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
This application 18/284,131 filed on 09/26/2023 is a 371 national phase of PCT/US 2022/019757 filed on 03/10/2022, and claims the benefit of provisional U.S. Patent Application No. 63/166,658, filed on 03/26/2021.
The priority date of claim 2 and its dependent claims is determined to be 03/26/2021, the filing date of provisional U.S. Patent Application No. 63/166,658.
Status of Claims
Applicant’s amendments to claims filed 04/27/2026 in response to the Non-Final Rejection mailed 01/27/2026 are acknowledged.
Claims 2, 4-6, 11, 13, 15, and 17 are amended.
Claims 1, 3, 7, and 12 have been canceled.
Claims 2, 4-6, 9-11, and 13-21 are pending and under examination.
Response to Remarks filed 04/27/2026
The amendments and arguments presented in the papers filed 04/27/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 01/27/2026 listed below have been reconsidered as indicated.
a) The 35 USC 112(b) indefiniteness rejections of claims 1-7 and 9-21 have been withdrawn in view of the cancellation of claim 1 and amendments to claims except as described below.
b) The rejection of claims 1-7 and 9-16 under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Srinivasan et al. (WO/2020/205644) is withdrawn in view of amendments to the claims and cancellation of claims 1, 3, 7, and 12.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Claim Interpretation
Claims 2 and 9 recite the limitation "B cell related gene". The instant specification states that a B cell related gene can be selected from “BLK, CD19, FCRL2, MS4A1, KIAA0125, TNFRSF17, TCL1A, SPIB, PNOC, and combinations thereof” and “Examples of B cell related genes can include, but are not limited to, BLK, BLNK, BTK, NFAM1, LYN, CD5, CD19, CD21, CD45, CD22, CD79A, CD79B, CD81, FYN, FCRL1, FCRL2, FCRL3, FCRL4, FCRL5, LAX, PIR, CR1, BAFF, CS1, LILRB1, LILRB2, LILRB3, LILRB4, LILRA3, LAIR1, and combinations thereof” (p. 10). No further requirements are provided that define a gene as “B cell related”. For purposes of examination, any of the genes listed in the specification is considered to be a “B cell related gene”.
Claims 2, and 10 recite the limitation “CD8+ T cell related gene”. The instant specification states that a CD8+ T cell related gene can be selected from “CD8A, GZMA, GZMB, IFNG, CXCL9, CXCL10, PRF1, TBX21 and combinations thereof” and that “Examples of CD8+ T cell related genes can include, but are not limited to, TNFRSF9, XCL1, XCL2, CRTAM, PSMB8, PSMB9, PSMB10, PSME2, TAP1, IRF1, FBOX6, ETV7, NKG7, GZMH, CCL4, LAG3, CD2, GBP5, CD3D, B2M, CD74, LAP3, CD7, HLA- DRA, HLA-C, HLA-DMA, and combinations thereof” (p. 11). No further requirements are provided that define a gene as “CD8+ T cell related”. For purposes of examination, any of the genes listed in the specification is considered to be a “CD8+ T cell related gene”.
Claim Rejections - 35 USC § 112(b)
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 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 2, 4-6, 9-11, and 13-21 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The following are new rejections necessitated by amendments
Claim 2 recites the limitation “identifying a B8T gene signature of the subject as a B8T high/high gene signature, based on the subject having both an increased RNA expression level of the B cell related gene and an increased RNA expression level of the CD8+ T cell related gene”. The phrase “B8T high/high gene signature” is unclear. The term “high” is a relative terms which renders the claim indefinite. It is unclear what criteria are used to define “high” values or what threshold would determine high versus not high. The term high is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
The limitation “having both an increased RNA expression level of the B cell related gene and an increased RNA expression level of the CD8+ T cell related gene” in claim 2 is unclear. The term “increased” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what the RNA expression level is required to be increased relative to. For example, the increase could be relative to a second sample from the same subject at a different time or different tissue, a reference, or a second sample from a different subject.
Claim 2 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01.
Claim 2 recites the limitations “(a) evaluating RNA expression level of a B cell related gene ---; (b) evaluating RNA expression level of a CD8+ T cell related gene---; (c) identifying a B8T gene signature of the subject as a B8T high/high gene signature---; (d) determining an immune checkpoint inhibitor (ICI) treatment outcome to be beneficial to the identified subject”. The omitted steps In claim 2 appear to be: steps directed towards identifying a subject with a B8T high/high gene signature, and selecting the subject based on a B8T high/high gene signature for treatment. As written the steps require identifying a B8T signature for a subject and not identifying a subject with a particular B8T signature. It is unclear what defines an identified subject as what is identified is a signature. Claim 2 should clearly delineate all active steps required for performing the claimed methods. For examination purposes it is interpreted that the identified subject of parts (d) and (e) is a subject that has been identified as having a B8T high/high gene signature.
Claims 4-6, 9-11 and 13-21 and 9-21 are similarly indefinite because they directly or indirectly depend from claim 2.
The following maintained rejection has been modified to address claim amendments filed on 04/27/2026.
Claim 11 recites the limitations “B8T high/high”, “B8T high/low”, “B8T low/high”, and “B8T low/low”. Claim 14 recites the limitations “B8T high/low” and “B8T low/high”. The terms “high/high”, “high/low”, “low/high”, and “low/low” are relative terms which render the claim indefinite. It is unclear what criteria are used to define high versus low values. It is also unclear how such values would be determined. The terms high and low are not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Response to Arguments against Claim Rejection - 35 U.S. C § 112(b)
The response asserts that the specification sufficiently describes that "high expression of intratumoral B cell gene signature (BCGS) and high expression of CD8+ T cell gene signature (CD8TGS) in a subject can be referred to as B8T high/high," "high expression of intratumoral B cell gene signature (BCGS) and low expression of CD8+ T cell gene signature (CD8TGS) in a subject can be referred to as B8T high/low," "low expression of intratumoral B cell gene signature (BCGS) and high expression of CD8+ T cell gene signature (CD8TGS) in a subject can be referred to as B8T low/high," and "low expression of intratumoral B cell gene signature (BCGS) and low expression of CD8+ T cell gene signature (CD8TGS) in a subject can be referred to as B8T low/low" (see, e.g., page 11 lines 9-18 of application as filed). Thus, the terms recited in claims 11, 12, and 14 are sufficiently defined by the specification (p. 6).
Applicant's arguments have been fully considered but are not persuasive.
While the specification clarifies the B cell and CD8+ T cell gene signature components used to define a high/high or other score, the specification does not make clear what standards or definition should be used to characterize an individual B cell or cd8+ T cell signature as high or low. Amended cla-im 2, which claims 11 and 14 depend from, recites “B8T high/high gene signature, based on the subject having both an increased RNA expression level of the B cell related gene and an increased RNA expression level of the CD8+ T cell related gene” as the basis of a high/high score. However the terms high and low remain indefinite as there is no clear standard for what level or amount of increase would be considered “high” or what level of expression would be defined as “low”.
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 2, 4-6, 9-11, and 13-21 remain/are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
This maintained rejection has been modified to address claim amendments filed on 04/27/2026.
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, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
Based upon 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 the statutory category of a process.
Step 2A, Prong One
The claims are taken to be directed to abstract ideas and laws of nature, judicial exceptions.
Claim 2 is directed to a method comprising “(a) evaluating RNA expression level of a B cell related gene to determine a B cell gene signature; (b) evaluating RNA expression level of a CD8+ T cell related gene to determine a CD8+ T cell gene signature; (c) identifying a B8T gene signature of the subject as a B8T high/high gene signature, based on the subject having both an increased RNA expression level of the B cell related gene and an increased RNA expression level of the CD8+ T cell related gene” and “(d) determining an immune checkpoint inhibitor (ICI) treatment outcome to be beneficial to the identified subject”. These limitations are abstract mental processes (see MPEP 2106.04(a)(2)(III)). As written, the evaluating, identifying, and determining steps encompass the mental step of looking at data reporting RNA expression and making mental judgements.
Claim 2 as a whole is directed to a process that involves the judicial exception of a law of nature (i.e. the correlation between B cell and CD8+ T cell gene expression signatures and treatment outcome). This relationship is a natural phenomenon that exists apart from any human action and constitutes a law of nature.
Claims 4-6, 9-11, and 13-21 depend from claim 2, and require the same steps of evaluating, analyzing, and determining.
Claim 15 is directed to a method comprising “identifying a prognostic biomarker in the subject, wherein the B8T gene signature and the identification of the prognostic biomarker are used in combination to determine treatment outcome in the subject”. This limitation is an abstract mental process (see MPEP 2106.04(a)(2)(III)). As written, the identifying step encompasses the mental step of looking at biomarker expression and gene expression and making mental judgements about treatment.
Claim 17 is directed to a method comprising “identifying the gender of the subject , wherein the B8T gene signature and the gender are used in combination to determine treatment outcome in the subject”. This limitation is an abstract mental process (see MPEP 2106.04(a)(2)(III)). As written, the identifying step encompasses the mental step of noting gender identity by looking at medical records and gene expression and making mental judgements about treatment.
Step 2A, Prong Two
The exception is not integrated into a practical application of the exception. The claims do not recite any additional elements that integrate the exception into a practical application of the exception.
While claim 2 recites ” (e) administering [[a]]the ICI treatment to the identified subject, thereby treating the cancer”, this is not an integration of the exception into a practical application. The claims do not include a step of administering a particular agent to the subject to treat a particular disease after determining that the subject having a disease will be responsive to that particular agent. See MPEP 2106.04(d)(2).
Step 2B
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. The claim does not add a specific limitation other than what is well-understood, routine, and conventional in the field. Steps directed to evaluating RNA expression, analyzing gene signatures and determining treatment outcome are recited at a high level of generality covering all conventional methods of assaying for gene expression. Methods of assaying for gene expression, analyzing gene signatures and determining treatment outcome were well-known, routine and conventional in the prior art as demonstrated in the 102 and 103 rejections documented below.
For these reasons, the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to Arguments against Claim Rejection - 35 U.S. C § 101
The response asserts that amended claim 2 does not encompass non-ICI
treatments within its scope, and thus meets the requirements of 2106.04( d)(2) (p. 7).
Applicant's arguments have been fully considered but are not persuasive.
Claims remain directed to a process that involves the judicial exception of a law of nature (i.e. the correlation between B cell and CD8+ T cell gene expression signatures and treatment outcome). While the claims do not encompass administering non-ICI treatments, the claimed ICI treatments are at a high level of generality and do not recite an action directed towards a particular treatment or prophylaxis for a disease or medical condition. Immune checkpoint inhibitor (ICI) treatments encompass a large class of treatments and the claims do not require a specific or particular ICI treatment in response to a specific classification or prediction score. Thus, the generic treatment steps fail to add significantly more.
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 2, 4-6, 9-11, and 13-16 are rejected under 35 U.S.C. 103 as being unpatentable over Srinivasan et al. (WO/2020/205644, on IDS dated 04/12/2024).
These are new rejections necessitated by claim amendments filed on 04/27/2026.
Regarding claim 2, Srinivasan teaches methods of treating a patient having a tumor (a subject having cancer), the method comprising: determining a tumor microenvironment (TME) signature to determine patient response to a therapeutic agent (para 5). Srinivasan teaches the signature may be detected by RNA sequencing (para 150), providing RNA expression. Srinivasan teaches a TME signature may comprise a B cell signature (para 7 and example 4) or CD8+T cell signature (para 7 and example 3), or combinations of subsets of genes from B cells and CD8+ T cells (paras 4, 174). Srinivasan teaches obtaining the expression level of genes in a TME signature and calculating a TME gene signature to classify a patient as biomarker positive or biomarker negative (para 25) and that Srinivasan further teaches that a biomarker positive patient is determined to be likely experience a DCB (durable clinical benefit, i.e. a beneficial outcome) with a therapeutic agent (para 127). Srinivasan teaches administering therapeutic agents to a biomarker positive patient (para 21). Srinivasan teaches therapeutic agents comprise immune checkpoint inhibitors (paras 34-36) and teaches administering an immune checkpoint inhibitor (para 378).
Srinivasan does not teach verbatim “(c) identifying a B8T gene signature of the subject as a B8T high/high gene signature, based on the subject having both an increased RNA expression level of the B cell related gene and an increased RNA expression level of the CD8+ T cell related gene”.
However, Srinivasan teaches a patient with high DCB (durable clinical benefit, i.e. a beneficial outcome) from a therapeutic agent has high B cell expression (para 129) and a patient with DCB has high CXCL9 expression (paras 133, 320), which reads on a signature that is B cell signature high/CD8+ T cell signature high as required by the limitation. Further, Srinivasan teaches that high expression of one or more genes comprising CD19 (B cell related gene) and CD8A (CD8+ T cell related gene) is associated with a positive biomarker classification for DCB with the therapeutic agent (paras 133, 320).
Therefore, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Srinivasan to arrive at the instantly claimed invention. The modification would have entailed using the combination of B cell signature and CD8+T cell signature to identify patients likely to experience durable clinical benefit with a therapeutic agent. Srinivasan teaches that high B cell gene expression and high CD8+ T cell gene expression is individually associated with durable clinical benefit, and that high expression of a combination of B cell and cd8+ T cell related genes are possible- yielding a high/high signature of B cell/CD8+ T cell expression, and further that high expression of a combination of these genes is associated with a beneficial outcome from a therapeutic agent. One would have been motivated to combine B cell gene expression and CD8+ T cell gene expression as the indicators of a positive biomarker classification for DCB with the therapeutic agent by the fact that both B cell and CD8+ T cell gene expression were individually associated with DCB. The modification would further have entailed selecting an immune checkpoint inhibitor as the therapeutic agent. Selecting the appropriate therapeutic agent is deemed merely a matter of judicious selection and routine optimization which would have been well within the purview of the skilled artisan. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 4, Srinivasan teaches performing the methods on metastatic tumors that have undergone surgical removal (para 378), which reads on metastatic solid tumor.
Regarding claim 5, Srinivasan teaches the cancer is bladder cancer (paras 32, 62, 270).
Regarding claim 6, Srinivasan teaches cancers selected from bladder cancer, breast cancer, and cervical cancer (para 270).
Regarding claim 9, Srinivasan teaches the B-cell signature comprises expression of CD19 (para 104).
Regarding claim 10, Srinivasan teaches signatures comprising CD8A (para 106), which reads on a CD8+ T cell related gene.
Regarding claim 11, Srinivasan teaches B cell signatures that are high and low correlated with durable clinical benefit (Fig. 5) and CD8+ T cell signatures that are high and low correlated with durable clinical benefit (Fig. 3), which reads on B8T signatures that are high/high, B8T high/low, B8T low/high, and B8T low/low, where the first element is B cell signatures and the second element is CD8+ T cell signatures.
Regarding claim 13, Srinivasan teaches using the method to determine durable clinical benefits (para 2), defined as progression-free survival (para 289).
Regarding claim 14, Srinivasan teaches low B cell signatures associated with no DCB (durable clinical benefit, i.e. a non-beneficial outcome) (Fig. 5) and CD8+ T cell signatures that are low associated with durable clinical benefit (Fig. 3), which reads on B8T signatures that are low/high and B8T high/low, where the first element is B cell signatures and the second element is CD8+ T cell signatures.
Regarding claims 15 and 16, Srinivasan teaches identifying the tumor mutational burden in patients and correlation with durable clinical benefit (Example 2, Fig. 2).
Claims 17-21 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Srinivasan et al. (WO/2020/205644. On IDS dated 04/12/2024) as applied to claims 2, 4-6, 9-11, and 13-16 above, and further in view of Conforti et al. (Cancer immunotherapy efficacy and patients' sex: a systematic review and meta-analysis. 2018. Lancet Oncology. 19(6):737-746. On IDS dated 04/12/2024).
The following rejections are modified as necessitated by claim amendments to independent claim.
Regarding claim 17, Srinivasan teaches identifying the gender of a subject (Tables 3 and 4), but does not teach identifying the gender of the subject, wherein the B8T gene signature and the gender are used in combination to determine treatment outcome in the subject.
Conforti teaches differences in immune checkpoint inhibitor efficacy between men and women (p. 737, Summary).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Srinivasan and Conforti to arrive at the instantly claimed invention. The modification would have entailed using the gender data collected by Srinivasan as a factor in determining a patient response to a therapeutic agent by adding it as a variable to consider as in Conforti. One would have been motivated to do so by the interest of both Srinivasan and Conforti in increasing predictiveness of treatment efficacy. Conforti teaches that sex-related dimorphism in immune system response is well known (p. 737, Summary), and Srinivasan is interested in considering complex factors responsible for determining treatment outcome (paras 2 and 3). There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claims 18-21, Srinivasan does not teach the treatment outcome is determined to be beneficial to the subject when the gender of the subject is identified as male (claim 18) or the treatment outcome is determined to be non-beneficial to the subject when the gender of the subject is identified as female (claim 19).
Conforti teaches examples wherein intervention is favored (treatment outcome is beneficial) when the subject is male; control is favored (treatment outcome is non-beneficial) when the subject is female; intervention is favored (treatment outcome is beneficial) when the subject is female; control is favored (treatment outcome is non-beneficial) when the subject is male (Fig. 2). Conforti states that there is heterogeneity in the efficacy of immune checkpoint inhibitors according to the patient’s sex (p. 743, col. 1) and that other factors could explain the association between sex and immune checkpoint inhibitor efficacy (p. 745, col. 1), including individual patent variables such as gene expression and mutations (p. 744).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Srinivasan and Conforti to arrive at the instantly claimed invention. The modification would have entailed using the gender data collected by Srinivasan as a factor in determining a patient response to a therapeutic agent by adding it as a variable to consider as in Conforti. One would have been motivated to do so by the interest of both Srinivasan and Conforti in increasing predictiveness of treatment efficacy. Conforti teaches that sex-related dimorphism in immune system response is well known (p. 737, Summary), and Srinivasan is interested in considering complex factors responsible for determining treatment outcome (paras 2 and 3). Further, Conforti recognizes that sex differences in treatment outcome is only one of many variables to be considered to understand heterogeneity of response. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Response to Arguments against Claim Rejection - 35 U.S. C § 103
The response asserts that Conforti does not cure the primary deficiencies of Srinivasan, and none of the cited references, alone or in combination, teach or suggest any of the subject matter in the claims as amended herein (p. 9).
Applicant's arguments have been fully considered but are not persuasive.
Applicant’s response does not present any arguments against Conforti. Thus the rejection is maintained with modifications necessitated by amendments as set forth above.
Conclusion
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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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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