Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair

Abstract

DNA repair by homologous recombination (HR) is critical for the maintenance of genome stability. Germline and somatic mutations in HR genes have been associated with an increased risk of developing breast (BC) and ovarian cancers (OvC). However, the extent of factors and pathways that are functionally linked to HR with clinical relevance for BC and OvC remains unclear. To gain a broader understanding of this pathway, we used multi-omics datasets coupled with machine learning to identify genes that are associated with HR and to predict their sub-function. Specifically, we integrated our phylogenetic-based co-evolution approach (CladePP) with 23 distinct genetic and proteomic screens that monitored, directly or indirectly, DNA repair by HR. This omics data integration analysis yielded a new database (HRbase) that contains a list of 464 predictions, including 76 gold standard HR genes. Interestingly, the spliceosome machinery emerged as one major pathway with significant cross-platform interactions with the HR pathway. We functionally validated 6 spliceosome factors, including the RNA helicase SNRNP200 and its co-factor SNW1. Importantly, their RNA expression correlated with BC/OvC patient outcome. Altogether, we identified novel clinically relevant DNA repair factors and delineated their specific sub-function by machine learning. Our results, supported by evolutionary and multi-omics analyses, suggest that the spliceosome machinery plays an important role during the repair of DNA double-strand breaks (DSBs).

Systematic proximal mapping of the classical RAD51 paralogs unravel functionally and clinically relevant interactors for genome stability

“…The spliceosome machine (KEGG:03040) emerged as a common pathway of the chemogenomic sub-groups (Fig 3C, S6 Table ). Indeed, we noted that several splicing factors are proximal interactors of the classical RAD51 paralogs at steady state and their targeting by CRISPR technology significantly modulates the response to genotoxic drugs (Fig 3D ), in line with phylogenetic co-evolution profiling data [44]. RAD51 paralogs are known to be essential in non-transformed human cells [13].…”

“…RNA-related processes have emerged as an integral component of the DNA damage response [51,52]. It is well established that the spliceosome machinery controls the transcription of established DNA repair genes [53,54], alongside putative regulators of these factors [44]. However, additional mechanisms of regulation of the DNA damage response have been attributed to the spliceosome machinery and its associated RNA binding proteins, including the signaling of the break, the remodeling of chromatin at DNA damage sites, DNA:RNA hybrids stabilization, RNA-templated DNA repair and liquid-liquid phase separation.…”

“…(E) Heatmap clustering representing the NormZ-scores of our selected preys alongside the classical RAD51 paralogs in a series of CRISPR screens published by [23]. (F) Representation of the percentage of S/G2 U2OS cells transfected with the indicated siRNA and displaying more than 9 IR-induced RAD51 foci as published in [44]. Each replicate is plotted on the x-and y-axis.…”

RNAPII-dependent ATM signaling at collisions with replication forks

“…For example, BRCA2the key mediator protein in HR-mediated DNA repair and an ATM substrate-broadly associates with RNAPII and is critical for fork stabilization 65,66 . Analogously, other RNAPII-associated factors, including DNA helicases (e.g., RECQ5 and DHX9) or spliceosomal RNA helicases may be activated by ATM to promote resolution of R loops, stabilize and remodel replication forks for efficient restart of DNA synthesis 19,[67][68][69] .…”

Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients

“…Alternative splicing is one of the major contributors to protein variation and diversity, which provide cancer cells the cellular plasticity to survive stress ( 123 ). With the availability of CPTAC data, emerging studies are investigating a multi-omics approach for integrated splice variants discovery but are limited to the purpose of disease monitoring and prognosis determination ( 124 , 125 ). Here, our scientific predicate (in this review) is that cancer-specific alternative splicing event is an untapped source of targets for therapeutic intervention, and a complete multi-omics characterization will enable the discovery, validation, and prioritization of the ASE targets.…”