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Molecular Cancer Research
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Chromatin, Epigenetics, and RNA Regulation

SMARCB1 Deficiency Integrates Epigenetic Signals to Oncogenic Gene Expression Program Maintenance in Human Acute Myeloid Leukemia

Shankha Subhra Chatterjee, Mayukh Biswas, Liberalis Debraj Boila, Debasis Banerjee and Amitava Sengupta
Shankha Subhra Chatterjee
1Stem Cell & Leukemia Lab, Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Translational Research Unit of Excellence (TRUE), Salt Lake, Kolkata, West Bengal, India.
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Mayukh Biswas
1Stem Cell & Leukemia Lab, Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Translational Research Unit of Excellence (TRUE), Salt Lake, Kolkata, West Bengal, India.
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Liberalis Debraj Boila
1Stem Cell & Leukemia Lab, Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Translational Research Unit of Excellence (TRUE), Salt Lake, Kolkata, West Bengal, India.
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Debasis Banerjee
2Clinical Hematology, Park Clinic, Gorky Terrace, Kolkata, West Bengal, India.
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Amitava Sengupta
1Stem Cell & Leukemia Lab, Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Translational Research Unit of Excellence (TRUE), Salt Lake, Kolkata, West Bengal, India.
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  • For correspondence: amitava.sengupta@iicb.res.in
DOI: 10.1158/1541-7786.MCR-17-0493 Published May 2018
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Abstract

SWI/SNF is an evolutionarily conserved multi-subunit chromatin remodeling complex that regulates epigenetic architecture and cellular identity. Although SWI/SNF genes are altered in approximately 25% of human malignancies, evidences showing their involvement in tumor cell–autonomous chromatin regulation and transcriptional plasticity are limiting. This study demonstrates that human primary acute myeloid leukemia (AML) cells exhibit near complete loss of SMARCB1 (BAF47 or SNF5/INI1) and SMARCD2 (BAF60B) associated with nucleation of SWI/SNFΔ. SMARCC1 (BAF155), an intact core component of SWI/SNFΔ, colocalized with H3K27Ac to target oncogenic loci in primary AML cells. Interestingly, gene ontology (GO) term and pathway analysis suggested that SMARCC1 occupancy was enriched on genes regulating Rac GTPase activation, cell trafficking, and AML-associated transcriptional dysregulation. Transcriptome profiling revealed that expression of these genes is upregulated in primary AML blasts, and loss-of-function studies confirmed transcriptional regulation of Rac GTPase guanine nucleotide exchange factors (GEF) by SMARCB1. Mechanistically, loss of SMARCB1 increased recruitment of SWI/SNFΔ and associated histone acetyltransferases (HAT) to target loci, thereby promoting H3K27Ac and gene expression. Together, SMARCB1 deficiency induced GEFs for Rac GTPase activation and augmented AML cell migration and survival. Collectively, these findings highlight tumor suppressor role of SMARCB1 and illustrate SWI/SNFΔ function in maintaining an oncogenic gene expression program in AML.

Implications: Loss of SMARCB1 in AML associates with SWI/SNFΔ nucleation, which in turn promotes Rac GTPase GEF expression, Rac activation, migration, and survival of AML cells, highlighting SWI/SNFΔ downstream signaling as important molecular regulator in AML. Mol Cancer Res; 16(5); 791–804. ©2018 AACR.

This article is featured in Highlights of This Issue, p. 743

Footnotes

  • Note: Supplementary data for this article are available at Molecular Cancer Research Online (http://mcr.aacrjournals.org/).

  • Received September 8, 2017.
  • Revision received January 11, 2018.
  • Accepted February 20, 2018.
  • Published first February 26, 2018.
  • ©2018 American Association for Cancer Research.
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Molecular Cancer Research: 16 (5)
May 2018
Volume 16, Issue 5
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SMARCB1 Deficiency Integrates Epigenetic Signals to Oncogenic Gene Expression Program Maintenance in Human Acute Myeloid Leukemia
Shankha Subhra Chatterjee, Mayukh Biswas, Liberalis Debraj Boila, Debasis Banerjee and Amitava Sengupta
Mol Cancer Res May 1 2018 (16) (5) 791-804; DOI: 10.1158/1541-7786.MCR-17-0493

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SMARCB1 Deficiency Integrates Epigenetic Signals to Oncogenic Gene Expression Program Maintenance in Human Acute Myeloid Leukemia
Shankha Subhra Chatterjee, Mayukh Biswas, Liberalis Debraj Boila, Debasis Banerjee and Amitava Sengupta
Mol Cancer Res May 1 2018 (16) (5) 791-804; DOI: 10.1158/1541-7786.MCR-17-0493
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