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 .
Election/Restrictions
Applicant's election with traverse of Inventive Group I in the reply filed on 7/21/2025 is acknowledged. The traversal is on the ground(s) that Marton at al. fails to teach use of Wnt7b, Wnt10a, or a combination thereof. This is not found persuasive because the claims still lack unity of invention because they do not make a contribution over the prior art as evidenced by the art rejections below.
The requirement is still deemed proper and is therefore made FINAL.
Claim Interpretation
Claims 1, 4, and 15 make use of the phrase “optionally wherein”, which means that any further limitation after said phrase is not a direct requirement of the claim. Therefore, only the parts of claims 1, 4, and 15 which come prior to the phrase “optionally wherein” will be examined on the merits. Applicant may, at their discretion, amend claims 1, 4, and 15 to distinctly state all requirements regarding the claims in question.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 1, 7, 9, and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. (Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma, 2016) in view of Kazuo et al. (JP 2014-176353 A)
Regarding Claims 1 and 15: Kim teaches use of single cell RNA sequencing (RNA-seq) to compare the expression profiles from biopsied metastatic renal cell carcinoma (mRCC), patient-derived xenografts (PDX) and primary renal cell carcinoma (pRCC) (pg 5, Single-cell RNA sequencing and quality assessment for expression profiling) and used single-cell dissociation of xenografted tumor specimens for both single-cell RNA sequencing (pg 11, Single-cell RNA sequencing and processing) and for short-term culture (pg 12, Primary in vitro short-term culture) This reads on the claimed method of generating an ex-vivo cell based system from a single-cell dissociated tissue sample obtained from a subject and performing single-cell RNA sequencing on said tissue sample. This further reads on the claimed method of the original tissue sample being a tumor or metastatic tumor tissue sample. Lastly, this reads on the method of claim 15 of an ex-vivo cell-based system derived by the method of claim 1.
Kim further teaches use of basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) in the use of their xenograft-based short term culture (pg 12, Primary in vitro short-term culture) which reads on the claimed method of use of the addition of growth factors or cell signaling molecules in the media of the ex vivo cell-based model. Kim fails to teach on the claimed method of use of WNT7B or WNT10A in the media in addition to co-culture with fibroblasts.
Kazuo et al. teaches a method of expanding human hematopoietic stem cells (0001) with use of a medium comprising growth or expansion factors, chemokines, cytokines, and other factors to promote cell survival and proliferation. (0033) Kazuo further specifies use of Wnt7b as a factor used to increase proliferation and cell survival (0033) which reads on use of Wnt7b or Wnt10A or a combination thereof in the culture media.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the sequence-based analysis and culture method of Kim with the culture media factors and co-culture method as taught by Kauzo to create an ex vivo cell culture model comprising Wnt7Bb or Wnt10A in the media comprising co-culturing the tissue-based cell sample with fibroblasts. One would have been motivated and had a reasonable expectation of success at doing so based on the teachings of Kazuo, who state that the addition of growth factors can increase cell proliferation, amplification and survival of cells in culture and that co-culture can aid in proliferation.
Regarding Claims 7 and 9: Kim et al. teaches use of xenograft tumor specimens being dissociated into a single cell suspension and being cultured in neurobasal media supplemented with N2, bFGF, EGF, neuregulin 1, and insulin-like growth factor. (Pg 12, Primary in vitro short-term culture) This reads both on the medium further comprising the addition of one or more additional growth factors or cell signaling molecules (claim 7) and the method of the medium not comprising a TGFb inhibitor (claim 9).
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. (Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma, 2016) in view of Kazuo et al. (JP 2014-176353 A) and Agbunag et al. (Oncogenic K-ras Drives Cell Cycle Progression and Phenotypic Conersion of Primary Pancreatic Duct Epithelial Cells, 2004)
The teachings of Kim and Kazuo are described above. Both Kim and Kazuo fail to teach manipulation of the media or culture conditions to revert the phenotype of the cells in culture.
Regarding Claim 4: Kim teaches use of single-cell analysis and transcriptome profiling to examine the growth inhibitory effects of afatinib and dasatinib on cells in culture. (Pg 6, Evaluation of the single-cell analysis-driven therapeutic strategy) This reads on use of single-cell RNA analysis performed before and after establishing the cells of the claimed invention in an ex vivo cell-based system. After these results were obtained, a combination therapy was tried and it was found that the combination treatment of afatinib and dasatinib was much more effective than individual treatment, which had a more efficient inhibition of downstream AKT and ERK phosphorylation in PDX-mRCC cells. (Pg 6-7, Evaluation of the single-cell analysis-driven therapeutic strategy) Kim fails to teach modification of the cell culture media to make the cellular phenotype revert.
Agbunag et al. teaches a method of modeling pancreatic ductal adenocarcinoma (PDA) and that k-ras mutations are one of the first genetic changes to be detected with early PDA formation. (Pg 5659, Introduction) To model this, primary pancreatic duct epithelial cells (PDEC) were established in culture and said cells were introduced to k-ras, causing a significant increase in cell size, mimicking the phenotype of PDA. (Pg 5659-5661, Results and Discussion) PDEC cells were then microinjected with both k-ras and a P13K inhibitor, which failed to lead to an increase in cell size. (Pg 5661, Results and Discussion) This reads on the claimed method of modifying the medium or conditions to revert the expression space between the current phenotype (enlarged k-ras exposed PDEC which mimic PDA) to non-enlarged PDEC cells (with the addition of the P13K inhibitor).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the condition manipulation of the addition of a P13K inhibitor to cause a phenotype change to PDEC cells as taught by Agbunag with the single cell dissociation method taught by Kim and the media factors and co-culture method as taught by Kauzo to use single-cell RNA sequencing to determine the phenotype of cells in culture before and after a phenotypic change in the culture has been observed with the phenotypic change being caused by manipulation of the cell culture media or conditions. One would have been motivated to do so and had a reasonable expectation of success based on the teachings of Agbunag which detail use of a P13K inhibitor microinjected into the cells in culture with k-ras which result in the inhibition of the phenotypic change caused by just k-ras of increased cell size.
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. (Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma, 2016) in view of Kazuo et al. (JP 2014-176353 A) and Boj et al. (Organoid Models of Human and Mouse Ductal Pancreatic Cancer, 2015)
The teachings of Kim and Kazuo are described above. Both Kim and Kazuo fail to teach use of a pancreatic ductal adenocarcinoma (PDAC) tumor as the source for the method of culture of claim 1.
Regarding claim 10: Boj et al. teaches a method of isolating murine primary pancreatic ductal tumors and establishing an organoid model in culture of said tumors to show in vitro how pancreatic ductal adenocarcinoma progresses. (Pg 327, Tumor-Derived Organoids Provide a Model for Murine PDA Progression)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teaching of Boj of use of murine PDA tumors in primary culture with the single cell dissociation method taught by Kim and the media factors and co-culture method as taught by Kauzo to create a culture method with cells derived from a PDAC tumor. One would have had motivation and a reasonable expectation of success based on the teachings of Boj, who detail a method of extraction of primary murine PDAC tumors which were used to establish organoid models in culture.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. (Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma, 2016) in view of Kazuo et al. (JP 2014-176353 A) and Castro (Interferon-Gamma at the Crossroads of Tumor Immune Surveillance or Evasion, 2018)
The teachings of Kim and Kazuo are disclosed above. Both Kim and Kazuo fail to teach use of IFNγ in their culture media.
Regarding Claim 14: Castro et al. teaches that IFNγ plays a role in the tumor microenvironment in that it is antiproliferative, anti-angiogenic, and has pro-apoptotic effects and may favor tumor immune invasion. (pg 6, IFNγ Actions on Transformed cells and the Tumor microenvironment)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teaching of Castro of use of IFNγ in the culture media with the sequence-based analysis and culture method of Kim with the culture media factors and co-culture method as taught by Kauzo to create an ex vivo cell culture model comprising IFNγ in the culture media. One would have been motivated and had a reasonable expectation of success at doing so based on the teaching of Castro, who states that IFNγ is antiproliferative, anti-angiogenic, and may favor tumor immune invasion.
Response to Arguments
Applicant has argued that neither Kim nor Kazuo teach a method of maintaining the in vivo phenotype of a primary metastatic tumor in single-cell culture regarding claims 1 and 15. This argument is unpersuasive. Kim teaches a method of dissociating xenograft tumor specimens into a single cell suspension and placing them into a neurobasal media with the intent to run drug sensitivity assays on said cultures. (pg 12, Primary in vitro short term culture) In order to be able to run drug sensitivity assays and gain meaningful results, it is obvious that the primary xenograft tumor specimens in culture would have to maintain their in vivo phenotype.
Applicant further argues that a person of ordinary skill in the art would have no motivation to combine the teachings of Kazuo of the addition of WNT7B and WNT10A “among numerous factors” with the teachings of Kim to create a media comprising WNT7B and/or WNT10A. This is unpersuasive because Kazuo teaches that WNT7B, among other factors, is known to promote cell survival, maintenance, proliferation, amplification, and self-replication. (0033) This taken in the context of Kim of the teaching of a short-term culture of primary xenografted tumor cells would result in the formation of a media which is better suited to long-term culture, as the factors taught by Kazuo are stated to promote cell survival, proliferation, and maintenance. Furthermore, per MPEP 2141.II.C "A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton."KSR, 550 U.S. at 421, 82 USPQ2d at 1397. "[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle."Id. at 420, 82 USPQ2d at 1397. Office personnel may also take into account "the inferences and creative steps that a person of ordinary skill in the art would employ."Id. at 418, 82 USPQ2d at 1396.
Applicant further argues that claims 4, 7, 9, 10, and 14 are dependent on claim 1 and are therefore allowable on the same basis as claim 1. However, as the above discussion rendered said arguments unpersuasive, the arguments regarding 4, 7, 9, 10, and 14 are unpersuasive on the same basis.
Based on the above discussion, the rejections of claims 1, 4, 7, 9, 10, 14, and 15 are upheld.
Conclusion
THIS ACTION IS MADE FINAL. 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 HANNA M THUESON whose telephone number is (571) 272-3680. The examiner can normally be reached M-F 7:30-5 EST. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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/HANNA MARIE THUESON/Examiner, Art Unit 1638
/Tracy Vivlemore/Supervisory Primary Examiner, Art Unit 1638
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