致病性 BRCA1 或 BRCA2 种系突变会导致遗传性乳腺癌、卵巢癌、前列腺癌和胰腺癌。矛盾的是，BRCA1 或 BRCA2 (bBRCA1/2) 的双等位基因失活具有胚胎致死性，并会降低细胞增殖。促进 bBRCA1/2 肿瘤发生的补偿机制仍不清楚。我们鉴定了人类 bBRCA1/2 肿瘤中富含的反复遗传改变，并通过实验验证了这些改变是否改善了细胞模型中的增殖。我们通过 TCGA 和 ICGC 分析了 bBRCA1/2 乳腺癌和卵巢癌的突变和拷贝数改变 (CNA)。我们使用 Fisher 精确检验来鉴定与缺乏同源重组缺陷证据的对照肿瘤相比，bBRCA1/2 肿瘤中富集的 CNA。通过基因表达及其在全基因组 CRISPR/Cas9 筛选中对增殖的影响，进一步筛选了位于 bBRCA1/2 肿瘤中富集的 CNA 区域的基因。通过体外克隆存活和功能测定对一组候选基因进行了功能验证，以验证它们在 bBRCA1/2 突变情况下对增殖的影响。我们发现 bBRCA1/2 肿瘤中复发性大规模基因组缺失的频率明显高于组织学上的频率匹配对照（乳腺癌和卵巢癌中 n = 238 个细胞带）。在删除的区域内，我们在全基因组 CRISPR 筛选中发现了 277 个 BRCA1 相关基因和 218 个 BRCA2 相关基因，这些基因在 bBRCA1/2 中表达减少且增殖增加，但在野生型细胞中则不然。通过克隆增殖测定对 20 个候选基因进行体外验证，验证了 9 个基因，包括 RIC8A 和 ATMIN（ATM 相互作用蛋白）。我们发现 RIC8A 缺失，这种情况在 bBRCA1/2 肿瘤中经常发生，并且在 BRCA1 和 BRCA2 缺失的情况下综合可行。此外，我们发现转移性同源重组缺陷癌症会获得 RIC8A 功能丧失突变。最后，我们发现 RIC8A 不能挽救同源重组缺陷，但可能影响 bBRCA1/2 肿瘤的有丝分裂，可能导致微核形成增加。这项研究通过识别合成活力相互作用和受影响的因果驱动基因，提供了一种解决肿瘤抑制悖论的方法通过大规模 CNA 在人类癌症中的应用。© 2024。作者。

Pathogenic BRCA1 or BRCA2 germline mutations contribute to hereditary breast, ovarian, prostate, and pancreatic cancer. Paradoxically, bi-allelic inactivation of BRCA1 or BRCA2 (bBRCA1/2) is embryonically lethal and decreases cellular proliferation. The compensatory mechanisms that facilitate oncogenesis in bBRCA1/2 tumors remain unclear.We identified recurrent genetic alterations enriched in human bBRCA1/2 tumors and experimentally validated if these improved proliferation in cellular models. We analyzed mutations and copy number alterations (CNAs) in bBRCA1/2 breast and ovarian cancer from the TCGA and ICGC. We used Fisher's exact test to identify CNAs enriched in bBRCA1/2 tumors compared to control tumors that lacked evidence of homologous recombination deficiency. Genes located in CNA regions enriched in bBRCA1/2 tumors were further screened by gene expression and their effects on proliferation in genome-wide CRISPR/Cas9 screens. A set of candidate genes was functionally validated with in vitro clonogenic survival and functional assays to validate their influence on proliferation in the setting of bBRCA1/2 mutations.We found that bBRCA1/2 tumors harbor recurrent large-scale genomic deletions significantly more frequently than histologically matched controls (n = 238 cytobands in breast and ovarian cancers). Within the deleted regions, we identified 277 BRCA1-related genes and 218 BRCA2-related genes that had reduced expression and increased proliferation in bBRCA1/2 but not in wild-type cells in genome-wide CRISPR screens. In vitro validation of 20 candidate genes with clonogenic proliferation assays validated 9 genes, including RIC8A and ATMIN (ATM-Interacting protein). We identified loss of RIC8A, which occurs frequently in both bBRCA1/2 tumors and is synthetically viable with loss of both BRCA1 and BRCA2. Furthermore, we found that metastatic homologous recombination deficient cancers acquire loss-of-function mutations in RIC8A. Lastly, we identified that RIC8A does not rescue homologous recombination deficiency but may influence mitosis in bBRCA1/2 tumors, potentially leading to increased micronuclei formation.This study provides a means to solve the tumor suppressor paradox by identifying synthetic viability interactions and causal driver genes affected by large-scale CNAs in human cancers.© 2024. The Author(s).