Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns.

ABSTRACT: Cell lines are commonly used as cancer models. The tissue of origin provides context for understanding biological mechanisms and predicting therapy response. We therefore systematically examined whether cancer cell lines exhibit features matching the presumed cancer type of origin. Gene expression and DNA methylation classifiers trained on ~9000 tumors identified 35 (of 614 examined) cell lines that better matched a different tissue or cell type than the one originally assigned. Mutational patterns further supported most reassignments. For instance, cell lines identified as originating from the skin often exhibited a UV mutational signature. We cataloged 366 "golden set" cell lines in which transcriptomic and epigenomic profiles strongly resemble the cancer type of origin, further proposin

SUBMITTER: Salvadores M 

PROVIDER: S-EPMC7458440 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature