The RecQ DNA helicase WRN is a synthetic lethal target for cancers with microsatellite instability (MSI), a form of genetic hypermutability arising from impaired mismatch repair 1-4 . WRN depletion induces widespread DNA double strand breaks (DSBs) in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI cancers from DSBs remains unclear. Here, we demonstrate that TAdinucleotide repeats are highly unstable in MSI cells and exhibit surprisingly large-scale expansions, distinct from previously described insertion/deletion mutations of a few nucleotides 5 . We show that expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and necessitate unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to MUS81 nuclease cleavage, leading to massive chromosome shattering. Thus, our study uncovers a distinct biomarker within MSI tumors that underlies the synthetic lethal dependence on WRN, thereby supporting the development of WRN-based therapeutics.

Transforming growth factor-β (TGF-β) is major inducer of epithelial to mesenchymal transition (EMT), which associates with cancer cell metastasis and resistance to chemotherapy and targeted drugs, through both transcriptional and non-transcriptional mechanisms. We previously reported that in cancer cells, heightened mitogenic signaling allows TGF-β-activated Smad3 to interact with poly(RC) binding protein 1 (PCBP1) and together they regulate many alternative splicing events that favors expression of protein isoforms essential for EMT, cytoskeletal rearrangement, and adherens junction signaling. Here, we show that the exclusion of TGF-β-activated kinase 1 (TAK1) variable exon 12 requires another RNA-binding protein, Fox-1 homolog 2 (Rbfox2), which binds intronic sequences in front of exon 12 independently of the Smad3-PCBP1 complex. Functionally, exon 12-excluded TAK1∆E12 and full length TAK1FL are distinct. The short isoform TAK1∆E12 is constitutively active and supports TGF-β-induced EMT and nuclear factor kappa B (NF-κB) signaling, whereas the full-length isoform TAK1FL promotes TGF-β-induced apoptosis. These observations offer a harmonious explanation for how a single TAK1 kinase can mediate the opposing responses of cell survival and apoptosis in response to TGF-β. They also reveal a propensity of the alternatively spliced TAK1 isoform TAK1∆E12 to cause drug resistance due to its activity in supporting EMT and NF-κB survival signaling.