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Article

Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models

1
Department of Biochemistry and Molecular Biology I, University of Granada, 18071 Granada, Spain
2
GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, 18016 Granada, Spain
3
Health Research Institute of Granada (ibs.Granada), 18014 Granada, Spain
4
Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
5
School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
6
Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
7
Genes and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain
8
Solid Tumors Program, Centro de Investigación Médica Aplicada and Department of Pathology, Anatomy and Physiology, University of Navarra Pamplona, 31009 Pamplona, Spain
9
Navarra’s Health Research Institute (IDISNA) and CIBERONC, 31008 Pamplona, Spain
10
Department of Physiology, University of Valencia, 46100 Burjassot, Valencia, Spain
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Cancers 2020, 12(12), 3712; https://doi.org/10.3390/cancers12123712
Received: 29 October 2020 / Revised: 29 November 2020 / Accepted: 8 December 2020 / Published: 10 December 2020
(This article belongs to the Special Issue Non-small Cell Lung Cancer--Tumor Biology)
Mammalian SWI/SNF complexes regulate gene expression by reorganizing the way DNA is packaged into chromatin. SWI/SNF subunits are recurrently altered in tumors at multiple levels, including DNA mutations as well as alteration of the levels of RNA and protein. Cancer cell lines are often used to study SWI/SNF function, but their patterns of SWI/SNF alterations can be complex. Here, we present a comprehensive characterization of DNA mutations and RNA and protein expression of SWI/SNF members in 38 lung adenocarcinoma (LUAD) cell lines. We show that over 85% of our cell lines harbored at least one alteration in one SWI/SNF subunit. In addition, over 75% of our cell lines lacked expression of at least one SWI/SNF subunit at the protein level. Our catalog will help researchers choose an appropriate cell line model to study SWI/SNF function in LUAD.
Mammalian SWI/SNF (SWitch/Sucrose Non-Fermentable) complexes are ATP-dependent chromatin remodelers whose subunits have emerged among the most frequently mutated genes in cancer. Studying SWI/SNF function in cancer cell line models has unveiled vulnerabilities in SWI/SNF-mutant tumors that can lead to the discovery of new therapeutic drugs. However, choosing an appropriate cancer cell line model for SWI/SNF functional studies can be challenging because SWI/SNF subunits are frequently altered in cancer by various mechanisms, including genetic alterations and post-transcriptional mechanisms. In this work, we combined genomic, transcriptomic, and proteomic approaches to study the mutational status and the expression levels of the SWI/SNF subunits in a panel of 38 lung adenocarcinoma (LUAD) cell lines. We found that the SWI/SNF complex was mutated in more than 76% of our LUAD cell lines and there was a high variability in the expression of the different SWI/SNF subunits. These results underline the importance of the SWI/SNF complex as a tumor suppressor in LUAD and the difficulties in defining altered and unaltered cell models for the SWI/SNF complex. These findings will assist researchers in choosing the most suitable cellular models for their studies of SWI/SNF to bring all of its potential to the development of novel therapeutic applications. View Full-Text
Keywords: SWI/SNF complex; lung cancer; lung adenocarcinoma; epigenetics; cell models; multi-omics SWI/SNF complex; lung cancer; lung adenocarcinoma; epigenetics; cell models; multi-omics
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MDPI and ACS Style

Peinado, P.; Andrades, A.; Cuadros, M.; Rodriguez, M.I.; Coira, I.F.; Garcia, D.J.; Álvarez-Perez, J.C.; Baliñas-Gavira, C.; Arenas, A.M.; Patiño-Mercau, J.R.; Sanjuan-Hidalgo, J.; Romero, O.A.; Montuenga, L.M.; Carretero, J.; Sanchez-Cespedes, M.; Medina, P.P. Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models. Cancers 2020, 12, 3712. https://doi.org/10.3390/cancers12123712

AMA Style

Peinado P, Andrades A, Cuadros M, Rodriguez MI, Coira IF, Garcia DJ, Álvarez-Perez JC, Baliñas-Gavira C, Arenas AM, Patiño-Mercau JR, Sanjuan-Hidalgo J, Romero OA, Montuenga LM, Carretero J, Sanchez-Cespedes M, Medina PP. Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models. Cancers. 2020; 12(12):3712. https://doi.org/10.3390/cancers12123712

Chicago/Turabian Style

Peinado, Paola, Alvaro Andrades, Marta Cuadros, Maria I. Rodriguez, Isabel F. Coira, Daniel J. Garcia, Juan C. Álvarez-Perez, Carlos Baliñas-Gavira, Alberto M. Arenas, Juan R. Patiño-Mercau, Juan Sanjuan-Hidalgo, Octavio A. Romero, Luis M. Montuenga, Julian Carretero, Montserrat Sanchez-Cespedes, and Pedro P. Medina 2020. "Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models" Cancers 12, no. 12: 3712. https://doi.org/10.3390/cancers12123712

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