BCL7A is silenced by hypermethylation to promote acute myeloid leukemia

The online version contains supplementary material available at https:// doi. org/ 10. 1186/ s40364‑ 023‑ 00472‑x. Additional file 1: Supplementary Figure 1. Diagram displaying CpG‑ methylation status around the BCL7A TSS. Genomic DNA from the NB4 cell line was subjected to bisulfite conversion and used for subsequent TA‑ cloning. Supplementary Figure 2. Schematic representation of the differ‑ ent lentiviral plasmids used in the experimental procedures. The specific region of the long isoform of BCL7A is colored in blue. Supplementary Figure 3. Western blot including the Decitabine (DAC) treatment over the NB4 cell line shown in Fig. 2c. Supplementary Figure 4. Protein‑protein interactions between BCL7A and SMARCA4 as determined by Mashtalir et al (2020). Supplementary Figure 5. DepMap AML cell lines collection data showing BCL7A Methylation Fraction (1kb upstream TSS) vs BCL7Aex‑ pression level. NB4 and M07e are marked. Supplementary Figure 6. Competition cell growth effect of BCL7A expression restoration on in vitro proliferation. Supplementary Table 1. Additional file 2: Supplementary Table 2. Differential expression analysis resultsP.P.M.’s laboratory is funded by Consejería de Universidad, Investigación e Innovación de la Junta de Andalucía and FEDER (P20‑00688), Aula de Investigación sobre la Leucemia infantil: Heroes contra la Leucemia, the Ministry of Science and Innovation of Spain (grant PID2021‑126111OB‑I00), Junta de Andalucía (grants PIGE‑0440–2019, PI‑0135–2020), the University of Granada (grants B‑CTS‑126‑UGR18, B‑CTS‑480‑UGR20, and E‑CTS‑304‑UGR20), and the Spanish Association for Cancer Research (LABORATORY‑AECC‑2018). J.R.P‑M, A.A, and M.S.B‑C were supported by fellowships FPU18/03709, FPU17/00067, and FPU19/00576 respectively funded by the Spanish Ministry of Science, Innovation and UniversitiesBackground Recent massive sequencing studies have revealed that SWI/SNF complexes are among the most fre‑ quently altered functional entities in solid tumors. However, the role of SWI/SNF in acute myeloid leukemia is poorly understood. To date, SWI/SNF complexes are thought to be oncogenic in AML or, at least, necessary to support leuke‑ mogenesis. However, mutation patterns in SWI/SNF genes in AML are consistent with a tumor suppressor role. Here, we study the SWI/SNF subunit BCL7A, which has been found to be recurrently mutated in lymphomas, but whose role in acute myeloid malignancies is currently unknown. Methods Data mining and bioinformatic approaches were used to study the mutational status of BCL7A and the correlation between BCL7A expression and promoter hypermethylation. Methylation‑specific PCR, bisulfite sequenc‑ ing, and 5‑aza‑2’‑deoxycytidine treatment assays were used to determine if BCL7A expression was silenced due to promoter hypermethylation. Cell competition assays after BCL7A expression restoration were used to assess the role of BCL7A in AML cell line models. Differential expression analysis was performed to determine pathways and genes altered after BCL7A expression restoration. To establish the role of BCL7A in tumor development in vivo, tumor growth was compared between BCL7A‑expressing and non‑expressing mouse xenografts using in vivo fluorescence imaging. Results BCL7A expression was inversely correlated with promoter methylation in three external cohorts: TCGA‑LAML (N = 160), TARGET‑AML (N = 188), and Glass et al. (2017) (N = 111). The AML‑derived cell line NB4 silenced the BCL7A expression via promoter hypermethylation. Ectopic BCL7A expression in AML cells decreased their competitive ability compared to control cells. Additionally, restoration of BCL7A expression reduced tumor growth in an NB4 mouse xenograft model. Also, differential expression analysis found that BCL7A restoration altered cell cycle pathways and modified significantly the expression of genes like HMGCS1, H1-0, and IRF7 which can help to explain its tumor sup‑ pressor role in AML. Conclusions BCL7A expression is silenced in AML by promoter methylation. In addition, restoration of BCL7A expres‑ sion exerts tumor suppressor activity in AML cell lines and xenograft models.Consejería de Universidad, Investigación e Innovación de la Junta de Andalucía and FEDER (P20‑00688)Ministry of Science and Innovation of Spain (grant PID2021‑126111OB‑I00)Junta de Andalucía (grants PIGE‑0440–2019, PI‑0135–2020)University of Granada (B‑CTS‑126‑UGR18, B‑CTS‑480‑UGR20, E‑CTS‑304‑UGR20)Spanish Association for Cancer Research (LABORATORY‑AECC‑2018)Spanish Ministry of Science, Innovation and Universities FPU18/03709, FPU17/00067, FPU19/0057

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

Simple Summary: 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. Abstract: 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 di erent SWI/SNF subunits. These results underline the importance of the SWI/SNF complex as a tumor suppressor in LUAD and the di culties 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.Ministry of Economy of Spain SAF2015-67919-RJunta de Andalucía CS2016-3 P12-BIO1655 PIGE-0440-2019 Pl-0245-2017 PI-0135-2020University of Granada PPJIA2019-0 B-CTS-126-UGR18International Association for the Study of Lung Cancer (IASLC)Spanish Association for Cancer Research (LAB-AECC)PhD "La Caixa Foundation" LCF/BQ/DE15/10360019"Fundacion Benefica Anticancer Santa Candida y San Francisco Javier" predoctoral fellowshipEuropean Commission 837897Spanish Ministry of Education, Culture and Sports FPU fellowship FPU17/00067 FPU17/01258 FPU18/03709PhD FPI-fellowship BES-2013-064596Fundación Científica de la Asociación Española Contra el Cáncer GCB14-2170Fundación Ramon ArecesInstituto de Salud Carlos III-Fondo de Investigación Sanitaria-Fondo Europeo de Desarrollo Regional `Una manera de hacer Europa' (FEDER) PI19/0009

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

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

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

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

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

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