MC38 colorectal tumor cell lines from two different sources display substantial differences in transcriptome, mutanome and neoantigen expression

Frontiers in Immunology, vol. 14, pp. 1102282

Abstract

Introduction The cell line MC38 is a commonly used murine model for colorectal carcinoma. It has a high mutational burden, is sensitive to immune checkpoint immunotherapy and endogenous CD8+ T cell responses against neoantigens have been reported. Methods Here, we re-sequenced exomes and transcriptomes of MC38 cells from two different sources, namely Kerafast (originating from NCI/NIH, MC38-K) and the Leiden University Medical Center cell line collection (MC38-L), comparing the cell lines on the genomic and transcriptomic level and analyzing their recognition by CD8+ T cells with known neo-epitope specificity. Results The data reveals a distinct structural composition of MC38-K and MC38-L cell line genomes and different ploidies. Further, the MC38-L cell line harbored about 1.3-fold more single nucleotide variations and small insertions and deletions than the MC38-K cell line. In addition, the observed mutational signatures differed; only 35.3% of the non-synonymous variants and 5.4% of the fusion gene events were shared. Transcript expression values of both cell lines correlated strongly (p = 0.919), but we found different pathways enriched in the genes that were differentially upregulated in the MC38-L or MC38-K cells, respectively. Our data show that previously described neoantigens in the MC38 model such as Rpl18 mut and Adpgk mut were absent in the MC38-K cell line resulting that such neoantigen-specific CD8+ T cells recognizing and killing MC38-L cells did not recognize or kill MC38-K cells. Conclusion This strongly indicates that at least two sub-cell lines of MC38 exist in the field and underlines the importance of meticulous tracking of investigated cell lines to obtain reproducible results, and for correct interpretation of the immunological data without artifacts. We present our analyses as a reference for researchers to select the appropriate sub-cell line for their own studies.

Authors 10

1. Barbara Schrörs

   University Medical Center of the Johannes Gutenberg University Mainz · Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz

   Affiliation as printed

   TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany

2. Brett J. Hos Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center, Leiden, Netherlands

3. Ikra Yildiz

   University Medical Center of the Johannes Gutenberg University Mainz · Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz

   Affiliation as printed

   TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany

4. Martin Löwer

   University Medical Center of the Johannes Gutenberg University Mainz · Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz

   Affiliation as printed

   TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany

5. Franziska Lang

   University Medical Center of the Johannes Gutenberg University Mainz · Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz

   Affiliation as printed

   TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany

6. Christoph Holtsträter

   University Medical Center of the Johannes Gutenberg University Mainz · Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz

   Affiliation as printed

   TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany

7. Mathias Vormehr

   BioNTech (Germany)

   Affiliation as printed

   BioNTech SE, Mainz, Germany

8. Uğur Şahin

   University Medical Center of the Johannes Gutenberg University Mainz · BioNTech (Germany)

   Affiliation as printed

   BioNTech SE, Mainz, Germany

   Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany

9. FERRY A. OSSENDORP corresponding Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center, Leiden, Netherlands

10. Mustafa Diken corresponding

    University Medical Center of the Johannes Gutenberg University Mainz · BioNTech (Germany) · Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz

    Affiliation as printed

    BioNTech SE, Mainz, Germany

    TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany