The LL-100 panel: 100 cell lines for blood cancer studies

Hilmar Quentmeier,Hans G Drexler,Cord C Uphoff,Wilhelm G Dirks,Sonja Eberth,Claudia Pommerenke,Klaus Steube,Stefan Nagel,Roderick A F Macleod,Max Koeppel

doi:10.1038/s41598-019-44491-x

Hilmar Quentmeier, Hans G Drexler + Show 8 more

Open Access

https://doi.org/10.1038/s41598-019-44491-x

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Abstract

For many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and non-inherent virus contamination. Whole exome sequencing and RNA-sequencing of the 100 cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. We show that such comprehensive sequencing data can be used to find lymphoma-subtype-characteristic copy number aberrations, mRNA isoforms, transcription factor activities and expression patterns of NKL homeobox genes. These exemplary studies confirm that the novel LL-100 panel will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.

Highlights

Human cancer cell lines form a renewable resource and are vital models for studying the cellular and molecular mechanisms underlying tumorigenesis as well as for anti-cancer drug screening[1,2]
Sequencing data have been deposited at ENA under the accession number PRJEB30297 for whole exome sequencing (WES) and PRJEB30312 for RNA-seq, respectively
Based on the analysis of WES and RNA-seq data we show the usefulness of the LL-100 panel for LL research in five exemplary studies

Summary

Introduction

Human cancer cell lines form a renewable resource and are vital models for studying the cellular and molecular mechanisms underlying tumorigenesis as well as for anti-cancer drug screening[1,2]. The National Cancer Institute (NCI) tumor cell line panel (known as NCI-60 as 60 cancer cell lines were assembled) was developed in the 1980s as an in vitro drug discovery tool intended to supplant animal studies in drug screening (reviewed in[7]). Later in the 2000s, the NCI-60 panel transitioned from a drug-discovery pipeline to a more general research tool in support of the cancer research community[7,8] Another panel incorporating a reduced number of cell lines of particular interest which had been derived from several solid tumor types was established in Japan[9]. We present transcriptome and exome sequencing data of a panel of 100 authenticated LL cell lines (LL-100) and selected examples of their utilization

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