Abstract 555: Longitudinal exome-scale liquid biopsy monitoring of evolving therapeutic resistance mechanisms in head and neck squamous cell carcinoma patients receiving anti-PD-1 therapy
Authors: Abbott Charles W. , Bedi Nikita , Zhang Simo V. , Northcott Josette , LI Robin , Pyke Rachel Marty , Levy Eric , Chernock Rebecca , Mansour Mena , Colevas A. Dimitrios , Lyle John , Sunwoo John B. , Boyle Sean , Chen Richard 
Published: July 2021

Background Typical liquid biopsy panels capture a relatively small number of variants, and likely under-represent the heterogeneity of resistance in late-stage cancers. This reduced scope can result in overlooked therapeutic biomarkers which respond dynamically to treatment, as well as potentially missed resistance mechanisms and pathway-level events. To address the challenges associated with identifying multiple concurrent heterogeneous resistance mechanisms in individual patients, we evaluated longitudinal whole exome sequencing of cell free DNA (cfDNA) and solid tumor biopsies from head and neck squamous cell carcinoma (HNSCC) patients that received anti-PD1 therapy. Using this approach, we identified evolving variant and pathway-level resistance mechanisms in cfDNA, as a complement to tumor biopsy derived information, and identified differences in putative neoantigens found in tissue and cfDNA.

Methods Pre- and post-intervention matched tumor, normal and plasma samples were obtained from a pilot cohort of 13 patients with HNSCC. Following baseline sample collection, all patients received a single dose of nivolumab. The primary tumor was then resected, approximately one month later when possible, or a second biopsy was collected where resection was impractical. Paired tumor and normal samples were profiled using ImmunoID NeXTTM, an augmented exome/transcriptome platform and analysis pipeline. Exome-scale cfDNA profiling of matched plasma samples was performed using the NeXT Liquid BiopsyTM platform to detect somatic variants. Data from these two platforms were then compared with corresponding clinical findings.

Results We observed a rapid evolution of the tumor microenvironment and disease mutation profile following therapy, with strong concordance detected between plasma and tumor variants at each timepoint. Post-therapy interrogation of cfDNA revealed dynamic changes in numerous oncogenes and clinically relevant pathways, such as ERK1/2 and MAPK, that were not observed in solid tumor. These findings suggest that single-lesion biopsy of the primary tumor misses co-occurring, clinically relevant resistance alterations. Median post-treatment neoantigen count was reduced in solid tumor, but increased in cfDNA. HLA-specific loss of heterozygosity (LOH) was identified in a number of subjects, likely resulting in reduced neoepitope presentation in those cases.

Conclusions Exome-wide somatic events were reliably detected in cfDNA, providing additional potential biomarkers to complement those identified in solid tumor. As we increase our cohort size, we expect that identification of biomarkers from both exome scale tissue biopsy and cfDNA will provide a more comprehensive view into therapeutic response and resistance mechanisms in HNSCC patients missed with typical liquid biopsy panels.

Citation Format: Charles W. Abbott, Nikita Bedi, Simo V. Zhang, Josette Northcott, Robin LI, Rachel Marty Pyke, Eric Levy, Rebecca Chernock, Mena Mansour, A. Dimitrios Colevas, John Lyle, John B. Sunwoo, Sean Boyle, Richard Chen. Longitudinal exome-scale liquid biopsy monitoring of evolving therapeutic resistance mechanisms in head and neck squamous cell carcinoma patients receiving anti-PD-1 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 555.