Frameshift events predict anti-PD-1/L1 response in head and neck cancer

Abstract

Programmed cell death protein 1 (PD-1) inhibitors have efficacy in treating squamous cell carcinoma of the head and neck (SCCHN), but objective response rates are low. PD-1 ligand (PD-L1) expression alone is not considered a robust predictor of response and additional biomarkers are needed. This 3-year observational cohort followed 126 SCCHN patients treated with anti-PD-1/L1 therapy. Prior to treatment, 81 (64%) had targeted massively parallel tumor sequencing. Of these, 42 (52%) underwent fluorescence-activated cell sorting and PD-L1 immunohistochemistry for tumor immunoprofiling. Six (5%) complete responses (CRs) and 11 (9%) partial responses (PRs) were observed. Those treated with prior chemotherapy (98, 78%) versus only surgery and/or radiation had longer overall survival (OS) (10 vs. 3 months, P = 0.02). Smokers had a higher total mutational burden (TMB) (P = 0.01). Virus-positive patients had a lower TMB (P < 0.01) and improved OS (P = 0.02). Among virus-negative responders, NOTCH1 and SMARCA4 were more frequently mutated and frameshift events in tumor suppressor genes occurred more frequently (P = 0.03). Higher TMB and CD8+ T cell infiltrates predicted anti-PD-1/L1 benefit (P < 0.01, P < 0.01, respectively) among virus-negative tumors. TIM-3/LAG-3 coexpression with PD-1 was higher on T cells among nonresponders (P = 0.03 and 0.02, respectively). Somatic frameshift events in tumor suppressor genes and higher TMB among virus-negative SCCHN tumors predict anti-PD-1/L1 response.

Keywords: Genetics; Head & neck cancer; Immunotherapy; Molecular genetics; Oncology.

Conflict of interest statement

Conflict of interest: GJH receives institutional research support from BMS and EMD Serono. JDS serves on the scientific advisory board for BMS, Debiopharm, Nanobiotix, and Astra Zeneca. JHL receives institutional research support from Bayer, BMS, Novartis, and Millennium. RIH receives institutional support and consults for BMS, Merck, Astra Zeneca, Pfizer, and Celgene in addition to consulting for Eisai and Genzyme, and is also a member of the National Comprehensive Cancer Network head and neck cancer panel. RU is on the scientific advisory board at Merck.

Figures

Figure 1. Correlating total mutational burden with response to PD-1/L1 blockade in SCCHN.

(A) Normalized total mutational burden (TMB) among tumor samples (n = 81) arranged from highest to lowest according to anti–PD-1/L1 response. A (+) denotes virus-positive disease. Responders show significantly increased TMB compared with nonresponders. HPV-negative patients with higher TMB demonstrate prolonged overall survival (OS). Greater TMB among (B) former or current (F/C) smokers compared with never (N) smokers, and (C) among patients with virus-mediated [HPV or EBV] disease. SCCHN, squamous cell carcinoma of the head and neck; CR, complete response; PR, partial response; SD, stable disease; PD, progressive disease; EBV, Epstein-Barr virus; HPV, human papillomavirus. Horizontal bars show median and 95% confidence intervals. Mann-Whitney U test, log-rank testing.

Figure 2. Genomic landscape among anti–PD-1/L1 responders in SCCHN.

(A) Genomic mutational landscape among anti–PD-1/L1 responders (n = 12) and those with SD (n = 20) using a targeted next-generation sequencing platform highlighting total mutational burden (TMB) grouped by high (red, > 10 mutations/Mb), medium (orange, 5–10 mutations/Mb), and low (blue, < 5 mutations/Mb). (B) Primary site of disease (key: top right), viral status (EBV+ or HPV+) and smoking status are shown. (C) The mutational plot shows somatic alterations in order of frequency (highest on top). Somatic mutation key: blue (missense), purple (nonsense), orange (in-frame or frameshift). SA, splice acceptor; SS, splice site; SR, splice region; P, promoter alteration. Only those alterations occurring in 3 or more tumor samples are included in the grid with the exception of genes involved in mismatch repair (MMR). (D) Mutational signatures are displayed (key: lower right). (E) Total indel count (TIC) per tumor sample. (F) Fraction of the genome that is copy-number altered. (G) Proportion of patients with key mutations by response. *P < 0.01 ( χ2 test, 2-sided). SCCHN, squamous cell carcinoma of the head and neck; UV, ultraviolet; CR, complete response; PR, partial response; SD, stable disease; OPC, oropharynx; OC, oral cavity; NPC, nasopharynx; LAR, larynx, hypopharynx; CUT, cutaneous; CUP, carcinoma of unknown primary; APOBEC, apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like.

Figure 3. Copy-number alteration events among anti–PD-1/L1 responders in SCCHN.

Copy-number variation (CNV) plot showing losses and gains in order of gene loci among those genes with the greatest frequency of alteration among the cohort (≥8 events). CNV key: light blue (single copy loss), dark blue (homozygous deletion), pink (low copy gain), red (amplification). SCCHN, squamous cell carcinoma of the head and neck; CR, complete response; PR, partial response; SD, stable disease.

Figure 4. Correlating immunophenotype with response among anti–PD-1/L1 treated patients with SCCHN.

(A) Increased tumor CD8+ T cell infiltration and PD-L1+ infiltrating monocytes among anti–PD-1/L1 responders. Matched PD-1+ CD8+ T cell component (light blue columns). A (+) indicates a virus-mediated tumor. PD-L1 tumor positivity (%) by immunohistochemistry (n = 42). (B) Immune cell phenotyping shows greater effector memory (EM) CD8+ T cells among anti–PD-1/L1 responders (n = 8). (C) Immune checkpoint coexpression appears increased among anti–PD-1/L1 nonresponders (n = 34). Horizontal bars reflect median and 95% confidence intervals. *P < 0.05 determined by Mann-Whitney test, Spearman’s ρ. SCCHN, squamous cell carcinoma of the head and neck; CM, central memory; CR, complete response; PR, partial response; SD, stable disease; PD, progressive disease.