Influence of tumor mutational burden, inflammatory gene expression profile, and PD-L1 expression on response to pembrolizumab in head and neck squamous cell carcinoma

Robert I Haddad, Tanguy Y Seiwert, Laura Q M Chow, Shilpa Gupta, Jared Weiss, Iris Gluck, Joseph P Eder, Barbara Burtness, Makoto Tahara, Bhumsuk Keam, Hyunseok Kang, Kei Muro, Andrew Albright, Robin Mogg, Mark Ayers, Lingkang Huang, Jared Lunceford, Razvan Cristescu, Jonathan Cheng, Ranee Mehra, Robert I Haddad, Tanguy Y Seiwert, Laura Q M Chow, Shilpa Gupta, Jared Weiss, Iris Gluck, Joseph P Eder, Barbara Burtness, Makoto Tahara, Bhumsuk Keam, Hyunseok Kang, Kei Muro, Andrew Albright, Robin Mogg, Mark Ayers, Lingkang Huang, Jared Lunceford, Razvan Cristescu, Jonathan Cheng, Ranee Mehra

Abstract

Background: To characterize genomic determinants of response to pembrolizumab in recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) in the KEYNOTE-012 study.

Methods: Associations between biomarkers (tumor mutational burden (TMB), neoantigen load (NL), 18-gene T-cell-inflamed gene expression profile (TcellinfGEP), and PD-L1 combined positive score (CPS)) and clinical outcomes with pembrolizumab were assessed in patients with R/M HNSCC (n=192). Tumor human papillomavirus (HPV) status was also evaluated with the use of p16 immunohistochemistry and whole exome sequencing (WES; HPV+, mapping >20 HPV reads) in pretreatment tumor samples (n=106).

Results: TMB, clonality-weighted TMB, and TcellinfGEP were significantly associated with objective response (p=0.0276, p=0.0201, and p=0.006, respectively), and a positive trend was observed between NL and PD-L1 CPS and clinical response (p=0.0550 and p=0.0682, respectively). No correlation was observed between TMB and TcellinfGEP (Spearman ρ=-0.026) or TMB and PD-L1 (Spearman ρ=0.009); a correlation was observed between TcellinfGEP and PD-L1 (Spearman ρ=0.511). HPV status by WES and p16 immunohistochemistry showed concordance (84% ҡ=0.573) among patients whose HPV results were available using both methods.

Conclusions: TMB and inflammatory biomarkers (TcellinfGEP and PD-L1) may represent distinct and complementary biomarkers predicting response to anti-programmed death 1 therapies in HNSCC; further study of these relationships in randomized clinical trials is needed.

Trial registration number: NCT01848834.

Keywords: gene expression profiling; head and neck neoplasms; immunotherapy; programmed cell death 1 receptor; tumor biomarkers.

Conflict of interest statement

Competing interests: RIH: research grant (to institution) from Merck; consultant/ad board member for Merck, BMS, Astra Zeneca, Pfizer, Genentech, Kura, Celgene, Eisai, Loxo, Immunomic, GSK, Gilead, Vaccinex, EMD Serono, BioNTech, Achilles; royalties from Up to Date; data safety monitoring board for Nanobiotix, ISA. TYS: grant (to institution) from Merck, Nanobiotix, Regeneron, Bristol Myers Squibb, AstraZeneca; honorarium from Merck, Nanobiotix, Regeneron, Innate Pharma, AstraZeneca, eTheRNA, Nektar. LQMC: grants from Merck, Lily/Imclone, Bristol Myers Squibb, AstraZeneca/MedImmune, Pfizer, Seattle Genetics, Dynavax, Alkermes, Novartis; personal fees from Merck, Pfizer, Dynavax, Synthrox, Alkermes, Cullinan, Elicio, Genentech, Novartis, Daiichi Sankyo, Gilead, Regeneron/Sanofi Genzyme. SG: consultant to Seattle Genetics. JW: research grant (to institution) from Merck; research grant from Merck, AstraZeneca, Celgene, G1; personal fees from AstraZeneca, EMD Serono, Genentech, Inivata, Celgene, G1, Jounce, AbbVie, Rakuten. IG: has nothing to disclose. JPE: has nothing to disclose. BB: grants from Merck, Bristol Myers Squibb, Fox Chase Cancer Center; personal fees from Merck, AstraZeneca, Fox Chase Cancer Center. MT: research grant from MSD, Ono Pharmaceutical, Bristol Myers Squibb, Bayer, Eisai, Merck Biopharma, Pfizer, Rakuten Medical, Novartis; personal fees from MSD, Ono Pharmaceutical, Bristol Myers Squibb, Bayer, Eisai, Merck Biopharma, LOXO, Pfizer, Celgene, Rakuten Medical, Amgen, Novartis. BK: grants from Ono Pharmaceutical, MSD Oncology, AstraZeneca; personal fees from MSD Oncology, AstraZeneca, Genexis, Handok. HK: research grant from Merck, Kura Oncology, Lilly, Exelixis, Elevar Therapeutics, Ayala Pharmaceuticals, Novartis; consulting for PIN Therapeutics, Mitoimmune; advisory board for Bayer, GlaxoSmithKline, Prelude Therapeutics, Achilles Therapeutics. KM: research grant from Solasio Pharma, Pfizer, Amgen, Daiichi Sankyo, Parexel International, MSD, Merck Serono; research grant and honorarium from Sanofi, Ono, Taiho, consulting and honorarium from Eli Lilly, Chugai, honorarium from Takeda, Bristol Myers Squibb, Bayer. AA: employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA and stockholder of Merck & Co., Inc., Kenilworth, NJ, USA. RM: employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA and stockholder of Merck & Co., Inc., Kenilworth, NJ, USA. MA: employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA and stockholder of Merck & Co., Inc., Kenilworth, NJ, USA; patent (US20180327848) issued for RNA Gene Signatures (inventor of 18-gene T-cell inflamed signature). LH: employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA and stockholder of Merck & Co., Inc., Kenilworth, NJ, USA. JL: employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA and stockholder of Merck & Co., Inc., Kenilworth, NJ, USA; patent (US20180327848) issued for RNA Gene Signatures (inventor of 18-gene T-cell inflamed signature). RC: employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA and stockholder of Merck & Co., Inc., Kenilworth, NJ, USA; patent pending for angiogenesis and mMDSC gene expression-based biomarker of tumor response to PD-1 antagonists (patent 2020/167619). JC: former employee of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA and stockholder of Merck & Co., Inc., Kenilworth, NJ, USA. RM: research grant from AstraZeneca, Merck; consulting/advisory board for Rakuten Medical.

© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

Figures

Figure 1
Figure 1
Association between biomarkers and response in the overall patient population. (A) TMB, (B) TMB weighted by clonality, (C) NL, (D) T-cell-inflamed GEP, and (E) PD-L1 CPS. CPS, combined positive score; CR, complete response; GEP, gene expression profile; NL, neoantigen load; NR, non-responder; PD-L1, programmed death ligand 1; PR, partial response; R, responder; TMB, tumor mutational burden.
Figure 2
Figure 2
AUROC curve by biomarker. AUROC, area under the receiver operating characteristic; CPS, combined positive score; GEP, gene expression profile; PD-L1, programmed death ligand 1; TMB, tumor mutational burden; WES, whole exome sequencing.
Figure 3
Figure 3
Association between biomarkers and PFS and OS in the overall patient population at prespecified cut-offs. (A) TMB and PFS, (B) TMB and OS, (C) T-cell-inflamed GEP and PFS, (D) T-cell-inflamed GEP and OS, (E) PD-L1 CPS and PFS, and (F) PD-L1 CPS and OS. CPS, combined positive score; GEP, gene expression profile; OS, overall survival; PD-L1, programmed death ligand 1; PFS, progression-free survival; TMB, tumor mutational burden.
Figure 4
Figure 4
Correlation between (A) TMB and T-cell-inflamed GEP or (B) TMB and PD-L1 CPS and the response rate (95% CI) of the dual biomarkers (C) TMB and PD-L1 CPS, (D) TMB and T-cell-inflamed GEP, and (E) T-cell-inflamed GEP and PD-L1 CPS in the overall patient population. Dashed horizontal lines represent clinically applicable TMB threshold of ≥175 mut/exome. Dashed vertical line represents discovery cut-off for the T-cell-inflamed GEP (≥−.318) selected through analysis of data across multiple tumor types or the PD-L1 cut-off of CPS 1. CPS, combined positive score; CR, complete response; GEP, gene expression profile; mut/exome, mutations/exome; NR, non-responder; PD-L1, programmed death ligand 1; PR, partial response; R, responder; TMB, tumor mutational burden.
Figure 5
Figure 5
Biomarker distribution by HPV status for (A) TMB, (B) T-cell-inflamed GEP, and (C) PD-L1 CPS. CPS, combined positive score; GEP, gene expression profile; HPV, human papillomavirus; TMB, tumor mutational burden; WES, whole exome sequencing.
Figure 6
Figure 6
Association between biomarkers and response by HPV status for (A) TMB, (B) T-cell-inflamed GEP, and (C) PD-L1. CPS, combined positive score; CR, complete response; GEP, gene expression profile, HPV, human papillomavirus; NR, non-responder; PD-L1, programmed death ligand 1; PR, partial response; R, responder; TMB, tumor mutational burden; WES, whole exome sequencing.

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