RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability

Provasek, V.; Bacolla, A.; Rangaswamy, S.; Mitra, J.; Kodavati, M.; Yusuf, I.; Malojirao, V.; Vasquez, V.; Britz, G. W.; Li, G.-M.; Xu, Z.; Mitra, S.; Garruto, R. M.; Tainer, J.; Hegde, M.

doi:10.1101/2024.05.16.594552

bioRxiv · 10.1101/2024.05.16.594552

RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability

Provasek, V.·Bacolla, A.·Rangaswamy, S.·Mitra, J.·Kodavati, M.·Yusuf, I.·Malojirao, V.·Vasquez, V.·Britz, G. W.·Li, G.-M.·Xu, Z.·Mitra, S.·Garruto, R. M.·Tainer, J.·Hegde, M.

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Abstract

TDP43 is an RNA/DNA binding protein increasingly recognized for its role in neurodegenerative conditions, including amyotrophic lateral sclerosis and frontotemporal dementia (FTD). As characterized by its aberrant nuclear export and cytoplasmic aggregation, TDP43 proteinopathy is a hallmark feature in over 95% of ALS/FTD cases, leading to the formation of detrimental cytosolic aggregates and a reduction in nuclear functionality within neurons. Building on our prior work linking TDP43 proteinopathy to the accumulation of DNA double-strand breaks (DSBs) in neurons, the present investigation uncovers a novel regulatory relationship between TDP43 and DNA mismatch repair (MMR) gene expressions. Here, we show that TDP43 depletion or overexpression directly affects the expression of key MMR genes. Alterations include MLH1, MSH2, MSH3, MSH6, and PMS2 levels across various primary cell lines, independent of their proliferative status. Our results specifically establish that TDP43 selectively influences the expression of MLH1 and MSH6 by influencing their alternative transcript splicing patterns and stability. We furthermore find aberrant MMR gene expression is linked to TDP43 proteinopathy in two distinct ALS mouse models and post-mortem brain and spinal cord tissues of ALS patients. Notably, MMR depletion resulted in the partial rescue of TDP43 proteinopathy-induced DNA damage and signaling. Moreover, bioinformatics analysis of the TCGA cancer database reveals significant associations between TDP43 expression, MMR gene expression, and mutational burden across multiple cancers. Collectively, our findings implicate TDP43 as a critical regulator of the MMR pathway and unveil its broad impact on the etiology of both neurodegenerative and neoplastic pathologies.

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Provasek, V., Bacolla, A., Rangaswamy, S., Mitra, J., Kodavati, M., Yusuf, I., Malojirao, V., Vasquez, V., Britz, G. W., Li, G.-M., Xu, Z., Mitra, S., Garruto, R. M., Tainer, J., Hegde, M.. 2024-05-17. RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability. https://doi.org/10.1101/2024.05.16.594552

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