SLUG‐related partial epithelial‐to‐mesenchymal transition is a transcriptomic prognosticator of head and neck cancer survival

Abstract

Partial epithelial-to-mesenchymal transition (pEMT) contributes to cellular heterogeneity that is associated with nodal metastases and unfavorable clinical parameters in head and neck squamous cell carcinomas (HNSCCs). We developed a single-cell RNA sequencing signature-based pEMT quantification through cell type-dependent deconvolution of bulk RNA sequencing and microarray data combined with single-sample scoring of molecular phenotypes (Singscoring). Clinical pEMT-Singscores served as molecular classifiers in multivariable Cox proportional hazard models and high scores prognosticated poor overall survival and reduced response to irradiation as independent parameters in large HNSCC cohorts [The Cancer Genome Atlas (TCGA), MD Anderson Cancer Centre (MDACC), Fred Hutchinson Cancer Research Center (FHCRC)]. Differentially expressed genes confirmed enhanced cell motility and reduced oxidative phosphorylation and epithelial differentiation in pEMT high patients. In patients and cell lines, the EMT transcription factor SLUG correlated most strongly with pEMT-Singscores and promoted pEMT, enhanced invasion, and resistance to irradiation in vitro. SLUG protein levels in HNSCC predicted disease-free survival, and its peripheral expression at the interphase to the tumor microenvironment was significantly increased in relapsing patients. Hence, pEMT-Singscores represent a novel risk predictor for HNSCC stratification regarding clinical outcome and therapy response that is partly controlled by SLUG.

Epithelial-to-Mesenchymal Transition-Derived Heterogeneity in Head and Neck Squamous Cell Carcinomas

“…We described a similar preferential loss of the epithelial marker EpCAM along with a gain of the mesenchymal marker Vimentin at the edges of tumor areas in HNSCC [ 66 ]. Comparably, while some primary tumors were characterized by a homogeneous expression of the EMT transcription factor (EMT-TF) SLUG, a preferential strong expression at the edges of tumor areas was associated with recurrences [ 67 ]. Spatially distinct induction of EMT and pEMT represents a source of ITH and plasticity that may support tumor bud formation, MRD, treatment resistance, and local/loco-regional invasion in HNSCC.…”

“…SLUG induces the expression of stem cell markers, enhanced resistance to cisplatin, and was associated with tumor cell invasion in HNSCC xenografts in the mouse [ 112 ]. Furthermore, SLUG was associated with the expression of a 15-gene signature of partial EMT defined in oral carcinomas, which was correlated with the nodal status of patients (see “EMT gene signatures”) [ 44 , 67 ]. However, enhanced SLUG expression correlated with the pEMT signature in tumors of individual patients, but this correlation was not observed at the single cell level in primary tumors [ 44 ].…”

“…However, enhanced SLUG expression correlated with the pEMT signature in tumors of individual patients, but this correlation was not observed at the single cell level in primary tumors [ 44 ]. High expression of SLUG in primary HNSCC was a marker for reduced disease-free survival and was linked to tumor recurrence and the expression of EGFR [ 67 ]. Based on the ability of SLUG to promote treatment resistance, Riechelmann and colleagues compared the clinical outcome of HNSCC patients receiving either primary radiotherapy (RT) or radiochemotherapy (RCT) with patients receiving surgery with or without subsequent adjuvant RT/CRT in dependency of SLUG expression.…”

“…The resulting large cohorts served to compute a risk score based on the expression of the 15 common pEMT genes using single-sample scoring of molecular phenotypes (Singscores) [ 133 ]. pEMT-Singscores were identified as an independent prognosticator of OS in all three cohorts and as an independent prognosticator of OS in the sub-cohort of irradiated patients of TCGA [ 67 ]. An analysis of differentially expressed genes and related GO-terms showed that pEMT is associated with an up-regulation of cell motility and a down-regulation of epithelial differentiation and oxidative phosphorylation [ 67 ].…”

“…pEMT-Singscores were identified as an independent prognosticator of OS in all three cohorts and as an independent prognosticator of OS in the sub-cohort of irradiated patients of TCGA [ 67 ]. An analysis of differentially expressed genes and related GO-terms showed that pEMT is associated with an up-regulation of cell motility and a down-regulation of epithelial differentiation and oxidative phosphorylation [ 67 ]. Correlation analyses further defined SLUG as most strongly associated with single genes of the pEMT signature and with pEMT-Sinscores in patients and cell lines.…”