Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2.

Melanie L Bailey,Amy Hin Yan Tong,Andrea Habsid,David Tieu,Katherine Chan,Jason Moffat,Philip Hieter

doi:10.26508/lsa.202101083

Abstract

STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2 Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.

Highlights

Cohesin is a well-conserved structural ring complex that physically tethers two DNA segments to ensure proper chromatin organization and function
For HAP1 and RPE1 lines, we generated STAG2 KO clones using one of two single guide RNAs that targeted STAG2 exonic DNA (Fig S1A and Table S1). Both HAP1 and RPE1 lines have been screened with CRISPR-Cas9 previously (Hart et al, 2015, 2017; Brown et al, 2019; Aregger et al, 2020), which we felt would be helpful in analyzing results from our isogenic STAG2 screens
More studies have recognized that many genetic interactions are influenced by genetic and environmental factors including cell line background, epigenetic profiles and various endogenous and exogenous stresses (Ryan et al, 2018; Shen & Ideker, 2018)

Summary

Introduction

Cohesin is a well-conserved structural ring complex that physically tethers two DNA segments to ensure proper chromatin organization and function. Mitotic cohesin consists of three core ring components, SMC1A, SMC3, and RAD21, as well as several accessory factors including one of two SCC3 paralogs, either STAG1 or STAG2 (Uhlmann, 2016). These two paralogs are thought to be mainly interchangeable in the complex, more recent data have indicated separate roles for cohesin-STAG1 and cohesinSTAG2 in a small number of functions (Kong et al, 2014; Daniloski & Smith, 2017; Kojic et al, 2018; Casa et al, 2020). Loss of STAG2 has been shown to be synthetic lethal with its paralog STAG1 (Benedetti et al, 2017; van der Lelij et al, 2017, 2020; Liu et al, 2018; Viny et al, 2019)

Methods

Results

Conclusion