Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1

Abstract

New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a 55-year-old male with OAC without recombinant-DNA transformation. Somatic genetic variations from MFD-1, tumour, normal oesophagus, and leucocytes were analysed with SNP6. WGS was performed in tumour and leucocytes. RNAseq was performed in MFD-1, and two classic OAC cell lines FLO1 and OE33. Transposase-accessible chromatin sequencing (ATAC-seq) was performed in MFD-1, OE33, and non-neoplastic HET1A cells. Functional studies were performed. MFD-1 had a high SNP genotype concordance with matched germline/tumour. Parental tumour and MFD-1 carried four somatically acquired mutations in three recurrent mutated genes in OAC: TP53, ABCB1 and SEMA5A, not present in FLO-1 or OE33. MFD-1 displayed high expression of epithelial and glandular markers and a unique fingerprint of open chromatin. MFD-1 was tumorigenic in SCID mouse and proliferative and invasive in 3D cultures. The clinical utility of whole genome sequencing projects will be delivered using accurate model systems to develop molecular-phenotype therapeutics. We have described the first such system to arise from the oesophageal International Cancer Genome Consortium project.

Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state

“…ChIP, ChIP-seq, and ATAC-seq analysis ChIP, ChIP-seq (Wiseman et al 2015), and ATAC-seq (Garcia et al 2016;Britton et al 2017) were performed and analyzed essentially as described previously (for details, see Supplemental Methods). For ATAC-seq, differential accessible regions with a linear fold change > 5 and a Q-value < 0.05 were considered significant and were subject to further analyses.…”

Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma

“…PDE5 was highly and ubiquitously expressed in esophageal cancer tissue with low expression in normal tissue (Figure 2A). In matched normal esophageal fibroblasts (NOFs) and CAFs, 2 commonly used EAC cell lines and a primary epithelial esophageal cancer cell line extracted in our laboratory (MFD-1) 36 , variable PDE5 expression was observed, determined by cell sub-type. There was little or no PDE5 protein expression in the cancer cell lines with highest expression in CAFs (Figure 2B).…”

“…To explore this, we took a single cell whole-transcriptomic approach using droplet-based microfluidics and single cell RNA sequencing (DropSeq) to analyse the gene expression of individual CAFs and esophageal cancer cells in direct co-culture 38 . CAFs were grown in isolation or in co-culture with esophageal cancer cell line, MFD-1 36 . Cells were treated with vardenafil for 72 hours before analysis.…”

“…CAFs were grown in isolation or in co-culture MFD-1 cell line 36 . Cells were treated with vardenafil for 72 hours before analysis.…”

Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma

“…Therefore, MCM7 overexpression leads to both increased proliferation and perturbation of MCM complex activity. Finally, we reduced MCM7 expression levels in MFD-1 cells that were recently derived from an EAC patient of our OCCAMS cohort (36). MFD-1 cells have four-fold higher MCM7 basal expression compared to the diploid FLO-1 cells ( Figure 4G).…”