Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types
| Autor: | J Charalel, Marina Sirota, Katharine Yu, Christina Yau, Theodore C. Goldstein, Bin Chen, Denise M. Wolf, Atul J. Butte, Dvir Aran, L.J. van 't Veer |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
General Physics and Astronomy Datasets as Topic 02 engineering and technology Transcriptome Neoplasms 2.1 Biological and endogenous factors Aetiology lcsh:Science Cancer Regulation of gene expression Multidisciplinary Tumor 021001 nanoscience & nanotechnology 3. Good health Gene Expression Regulation Neoplastic Correlation analysis 0210 nano-technology Sequence Analysis Science Computational biology Biology Article General Biochemistry Genetics and Molecular Biology Cell Line 03 medical and health sciences Pancreatic Cancer Rare Diseases Cell Line Tumor Cancer genome Pancreatic cancer medicine Genetics Humans Cancer models Data mining Gene Neoplastic Sequence Analysis RNA Cancer cell line encyclopedia Gene Expression Profiling Human Genome General Chemistry medicine.disease 030104 developmental biology Gene Expression Regulation Cell culture RNA lcsh:Q Gene expression Digestive Diseases |
| Zdroj: | Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019) Nature communications, vol 10, iss 1 Nature Communications |
| ISSN: | 2041-1723 |
| Popis: | Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia to evaluate cell lines as models of primary tumors across 22 tumor types. We perform correlation analysis and gene set enrichment analysis to understand the differences between cell lines and primary tumors. Additionally, we classify cell lines into tumor subtypes in 9 tumor types. We present our pancreatic cancer results as a case study and find that the commonly used cell line MIA PaCa-2 is transcriptionally unrepresentative of primary pancreatic adenocarcinomas. Lastly, we propose a new cell line panel, the TCGA-110-CL, for pan-cancer studies. This study provides a resource to help researchers select more representative cell line models. Cell lines are used ubiquitously in cancer research but how well they represent the tumor type they were derived from is variable. Here, the authors compare transcriptomic profiles of 22 tumor types and cell lines and propose a new comprehensive cell line panel for pan-cancer studies. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|