BCL7A is silenced by hypermethylation to promote acute myeloid leukemia

Juan Rodrigo Patiño-Mercau; Carlos Baliñas-Gavira; Alvaro Andrades; Maria S Benitez-Cantos; Ana Ercegovič Rot; Maria Isabel Rodriguez; Juan Carlos Álvarez-Pérez; Marta Cuadros; Pedro P Medina

doi:10.1186/s40364-023-00472-x

BCL7A is silenced by hypermethylation to promote acute myeloid leukemia

Biomark Res. 2023 Mar 20;11(1):32. doi: 10.1186/s40364-023-00472-x.

Authors

Juan Rodrigo Patiño-Mercau^#^{1

2}, Carlos Baliñas-Gavira^#^{1

3}, Alvaro Andrades^{1

2

4}, Maria S Benitez-Cantos^{1

4

5}, Ana Ercegovič Rot^{1

6

7}, Maria Isabel Rodriguez^{1

4

5}, Juan Carlos Álvarez-Pérez^{1

2

4}, Marta Cuadros^{1

4

5}, Pedro P Medina^{8

9

10}

Affiliations

¹ Gene Expression Regulation and Cancer Group (CTS-993), GENYO, Centre for Genomics and Oncological Research: Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain.
² Department of Biochemistry and Molecular Biology I, Facultad de Ciencias, University of Granada, Avda. de Fuentenueva S/N, 18071, Granada, Spain.
³ Present Address: Institut Curie, Paris Sciences Et Lettres Research University, Sorbonne University, INSERM U934/CNRS UMR3215, Paris, France.
⁴ Health Research Institute of Granada (Ibs.Granada), Granada, Spain.
⁵ Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain.
⁶ Present Address: International Postgraduate School Jožef Stefan, Ljubljana, Slovenia.
⁷ Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.
⁸ Gene Expression Regulation and Cancer Group (CTS-993), GENYO, Centre for Genomics and Oncological Research: Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain. pedromedina@ugr.es.
⁹ Department of Biochemistry and Molecular Biology I, Facultad de Ciencias, University of Granada, Avda. de Fuentenueva S/N, 18071, Granada, Spain. pedromedina@ugr.es.
¹⁰ Health Research Institute of Granada (Ibs.Granada), Granada, Spain. pedromedina@ugr.es.

^# Contributed equally.

Abstract

Background: Recent massive sequencing studies have revealed that SWI/SNF complexes are among the most frequently 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 leukemogenesis. 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 sequencing, 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 suppressor role in AML.

Conclusions: BCL7A expression is silenced in AML by promoter methylation. In addition, restoration of BCL7A expression exerts tumor suppressor activity in AML cell lines and xenograft models.

Keywords: AML; DNA hypermethylation; SWI/SNF complex; Tumor suppressor.