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 .
Status of Claims
Applicant' s amendment filed 09/02/2025 is acknowledged. Claims 1-4, 6-13, 15-18, and 20-21 have been amended. Claims 1-21 are pending in the instant application and the subject of this final office action.
All of the amendments and arguments have been reviewed and considered. Any rejections or objections not reiterated herein have been withdrawn in light of amendments to the claims or as discussed in this office action.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Previous Rejection
Status of Prior Rejections/Objections:
The objections to the drawings is withdrawn in view of Applicant’s submission that there was no intention to have color drawings.
The objections to the specification are withdrawn in view of the amended specification.
The objections to claims 2-3, 8, 10, and 16-17 are withdrawn in view of the amendments.
The 112(a) rejections to claims 1-7 and 10-21 are withdrawn in view of the amendments.
The 112(b) rejections to claims 1-9, 12, and 15-21 are withdrawn in view of the amendments.
The 101 rejections to claims 1-21 are withdrawn in view of the amendments.
The prior art rejections under 103 directed to claims 1-4, 6-18, and 20-21 in view of Jung, Lyons, and Porrello and claims 5 and 19 in view of Jung, Lyons, and Porrello and further in view of De Keukeleire are withdrawn in view of the amendments to the claims.
New Ground(s) of Rejections
The new ground(s) of rejections were necessitated by applicant’s amendment of the claims.
Claim Rejections - 35 USC § 103
Claims 1-4, 6-18, and 20-21 are rejected under 35 U.S.C. 103 as being unpatentable over Jung (Jung AC, et al. Biological and clinical relevance of transcriptionally active human papillomavirus (HPV) infection in oropharynx squamous cell carcinoma. Int J Cancer. 2010 Apr 15;126(8):1882-1894), Lyons (Lyons YA, et al. Immune cell profiling in cancer: molecular approaches to cell-specific identification. NPJ Precis Oncol. 2017 Aug 15;1(1):26.), Porrello (Porrello A et al. Factor XIIIA-expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking. Nat Commun. 2018 May 18;9(1):1988; as cited in the IDS dated 06/12/2023), and Han (Han M, et al. Predictors of Mortality in HPV-Associated Oropharynx Carcinoma Treated With Surgery Alone. Laryngoscope. 2020 Jul;130(7):E423-E435)
Regarding claims 1 and 3, Jung teaches collecting tumor samples from patients surgically
treated for primary head and neck tumors, wherein all tumors were squamous cell carcinomas (pg. 1883, Patients, para 1; pg. 1883, Tumor Samples, para 1). Jung teaches detecting a level of expression of SYNGR3 by qRT-PCR [i.e., gene product is mRNA; instant claim 3], wherein HPV+ samples are compared to HPV- samples [i.e., a control samples] (pg. 1888, col 2, para 1; Supplementary Fig. 1).
Jung further teaches that HPV transcription discriminated samples with the selected deregulated genes [including SYNGR3] better than the sole presence of the HPV DNA (pg. 1888, col 2, para 1). Jung teaches that increased SYNGR3 expression is correlated with actively transcribing HPV infected tumors (HPV RNA+) when compared to HPV DNA- RNA- tumors [i.e., control/reference samples] (Supplemental Figure 1).
Jung teaches that HPV presence should be considered as a stratification factor, wherein reliable biomarkers are required to discriminate this subgroup of HNSCC patients for appropriate specific treatment (pg. 1882, col 2, para 1, spanning pg. 1883). Jung teaches that reliable biomarkers of a transcriptionally active HPV could be considered as alternative or additional indicators of HPV-related tumorigenesis (pg. 1893, col 1, para 1, spanning col 2), wherein SYNGR3 expression is correlated with transcriptional activity of HPV (Supplemental Figure 1C). Jung teaches treating with surgery alone, with surgery and postoperative adjuvant radiotherapy, and with surgery and postoperative adjuvant chemoradiotherapy (pg. 1883, Tumor samples, para 2).
Therefore, Jung teaches use of SYNGR3 as a biomarker for stratification of patients [i.e., diagnosis] into HNSCC subgroups for the purpose of treating.
Jung further teaches that pathological observations have shown that HPV-positive lesions tend to be permeated by infiltrating lymphocytes and that some genes involved in the cell-based immune response were also markedly up-regulated in the HPV-related tumors (pg. 1891, col 2, para 2, spanning pg. 1892).
Jung teaches finding that HPV is heterogeneously distributed and usually organized in clusters in samples from HPV-related HNSCC [using chromogenic in situ hybridization] (pg. 1891, col 2, para 1).
Jung teaches that HPV-related HNSCC correlates with improved prognosis and that this more favorable outcome may be partly explained by enhanced sensitivity to chemotherapy and radiations (pg. 1882, para 2, spanning pg. 1883).
Jung does not explicitly teach that the sample of Jung comprises one or more immune cells or that the SYNGR3 is detected in the one or more immune cells.
Jung does not explicitly teach that the treatment stratification is directed to a de-escalation treatment protocol that reduces side effects.
Lyons teaches single-cell RNA-Seq to overcome challenges presented by heterogeneity within a population by enabling the investigation of single cells in order to determine their phenotype and the significance of their differences (pg. 3, col 1, para 1), wherein single-cell analysis of tumor-infiltrating T cells can illustrate varying phenotypes of T cells to (Methods for gene expression profiling of immune cells, para 2).
Lyons teaches the importance of using the cancer immune phenotype to tailor therapy, wherein expression profiling of immune cells as an immune signature has demonstrated significant differences in overall survival in a variety of cancers (pg. 6, Conclusions).
Lyons teaches that it has been demonstrated that knowledge of the location and density of immune cells may be more prognostic than the TNM staging guidelines and the importance of incorporating immune response into the classification of disease (Clinical use of immune profiles, para 2). Lyons teaches determining response by evaluating immune cell populations from treated and untreated tumor samples (Abstract).
Lyons further teaches that the immune contexture of primary tumors has provided information that can be equally effective, and even superior, in predicting progression-free and overall survival in cancers comprising head and neck cancer, wherein the studies included those on head and neck cancers (Introduction, para 1). Lyons further teaches that gene signatures can be used to predict response to therapy by evaluating gene expression in immune system cells of tumor tissue (Introduction, para 2).
Porrello teaches immune cell subtype signatures, including a Th1 signature comprising SYNGR3 (Supplementary Data 7), developed based genes whose expression is strongly associated with specific immune cell types based on prior art (Modified immunome signature, para 1). Porello teaches applying this immunome signature in LUSC [lung cancer] samples to determine the level of different immune infiltrates (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1). Porello further teaches that immunogenomic approaches can be used to re-classify cancer subtypes (pg. 12, col 1, para 1), and that the scoring method of the signature has advantages over other methods in that it is unambiguous and sample can be relatively enriched with respect to the broadest range of immune cell types (from none to all) (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1).
Therefore, in view of Lyons that head and neck cancers have an immune contexture [i.e., one or more immune cells] and of Porrello that SYNGR3 is a marker of a type of immune cell, Jung teaches that the sample comprises one or more immune cells and that the SYNGR3 is detected in the one or more immune cells [i.e., wherein high TIL samples would have greater than control expression consistent with the bulk data].
Han teaches the de-escalation limitation by teaching de-intensifying treatment toxicity by treating with surgery alone (instant claim 2) for HPV+ oral pharyngeal SCC [OPSCC, i.e., a subset of HNSCC] (pg. E424, col 2, para 4; see also pg. E434, col 1, para 1). Han teaches that a protocol of surgery alone has a possibility of a better QOL impact [i.e., reduced side effects associated with treatment] compared to definitive chemoradiation and adjuvant (chemo)radiation protocols, given that radiation and chemotherapy have long- term side effects that worsen QOL and function (pg. E434, col 1, para 1).
Han further teaches that patients who underwent primary surgery for OPSCC demonstrated a better quality of life and that primary surgical treatment has a comparable overall survival to primary chemoradiation (pg. E423, col 2, para 1).
Han teaches overall survival as an end point for analyzing the results of the protocol change (entire document, e.g., pg. E434, col 1, para 1-4, spanning col 2).
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 method of Jung with the single cell RNA seq method of Lyons before the effective filing date. The artisan would have been motivated to do so to overcome the issues with heterogeneity taught by Jung and Lyons. There would have been a strong expectation of success, as Porrello teaches expression of SYNGR3 in an immune cell type. Further, each of Jung and Lyons are directed to molecular markers in cancers.
Likewise, it would have been obvious to one of ordinary skill in the art before the effective filing date to treat subjects with a greater level of expression in a sample of one or more immune cells identified in the method of Jung in view of Lyons and Porrello with the surgery-only de-intensification protocol of Han. Such a substitution would have been motivated by the potential to reduce/eliminate side effects relative to the “definitive” standard-of-care protocols, as taught by Han. It likewise would have been obvious in view of Jung, Lyons that the treatments may be diagnosed by biomarkers correlated with HPV status in the tumor of the patient, motivated by improving patient prognosis by matching them a therapy they have enhanced sensitivity, as taught by Jung. There would have been a reasonable expectation of success as such are directed to molecular identifiers of cancer and/or cancer prognosis and represent the application of a known technique to a known method.
Regarding claim 4, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches detecting a level of expression of CDKN2A [i.e., the gene of p16] in the sample using an Affymetrix microarray pg. 1887, Transcriptome analysis, para 1, spanning pg. 1888) and qRT-PCR (pg. 1888, col 2, para 1; Supplemental Fig. 1), comparing HPV+ lesions from HNSCC patients to HPV- [i.e., control] lesions and identifying p16 overexpression (pg. 1888, col 1, para 1; Supporting Information, Table 1; pg. 1888, col 2, para 1; Supplemental Fig. 1).
CDKN2A/p16 is among the “reliable biomarkers”, as discussed above, for indicating HPV.
Thus, Jung further teaches detecting a level of expression of a p16 gene in the sample, comparing said level to controls, and discriminating samples [i.e., diagnosing a subject] based on the level of expression of biomarkers comprising SYNGR3 and p16.
Regarding claim 6, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches quantifying SYNGR3 using qRT-PCR and comparing quantified expression levels between HPV DNA+/RNA+ subjects and HPV DNA-/RNA- subjects [i.e., controls] (pg. 1888, col 2, para 1; Supplemental Fig. 1).
Regarding claim 7, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches performing HPV in situ hybridization on the samples (pg. 1884, Chromogenic in situ hybridation [sic], para 1; Fig. 1)
Regarding claim 8, Jung teaches analysis of SYNGR3 by qRT-PCR (pg. 1888, col 2, para 1; Supplemental Fig. 1) in samples from patients with primary head and neck squamous cell carcinoma (pg. 1883, Patients, para 1; pg. 1883, Tumor samples, para 1-2).
Jung further teaches that HPV transcription discriminated samples with the selected deregulated genes [including SYNGR3] better than the sole presence of the HPV DNA (pg. 1888, col 2, para 1).
Jung teaches that HPV presence should be considered as a stratification factor, wherein reliable biomarkers are required to discriminate this subgroup of HNSCC patients for appropriate specific treatment (pg. 1882, col 2, para 1, spanning pg. 1883). Jung teaches that reliable biomarkers of a transcriptionally active HPV could be considered as alternative or additional indicators of HPV-related tumorigenesis (pg. 1893, col 1, para 1, spanning col 2), wherein SYNGR3 expression is correlated with transcriptional activity of HPV (Supplemental Fig. 1C). Jung teaches treating with surgery alone, with surgery and postoperative adjuvant radiotherapy, and with surgery and postoperative adjuvant chemoradiotherapy (pg. 1883, Tumor samples, para 2).
Therefore, Jung teaches overexpression of SYNGR3 as a biomarker for stratification of therapies and treating patients with therapies including the standard-of-care, i.e., a protocol for patients with HPV-positive HNSCC.
Jung further teaches that pathological observations have shown that HPV-positive lesions tend to be permeated by infiltrating lymphocytes and that some genes involved in the cell-based immune response were also markedly up-regulated in the HPV-related tumors (pg. 1891, col 2, para 2, spanning pg. 1892).
Jung teaches finding that HPV is heterogeneously distributed and usually organized in clusters in samples from HPV-related HNSCC [using chromogenic in situ hybridization] (pg. 1891, col 2, para 1).
Jung does not explicitly teach that the overexpression of SYNGR3 is identified in one or more immune cells in the HNSCC.
Jung does not explicitly teach that the treatment stratification is directed to a de-escalation treatment protocol that reduces side effects.
Lyons partially rectifies the immune cell limitation by teaching single-cell RNA-Seq to overcome challenges presented by heterogeneity within a population by enabling the investigation of single cells in order to determine their phenotype and the significance of their differences (pg. 3, col 1, para 1), wherein single-cell analysis of tumor-infiltrating T cells can illustrate varying phenotypes of T cells to (Methods for gene expression profiling of immune cells, para 2).
Lyons teaches the importance of using the cancer immune phenotype to tailor therapy, wherein expression profiling of immune cells as an immune signature has demonstrated significant differences in overall survival in a variety of cancers (pg. 6, Conclusions).
Lyons teaches that it has been demonstrated that knowledge of the location and density of immune cells may be more prognostic than the TNM staging guidelines and the importance of incorporating immune response into the classification of disease (Clinical use of immune profiles, para 2). Lyons teaches determining response by evaluating immune cell populations from treated and untreated tumor samples (Abstract).
Lyons further teaches that the immune contexture of primary tumors has provided information that can be equally effective, and even superior, in predicting progression-free and overall survival in cancers comprising head and neck cancer, wherein the studies included those on head and neck cancers (Introduction, para 1). Lyons further teaches that gene signatures can be used to predict response to therapy by evaluating gene expression in immune system cells of tumor tissue (Introduction, para 2).
Porrello further rectifies the immune cell limitation by teaching immune cell subtype signatures, including a Th1 signature comprising SYNGR3 (Supplementary Data 7), developed based genes whose expression is strongly associated with specific immune cell types based on prior art (Modified immunome signature, para 1). Porello teaches applying this immunome signature in LUSC [lung cancer] samples to determine the level of different immune infiltrates (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1). Porello further teaches that immunogenomic approaches can be used to re-classify cancer subtypes (pg. 12, col 1, para 1), and that the scoring method of the signature has advantages over other methods in that it is unambiguous and sample can be relatively enriched with respect to the broadest range of immune cell types (from none to all) (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1).
Han rectifies the de-escalation limitation by teaching de-intensifying treatment toxicity by treating with surgery alone for HPV+ oral pharyngeal SCC [OPSCC, i.e., a subset of HNSCC] (pg. E424, col 2, para 4; see also pg. E434, col 1, para 1). Han teaches that a protocol of surgery alone has a possibility of a better QOL impact [i.e., reduced side effects associated with treatment] compared to definitive chemoradiation and adjuvant (chemo)radiation protocols, given that radiation and chemotherapy have long- term side effects that worsen QOL and function (pg. E434, col 1, para 1).
Han further teaches that patients who underwent primary surgery for OPSCC demonstrated a better quality of life and that primary surgical treatment has a comparable overall survival to primary chemoradiation (pg. E423, col 2, para 1).
Han teaches overall survival as an end point for analyzing the results of the protocol change (entire document, e.g., pg. E434, col 1, para 1-4, spanning col 2).
Therefore, would have been obvious to combine the method of Jung with the single cell RNA seq method of Lyons before the effective filing date. The artisan would have been motivated to do so to overcome the issues with heterogeneity taught by Jung and Lyons. There would have been a strong expectation of success as Porrello teaches expression of SYNGR3 in an immune cell type. Further, Jung and Lyons are directed to molecular markers in cancers.
Further, it would have been obvious to one of ordinary skill in the art before the effective filing date to treat subjects with a greater level of expression in a sample of one or more immune cells identified in the method of Jung in view of Lyons and Porrello with the surgery-only de-intensification protocol of Han. Such a substitution would have been motivated by the potential to reduce/eliminate side effects relative to the “definitive” standard-of-care protocols, as taught by Han. It likewise would have been obvious in view of Jung, Lyons that the treatments may be diagnosed by biomarkers correlated with HPV status in the tumor of the patient, motivated by improving patient prognosis by matching them a therapy they have enhanced sensitivity, as taught by Jung. There would have been a reasonable expectation of success as such are directed to molecular identifiers of cancer and/or cancer prognosis and represent the application of a known technique to a known method.
Regarding claim 9, in the method of Jung in view of Lyons and Porrello, Jung teaches further analyzing said samples for CDKN2A [i.e., the gene of p16] by qRT-PCR (pg. 1888, col 2, para 1; Supplemental Fig. 1; pg. 1883, Patients, para 1; pg. 1883, Tumor samples, para 1-2).
Jung teaches that HPV transcription discriminated samples with the selected deregulated genes [including SYNGR3 and CDKN2A] better than the sole presence of the HPV DNA (pg. 1888, col 2, para 1).
Thus, Jung further teaches assessing p16 expression in the HNSCC tumor in the method of diagnosing.
Regarding claim 10, Jung teaches:
determining a SYNGR3 status of a subject based on a level of SYNGR3 (Supplemental Fig. 1; pg. 1888, col 1, para 2; pg. 1888, col 2, para 1) and a p16 status based on a level of p16 gene [i.e., CDKN2A] expression in the tumor of the subject (Supplemental Fig. 1; pg. 1888, col 1, para 2; pg. 1888, col 2, para 1);
use of differentially expressed genes [i.e., SYNGR3 and CDKN2A] as biomarkers for HPV-positive HNSCC (pg. 1883, col 1, para 1; pg. 1888, col 2, para 1-2); and
stratifying patients based on HPV presence and discriminating HNSCC patients into appropriate treatment subgroups based on biomarkers (pg. 1882, col 2, para 2, spanning pg. 1883; pg. 1893, col 1, para 1, spanning col 2) and treating with surgery alone, with surgery and postoperative adjuvant radiotherapy, and with surgery and postoperative adjuvant chemoradiotherapy (pg. 1883, Tumor samples, para 2).
Jung further teaches that pathological observations have shown that HPV-positive lesions tend to be permeated by infiltrating lymphocytes and that some genes involved in the cell-based immune response were also markedly up-regulated in the HPV-related tumors (pg. 1891, col 2, para 2, spanning pg. 1892).
Jung further teaches finding that HPV is heterogeneously distributed and usually organized in clusters in samples from HPV-related HNSCC [using chromogenic in situ hybridization] (pg. 1891, col 2, para 1).
Jung does not explicitly teach that the overexpression of SYNGR3 is identified in one or more immune cells in the HNSCC.
Jung does not explicitly teach that the treatment stratification is directed to a de-escalation treatment protocol that reduces side effects.
Lyons partially rectifies the immune cell limitation by teaching single-cell RNA-Seq to overcome challenges presented by heterogeneity within a population by enabling the investigation of single cells in order to determine their phenotype and the significance of their differences (pg. 3, col 1, para 1), wherein single-cell analysis of tumor-infiltrating T cells can illustrate varying phenotypes of T cells to (Methods for gene expression profiling of immune cells, para 2).
Lyons teaches the importance of using the cancer immune phenotype to tailor therapy, wherein expression profiling of immune cells as an immune signature has demonstrated significant differences in overall survival in a variety of cancers (pg. 6, Conclusions).
Lyons teaches that it has been demonstrated that knowledge of the location and density of immune cells may be more prognostic than the TNM staging guidelines and the importance of incorporating immune response into the classification of disease (Clinical use of immune profiles, para 2). Lyons teaches determining response by evaluating immune cell populations from treated and untreated tumor samples (Abstract).
Lyons further teaches that the immune contexture of primary tumors has provided information that can be equally effective, and even superior, in predicting progression-free and overall survival in cancers comprising head and neck cancer, wherein the studies included those on head and neck cancers (Introduction, para 1). Lyons further teaches that gene signatures can be used to predict response to therapy by evaluating gene expression in immune system cells of tumor tissue (Introduction, para 2).
Porrello further rectifies the immune cell limitation by teaching immune cell subtype signatures, including a Th1 signature comprising SYNGR3 (Supplementary Data 7), developed based genes whose expression is strongly associated with specific immune cell types based on prior art (Modified immunome signature, para 1). Porello teaches applying this immunome signature in LUSC [lung cancer] samples to determine the level of different immune infiltrates (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1). Porello further teaches that immunogenomic approaches can be used to re-classify cancer subtypes (pg. 12, col 1, para 1), and that the scoring method of the signature has advantages over other methods in that it is unambiguous and sample can be relatively enriched with respect to the broadest range of immune cell types (from none to all) (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1).
Han rectifies the de-escalation limitation by teaching de-intensifying treatment toxicity by treating with surgery alone (instant claim 12) for HPV+ oral pharyngeal SCC [OPSCC, i.e., a subset of HNSCC] (pg. E424, col 2, para 4; see also pg. E434, col 1, para 1). Han teaches that a protocol of surgery alone has a possibility of a better QOL impact [i.e., reduced side effects associated with treatment] compared to definitive chemoradiation and adjuvant (chemo)radiation protocols, given that radiation and chemotherapy have long- term side effects that worsen QOL and function (pg. E434, col 1, para 1).
Han further teaches that patients who underwent primary surgery for OPSCC demonstrated a better quality of life and that primary surgical treatment has a comparable overall survival to primary chemoradiation (pg. E423, col 2, para 1).
Han teaches overall survival as an end point for analyzing the results of the protocol change (entire document, e.g., pg. E434, col 1, para 1-4, spanning col 2).
Therefore, would have been obvious to combine the method of Jung with the single cell RNA seq method of Lyons before the effective filing date. The artisan would have been motivated to do so to overcome the issues with heterogeneity taught by Jung and Lyons. There would have been a strong expectation of success as Porrello teaches expression of SYNGR3 in an immune cell type. Further, Jung and Lyons are directed to molecular markers in cancers.
Further, it would have been obvious to one of ordinary skill in the art before the effective filing date to treat subjects with a greater level of expression in a sample of one or more immune cells identified in the method of Jung in view of Lyons and Porrello with the surgery-only de-intensification protocol of Han. Such a substitution would have been motivated by the potential to reduce/eliminate side effects relative to the “definitive” standard-of-care protocols, as taught by Han. It likewise would have been obvious in view of Jung, Lyons that the treatments may be diagnosed by biomarkers correlated with HPV status in the tumor of the patient, motivated by improving patient prognosis by matching them a therapy they have enhanced sensitivity, as taught by Jung. There would have been a reasonable expectation of success as such are directed to molecular identifiers of cancer and/or cancer prognosis and represent the application of a known technique to a known method.
Regarding claim 9, in the method of Jung in view of Lyons and Porrello, Jung teaches further analyzing said samples for CDKN2A [i.e., the gene of p16] by qRT-PCR (pg. 1888, col 2, para 1; Supplemental Fig. 1; pg. 1883, Patients, para 1; pg. 1883, Tumor samples, para 1-2).
Jung teaches that HPV transcription discriminated samples with the selected deregulated genes [including SYNGR3 and CDKN2A] better than the sole presence of the HPV DNA (pg. 1888, col 2, para 1).
Thus, Jung further teaches assessing p16 expression in the HNSCC tumor in the method of diagnosing.
Regarding claim 11, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches that the presence of the HPV genome was also assessed by a chromogenic in situ [hybridization] colorimetric approach using HPV16-specific oligonucleotide probes (pg. 1886, Chromogenic in situ hybridization (CISH), para 1). Jung further teaches that HPV transcription discriminated samples with the selected deregulated genes better than the sole presence of the HPV DNA (pg. 1888, col 2, para 1).
Jung further teaches that CISH enables visualization of HPV heterogeneity in the tumor sample (Fig. 1 a and b; pg. 1886, Chromogenic in situ hybridization (CISH), para 1).
Therefore, it would have been prima facie obvious to improve the ability to distinguish HPV-positive HNSCC subjects by employing CISH for HPV16 as taught by Jung in the method of Jung in view of Lyons and Porrello, in order to visualize the heterogeneity of the HPV distribution in an in situ context. There would have been a strong expectation of success as Jung teaches the necessary methods for CISH.
Regarding claim 13, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches quantifying the SYNGR3 level by qRT-PCR of HPV+ and HPV- [i.e., control] subjects and comparing the levels (Supplementary Fig. 1; pg. 1888, col 2, para 1).
Regarding claim 14, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches comparing HPV+ samples to HPV- samples (Supplementary Fig. 1; pg. 1888, col 2, para 1), wherein a control subject may be interpreted to be a reference sample, absent a limiting definition of “reference sample” in the instant specification. See also MPEP 2111.
Regarding claims 15-17, Jung teaches collecting tumor samples from patients treated for primary head and neck tumors, wherein all tumors were squamous cell carcinomas (pg. 1883, Patients, para 1; pg. 1883, Tumor Samples, para 1). Jung teaches detecting a level of expression of SYNGR3 by qRT-PCR [i.e., gene product is mRNA], wherein HPV+ samples are compared to a median of the HPV- samples [i.e., a reference level] (pg. 1888, col 2, para 1; Supplementary Fig. 1; instant claim 17).
Jung further teaches that HPV transcription discriminated samples with the selected deregulated genes [including SYNGR3] better than the sole presence of the HPV DNA (pg. 1888, col 2, para 1). Jung teaches that increased SYNGR3 expression is correlated with actively transcribing HPV infected tumors (HPV RNA+) when compared to HPV DNA- RNA- tumors [i.e., control/reference samples] (Supplemental Figure 1).
Jung teaches that HPV presence should be considered as a stratification factor [for chemotherapy and radiation], wherein reliable biomarkers are required to discriminate this subgroup of HNSCC patients for appropriate specific treatment (pg. 1882, col 2, para 1, spanning pg. 1883). Jung teaches that reliable biomarkers of a transcriptionally active HPV could be considered as alternative or additional indicators of HPV-related tumorigenesis (pg. 1893, col 1, para 1, spanning col 2), wherein SYNGR3 expression is correlated with transcriptional activity of HPV (Supplemental Figure 1C). Jung teaches treating with surgery alone, with surgery and postoperative adjuvant radiotherapy, and with surgery and postoperative adjuvant chemoradiotherapy (pg. 1883, Tumor samples, para 2).
Therefore, Jung teaches use of SYNGR3 as a biomarker for stratification of patients [i.e., diagnosis], stratification of patients in to HNSCC subgroups for the purpose of treating with different therapies, and treating patients with therapies including the standard-of-care, i.e., a protocol for patients with HPV-positive HNSCC.
Jung further teaches that pathological observations have shown that HPV-positive lesions tend to be permeated by infiltrating lymphocytes and that some genes involved in the cell-based immune response were also markedly up-regulated in the HPV-related tumors (pg. 1891, col 2, para 2, spanning pg. 1892).
Jung teaches that HPV-related HNSCC correlates with improved prognosis and that this more favorable outcome may be partly explained by enhanced sensitivity to chemotherapy and radiations (pg. 1882, para 2, spanning pg. 1883).
Jung teaches finding that HPV is heterogeneously distributed and usually organized in clusters in samples from HPV-related HNSCC [using chromogenic in situ hybridization] (pg. 1891, col 2, para 1).
Jung does not explicitly teach that the sample of Jung comprises one or more immune cells or that the SYNGR3 is detected in the one or more immune cells.
Jung does not explicitly teach that the treatment stratification is directed to a de-escalation treatment protocol that reduces side effects.
Lyons partially rectifies the immune cell limitation by teaching single-cell RNA-Seq to overcome challenges presented by heterogeneity within a population by enabling the investigation of single cells in order to determine their phenotype and the significance of their differences (pg. 3, col 1, para 1), wherein single-cell analysis of tumor-infiltrating T cells can illustrate varying phenotypes of T cells to (Methods for gene expression profiling of immune cells, para 2).
Lyons teaches the importance of using the cancer immune phenotype to tailor therapy, wherein expression profiling of immune cells as an immune signature has demonstrated significant differences in overall survival in a variety of cancers (pg. 6, Conclusions).
Lyons teaches that it has been demonstrated that knowledge of the location and density of immune cells may be more prognostic than the TNM staging guidelines and the importance of incorporating immune response into the classification of disease (Clinical use of immune profiles, para 2). Lyons teaches determining response by evaluating immune cell populations from treated and untreated tumor samples (Abstract).
Lyons further teaches that the immune contexture of primary tumors has provided information that can be equally effective, and even superior, in predicting progression-free and overall survival in cancers comprising head and neck cancer, wherein the studies included those on head and neck cancers (Introduction, para 1). Lyons further teaches that gene signatures can be used to predict response to therapy by evaluating gene expression in immune system cells of tumor tissue (Introduction, para 2).
Porrello further rectifies the immune cell limitation by teaching immune cell subtype signatures, including a Th1 signature comprising SYNGR3 (Supplementary Data 7), developed based genes whose expression is strongly associated with specific immune cell types based on prior art (Modified immunome signature, para 1). Porello teaches applying this immunome signature in LUSC [lung cancer] samples to determine the level of different immune infiltrates (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1). Porello further teaches that immunogenomic approaches can be used to re-classify cancer subtypes (pg. 12, col 1, para 1), and that the scoring method of the signature has advantages over other methods in that it is unambiguous and sample can be relatively enriched with respect to the broadest range of immune cell types (from none to all) (pg. 15, Analysis of the immune cell types: scoring of different infiltrates, para 1).
Han rectifies the de-escalation limitation by teaching de-intensifying treatment toxicity by treating with surgery alone (instant claim 16) for HPV+ oral pharyngeal SCC [OPSCC, i.e., a subset of HNSCC] (pg. E424, col 2, para 4; see also pg. E434, col 1, para 1). Han teaches that a protocol of surgery alone has a possibility of a better QOL impact [i.e., reduced side effects associated with treatment] compared to definitive chemoradiation and adjuvant (chemo)radiation protocols, given that radiation and chemotherapy have long- term side effects that worsen QOL and function (pg. E434, col 1, para 1).
Han further teaches that patients who underwent primary surgery for OPSCC demonstrated a better quality of life and that primary surgical treatment has a comparable overall survival to primary chemoradiation (pg. E423, col 2, para 1).
Han teaches overall survival as an end point for analyzing the results of the protocol change (entire document, e.g., pg. E434, col 1, para 1-4, spanning col 2).
Therefore, would have been obvious to combine the method of Jung with the single cell RNA seq method of Lyons before the effective filing date. The artisan would have been motivated to do so to overcome the issues with heterogeneity taught by Jung and Lyons. There would have been a strong expectation of success as Porrello teaches expression of SYNGR3 in an immune cell type. Further, Jung and Lyons are directed to molecular markers in cancers.
Further, it would have been obvious to one of ordinary skill in the art before the effective filing date to treat subjects with a greater level of expression in a sample of one or more immune cells identified in the method of Jung in view of Lyons and Porrello with the surgery-only de-intensification protocol of Han. Such a substitution would have been motivated by the potential to reduce/eliminate side effects relative to the “definitive” standard-of-care protocols, as taught by Han. It likewise would have been obvious in view of Jung, Lyons that the treatments may be diagnosed by biomarkers correlated with HPV status in the tumor of the patient, motivated by improving patient prognosis by matching them a therapy they have enhanced sensitivity, as taught by Jung. There would have been a reasonable expectation of success as such are directed to molecular identifiers of cancer and/or cancer prognosis and represent the application of a known technique to a known method.
Regarding claim 18, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches detecting a level of expression of CDKN2A [i.e., the gene of p16] in the sample using an Affymetrix microarray pg. 1887, Transcriptome analysis, para 1, spanning pg. 1888) and qRT-PCR (pg. 1888, col 2, para 1; Supplemental Fig. 1), comparing HPV+ lesions from HNSCC patients to HPV- [i.e., control] lesions, wherein a median level of the HPV- lesions is determined [i.e., a reference level], and identifying p16 overexpression (pg. 1888, col 1, para 1; Supporting Information, Table 1; pg. 1888, col 2, para 1; Supplemental Fig. 1).
Jung teaches stratifying according to HPV-DNA status (pg. 1888, col 2, para 1; Supplemental Fig. 1). Jung further teaches that HPV transcription discriminated samples with the selected deregulated genes better than the sole presence of the HPV DNA (pg. 1888, col 2, para 1).
Thus, Jung further teaches detecting a level of expression of a p16 gene in the sample, comparing said level to controls, and discriminating samples [i.e., diagnosing a subject] based on the level of expression of biomarkers comprising SYNGR3 and p16.
Regarding claim 20, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches quantifying SYNGR3 using qRT-PCR in HPV+ samples (pg. 1888, col 2, para 1; Supplemental Fig. 1) and comparing the quantified expression level to the median of the HPV- samples [i.e., a reference level] of the SYNGR3 expression level (Supplemental Fig. 1).
Regarding claim 21, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches performing HPV in situ hybridization on the samples (pg. 1884, Chromogenic in situ hybridation [sic], para 1; Fig. 1).
Claim 5 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Jung (Jung AC, et al. Biological and clinical relevance of transcriptionally active human papillomavirus (HPV) infection in oropharynx squamous cell carcinoma. Int J Cancer. 2010 Apr 15;126(8):1882-1894), Lyons (Lyons YA, et al. Immune cell profiling in cancer: molecular approaches to cell-specific identification. NPJ Precis Oncol. 2017 Aug 15;1(1):26.), and Porrello (Porrello A et al. Factor XIIIA-expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking. Nat Commun. 2018 May 18;9(1):1988; as cited in the IDS dated 06/12/2023), and Han (Han M, et al. Predictors of Mortality in HPV-Associated Oropharynx Carcinoma Treated With Surgery Alone. Laryngoscope. 2020 Jul;130(7):E423-E435) as applied to claim 1 above, and further in view of De Keukeleire (De Keukeleire SJ, et al. Immuno-Oncological Biomarkers for Squamous Cell Cancer of the Head and Neck: Current State of the Art and Future Perspectives. Cancers (Basel). 2021 Apr 4;13(7):1714).
Regarding claim 5, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches assessing the presence of the HPV genome through CISH (pg. 1886, Chromogenic in situ hybridization (CISH), para 1), but fails to teach detection of a gene expression/expression product with ISH or IHC.
De Keukeleire teaches detection of HPV through in situ hybridization or immunohistochemical techniques using P16 overexpression (pg. 5, 3.1.1. HPV/P16 Status, para 1, spanning pg. 6).
De Keukeleire further teaches P16 and/or HPV positivity in OPSCC is correlated with better response to radio- and chemotherapy, a more favorable OS and lower likelihood of relapse in comparison to OPSCC with negative P16 and/or HPV status (pg. 6, para 1). De Keukeleire teaches sensitivity and specificity rates for the marker (pg. 5, 3.1.1. HPV/P16 Status, para 1, spanning pg. 6)
Therefore, it would have been obvious in the method of Jung in view of Lyons and Porrello to further use either in situ hybridization or immunohistochemical techniques to assess overexpression of p16 as taught by De Keukeleire, motivated by the desire to be able improve the prediction of patient responses to treatments as taught by De Keukeleire. There would be a strong expectation of success as IHC and ISH of p16 is predictable as taught by De Keukeleire (i.e., the sensitivity and specificity rates are known).
Claim 19 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Jung (Jung AC, et al. Biological and clinical relevance of transcriptionally active human papillomavirus (HPV) infection in oropharynx squamous cell carcinoma. Int J Cancer. 2010 Apr 15;126(8):1882-1894), Lyons (Lyons YA, et al. Immune cell profiling in cancer: molecular approaches to cell-specific identification. NPJ Precis Oncol. 2017 Aug 15;1(1):26.), and Porrello (Porrello A et al. Factor XIIIA-expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking. Nat Commun. 2018 May 18;9(1):1988; as cited in the IDS dated 06/12/2023), and Han (Han M, et al. Predictors of Mortality in HPV-Associated Oropharynx Carcinoma Treated With Surgery Alone. Laryngoscope. 2020 Jul;130(7):E423-E435) as applied to claim 15 above, and further in view of De Keukeleire (De Keukeleire SJ, et al. Immuno-Oncological Biomarkers for Squamous Cell Cancer of the Head and Neck: Current State of the Art and Future Perspectives. Cancers (Basel). 2021 Apr 4;13(7):1714).
Regarding claim 19, in the method of Jung in view of Lyons, Porrello, and Han, Jung teaches assessing the presence of the HPV genome through CISH (pg. 1886, Chromogenic in situ hybridization (CISH), para 1), but fails to teach detection of a gene expression/expression product with ISH or IHC.
De Keukeleire teaches detection of HPV through in situ hybridization or immunohistochemical techniques using P16 overexpression (pg. 5, 3.1.1. HPV/P16 Status, para 1, spanning pg. 6).
De Keukeleire further teaches P16 and/or HPV positivity in OPSCC is correlated with better response to radio- and chemotherapy, a more favorable OS and lower likelihood of relapse in comparison to OPSCC with negative P16 and/or HPV status (pg. 6, para 1). De Keukeleire teaches sensitivity and specificity rates for the marker (pg. 5, 3.1.1. HPV/P16 Status, para 1, spanning pg. 6)
Therefore, it would have been obvious in the method of Jung in view of Lyons and Porrello to further use either in situ hybridization or immunohistochemical techniques to assess overexpression of p16 as taught by De Keukeleire, motivated by the desire to be able improve the prediction of patient responses to treatments as taught by De Keukeleire. There would be a strong expectation of success as IHC and ISH of p16 is predictable as taught by De Keukeleire (i.e., the sensitivity and specificity rates are known).
Response to Arguments
Applicant’s arguments, see pg. 14-17, filed 09/02/2025, with respect to the rejection(s) of claim(s) 1-21 under 103 regarding the lack of teaching of the de-escalating protocol in the amended claims have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Han (2019).
Applicant's remaining arguments filed 09/02/2025 have been fully considered but they are not persuasive.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
In the instant case, while Jung does not explicitly teach detecting SYNGR3 in the one or more immune cells as claimed, Jung does teach detecting SYNGR3 in a bulk sample from HPV+ HNSCC tumors and that HPV-positive lesions tend to be permeated by infiltrating lymphocytes, and other elevated genes reflective of an inflammatory response in the stromal microenvironment (Jung, pg. 1891, col 2, para 2, spanning pg. 1892). In view of the teachings of Lyons and Porrello, as discussed in further detail in the 103 rejection above, it would have been obvious to analyze the immune cells of the samples of Jung to address the issue of the heterogenous distribution of HPV discussed in Jung with the method of Lyons, wherein Porrello teaches SYNGR3 is a marker of a type of infiltrating lymphocyte in tumors (TILs). Thus, it would be expected that SYNGR3—known to be elevated in HNSCC and a marker of a type of TILs—would be increased in a subset of an HNSCC sample comprising of immune cells from an HPV+ HNSCC tumor in which the level of SYNGR3 is detected relative to a control/reference with lower TILs.
Given, then, that Jung teaches that HPV presence should be considered as a stratification factor for treatment (pg. 1882, col 2, para 1, spanning pg. 1883) and that RNA expression is relevant to HPV-positive patient’s clinical outcomes, wherein reliable biomarkers of transcriptionally active HPV (of which SYNGR3 and the gene of p16 are among the top correlated; see Supplementary Fig. 1) could be considered as indicators (pg. 1893, col 1, para 1), and the combination with Lyons and Porrello that addresses the heterogeneity to improve the assay for HPV+ HNSCC diagnosis, in view of Han’s teaching of treating HPV+ HNSCC subtypes with surgery-only de-intensified [i.e., de-escalating protocol] treatment motivated by the desire to reduce/eliminate the taught side effects, all limitations would have been obvious in the combined invention before the effective filing date.
It is further noted that while Porrello does not teach HNSCC, the artisan would reasonably expect the expression markers of tumor infiltrating leukocytes to be applicable to a wide variety of solid tumor types. Indeed, the Applicant utilizes the “Immunome” signature of Porrello in their analysis of HNSCC (pg. 39, para 1).
For these reasons, the arguments are not found persuasive.
Conclusion
No claims are 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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/EMMA R HOPPE/Examiner, Art Unit 1683
/NANCY J LEITH/Primary Examiner, Art Unit 1636