the information from the two methods is orthogonal, it is expected to greatly improve discrimination and diagnosis of the disease state” (Eberlin et al., page 2130, column 2).
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 subjected the blood samples comprising circulating tumor cells taught by Sakamoto et al. to the orthogonal non-destructive MS and histology profiling techniques taught by Eberlin et al. The ordinary artisan would have been motivated to apply the orthogonal, sequential tumor cell detection techniques by ambient ionization MS and histology, taught by Eberlin et al., to the diagnostic system taught by Sakamoto et al. comprising parallel ambient ionization MS and histology because of the teaching of Eberlin et al. that “The ability to perform DESI-MS imaging and histochemical analysis of the same tissue section is important for accurate correlation between molecular signatures and disease state. Because the information from the two methods is orthogonal, it is expected to greatly improve discrimination and diagnosis of the disease state. This is especially true in the analysis of cancerous tissue sections, which are very often highly heterogeneous…” (Eberlin et al., page 2130, column 2). The ordinary artisan would have had a reasonable expectation that exchanging the (presumably) destructive ambient ionization MS technique and parallel histology techniques taught by Sakamoto et al. with the non-destructive ambient ionization followed by histology on the same cells, as taught by Eberlin et al. would have successfully improved the identification of single circulating tumor cells because of the teaching of Eberlin et al. that orthogonal characterization of the same tissue sample (the same cells) predictably improves discrimination and diagnosis of disease state.
Regarding claim 6, Sakamoto et al. teach the cancer cells (CTCs) are human oral squamous cell carcinoma cells (i.e. a head and neck cancer) (Sakamoto et al., page 763, column 1, paragraph 3) and Kawada et al. teach the cancer is a head and neck cancer giving rise to CTCs (Kawada et al., page 2181, column 1, paragraph 3).
Regarding claim 9, Eberlin et al. do not appear to explicitly teach that the surface on which tissues are analyzed in series by conventional histology/immunochemistry and 2D DESI-MSI is “a slide”. However, Feider et al. demonstrate that DESI ionizes samples off of a slide (Feider et al., Figure 2, top panel, image 2; reproduced below for convenience)
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Regarding claims 10-11, Sakamoto et al. teach obtaining a reference profile (healthy donor blood without spiked SAS cells) from the same subject to identify tumor-associated MS peaks (i.e. detecting the presence of CTCs by comparing the profile to a reference profile) (Sakamoto et al., figure 2 and 3 and page 759, column 1-2 bridging paragraph).
Regarding claims 13-19, the present claims do not recite any method steps and thus do not further limit the claimed method. These claims merely recite the presence of various fatty acid and metabolite molecules inherent to the presence of CTCs in a sample.
Regarding claim 20, Sakamoto et al. teach filtering the fluid sample to exclude white blood cells (i.e. leukocytes) from the PBMC fraction (i.e. the buffy coat) using a CellSieve Microfiltration Assay and a low-pressure filtration system (Sakamoto et al., page 760, column 2, paragraph 1).
Regarding claim 22, Sakamoto et al. teach the buffy coat layer (i.e. PBMC fraction) is separated from blood by a Ficoll-Hypaque gradient (Sakamoto et al., figure 1 and page 759, column 2, paragraph 3).
Response to arguments
Rather than addressing each of the specific combinations of references cited in the 103 rejections of record, the response characterizes the rejections:
“The claims are rejected Sakamoto, optionally taken with Eberlin et al. (2011), Porcari et al. (2018), Katz et al. (2011), Feider et al. (2019), Li et al. (2013), Eberlin et al. (2014a), Eberlin et al. (2014b), Zhang et al. (2017), San et al. (2017), Sans et al. (2019), De Giorgi et al. (2010), Tang et al. (2018), Wu et al. (2013), Tong et al. (2007), StemCell Tech (2018), Hosokawa et al. (2013), and/or Kawada et al. (2017). Given that Sakamoto is said on its own to obviate claim 1, and that the supporting references all seem primarily directed to features of dependent claims, applicant's comments will address the deficiencies of Sakamoto.”
It is noted that the rejections of record are not “optional” combinations of the prior art references, but are applied to specific claims under specifically stated alternative claim interpretations in light of the indefiniteness rejections of record. The references are cited in combination, requiring each of the references as cited in the rejections of record with none of the references cited as “optional” in the rejections of record.
The response further asserts that the inclusion of claim language from prior claim 9 (i.e. narrowing “ambient ionization MS” to “2D DESI-MSI” into the independent claim obviates all of the rejections except for Sakamoto et al. in view of Eberlin et al. and Feider et al.
The response asserts that “a reference must be used as a whole and not just for particular aspects of its teachings”, citing MPEP 2143.02, and asserts “Sakamoto is wholly inconsistent with a surface-fixed sample and therefore inconsistent with the present claims, as well as with the teachings of Eberlin”.
This argument has been thoroughly considered and is not persuasive.
MPEP 2143.02 states: “In determining the differences between the prior art and the claims, the question under 35 U.S.C. 103 is not whether the differences themselves would have been obvious, but whether the claimed invention as a whole would have been obvious.”
As described in the rejections of record and the revised rejections above, the difference apparently at issue between the primary reference (Sakamoto et al.) which teaches analyzing CTCs from buffy coat using PESI-MS (a liquid sampling method) and conventional immunohistochemistry in parallel (i.e. on different cells as PESI-MS is destructive to the sampled cells), whereas the claimed invention analyzes CTCs from buffy coat using 2D DESI-MSI (ionization of analyte from a sample disposed on a slide).
As described in the rejections above, the secondary reference (Eberlin) teaches specific predictable advantages of analyzing tissues disposed on a surface using 2D DESI-MSI including the ability to analyze the same cells by 2D DESI-MSI and conventional histological techniques.
The combination of references detailed above provide specific motivation (including those described above) to analyze tumor samples using sequential, orthogonal 2D DESI-MSI and histology on the same cells rather than destructive and/or parallel PESI MS and histology on different cells (i.e. sampling from a heterogenous liquid sample).
As such, the assertion that “Sakamoto is inconsistent with… the present claims and Eberlin” is not persuasive at least in view of the specific motivating teachings of Eberlin described above.
The response further asserts that the combination of teachings of Sakamoto with the teachings of Eberlin would change the principle of operation of the primary reference.
This assertion has been thoroughly considered and is not persuasive.
Sakamoto et al. teaches using PESI MS to analyze CTCs in blood samples. The specific teachings of Eberlin motivate the ordinary artisan to utilize 2D DESI MS, rather than PESI MS for analyzing samples of cancerous tissue in series using multiple non-destructive analytical techniques on the same cells (MS, histology, immunohistochemistry, etc). Further, as described above, Feider et al. teach that both PESI and 2D DESI were well known techniques for ionizing analytes prior to MS analysis prior to the filing date of the claimed invention.
In view of the teachings of Sakamoto comprising detecting circulating tumor cells in buffy coat samples by parallel mass spectrometry and conventional histological techniques, the predictable improvements to the discrimination and diagnosis of circulating tumor cells compared to samples not containing circulating tumor cells taught by Eberlin et al. afforded by the sequential and orthogonal 2D DESI-MSI and conventional histology, and the minimal technical adjustment and negligible experimentation required to modify the solution-based PESI methods taught by Sakamoto et al. with the surface-based 2D DESI-MSI methods taught by Eberlin et al. (i.e. disposing a portion of the liquid tissue buffy coat onto a surface, as taught by Eberlin et al. for other tissue types (e.g. tumor slices)), it is the position of the examiner that, in contrast to the facts in the cited In re Ratti, the cited combination of reference would not “require a substantial reconstruction and redesign of the elements shown in [the primary reference] as well as a change in the basic principle under which the [primary reference] construction was designed to operate." because both techniques were known in the art for analyzing cancer cells in tissues (e.g. solid or isolated blood cells) and Eberlin specifically teaches advantages of 2D DESI-MSI over other ionization-MS techniques in the art.
The response further asserts “2D-DESI approach permits imaging of cells in a sample… in a way PESI does not” and “an additional advantage afforded by … 2D-DESI is compatibility with the FISH analysis of claim 3… creating a more robust and powerful analysis”. This assertion appears to be a summary of the predictable advantages of 2D DESI that were well known in the prior art (and specifically taught by the cited Eberlin reference herein). This assertion does not persuasively distinguish the claimed invention from the prior art.
The response states “In response to your recent email I would argue the following:” (pg 9). There has not been any email correspondence between the examiner and any representative for applicant. It is unclear whether this is an inadvertent “copy and paste” error in the response.
The response further extols the benefits of 2D DESI-MSI over PESI “PESI only provides a “bulk” measurement. This is likewise not persuasive, as this assertion also appears to be a summary of the predictable advantages of 2D DESI that were well known in the prior art (and specifically taught by the cited Eberlin reference herein).
The response states a poster by the inventors is attached to the response purportedly demonstrating “information [that] is impossible to obtain by PESI. Thus, the development of 2D-DESI is a major advance in the application of mass spectrometry to cancer diagnostics”.
It is noted that no such poster has been filed, is attached to the remarks, no IDS has been filed with the response, and no declarations have been filed with the response. It is unclear to what poster and figures the response is referencing. The written summary of the figures quoted above is not persuasive, as this assertion also appears to be a summary of the predictable advantages of 2D DESI that were well known in the prior art (and specifically taught by the cited Eberlin reference herein).
Claims 3-4, 7, 28, and 35 are rejected under 35 U.S.C. 103 as being unpatentable over Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al., as applied to claims 1, 2, 6, 9-11, 13-20, and 22 above, and further in view of Porcari et al., “Multicenter Study Using Desorption-Electrospray-Ionization-Mass-Spectrometry Imaging for Breast-Cancer Diagnosis”, Analytical Chem. 2018, 90, 11324-11332, and Katz et al., US 2011/0189670 A1, published August 4, 2011.
This is a new grounds of rejection necessitated by the addition of claim 35 and the amendment of claim 28 now depending on claim 3 rather than claim 1.
Regarding claims 3 and 7, Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. teach a method of treating cancer comprising detecting cancer cells in blood samples from a subject compared to non-cancer controls by isolating the buffy coat portion of a blood sample and performing 2D DESI-MSI to detect the presence of a circulating tumor cell and further treating subjects having CTCs with an anti-tumor therapy comprising chemotherapy.
Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. further teach integrating 2D DESI-MSI with conventional histology (e.g. H&E stain) and immunohistochemistry (e.g. p63 IHC) on the same cells (Eberlin et al., figure 3)
Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. do not teach also hybridizing the CTCs with labeled nucleic acid probes to detect the CTCs by FISH.
However, Porcari et al. teach detecting breast cancer tumor cells in tissues using 2D DESI-MS imaging using histologically compatible solvents paired with orthogonal detection using immunohistochemistry and FISH for HER2 status (i.e. one or more labeled nucleic acid probes) (Porcari et al., page 11325, column 2 and page 11328, column 2, paragraph 2).
Katz et al. teach detecting circulating tumor cells using FISH comprising fluorescent genomic specific probes for genetic markers that are most frequently amplified or deleted in CTCs (Katz et al., abstract and paragraph 0017). Katz et al. specifically teach that the fluorescent probes comprise probes for 3p22.1, combined with a centromeric 3 (i.e. cep3), a 10q22.3 probe, and a cep10 probe (Katz et al., paragraph 0017).
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 combined the method taught by Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. comprising detecting CTCs in buffy coat samples from subjects using 2D DESI-MSI with the methods taught by Porcari et al. and Katz et al. specifically combining 2D DESI-MSI for detection of tumor cells in tissues with orthogonal confirmatory detection of the tumor cells by FISH (Porcari et al.) and the method of detecting circulating tumor cells using the specifically recited FISH probes (Katz et al.) The ordinary artisan would have been motivated to combine the 2D DESI-MSI techniques for detection of CTCs, taught by Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. with the combination method taught by Porcari et al. using the specific probes taught by Katz et al. because Porcari et al. use FISH probes for genomic abnormalities particular to the tumor cells of interest (HER2 status and breast cancer) as “gold standard” confirmatory evidence for the MS detection data (Porcari et al., page 11328, column 2, paragraph 2). Katz et al. teach that the specific recited probes specifically recognize genetic markers that are most frequently amplified or deleted in CTCs (i.e. the target of the method taught by Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al.)(Katz et al., paragraph 0017). Therefore, the ordinary artisan would have had a reasonable expectation that the FISH probes taught by Katz et al. would have provided “gold standard” confirmatory evidence combined with the histology-compatible ambient ionization mass spectrometry taught by Porcari et al. when applied to the CTC-detection method taught by Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al.
Regarding claim 4, Katz et al. teach that the labels can be fluorescent or chromogenic (Katz et al., paragraph 0013).
Regarding claim 28, Sakamoto et al. teach detecting over 1,100 peaks in a serial dilution assay of SAS cells spiked into human blood and: (a) assessing all observed differences (i.e. abnormalities) in the mass spectra between the reference and cancer-cell containing samples for marker peaks and: (b) those that were specifically altered in the presence of SAS cells (the simulated CTCs) (i.e. detecting comprises assessing all abnormalities or gains only).
Regarding claim 35, Katz et al. further teach additional probes useful for detecting circulating tumor cells comprise a centromeric 7/7p12 EGFR probe, cep7/7p22.1 probes, cep17 and 9p21.3 probes, EGFP/cep and 10/cep10q probes, cep 10 and cep 10q probes (Katz et al. paragraph 0017), among others.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. as applied to claims 1, 2, 6, 9-11, 13-20, and 22 above, and further in view of Li et al., “Lipid profiling for early diagnosis and progression of colorectal cancer using direct-infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry”, Rapid Commun Mass Spectrom. 2013, 27, 24-34.
This rejection has been updated as necessitated by the amendments to the claims.
Regarding claim 12, as described above, Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. teach a method of detecting circulating tumor cells in the buffy coat fraction of a blood sample from a subject by subjecting the sample to nondestructive 2D DESI-MS imaging, wherein the MS profile from the sample comprising circulating tumor cells is compared to a reference profile from a matched control derived from the same donor.
Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. do not teach that the reference profile may be obtained from a different subject.
However, Li et al. teach a method comprising analyzing serum metabolites from colorectal cancer patients and healthy control patients by mass spectrometry. Li et al. teach that comparison between lipidomic markers apparent in the MS profiles obtained from the blood of healthy subjects and those of early-stage subjects with colorectal cancer outperformed the established carcinoembryonic antigen (CEA) biomarker typically used for diagnosis of colorectal cancer (Li et al., abstract).
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 Sakamoto et al. in view of Eberlin et al. comprising comparing MS profiles between samples comprising CTCs and non-CTC-containing samples/regions from a single subject such that the comparison is made between subjects with CTCs and those that do not have CTCs (i.e. healthy controls). The ordinary artisan would have been motivated to make such a modification with a reasonable expectation of success because of the teaching of Li et al. that cancer biomarkers detectable by MS are not confined to the blood fraction comprising circulating tumor cells. Rather Li et al. teach that CRC-diagnostic lipid biomarkers are detectable in serum (Li et al., abstract) and therefore, would likely remain in control samples obtained from the blood of a subject with CTCs, even if said control sample were depleted of CTCs (i.e. if cell-free serum was used as control).
Claims 13-19 are rejected under 35 U.S.C. 103 as being unpatentable over Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. as applied to claims 1, 2, 6, 9-11, 13-19, 20, and 22 above, and further in view of Eberlin et al. 2014(a), “Molecular assessment of surgical-resection margins of gastric cancer by mass-spectrometric imaging”, PNAS vol. 111, no. 7, pp 2436-2441, published February 18, 2014, Eberlin et al. 2014(b), “Alteration of the lipid profile in lymphomas induced by MYC overexpression”, PNAS vol. 111, no. 29, pp 10450-10455, published July 22, 2014, Zhang et al., “Detection of Metastatic Breast and Thyroid Cancer in Lymph Nodes by Desorption Electrospray Ionization Mass Spectrometry Imaging”, J. Am. Soc. Mass Spectrom. (2017) 28:1166-1174, published February 26, 2017, Sans et al., “Metabolic Markers and Statistical Prediction of Serous Ovarian Cancer Aggressiveness by Ambient Ionization Mass Spectrometry Imaging”, Cancer Res. 77(11):2903-2913, published June 1, 2017, Sans et al., 2019, “Performance of the MasSpec Pen for Rapid Diagnosis of Ovarian Cancer”, Clin Chem. 2019 May; 65(5):674-683, published May 1, 2019, and Porcari et al., “Multicenter Study Using Desorption-Electrospray-Ionization-Mass-Spectrometry Imaging for Breast-Cancer Diagnosis”, Analytical Chem. 2018, 90, 11324-11332.
This rejection has been updated as necessitated by the amendments to the claims.
Regarding claim 1, as described above, Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. teach a method of detecting circulating tumor cells in the buffy coat fraction of a blood sample from a subject by subjecting the sample to nondestructive 2D DESI-MS imaging, wherein the MS profile from the sample comprising circulating tumor cells is compared to a reference profile from a matched control derived from the same donor.
It is noted that the claim language recited by claims 13-19, “wherein the profile comprises…” [certain fatty acid and/or metabolite molecules and m/z signals in the MS data] does not positively recite any particular method steps or limitations upon previously recited method steps and rather appears to require that specific naturally occurring CTC biomarkers are present in the sample. As discussed above, the presence of these biomarkers is inherent to the method of claim 1 wherein a buffy coat sample comprising CTCs is subjected to ambient ionization mass spectrometry.
However, in the interest of compact prosecution, each of the recited m/z “species” recited by the claims were known in the art as markers of various tumor cells as taught by the cited art.
Regarding claim 13, Eberlin et al., 2014(a) teach fatty acid and metabolites and an analyte with m/z of 303 (i.e. ~303.223) is present in mass spectra of gastric cancer (Eberlin et al., 2014(a), figure 1). Sans et al. teach species with m/z ratios of 215.033 and 283.264 are present in mass spectra of high grade serous ovarian cancer (Sans et al., table 1). Finally, Porcari et al. teach a species with m/z ratio of 255.233 is present in mass spectra of breast cancer tissues.
Regarding claim 14, Sans et al. teach a Ceramide with m/z of 656.576 is present in mass spectra of serous ovarian cancer (Sans et al., figure 1 C). Porcari et al. teach species with m/z ratios of 572.481 and 682.592 (i.e. 572.48 and 682.694) are present in mass spectra of breast cancer tissues (Porcari et al., figure 2).
Regarding claim 15, Eberlin et al., 2014(a) teach a species with m/z of 723 (i.e. 722.513) is present in gastric cancer(Eberlin et al., 2014(a), Figure 1). Sans et al., 2019 teach a glycerophosphoethanolamine species with m/z of 750.546 is present in low grade serous ovarian carcinoma (Sans et al., page 676, column 2). Finally, Zhang et al. teach a species with m/z of 766.539 (i.e. 766.542) is present in metastatic lymph nodes (Zhang et al., figure 2).
Regarding claim 16, Eberlin et al., 2014(a) teach a species with m/z ratio of 723.5 (i.e. 723.499) is present in gastric cancer (Eberlin et al., figure 1). Sans et al. teach a species with m/z of 725 (i.e. 725.495) is present in ovarian carcinoma (Sans et al., figure 4).
Regarding claim 17, Eberlin et al., 2014(a) teach species with m/z ratios of 788.5 and 810 (i.e. 788.545 and 810.529) are present in gastric cancer (Eberlin et al., 2014(a), figure 1).
Regarding claim 18, Eberlin et al., 2014(b) teach species with m/z ratios of 747.5166 (i.e. 747.52) and 773.5325 (i.e. 773.534) are present in lymphomas (Eberlin et al., 2014(b), Figure 1).
Regarding claim 19, Eberlin et al., 2014(b) teach species with m/z ratios of 861.5479 (i.e. 861.551) and 885.5478 (i.e. 885.550) are present in lymphomas (Eberlin et al., 2014(b), Figure 1). Eberlin et al., 2014(a) teach a species with a m/z ratio of 836 (i.e. 835.535) is present in gastric cancer (Eberlin et al., 2014(a), Figure 1). Finally, Zhang et al. teach a species with a m/z ratio of 857.518 (i.e. 857.520) is present in metastatic thyroid cancer (Zhang et al., figure 2).
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 measured any one or any combination of the known fatty acid and/or metabolite species known in the art at least from the cited references all published more than one year prior to the effective filing date of the claimed invention. The ordinary artisan would have been motivated to measure any of these known species by ambient ionization mass spectrometry according to the method taught by Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. with the predictable result of detecting CTCs in a subject because each of the cited references teach the recited fatty acid and/or metabolite species “(with or and species)” having m/z ratios as recited by the claims are known markers of cancer cells capable of differentiating between normal tissue and adjacent tumor cells (i.e. can differentiate between normal cells and tumor cells). Further, several of the cited references explicitly identify the cited markers in metastatic tumors (i.e. those that give rise to circulating tumor cells).
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. as applied to claims 1, 2, 6, 9-11, 13-20, and 22 above, and further in view of De Giorgi et al., “Application of a Filtration- and Isolation-by-Size Technique for the Detection of Circulating Tumor Cells in Cutaneous Melanoma”, Journal of Investigative Dermatology (2010) 130, 2440-2447, and Tang et al., “Blood-Based Biopsies- Clinical Utility Beyond Circulating Tumor Cells”, Cytometry Part A 93A: 1246-1250, 2018.
Regarding claims 1 and 20-21, as described above, Sakamoto et al. in view of Eberlin et al., 2011, Feider et al., and Kawada et al. teach a method of detecting circulating tumor cells in the buffy coat fraction of a blood sample from a subject by subjecting the sample to nondestructive 2D DESI-MS imaging, wherein the MS profile from the sample comprising circulating tumor cells is compared to a reference profile from a matched control derived from the same donor.
Sakamoto et al. further teach filtering the fluid sample to exclude white blood cells (i.e. leukocytes) from the PBMC fraction (i.e. the buffy coat) using a CellSieve Microfiltration Assay and a low-pressure filtration system (i.e. a vacuum apparatus) (Sakamoto et al., page 760, column 2, paragraph 1).
Sakamoto et al. do not teach the pore size of the membrane filter. However, Tang et al. teach capturing circulating tumor cells on a CellSieve Microfiltration membrane with 7 µm diameter pores (Tang et al., figure 1 and page 1247, column 1). Similarly, De Giorgi et al. teach isolating epithelial tumor cells from circulating peripheral blood (i.e. circulating tumor cells) using an “ISET” membrane with 8 µm diameter pores.
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 used a vacuum apparatus (as taught by Sakamoto et al. and Tang et al.) comprising a filter membrane with pores having a diameter between 7 and 8 (i.e. 7.5) µm. The ordinary artisan would have recognized that a filter with 7.5 µm pores would have predictably captured CTCs from blood because Tang et al. and Sakamoto et al. capture CTCs with a filter having 7 µm diameter pores, and De Giorgi et al. capture CTCs with a filter having 8 µm diameter pores because Tang, Sakamoto, and De Giorgi et al. each teach using such filters for the same purpose and the claimed filter pore diameter falls within the range of suitable pore sizes established at least by the cited prior art.
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.
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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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