Repression of transcription at DNA breaks requires cohesin throughout interphase and prevents genome instability

Cohesin subunits are frequently mutated in cancer, but how they function as tumor suppressors is unknown. Cohesin mediates sister chromatid cohesion, but this is not always perturbed in cancer cells. Here, we identify a previously unknown role for cohesin. We find that cohesin is required to repress transcription at DNA double-strand breaks (DSBs). Notably, cohesin represses transcription at DSBs throughout interphase, indicating that this is distinct from its known role in mediating DNA repair through sister chromatid cohesion. We identified a cancer-associated SA2 mutation that supports sister chromatid cohesion but is unable to repress transcription at DSBs. We further show that failure to repress transcription at DSBs leads to large-scale genome rearrangements. Cancer samples lacking SA2 display mutational patterns consistent with loss of this pathway. These findings uncover a new function for cohesin that provides insights into its frequent loss in cancer

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Distinct response of adult neural stem cells to low versus high dose ionising radiation.

Radiosusceptibility is the sensitivity of a biological organism to ionising radiation (IR)-induced carcinogenesis, an outcome of IR exposure relevant following low doses. The tissue response is strongly influenced by the DNA damage response (DDR) activated in stem and progenitor cells. We previously reported that in vivo exposure to 2 Gy X-rays activates apoptosis, proliferation arrest and premature differentiation in neural progenitor cells (transit amplifying cells and neuroblasts) but not in neural stem cells (NSCs) of the largest neurogenic region of the adult brain, the subventricular zone (SVZ). These responses promote adult quiescent NSC (qNSC) activation after 2 Gy. In contrast, neonatal (P5) SVZ neural progenitors continue proliferating and do not activate qNSCs. Significantly, the human and mouse neonatal brain is radiosusceptible. Here, we examine the response of stem and progenitor cells in the SVZ to low IR doses (50–500 mGy). We observe a linear dose-response for apoptosis but, in contrast, proliferation arrest and neuroblast differentiation require a threshold dose of 200 or 500 mGy, respectively. Importantly, qNSCs were not activated at doses below 500 mGy. Thus, full DDR activation in the neural stem cell compartment in vivo necessitates a threshold dose, which can be considered of significance when evaluating IR-induced cancer risk and dose extrapolation

Novel synthetic lethality screening method identifies TIP60-dependent radiation sensitivity in the absence of BAF180

In recent years, research into synthetic lethality and how it can be exploited in cancer treatments has emerged as major focus in cancer research. However, the lack of a simple to use, sensitive and standardised assay to test for synthetic interactions has been slowing the efforts. Here we present a novel approach to synthetic lethality screening based on co-culturing two syngeneic cell lines containing individual fluorescent tags. By associating shRNAs for a target gene or control to individual fluorescence labels, we can easily follow individual cell fates upon siRNA treatment and high content imaging. We have demonstrated that the system can recapitulate the functional defects of the target gene depletion and is capable of discovering novel synthetic interactors and phenotypes. In a trial screen, we show that TIP60 exhibits synthetic lethality interaction with BAF180, and that in the absence of TIP60, there is an increase micronuclei dependent on the level of BAF180 loss, significantly above levels seen with BAF180 present. Moreover, the severity of the interactions correlates with proxy measurements of BAF180 knockdown efficacy, which may expand its usefulness to addressing synthetic interactions through titratable hypomorphic gene expression

La déficience de PBRM1 confère une létalité synthétique aux inhibiteurs de la réparation de l'ADN dans le cancer

International audienceInactivation of Polybromo 1 (PBRM1), a specific subunit of the PBAF chromatin remodeling complex, occurs frequently in cancer, including 40% of clear cell renal cell carcinomas (ccRCC). To identify novel therapeutic approaches to targeting PBRM1-defective cancers, we used a series of orthogonal functional genomic screens that identified PARP and ATR inhibitors as being synthetic lethal with PBRM1 deficiency. The PBRM1/PARP inhibitor synthetic lethality was recapitulated using several clinical PARP inhibitors in a series of in vitro model systems and in vivo in a xenograft model of ccRCC. In the absence of exogenous DNA damage, PBRM1-defective cells exhibited elevated levels of replication stress, micronuclei, and R-loops. PARP inhibitor exposure exacerbated these phenotypes. Quantitative mass spectrometry revealed that multiple R-loop processing factors were downregulated in PBRM1-defective tumor cells. Exogenous expression of the R-loop resolution enzyme RNase H1 reversed the sensitivity of PBRM1-deficient cells to PARP inhibitors, suggesting that excessive levels of R-loops could be a cause of this synthetic lethality. PARP and ATR inhibitors also induced cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) innate immune signaling in PBRM1-defective tumor cells. Overall, these findings provide the preclinical basis for using PARP inhibitors in PBRM1-defective cancers. SIGNIFICANCE: This study demonstrates that PARP and ATR inhibitors are synthetic lethal with the loss of PBRM1, a PBAF-specific subunit, thus providing the rationale for assessing these inhibitors in patients with PBRM1-defective cancer.L'inactivation de Polybromo 1 (PBRM1), une sous-unité spécifique du complexe de remodelage de la chromatine PBAF, se produit fréquemment dans le cancer, y compris dans 40% des carcinomes rénaux à cellules claires (ccRCC). Afin d'identifier de nouvelles approches thérapeutiques pour cibler les cancers déficients en PBRM1, nous avons utilisé une série de cribles génomiques fonctionnels orthogonaux qui ont identifié les inhibiteurs PARP et ATR comme étant synthétiquement létaux en cas de déficience en PBRM1. La létalité synthétique des inhibiteurs de PBRM1/PARP a été récapitulée en utilisant plusieurs inhibiteurs cliniques de PARP dans une série de systèmes modèles in vitro et in vivo dans un modèle de xénogreffe de ccRCC. En l'absence de lésions exogènes de l'ADN, les cellules déficientes en PBRM1 présentaient des niveaux élevés de stress de réplication, de micronoyaux et de boucles R. L'exposition à un inhibiteur de PARP a exacerbé la létalité synthétique. L'exposition à un inhibiteur de PARP a exacerbé ces phénotypes. La spectrométrie de masse quantitative a révélé que plusieurs facteurs de traitement des boucles R étaient régulés à la baisse dans les cellules tumorales défectueuses de PBRM1. L'expression exogène de l'enzyme de résolution des boucles R, la RNase H1, a inversé la sensibilité des cellules PBRM1 déficientes aux inhibiteurs de la PARP, ce qui suggère que des niveaux excessifs de boucles R pourraient être une cause de cette létalité synthétique. Les inhibiteurs de PARP et d'ATR ont également induit une signalisation immunitaire innée de type GMP cyclique-AMP synthase/stimulateur des gènes de l'interféron (cGAS/STING) dans les cellules tumorales déficientes en PBRM1. Dans l'ensemble, ces résultats fournissent une base préclinique pour l'utilisation des inhibiteurs de PARP dans les cancers déficients en PBRM1. SIGNIFICATION : Cette étude démontre que les inhibiteurs de PARP et d'ATR sont synthétiquement létaux en cas de perte de PBRM1, une sous-unité spécifique du PBAF, ce qui justifie l'évaluation de ces inhibiteurs chez les patients atteints d'un cancer déficient en PBRM1