A novel role for cohesin-STAG2 in R loop homeostasis

In recent years, structural maintenance of chromosomes (SMC) complexes have emerged as critical ring-shaped and ATP-dependent DNA tethers and loop extruders. The most well-known SMC complex, cohesin, has vital importance in nearly all aspects of chromosome metabolism, including gene expression, nuclear architecture, DNA replication and repair, and mitotic chromosome segregation. Against this backdrop, large-scale cancer sequencing projects revealed frequent mutations in cohesin subunits in tumors at multiple organ sites. How these mutations promote cancer, and whether they create collateral vulnerabilities that could be targeted therapeutically, are important unsolved problems. Building on our previous studies of cohesin and DNA replication, we analyzed cells that lacked STAG2, the most frequently mutated cohesin subunit and a TCGA-designated pan-cancer driver. We discovered that STAG2-deficient cells are prone to accumulation of R-loops and experience all the hallmarks of replication stress. They are also “addicted” to R-loop mitigating factors, including RNAse H2 and the Fanconi Anemia pathway. Via NER endonucleases, STAG2-deficient cells produce cytoplasmic R-loop fragments that trigger innate immune signaling. We propose studies that will dissect the mechanisms that underlie R-loop homeostasis, gene regulation, and avoidance of replication-transcription conflicts. This information will expand and deepen our understanding of how STAG2 regulates the genome under normal conditions and how its loss impacts cancer cells. This information is needed to develop more effective and less toxic cancer therapies. Project Number: 1R01GM164615-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Prasad Jallepalli | Institution: SLOAN-KETTERING INST CAN RESEARCH, NEW YORK, NY | Award Amount: $534,644 | Activity Code: R01 | Study Section: Molecular Genetics Study Section[MG] View on NIH RePORTER: https://reporter.nih.gov/project-details/11346739