Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveals distinct cancer-associated fibroblasts in head and neck squamous cell carcinoma

Qian Zhang; Yuxin Wang; Chengwan Xia; Liang Ding; Yumei Pu; Xiaobei Hu; Huiming Cai; Qingang Hu

doi:10.21037/atm-21-2767

Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveals distinct cancer-associated fibroblasts in head and neck squamous cell carcinoma

Ann Transl Med. 2021 Jun;9(12):1017. doi: 10.21037/atm-21-2767.

Authors

Qian Zhang¹, Yuxin Wang¹, Chengwan Xia¹, Liang Ding², Yumei Pu¹, Xiaobei Hu³, Huiming Cai⁴, Qingang Hu¹

Affiliations

¹ Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
² Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
³ Department of Orthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
⁴ Nanjing Nuoyuan Medical Devices Co., Ltd., Nanjing, China.

Abstract

Background: The heterogeneity of cancer-associated fibroblasts (CAFs) in head and neck squamous cell carcinoma (HNSCC) has been widely acknowledged, but has not yet been elucidated. The potential roles and clinical relevance of CAFs subclusters in HNSCC progression remain obscure.

Methods: In this study, we combined single-cell and bulk tissue transcriptome profiles of HNSCC with clinical data from The Cancer Genome Atlas (TCGA). The Seurat package was used to perform single-cell RNA-seq analysis to distinguish distinct CAFs subtypes. Prognostic relevance of several CAFs markers was assessed and functional analysis was also performed.

Results: We identified eight CAFs subclusters; of these, seven showed enhanced expression levels in HNSCC tumor tissues compared to normal tissue, and three (clusters 0, 3, and 4) were associated with poorer overall survival. Further functional analysis revealed that cluster 0 was characterized by myofibroblasts with high alpha smooth muscle actin (aSMA) expression and enrichment in smooth muscle contraction. The cluster 3 exhibited expression of extracellular matrix (ECM)-related genes and was enriched in epithelial-mesenchymal transition (EMT)-related gene sets. Cluster 4 expressed high levels of the major histocompatibility complex (MHC) class II family, which was characterized as antigen-presenting CAFs.

Conclusions: We determined CAFs heterogeneity in HNSCC. 8 CAFs subclusters were recognized and 3 of which were prognosis related. The 3 CAFs subclusters showed distinct phenotypes enriched in myofibroblast function, ECM remodeling and antigen-presenting function respectively.

Keywords: Head and neck squamous cell carcinoma (HNSCC); cancer-associated fibroblasts (CAFs); prognosis; tumour heterogeneity.