Tumor slice culture system to assess drug response of primary breast cancer

Genome Instability and Cance

Frequent homologous recombination deficiency in high-grade endometrial carcinomas

Purpose The elevated levels of somatic copy number alterations (SCNA) in a subset of high-risk endometrial cancers (EC) are suggestive of defects in pathways governing genome integrity. We sought to assess the prevalence of homologous recombination deficiency (HRD) in EC and its association with histopathological and molecular characteristics. Experimental Design Fresh tumor tissue was prospectively collected from 36 EC, and functional HRD was examined by the ability of replicating tumor cells to accumulate RAD51 protein at DNA double strand breaks (RAD51 foci) induced by ionizing radiation. Genomic alterations were determined by next generation sequencing and array comparative genomic hybridization/SNP array. The prevalence of BRCA-associated genomic scars-a surrogate marker for HRD-was determined in the TCGA EC cohort. Results Most EC included in the final analysis (n=25) were of non-endometrioid (52%), grade 3 (60%) histology and FIGO-stage I (72%). HRD was observed in 24% (n=6) of cases and was restricted to non-endometrioid EC (NEEC), with 46% of NEEC being HRD compared to none of the endometrioid EC (EEC, P=0.014). All but one of the HRD cases harboured either a pathogenic BRCA1 variant or high somatic copy number losses of HR genes. Analysis of TCGA cases supported these results, with BRCA-associated genomic scars present in up to 48% (63/132) of NEEC vs. 12% (37/312) of EEC (P≺0.001). Conclusions HRD occurs in EC, and is largely restricted to non-endometrioid, TP53-mutant EC. Evaluation of HRD may help select patients that could benefit from treatments targeting this defect, including platinum compounds and PARP inhibitors.</p

Frequent homologous recombination deficiency in high-grade endometrial carcinomas

Purpose The elevated levels of somatic copy number alterations (SCNA) in a subset of high-risk endometrial cancers (EC) are suggestive of defects in pathways governing genome integrity. We sought to assess the prevalence of homologous recombination deficiency (HRD) in EC and its association with histopathological and molecular characteristics. Experimental Design Fresh tumor tissue was prospectively collected from 36 EC, and functional HRD was examined by the ability of replicating tumor cells to accumulate RAD51 protein at DNA double strand breaks (RAD51 foci) induced by ionizing radiation. Genomic alterations were determined by next generation sequencing and array comparative genomic hybridization/SNP array. The prevalence of BRCA-associated genomic scars-a surrogate marker for HRD-was determined in the TCGA EC cohort. Results Most EC included in the final analysis (n=25) were of non-endometrioid (52%), grade 3 (60%) histology and FIGO-stage I (72%). HRD was observed in 24% (n=6) of cases and was restricted to non-endometrioid EC (NEEC), with 46% of NEEC being HRD compared to none of the endometrioid EC (EEC, P=0.014). All but one of the HRD cases harboured either a pathogenic BRCA1 variant or high somatic copy number losses of HR genes. Analysis of TCGA cases supported these results, with BRCA-associated genomic scars present in up to 48% (63/132) of NEEC vs. 12% (37/312) of EEC (P≺0.001). Conclusions HRD occurs in EC, and is largely restricted to non-endometrioid, TP53-mutant EC. Evaluation of HRD may help select patients that could benefit from treatments targeting this defect, including platinum compounds and PARP inhibitors

The impact of coding germline variants on contralateral breast cancer risk and survival.

Evidence linking coding germline variants in breast cancer (BC)-susceptibility genes other than BRCA1, BRCA2, and CHEK2 with contralateral breast cancer (CBC) risk and breast cancer-specific survival (BCSS) is scarce. The aim of this study was to assess the association of protein-truncating variants (PTVs) and rare missense variants (MSVs) in nine known (ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53) and 25 suspected BC-susceptibility genes with CBC risk and BCSS. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated with Cox regression models. Analyses included 34,401 women of European ancestry diagnosed with BC, including 676 CBCs and 3,449 BC deaths; the median follow-up was 10.9 years. Subtype analyses were based on estrogen receptor (ER) status of the first BC. Combined PTVs and pathogenic/likely pathogenic MSVs in BRCA1, BRCA2, and TP53 and PTVs in CHEK2 and PALB2 were associated with increased CBC risk [HRs (95% CIs): 2.88 (1.70-4.87), 2.31 (1.39-3.85), 8.29 (2.53-27.21), 2.25 (1.55-3.27), and 2.67 (1.33-5.35), respectively]. The strongest evidence of association with BCSS was for PTVs and pathogenic/likely pathogenic MSVs in BRCA2 (ER-positive BC) and TP53 and PTVs in CHEK2 [HRs (95% CIs): 1.53 (1.13-2.07), 2.08 (0.95-4.57), and 1.39 (1.13-1.72), respectively, after adjusting for tumor characteristics and treatment]. HRs were essentially unchanged when censoring for CBC, suggesting that these associations are not completely explained by increased CBC risk, tumor characteristics, or treatment. There was limited evidence of associations of PTVs and/or rare MSVs with CBC risk or BCSS for the 25 suspected BC genes. The CBC findings are relevant to treatment decisions, follow-up, and screening after BC diagnosis

BRCA2 hypomorphic missense variants confer moderate risks of breast cancer

Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case–control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; P = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; P = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; P = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; P = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants