1
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Morganti S, Marra A, De Angelis C, Toss A, Licata L, Giugliano F, Taurelli Salimbeni B, Berton Giachetti PPM, Esposito A, Giordano A, Bianchini G, Garber JE, Curigliano G, Lynce F, Criscitiello C. PARP Inhibitors for Breast Cancer Treatment: A Review. JAMA Oncol 2024; 10:658-670. [PMID: 38512229 DOI: 10.1001/jamaoncol.2023.7322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Importance Poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors have revolutionized the treatment of patients with germline BRCA1/2-associated breast cancer, representing the first targeted therapy capable of improving outcomes in patients with hereditary tumors. However, resistance to PARP inhibitors occurs in almost all patients. Observations This narrative review summarizes the biological rationale behind the use of PARP inhibitors in breast cancer, as well as the available evidence, recent progress, and potential future applications of these agents. Recent studies have shown that the benefit of PARP inhibitors extends beyond patients with germline BRCA1/2-associated metastatic breast cancer to patients with somatic BRCA1/2 variants and to those with germline PALB2 alterations. Moreover, these agents proved to be effective both in the metastatic and adjuvant settings. However, patients with metastatic breast cancer usually do not achieve the long-term benefit from PARP inhibitors observed in other tumor types. Mechanisms of resistance have been identified, but how to effectively target them is largely unknown. Ongoing research is investigating both novel therapeutics and new combination strategies to overcome resistance. PARP1-selective inhibitors, by sparing the hematological toxic effects induced by the PARP2 blockade, are promising agents to be combined with chemotherapy, antibody-drug conjugates, and other targeted therapies. Conclusions and Relevance Although the efficacy of PARP inhibitors is well established, many questions persist. Future research should focus on identifying predictive biomarkers and therapeutic strategies to overcome resistance. Integrating well-designed translational efforts into all clinical studies is thereby crucial to laying the groundwork for future insights from ongoing research.
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Affiliation(s)
- Stefania Morganti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University Federico II, Naples, Italy
- Laster and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Angela Toss
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Licata
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
- School of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Giugliano
- European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- INSERM U981-Molecular Predictors and New Targets in Oncology, PRISM Center for Precision Medicine, Gustave Roussy, Villejuif, France
| | | | | | - Angela Esposito
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Antonio Giordano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Giampaolo Bianchini
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
- School of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Giuseppe Curigliano
- European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Filipa Lynce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Carmen Criscitiello
- European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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Pan J, Wang Y, Huang S, Mao S, Ling Q, Li C, Li F, Yu M, Huang X, Huang J, Lv Y, Li X, Ye W, Wang H, Wang J, Jin J. High expression of BCAT1 sensitizes AML cells to PARP inhibitor by suppressing DNA damage response. J Mol Med (Berl) 2024; 102:415-433. [PMID: 38340163 DOI: 10.1007/s00109-023-02409-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 11/27/2023] [Accepted: 12/11/2023] [Indexed: 02/12/2024]
Abstract
Previous evidence has confirmed that branched-chain aminotransferase-1 (BCAT1), a key enzyme governing branched-chain amino acid (BCAA) metabolism, has a role in cancer aggression partly by restricting αKG levels and inhibiting the activities of the αKG-dependent enzyme family. The oncogenic role of BCAT1, however, was not fully elucidated in acute myeloid leukemia (AML). In this study, we investigated the clinical significance and biological insight of BCAT1 in AML. Using q-PCR, we analyzed BCAT1 mRNAs in bone marrow samples from 332 patients with newly diagnosed AML. High BCAT1 expression independently predicts poor prognosis in patients with AML. We also established BCAT1 knockout (KO)/over-expressing (OE) AML cell lines to explore the underlying mechanisms. We found that BCAT1 affects cell proliferation and modulates cell cycle, cell apoptosis, and DNA damage/repair process. Additionally, we demonstrated that BCAT1 regulates histone methylation by reducing intracellular αKG levels in AML cells. Moreover, high expression of BCAT1 enhances the sensitivity of AML cells to the Poly (ADP-ribose) polymerase (PARP) inhibitor both in vivo and in vitro. Our study has demonstrated that BCAT1 expression can serve as a reliable predictor for AML patients, and PARP inhibitor BMN673 can be used as an effective treatment strategy for patients with high BCAT1 expression. KEY MESSAGES: High expression of BCAT1 is an independent risk factor for poor prognosis in patients with CN-AML. High BCAT1 expression in AML limits intracellular αKG levels, impairs αKG-dependent histone demethylase activity, and upregulates H3K9me3 levels. H3K9me3 inhibits ATM expression and blocks cellular DNA damage repair process. Increased sensitivity of BCAT1 high expression AML to PARP inhibitors may be used as an effective treatment strategy in AML patients.
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Affiliation(s)
- Jiajia Pan
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Yungui Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Shujuan Huang
- Department of Hematology, the First Affiliated Hospital of University of Science and Technology of China, Anhui, Hefei, China
| | - Shihui Mao
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Qing Ling
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Chenying Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Fenglin Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Mengxia Yu
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Xin Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Jiansong Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Yunfei Lv
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Xia Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Wenle Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Huafeng Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China
| | - Jinghan Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China.
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China.
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Zhejiang, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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He H, Yang W, Shi Y, Chen X, Chen X, Hu X, Li X, Yang Y, Liu Z, Ye T, Wang N, Yu L. Design and synthesis of the first PARP-1 and proteasome dual inhibitors to treat breast cancer. Eur J Med Chem 2024; 264:115943. [PMID: 38039793 DOI: 10.1016/j.ejmech.2023.115943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/28/2023] [Accepted: 11/05/2023] [Indexed: 12/03/2023]
Abstract
PARP-1 is a crucial factor in repairing DNA single strand damage and maintaining genomic stability. However, the use of PARP-1 inhibitors is limited to combination with chemotherapy or radiotherapy, or as a single agent for indications carrying HRR defects. The ubiquitin-proteasome system processes the majority of cellular proteins and is the principal manner by which cells regulate protein homeostasis. Proteasome inhibitors can cooperate with PARP-1 inhibitors to inhibit DNA homologous recombination repair function. In this study, we designed and synthesized the first dual PARP-1 and proteasome inhibitor based on Olaparib and Ixazomib. Both compounds 42d and 42i exhibited excellent proliferation inhibition and dual-target synergistic effects on cells that were insensitive to PARP-1 inhibitors. Further mechanistic evaluations revealed that 42d and 42i could inhibit homologous recombination repair function by down-regulating the expression of BRCA1 and RAD51. Additionally, 42i induced more significant apoptosis and showed better inhibitory effect on cell proliferation in clonal formation experiments in breast cancer cells than 42d. In summary, our study presented a new class of dual PARP-1/proteasome inhibitors with significant synergistic effects for the treatment of breast cancer.
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Affiliation(s)
- Hualong He
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wan Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yaojie Shi
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xinyi Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiang Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyue Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yingyue Yang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhihao Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Tinghong Ye
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ningyu Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Luoting Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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4
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Dias Nunes J, Demeestere I, Devos M. BRCA Mutations and Fertility Preservation. Int J Mol Sci 2023; 25:204. [PMID: 38203374 PMCID: PMC10778779 DOI: 10.3390/ijms25010204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Hereditary cancers mostly affect the adolescent and young adult population (AYA) at reproductive age. Mutations in BReast CAncer (BRCA) genes are responsible for the majority of cases of hereditary breast and ovarian cancer. BRCA1 and BRCA2 act as tumor suppressor genes as they are key regulators of DNA repair through homologous recombination. Evidence of the accumulation of DNA double-strand break has been reported in aging oocytes, while BRCA expression decreases, leading to the hypothesis that BRCA mutation may impact fertility. Moreover, patients exposed to anticancer treatments are at higher risk of fertility-related issues, and BRCA mutations could exacerbate the treatment-induced depletion of the ovarian reserve. In this review, we summarized the functions of both genes and reported the current knowledge on the impact of BRCA mutations on ovarian ageing, premature ovarian insufficiency, female fertility preservation strategies and insights about male infertility. Altogether, this review provides relevant up-to-date information on the impact of BRCA1/2 mutations on fertility. Notably, BRCA-mutated patients should be adequately counselled for fertility preservation strategies, considering their higher sensitivity to chemotherapy gonadotoxic effects.
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Affiliation(s)
- Joana Dias Nunes
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.D.N.); (M.D.)
| | - Isabelle Demeestere
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.D.N.); (M.D.)
- Fertility Clinic, HUB-Erasme Hospital, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Melody Devos
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.D.N.); (M.D.)
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5
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Lee H, Ha S, Choi S, Do S, Yoon S, Kim YK, Kim WY. Oncogenic Impact of TONSL, a Homologous Recombination Repair Protein at the Replication Fork, in Cancer Stem Cells. Int J Mol Sci 2023; 24:ijms24119530. [PMID: 37298484 DOI: 10.3390/ijms24119530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
We investigated the role of TONSL, a mediator of homologous recombination repair (HRR), in stalled replication fork double-strand breaks (DSBs) in cancer. Publicly available clinical data (tumors from the ovary, breast, stomach and lung) were analyzed through KM Plotter, cBioPortal and Qomics. Cancer stem cell (CSC)-enriched cultures and bulk/general mixed cell cultures (BCCs) with RNAi were employed to determine the effect of TONSL loss in cancer cell lines from the ovary, breast, stomach, lung, colon and brain. Limited dilution assays and ALDH assays were used to quantify the loss of CSCs. Western blotting and cell-based homologous recombination assays were used to identify DNA damage derived from TONSL loss. TONSL was expressed at higher levels in cancer tissues than in normal tissues, and higher expression was an unfavorable prognostic marker for lung, stomach, breast and ovarian cancers. Higher expression of TONSL is partly associated with the coamplification of TONSL and MYC, suggesting its oncogenic role. The suppression of TONSL using RNAi revealed that it is required in the survival of CSCs in cancer cells, while BCCs could frequently survive without TONSL. TONSL dependency occurs through accumulated DNA damage-induced senescence and apoptosis in TONSL-suppressed CSCs. The expression of several other major mediators of HRR was also associated with worse prognosis, whereas the expression of error-prone nonhomologous end joining molecules was associated with better survival in lung adenocarcinoma. Collectively, these results suggest that TONSL-mediated HRR at the replication fork is critical for CSC survival; targeting TONSL may lead to the effective eradication of CSCs.
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Affiliation(s)
- Hani Lee
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sojung Ha
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Muscle Physiome Research Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - SeokGyeong Choi
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Soomin Do
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sukjoon Yoon
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Yong Kee Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Muscle Physiome Research Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Research Institute of Pharmacal Research, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Woo-Young Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Research Institute of Pharmacal Research, Sookmyung Women's University, Seoul 04310, Republic of Korea
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6
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Homologous Recombination Deficiency in Ovarian Cancer: from the Biological Rationale to Current Diagnostic Approaches. J Pers Med 2023; 13:jpm13020284. [PMID: 36836518 PMCID: PMC9968181 DOI: 10.3390/jpm13020284] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
The inability to efficiently repair DNA double-strand breaks using the homologous recombination repair pathway is defined as homologous recombination deficiency (HRD). This molecular phenotype represents a positive predictive biomarker for the clinical use of poly (adenosine diphosphate [ADP]-ribose) polymerase inhibitors and platinum-based chemotherapy in ovarian cancers. However, HRD is a complex genomic signature, and different methods of analysis have been developed to introduce HRD testing in the clinical setting. This review describes the technical aspects and challenges related to HRD testing in ovarian cancer and outlines the potential pitfalls and challenges that can be encountered in HRD diagnostics.
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7
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Crum CP, Yoon JY, Feltmate CM. Clinical commentary extra-uterine high-grade serous carcinoma: Two pathways, two preventions? Gynecol Oncol 2023; 169:1-3. [PMID: 36459857 DOI: 10.1016/j.ygyno.2022.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Christopher P Crum
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, United States of America.
| | - Ju-Yoon Yoon
- Department of Laboratory Medicine and Pathobiology, St. Michaels Hospital: Unity Health, 2 Carter Wing, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| | - Colleen M Feltmate
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, United States of America
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8
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Kim J, Jeong K, Jun H, Kim K, Bae JM, Song MG, Yi H, Park S, Woo GU, Lee DW, Kim TY, Lee KH, Im SA. Mutations of TP53 and genes related to homologous recombination repair in breast cancer with germline BRCA1/2 mutations. Hum Genomics 2023; 17:2. [PMID: 36604691 PMCID: PMC9817339 DOI: 10.1186/s40246-022-00447-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Germline mutations of breast cancer susceptibility gene BRCA1 and BRCA2 (gBRCA1/2) are associated with elevated risk of breast cancer in young women in Asia. BRCA1 and BRCA2 proteins contribute to genomic stability through homologous recombination (HR)-mediated double-strand DNA break repair in cooperation with other HR-related proteins. In this study, we analyzed the targeted sequencing data of Korean breast cancer patients with gBRCA1/2 mutations to investigate the alterations in HR-related genes and their clinical implications. MATERIALS AND METHODS Data of the breast cancer patients with pathogenic gBRCA1/2 mutations and qualified targeted next-generation sequencing, SNUH FiRST cancer panel, were analyzed. Single nucleotide polymorphisms, small insertions, and deletions were analyzed with functional annotations using ANNOVAR. HR-related genes were defined as ABL1, ATM, ATR, BARD1, BRCA1, BRCA2, CDKN1A, CDKN2A, CHEK1, CHEK2, FANCA, FANCD2, FANCG, FANCI, FANCL, KDR, MUTYH, PALB2, POLE, POLQ, RAD50, RAD51, RAD51D, RAD54L, and TP53. Mismatch-repair genes were MLH1, MSH2, and MSH6. Clinical data were analyzed with cox proportional hazard models and survival analyses. RESULTS Fifty-five Korean breast cancer patients with known gBRCA1/2 mutations and qualified targeted NGS data were analyzed. Ethnically distinct mutations in gBRCA1/2 genes were noted, with higher frequencies of Val1833Ser (14.8%), Glu1210Arg (11.1%), and Tyr130Ter (11.1%) in gBRCA1 and Arg2494Ter (25.0%) and Lys467Ter (14.3%) in gBRCA2. Considering subtypes, gBRCA1 mutations were associated with triple-negative breast cancers (TNBC), while gBRCA2 mutations were more likely hormone receptor-positive breast cancers. At least one missense mutation of HR-related genes was observed in 44 cases (80.0%). The most frequently co-mutated gene was TP53 (38.1%). In patients with gBRCA1/2 mutations, however, genetic variations of TP53 occurred in locations different from the known hotspots of those with sporadic breast cancers. The patients with both gBRCA1/2 and TP53 mutations were more likely to have TNBC, high Ki-67 values, and increased genetic mutations, especially of HR-related genes. Survival benefit was observed in the TP53 mutants of patients with gBRCA2 mutations, compared to those with TP53 wild types. CONCLUSION Our study showed genetic heterogeneity of breast cancer patients with gBRCA1 and gBRCA2 mutations in the Korean populations. Further studies on precision medicine are needed for tailored treatments of patients with genetic diversity among different ethnic groups.
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Affiliation(s)
- Jinyong Kim
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul, 03080 Republic of Korea
| | - Kyeonghun Jeong
- grid.31501.360000 0004 0470 5905Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XTransdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyeji Jun
- grid.412484.f0000 0001 0302 820XTransdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kwangsoo Kim
- grid.412484.f0000 0001 0302 820XTransdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jeong Mo Bae
- grid.412484.f0000 0001 0302 820XDepartment of Pathology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Myung Geun Song
- grid.412484.f0000 0001 0302 820XBiomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hanbaek Yi
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul, 03080 Republic of Korea
| | - Songyi Park
- grid.415735.10000 0004 0621 4536Division of Hematology/Oncology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Go-un Woo
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul, 03080 Republic of Korea
| | - Dae-Won Lee
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul, 03080 Republic of Korea
| | - Tae-Yong Kim
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul, 03080 Republic of Korea
| | - Kyung-Hun Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
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9
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Ragupathi A, Singh M, Perez AM, Zhang D. Targeting the BRCA1/ 2 deficient cancer with PARP inhibitors: Clinical outcomes and mechanistic insights. Front Cell Dev Biol 2023; 11:1133472. [PMID: 37035242 PMCID: PMC10073599 DOI: 10.3389/fcell.2023.1133472] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
BRCA1 and BRCA2 play a critical role in a variety of molecular processes related to DNA metabolism, including homologous recombination and mediating the replication stress response. Individuals with mutations in the BRCA1 and BRCA2 (BRCA1/2) genes have a significantly higher risk of developing various types of cancers, especially cancers of the breast, ovary, pancreas, and prostate. Currently, the Food and Drug Administration (FDA) has approved four PARP inhibitors (PARPi) to treat cancers with BRCA1/2 mutations. In this review, we will first summarize the clinical outcomes of the four FDA-approved PARPi in treating BRCA1/2 deficient cancers. We will then discuss evidence supporting the hypothesis that the cytotoxic effect of PARPi is likely due to inducing excessive replication stress at the difficult-to-replicate (DTR) genomic regions in BRCA1/2 mutated tumors. Finally, we will discuss the ongoing preclinical and clinical studies on how to combine the PARPi with immuno-oncology drugs to further improve clinical outcomes.
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10
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Wu X, Guo M, Cui J, Cai H, Wang SM. Heterozygotic Brca1 mutation initiates mouse genome instability at embryonic stage. Oncogenesis 2022; 11:41. [PMID: 35869059 PMCID: PMC9307611 DOI: 10.1038/s41389-022-00417-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 12/12/2022] Open
Abstract
BRCA1 mutation is the genetic predisposition in causing genome instability towards cancer. BRCA1 mutation is predominantly germline inherited at the fertilization. However, when the inherited mutation initiates genome instability in the mutation carriers remains largely elusive. We used a heterozygotic Brca1-knockout mouse as a model to investigate the issue. Through whole-genome sequencing and bioinformatics analysis, we monitored genome status across the developmental stages from embryo to adulthood in the mouse model. We observed that genome instability as reflected by structural variation, indel and copy number variation already appeared at 10.5-day embryo and progressively towards adulthood. We also observed that the genome instability was not linearly accumulated but dynamically changed along the developmental process, affecting many oncogenic genes and pathways including DNA damage repair, estrogen signaling, and oncogenesis. We further observed that many genome abnormalities in the cancer caused by Brca1 mutation were originated at embryonic stage, and Trp53 (TP53) mutation was not essential for the Brca1 mutation-caused genome instability in the non-cancer cells. Our study revealed that heterozygotic Brca1 mutation alone can cause genome instability at embryonic stage, highlighting that prevention of BRCA1 mutation-related cancer in humans may need to start earlier than currently considered.
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11
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Congregado B, Rivero I, Osmán I, Sáez C, Medina López R. PARP Inhibitors: A New Horizon for Patients with Prostate Cancer. Biomedicines 2022; 10:1416. [PMID: 35740437 PMCID: PMC9220343 DOI: 10.3390/biomedicines10061416] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 11/23/2022] Open
Abstract
The introduction of PARP inhibitors (PARPi) in prostate cancer is a milestone and provides a pathway to hope in fighting this disease. It is the first time that drugs, based on the concept of synthetic lethality, have been approved for prostate cancer. In addition, it is also the first time that genetic mutation tests have been included in the therapeutic algorithm of this disease, representing a significant step forward for precision and personalized treatment of prostate cancer. The objectives of this review are: (1) understanding the mechanism of action of PARPi in monotherapy and combinations; (2) gaining insights on patient selection for PARPi; (3) exposing the pivotal studies that have allowed its approval, and; (4) offering an overview of the ongoing trials. Nevertheless, many unsolved questions remain, such as the number of patients who could potentially benefit from PARPi, whether to use PARPi in monotherapy or in combination, and when is the best time to use them in advanced or localized disease. To answer these and other questions, many clinical trials are underway. Some of them have recently demonstrated promising results that may favor the introduction of new combinations in metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Belén Congregado
- Urology and Nephrology Department, University Hospital Virgen del Rocío, 41013 Seville, Spain; (I.R.); (I.O.); (R.M.L.)
| | - Inés Rivero
- Urology and Nephrology Department, University Hospital Virgen del Rocío, 41013 Seville, Spain; (I.R.); (I.O.); (R.M.L.)
| | - Ignacio Osmán
- Urology and Nephrology Department, University Hospital Virgen del Rocío, 41013 Seville, Spain; (I.R.); (I.O.); (R.M.L.)
| | - Carmen Sáez
- Department of Pathology, Biomedical Institute of Seville (IBIS), 41013 Seville, Spain;
| | - Rafael Medina López
- Urology and Nephrology Department, University Hospital Virgen del Rocío, 41013 Seville, Spain; (I.R.); (I.O.); (R.M.L.)
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12
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Yoon JY, Chapel D, Goebel E, Qian X, Mito J, Horowitz N, Miron A, Soong TR, Xian W, Crum CP. Molecular catastrophe, the peritoneal cavity and ovarian cancer prevention. J Pathol 2022; 257:255-261. [PMID: 35238033 DOI: 10.1002/path.5891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/06/2022] [Accepted: 02/28/2022] [Indexed: 11/06/2022]
Abstract
The current theory of carcinogenesis for the deadliest of "ovarian" cancers - high-grade serous carcinoma (HGSC) - holds that the malignancy develops first in the fallopian tube and spreads to the ovaries, peritoneum and/or regional lymph nodes. This is based primarily on the observation of early forms of serous neoplasia (serous tubular intraepithelial lesions (STILs), and serous tubular intraepithelial carcinomas (STICS)) in the fimbria of women undergoing risk reduction surgery. However, these lesions are uncommon in the general population, confer a low risk (5%) of HGSC following their removal in at-risk women with germ-line BRCA1/2 mutations and require 4 or more years to recur as intraperitoneal HGSC. These features suggest that isolated STILs and STICs behave as precursors with uncertain cancer risk rather than carcinomas. Their evolution to HGSC after escape from the tube could proceed step-wise with multiple biologic events; however, it is unclear whether immediately adjacent HGSCs in the setting of advanced disease evolved in the same fashion. The latter scenario could also be explained by a "catastrophic" model in which STICs suddenly develop with invasive and metastatic potential, overwhelming or obscuring the site of origin. Moreover, a similar model might explain the sudden emergence of HGSC in the peritoneal cavity following escape of precursor cells years before. Long term follow-up data from opportunistic or prophylactic salpingectomy should shed light on where malignant transformation occurs, as well as the time-line from precursor to metastatic HGSC. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ju Yoon Yoon
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Boston, MA.,Department of Laboratory Medicine, St. Michaels Hospital, Unity Health Toronto, Toronto, Ontario
| | - David Chapel
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Boston, MA.,Department of Pathology, University of Michigan Medical Center, Ann Arbor, MI
| | - Emily Goebel
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre and Western University, London, Ontario
| | - Xiaohua Qian
- Department of Pathology, Division of Cytopathology, Stanford University Medical Center, Palo Alto, CA
| | - Jeffrey Mito
- Department of Pathology, Division of Cytopathology, Brigham and Women's Hospital, Boston, MA
| | - Neil Horowitz
- Division of Gynecologic Oncology, Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | | | - T Rinda Soong
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Wa Xian
- University of Houston Stem Cell Center, Houston, TX
| | - Christopher P Crum
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Boston, MA
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13
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Barbalho D, Sandoval R, Santos E, Pisani J, Quirino C, Garicochea B, Rossi B, Achatz MI. Novel Insights From the Germline Landscape of Breast Cancer in Brazil. Front Oncol 2022; 11:743231. [PMID: 35155181 PMCID: PMC8831886 DOI: 10.3389/fonc.2021.743231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 12/31/2021] [Indexed: 11/22/2022] Open
Abstract
Introduction Breast cancer patients with germline pathogenic variants may benefit from risk-reducing surgeries, intensive screening, and targeted cancer therapies. There is a paucity of data regarding prevalence and distribution of germline pathogenic variants in the Brazilian population. Our primary endpoint was the description of prevalence and distribution of germline pathogenic variants among breast cancer patients who underwent next-generation sequencing (NGS) panel testing. Secondary endpoint was the assessment of predictive factors of a positive test. Methods We analyzed NGS results, personal, and family history data from a prospectively collected cohort of breast cancer patients from August 2013 to May 2019. Exact logistic regression was used to perform multivariable analysis. Results Of 370 breast cancer patients, we found 59 pathogenic variants in 57 (15%) patients. Pathogenic variants were identified in BRCA1 (24%), ATM (14%), BRCA2 (10%), TP53 (8%), PALB2 (8%), CHEK2 (7%), CDH1 (3%), RAD51C (3%), MITF (2%), PMS2 (2%), RAD51D (2%), and TERT (2%). Monoallelic MUTYH pathogenic variants were found in 15%. After multivariable analysis, age of diagnosis (OR 0.89, 95% CI: 0.81–0.95, for each year increase), triple-negative subtype (OR 17.2, 95% CI: 3.74–114.72), and number of breast cancers in the family (OR 2.46, 95% CI 1.57–4.03, for each additional case) were associated with BRCA1 pathogenic variants. In the present study, a quarter of triple-negative breast cancer patients harbored a germline pathogenic variant and two-thirds of those were BRCA1 carriers. Conclusions Prevalence and distribution of germline pathogenic variants in this Brazilian sample of breast cancer patients are mostly similar to other populations. However, there is a trend to an overrepresentation of TP53 pathogenic variants that merits confirmation in further studies. Early-onset breast cancer patients should be offered genetic counseling, particularly those with triple-negative subtype.
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Affiliation(s)
- Daniel Barbalho
- Department of Breast Surgery, Hospital Sirio-Libanês, São Paulo, Brazil
| | - Renata Sandoval
- Department of Oncogenetics, Hospital Sirio-Libanês, São Paulo, Brazil
| | - Erika Santos
- Department of Oncogenetics, Hospital Sirio-Libanês, São Paulo, Brazil
| | - Janina Pisani
- Department of Oncogenetics, Hospital Sirio-Libanês, São Paulo, Brazil
| | - Carla Quirino
- Department of Oncogenetics, Hospital Sirio-Libanês, São Paulo, Brazil
| | - Bernardo Garicochea
- Department of Oncogenetics, Hospital Sirio-Libanês, São Paulo, Brazil.,Centro Paulista de Oncologia, Oncoclinicas, São Paulo, Brazil
| | - Benedito Rossi
- Department of Oncogenetics, Hospital Sirio-Libanês, São Paulo, Brazil
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14
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Reisel D, Baran C, Manchanda R. Preventive population genomics: The model of BRCA related cancers. ADVANCES IN GENETICS 2021; 108:1-33. [PMID: 34844711 DOI: 10.1016/bs.adgen.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Preventive population genomics offers the prospect of population stratification for targeting screening and prevention and tailoring care to those at greatest risk. Within cancer, this approach is now within reach, given our expanding knowledge of its heritable components, improved ability to predict risk, and increasing availability of effective preventive strategies. Advances in technology and bioinformatics has made population-testing technically feasible. The BRCA model provides 30 years of insight and experience of how to conceive of and construct care and serves as an initial model for preventive population genomics. Population-based BRCA-testing in the Jewish population is feasible, acceptable, reduces anxiety, does not detrimentally affect psychological well-being or quality of life, is cost-effective and is now beginning to be implemented. Population-based BRCA-testing and multigene panel testing in the wider general population is cost-effective for numerous health systems and can save thousands more lives than the current clinical strategy. There is huge potential for using both genetic and non-genetic information in complex risk prediction algorithms to stratify populations for risk adapted screening and prevention. While numerous strides have been made in the last decade several issues need resolving for population genomics to fulfil its promise and potential for maximizing precision prevention. Healthcare systems need to overcome significant challenges associated with developing delivery pathways, infrastructure expansion including laboratory services, clinical workforce training, scaling of management pathways for screening and prevention. Large-scale real world population studies are needed to evaluate context specific population-testing implementation models for cancer risk prediction, screening and prevention.
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Affiliation(s)
- Dan Reisel
- EGA Institute for Women's Health, University College London, London, United Kingdom
| | - Chawan Baran
- Wolfson Institute of Preventive Medicine, CRUK Barts Centre, Queen Mary University of London, Charterhouse Square, London, United Kingdom
| | - Ranjit Manchanda
- Wolfson Institute of Preventive Medicine, CRUK Barts Centre, Queen Mary University of London, Charterhouse Square, London, United Kingdom; Department of Gynaecological Oncology, St Bartholomew's Hospital, London, United Kingdom; Department of Health Services Research, London School of Hygiene & Tropical Medicine, London, United Kingdom.
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15
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Tarpey MD, Amorese AJ, LaFave ER, Minchew EC, Fisher-Wellman KH, McClung JM, Hvastkovs EG, Spangenburg EE. Skeletal Muscle Function Is Dependent Upon BRCA1 to Maintain Genomic Stability. Exerc Sport Sci Rev 2021; 49:267-273. [PMID: 34091499 PMCID: PMC8495729 DOI: 10.1249/jes.0000000000000265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Breast Cancer gene 1 (BRCA1) is a large, multifunctional protein that regulates a variety of mechanisms in multiple different tissues. Our work established that Brca1 is expressed in skeletal muscle and localizes to the mitochondria and nucleus. Here, we propose BRCA1 expression is critical for the maintenance of force production and mitochondrial respiration in skeletal muscle.
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Affiliation(s)
- Michael D. Tarpey
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Adam J. Amorese
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Elizabeth R. LaFave
- East Carolina University, Department of Chemistry, 300 Science and Technology Bldg., Greenville, NC 27858
| | - Everett C. Minchew
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Kelsey H. Fisher-Wellman
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
| | - Joseph M. McClung
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
| | - Eli G. Hvastkovs
- East Carolina University, Department of Chemistry, 300 Science and Technology Bldg., Greenville, NC 27858
| | - Espen E. Spangenburg
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
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16
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Berger ER, Golshan M. Surgical Management of Hereditary Breast Cancer. Genes (Basel) 2021; 12:1371. [PMID: 34573353 PMCID: PMC8470490 DOI: 10.3390/genes12091371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/26/2022] Open
Abstract
The identification that breast cancer is hereditary was first described in the nineteenth century. With the identification of the BRCA1 and BRCA 2 breast/ovarian cancer susceptibility genes in the mid-1990s and the introduction of genetic testing, significant advancements have been made in tailoring surveillance, guiding decisions on medical or surgical risk reduction and cancer treatments for genetic variant carriers. This review discusses various medical and surgical management options for hereditary breast cancers.
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Affiliation(s)
- Elizabeth R. Berger
- Department of Surgery, School of Medicine, Yale University, New Haven, CT 06511, USA;
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17
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Abstract
Technological innovation and rapid reduction in sequencing costs have enabled the genomic profiling of hundreds of cancer-associated genes as a component of routine cancer care. Tumour genomic profiling can refine cancer subtype classification, identify which patients are most likely to benefit from systemic therapies and screen for germline variants that influence heritable cancer risk. Here, we discuss ongoing efforts to enhance the clinical utility of tumour genomic profiling by integrating tumour and germline analyses, characterizing allelic context and identifying mutational signatures that influence therapy response. We also discuss the potential clinical utility of more comprehensive whole-genome and whole-transcriptome sequencing and ultra-sensitive cell-free DNA profiling platforms, which allow for minimally invasive, serial analyses of tumour-derived DNA in blood.
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Affiliation(s)
- Debyani Chakravarty
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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18
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The Genetic Analyses of French Canadians of Quebec Facilitate the Characterization of New Cancer Predisposing Genes Implicated in Hereditary Breast and/or Ovarian Cancer Syndrome Families. Cancers (Basel) 2021; 13:cancers13143406. [PMID: 34298626 PMCID: PMC8305212 DOI: 10.3390/cancers13143406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
The French Canadian population of the province of Quebec has been recognized for its contribution to research in medical genetics, especially in defining the role of heritable pathogenic variants in cancer predisposing genes. Multiple carriers of a limited number of pathogenic variants in BRCA1 and BRCA2, the major risk genes for hereditary breast and/or ovarian cancer syndrome families, have been identified in French Canadians, which is in stark contrast to the array of over 2000 different pathogenic variants reported in each of these genes in other populations. As not all such cancer syndrome families are explained by BRCA1 and BRCA2, newly proposed gene candidates identified in other populations have been investigated for their role in conferring risk in French Canadian cancer families. For example, multiple carriers of distinct variants were identified in PALB2 and RAD51D. The unique genetic architecture of French Canadians has been attributed to shared ancestry due to common ancestors of early settlers of this population with origins mainly from France. In this review, we discuss the merits of genetically characterizing cancer predisposing genes in French Canadians of Quebec. We focused on genes that have been implicated in hereditary breast and/or ovarian cancer syndrome families as they have been the most thoroughly characterized cancer syndromes in this population. We describe how genetic analyses of French Canadians have facilitated: (i) the classification of variants in BRCA1 and BRCA2; (ii) the identification and classification of variants in newly proposed breast and/or ovarian cancer predisposing genes; and (iii) the identification of a new breast cancer predisposing gene candidate, RECQL. The genetic architecture of French Canadians provides a unique opportunity to evaluate new candidate cancer predisposing genes regardless of the population in which they were identified.
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19
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Abstract
Thirty years on from the launch of the Human Genome Project, Richard Gibbs reflects on the promises that this voyage of discovery bore. Its success should be measured by how this project transformed the rules of research, the way of practising biological discovery and the ubiquitous digitization of biological science. Thirty years on from the launch of the Human Genome Project, Richard Gibbs reflects on the promisesthat this voyage of discovery bore. Its success should be measured by how this project transformed the rules of research, the way of practising biological discovery and the ubiquitous digitization of biological science. Richard Gibbs, AC, PhD is a human geneticist and the Founding Director of the Baylor College of Medicine Human Genome Sequencing Center (HGSC). He graduated from the University of Melbourne in Genetics and Radiation Biology and moved to Houston, TX, to study the molecular basis of genetic disease. He developed basic methods for DNA and mutation analysis and was an early contributor to the Human Genome Project (HGP), leading one of five sites that generated the majority of the sequence. Since the completion of the HGP, he has led multiple genome projects including the generation of the first personalized whole-genome diploid human sequences. His group pioneered the oligonucleotide exon-capture methods that are widely used today for whole-exome sequencing, and he is currently leading programmes for translation of genomic data into the clinic.
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20
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BRCAness as a prognostic indicator in patients with early breast cancer. Sci Rep 2020; 10:21173. [PMID: 33273622 PMCID: PMC7713365 DOI: 10.1038/s41598-020-78016-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/14/2020] [Indexed: 11/28/2022] Open
Abstract
BRCAness is defined as a phenotypic copy of germline BRCA mutations, which describes presence of homologous recombination defects in sporadic cancers. We detected BRCAness by multiplex ligation-dependent probe amplification (MLPA) and explored whether BRCAness can be used as a predictor of prognosis. BRCAness status was classified for total 121 breast cancer patients. Forty-eight patients (39.7%) were identified as BRCAness positive. Tumors of BRCAness were more likely to be hormone receptors negative (95.8% vs. 50.7%, P < 0.001), nuclear grade III (76.1% vs. 48.4%, P = 0.001) and triple-negative breast cancer subtype (91.6% vs. 42.5%, P < 0.001). Five-year disease free survival (DFS) (54.0% vs. 88.0%, P < 0.001) and overall survival (OS) (76.3% vs. 93.1%, P = 0.002) were significantly lower in BRCAness patients. In neoadjuvant chemotherapy subgroup analysis, clinical response rate for taxane-based regimen was significantly lower in BRCAness patients (58.3% vs. 77.8%, P = 0.041). Cox regression multivariate analysis showed that BRCAness was the independent prognostic factor for DFS (HR 2.962, 95%CI 1.184–7.412, P = 0.020), but not for OS (HR 2.681, 95%CI 0.618–11.630, P = 0.188). BRCAness is associated with specific characteristics and may suggest resistance to taxane-based chemotherapy. BRCAness can be used as a negative prognostic indicator for breast cancer.
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21
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Abstract
Effective cancer prevention requires the discovery and intervention of a factor critical to cancer development. Here we show that ovarian progesterone is a crucial endogenous factor inducing the development of primary tumors progressing to metastatic ovarian cancer in a mouse model of high-grade serous carcinoma (HGSC), the most common and deadliest ovarian cancer type. Blocking progesterone signaling by the pharmacologic inhibitor mifepristone or by genetic deletion of the progesterone receptor (PR) effectively suppressed HGSC development and its peritoneal metastases. Strikingly, mifepristone treatment profoundly improved mouse survival (∼18 human years). Hence, targeting progesterone/PR signaling could offer an effective chemopreventive strategy, particularly in high-risk populations of women carrying a deleterious mutation in the BRCA gene.
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22
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PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-Deficient Cells. Mol Cell 2020; 80:327-344.e8. [PMID: 32966758 DOI: 10.1016/j.molcel.2020.08.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/22/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Stabilization of stalled replication forks is a prominent mechanism of PARP (Poly(ADP-ribose) Polymerase) inhibitor (PARPi) resistance in BRCA-deficient tumors. Epigenetic mechanisms of replication fork stability are emerging but remain poorly understood. Here, we report the histone acetyltransferase PCAF (p300/CBP-associated) as a fork-associated protein that promotes fork degradation in BRCA-deficient cells by acetylating H4K8 at stalled replication forks, which recruits MRE11 and EXO1. A H4K8ac binding domain within MRE11/EXO1 is required for their recruitment to stalled forks. Low PCAF levels, which we identify in a subset of BRCA2-deficient tumors, stabilize stalled forks, resulting in PARPi resistance in BRCA-deficient cells. Furthermore, PCAF activity is tightly regulated by ATR (ataxia telangiectasia and Rad3-related), which phosphorylates PCAF on serine 264 (S264) to limit its association and activity at stalled forks. Our results reveal PCAF and histone acetylation as critical regulators of fork stability and PARPi responses in BRCA-deficient cells, which provides key insights into targeting BRCA-deficient tumors and identifying epigenetic modulators of chemotherapeutic responses.
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23
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Hur JY, Kim JY, Ahn JS, Im YH, Lee J, Kwon M, Park YH. Clinical Characteristics of Korean Breast Cancer Patients Who Carry Pathogenic Germline Mutations in Both BRCA1 and BRCA2: A Single-Center Experience. Cancers (Basel) 2020; 12:cancers12051306. [PMID: 32455662 PMCID: PMC7281087 DOI: 10.3390/cancers12051306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 11/22/2022] Open
Abstract
There are few reports of breast cancer patients who carry germline mutations in both germline breast cancer susceptibility genes 1 (gBRCA1) and 2 (gBRCA2). In this study, we analyzed the clinical, pathological, and genomic characteristics of Korean breast cancer patients with both gBRCA1 and gBRCA2 mutations. Medical records of patients who received gBRCA1 and gBRCA2 testing at Samsung Medical Center between January 2007 to October 2018 were retrospectively reviewed. Genomic DNA was isolated from peripheral blood leukocytes. Among a total of 2720 patients, four patients with both gBRCA1 and gBRCA2 mutations were identified (4/2720; 0.14%). Seven patients who had a gBRCA1 mutation and gBRCA2 variants of uncertain significance (VUS) were also identified. In those patients with both gBRCA1 and gBRCA2 mutations, the mean age at diagnosis for breast cancer was 36 years (range, 31–43 years). All four tumors were infiltrating ductal carcinomas and three of the tumors were estrogen receptor-negative, progesterone receptor-negative, and human epidermal growth factor receptor 2-negative (triple-negative). All four patients who carried germline mutations in both BRCA1 and BRCA2 had a family history of breast/ovarian cancer. Pathologic stage was II in three patients and I in one patient. Breast cancer patients with both gBRCA1 and gBRCA2 mutations were rare, young at diagnosis, and all but one tumor was triple-negative based on our single-center experience.
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Affiliation(s)
- Joon Young Hur
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.Y.H.); (J.-Y.K.); (J.S.A.); (Y.-H.I.); (J.L.); (M.K.)
- Division of Hematology and Oncology, Department of Internal Medicine, Hanyang University Guri Hospital, Guri 11923, Korea
| | - Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.Y.H.); (J.-Y.K.); (J.S.A.); (Y.-H.I.); (J.L.); (M.K.)
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.Y.H.); (J.-Y.K.); (J.S.A.); (Y.-H.I.); (J.L.); (M.K.)
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.Y.H.); (J.-Y.K.); (J.S.A.); (Y.-H.I.); (J.L.); (M.K.)
| | - Jiyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.Y.H.); (J.-Y.K.); (J.S.A.); (Y.-H.I.); (J.L.); (M.K.)
| | - Minsuk Kwon
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.Y.H.); (J.-Y.K.); (J.S.A.); (Y.-H.I.); (J.L.); (M.K.)
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.Y.H.); (J.-Y.K.); (J.S.A.); (Y.-H.I.); (J.L.); (M.K.)
- Correspondence:
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Hatano Y, Tamada M, Matsuo M, Hara A. Molecular Trajectory of BRCA1 and BRCA2 Mutations. Front Oncol 2020; 10:361. [PMID: 32269964 PMCID: PMC7109296 DOI: 10.3389/fonc.2020.00361] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Every cancer carries genomic mutations. Although almost all these mutations arise after fertilization, a minimal count of cancer predisposition mutations are already present at the time of genesis of germ cells. Of the cancer predisposition genes identified to date, BRCA1 and BRCA2 have been determined to be associated with hereditary breast and ovarian cancer syndrome. Such cancer predisposition genes have recently been attracting attention owing to the emergence of molecular genetics, thus, affecting the strategy of cancer prevention, diagnostics, and therapeutics. In this review, we summarize the molecular significance of these two BRCA genes. First, we provide a brief history of BRCA1 and BRCA2, including their identification as cancer predisposition genes and recognition as members in the Fanconi anemia pathway. Next, we describe the molecular function and interaction of BRCA proteins, and thereafter, describe the patterns of BRCA dysfunction. Subsequently, we present emerging evidence on mutational signatures to determine the effects of BRCA disorders on the mutational process in cancer cells. Currently, BRCA genes serve as principal targets for clinical molecular oncology, be they germline or sporadic mutations. Moreover, comprehensive cancer genome analyses enable us to not only recognize the current status of the known cancer driver gene mutations but also divulge the past mutational processes and predict the future biological behavior of cancer through the molecular trajectory of genomic alterations.
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Affiliation(s)
- Yuichiro Hatano
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Maho Tamada
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Mikiko Matsuo
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
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Germline mutations of multiple breast cancer-related genes are differentially associated with triple-negative breast cancers and prognostic factors. J Hum Genet 2020; 65:577-587. [PMID: 32029870 DOI: 10.1038/s10038-020-0729-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/30/2022]
Abstract
Genetic testing for BRCA1/2 mutations has become the standard clinical practice. Recent findings suggest the clinical significance of multigene panel testing of BRCA1/2 and other cancer-related genes. However, the clinical features of patients with breast cancer with germline mutations identified using multigene panels remain unclear. In this study, DNA samples from 583 Chinese women with breast cancer were subjected to target sequencing for 54 cancer-related genes using a pre-capture pooling method followed by next-generation sequencing. We identified 79 pathogenic germline mutations in 21 cancer-related genes. Forty-five patients (7.7%) harbored BRCA1/2 mutations, and 38 patients (6.5%) carried pathogenic mutations in the remaining 19 genes. PALB2 was the most commonly (1.2%) mutated gene other than BRCA1/2. Most of the identified pathogenic mutations were novel, suggesting mutation screening by using multigene panel testing is important particularly for non-European populations. Mutations in BRCA1/2 and the other cancer-related genes were differentially associated with clinical features. BRCA1 mutation carriers were strongly associated with triple-negative breast cancer (TNBC), whereas BRCA2 mutation carriers were not. Tumors in BRCA1-mutation carriers had a high histological grade. Patients with BRCA2-mutated breast cancers were likely to develop E-cadherin-negative tumors with bone metastases. Furthermore, mutations in PALB2 were strongly associated with TNBC. We demonstrated the usefulness of multigene panel testing and observed that a substantial proportion of patients with breast cancer had hereditary risk factors. Identifying differential associations between mutation status and clinical features will advance our understanding regarding the pathologies of this heterogeneous disease.
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Lal A, Ramazzotti D, Weng Z, Liu K, Ford JM, Sidow A. Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations. BMC Med Genomics 2019; 12:84. [PMID: 31182087 PMCID: PMC6558765 DOI: 10.1186/s12920-019-0545-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/31/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to breast and ovarian cancer, and there remains a need to identify the specific genomic mechanisms by which cancer evolves in these patients. Here we present a systematic genomic analysis of breast tumors with BRCA1 and BRCA2 mutations. METHODS We analyzed genomic data from breast tumors, with a focus on comparing tumors with BRCA1/BRCA2 gene mutations with common classes of sporadic breast tumors. RESULTS We identify differences between BRCA-mutated and sporadic breast tumors in patterns of point mutation, DNA methylation and structural variation. We show that structural variation disproportionately affects tumor suppressor genes and identify specific driver gene candidates that are enriched for structural variation. CONCLUSIONS Compared to sporadic tumors, BRCA-mutated breast tumors show signals of reduced DNA methylation, more ancestral cell divisions, and elevated rates of structural variation that tend to disrupt highly expressed protein-coding genes and known tumor suppressors. Our analysis suggests that BRCA-mutated tumors are more aggressive than sporadic breast cancers because loss of the BRCA pathway causes multiple processes of mutagenesis and gene dysregulation.
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Affiliation(s)
- Avantika Lal
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Present address: NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, CA 95051 USA
| | - Daniele Ramazzotti
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Department of Computer Science, Stanford University, Stanford, CA 94305 USA
| | - Ziming Weng
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
| | - Keli Liu
- Department of Statistics, Stanford University, Stanford, CA 94305 USA
| | - James M. Ford
- Department of Medicine, Stanford University, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
| | - Arend Sidow
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
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Genetic Testing to Guide Risk-Stratified Screens for Breast Cancer. J Pers Med 2019; 9:jpm9010015. [PMID: 30832243 PMCID: PMC6462925 DOI: 10.3390/jpm9010015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 12/14/2022] Open
Abstract
Breast cancer screening modalities and guidelines continue to evolve and are increasingly based on risk factors, including genetic risk and a personal or family history of cancer. Here, we review genetic testing of high-penetrance hereditary breast and ovarian cancer genes, including BRCA1 and BRCA2, for the purpose of identifying high-risk individuals who would benefit from earlier screening and more sensitive methods such as magnetic resonance imaging. We also consider risk-based screening in the general population, including whether every woman should be genetically tested for high-risk genes and the potential use of polygenic risk scores. In addition to enabling early detection, the results of genetic screens of breast cancer susceptibility genes can be utilized to guide decision-making about when to elect prophylactic surgeries that reduce cancer risk and the choice of therapeutic options. Variants of uncertain significance, especially missense variants, are being identified during panel testing for hereditary breast and ovarian cancer. A finding of a variant of uncertain significance does not provide a basis for increased cancer surveillance or prophylactic procedures. Given that variant classification is often challenging, we also consider the role of multifactorial statistical analyses by large consortia and functional tests for this purpose.
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Palazzo L, Ahel I. PARPs in genome stability and signal transduction: implications for cancer therapy. Biochem Soc Trans 2018; 46:1681-1695. [PMID: 30420415 PMCID: PMC6299239 DOI: 10.1042/bst20180418] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 01/03/2023]
Abstract
The poly(ADP-ribose) polymerase (PARP) superfamily of enzymes catalyses the ADP-ribosylation (ADPr) of target proteins by using nicotinamide adenine dinucleotide (NAD+) as a donor. ADPr reactions occur either in the form of attachment of a single ADP-ribose nucleotide unit on target proteins or in the form of ADP-ribose chains, with the latter called poly(ADP-ribosyl)ation. PARPs regulate many cellular processes, including the maintenance of genome stability and signal transduction. In this review, we focus on the PARP family members that possess the ability to modify proteins by poly(ADP-ribosyl)ation, namely PARP1, PARP2, Tankyrase-1, and Tankyrase-2. Here, we detail the cellular functions of PARP1 and PARP2 in the regulation of DNA damage response and describe the function of Tankyrases in Wnt-mediated signal transduction. Furthermore, we discuss how the understanding of these pathways has provided some major breakthroughs in the treatment of human cancer.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
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30
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Challenges in the identification of inherited risk of ovarian cancer: where should we go from here? Gynecol Oncol 2018; 152:3-6. [PMID: 30538055 DOI: 10.1016/j.ygyno.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Robert M, Patsouris A, Frenel JS, Gourmelon C, Augereau P, Campone M. Emerging PARP inhibitors for treating breast cancer. Expert Opin Emerg Drugs 2018; 23:211-221. [DOI: 10.1080/14728214.2018.1527900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Marie Robert
- René Gauducheau, Institut de Cancérologie de l’Ouest, St Herblain, France
| | - Anne Patsouris
- Paul Papin, Institut de Cancérologie de l’Ouest, Angers, France
| | | | - Carole Gourmelon
- René Gauducheau, Institut de Cancérologie de l’Ouest, St Herblain, France
| | - Paule Augereau
- Paul Papin, Institut de Cancérologie de l’Ouest, Angers, France
| | - Mario Campone
- René Gauducheau, Institut de Cancérologie de l’Ouest, St Herblain, France
- Medical oncology, Centre de Recherche en Cancérologie Nantes-Angers (CRNA), Saint-Herblain, France
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Yang X, Li J, Fang Y, Zhang Z, Jin D, Chen X, Zhao Y, Li M, Huan L, Kent TA, Dong JF, Jiang R, Yang S, Jin L, Zhang J, Zhong TP, Yu F. Rho Guanine Nucleotide Exchange Factor ARHGEF17 Is a Risk Gene for Intracranial Aneurysms. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2018; 11:e002099. [PMID: 29997225 PMCID: PMC6141028 DOI: 10.1161/circgen.117.002099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/22/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND Intracranial aneurysm (IA) is usually a late-onset disease, affecting 1% to 3% of the general population and leading to life-threatening subarachnoid hemorrhage. Genetic susceptibility has been implicated in IAs, but the causative genes remain elusive. METHODS We performed next-generation sequencing in a discovery cohort of 20 Chinese IA patients. Bioinformatics filters were exploited to search for candidate deleterious variants with rare and low allele frequency. We further examined the candidate variants in a multiethnic sample collection of 86 whole exome sequenced unsolved familial IA cases from 3 previously published studies. RESULTS We identified that the low-frequency variant c.4394C>A_p.Ala1465Asp (rs2298808) of ARHGEF17 was significantly associated with IA in our Chinese discovery cohort (P=7.3×10-4; odds ratio=7.34). It was subsequently replicated in Japanese familial IA patients (P=0.039; odds ratio=4.00; 95% confidence interval=0.832-14.8) and was associated with IA in the large Chinese sample collection comprising 832 sporadic IA-affected and 599 control individuals (P=0.041; odds ratio=1.51; 95% confidence interval=1.02-Inf). When combining the sequencing data of all familial IA patients from 4 different ethnicities (ie, Chinese, Japanese, European American, and French-Canadian), we identified a significantly increased mutation burden for ARHGEF17 (21/106 versus 11/306; P=8.1×10-7; odds ratio=6.6; 95% confidence interval=2.9-15.8) in cases as compared with controls. In zebrafish, arhgef17 was highly expressed in the brain blood vessel. arhgef17 knockdown caused blood extravasation in the brain region. Endothelial lesions were identified exclusively on cerebral blood vessels in the arhgef17-deficient zebrafish. CONCLUSIONS Our results provide compelling evidence that ARHGEF17 is a risk gene for IA.
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Affiliation(s)
- Xinyu Yang
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.)
| | - Jiani Li
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (J.L., F.Y.)
| | - Yabo Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhong Shan Hospital, Fudan University, Shanghai, China (Y.F., D.J., X.C., L.J., T.P.Z.)
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, East China Normal University School of Life Sciences (Y.F., D.J., L.J., T.P.Z.)
| | - Zhen Zhang
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.)
| | - Daqing Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhong Shan Hospital, Fudan University, Shanghai, China (Y.F., D.J., X.C., L.J., T.P.Z.)
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, East China Normal University School of Life Sciences (Y.F., D.J., L.J., T.P.Z.)
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhong Shan Hospital, Fudan University, Shanghai, China (Y.F., D.J., X.C., L.J., T.P.Z.)
| | - Yan Zhao
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.)
| | - Mengqi Li
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.)
| | - Linchun Huan
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.)
- Department of Neurosurgery, Linyi People's Hospital, Shandong, China (L.H.)
| | - Thomas A Kent
- Engineering Medicine, Texas A&M Health Science Center and College of Engineering, Houston (T.A.K.)
| | - Jing-Fei Dong
- Blood Works Northwest Research Institute, Seattle, WA (J.-F.D.)
- Division of Hematology, Department of Medicine, University of Washington School of Medicine, Seattle (J.-F.D.)
| | - Rongcai Jiang
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.)
| | - Shuyuan Yang
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.)
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhong Shan Hospital, Fudan University, Shanghai, China (Y.F., D.J., X.C., L.J., T.P.Z.)
| | - Jianning Zhang
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.).
| | - Tao P Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhong Shan Hospital, Fudan University, Shanghai, China (Y.F., D.J., X.C., L.J., T.P.Z.).
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, East China Normal University School of Life Sciences (Y.F., D.J., L.J., T.P.Z.)
| | - Fuli Yu
- Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, China (X.Y., Z.Z., Y.Z., M.L., L.H., R.J., S.Y., J.Z., F.Y.).
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (J.L., F.Y.)
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Gene-Specific Genetic Complementation between Brca1 and Cobra1 During Mouse Mammary Gland Development. Sci Rep 2018; 8:2731. [PMID: 29426838 PMCID: PMC5807304 DOI: 10.1038/s41598-018-21044-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/29/2018] [Indexed: 12/22/2022] Open
Abstract
Germ-line mutations in breast cancer susceptibility gene, BRCA1, result in familial predisposition to breast and ovarian cancers. The BRCA1 protein has multiple functional domains that interact with a variety of proteins in multiple cellular processes. Understanding the biological consequences of BRCA1 interactions with its binding partners is important for elucidating its tissue-specific tumor suppression function. The Cofactor of BRCA1 (COBRA1) is a BRCA1-binding protein that, as a component of negative elongation factor (NELF), regulates RNA polymerase II pausing during transcription elongation. We recently identified a genetic interaction between mouse Brca1 and Cobra1 that antagonistically regulates mammary gland development. However, it remains unclear which of the myriad functions of Brca1 are required for its genetic interaction with Cobra1. Here, we show that, unlike deletion of Brca1 exon 11, separation-of-function mutations that abrogate either the E3 ligase activity of its RING domain or the phospho-recognition property of its BRCT domain are not sufficient to rescue the mammary developmental defects in Cobra1 knockout mice. Furthermore, deletion of mouse Palb2, another breast cancer susceptibility gene with functional similarities to BRCA1, does not rescue Cobra1 knockout-associated mammary defects. Thus, the Brca1/Cobra1 genetic interaction is both domain- and gene-specific in the context of mammary gland development.
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Menendez JA, Folguera-Blasco N, Cuyàs E, Fernández-Arroyo S, Joven J, Alarcón T. Accelerated geroncogenesis in hereditary breast-ovarian cancer syndrome. Oncotarget 2017; 7:11959-71. [PMID: 26943589 PMCID: PMC4914261 DOI: 10.18632/oncotarget.7867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/21/2016] [Indexed: 12/21/2022] Open
Abstract
The geroncogenesis hypothesis postulates that the decline in metabolic cellular health that occurs naturally with aging drives a "field effect" predisposing normal tissues for cancer development. We propose that mutations in the cancer susceptibility genes BRCA1/2 might trigger "accelerated geroncogenesis" in breast and ovarian epithelia. By speeding up the rate at which the metabolic threshold becomes "permissive" with survival and expansion of genomically unstable pre-tumoral epithelial cells, BRCA haploinsufficiency-driven metabolic reprogramming would operate as a bona fide oncogenic event enabling malignant transformation and tumor formation in BRCA carriers. The metabolic facet of BRCA1 one-hit might involve tissue-specific alterations in acetyl-CoA, α-ketoglutarate, NAD+, FAD, or S-adenosylmethionine, critical factors for de/methylation or de/acetylation dynamics in the nuclear epigenome. This in turn might induce faulty epigenetic reprogramming at the "install phase" that directs cell-specific differentiation of breast/ovarian epithelial cells, which can ultimately determine the penetrance of BRCA defects during developmental windows of susceptibility. This model offers a framework to study whether metabolic drugs that prevent or revert metabolic reprogramming induced by BRCA haploinsufficiency might displace the "geroncogenic risk" of BRCA carriers to the age typical for those without the mutation. The identification of the key nodes that directly communicate changes in cellular metabolism to the chromatin in BRCA haploinsufficient cells may allow the epigenetic targeting of genomic instability using exclusively metabolic means. The validation of accelerated geroncogenesis as an inherited "one-hit" metabolic "field effect" might offer new strategies to therapeutically revisit the apparently irreversible genetic-hereditary fate of women with hereditary breast-ovarian cancer syndrome.
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Affiliation(s)
- Javier A Menendez
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Salt, Catalonia, Spain
| | - Núria Folguera-Blasco
- Computational and Mathematical Biology Research Group, Centre de Recerca Matemàtica (CRM), Barcelona, Spain
| | - Elisabet Cuyàs
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Salt, Catalonia, Spain
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Campus of International Excellence Southern Catalonia, Reus, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Campus of International Excellence Southern Catalonia, Reus, Spain
| | - Tomás Alarcón
- Computational and Mathematical Biology Research Group, Centre de Recerca Matemàtica (CRM), Barcelona, Spain.,Institució Catalana d'Estudis i Recerca Avançats (ICREA), Barcelona, Spain.,Departament de Matemàtiques, Universitat Autònoma de Barcelona, Barcelona, Spain.,Barcelona Graduate School of Mathematics (BGSMath), Barcelona, Spain
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Rao S, Cronin SJF, Sigl V, Penninger JM. RANKL and RANK: From Mammalian Physiology to Cancer Treatment. Trends Cell Biol 2017; 28:213-223. [PMID: 29241686 DOI: 10.1016/j.tcb.2017.11.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/24/2022]
Abstract
The tumor necrosis factor (TNF) receptor RANK (TNFRSF11A) and its ligand RANKL (TNFSF11) regulate osteoclast development and bone metabolism. They also control stem cell expansion and proliferation of mammary epithelial cells via the sex hormone progesterone. As such, RANKL and RANK have been implicated in the onset of hormone-induced breast cancer. Recently, RANK/RANKL were identified as crucial regulators for BRCA1 mutation-driven breast cancer. Current prevention strategies for BRCA1 mutation carriers are associated with wide-ranging risks; therefore, the search for alternative, non-invasive strategies is of paramount importance. We summarize here the functions of the RANKL/RANK pathway in mammalian physiology and focus on its recently uncovered role in breast cancer. We propose that anti-RANKL therapy should be pursued as a preventative strategy for breast cancer.
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Affiliation(s)
- Shuan Rao
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria; These authors contributed equally to this work
| | - Shane J F Cronin
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria; These authors contributed equally to this work
| | - Verena Sigl
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria.
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Sigl V, Jones LP, Penninger JM. RANKL/RANK: from bone loss to the prevention of breast cancer. Open Biol 2017; 6:rsob.160230. [PMID: 27881737 PMCID: PMC5133443 DOI: 10.1098/rsob.160230] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/21/2016] [Indexed: 12/13/2022] Open
Abstract
RANK and RANKL, a receptor ligand pair belonging to the tumour necrosis factor family, are the critical regulators of osteoclast development and bone metabolism. Besides their essential function in bone, RANK and RANKL have also been identified as the key factors for the formation of a lactating mammary gland in pregnancy. Mechanistically, RANK and RANKL link the sex hormone progesterone with stem cell expansion and proliferation of mammary epithelial cells. Based on their normal physiology, RANKL/RANK control the onset of hormone-induced breast cancer through the expansion of mammary progenitor cells. Recently, we and others were able to show that RANK and RANKL are also critical regulators of BRCA1-mutation-driven breast cancer. Currently, the preventive strategy for BRCA1-mutation carriers includes preventive mastectomy, associated with wide-ranging risks and psychosocial effects. The search for an alternative non-invasive prevention strategy is therefore of paramount importance. As our work strongly implicates RANK and RANKL as key molecules involved in the initiation of BRCA1-associated breast cancer, we propose that anti-RANKL therapy could be a feasible preventive strategy for women carrying BRCA1 mutations, and by extension to other women with high risk of breast cancer.
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Affiliation(s)
- Verena Sigl
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr Bohrgasse 3, 1030 Vienna, Austria
| | - Laundette P Jones
- School of Medicine, Department of Pharmacology, University of Maryland, Baltimore, MD 21201, USA
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr Bohrgasse 3, 1030 Vienna, Austria
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37
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Powers B, Pal T, Laronga C. Considerations in Testing for Inherited Breast Cancer Predisposition in the Era of Personalized Medicine. Surg Oncol Clin N Am 2017; 27:1-22. [PMID: 29132555 DOI: 10.1016/j.soc.2017.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Technological advances realized through next-generation sequencing technologies coupled with the loss of the ability to patent genes have led to reduction in costs for genetic testing. As a result, more people are being identified with inherited breast cancer syndromes that may affect recommendations for surveillance and risk reduction. Surgeons, at the forefront for patients newly diagnosed with breast cancer, must keep current with the changing landscape of genetics to continue to provide appropriate counsel and care. This article provides an overview of individuals at risk for inherited cancer predisposition and recommendations for surveillance and management.
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Affiliation(s)
- Benjamin Powers
- Department of Breast Oncology, H. Lee Moffitt Cancer Center, 10920 N. Mckinley Drive, Tampa, FL 33612, USA
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Christine Laronga
- Department of Breast Oncology, H. Lee Moffitt Cancer Center, 10920 N. Mckinley Drive, Tampa, FL 33612, USA.
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Sau A, Cabrita MA, Pratt MAC. NF-κB at the Crossroads of Normal Mammary Gland Biology and the Pathogenesis and Prevention of BRCA1-Mutated Breast Cancer. Cancer Prev Res (Phila) 2017; 11:69-80. [PMID: 29101208 DOI: 10.1158/1940-6207.capr-17-0225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/03/2017] [Accepted: 10/27/2017] [Indexed: 11/16/2022]
Abstract
Recent studies have shown that progesterone receptor (PR)-expressing cells respond to progesterone in part through the induction of the receptor activator of NF-κB ligand (RANKL), which acts in a paracrine manner to induce expansion of a RANK-expressing luminal progenitor cell population. The RANK+ population in human breast tissue from carriers of BRCA1 mutations (BRCA1mut/+) as well as the luminal progenitor population in Brca1-deficient mouse mammary glands is abnormally amplified. Remarkably, mouse Brca1+/- and human BRCA1mut/+ progenitor cells are able to form colonies in vitro in the absence of progesterone, demonstrating a hormone-independent proliferative capacity. Our research has demonstrated that proliferation in BRCA1-deficient cells results in a DNA damage response (DDR) that activates a persistent NF-κB signal, which supplants progesterone/RANKL signaling for an extended time period. Thus, the transcriptional targets normally activated by RANKL that promote a proliferative response in luminal progenitors can contribute to the susceptibility of mammary epithelial cells to BRCA1-mutated breast cancers as a consequence of DDR-induced NF-κB. Together, these latest findings mark substantial progress in uncovering the mechanisms driving high rates of breast tumorigenesis in BRCA1 mutation carriers and ultimately reveal possibilities for nonsurgical prevention strategies. Cancer Prev Res; 11(2); 69-80. ©2017 AACR.
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Affiliation(s)
- Andrea Sau
- University of Ottawa, Ottawa, Ontario, Canada
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Robert M, Frenel JS, Gourmelon C, Patsouris A, Augereau P, Campone M. Olaparib for the treatment of breast cancer. Expert Opin Investig Drugs 2017; 26:751-759. [DOI: 10.1080/13543784.2017.1318847] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Marie Robert
- Medical oncology, Institut de Cancérologie de l’Ouest, René Gauducheau, St Herblain, France
| | - Jean-Sébastien Frenel
- Medical oncology, Institut de Cancérologie de l’Ouest, René Gauducheau, St Herblain, France
| | - Carole Gourmelon
- Medical oncology, Institut de Cancérologie de l’Ouest, René Gauducheau, St Herblain, France
| | - Anne Patsouris
- Medical oncology, Institut de Cancérologie de l’Ouest, Paul Papin, Angers, France
| | - Paule Augereau
- Medical oncology, Institut de Cancérologie de l’Ouest, Paul Papin, Angers, France
| | - Mario Campone
- Medical oncology, Institut de Cancérologie de l’Ouest, René Gauducheau, St Herblain, France
- Centre de Recherche en Cancérologie Nantes-Angers (CRNA), France
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40
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Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, Nik-Zainal S. HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. Nat Med 2017; 23:517-525. [PMID: 28288110 PMCID: PMC5833945 DOI: 10.1038/nm.4292] [Citation(s) in RCA: 639] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/24/2017] [Indexed: 12/12/2022]
Abstract
Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition.
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Affiliation(s)
- Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Lucy R. Yates
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Guys and St Thomas’ NHS Trust, London, UK
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, SE-223 81, Sweden
| | - Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Manasa Ramakrishna
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Hodgkin Building, Chesterford Research Park, Little Chesterford, Cambridge CB10 1XL, UK
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sandrine Boyault
- Centre Léon Bérard, Translational Research Lab Department, 28, rue Laënnec, 69373 Lyon Cedex 08, France
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Peter T. Simpson
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Queensland 4029, Australia
| | - Tari A. King
- Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, United States
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jorunn E. Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University, Seoul, 133-791, South Korea
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, SE-223 81, Sweden
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire, CB10 1SD
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, 6525GA, Nijmegen, Netherlands
| | - Marc J. van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radium Hospital Oslo 0310, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo 0310, Norway
| | - John W.M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Paul N. Span
- Department of Radiation Oncology, and department of Laboratory Medicine, Radboud university medical center, Nijmegen 6525GA, The Netherlands
| | - Sunil R Lakhani
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Queensland 4029, Australia
- Pathology Queensland, The Royal Brisbane and Women’s Hospital, Brisbane, Queensland 4029, Australia
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology and INSERM U934, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium
| | - Andrew Tutt
- Breast Cancer Now Research Unit, King’s College, London, UK
- Breast Cancer Now Toby Robin’s Research Centre, Institute of Cancer Research, London, UK
| | - Alastair M. Thompson
- Department of Breast Surgical Oncology, University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, Texas 77030, USA
| | - Steven Van Laere
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- HistoGeneX NV, Wilrijk, Belgium
| | - Andrea L. Richardson
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115 USA
- Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Alain Viari
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655, Avenue de l'Europe, 38330 Montbonnot-Saint Martin, France
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
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41
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Affiliation(s)
- Sonia S Kupfer
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition, University of Chicago, Chicago, Illinois.
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42
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Abstract
PARP inhibitors (PARPi), a cancer therapy targeting poly(ADP-ribose) polymerase, are the first clinically approved drugs designed to exploit synthetic lethality, a genetic concept proposed nearly a century ago. Tumors arising in patients who carry germline mutations in either BRCA1 or BRCA2 are sensitive to PARPi because they have a specific type of DNA repair defect. PARPi also show promising activity in more common cancers that share this repair defect. However, as with other targeted therapies, resistance to PARPi arises in advanced disease. In addition, determining the optimal use of PARPi within drug combination approaches has been challenging. Nevertheless, the preclinical discovery of PARPi synthetic lethality and the route to clinical approval provide interesting lessons for the development of other therapies. Here, we discuss current knowledge of PARP inhibitors and potential ways to maximize their clinical effectiveness.
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Affiliation(s)
- Christopher J Lord
- The Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Alan Ashworth
- University of California, San Francisco (UCSF), Helen Diller Family Comprehensive Cancer Center, 1450 Third Street, San Francisco, CA 94158, USA.
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Schubert S, Ripperger T, Rood M, Petkidis A, Hofmann W, Frye-Boukhriss H, Tauscher M, Auber B, Hille-Betz U, Illig T, Schlegelberger B, Steinemann D. GT198 (PSMC3IP) germline variants in early-onset breast cancer patients from hereditary breast and ovarian cancer families. Genes Cancer 2017; 8:472-483. [PMID: 28435519 PMCID: PMC5369655 DOI: 10.18632/genesandcancer.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
GT198, located 470 kb downstream of BRCA1, encodes for the nuclear PSMC3-interacting protein, which functions as co-activator of steroid hormone-mediated gene expression, and is involved in RAD51 and DMC1-mediated homologous recombination during DNA repair of double-strand breaks. Recently, germline variants in GT198 have been identified in hereditary breast and ovarian cancer (HBOC) patients, mainly in cases with early-onset. We screened a cohort of 166 BRCA1/2 mutation-negative HBOC patients, of which 56 developed early-onset breast cancer before the age of 36 years, for GT198 variants. We identified 7 novel or rare GT198 variants in 8 out of 166 index patients: c.-115G>A (rs191843707); c.-70T>A (rs752276800); c.-37A>T (rs199620968); c.-24C>G (rs200359709); c.519G>A p.(Trp173*); c.537+51G>C (rs375509656); c.*24G>A. Three out of 7 identified variants (c.-115G>A, c.519G>A and c.*24G>A) with putative pathogenic impact were found in HBOC patients with breast cancer onset at ≤ 36 years. The nonsense mutation c.519G>A p.(Trp173*) was located within the DNA binding domain of GT198 and is predicted to induce nonsense-mediated mRNA decay. Functional analyses of c.-115G>A, and c.*24A>G indicated an influence of these variants on gene expression. This is the second study that gives evidence for an association between pathogenic GT198 germline variants and early-onset breast cancer in HBOC.
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Affiliation(s)
- Stephanie Schubert
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Melanie Rood
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Anthony Petkidis
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Marcel Tauscher
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ursula Hille-Betz
- Department of Obstetrics and Gynecology, Hannover Medical School, Hannover, Germany
| | - Thomas Illig
- Department of Human Genetics, Hannover Medical School, Hannover, Germany.,Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | | | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
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Rapid and cost-effective high-throughput sequencing for identification of germline mutations of BRCA1 and BRCA2. J Hum Genet 2017; 62:561-567. [DOI: 10.1038/jhg.2017.5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/26/2016] [Accepted: 12/05/2016] [Indexed: 12/30/2022]
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45
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Dhillon KK, Bajrami I, Taniguchi T, Lord CJ. Synthetic lethality: the road to novel therapies for breast cancer. Endocr Relat Cancer 2016; 23:T39-55. [PMID: 27528623 DOI: 10.1530/erc-16-0228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 12/12/2022]
Abstract
When the BRCA1 and BRCA2 tumour suppressor genes were identified in the early 1990s, the immediate implications of mapping, cloning and delineating the sequence of these genes were that individuals in families with a BRCA gene mutation could be tested for the presence of a mutation and their risk of developing cancer could be predicted. Over time though, the discovery of BRCA1 and BRCA2 has had a much greater influence than many might have imagined. In this review, we discuss how the discovery of BRCA1 and BRCA2 has not only provided an understanding of the molecular processes that drive tumourigenesis but also reignited an interest in therapeutically exploiting loss-of-function alterations in tumour suppressor genes.
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Affiliation(s)
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
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Muñoz-Fontela C, Mandinova A, Aaronson SA, Lee SW. Emerging roles of p53 and other tumour-suppressor genes in immune regulation. Nat Rev Immunol 2016; 16:741-750. [PMID: 27667712 DOI: 10.1038/nri.2016.99] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tumour-suppressor genes are indispensable for the maintenance of genomic integrity. Recently, several of these genes, including those encoding p53, PTEN, RB1 and ARF, have been implicated in immune responses and inflammatory diseases. In particular, the p53 tumour- suppressor pathway is involved in crucial aspects of tumour immunology and in homeostatic regulation of immune responses. Other studies have identified roles for p53 in various cellular processes, including metabolism and stem cell maintenance. Here, we discuss the emerging roles of p53 and other tumour-suppressor genes in tumour immunology, as well as in additional immunological settings, such as virus infection. This relatively unexplored area could yield important insights into the homeostatic control of immune cells in health and disease and facilitate the development of more effective immunotherapies. Consequently, tumour-suppressor genes are emerging as potential guardians of immune integrity.
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Affiliation(s)
- César Muñoz-Fontela
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Anna Mandinova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Building 149 13th Street, Charlestown, Massachusetts 02129, USA.,Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA.,Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Stuart A Aaronson
- Department of Oncological Sciences, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, USA
| | - Sam W Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Building 149 13th Street, Charlestown, Massachusetts 02129, USA.,Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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47
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Lodovichi S, Vitello M, Cervelli T, Galli A. Expression of cancer related BRCA1 missense variants decreases MMS-induced recombination in Saccharomyces cerevisiae without altering its nuclear localization. Cell Cycle 2016; 15:2723-31. [PMID: 27484786 DOI: 10.1080/15384101.2016.1215389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
BRCA1 tumor suppressor gene is found mutated in familial breast and ovarian cancer. Most cancer related mutations were found located at the RING (Really Interesting New Gene) and at the BRCT (BRca1 C-Terminal) domain. However, 20 y after its identification, the biological role of BRCA1 and which domains are more relevant for tumor suppression are still being elucidated. We previously reported that expression of BRCA1 cancer related variants in the RING and BRCT domain increases spontaneous homologous recombination in yeast indicating that BRCA1 may interact with yeast DNA repair/recombination. To finally demonstrate whether BRCA1 interacts with yeast DNA repair, we exposed yeast cells expressing BRCA1wt, the cancer-related variants C-61G and M1775R to different doses of the alkylating agent methyl methane-sulfonate (MMS) and then evaluated the effect on survival and homologous recombination. Cells expressing BRCA1 cancer variants were more sensitive to MMS and less inducible to recombination as compared to cell expressing BRCA1wt. Moreover, BRCA1-C61G and -M1775R did not change their nuclear localization form as compared to the BRCA1wt or the neutral variant R1751Q indicating a difference in the DNA damage processing. We propose a model where BRCA1 cancer variants interact with the DNA double strand break repair pathways producing DNA recombination intermediates, that maybe less repairable and decrease MMS-induced recombination and survival. Again, this study strengthens the use of yeast as model system to characterize the mechanisms leading to cancer in humans carrying the BRCA1 missense variant.
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Affiliation(s)
- Samuele Lodovichi
- a Yeast Genetics and Genomics, Institute of Clinical Physiology , CNR, Pisa , Italy
| | - Martina Vitello
- a Yeast Genetics and Genomics, Institute of Clinical Physiology , CNR, Pisa , Italy
| | - Tiziana Cervelli
- a Yeast Genetics and Genomics, Institute of Clinical Physiology , CNR, Pisa , Italy
| | - Alvaro Galli
- a Yeast Genetics and Genomics, Institute of Clinical Physiology , CNR, Pisa , Italy
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48
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Bunnell AE, Garby CA, Pearson EJ, Walker SA, Panos LE, Blum JL. The Clinical Utility of Next Generation Sequencing Results in a Community-Based Hereditary Cancer Risk Program. J Genet Couns 2016; 26:105-112. [PMID: 27276934 DOI: 10.1007/s10897-016-9985-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/31/2016] [Indexed: 01/07/2023]
Abstract
Since the 2013 Supreme Court ruling on BRCA1/BRCA2 patenting, hereditary cancer gene panels now include BRCA1 and BRCA2, making these panels an option for first-tier testing. However, questions remain about the clinical utility and implications of these panels for medical management with inclusion of genes of unknown to moderate penetrance. To better understand how use of these panels affected our practice, we reviewed patients who underwent testing in our clinic from July 1, 2013 through May 23, 2014. Indications for testing included personal and/or family history of breast and/or ovarian cancer. A total of 136 patients underwent panel testing via a single commercial laboratory; 12 (8.8 %) patients were positive for a pathogenic or likely pathogenic mutation (four BRCA2 mutations, two TP53 mutations, one CDH1 mutation, two ATM mutations, and one patient each with a CHEK2, NBN, or PALB2 mutation). Of these positive patients, 100 % met the National Comprehensive Cancer Network (NCCN) guidelines for Hereditary Breast and Ovarian Cancer genetic testing (2.2014). Mutations in seven of twelve (58 %) patients led to changes in medical management; three of seven (43 %) had a non-BRCA1 or BRCA2 gene mutation. Our findings suggest that there is clinical utility of panels that include genes of unknown to moderate penetrance.
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Affiliation(s)
- A E Bunnell
- Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, 3410 Worth St, Dallas, TX, 75248, USA
| | - C A Garby
- Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, 3410 Worth St, Dallas, TX, 75248, USA
| | - E J Pearson
- Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, 3410 Worth St, Dallas, TX, 75248, USA
| | - S A Walker
- Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, 3410 Worth St, Dallas, TX, 75248, USA
| | - L E Panos
- Ambry Genetic Laboratories, Aliso Viejo, CA, 92656, USA
| | - Joanne L Blum
- Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, 3410 Worth St, Dallas, TX, 75248, USA. .,Texas Oncology, Baylor Charles A. Sammons Cancer Center, 3410 Worth St, Dallas, TX, 75248, USA.
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49
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Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution. Nat Commun 2016; 7:11620. [PMID: 27216078 PMCID: PMC4890182 DOI: 10.1038/ncomms11620] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/14/2016] [Indexed: 02/06/2023] Open
Abstract
The exact timing and contribution of epigenetic reprogramming to carcinogenesis are unclear. Women harbouring BRCA1/2 mutations demonstrate a 30–40-fold increased risk of high-grade serous extra-uterine Müllerian cancers (HGSEMC), otherwise referred to as ‘ovarian carcinomas', which frequently develop from fimbrial cells but not from the proximal portion of the fallopian tube. Here we compare the DNA methylome of the fimbrial and proximal ends of the fallopian tube in BRCA1/2 mutation carriers and non-carriers. We show that the number of CpGs displaying significant differences in methylation levels between fimbrial and proximal fallopian tube segments are threefold higher in BRCA mutation carriers than in controls, correlating with overexpression of activation-induced deaminase in their fimbrial epithelium. The differentially methylated CpGs accurately discriminate HGSEMCs from non-serous subtypes. Epigenetic reprogramming is an early pre-malignant event integral to BRCA1/2 mutation-driven carcinogenesis. Our findings may provide a basis for cancer-preventative strategies. Women with germline variants in BRCA genes are predisposed to ovarian cancer. In this study, the authors demonstrate that fimbrial tissue from the ovary, the site of ovarian cancer, in BRCA mutant carriers contains marked DNA methylation changes compared with the proximal region of the ovary.
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50
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Nair SJ, Zhang X, Chiang HC, Jahid MJ, Wang Y, Garza P, April C, Salathia N, Banerjee T, Alenazi FS, Ruan J, Fan JB, Parvin JD, Jin VX, Hu Y, Li R. Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development. Nat Commun 2016; 7:10913. [PMID: 26941120 PMCID: PMC4785232 DOI: 10.1038/ncomms10913] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/29/2016] [Indexed: 12/14/2022] Open
Abstract
The breast cancer susceptibility gene BRCA1 is well known for its function in double-strand break (DSB) DNA repair. While BRCA1 is also implicated in transcriptional regulation, the physiological significance remains unclear. COBRA1 (also known as NELF-B) is a BRCA1-binding protein that regulates RNA polymerase II (RNAPII) pausing and transcription elongation. Here we interrogate functional interaction between BRCA1 and COBRA1 during mouse mammary gland development. Tissue-specific deletion of Cobra1 reduces mammary epithelial compartments and blocks ductal morphogenesis, alveologenesis and lactogenesis, demonstrating a pivotal role of COBRA1 in adult tissue development. Remarkably, these developmental deficiencies due to Cobra1 knockout are largely rescued by additional loss of full-length Brca1. Furthermore, Brca1/Cobra1 double knockout restores developmental transcription at puberty, alters luminal epithelial homoeostasis, yet remains deficient in homologous recombination-based DSB repair. Thus our genetic suppression analysis uncovers a previously unappreciated, DNA repair-independent function of BRCA1 in antagonizing COBRA1-dependent transcription programme during mammary gland development. COBRA1 is a BRCA1-binding protein and, as part of the negative elongation factor, regulates RNA polymerase II pausing and transcription elongation. Here, the authors show that tissue-specific deletion of mouse Cobra1 inhibits postnatal mammary gland development and that the mammary defects can be rescued by additional deletion of Brca1 in a DNA repair-independent manner.
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Affiliation(s)
- Sreejith J Nair
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Xiaowen Zhang
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Huai-Chin Chiang
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Md Jamiul Jahid
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Yao Wang
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Paula Garza
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Craig April
- Research and Development, Illumina, Inc., San Diego, California 92122, USA
| | - Neeraj Salathia
- Research and Development, Illumina, Inc., San Diego, California 92122, USA
| | - Tapahsama Banerjee
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fahad S Alenazi
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Jian-Bing Fan
- Research and Development, Illumina, Inc., San Diego, California 92122, USA
| | - Jeffrey D Parvin
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Victor X Jin
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Yanfen Hu
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Rong Li
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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