SMARCA1: A MASTER EPIGENETIC REGULATOR OF DIFFERENTIATION, EPITHELIAL-TO-MESENCHYMAL TRANSITION (EMT), AND THERAPEUTIC RESISTANCE IN RHABDOMYOSARCOMA

Author

Ashwaq Aljabri, Southern Illinois University CarbondaleFollow

Date of Award

5-1-2025

Degree Name

Doctor of Philosophy

Department

Molecular Biology, Microbiology and Biochemistry

First Advisor

Davie, Judy

Second Advisor

Yohe, Marielle

Abstract

This dissertation characterized SMARCA1, an ISWI-family chromatin remodeler, as a multifunctional regulator in rhabdomyosarcoma (RMS), a pediatric cancer arising from the failure of muscle precursor cells to complete differentiation. Through comprehensive multi-omics approaches including CRISPR/Cas9 gene editing, RNA-seq, ATAC-seq, and CUT&RUN analyses, this work elucidates how SMARCA1 functions at the intersection of critical oncogenic pathways to influence differentiation, epithelial-to-mesenchymal transition (EMT), and therapeutic resistance. This research originated from a previous discovery of SMARCA1 as a binding partner of MyoG (unpublished data), which raised fundamental questions about its role in skeletal muscle and rhabdomyosarcoma. In this study, initial results revealed that SMARCA1 directly modulates chromatin accessibility and transcriptional activation of the tumor suppressor EGR1 and key Wnt signaling regulators, with a complex dose-dependent relationship between SMARCA1 levels and differentiation outcomes. Our work demonstrated that SMARCA5, another ISWI family member, primarily regulates cell proliferation and survival through the mTOR pathway. Initially guided by computational analyses of co-expression patterns, the role of SMARCA1 as a master regulator of EMT in fusion-positive RMS was confirmed in this study through next-generation sequencing approaches (RNA-seq, ATAC-seq, and CUT&RUN). These comprehensive genomic analyses revealed that SMARCA1 directly controls key EMT transcription factors (SNAI1, SNAI2, ZEB1, ZEB2, MYCN) and physically interacts with epigenetic modifiers like HDAC2 to coordinate TGF-β signaling through multiple pathways. Following SMARCA1 depletion, cell migration, invasion, and 3D spheroid formation were severely impaired, highlighting its essential role in maintaining the aggressive phenotype of RMS cells. This study further investigated therapeutic resistance mechanisms which revealed that SMARCA1 mediates resistance to MEK inhibitors in RMS subtypes. In fusion-positive RMS, SMARCA1 levels were observed to increase following trametinib treatment, and its knockout dramatically sensitized cells to MEK inhibition. The resistant cells showed extensive reprogramming, including global chromatin remodeling, enhanced expression of EMT factors, and activation of survival pathways including TGF-β and PI3K signaling. This work establishes SMARCA1 as a central epigenetic regulator in rhabdomyosarcoma with distinct yet interconnected functions contributing to pathogenesis and therapeutic resistance. The findings position SMARCA1 as a promising therapeutic target, particularly in combination approaches targeting the SMARCA1-TGFBR1 axis alongside MEK inhibitors to overcome the aggressive nature and treatment resistance of rhabdomyosarcoma.