Ye Xu

Background: The high risk of contralateral breast cancer (CBC) in carriers of germline BRCA1/2 pathogenic variants (PVs) is well established, whereas differences in tumor subtype and risk of CBC between BRCA1 and BRCA2 carriers remain largely unknown. Methods: This cohort study included 738 unselected Chinese patients with breast cancer who carried BRCA1/2 PVs (289 BRCA1 and 449 BRCA2 carriers) and were treated at Peking University Cancer Hospital between October 2003 and August 2021. Tumor subtypes and the cumulative incidence of CBC were analyzed in both BRCA1 and BRCA2 carriers. Results: After a median follow-up of 9.0 years, 52 (18.0%) of 289 BRCA1 carriers and 49 (10.9%) of 449 BRCA2 carriers had developed CBC. The 10-year cumulative incidence of CBC was significantly higher in BRCA1 than in BRCA2 carriers (18.9% vs. 11.7%; p = 0.01). Among patients aged 40 years or younger, the 10-year cumulative incidence of CBC was higher in BRCA1 carriers than in BRCA2 carriers (27.5% vs. 12.5%; p = 0.007; adjusted hazard ratio, 2.58 [95% CI, 1.06–6.29]; p = 0.04). In addition, among BRCA1 carriers who developed CBC, the majority of primary tumors (62.7%) were triple-negative breast cancers (TNBCs). Among these patients with primary TNBC, approximately 77.4% of contralateral breast tumors were also TNBC. In contrast, primary and contralateral tumors in BRCA2 carriers were predominantly hormone receptor-positive (72.9% and 66.7%, respectively). Conclusions:BRCA1 carriers have a higher CBC risk than BRCA2 carriers. TNBC is the predominant phenotype of both primary and subsequent contralateral tumors in BRCA1 carriers. These findings provide useful data to inform the optimal management of CBC risk in BRCA1/2 carriers.

Purpose: To evaluate the pathogenicity of BRCA2 variants of uncertain significance (VUS) located within the functionally critical exons 15–26 using published SGE data, and to reclassify these VUS by integrating clinical phenotypes. Methods: A total of 15,092 breast cancer patients were enrolled in this study, among which 457 distinct BRCA2 VUS were identified in 1051 carriers. Based on SGE scores, 88 BRCA2 VUSs within exons 15–26 were functionally assessed and carriers reclassified as functionally pathogenic, functionally benign, or remaining VUS. Clinicopathological characteristics were subsequently compared across variant groups. Results: Of these 88 evaluated BRCA2 VUSs (187 carriers), 15 were reclassified as functionally pathogenic (20 carriers), 66 as functionally benign (154 carriers), and 7 remained VUS (13 carriers). Compared with non-carriers, carriers with functionally pathogenic variants exhibited a significantly higher prevalence of a family history of any cancer (65.0% vs. 31.1%, p = 0.002), particularly breast and/or ovarian cancer (35.0% vs. 10.0%, p = 0.002), as well as a trend toward a higher incidence of bilateral breast cancer (10.0% vs. 2.4%, p = 0.085). In contrast, individuals harboring functionally benign variants demonstrated clinicopathological characteristics similar to non-carriers. Conclusion: SGE-based functional scoring system provides a reliable approach for reclassifying BRCA2 VUS. When integrated with clinical phenotypes, it enhanced the accuracy of pathogenicity assessment.

Pathogenic germline variants in the BRCA1 gene significantly increase the lifetime risk of breast cancer and are frequently associated with early‐onset and triple‐negative disease. However, the chronology of genetic events during breast tumor evolution in BRCA1 carriers remains unclear. In this study, 57 primary breast tumors from 57 BRCA1 carriers were analyzed, including formalin‐fixed paraffin‐embedded specimens and fresh‐frozen specimens. Formalin‐fixed paraffin‐embedded tumors were microdissected into normal mammary tissue, carcinoma in situ, and invasive carcinoma components for deep target‐region sequencing, whereas fresh‐frozen tumors underwent whole‐exome sequencing and bulk transcriptome sequencing. Compared with non‐carriers from The Cancer Genome Atlas, breast cancers from BRCA1 carriers showed a distinct mutational landscape characterized by a high prevalence of TP53 mutations and a reduced frequency of PIK3CA and GATA3 alterations. Based on the initiating driver event, BRCA1 ‐associated tumors were classified into three subgroups: TP53 , PI(3)K‐AKT pathway, and unclassified. The TP53 ‐driven subgroup was strongly associated with the triple‐negative phenotype, loss of heterozygosity at the BRCA1 locus, and elevated genomic instability. TP53 truncating mutations were enriched in BRCA1 carriers compared with non‐carriers and showed a trend toward worse outcomes, potentially related to lower homologous recombination deficiency scores and activation of epithelial‐mesenchymal transition pathways. These findings highlight the distinct mutational architecture of breast cancers from BRCA1 carriers and suggest that TP53 truncating mutations may define a particularly aggressive subtype that warrants further investigation.

PURPOSE: The atlas of immune microenvironment at single-cell level in BRCA1/2 -mutated breast cancer is largely unknown and whether an immune signature on the basis of single-cell atlas is associated with response to neoadjuvant chemotherapy remains to be investigated. MATERIALS AND METHODS: The immune microenvironment between BRCA1/2 -mutated and BRCA wild-type breast tumors was explored using single-cell RNA sequencing (scRNA-seq) assay and was validated in an independent cohort of 40 BRCA1/2 carriers and 56 noncarriers via immunohistochemistry assay (IHC). Bulk RNA-seq was performed using RNA extracted from fresh-frozen pretreatment core-needle tumor tissues in 80 BRCA1/2 carriers with operable primary human epidermal growth factor receptor 2–negative tumors who received neoadjuvant chemotherapy, and the associations between immune cell subtypes defined by scRNA-seq and pathologic complete response (pCR) were investigated. RESULTS: BRCA1/2 -mutated tumors exhibited an enriched immune microenvironment compared with the wild-type counterparts at single-cell level, particularly regulatory T cells and exhausted T cells, which were validated in the IHC cohort. Among the neoadjuvant chemotherapy cohort of 80 BRCA1/2 carriers, 36.2% achieved a pCR. We established an immune signature on the basis of the single-cell and bulk RNA-seq data, named BRCA-IM. The BRCA-IM model exhibited an excellent prediction of pCR in the neoadjuvant chemotherapy cohort, with AUC values of 0.81(95% CI, 0.69 to 0.92) in the training set and 0.91(95% CI, 0.79 to 1.00) in the test set, respectively; and the BRCA-IM model remained as an independent predictor for pCR after adjusting for other factors. Moreover, higher BRCA-IM scores were significantly associated with more favorable survival in the neoadjuvant chemotherapy cohort. CONCLUSION: BRCA1/2 -mutated breast cancer shows an enriched tumor immune microenvironment, and the BRCA-IM model exhibits a good performance in prediction of pCR in BRCA1/2 -mutated tumors.

PURPOSE: The absolute cumulative risk of contralateral breast cancer (CBC) for patients with BRCA1/ 2 variants is unknown. The purpose of this study was to develop a CBC risk prediction model for assessing CBC risk for BRCA1/ 2 carriers.METHODS: The primary cohort of 491 patients with BRCA1/ 2 variants was derived from a large series of unselected patients with breast cancer. A nomogram was established on the basis of the results of a multivariate Cox regression analysis from this cohort. This model, named BRCA-CRisk, was further validated by an independent cohort of 205 patients with BRCA1/ 2 variants. Discrimination and calibration of the model were assessed.RESULTS: In the primary cohort of 491 patients, 66 developed contralateral breast cancer after a median follow-up of 7.0 years. Four variables were significantly associated with risk of CBC and were incorporated in the establishment of the BRCA-CRisk prediction model: younger age at first breast cancer (with continuous variable, P = .002), positive first-degree family history of breast and/or ovarian cancer (hazard ratio [HR], 1.89; 95% CI, 1.16 to 3.08; P = .011), variant located near the 3′ region of BRCA (HR, 2.01; 95% CI, 1.23 to 3.30; P = .006), and endocrine therapy (HR, 0.54; 95% CI, 0.33 to 0.88; P = .013). The area under the time-dependent curves for the 5- and 10-year cumulative risks of CBC were 0.775 and 0.702, respectively. The model was well validated in the independent cohort of 205 BRCA1/ 2 carriers, with area under the curves of 0.750 and 0.691 for 5 and 10 years, respectively.CONCLUSION: BRCA-CRisk model provides a useful tool for assessing the absolute cumulative risk of CBC for BRCA1/ 2 carriers and may help carriers and clinicians optimally select risk-reducing strategies on the basis of individual CBC risk.

Hyperactivation of Wnt signaling is crucial in tumor formation. Fully elucidating the molecular details of how the cancer-specific Wnt signaling pathway is activated or contributes to tumorigenesis will help in determining future treatment strategies. Here, we aimed to explore the contribution of CUEDC2, a novel CUE-domain-containing protein, to the activation of Wnt signaling and the tumorigenesis of triple-negative breast cancer (TNBC) and to determine the underlying mechanisms. TNBC patient samples and disease-free survival (DFS) data were used to determine the association between CUEDC2 and TNBC progression. The effects of CUEDC2 on TNBC were examined in TNBC cells in vitro and in subcutaneous xenograft tumors in vivo. Gene knockdown, immunoprecipitation plus liquid chromatography–tandem mass spectrometry, pull-down, co-immunoprecipitation, localized surface plasmon resonance, and nuclear translocation analysis were used to uncover the mechanisms of CUEDC2 in regulating Wnt signaling and TNBC development. CUEDC2 is sufficient to maintain the hyperactivation of Wnt signaling required for TNBC tumorigenesis. The contribution of CUEDC2 plays a major role in determining the outcome of oncogenic Wnt signaling both in vitro and in vivo. Mechanistically, the CUE domain in CUEDC2 directly bound to the ARM (7–9) domain in β-catenin, promoted β-catenin nuclear translocation and enhanced the expression of β-catenin targeted genes. More importantly, an 11-amino-acid competitive peptide targeting the CUE domain in CUEDC2 blocked the interactions of CUEDC2 and β-catenin and abrogated the malignant phenotype of TNBC cells in vitro and in vivo. We observed that TNBC patients who exhibited higher levels of CUEDC2 showed marked hyperactivation of the Wnt signaling pathway and poor clinical outcomes, highlighting the clinical relevance of our findings. CUEDC2 promotes TNBC tumor growth by enhancing Wnt signaling through directly binding to β-catenin and accelerating its nuclear translocation. Targeting the interactions of CUEDC2 and β-catenin may be a valuable strategy for combating TNBC.

Characterizing the pathogenicity of BRCA1 variants of uncertain significance (VUSs) is a major bottleneck in clinical management of BRCA1-associated breast cancer. Saturation genome editing (SGE) was recently reported as an innovative laboratory-based approach to assess the pathogenicity of BRCA1 variants. We combined clinical phenotypes and SGE score to identify the pathogenicity of BRCA1 VUSs detected in a cohort of 8,085 breast cancer patients. According to SGE function score, 33 out of 144 BRCA1 VUSs detected were classified into “loss of function” (n = 13), “intermediate” (n = 2), and “functional” (n = 18) groups. Compared with non-carriers, “loss of function” VUS carriers (n = 19) presented significantly worse clinicopathological characteristics. These included younger age at breast cancer diagnosis (44.4 years vs. 51.2 years, P = 0.01), stronger family history of any cancer (57.9% vs. 32.3%, P = 0.017) especially breast or ovarian cancer (47.4% vs. 9.3%, P < 0.001), more bilateral breast cancer (31.6% vs. 3.4%, P < 0.001), and triple-negative breast cancer (47.4% vs. 12.8%, P < 0.001), which were comparable to those of pathogenic variant carriers. In contrast, the clinical phenotypes of “functional” VUS carriers were similar to those of non-carriers. These results indicated that SGE was a reliable method in BRCA1 variant classification. Combining SGE function score and the available evidence, twelve out of 33 BRCA1 VUSs were reclassified as pathogenic or likely pathogenic variants and one was benign.

To investigate the prevalence and clinical relevance of PALB2 germline mutations in BRCA1/2-negative breast cancer patients.

BRCA1/2 genes are the most frequently germline mutated DNA‐repair genes and the survival of BRCA1/2 carriers has been extensively explored in breast cancer. However, the prevalence of germline mutations in non‐BRCA1/2 DNA‐repair genes and the survival of carriers are largely unknown in a large cohort of unselected breast cancer patients. Germline mutations in 16 DNA‐repair genes were determined using a multigene panel in 7657 BRCA1/2‐negative breast cancer patients who were unselected for family history of cancer or age at diagnosis. Among the 7657 BRCA1/2‐negative breast cancer patients, 257 (3.4%) carried at least one pathogenic germline mutation in the 16 DNA‐repair genes. The prevalence of DNA‐repair gene mutation was significant higher in familial breast cancers (5.2%, P=0.002) and early‐onset breast cancers (diagnosed at and before age of 40) (4.5%, P=0.003) than that of sporadic breast cancers (2.9%) (diagnosed above age of 40), respectively. The DNA‐repair gene mutation carriers were significantly more likely to have a larger tumor (P=0.04) and axillary lymph‐node metastasis (P=0.03). Moreover, DNA‐repair gene mutation was an independent unfavorable factor for recurrence‐free survival [adjusted hazard ratio (HR) =1.38, 95% CI: 1.00‐1.91, P=0.05] and disease‐specific survival (adjusted HR=1.63, 95% CI: 1.04–2.57, P=0.03) in this cohort. Overall, 3.4% of BRCA1/2‐negative breast cancer patients carried germline mutations in the 16 DNA‐repair genes, and the DNA‐repair gene mutation carriers exhibited an aggressive phenotype and had a poor survival compared with noncarriers.