Identification of therapeutic targets for Head and Neck Squamous Cell Carcinoma (HNSCC)


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Ahmad Malik1
1University of Toronto

Abstract

Background

Head and Neck Squamous Cell Carcinomas (HNSCC) are a major health problem with a five-year survival rate of less than 50%. The low survival rate is attributed to the relapse at the primary site or distal metastasis. Tumor-initiating cells (TICs), a small proportion of stem cell-like cells in the tumor, are thought to be the primary reason for relapse. Transcriptomics studies have revealed differential gene expression between TICs and bulk tumor cells. Super-enhancers (SE), have been implicated in regulating nearby genes. Characterizing SE in human HNSCC TICs will help identify therapeutic targets against these cells.

Method

TICs were isolated from primary HNSCC tumors; TIC and bulk SE profiles were elucidated using ATAC sequencing and bioinformatics pipelines. Motif analysis was performed using Bulk and TIC specific SE regions. To understand TICs heterogeneity, a scRNA sequencing experiment was performed using 1000 TICs and 2000 bulk tumor cells.

Results

TICs and bulk tumor cells share 127 SE; 58 and 53 SE are exclusive to TICs and Bulk populations, respectively. TIC-specific SE are enriched for motifs of known oncogenic transcription regulators that are known to drive a number of processes in HNSCC tumors such as proliferation, invasion, and metastasis. scRNA seq revealed that HNSCC TICs are a heterogeneous population and differ significantly from the bulk population. We also identified novel markers to enrich stem-cell-like clusters in our data.

Conclusion

Despite the shared genetic mutations, the HNSCC TICs and Bulk populations have very different characteristics. TICs have a very high tumor initiation ability as observed in limited dilution assays. Epigenetic profiling revealed TIC and bulk specific enhancer signatures and through motif enrichment, we were able to infer the potential mechanisms through which TIC phenotype is achieved. We are currently functionally testing the potential TIC-specific therapeutic targets using in vitro and in vivo CRISPR-Cas9 strategies.