Using Whole-Genome Analysis on Cancer Tissue of Patients With Platinum-refractory Head and Neck Squamous Cell Carcinoma Who Underwent Nivolumab to Precisely Predict Responders: An Observational Biomarker Study

1-1 PD-1 pathway as a novel and effective pathway in cancer treatment The programmed death 1 (PD-1) receptor, which is expressed on activated T cells, is engaged by ligands PD-L1 and PD-L2, which are expressed by tumor cells and infiltrating immune cells 1. Tumor PD-L1 expression is commonly seen in a broad spectrum of cancers, and the interaction between PD-1 and PD-L1, PD-L2 ligands inhibits T-cell activation and promotes tumor immune escape (i.e., the mechanism by which tumor cells escape recognition and elimination by the immune system) 2, 3. Immune checkpoint inhibitors (ICI) developed on the basis of the above mechanism have shown their success with good treatment efficacy in patients with melanoma4-8, lung cancer3, 7, 9-21, and renal cell carcinoma12, 22-24 to date. Owing to the mechanism of targeting probably very common pathways of cancer (PD-1 pathway), ICIs seems to be equally effective in a wide range of cancers with a similar response rate of 20-30% 25, which indicates a common immune defect on PD-1 pathway exists amongst the various type of cancer.

1-2 Subpopulation selection could possibly contribute better efficacy Recently, two PD1 inhibitors, Nivolumab and Pembrolizumab, showed their different results in large-scale clinical trials 11, 14. Subpopulation selection strategies in these 2 trials have been widely considered as one of the major reasons. A precise selection of patients with the best response is critically warranted and a truly unmet need, given PD-L1 cannot clearly stratify patients who will benefit most from Nivolumab.

1-3 No available biomarkers to predict severe irAEs is an unmet need Another problem is that all ICIs have occasionally severe and sometimes life-threatening immune-related adverse events (irAEs). At present, no good biomarker is available to predict such irAEs. It is imperative to identify the biomarkers that can predict the risk of severe irAEs 25.

1-4 NGS technology could probably provide solutions to the above 2 problems Next-generation sequencing (NGS) technology has been introduced in recent years (Fig. 1), and allows the analysis of genomes, including those representing disease states 26, 27. Generally speaking, there are three NGS approaches to improve diagnostics for cancer gene mutations: (1) targeted enrichment of a set of genes (gene panel), (2) whole-exome sequencing (WES), and (3) whole-genome sequencing (WGS) 28. When comparing the three options, it is clear that-theoretically-WGS is the superior approach as it will produce the most complete data set on an individual's genome (Table 1)28. A recent study 29 concluded that WGS offers significant advantages of (a) more coverage of the exome, (b) detection of intronic variants, and (c) calling of all structural variants, including single exon deletions; however, the costs and testing time limited the routine use of WGS. In brief, WGS for cancer patients before treatment could most possibly help to select patients with specific signature(s) to receive specific treatment in a manner of precision medicine 30-37.

1-5 Host immunity (inherent, host) and Cancer (somatic, acquired) interaction could only be seen in whole genome analysis By means of WGS, we could approach the question of how to identify the responders from Nivolumab in the direction of "cancer part (somatic)" conventionally. In another way, we could also approach this question by "host part", which is also the advantages of WGS testing.