Abstract

Genomic information encoded in DNA is compacted within the cell nucleus through the hierarchical organization of chromatin. The accessibility of this information to the transcriptional machinery is regulated by dynamic changes in chromatin structure, mediated by chromatin remodeling complexes and histone modifications. Among these, the SWI/SNF complex plays a central role by utilizing ATP hydrolysis to alter nucleosome positioning and chromatin accessibility. Genetic inactivation of genes encoding subunits of the SWI/SNF complex has been identified in approximately 20% of human cancers. One of the most frequently affected subunits is SNF5, a potent tumor suppressor whose loss is observed across multiple malignancies. In particular, mutations in the SMARCB1 gene, which encodes the SNF5 subunit of the SWI/SNF complex, represent the driver genetic alteration underlying malignant rhabdoid tumors (MRT). However, oncogenesis in this context is not solely attributable to the loss of functional SNF5. Accumulating evidence indicates that the continued presence and activity of BRG1, the ATPase catalytic subunit of the SWI/SNF complex, is required to sustain tumorigenesis. Thus, malignant transformation arises from the combined loss of SNF5 tumor-suppressive function and persistent BRG1-dependent chromatin remodeling activity. This dependency suggests that pharmacological inhibition of SWI/SNF ATPase activity may represent a viable therapeutic strategy for tumors characterized by SNF5 deficiency. Further supporting the tumor-suppressive role of SNF5, experimental re-expression of SNF5 in rhabdoid tumor cells has been shown to arrest cell proliferation while inducing cellular senescence and apoptosis. These effects are mediated, at least in part, through transcriptional activation of {P16INK4a}, a key cell cycle regulator and tumor suppressor.

Content

Introduction
Genomic information is stored within DNA localized in the nucleus of every diploid cell, where it is packaged into chromatin. Chromatin is composed of DNA associated with histone proteins and additional non-histone components, and it exists in two major structural states: heterochromatin and euchromatin. When DNA is condensed into heterochromatin, gene expression is generally repressed, whereas euchromatin is associated with transcriptionally permissive regions. These structural differences are reflected by distinct epigenetic marks, as heterochromatin is characterized by hypoacetylated histones and elevated levels of H3K9 methylation (H3K9me) ^1,2.


Figure 1. Illustration of how ATP-dependent chromatin remodeling complexes, such as SWI/SNF, modulate nucleosome structure. DNA is wrapped around histone octamers to form chromatin, and the complex uses ATP hydrolysis to slide, eject, or reposition nucleosomes, thereby regulating accessibility to transcriptional machinery and influencing gene expression.

Chromatin remodeling complexes, such as the SWI/SNF complex, regulate transitions between these chromatin states by exploiting the energy derived from ATP hydrolysis. Through mechanisms including nucleosome sliding, histone ejection, unwrapping, or histone dimer exchange, these complexes dynamically modulate DNA accessibility and transcriptional competence ^1,2. The SWI/SNF complex is a large and heterogeneous multiprotein assembly composed of several variable and core subunits. Among the core components, SMARCB1 plays a pivotal role in maintaining proper transcriptional regulation. Mutations affecting this subunit are observed in a wide spectrum of cancers, most notably in malignant rhabdoid tumors (MRT), which are rare but highly aggressive pediatric malignancies ³. Rhabdoid tumors are characterized by extremely poor clinical outcomes and are molecularly defined by the loss of SMARCB1, the gene encoding the SMARCB1 subunit. SMARCB1 is located on chromosome 22q11, and its inactivation represents the hallmark genetic lesion of MRT ⁴. Functionally, SMARCB1 is essential for the activation of enhancers regulating genes involved in cellular differentiation and development, while simultaneously repressing transcription of the oncogenic factor MYC. Loss of SMARCB1, in conjunction with sustained SMARCA4 ATPase activity required for cell proliferation, creates a permissive environment for tumor initiation and progression ⁵.
In addition, SMARCB1 plays a critical role in cell cycle control through regulation of the CDKN2A locus, which encodes the tumor suppressors P16INK4a and CDKN2A. SMARCB1 promotes transcription of P16INK4a while downregulating the expression of multiple cyclins and CDK4, a cyclin-dependent kinase implicated in cell cycle progression and metastasis ^6,7. P16INK4a exerts its tumor-suppressive function by controlling the activity of Rb, a key transcriptional corepressor. In its hypophosphorylated state, Rb binds to E2F transcription factors, repressing genes required for the G1–S phase transition of the cell cycle ^6,7. Upon mitogenic stimulation, cyclin-CDK4 complexes phosphorylate Rb, leading to its dissociation from E2F and allowing transcription of genes necessary for S-phase entry ^6,7.


Figure 2. Schematic representation of Rb regulation of E2F activity in the context of CDKN2A transcription. When P16INK4a is expressed, Rb remains in a hypophosphorylated, active state, binding E2F and repressing genes required for G1–S phase progression. Loss of P16INK4a or SMARCB1 deficiency disrupts this regulation, leading to uncontrolled E2F-driven transcription and cell cycle progression.

By inducing P16INK4a expression, SMARCB1 inhibits CDK4-mediated phosphorylation of Rb, thereby maintaining Rb in its active repressive state and preventing inappropriate cell cycle progression ^6,7.
Rhabdoid tumors predominantly arise in pediatric patients and are classified as malignant embryonal tumors of the central nervous system. In approximately 20–35% of cases, they are associated with germline biallelic alterations of SMARCB1. Loss of SMARCB1 leads to dysregulation of enhancers controlling EZH2, the catalytic methyltransferase of the PRC2 complex, which normally antagonizes SWI/SNF complex activity during development. This imbalance disrupts normal embryonic differentiation programs and contributes to oncogenic transformation ^8,9.

SWI/SNF complex
The SWI/SNF complex is a multi-subunit, ATP-dependent chromatin remodeler that utilizes the energy derived from ATP hydrolysis to reorganize nucleosomes and modulate chromatin accessibility ^10,11.
In mammals, the SWI/SNF complex is also referred to as the BAF complex. It comprises 12 to 15 subunits encoded by 29 different genes, with the ATPase subunit serving as the catalytic core. The complex exhibits significant heterogeneity due to the combinatorial assembly of its variable subunits ¹².

Figure 3. Composition of the BAF complex (SWI/SNF in mammals) showing all core and variable subunits, including the ATPase catalytic domain SMARCA4 and the tumor suppressor SMARCB1. The diagram highlights the heterogeneity of the complex and the interactions among subunits that enable chromatin remodeling, enhancer activation, and transcriptional regulation.

SWI/SNF complex is frequently localized near acetylated H3K27 histones, a mark associated with transcriptional activation and chromatin opening. Its activity counteracts the function of PRC2, which deposits the repressive H3K27 trimethylation mark ¹³.
The SWI/SNF complex regulates tissue and organ development, including the differentiation of oligodendrocytes and neurons ¹⁴. Functionally, it forms a C-shaped clamp around the nucleosome, stabilizing interactions between nucleosomes, SMARCB1, and other subunits. The BRG1 ATPase subunit uses ATP hydrolysis to disrupt histone-DNA contacts, allowing DNA to be sandwiched between SMARCA4 and SMARCB1. This facilitates nucleosome sliding or ejection, promoting chromatin accessibility and transcriptional activation ^5,15,16.
Through these mechanisms, the SWI/SNF complex influences a variety of cellular processes, including cell cycle control, differentiation, apoptosis, and metabolism. Mutations in the complex are linked to multiple cancers, including rhabdoid tumors ^15,16.


Figure 4. Representation of the antagonistic regulation of gene expression by SWI/SNF and PRC2 complexes. SWI/SNF promotes transcriptional activation by opening chromatin and facilitating histone H3K27 acetylation, while PRC2 represses transcription by depositing H3K27 trimethylation marks. Loss of SMARCB1 in rhabdoid tumors impairs SWI/SNF activity, resulting in widespread epigenetic dysregulation and altered gene expression.

Rhabdoid Tumor and SMARCB1
Rhabdoid tumors (RT) are rare, aggressive, and malignant neoplasms, primarily affecting infants and young children. They arise in the brain, kidney, and soft tissues. SMARCB1, a core member of the chromatin remodeling complex, acts as a tumor suppressor in this context. Accordingly, MRT pathogenesis is driven by epigenetic dysregulation.
These tumors develop due to biallelic inactivation of the SMARCB1 gene, or through subsequent acquisition of mutations or deletions. SMARCB1 encodes the SMARCB1 subunit of the human SWI/SNF complex, which remodels chromatin in an ATP-dependent manner to activate gene transcription. Approximately 25–30% of MRT patients harbor germline SMARCB1 mutations, typically de novo, or experience deletions at 22q11.
Loss of SMARCB1 prevents removal of repressive H3K27 trimethylation marks deposited by PRC2, leading to widespread epigenetic dysregulation, developmental arrest, and abnormal cellular proliferation ¹⁷.
The regulation of gene expression by the SWI/SNF and PRC2 complexes is depicted in the figure. SWI/SNF complex includes SMARCB1 and interacts with numerous cofactors and histone acetyltransferases to activate target gene expression. 


Figure 5. Illustration of the diverse roles of SWI/SNF in cellular processes. The complex regulates enhancer accessibility, transcription of tumor suppressors like P16INK4a, repression of oncogenes such as MYC, and maintenance of proper cell cycle control. SMARCA4-dependent super-enhancers are essential for sustaining rhabdoid tumor gene expression programs, while SMARCB1 loss shifts the balance toward oncogenic transcription.

Acetylation of H3K27 marks transcriptionally active regions, whereas the opposing PRC2 complex interacts with DNA methyltransferases and deacetylases to silence genes. In rhabdoid tumors, loss of SMARCB1 disrupts normal SWI/SNF complex function, resulting in altered gene expression. Re-expression of SMARCB1 restores H3K27 acetylation at multiple loci ¹⁷.

SMARCA4 Role in MRT ¹⁸
The SWI/SNF complex contains the ATPase subunit SMARCA4, which harnesses ATP hydrolysis to drive chromatin remodeling. SMARCA4 maintains chromatin accessibility at specific enhancer regions, making it essential for sustaining rhabdoid gene expression programs. Many active super-enhancers in rhabdoid tumor cell lines are dependent on SMARCA4 to remain open.
SMARCA4-dependent sites regulate genes controlling signaling, cell cycle, apoptosis, angiogenesis, and migration, thereby influencing rhabdoid-specific transcriptional programs. Dysregulation due to SWI/SNF complex mutations follows a two-step process: collapse of enhancers linked to differentiation and development, coupled with upregulation of enhancers controlling pro-tumorigenic programs.

MYC Role in MRT ^19,20
Loss of SMARCB1 disrupts key molecular pathways and upregulates MYC, driving oncogenesis. Experimental reconstitution of SMARCB1 in MRT cell lines reduces MYC mRNA expression and proliferation, demonstrating that MYC is required for MRT growth. SMARCB1 restoration also decreases chromatin accessibility at the MYC super-enhancer and promoter.
Thus, MYC functions as a driver oncogene in MRT, while SMARCB1 loss is necessary for tumorigenesis, as it eliminates the SMARCB1 subunit of SWI/SNF complex that normally restrains MYC expression. SMARCA4 further facilitates MYC activation by promoting chromatin accessibility at MYC-associated loci. SMARCB1 directly binds MYC to inhibit its transcriptional activity in wild-type cells. Loss of SMARCB1 releases MYC to bind its targets, promoting oncogenesis, suggesting that MYC inhibition could represent a therapeutic strategy in SMARCB1-deficient tumors ²¹.

P16INK4a Role in MRT ²¹
SMARCB1, which encodes SMARCB1, is also critical for regulating P16INK4a, a potent tumor suppressor that modulates Rb activity. Rb functions as a corepressor by binding E2F transcription factors, silencing genes necessary for G1–S phase progression.
SMARCB1-deficient cells exhibit reduced P16INK4a expression, resulting in unchecked S-phase progression and increased proliferation. Re-expression of SMARCB1 restores P16INK4a levels, enhancing CDK4 inhibition and proper G0/G1 checkpoint activity ²¹.
SMARCB1 is required for SMARCA4 recruitment to the P16INK4a promoter. In the absence of SMARCB1, SMARCA4 cannot activate P16INK4a, leaving this pathway in the OFF state and allowing SMARCA4-dependent MYC activation to drive oncogenesis. Reconstitution of SMARCB1 in MRT restores P16INK4a transcription and protein expression, thereby inhibiting cell cycle progression by preventing cyclin–CDK4 activation. In MRT cells lacking functional SMARCB1, cyclin D is expressed while P16INK4a is suppressed, accelerating the G1–S transition.

Conclusion
Malignant rhabdoid tumor (MRT) is a rare and aggressive pediatric malignancy that requires a multidisciplinary clinical approach. It is therefore crucial to consider the penetrance of tumors in children with 22q11 deletions encompassing SMARCB1 and to evaluate the incidence of mosaicism ²².
Inactivation of individual subunits of the SWI/SNF complex can contribute to tumorigenesis. In particular, MRT arises predominantly from loss of the SMARCB1 subunit ¹⁰. SMARCB1 deficiency not only initiates tumorigenesis but also sustains an oncogenic state, in part through dysregulated MYC expression ¹¹.
The identification of SMARCB1 mutations, deletions, or duplications in MRT has shifted attention toward the downstream targets and protein-binding partners of SMARCB1. Therapeutic strategies aimed at mimicking SMARCB1 function or modulating its targets, such as cyclin D, PLK1, P16INK4a, CBLIF, AKT1, and HEDGEHOG, hold potential for a multi-targeted approach to treat MRT ²². Given the limited clinical experience and the poor prognosis associated with MRT, there is a pressing need to develop novel therapeutic strategies and improve translational approaches to effectively target these aggressive tumors ²².