Mining the genetic information of cancer cell lines for future therapy development

Mainz, September 15, 2014 – Cancer cell lines are a tremendous resource for cancer biology and therapy development: they are a tool to examine the genetic origin of cancers; to identify potential novel tumor targets, such as tumor antigens for vaccine development; and to use in preclinical studies. Mutations, gene expression, and drug sensitivity have been determined for many cell lines using next-generation sequencing (NGS). However, the HLA type and HLA expression of cell lines, characterizations necessary for the development of cancer vaccines, are largely incomplete and, when available, distributed in many publications.

In a new research paper in the September issue of OncoImmunology, TRON scientists determined the HLA type and HLA expression of 167 cancer and 10 non-cancer cell lines.
Using standard NGS RNA-Seq short reads from “whole transcriptome” sequencing and mapping reads to known HLA types, the study by TRON documents previously unreported HLA class I and II genotypes and their expression. The results are a fundamental resource for all researchers selecting cancer cell lines based on the HLA type and HLA expression, as well as for the development of immunotherapeutic tools for cancer immunotherapies.

Boegel, S., Loewer, M., Bukur, T., Sahin, U., Castle, J.C. A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines. OncoImmunology. 11 Sep. 2014.