Molecular and genomic characterisation of a panel of human anal cancer cell lines

Abstract

Anal cancer is a rare disease that has doubled in incidence over the last four decades. Current treatment and survival of patients with this disease has not changed substantially over this period of time, due, in part, to a paucity of preclinical models to assess new therapeutic options. To address this hiatus, we set-out to establish, validate and characterise a panel of human anal squamous cell carcinoma (ASCC) cell lines by employing an explant technique using fresh human ASCC tumour tissue. The panel of five human ASCC cell lines were validated to confirm their origin, squamous features and tumourigenicity, followed by molecular and genomic (whole-exome sequencing) characterisation. This panel recapitulates the genetic and molecular characteristics previously described in ASCC including phosphoinositide-3-kinase (PI3K) mutations in three of the human papillomavirus (HPV) positive lines and TP53 mutations in the HPV negative line. The cell lines demonstrate the ability to form tumouroids and retain their tumourigenic potential upon xenotransplantation, with varied inducible expression of major histocompatibility complex class I (MHC class I) and Programmed cell death ligand 1 (PD-L1). We observed differential responses to standard chemotherapy, radiotherapy and a PI3K specific molecular targeted agent in vitro, which correlated with the clinical response of the patient tumours from which they were derived. We anticipate this novel panel of human ASCC cell lines will form a valuable resource for future studies into the biology and therapeutics of this rare disease.

Unraveling Emerging Anal Cancer Clinical Biomarkers from Current Immuno-Oncogenomics Advances

“…In a HPV+ cohort, CD8+ TILs with high expression of PD-L1 were associated with better overall survival than CD8+ TILs with low expression of PD-L1. When PD-1 expression on TILs was analyzed by compartment, an association with survival was found for PD-1 expressing TILs in the tumor, and at the edge of the tumor but not for stromal TILs expressing PD-1 [ 14 ]. As discussed above, TILs are more abundant in HPV-positive tumors when compared with HPV-negative tumors.…”

The Drivers, Mechanisms, and Consequences of Genome Instability in HPV-Driven Cancers

“…Other than age-related mutations, the most prominent single nucleotide mutation signature in cervical cancers and other HPV-driven cancers is from the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) enzyme family, a group of proteins used as a host defence mechanism in response to viral infection and endogenous retroviral activation [6,149]. APOBEC-family enzymes induce a characteristic cytosine deamination, which is seen widely across HPV-driven cancers including cervical cancer, HNSCCs, anal cancer, penile cancer and vulvar cancer, and can account for up to 68% of mutations within affected tumours [149][150][151][152][153][154]. APOBEC enzymes deaminate cytosine bases to uridine at single stranded DNA and RNA, which subsequently results in a C > T transition when inflicted on the genome [155].…”

Understanding the molecular biology of anal squamous cell carcinoma

“…This biology is also consistent with a panel of recently developed anal cancer cell lines. 7 PIK3CA mutations were found in three HPV+ve SCCA primary lines, with 2 showing some sensitivity to the PI3Kα-specific inhibitor BYL719 (Alpelisib), demonstrating the potential therapeutic utility of targeting this pathway. Two HPV+ve cell lines (one of primary origin the other derived from locally recurrent disease) also harboured KMT2C mutations.…”