6 research outputs found
BCL7A is silenced by hypermethylation to promote acute myeloid leukemia
The online version contains supplementary material available at https:// doi.
org/ 10. 1186/ s40364â 023â 00472âx.
Additional file 1: Supplementary Figure 1. Diagram displaying CpGâ
methylation status around the BCL7A TSS. Genomic DNA from the NB4 cell
line was subjected to bisulfite conversion and used for subsequent TAâ
cloning. Supplementary Figure 2. Schematic representation of the differâ
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. Proteinâprotein
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 BCL7Aexâ
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.âs laboratory is funded by ConsejerĂa de Universidad, InvestigaciĂłn e InnovaciĂłn de la Junta de AndalucĂa and FEDER (P20â00688), Aula de InvestigaciĂłn sobre la Leucemia infantil: Heroes contra la Leucemia, the Ministry of Science and Innovation of Spain (grant PID2021â126111OBâI00), Junta de AndalucĂa (grants PIGEâ0440â2019, PIâ0135â2020), the University of Granada (grants BâCTSâ126âUGR18, BâCTSâ480âUGR20, and EâCTSâ304âUGR20), and the Spanish Association for Cancer Research (LABORATORYâAECCâ2018). J.R.PâM, A.A, and M.S.BâC 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 freâ
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 leukeâ
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. Methylationâspecific PCR, bisulfite sequencâ
ing, and 5âazaâ2ââdeoxycytidine 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 BCL7Aâexpressing and nonâexpressing mouse xenografts using in vivo fluorescence imaging.
Results BCL7A expression was inversely correlated with promoter methylation in three external cohorts: TCGAâLAML
(N = 160), TARGETâAML (N = 188), and Glass et al. (2017) (N = 111). The AMLâderived 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 supâ
pressor role in AML.
Conclusions BCL7A expression is silenced in AML by promoter methylation. In addition, restoration of BCL7A expresâ
sion exerts tumor suppressor activity in AML cell lines and xenograft models.ConsejerĂa de Universidad, InvestigaciĂłn e InnovaciĂłn de la Junta de AndalucĂa and FEDER (P20â00688)Ministry of Science and Innovation of Spain (grant PID2021â126111OBâI00)Junta de AndalucĂa (grants PIGEâ0440â2019, PIâ0135â2020)University of Granada (BâCTSâ126âUGR18, BâCTSâ480âUGR20, EâCTSâ304âUGR20)Spanish Association for Cancer Research (LABORATORYâAECCâ2018)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 AndalucĂa
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-2013-064596FundaciĂłn CientĂfica de la AsociaciĂłn Española Contra el CĂĄncer
GCB14-2170FundaciĂłn Ramon ArecesInstituto de Salud Carlos III-Fondo de InvestigaciĂłn 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