BRCA1 deficiency is a recurrent event in early-onset triple-negative breast cancer: a comprehensive analysis of germline mutations and somatic promoter methylation.

PURPOSE: BRCA1 germline mutation is closely associated with triple-negative breast cancer. BRCA deficiency leads to impaired DNA repair and tumor development, and understanding this deficiency, in both hereditary and sporadic scenarios, is of great clinical and biological interest. Here, we investigated germline or somatic events that might lead to BRCA1 impairment in triple-negative breast cancer. We also analyzed the clinical implications associated with BRCA deficiency. METHODS: Next-generation sequencing for the BRCA1/2 genes and multiplex ligation-dependent probe amplification (MLPA) for the BRCA1 gene were performed for mutation screening. A customized bisulfite next-generation sequencing approach was used for assessing BRCA1 promoter methylation status in tumor tissue. RESULTS: A total of 131 triple-negative cases were assessed, and germline pathogenic variants were detected in 13.0% of all cases and in 26% of cases diagnosed in young women. Most germline pathogenic variants (88.2%) occurred in the BRCA1 gene. BRCA1 promoter hypermethylation was detected in 20.6% of tumors; none of these tumors were in BRCA1/2 pathogenic variant carriers. BRCA1 impairment by either germline or somatic events was significantly more frequent in young women (55% in those ≤ 40 years; 33% in those 41-50 years; 22% in those > 50 years of age) and associated with better overall and disease-free survival rates in this group of patients. CONCLUSIONS: BRCA1 deficiency was recurrent in early-onset triple-negative breast cancer in Brazilian patients and associated with improved survival. With the new treatment modalities being investigated, including poly (ADP-ribose)-polymerase (PARP) inhibitor therapy, our results suggest that a significant proportion of young women with this subtype of tumor might benefit from PARP inhibitor treatment, which warrants further investigation.

Triple-Negative Breast Cancer circRNAome Reveals Hsa_circ_0072309 as a Potential Risk Biomarker.

Circular RNAs (circRNAs) are a class of long non-coding RNAs that have the ability to sponge RNA-Binding Proteins (RBPs). Triple-negative breast cancer (TNBC) has very aggressive behavior and poor prognosis for the patient. Here, we aimed to characterize the global expression profile of circRNAs in TNBC, in order to identify potential risk biomarkers. For that, we obtained RNA-Seq data from TNBC and control samples and performed validation experiments using FFPE and frozen tissues of TNBC patients and controls, followed by in silico analyses to explore circRNA-RBP interactions. We found 16 differentially expressed circRNAs between TNBC patients and controls. Next, we mapped the RBPs that interact with the top five downregulated circRNAs (hsa_circ_0072309, circ_0004365, circ_0006677, circ_0008599, and circ_0009043) and hsa_circ_0000479, resulting in a total of 16 RBPs, most of them being enriched to pathways related to cancer and gene regulation (e.g., AGO1/2, EIF4A3, ELAVL1, and PTBP1). Among the six circRNAs, hsa_circ_0072309 was the one that presented the most confidence results, being able to distinguish TNBC patients from controls with an AUC of 0.78 and 0.81, respectively. This circRNA may be interacting with some RBPs involved in important cancer-related pathways and is a novel potential risk biomarker of TNBC.

Aspectos moleculares envolvidos no surgimento do Tumor Triplo-Negativo de Mama em pacientes portadoras ou não de mutação germinativa em BRCA1 / Molecular aspects involved in development of triple-negative breast cancer in patients with or without germline mutation in BRCA1

O Câncer de Mama Triplo-Negativo (CMTN), caracterizado pela perda de expressão dos receptores de estrógeno (RE), de progesterona (RP) e pela não super-expressão/amplificação do receptor do fator de crescimento epidermal humano do tipo 2 (HER-2), é considerado um subtipo bastante agressivo e heterogêneo molecularmente. Clinicamente, o CMTN apresenta prognóstico ruim, altas taxas de recorrência e menor sobrevida global em relação aos outros subtipos de câncer de mama. Ele corresponde a aproximadamente 15% dos casos de câncer de mama e não apresenta nenhuma terapia alvo efetiva. Mutação patogênica germinativa nos genes BRCA1 e BRCA2 leva a um aumento de risco para o desenvolvimento de Câncer de Mama e Ovário, sendo que mutação germinativa em BRCA1 está associada ao desenvolvimento de CMTN, especialmente em pacientes diagnosticadas antes dos 50 anos. A deficiência de BRCA1 leva ao mecanismo ineficiente do reparo do DNA e ao desenvolvimento do tumor. Recentemente, nosso grupo classificou as pacientes diagnosticadas com CMTN em grupo Hereditário (com mutação patogênica germinativa em BRCA1) e grupo Esporádico (sem mutação germinativa em BRCA1). Estes foram ainda classificados em tumores BRCA1-deficiente (com hipermetilação no promotor de BRCA1) e em tumores BRCA1-proficiente (sem hipermetilação no promotor de BRCA1 e sem mutação germinativa em BRCA1). As diferenças moleculares entre esses grupos de CMTN são de grande interesse clínico e biológico, embora ainda não sejam conhecidas. Dentro desse contexto, nosso objetivo foi investigar o perfil transcricional de CMTN sob diferentes aspectos de deficiência de BRCA1. Para isso, foi avaliado o sequenciamento do RNA (RNA-Seq) de 37 casos de CMTN em idade jovem (≤ 50 anos), sendo 9 casos Hereditário (com mutação patogênica germinativa em BRCA1) e 28 casos Esporádico. Dos casos Esporádicos, 9 foram BRCA1-deficiente (com o promotor de BRCA1 hipermetilado) e 19 BRCA1-proficiente (com o promotor de BRCA1 não hipermetilado). Utilizamos o RNA total a partir das 37 amostras tumorais e 25 amostras normais pareadas adjacentes ao tumor. As bibliotecas de cDNA foram construídas a partir do RNA total através do método de depleção do rRNA e sequenciadas na plataforma NextSeq (Illumina). Para a normalização dos dados de expressão de cada gene, foi aplicada a medida FPKM. Os critérios para a obtenção dos genes diferencialmente expressos (GDEs), nas amostras tumorais em relação às normais, foram fold change ≥ 4,0 e ≤ - 4,0 e p valor ajustado ≤ 0,05). Para classificação molecular dos tumores TN, foi utilizada a ferramenta online TNBCtype. As curvas de sobrevida global de acordo com essa classificação molecular foram calculadas através do método de Kaplan-Meier. Para verificar os processos biológicos envolvidos com a tumorigênese do CMTN, os GDEs foram submetidos a uma análise funcional in silico através do programa Ingenuity Pathway Analysis (IPA). Em média, 48.627.204 milhões de sequências foram geradas por amostra, das quais 79,5% foram mapeadas no genoma humano referência, revelando, em média, 15.071 genes expressos com pelo menos 10 sequências única mapeada por amostra. O perfil transcricional das amostras CMTN permitiu a classificação nos 7 subtipos moleculares de CMTN, sendo a maioria das amostras classificadas no subtipo imunomodulador (IM) e mesenquimal (M). No grupo das amostras BRCA1-deficiente, observamos um predomínio do subtipo IM enquanto que, nas amostras BRCA1-proficiente, houve um maior número de amostras classificadas em M. Não observamos diferença nas curvas de sobrevida global entre os dois grupos de amostras. Porém, os resultados mostraram que o subtipo IM parece ter uma tendência de melhor sobrevida global comparado com os outros subtipos, independente do status de BRCA1. A expressão diferencial das amostras tumorais em relação às amostras normais no grupo de CMTN Hereditário revelou 1965 GDEs, sendo 589 mais expressos e 1376 menos expressos no tumor; e, no grupo de CMTN Esporádico, a análise revelou 1837 GDEs, sendo 645 mais expressos e 1192 menos expressos no tumor. A partir dos GDEs de cada grupo, a análise do IPA mostrou que os dois grupos apresentaram vias canônicas enriquecidas comuns significantemente ativadas e envolvidas, de forma geral, com a Regulação do ciclo celular. Entretanto, as vias canônicas significantemente inibidas mostraram-se exclusivas em cada grupo: a via de Sinalização do receptor do glutamato foi a mais significativa (z-score = -2,12) nas amostras de CMTN Hereditário; e a via de Ativação de LXR/RXR foi a mais significativa (z-score = -2,98) nas amostras CMTN Esporádico. Além disso, observamos reguladores transcricionais significantemente ativados e inibidos exclusivamente em cada grupo. Os genes TNF e E2F1 foram os mais significantemente ativados apenas nas amostras de CMTN Hereditário (z-score = 4,06) e de CMTN Esporádico (z-score = 2,22), respectivamente. Por outro lado, o microRNA mir-21 e o gene PPARG foram os reguladores inibidos exclusivamente nas amostras CMTN Hereditário (-score = -4,68) e nas amostras CMTN Esporádico (z-score = -4,24), respectivamente. Esse estudo, de forma geral, revelou potenciais vias e genes reguladores de cascatas de sinalização envolvidos na tumorigênese do CMTN no contexto da deficiência de BRCA1, contribuindo na elucidação da complexidade funcional de tumores TN

Triple-negative breast cancer (TNBC), characterized by lack of expression of the estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), results in aggressive biology, early peak of recurrence, and shorter overall survival than other subtypes. It comprises approximately 15% of breast cancer cases and yet there is no effective therapy. Mutations in the BRCA1 and BRCA2 genes are associated with increased risk of breast and ovarian cancers since germline mutation in BRCA1 is associated with the development of TNBC, especially in patients diagnosed before age 50. BRCA deficiency leads to impaired DNA repair and tumor development. Recently, our group classified TNBC patients into hereditary BRCA1-mutated and sporadic BRCA1-proficient. These were further classified into BRCA1-deficient tumors (with BRCA1 promotor hypermethylation) and BRCA1-proficient tumors (no BRCA1 promoter hypermethylation neither BRCA1 germline mutation). Molecular differences between hereditary and sporadic TNBC groups are clinically and biologically interesting although it remains unclear. In this context, we aimed to investigate the transcriptional profile of TNBC-associated or not with BRCA1 deficiency. For that, RNA sequencing (RNA-seq) from 37 early-onset TNBC (≤ 50 years old) was evaluated, comprising 9 Hereditary (with BRCA1 germline pathogenic mutation) and 28 Sporadic cases, of which 9 BRCA1-deficient and 19 BRCA1-proficient. Total RNA from 37 tumors samples and 25 adjacent normal samples of paired cases were used to constructed RNAseq libraries by depleting ribosomal RNA and sequenced on Illumina NextSeq 500 platform. Expression values were normalized by FPKM. Differentially expressed genes (DEGs) between tumor and normal samples were obtained using fold-change ≥ |4| and p value adjusted ≤ 0.05 as statistical criteria. The TNBC samples were subtyping using the web-based prediction tool TNBCType. Overall survival curves were calculated using the Kaplan.Meir method. IPA software was used to detect activated/inactivated canonical pathways and relevant upstream regulators, considering a z-score ≤-2.0 and ≥ 2.0, respectively. On average, 49 million reads were generated per sample, of which 79.5% were mapped to the human reference genome revealing 15,071 expressed genes with at least 10 reads per sample. From the transcriptional profile of TNBC samples we classified into seven TNBC subtypes being the majority of tumors classified as immunomodulatory (IM) and mesenchymal (M) subtype. We detected no difference in overall survival for both groups. However, trends towards better overall were observed for TNBC samples classified as IM compared with other subtypes, without associations with BRCA1 status. Differential gene expression analysis between tumor and normal samples in the hereditary group revealed 1,965 DEGs, being 589 upregulated and 1,376 downregulated; and in the sporadic group, the analysis revealed 1,837 DEGs, being 645 upregulated and 1,192 downregulated. Using the DEGs of each group, the IPA analysis revealed that Cell Cycle Regulation signaling was activated in both groups. Regarding inactivated pathways, we detected the Glutamate Receptor signaling (z-score = -2,12) in hereditary TNBC and the LXR/RXR activation in sporadic TNBC (z-score = -2,98). Also, the IPA analysis revealed relevant specific transcription regulators of each group. The TNF and E2F1 were the most significantly activated genes in hereditary- and sporadic-TNBC, respectively. On the other hand, the mir-21 and PPARG were the most significantly unique inhibited regulators in hereditary and sporadic, respectively. In general, this study unveiled potential pathways and regulatory genes for signaling cascades involved in TNBC tumorigenesis considering the deficiency of BRCA1, contributing to the elucidation of the functional complexity of the tumorigenic process of TNBC patients