Single-cell sequencing and its applications in head and neck cancer

Zongtai Qi, Thomas Barrett, Anuraag S. Parikh, Itay Tirosh, Sidharth V. Puram

Research output: Contribution to journalReview articlepeer-review

25 Scopus citations


Head and neck squamous cell carcinoma (HNSCC), like many tumors, is characterized by significant intra-tumoral heterogeneity, namely transcriptional, genetic, and epigenetic differences that define distinct cellular subpopulations. While it has been established that intra-tumoral heterogeneity may have prognostic significance in HNSCC, we are only beginning to describe and define such heterogeneity at a cellular resolution. Recent advances in single-cell sequencing technologies have been critical in this regard, opening new avenues in our understanding of more nuanced tumor biology by identifying distinct cellular subpopulations, dissecting signaling within the tumor microenvironment, and characterizing cellular genomic mutations and copy number aberrations. The combined effect of these insights is likely to be robust and meaningful changes in existing diagnostic and treatment algorithms through the application of novel biomarkers as well as targeted therapeutics. Here, we review single-cell technological and computational advances at the genomic, transcriptomic, and epigenomic levels, and discuss their applications in cancer research and clinical practice, with a specific focus on HNSCC.

Original languageEnglish
Article number104441
JournalOral Oncology
StatePublished - Dec 2019


  • Diagnostic biomarker
  • Head and neck cancer
  • Immunotherapy
  • Single cell
  • Single cell RNA sequencing
  • Single cell sequencing
  • Squamous cell carcinoma
  • Technology development
  • Tumor heterogeneity


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