As a key component of the SWI/SNF complex, SMARCB1 plays a crucial epigenetic regulatory role in tumorigenesis. Increasing studies have observed SMARCB1 deficiency in various solid tumors, including bladder cancer. Hence, it is imperative to elucidate the impact of SMARCB1 deficiency on bladder cancer and the epigenetic mechanisms underlying the development and progression of SMARCB1-deficient bladder cancer.

Immunohistochemistry on human bladder cancer samples was conducted to evaluate the clinical relevance of SMARCB1. SMARCB1 knockout bladder cancer cell lines were constructed by CRISPR/Cas9 gene editing technology. In vitro functional assays, including CCK-8, colony formation and transwell assays, as well as a in vivo nude mouse subcutaneous tumor model, were performed to demonstrate the oncogenic effects of SMARCB1 deficiency. Potential interactors of SMARCB1 were identified by Mass spectrometry and co-immunoprecipitation assays. RNA-sequencing, ATAC-sequencing and CUT&Tag analysis provided insights into the downstream transcriptional regulatory mechanisms.

SMARCB1 was significantly downregulated in clincial bladder cancer tissues compared with adjacent normal tissues, and patients with low SMARCB1 expression exhibited shorter overall survival. In vitro and in vivo experiments confirmed that SMARCB1 deficiency markedly promoted bladder cancer proliferation and metastasis. Transcriptome sequencing analysis of bladder cancer cell lines revealed that SMARCB1 knockout led to significant upregulation of MYC target genes and hypoxia-related pathways, while oxidative phosphorylation was notably downregulated. Further validation demonstrated that SMARCB1 loss aberrantly upregulated glycolysis, lactate production, and its derived lactylation levels. Mass spectrometry and co-immunoprecipitation assays identified MECP2 as a key interacting protein of SMARCB1. Mechanistically, SMARCB1 deficiency enhanced the binding between the MECP2 and lactyltransferase KAT2A, thereby increasing MECP2 lactylation levels. This aberrant modification further activated MECP2-mediated transcriptional regulation of the oncogene ITGB8, driving malignant progression in bladder cancer.

Our data demonstrated the important role and epigenetic mechanisms of SMARCB1 deficiency in the malignant progression of bladder cancer. Therapeutic targeting KAT2A-MECP2 interaction enhanced by SMARCB1 deficiency might present a promising avenue for the management of SMARCB1-deficient bladder cancer.