Functional genomic analysis identifies drug targetable pathways in invasive and metastatic cutaneous squamous cell carcinoma

Abstract

Although cutaneous squamous cell carcinoma (cSCC) is treatable in the majority of cases, deadly invasive and metastatic cases do occur. To date there are neither reliable predictive biomarkers of disease progression nor FDA-approved targeted therapies as standard of care. To address these issues, we screened patient-derived primary cultured cells from invasive/metastatic cSCC with 107 small-molecule inhibitors. In-house bioinformatics tools were used to cross-analyze drug responses and DNA mutations in tumors detected by whole-exome sequencing (WES). Aberrations in molecular pathways with evidence of potential drug targets were identified, including the Eph-ephrin and neutrophil degranulation signaling pathways. Using a screening panel of siRNAs, we identified EPHA6 and EPHA7 as targets within the Eph-ephrin pathway responsible for mitigating decreased cell viability. These studies form a plausible foundation for detecting biomarkers of high-risk progressive disease applicable in dermatopathology and for patient-specific therapeutic options for invasive/metastatic cSCC.

Comprehensive Mutational and Phenotypic Characterization of New Metastatic Cutaneous Squamous Cell Carcinoma Cell Lines Reveal Novel Drug Susceptibilities

“…The metastatic cell lines UT-SCC7, UT-SCC59A, and UT-SCC115 have not been validated molecularly, nor has evidence of tumorigenicity been published. This is also the case for an undesignated metastatic cSCC cell line recently developed [ 29 ]. MET4 and IC1MET form tumors in mice but phenotypic comparisons to their originating tumors are limited.…”

“…Dose-response screening and western blot analysis verified the sensitivity of the cell lines towards PIK-75, as well as the dual mTOR/PI3K-targeting dactolisib, thus permitting further pre-clinical studies on the PI3K/AKT/mTOR oncogenic pathway in metastatic cSCC. A recent study similarly identified sensitivity to dactolisib for invasive cell lines of cSCC [ 29 ]. According to the Genomics of Drug Sensitivity in Cancer Database ( ; Accessed 1 December 2020) the mean IC 50 for head and neck SCC cell lines using dactolisib (PIK-75 data not available) was notably higher (311 nM) than the range observed with our cell lines (22–80 nM), further supporting the sensitivity of our cell lines to this drug.…”

Molecular Alterations in Cutaneous Squamous Cell Carcinoma in Immunocompetent and Immunosuppressed Hosts—A Systematic Review

“…Novel somatic mutations in MLH1 (Q407*, Q426*, R423*) were also observed in an analysis of ten cases of high-risk cSCCHN [ 6 ]. In another study, EPHA6 and EPHA7 were identified as targets within the Eph-ephrin pathway, which is responsible for mitigating decreased cell viability in cSCC [ 23 ]. The authors also reported that RAC1 was the largest hub within the Eph-ephrin signaling pathway (degree = 14).…”

“…The authors also reported that RAC1 was the largest hub within the Eph-ephrin signaling pathway (degree = 14). Novel mutations in BPI were identified in the same study (HGVS DNA reference: g.36938975G > A, g.36954682C > T) [ 23 ].…”

Functional proteomics of patient derived head and neck squamous cell carcinoma cells reveal novel applications of trametinib

“…Cell culture methods have been previously described. 24 , 34 Primary tumor samples were collected from the operating room in DMEM/F12 Media, supplemented with 2x antibiotic/antimitotic (Invitrogen, Carlsbad, CA). Tissues were washed 3 times in fresh DMEM/F12 Media and minced before plating.…”