Genomic and signalling pathway characterization of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma.
Khanh B TranGregory GimenezPeter TsaiSharada KolekarEuan J RodgerAniruddha ChatterjeeAnower JabedJen-Hsing ShihWayne R JosephElaine S MarshallQian WangCristin G PrintMichael R EcclesBruce C BaguleyPeter R ShepherdPublished in: Pigment cell & melanoma research (2020)
Melanoma is a disease associated with a very high mutation burden and thus the possibility of a diverse range of oncogenic mechanisms that allow it to evade therapeutic interventions and the immune system. Here, we describe the characterization of a panel of 102 cell lines from metastatic melanomas (the NZM lines), including using whole-exome and RNA sequencing to analyse genetic variants and gene expression changes in a subset of this panel. Lines possessing all major melanoma genotypes were identified, and hierarchical clustering of gene expression profiles revealed four broad subgroups of cell lines. Immunogenotyping identified a range of HLA haplotypes as well as expression of neoantigens and cancer-testis antigens in the lines. Together, these characteristics make the NZM panel a valuable resource for cell-based, immunological and xenograft studies to better understand the diversity of melanoma biology and the responses of melanoma to therapeutic interventions.
Keyphrases
- gene expression
- single cell
- skin cancer
- genetic diversity
- copy number
- small cell lung cancer
- poor prognosis
- squamous cell carcinoma
- dna methylation
- stem cells
- rna seq
- transcription factor
- immune response
- papillary thyroid
- mesenchymal stem cells
- young adults
- binding protein
- long non coding rna
- childhood cancer
- genome wide identification