Mammalian SWI/SNF complexes in urothelial bladder cancer: analysis of the tumorbiological role of ARID1A and identification of potential ARID1A-deficiency-based therapeutic strategies
Reproductive Medicine, Urology
Final Report Abstract
ARID1A is a subunit of SWI/SNF chromatin remodeling complexes, which are necessary to control the positioning of nucleosomes. The ARID1A gene is frequently altered in cancer, especially in urothelial bladder cancer. We aimed to understand the function of ARID1A, with the prospect to develop ARID1A-based therapies for patients with urothelial bladder cancer. Therefore, we determined ARID1A-interacting proteins, deciphered the transcription program modulated by ARID1A, and characterized ARID1A-deficient urothelial bladder cancer cases regarding immune checkpoint inhibitor response. We observed ARID1A/cBAF complexes interacting with ribosomal proteins and the SMN splicing complex in two normal-like urothelial bladder cell lines (UROtsa and HBLAK), possibly linking ARID1A to translation and splicing. In support, in ARID1A knockout (UROtsa, normal-like urothelial bladder cell line; T24, malignant urothelial bladder cancer cell line), knockdown (HBLAK, normal-like urothelial bladder cell line), and a re-expression models (JMSU-1, malignant urothelial bladder cancer cell line which lacks functional ARID1A) changes in the gene expression programs could be linked to translational and splicing processes. Additionally, we found cell cycle/checkpoints and immune processes affected by the loss/gain of ARID1A. Furthermore, loss of ARID1A resulted in significantly less accessible chromatin in UROtsa cells, particularly near distal enhancers and introns. This supports findings by others that ARID1A-containing cBAF complexes are important at distal enhancers. Less accessible regions were mapped to gene clusters encoding proteins associated with EMT, cell cycle, and UV response. More accessible regions were linked to IFN response. To test the candidate pathways identified in the interactome, transcriptome, and genome analyses, we evaluated cellular proliferation, cell cycle progression, and alternative splicing. We observed a significantly decreased proliferation in colony formation assays of UROtsa and T24 ARID1A KO cells. Re-expression of ARID1A in JMSU-1 cells had little effect. Monitoring the cell cycle after synchronization with nocodazole, S-phase progression was slightly delayed in UROtsa and T24 ARID1A KO cells compared to their controls. Interestingly, cells appeared to harbor a G2/M checkpoint defect as a higher fraction of ARID1A KO cells reentered G1 phase after DNA damage prematurely, which might be relevant for cancer progression. Alternative splicing was verified for one candidate gene using RT-qPCR. Finally, we did not observe histological and immunohistochemical coregulation of CD8 or PD-L1 upon deregulating ARID1A. All in all, we presume that the altered cell cycle (checkpoints) and splicing could have major impacts on the cell behavior and may be exploited for treatment.
Publications
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ATAC-Seq and RNA-Seq datasets
Rebecca Schlößer
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Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal‐like and malignant urothelial cells. Molecular Oncology, 19(12), 3784-3805.
Schlösser, Rebecca M.; Krumbach, Florian; Corrales, Eyleen; Andrieux, Geoffroy; Preisinger, Christian; Liss, Franziska; Golzmann, Alexandra; Boerries, Melanie; Becker, Kerstin; Knüchel, Ruth; Garczyk, Stefan & Lüscher, Bernhard
