Abstract 1703: SMARCA2/4 degraders relieve the differentiation block in AML via changes in chromatin looping and accessibility
Authors: Aminov Sarah , Pradhan Kith , Sahu Srabani , Gordon-Mitchell Shanisha , Rabinovich Emma , Fromowitz Ariel , Chakraborty Joyeeta , Aluri Srinivas , Zhao Rongbao , Haque Nayem , Carbajal Milagros , Shastri Aditi , Steidl Ulrich , Samajdarr Susanta , Kumar Akhil , Ramachandra Murali , Coleman Robert A. , Stengel Kristy , Verma Amit K. 
Published: March 2024

Abstract
Acute Myeloid Leukemia (AML) is characterized by the unfettered proliferation and poor differentiation of myeloid cells causing reduced survival. The mammalian BAF complexes (also known as SWI/SNF) are important regulators of MYC and the cell cycle. There are three BAF complexes (cBAF, ncBAF and pBAF) that share several subunits. SMARCA2 and 4 are mutually exclusive ATPase subunits within the BAF complexes that use ATP hydrolysis and helicase activity to remodel chromatin via nucleosome sliding and removal. PBRM1 is a SMARCA4 associated factor present in pBAF. The association of SMARCA4 with regulatory elements of transcription factors makes it an intriguing target for AML. To evaluate the role of SMARC2/4 in AML, we analyzed RNA transcripts from highly purified primary AML initiating populations and control samples. Sorted leukemia stem cells (Lin-ve, CD34+, CD38-) overexpressed SMARCA2/4 when compared to healthy cells. A novel and highly selective SMARCA2/4 and PBRM1 PROTAC degrading agent AU-15330 was used to investigate the therapeutic effectiveness of targeting BAF complexes as well as the role of SMARCA2/4 in leukemic pathogenesis. Our data demonstrate that AU-15330 effectively degrades SMARCA2/4 and PBRM1 in human leukemia cell lines with varying mutational profiles; MV4-11 was the most sensitive cell line. When evaluating healthy CD34+ HSPCs as well as patient derived AML cells in colony assays, AU-15330 treatment increased differentiation in patient AML samples with minimal effects on healthy CD34+ cells. A xenograft of patient derived AML cells in irradiated mice was performed to determine the requirement of SMARCA2/4 in leukemia stem cell maintenance. Mice treated with AU-15330 had greater myeloid differentiation, fewer human cells in their bone marrows and reduced leukemia stem cell activity, seen in secondary transplants. To understand the underlying mechanism of how SMARCA2/4 and PBRM1 promote leukemic pathogenesis, we used a multi-omic analysis of transcription and chromatin dynamics in MV4-11 cells: ATAC-seq and RNA-seq identified downregulated genes with decreased accessibility, PRO-seq determined early transcriptional changes and HiChIP showed changes in enhancer promoter loops with SMARC2/4 degradation. Several leukemia related transcription factors as well as inflammatory genes were identified from these analyses as possible targets of the BAF complexes in the context of AML. Finally, to determine the effect of SMARCA2/4 degradation on pBAF association with chromatin, single cell imaging was performed of U2OS cells with HALO-tagged PBRM1 treated with the degrader or DMSO. pBAF in the degrader treated cells improved engagement with target chromatin however, a decrease in the stability of the complex binding to the nucleosome when compared to DMSO treated cells was shown. Taken together, these studies will determine the role of SMARCA2/4 in leukemia disease.
Citation Format: Sarah Aminov, Kith Pradhan, Srabani Sahu, Shanisha Gordon-Mitchell, Emma Rabinovich, Ariel Fromowitz, Joyeeta Chakraborty, Srinivas Aluri, Rongbao Zhao, Nayem Haque, Milagros Carbajal, Aditi Shastri, Ulrich Steidl, Susanta Samajdarr, Akhil Kumar, Murali Ramachandra, Robert A. Coleman, Kristy Stengel, Amit K. Verma. SMARCA2/4 degraders relieve the differentiation block in AML via changes in chromatin looping and accessibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1703.