T cell repertoire in peripheral blood as a potential biomarker for predicting response to concurrent cetuximab and nivolumab in head and neck squamous cell carcinoma

Xuefeng Wang, Jameel Muzaffar, Kedar Kirtane, Feifei Song, Matthew Johnson, Michael J Schell, Jiannong Li, Sean J Yoder, Jose R Conejo-Garcia, Jose A Guevara-Patino, Marcelo Bonomi, Priyanka Bhateja, James W Rocco, Conor E Steuer, Nabil F Saba, Christine H Chung, Xuefeng Wang, Jameel Muzaffar, Kedar Kirtane, Feifei Song, Matthew Johnson, Michael J Schell, Jiannong Li, Sean J Yoder, Jose R Conejo-Garcia, Jose A Guevara-Patino, Marcelo Bonomi, Priyanka Bhateja, James W Rocco, Conor E Steuer, Nabil F Saba, Christine H Chung

Abstract

Background: T cell receptor (TCR) signaling profile is a fundamental property that underpins both adaptive and innate immunity in the host. Despite its potential clinical relevance, the TCR repertoire in peripheral blood has not been thoroughly explored for its value as an immunotherapy efficacy biomarker in head and neck squamous cell carcinoma (HNSCC). The purpose of the present study is to characterize and compare the TCR repertoire in peripheral blood mononuclear cells (PBMC) from patients with HNSCC treated with the combination of cetuximab and nivolumab.

Methods: We used the immunoSEQ assay to sequence the TCR beta (TCR-B) chain repertoire from serially obtained PBMC at baseline and during the treatments from a total of 41 patients who received the combination (NCT03370276). Key TCR repertoire metrics, including diversity and clonality, were calculated and compared between patients with different therapy responses and clinical characteristics (eg, human papillomavirus (HPV) status and smoking history). Patient survival outcomes were compared according to patient groups stratified by the TCR-B clonotyping. To confirm the observed patterns in TCR spectrum, samples from patients who achieved complete response (CR) and partial response (PR) were further profiled with the immunoSEQ deep resolution assay.

Results: Our data indicated that the patients who achieved CR and PR had an increased TCR sequence diversity in their baseline samples, this tendency being more pronounced in HPV-negative patients or those with a smoking history. Notably, the CR/PR group had the lowest proportion of patients with oligoclonal TCR clones (2 out of 8 patients), followed by the stable disease group (9 out of 20 patients) and lastly the progressive disease group (7 out of 10 patients). An overall trend toward favorable patient survival was also observed in the polyclonal group. Finally, we reported the shared TCR clones across patients within the same response group, as well as the shared clones by aligning immunoSEQ reads with TCR data retrieved from The Cancer Genome Atlas- head and neck squamous cell carcinoma (TCGA-HNSC) cohort.

Conclusions: Our data suggest that, despite the great clinical heterogeneity of HNSCC and the limited responders in the present cohort, the peripheral TCR repertoires from pretreatment PBMC may be developed as biomarkers for the benefit of immunotherapy in HNSCC.

Keywords: head and neck neoplasms; immunotherapy.

Conflict of interest statement

Competing interests: CHC—honoraria from Bristol Myers Squibb, CUE, Sanofi, Mirati, Merck, and Exelixis for ad hoc Scientific Advisory Board participation. CS—honoraria from Armo, Bergen Bio, AbbVie, and Lilly Oncology for ad hoc Scientific Advisory Board participation. NS—honoraria from Pfizer, Merck, Aduro, Rakuten, CUE, and Blupoint, Eisai, AstraZeneca, WebMD, Mirati, Reach MD, Vaccinex, Kura, Biontech, GSK, Aduro, Pfizer for ad hoc Scientific Advisory Board or Data Safety Monitoring Committee and research funding Bristol Myers Squibb and Exelixis. JRCG—Honorarium from Alloy Therapeutics and Anixa Biosciences; stock options in Alloy Therapeutics, Anixa Biosciences and Compass Therapeutics; intellectual property with Anixa Biosciences and Compass Therapeutics; sponsored research supported by Anixa Biosciences.The other authors do not have conflict of interest to declare.

© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.

Figures

Figure 1
Figure 1
Patients with CR/PR have a less oligoclonal peripheral TCR expansion (higher TCR diversity) prior to the combination therapy. (A) Flowchart of PBMC sample selection for the survey and deep immunoSEQ TCR-B assay. (B) Distribution of four clonotype groups in the CR and PR patient group (defined based on relative abundance of the clone sequences). (C) Distribution of four clonotype groups in the PD patient group. (D) The proportion of patients with oligoclonal (the combined proportion of large and hyperexpanded clonotypes >25%) sequences in each response group. (E) Comparison of clonotype spectrums estimated from the survey and the follow-up DeepTCR-B sequencing based on matched CR/PR baseline PBMC samples. (F) Comparison of estimated clonotype frequencies of top clonotype groups from the survey and the follow-up deep and TCR-B sequencing. CR, complete response; HNSCC, head and neck squamous cell carcinoma; PBMC, peripheral blood mononuclear cells; PD, progressive disease; PR, partial response; SD, stable disease; TCR-B, TCR beta; TCR, T cell receptor.
Figure 2
Figure 2
The pretreatment peripheral TCR clonotyping is prognostic for overall survival. (A–C) Kaplan-Meier survival curves comparing patients with oligoclonal and polyclonal TCR repertories in (A) all patients; (B) HPV-negative patients and (C) who are ever smokers. (D) Summary of results from the Cox proportional hazards regression model (to test the association with clonotyping and overall survival) by adjusting age, smoking, productive templates. HPV, human papillomavirus; IHC, immunohistochemistry; TCR, T cell receptor.
Figure 3
Figure 3
Association between TCR repertoire diversity in baseline PBMC and clinical outcomes of patients with HNSCC. (A) The CR/PR patients have the lowest productive Simpson Clonality score, followed by SD and PD. (B) The never smoked patients with HNSCC show significantly lower productive Simpson clonality (p=0.015) in contrast to ever smokers. (C) The further stratification by HPV status shows the similar pattern of diversity discrepancy driven by smoking status. CR, complete response; HNSCC, head and neck squamous cell carcinoma; HPV, human papillomavirus; PBMC, peripheral blood mononuclear cells; PD, progressive disease; PR, partial response; SD, stable disease; TCR, T cell receptor.
Figure 4
Figure 4
The combination therapy induces clonotype modulation in CR patients, represented by the top clonotype profiles. (A–C) Tracking the relative abundance (estimated from DeepTCR) of top 10 most abundant clonotypes in three patients in CR: (A) MCC014(A), (B) MCC069, and (C) MCC055. (D) The density distribution of TCR aa sequences under positive and negative selection after the combination therapy. The log2FC (fold-change) is calculated by log2 transformation of clonotype (relative) frequency fold-change between EOT and pretreatment time points. CR, complete response; EOT, end of treatment; TCR, T cell receptor.
Figure 5
Figure 5
The GIANA clustering analysis revealed shared clonotypes across responder patients. (A) The clonotype clustering analysis of all HPV-negative responders (CR/PR) based on the distance calculated from the software GIANA. Sequences of special interest are marked with an asterisk (*). (B) The combined GIANA clustering reveals shared clones between peripheral TCR repertoires of CR patients and tumor samples from TCGA-HNSC. (C) The sequence logo plot shows the amino acid pattern of all CDR3 reads in CP/PR patients matched to the sequences retrieved from TCGA-HNSC. CDR3, complementarity-determining region 3; CR, complete response; PR, partial response; TCR, T cell receptor.

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