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Nacer DF, Vallon-Christersson J, Nordborg N, Ehrencrona H, Kvist A, Borg Å, Staaf J. Molecular characteristics of breast tumors in patients screened for germline predisposition from a population-based observational study. Genome Med 2023; 15:25. [PMID: 37060015 PMCID: PMC10103478 DOI: 10.1186/s13073-023-01177-4] [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: 10/26/2022] [Accepted: 04/05/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Pathogenic germline variants (PGVs) in certain genes are linked to higher lifetime risk of developing breast cancer and can influence preventive surgery decisions and therapy choices. Public health programs offer genetic screening based on criteria designed to assess personal risk and identify individuals more likely to carry PGVs, dividing patients into screened and non-screened groups. How tumor biology and clinicopathological characteristics differ between these groups is understudied and could guide refinement of screening criteria. METHODS Six thousand six hundred sixty breast cancer patients diagnosed in South Sweden during 2010-2018 were included with available clinicopathological and RNA sequencing data, 900 (13.5%) of which had genes screened for PGVs through routine clinical screening programs. We compared characteristics of screened patients and tumors to non-screened patients, as well as between screened patients with (n = 124) and without (n = 776) PGVs. RESULTS Broadly, breast tumors in screened patients showed features of a more aggressive disease. However, few differences related to tumor biology or patient outcome remained significant after stratification by clinical subgroups or PAM50 subtypes. Triple-negative breast cancer (TNBC), the subgroup most enriched for PGVs, showed the most differences between screening subpopulations (e.g., higher tumor proliferation in screened cases). Significant differences in PGV prevalence were found between clinical subgroups/molecular subtypes, e.g., TNBC cases were enriched for BRCA1 PGVs. In general, clinicopathological differences between screened and non-screened patients mimicked those between patients with and without PGVs, e.g., younger age at diagnosis for positive cases. However, differences in tumor biology/microenvironment such as immune cell composition were additionally seen within PGV carriers/non-carriers in ER + /HER2 - cases, but not between screening subpopulations in this subgroup. CONCLUSIONS Characterization of molecular tumor features in patients clinically screened and not screened for PGVs represents a relevant read-out of guideline criteria. The general lack of molecular differences between screened/non-screened patients after stratification by relevant breast cancer subsets questions the ability to improve the identification of screening candidates based on currently used patient and tumor characteristics, pointing us towards universal screening. Nevertheless, while that is not attained, molecular differences identified between PGV carriers/non-carriers suggest the possibility of further refining patient selection within certain patient subsets using RNA-seq through, e.g., gene signatures. TRIAL REGISTRATION The Sweden Cancerome Analysis Network - Breast (SCAN-B) was prospectively registered at ClinicalTrials.gov under the identifier NCT02306096.
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Affiliation(s)
- Deborah F Nacer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, SE-22381, Sweden
| | | | - Nicklas Nordborg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Hans Ehrencrona
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Kvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, SE-22381, Sweden.
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2
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Loss of function of BRCA1 promotes EMT in mammary tumors through activation of TGFβR2 signaling pathway. Cell Death Dis 2022; 13:195. [PMID: 35236825 PMCID: PMC8891277 DOI: 10.1038/s41419-022-04646-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/25/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
BRCA1 deficient breast cancers are aggressive and chemoresistant due, in part, to their enrichment of cancer stem cells that can be generated from carcinoma cells by an epithelial-mesenchymal transition (EMT). We previously discovered that BRCA1 deficiency activates EMT in mammary tumorigenesis. How BRCA1 controls EMT and how to effectively target BRCA1-deficient cancers remain elusive. We analyzed murine and human tumors and identified a role for Tgfβr2 in governing the molecular aspects of EMT that occur with Brca1 loss. We utilized CRISPR to delete Tgfβr2 and specific inhibitors to block Tgfβr2 activity and followed up with the molecular analysis of assays for tumor growth and metastasis. We discovered that heterozygous germline deletion, or epithelia-specific deletion of Brca1 in mice, activates Tgfβr2 signaling pathways in mammary tumors. BRCA1 depletion promotes TGFβ-mediated EMT activation in cancer cells. BRCA1 binds to the TGFβR2 locus to repress its transcription. Targeted deletion or pharmaceutical inhibition of Tgfβr2 in Brca1-deficient tumor cells reduces EMT and suppresses tumorigenesis and metastasis. BRCA1 and TGFβR2 expression levels are inversely related in human breast cancers. This study reveals for the first time that a targetable TGFβR signaling pathway is directly activated by BRCA1-deficiency in the induction of EMT in breast cancer progression.
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Li Y, Dong W, Zhang P, Zhang T, Ma L, Qu M, Ma X, Zhou X, He Q. Comprehensive Analysis of Regulatory Factors and Immune-Associated Patterns to Decipher Common and BRCA1/2 Mutation-Type-Specific Critical Regulation in Breast Cancer. Front Cell Dev Biol 2021; 9:750897. [PMID: 34733851 PMCID: PMC8558486 DOI: 10.3389/fcell.2021.750897] [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: 07/31/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background: BRCA1/2 mutations are closely related to high lifetime risk of breast cancer (BC). The objective of this study was to identify the genes, regulators, and immune-associated patterns underlying disease pathology in BC with BRCA1/2 somatic mutations and their associations with clinical traits. Methods: RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA; N = 36 BRCA1-mutant BC; N = 49 BRCA2-mutant BC; and N = 117 BRCA1/2-wild-type BC samples) were used for discovery, which included consensus network analysis, function enrichment, and analysis of hub genes; other TCGA data (N = 117 triple-negative BC) and two Gene Expression Omnibus database expression profiles were used as validation cohorts. Results: Consensus network analysis helped to identify specific co-expressed modules that showed positive correlations with tumor stage, number of positive lymph nodes, and margin status in BRCA1/2-mutant BC but lacking correlations in BRCA1/2-wild-type BC. Functional enrichment suggested potential mechanisms in BRCA1/2 carriers that could regulate the cell cycle, immune response, cellular metabolic processes, and cell migration, via enriched pathways including p53 and JAK-STAT signaling. Consensus network analysis identified the specific and common carcinogenic mechanisms involving BRCA mutations. Regulators cross-linking these modules include E2F or IRF transcription factor family, associated with cell cycle or immune response regulation module, respectively. Eight hub genes, including ISG15, BUB1, and TTK, were upregulated in several BRCA1/2-mutant BC datasets and showed prognostic value in BC. Furthermore, their genetic expression was related to higher levels of immune infiltration in BRCA1/2-mutant BC, which manifested as recruitment of T helper cells (Th1 cells), follicular helper T cells, and regulatory T cells, and T cell exhaustion. Moreover, important indicators for evaluation of BC immunotherapy, tumor mutational burden and neoantigen load also positively correlated with expression of some hub genes. Conclusion: We constructed a BRCA1/2 mutation-type-specific co-expressed gene network with related transcription factors and immune-associated patterns that could regulate and influence tumor metastasis and immune microenvironment, providing novel insights into the pathological process of this disease and the corresponding BRCA mutations.
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Affiliation(s)
- Yue Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Dong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pengqian Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ting Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ling Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meng Qu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xingcong Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoyan Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qian He
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Ruiz de la Cruz M, de la Cruz Montoya AH, Rojas Jiménez EA, Martínez Gregorio H, Díaz Velásquez CE, Paredes de la Vega J, de la Cruz Hernández-Hernández F, Vaca Paniagua F. Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases. Cancers (Basel) 2021; 13:cancers13194807. [PMID: 34638292 PMCID: PMC8508567 DOI: 10.3390/cancers13194807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/25/2022] Open
Abstract
Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.
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Affiliation(s)
- Miguel Ruiz de la Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | | | - Ernesto Arturo Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Héctor Martínez Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
| | - Jimena Paredes de la Vega
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Fidel de la Cruz Hernández-Hernández
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5623-1333 (ext. 39788)
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Bai F, Zhang LH, Liu X, Wang C, Zheng C, Sun J, Li M, Zhu WG, Pei XH. GATA3 functions downstream of BRCA1 to suppress EMT in breast cancer. Theranostics 2021; 11:8218-8233. [PMID: 34373738 PMCID: PMC8344017 DOI: 10.7150/thno.59280] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Purpose: Functional loss of BRCA1 is associated with poorly differentiated and metastatic breast cancers that are enriched with cancer stem cells (CSCs). CSCs can be generated from carcinoma cells through an epithelial-mesenchymal transition (EMT) program. We and others have previously demonstrated that BRCA1 suppresses EMT and regulates the expression of multiple EMT-related transcription factors. However, the downstream mediators of BRCA1 function in EMT suppression remain elusive. Methods: Depletion of BRCA1 or GATA3 activates p18INK4C , a cell cycle inhibitor which inhibits mammary epithelial cell proliferation. We have therefore created genetically engineered mice with Brca1 or Gata3 loss in addition to deletion of p18INK4C , to rescue proliferative defects caused by deficiency of Brca1 or Gata3. By using these mutant mice along with human BRCA1 deficient as well as proficient breast cancer tissues and cells, we investigated and compared the role of Brca1 and Gata3 loss in the activation of EMT in breast cancers. Results: We discovered that BRCA1 and GATA3 expressions were positively correlated in human breast cancer. Depletion of BRCA1 stimulated methylation of GATA3 promoter thereby repressing GATA3 transcription. We developed Brca1 and Gata3 deficient mouse system. We found that Gata3 deficiency in mice induced poorly-differentiated mammary tumors with the activation of EMT and promoted tumor initiating and metastatic potential. Gata3 deficient mammary tumors phenocopied Brca1 deficient tumors in the induction of EMT under the same genetic background. Reconstitution of Gata3 in Brca1-deficient tumor cells activated mesenchymal-epithelial transition, suppressing tumor initiation and metastasis. Conclusions: Our finding, for the first time, demonstrates that GATA3 functions downstream of BRCA1 to suppress EMT in controlling mammary tumorigenesis and metastasis.
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Affiliation(s)
- Feng Bai
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
- Department of Pathology, Shenzhen University Health Science Center, Shenzhen 518060, China
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA
| | - Li-Han Zhang
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan 450008, China
| | - Xiong Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Chuying Wang
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Chenglong Zheng
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Jianping Sun
- Department of Mathematics and Statistics, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Min Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Xin-Hai Pei
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen 518060, China
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6
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Greville G, Llop E, Howard J, Madden SF, Perry AS, Peracaula R, Rudd PM, McCann A, Saldova R. 5-AZA-dC induces epigenetic changes associated with modified glycosylation of secreted glycoproteins and increased EMT and migration in chemo-sensitive cancer cells. Clin Epigenetics 2021; 13:34. [PMID: 33579350 PMCID: PMC7881483 DOI: 10.1186/s13148-021-01015-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
Background Glycosylation, one of the most fundamental post-translational modifications, is altered in cancer and is subject in part, to epigenetic regulation. As there are many epigenetic-targeted therapies currently in clinical trials for the treatment of a variety of cancers, it is important to understand the impact epi-therapeutics have on glycosylation. Results Ovarian and triple negative breast cancer cells were treated with the DNA methyltransferase inhibitor, 5-AZA-2-deoxycytidine (5-AZA-dC). Branching and sialylation were increased on secreted N-glycans from chemo-sensitive/non-metastatic cell lines following treatment with 5-AZA-dC. These changes correlated with increased mRNA expression levels in MGAT5 and ST3GAL4 transcripts in ovarian cancer cell lines. Using siRNA transient knock down of GATA2 and GATA3 transcription factors, we show that these regulate the glycosyltransferases ST3GAL4 and MGAT5, respectively. Moreover, 5-AZA-dC-treated cells displayed an increase in migration, with a greater effect seen in chemo-sensitive cell lines. Western blots showed an increase in apoptotic and senescence (p21) markers in all 5-AZA-dC-treated cells. The alterations seen in N-glycans from secreted glycoproteins in 5-AZA-dC-treated breast and ovarian cancer cells were similar to the N-glycans previously known to potentiate tumour cell survival. Conclusions While the FDA has approved epi-therapeutics for some cancer treatments, their global effect is still not fully understood. This study gives insight into the effects that epigenetic alterations have on cancer cell glycosylation, and how this potentially impacts on the overall fate of those cells. Graphic abstract ![]()
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Affiliation(s)
- Gordon Greville
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland.,College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Esther Llop
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jane Howard
- College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Stephen F Madden
- Data Science Centre, Royal College of Surgeons in Ireland (RCSI), Dublin 2, Ireland
| | - Antoinette S Perry
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,School of Biology and Environmental Science, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Rosa Peracaula
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Pauline M Rudd
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Amanda McCann
- College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Radka Saldova
- GlycoScience Group, the National Institute for Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Mount Merrion, Blackrock, Co Dublin, Ireland. .,College of Health and Agricultural Science (CHAS), UCD School of Medicine, University College Dublin (UCD), Belfield, Dublin 4, Ireland.
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Chen PS, Hsu HP, Phan NN, Yen MC, Chen FW, Liu YW, Lin FP, Feng SY, Cheng TL, Yeh PH, Omar HA, Sun Z, Jiang JZ, Chan YS, Lai MD, Wang CY, Hung JH. CCDC167 as a potential therapeutic target and regulator of cell cycle-related networks in breast cancer. Aging (Albany NY) 2021; 13:4157-4181. [PMID: 33461170 PMCID: PMC7906182 DOI: 10.18632/aging.202382] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
According to cancer statistics reported in 2020, breast cancer constitutes 30% of new cancer cases diagnosed in American women. Histological markers of breast cancer are expressions of the estrogen receptor (ER), the progesterone receptor (PR), and human epidermal growth factor receptor (HER)-2. Up to 80% of breast cancers are grouped as ER-positive, which implies a crucial role for estrogen in breast cancer development. Therefore, identifying potential therapeutic targets and investigating their downstream pathways and networks are extremely important for drug development in these patients. Through high-throughput technology and bioinformatics screening, we revealed that coiled-coil domain-containing protein 167 (CCDC167) was upregulated in different types of tumors; however, the role of CCDC167 in the development of breast cancer still remains unclear. Integrating many kinds of databases including ONCOMINE, MetaCore, IPA, and Kaplan-Meier Plotter, we found that high expression levels of CCDC167 predicted poor prognoses of breast cancer patients. Knockdown of CCDC167 attenuated aggressive breast cancer growth and proliferation. We also demonstrated that treatment with fluorouracil, carboplatin, paclitaxel, and doxorubicin resulted in decreased expression of CCDC167 and suppressed growth of MCF-7 cells. Collectively, these findings suggest that CCDC167 has high potential as a therapeutic target for breast cancer.
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Affiliation(s)
- Pin-Shern Chen
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 70101, Taiwan, Republic of China
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, Republic of China
| | - Nam Nhut Phan
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh 700000, Vietnam
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China.,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China
| | - Feng-Wei Chen
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, Republic of China
| | - Yu-Wei Liu
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 70101, Taiwan, Republic of China
| | - Fang-Ping Lin
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 70101, Taiwan, Republic of China
| | - Sheng-Yao Feng
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 70101, Taiwan, Republic of China
| | - Tsung-Lin Cheng
- Department of Physiology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China.,Orthopedic Research Center, College of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China.,Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China
| | - Pei-Hsiang Yeh
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 70101, Taiwan, Republic of China
| | - Hany A Omar
- Sharjah Institute for Medical Research and College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates.,Department of Clinical Sciences, College of Pharmacy, Ajman University, Ajman 23000, United Arab Emirates.,Department of Pharmacology, Faculty of Pharmacy, BeniSuef University, Beni-Suef 62511, Egypt
| | - Zhengda Sun
- Kaiser Permanente, Northern California Regional Laboratories, The Permanente Medical Group, Berkeley, CA 94710, USA
| | - Jia-Zhen Jiang
- Emergency Department, Huashan Hospital North, Fudan University, Shanghai 201508, People's Republic of China
| | - Yi-Shin Chan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan, Republic of China
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, Republic of China
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan, Republic of China.,PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan, Republic of China
| | - Jui-Hsiang Hung
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 70101, Taiwan, Republic of China.,Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China
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Genome-Wide Gene Expression Analyses of BRCA1- and BRCA2-Associated Breast and Ovarian Tumours. Cancers (Basel) 2020; 12:cancers12103015. [PMID: 33081408 PMCID: PMC7603076 DOI: 10.3390/cancers12103015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 increase cumulative lifetime risk up to 75% for breast cancer and 76% for ovarian cancer. Genetic testing for BRCA1 and BRCA2 pathogenic variants has become an important part of clinical practice for cancer risk assessment and for reducing individual risk of developing cancer. Genetic testing can produce three outcomes: positive (a pathogenic variant), uninformative (no pathogenic variant) and uncertain significance (a variant of unknown clinical significance). More than one third of BRCA1 and BRCA2 variants identified have been classified as variants of uncertain significance, presenting a challenge for clinicians. To address this important clinical challenge, a number of studies have been undertaken to establish a gene expression phenotype for pathogenic BRCA1 and BRCA2 variant carriers in several diseased and normal tissues. However, the consistency of gene expression phenotypes described in studies has been poor. To determine if gene expression analysis has been a successful approach for variant classification, we describe the design and comparability of 23 published gene expression studies that have profiled cells from BRCA1 and BRCA2 pathogenic variant carriers. We show the impact of advancements in expression-based technologies, the importance of developing larger study cohorts and the necessity to better understand variables affecting gene expression profiles across different tissue types.
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9
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Glodzik D, Bosch A, Hartman J, Aine M, Vallon-Christersson J, Reuterswärd C, Karlsson A, Mitra S, Niméus E, Holm K, Häkkinen J, Hegardt C, Saal LH, Larsson C, Malmberg M, Rydén L, Ehinger A, Loman N, Kvist A, Ehrencrona H, Nik-Zainal S, Borg Å, Staaf J. Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers. Nat Commun 2020; 11:3747. [PMID: 32719340 PMCID: PMC7385112 DOI: 10.1038/s41467-020-17537-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Homologous recombination deficiency (HRD) is a defining characteristic in BRCA-deficient breast tumors caused by genetic or epigenetic alterations in key pathway genes. We investigated the frequency of BRCA1 promoter hypermethylation in 237 triple-negative breast cancers (TNBCs) from a population-based study using reported whole genome and RNA sequencing data, complemented with analyses of genetic, epigenetic, transcriptomic and immune infiltration phenotypes. We demonstrate that BRCA1 promoter hypermethylation is twice as frequent as BRCA1 pathogenic variants in early-stage TNBC and that hypermethylated and mutated cases have similarly improved prognosis after adjuvant chemotherapy. BRCA1 hypermethylation confers an HRD, immune cell type, genome-wide DNA methylation, and transcriptional phenotype similar to TNBC tumors with BRCA1-inactivating variants, and it can be observed in matched peripheral blood of patients with tumor hypermethylation. Hypermethylation may be an early event in tumor development that progress along a common pathway with BRCA1-mutated disease, representing a promising DNA-based biomarker for early-stage TNBC.
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Affiliation(s)
- Dominik Glodzik
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA, Cambridge, UK
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute, SE-17177, Stockholm, Sweden
| | - Mattias Aine
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, SE-22184, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Anna Karlsson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Shamik Mitra
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Division of Surgery, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Karolina Holm
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, SE-22184, Lund, Sweden
| | - Niklas Loman
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
- Department of Oncology, Skåne University Hospital, SE-22184, Lund, Sweden
| | - Anders Kvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Hans Ehrencrona
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, SE-22184, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-22184, Lund, Sweden
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, CB2 0QQ, Cambridge, UK
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden.
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10
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Amirfallah A, Arason A, Einarsson H, Gudmundsdottir ET, Freysteinsdottir ES, Olafsdottir KA, Johannsson OT, Agnarsson BA, Barkardottir RB, Reynisdottir I. High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer. PLoS One 2019; 14:e0221413. [PMID: 31442252 PMCID: PMC6707546 DOI: 10.1371/journal.pone.0221413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Background Fusion genes result from genomic structural changes, which can lead to alterations in gene expression that supports tumor development. The aim of the study was to use fusion genes as a tool to identify new breast cancer (BC) genes with a role in BC progression. Methods Fusion genes from breast tumors and BC cell lines were collected from publications. RNA-Seq data from tumors and cell lines were retrieved from databanks and analyzed for fusions with SOAPfuse or the analysis was purchased. Fusion genes identified in both tumors (n = 1724) and cell lines (n = 45) were confirmed by qRT-PCR and sequencing. Their individual genes were ranked by selection criteria that included correlation of their mRNA level with copy number. The expression of the top ranked gene was measured by qRT-PCR in normal tissue and in breast tumors from an exploratory cohort (n = 141) and a validation cohort (n = 277). Expression levels were correlated with clinical and pathological factors as well as the patients’ survival. The results were followed up in BC cohorts from TCGA (n = 818) and METABRIC (n = 2509). Results Vacuole membrane protein 1 (VMP1) was the most promising candidate based on specific selection criteria. Its expression was higher in breast tumor tissue than normal tissue (p = 1x10-4), and its expression was significantly higher in HER2 positive than HER2 negative breast tumors in all four cohorts analyzed. High expression of VMP1 associated with breast cancer specific survival (BCSS) in cohort 1 (hazard ratio (HR) = 2.31, CI 1.27–4.18) and METABRIC (HR = 1.26, CI 1.02–1.57), and also after adjusting for HER2 expression in cohort 1 (HR = 2.03, CI 1.10–3.72). BCSS was not significant in cohort 2 or TCGA cohort, which may be due to differences in treatment regimens. Conclusions The results suggest that high VMP1 expression is a potential marker of poor prognosis in HER2 positive BC. Further studies are needed to elucidate how VMP1 could affect pathways supportive of tumorigenesis.
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Affiliation(s)
- Arsalan Amirfallah
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Adalgeir Arason
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Hjorleifur Einarsson
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Eydis Thorunn Gudmundsdottir
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Edda Sigridur Freysteinsdottir
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Oskar Thor Johannsson
- Department of Oncology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjarni Agnar Agnarsson
- Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Rosa Bjork Barkardottir
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Inga Reynisdottir
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- * E-mail:
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11
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Care MA, Westhead DR, Tooze RM. Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer. NPJ Syst Biol Appl 2019; 5:13. [PMID: 30993001 PMCID: PMC6459838 DOI: 10.1038/s41540-019-0090-7] [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: 09/04/2018] [Accepted: 03/18/2019] [Indexed: 12/11/2022] Open
Abstract
Cancers converge onto shared patterns that arise from constraints placed by the biology of the originating cell lineage and microenvironment on programs driven by oncogenic events. Here we define consistent expression modules reflecting this structure in colon and breast cancer by exploiting expression data resources and a new computationally efficient approach that we validate against other comparable methods. This approach, Parsimonious Gene Correlation Network Analysis (PGCNA), allows comparison of network structures between these cancer types identifying shared modules of gene co-expression reflecting: cancer hallmarks, functional and structural gene batteries, copy number variation and biology of originating lineage. These networks along with the mapping of outcome data at gene and module level provide an interactive resource that generates context for relationships between genes within and between such modules. Assigning module expression values (MEVs) provides a tool to summarize network level gene expression in individual cases illustrating potential utility in classification and allowing analysis of linkage between module expression and mutational state. Exploiting TCGA data thus defines both recurrent patterns of association between module expression and mutation at data-set level, and exemplifies the polarization of mutation patterns with the leading edge of module expression at individual case level. We illustrate the scalable nature of the approach within immune response related modules, which in the context of breast cancer demonstrates the selective association of immune subsets, in particular mast cells, with the underlying mutational pattern. Together our analyses provide evidence for a generalizable framework to enhance molecular stratification in cancer.
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Affiliation(s)
- Matthew A. Care
- Section of Experimental Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, LS9 7TF UK
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT UK
| | - David R. Westhead
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT UK
| | - Reuben M. Tooze
- Section of Experimental Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, LS9 7TF UK
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12
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Lønning PE, Eikesdal HP, Løes IM, Knappskog S. Constitutional Mosaic Epimutations - a hidden cause of cancer? Cell Stress 2019; 3:118-135. [PMID: 31225507 PMCID: PMC6551830 DOI: 10.15698/cst2019.04.183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter hypermethylation is a key mechanism to facilitate cancer progression in many malignancies. While promoter hypermethylation can occur at later stages of the carcinogenesis process, constitutional methylation of key tumor suppressors may be an initiating event whereby cancer is started. Constitutional BRCA1 methylation due to cis-acting germline genetic variants is associated with a high risk of breast and ovarian cancer. However, this seems to be a rare event, restricted to a very limited number of families. In contrast, mosaic constitutional BRCA1 methylation is detected in 4-7% of newborn females without germline BRCA1 mutations. While the cause of such methylation is poorly understood, mosaic normal tissue BRCA1 methylation is associated with a 2-3 fold increased risk of high-grade serous ovarian cancer (HGSOC). As such, BRCA1 methylation may be the cause of a significant number of ovarian cancers. Given the molecular similarities between HGSOC and basal-like breast cancer, the findings with respect to HGSOC suggest that constitutional BRCA1 methylation could be a risk factor for basal-like breast cancer as well. Similar to BRCA1, some specific germline variants in MLH1 and MSH2 are associated with promoter methylation and a high risk of colorectal cancers in rare hereditary cases of the disease. However, as many as 15% of all colorectal cancers are of the microsatellite instability (MSI) "high" subtype, in which commonly the tumors harbor MLH1 hypermethylation. Constitutional mosaic methylation of MLH1 in normal tissues has been detected but not formally evaluated as a potential risk factor for incidental colorectal cancers. However, the findings with respect to BRCA1 in breast and ovarian cancer raises the question whether mosaic MLH1 methylation is a risk factor for MSI positive colorectal cancer as well. As for MGMT, a promoter variant is associated with elevated methylation across a panel of solid cancers, and MGMT promoter methylation may contribute to an elevated cancer risk in several of these malignancies. We hypothesize that constitutional mosaic promoter methylation of crucial tumor suppressors may trigger certain types of cancer, similar to germline mutations inactivating the same particular genes. Such constitutional methylation events may be a spark to ignite cancer development, and if associated with a significant cancer risk, screening for such epigenetic alterations could be part of cancer prevention programs to reduce cancer mortality in the future.
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Affiliation(s)
- Per E. Lønning
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Hans P. Eikesdal
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Inger M. Løes
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
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13
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Wang C, Bai F, Zhang LH, Scott A, Li E, Pei XH. Estrogen promotes estrogen receptor negative BRCA1-deficient tumor initiation and progression. Breast Cancer Res 2018; 20:74. [PMID: 29996906 PMCID: PMC6042319 DOI: 10.1186/s13058-018-0996-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/30/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Estrogen promotes breast cancer development and progression mainly through estrogen receptor (ER). However, blockage of estrogen production or action prevents development of and suppresses progression of ER-negative breast cancers. How estrogen promotes ER-negative breast cancer development and progression is poorly understood. We previously discovered that deletion of cell cycle inhibitors p16Ink4a (p16) or p18Ink4c (p18) is required for development of Brca1-deficient basal-like mammary tumors, and that mice lacking p18 develop luminal-type mammary tumors. METHODS A genetic model system with three mouse strains, one that develops ER-positive mammary tumors (p18 single deletion) and the others that develop ER-negative tumors (p16;Brca1 and p18;Brca1 compound deletion), human BRCA1 mutant breast cancer patient-derived xenografts, and human BRCA1-deficient and BRCA1-proficient breast cancer cells were used to determine the role of estrogen in activating epithelial-mesenchymal transition (EMT), stimulating cell proliferation, and promoting ER-negative mammary tumor initiation and metastasis. RESULTS Estrogen stimulated the proliferation and tumor-initiating potential of both ER-positive Brca1-proficient and ER-negative Brca1-deficient tumor cells. Estrogen activated EMT in a subset of Brca1-deficient mammary tumor cells that maintained epithelial features, and enhanced the number of cancer stem cells, promoting tumor progression and metastasis. Estrogen activated EMT independent of ER in Brca1-deficient, but not Brca1-proficient, tumor cells. Estrogen activated the AKT pathway in BRCA1-deficient tumor cells independent of ER, and pharmaceutical inhibition of AKT activity suppressed EMT and cell proliferation preventing BRCA1 deficient tumor progression. CONCLUSIONS This study reveals for the first time that estrogen promotes BRCA1-deficient tumor initiation and progression by stimulation of cell proliferation and activation of EMT, which are dependent on AKT activation and independent of ER.
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Affiliation(s)
- Chuying Wang
- Department of Medical Oncology, The First Affiliated hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710061 People’s Republic of China
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136 USA
| | - Feng Bai
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136 USA
| | - Li-han Zhang
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136 USA
| | - Alexandria Scott
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136 USA
| | - Enxiao Li
- Department of Medical Oncology, The First Affiliated hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710061 People’s Republic of China
| | - Xin-Hai Pei
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
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14
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Kinalis S, Nielsen FC, Talman ML, Ejlertsen B, Rossing M. Characterization of basal-like subtype in a Danish consecutive primary breast cancer cohort. Acta Oncol 2018; 57:51-57. [PMID: 29164968 DOI: 10.1080/0284186x.2017.1398837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Transcriptome analysis enables classification of breast tumors into molecular subtypes. BRCA1/2 predisposed patients are more likely to suffer from a basal-like subtype and this group of patients displays a more distinct phenotype and genotype. Hence, in-depth characterization of this separate entity is needed. MATERIAL AND METHODS Molecular subtyping was performed on a consecutive and unselected series of 1560 tumors from patients with primary breast cancer. Tumors were classified by the 256 gene expression signature (CIT) and associated with basic clinical characteristics and aggregated expression levels in the hallmark gene sets. RESULTS Of the 1560 samples, 168 were classified basal-like and 120 patients were screened for BRCA1/2 mutations, resulting in 19 BRCA1/2 carriers, 95 non-carriers and six patients carried variants of unknown significance. The BRCA1/2 carriers were significantly younger and there were no carriers above 60 years of age. The tumors showed a loss in DNA-repair profile, as well as an upregulation in proliferative cancer signaling pathways. A robust molecular signature for identification of the BRCA1/2 - carriers was infeasible in the current cohort. Patients with a basal like breast cancer had the lowest median age and the largest median tumor size. They were almost exclusively diagnosed in disease stage III. CONCLUSIONS Basal-like subtype is indeed a separate entity compared with other molecular breast cancer subtypes and the clinical course for this patient group should reflect the aggressiveness of this cancer. Taken together, patients being diagnosed with a basal-like breast cancer are in the youngest segment of breast cancer patients and are mainly diagnosed in stage III disease.
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Affiliation(s)
- Savvas Kinalis
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maj-Lis Talman
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bent Ejlertsen
- Denmark Danish Breast Cancer Cooperative Group, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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15
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Krüger K, Wik E, Knutsvik G, Nalwoga H, Klingen TA, Arnes JB, Chen Y, Mannelqvist M, Dimitrakopoulou K, Stefansson IM, Birkeland E, Aas T, Tobin NP, Jonassen I, Bergh J, Foulkes WD, Akslen LA. Expression of Nestin associates with BRCA1 mutations, a basal-like phenotype and aggressive breast cancer. Sci Rep 2017; 7:1089. [PMID: 28439082 PMCID: PMC5430803 DOI: 10.1038/s41598-017-00862-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/15/2017] [Indexed: 12/28/2022] Open
Abstract
We here examined whether Nestin, by protein and mRNA levels, could be a predictor of BRCA1 related breast cancer, a basal-like phenotype, and aggressive tumours. Immunohistochemical staining of Nestin was done in independent breast cancer hospital cohorts (Series I-V, total 1257 cases). Also, TCGA proteomic data (n = 103), mRNA microarray data from TCGA (n = 520), METABRIC (n = 1992), and 6 open access breast cancer datasets (n = 1908) were analysed. Patients with Nestin protein expression in tumour cells more often had BRCA1 germline mutations (OR 8.7, p < 0.0005, Series III), especially among younger patients (<40 years at diagnosis) (OR 16.5, p = 0.003). Nestin protein positivity, observed in 9–28% of our hospital cases (Series I-IV), was independently associated with reduced breast cancer specific survival (HR = 2.0, p = 0.035) and was consistently related to basal-like differentiation (by Cytokeratin 5, OR 8.7–13.8, p < 0.0005; P-cadherin OR 7.0–8.9, p < 0.0005; EGFR staining, OR 3.7–8.2, p ≤ 0.05). Nestin mRNA correlated significantly with Nestin protein expression (ρ = 0.6, p < 0.0005), and high levels were seen in the basal-like intrinsic subtype. Gene expression signalling pathways linked to high Nestin were explored, and revealed associations with stem-like tumour features. In summary, Nestin was strongly associated with germline BRCA1 related breast cancer, a basal-like phenotype, reduced survival, and stemness characteristics.
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Affiliation(s)
- Kristi Krüger
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway
| | - Elisabeth Wik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Gøril Knutsvik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Hawa Nalwoga
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Makerere University College of Health Sciences, P. O. Box 7072, Kampala, Uganda
| | - Tor A Klingen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Vestfold Hospital, Tønsberg, Norway
| | - Jarle B Arnes
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Ying Chen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Vestfold Hospital, Tønsberg, Norway.,Department of Pathology, Akershus University Hospital, Lørenskog, Norway
| | - Monica Mannelqvist
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway
| | - Konstantina Dimitrakopoulou
- Centre for Cancer Biomarkers CCBIO and Computational Biology Unit, Department of Informatics, University of, Bergen, Norway
| | - Ingunn M Stefansson
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Even Birkeland
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway
| | - Turid Aas
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Nicholas P Tobin
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Inge Jonassen
- Centre for Cancer Biomarkers CCBIO and Computational Biology Unit, Department of Informatics, University of, Bergen, Norway
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - William D Foulkes
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, 546 Pine Avenue West, Montreal, QC, H2W 1S6, Canada
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway. .,Department of Pathology, Haukeland University Hospital, Bergen, Norway.
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16
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Scott A, Bai F, Chan HL, Liu S, Ma J, Slingerland JM, Robbins DJ, Capobianco AJ, Pei XH. p16INK4a suppresses BRCA1-deficient mammary tumorigenesis. Oncotarget 2016; 7:84496-84507. [PMID: 27811360 PMCID: PMC5356676 DOI: 10.18632/oncotarget.13015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/25/2016] [Indexed: 11/25/2022] Open
Abstract
Senescence prevents the proliferation of genomically damaged, but otherwise replication competent cells at risk of neoplastic transformation. p16INK4A (p16), an inhibitor of CDK4 and CDK6, plays a critical role in controlling cellular senescence in multiple organs. Functional inactivation of p16 by gene mutation and promoter methylation is frequently detected in human breast cancers. However, deleting p16 in mice or targeting DNA methylation within the murine p16 promoter does not result in mammary tumorigenesis. How loss of p16 contributes to mammary tumorigenesis in vivo is not fully understood.In this article, we reported that disruption of Brca1 in the mammary epithelium resulted in premature senescence that was rescued by p16 loss. We found that p16 loss transformed Brca1-deficient mammary epithelial cells and induced mammary tumors, though p16 loss alone was not sufficient to induce mammary tumorigenesis. We demonstrated that loss of both p16 and Brca1 led to metastatic, basal-like, mammary tumors with the induction of EMT and an enrichment of tumor initiating cells. We discovered that promoter methylation silenced p16 expression in most of the tumors developed in mice heterozygous for p16 and lacking Brca1. These data not only identified the function of p16 in suppressing BRCA1-deficient mammary tumorigenesis, but also revealed a collaborative effect of genetic mutation of p16 and epigenetic silencing of its transcription in promoting tumorigenesis. To the best of our knowledge, this is the first genetic evidence directly showing that p16 which is frequently deleted and inactivated in human breast cancers, collaborates with Brca1 controlling mammary tumorigenesis.
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MESH Headings
- Animals
- BRCA1 Protein/genetics
- BRCA1 Protein/metabolism
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cells, Cultured
- Cyclin-Dependent Kinase Inhibitor p16/genetics
- Cyclin-Dependent Kinase Inhibitor p16/metabolism
- DNA Methylation
- Epithelial Cells/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mammary Neoplasms, Animal/genetics
- Mammary Neoplasms, Animal/metabolism
- Mammary Neoplasms, Animal/pathology
- Mice, Knockout
- Mice, Transgenic
- Promoter Regions, Genetic/genetics
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Affiliation(s)
- Alexandria Scott
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- The Sheila and David Fuente Graduate Program in Cancer Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Feng Bai
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ho Lam Chan
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Shiqin Liu
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jinshan Ma
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Joyce M Slingerland
- Braman Family Breast Cancer Institute, Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - David J. Robbins
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Anthony J. Capobianco
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Xin-Hai Pei
- Molecular Oncology Program, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- The Sheila and David Fuente Graduate Program in Cancer Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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17
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Sedghi M, Esfandiari E, Fazel-Najafabadi E, Salehi M, Salavaty A, Fattahpour S, Dehghani L, Nouri N, Mokarian F. Genomic rearrangement screening of the BRCA1 from seventy Iranian high-risk breast cancer families. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2016; 21:95. [PMID: 28163741 PMCID: PMC5244654 DOI: 10.4103/1735-1995.193167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/01/2016] [Accepted: 07/01/2016] [Indexed: 01/23/2023]
Abstract
Background: The second leading cause of cancer deaths in women is breast cancer. Germline mutations in susceptibility breast cancer gene BRCA1 increase the lifetime risk of breast cancer. Eighty-one large genomic rearrangements (LGRs) have been reported up to date in BRCA1 gene, and evaluation of these rearrangements helps with precise risk assessment in high-risk individuals. In this study, we have investigated LGRs in BRCA1 among Iranian high-risk breast cancer families. Materials and Methods: Seventy patients with breast cancer who were identified negative for point mutations or small deletions/insertions of BRCA1 gene were selected. Deletions and duplications of BRCA1 gene were evaluated using multiplex ligation-dependent probe amplification (MLPA). Results: Two deletions, deletion of exons 1A/1B-2 and exon 24, were detected in two patients with breast cancer. The former alteration was found in a woman with a strong family history of breast cancer while the latter one was detected in a woman with early onset of breast cancer. Conclusion: Although our data confirm that LGRs in BRCA1 comprise a relatively small proportion of mutations in hereditary breast cancer in the Iranian population, MLPA analysis might be considered for screening of LGRs in high-risk individuals. It is worth to note that our results are consistent with previous studies in various Asian and European countries.
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Affiliation(s)
- Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Esfandiari
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Esmat Fazel-Najafabadi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Division of Genetics and Molecular Biology, Medical School, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Salavaty
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shirin Fattahpour
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Leila Dehghani
- Department of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Isfahan Neurosciences Research Center, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nayerossadat Nouri
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fariborz Mokarian
- Department of Oncology, Isfahan University of Medical Sciences, Isfahan, Iran
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18
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Nielsen FC, van Overeem Hansen T, Sørensen CS. Hereditary breast and ovarian cancer: new genes in confined pathways. Nat Rev Cancer 2016; 16:599-612. [PMID: 27515922 DOI: 10.1038/nrc.2016.72] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic abnormalities in the DNA repair genes BRCA1 and BRCA2 predispose to hereditary breast and ovarian cancer (HBOC). However, only approximately 25% of cases of HBOC can be ascribed to BRCA1 and BRCA2 mutations. Recently, exome sequencing has uncovered substantial locus heterogeneity among affected families without BRCA1 or BRCA2 mutations. The new pathogenic variants are rare, posing challenges to estimation of risk attribution through patient cohorts. In this Review article, we examine HBOC genes, focusing on their role in genome maintenance, the possibilities for functional testing of putative causal variants and the clinical application of new HBOC genes in cancer risk management and treatment decision-making.
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Affiliation(s)
- Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
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19
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Dai X, Liu Z, Zhang S. Over-expression of EPS15 is a favorable prognostic factor in breast cancer. MOLECULAR BIOSYSTEMS 2016; 11:2978-85. [PMID: 26289382 DOI: 10.1039/c5mb00219b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As a crucial player in terminating growth factor signaling, EPS15 plays important roles in many malignancies including breast cancer. To explore the potential association of EPS15 with the clinical outcome of breast cancer, we conducted gene expression survival analysis using six independent datasets, checked its expression quantitative loci and their associated genes, and explored the networking of these genes with EPS15. Our results show that over-expression of EPS15 is significantly associated with a favorable clinical outcome of breast cancer, especially in tumors harbouring a positive estrogen receptor status. 21 unique SNPs were found to be associated with EPS15 expression. Among the neighboring genes of these SNPs, five (MTUS1, DOCK5, MSRA, SLIT3 and SKAP1) are genetically connected with EPS15 and its physical partners. These genes including EPS15 also show significant concurrent expressions, and four exhibit distinct relevance regarding patient survival. High expressions of EPS15 and MSRA show a distinct combinatorial favorable survival, suggesting the clinical relevance of their co-activation. In summary, over-expression of EPS15 is a potential favorable prognostic marker in breast cancer, which can be used clinically alone or together with other genes such as MSRA to avail therapeutic decision-making.
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Affiliation(s)
- Xiaofeng Dai
- School of Biotechnology, National Engineering Laboratory for Cereal Fermentation Technology, Jiang-Nan University, Wuxi 214122, China
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20
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Waldemarson S, Kurbasic E, Krogh M, Cifani P, Berggård T, Borg Å, James P. Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples. Breast Cancer Res 2016; 18:69. [PMID: 27357824 PMCID: PMC4928264 DOI: 10.1186/s13058-016-0732-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/19/2016] [Indexed: 12/11/2022] Open
Abstract
Background Breast cancer is a complex and heterogeneous disease that is usually characterized by histological parameters such as tumor size, cellular arrangements/rearrangments, necrosis, nuclear grade and the mitotic index, leading to a set of around twenty subtypes. Together with clinical markers such as hormone receptor status, this classification has considerable prognostic value but there is a large variation in patient response to therapy. Gene expression profiling has provided molecular profiles characteristic of distinct subtypes of breast cancer that reflect the divergent cellular origins and degree of progression. Methods Here we present a large-scale proteomic and transcriptomic profiling study of 477 sporadic and hereditary breast cancer tumors with matching mRNA expression analysis. Unsupervised hierarchal clustering was performed and selected proteins from large-scale tandem mass spectrometry (MS/MS) analysis were transferred into a highly multiplexed targeted selected reaction monitoring assay to classify tumors using a hierarchal cluster and support vector machine with leave one out cross-validation. Results The subgroups formed upon unsupervised clustering agree very well with groups found at transcriptional level; however, the classifiers (genes or their respective protein products) differ almost entirely between the two datasets. In-depth analysis shows clear differences in pathways unique to each type, which may lie behind their different clinical outcomes. Targeted mass spectrometry analysis and supervised clustering correlate very well with subgroups determined by RNA classification and show convincing agreement with clinical parameters. Conclusions This work demonstrates the merits of protein expression profiling for breast cancer stratification. These findings have important implications for the use of genomics and expression analysis for the prediction of protein expression, such as receptor status and drug target expression. The highly multiplexed MS assay is easily implemented in standard clinical chemistry practice, allowing rapid and cheap characterization of tumor tissue suitable for directing the choice of treatment. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0732-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofia Waldemarson
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | - Emila Kurbasic
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | - Morten Krogh
- Amber Biosciences AB, Skrivarevägen 9, 226 57, Lund, Sweden
| | - Paolo Cifani
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | | | - Åke Borg
- Department of Oncology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | - Peter James
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden. .,Turku Centre for Biotechnology, Åbo Akademi University, University of Turku Biocity, Tykistokatu 6, 20520, Turku, Finland.
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21
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Holm K, Staaf J, Lauss M, Aine M, Lindgren D, Bendahl PO, Vallon-Christersson J, Barkardottir RB, Höglund M, Borg Å, Jönsson G, Ringnér M. An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells. Breast Cancer Res 2016; 18:27. [PMID: 26923702 PMCID: PMC4770527 DOI: 10.1186/s13058-016-0685-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/09/2016] [Indexed: 12/15/2022] Open
Abstract
Background Aberrant DNA methylation is frequently observed in breast cancer. However, the relationship between methylation patterns and the heterogeneity of breast cancer has not been comprehensively characterized. Methods Whole-genome DNA methylation analysis using Illumina Infinium HumanMethylation450 BeadChip arrays was performed on 188 human breast tumors. Unsupervised bootstrap consensus clustering was performed to identify DNA methylation epigenetic subgroups (epitypes). The Cancer Genome Atlas data, including methylation profiles of 669 human breast tumors, was used for validation. The identified epitypes were characterized by integration with publicly available genome-wide data, including gene expression levels, DNA copy numbers, whole-exome sequencing data, and chromatin states. Results We identified seven breast cancer epitypes. One epitype was distinctly associated with basal-like tumors and with BRCA1 mutations, one epitype contained a subset of ERBB2-amplified tumors characterized by multiple additional amplifications and the most complex genomes, and one epitype displayed a methylation profile similar to normal epithelial cells. Luminal tumors were stratified into the remaining four epitypes, with differences in promoter hypermethylation, global hypomethylation, proliferative rates, and genomic instability. Specific hyper- and hypomethylation across the basal-like epitype was rare. However, we observed that the candidate genomic instability drivers BRCA1 and HORMAD1 displayed aberrant methylation linked to gene expression levels in some basal-like tumors. Hypomethylation in luminal tumors was associated with DNA repeats and subtelomeric regions. We observed two dominant patterns of aberrant methylation in breast cancer. One pattern, constitutively methylated in both basal-like and luminal breast cancer, was linked to genes with promoters in a Polycomb-repressed state in normal epithelial cells and displayed no correlation with gene expression levels. The second pattern correlated with gene expression levels and was associated with methylation in luminal tumors and genes with active promoters in normal epithelial cells. Conclusions Our results suggest that hypermethylation patterns across basal-like breast cancer may have limited influence on tumor progression and instead reflect the repressed chromatin state of the tissue of origin. On the contrary, hypermethylation patterns specific to luminal breast cancer influence gene expression, may contribute to tumor progression, and may present an actionable epigenetic alteration in a subset of luminal breast cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0685-5) contains supplementary material, which is available to authorized users.
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22
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Haploinsufficiency for BRCA1 leads to cell-type-specific genomic instability and premature senescence. Nat Commun 2015; 6:7505. [PMID: 26106036 PMCID: PMC4491827 DOI: 10.1038/ncomms8505] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/14/2015] [Indexed: 12/19/2022] Open
Abstract
Although BRCA1 function is essential for maintaining genomic integrity in all cell types, it is unclear why increased risk of cancer in individuals harbouring deleterious mutations in BRCA1 is restricted to only a select few tissues. Here we show that human mammary epithelial cells (HMECs) from BRCA1-mutation carriers (BRCA1(mut/+)) exhibit increased genomic instability and rapid telomere erosion in the absence of tumour-suppressor loss. Furthermore, we uncover a novel form of haploinsufficiency-induced senescence (HIS) specific to epithelial cells, which is triggered by pRb pathway activation rather than p53 induction. HIS and telomere erosion in HMECs correlate with misregulation of SIRT1 leading to increased levels of acetylated pRb as well as acetylated H4K16 both globally and at telomeric regions. These results identify a novel form of cellular senescence and provide a potential molecular basis for the rapid cell- and tissue- specific predisposition of breast cancer development associated with BRCA1 haploinsufficiency.
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23
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Wittersheim M, Büttner R, Markiefka B. Genotype/Phenotype correlations in patients with hereditary breast cancer. Breast Care (Basel) 2015; 10:22-6. [PMID: 25960721 DOI: 10.1159/000380900] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Of all breast cancer cases, 5-10% can be attributed to germline mutations, and the high-susceptibility genes BRCA1 and BRCA2 account for about 25-28% of these cases. For the remainder, several genes of moderate and low penetrance have been discovered. Histopathologic characteristics have been studied in small cohorts, but for most of the known non-BRCA1/2-associated hereditary breast cancers, the histologic and immunohistochemical phenotypes are not yet identified. Particularly BRCA1 tumors are associated with a distinct morphology and immunohistochemical characteristics that differ from sporadic breast cancer of age-matched controls. The recognition of features characteristic of these mutations can be helpful to identify patients likely to carry a germline mutation and to assess which gene should be screened for first, in families with a high occurrence of breast and ovarian cancer.
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24
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Saal LH, Vallon-Christersson J, Häkkinen J, Hegardt C, Grabau D, Winter C, Brueffer C, Tang MHE, Reuterswärd C, Schulz R, Karlsson A, Ehinger A, Malina J, Manjer J, Malmberg M, Larsson C, Rydén L, Loman N, Borg Å. The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine. Genome Med 2015; 7:20. [PMID: 25722745 PMCID: PMC4341872 DOI: 10.1186/s13073-015-0131-9] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/15/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is imperfect for predicting outcome, which results in overtreatment for many patients, and for others, leads to death from recurrent disease. Therefore, additional criteria are needed to better personalize care and maximize treatment effectiveness and survival. METHODS To address these challenges, the Sweden Cancerome Analysis Network - Breast (SCAN-B) consortium was initiated in 2010 as a multicenter prospective study with longsighted aims to analyze breast cancers with next-generation genomic technologies for translational research in a population-based manner and integrated with healthcare; decipher fundamental tumor biology from these analyses; utilize genomic data to develop and validate new clinically-actionable biomarker assays; and establish real-time clinical implementation of molecular diagnostic, prognostic, and predictive tests. In the first phase, we focus on molecular profiling by next-generation RNA-sequencing on the Illumina platform. RESULTS In the first 3 years from 30 August 2010 through 31 August 2013, we have consented and enrolled 3,979 patients with primary breast cancer at the seven hospital sites in South Sweden, representing approximately 85% of eligible patients in the catchment area. Preoperative blood samples have been collected for 3,942 (99%) patients and primary tumor specimens collected for 2,929 (74%) patients. Herein we describe the study infrastructure and protocols and present initial proof of concept results from prospective RNA sequencing including tumor molecular subtyping and detection of driver gene mutations. Prospective patient enrollment is ongoing. CONCLUSIONS We demonstrate that large-scale population-based collection and RNA-sequencing analysis of breast cancer is feasible. The SCAN-B Initiative should significantly reduce the time to discovery, validation, and clinical implementation of novel molecular diagnostic and predictive tests. We welcome the participation of additional comprehensive cancer treatment centers. TRIAL REGISTRATION ClinicalTrials.gov identifier NCT02306096.
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Affiliation(s)
- Lao H Saal
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22381 Lund, Sweden
| | - Johan Vallon-Christersson
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22381 Lund, Sweden
| | - Jari Häkkinen
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22381 Lund, Sweden
| | - Cecilia Hegardt
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22381 Lund, Sweden
| | - Dorthe Grabau
- />Department of Pathology, Skåne University Hospital, SE-22185 Lund, Sweden
| | - Christof Winter
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
| | - Christian Brueffer
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
| | - Man-Hung Eric Tang
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
| | - Christel Reuterswärd
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />Department of Clinical Sciences, SCIBLU Genomics, Lund University, SE-22381 Lund, Sweden
| | - Ralph Schulz
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />Department of Clinical Sciences, SCIBLU Genomics, Lund University, SE-22381 Lund, Sweden
| | - Anna Karlsson
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />Department of Clinical Sciences, SCIBLU Genomics, Lund University, SE-22381 Lund, Sweden
| | - Anna Ehinger
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />Department of Pathology and Cytology, Blekinge County Hospital, SE-37185 Karlskrona, Sweden
| | - Janne Malina
- />Department of Pathology, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Jonas Manjer
- />Department of Surgery, Lund University and Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Martin Malmberg
- />Department of Oncology, Skåne University Hospital, SE-22185 Lund, Sweden
| | - Christer Larsson
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />Department of Laboratory Medicine, Division of Molecular Pathology, Lund University, SE-22185 Lund, Sweden
| | - Lisa Rydén
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />Department of Surgery, Lund University and Skåne University Hospital, SE-22185 Lund, Sweden
| | - Niklas Loman
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />Department of Oncology, Skåne University Hospital, SE-22185 Lund, Sweden
| | - Åke Borg
- />Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Medicon Village 404-A2, SE-22381 Lund, Sweden
- />Lund University Cancer Center, SE-22381 Lund, Sweden
- />CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22381 Lund, Sweden
- />Department of Clinical Sciences, SCIBLU Genomics, Lund University, SE-22381 Lund, Sweden
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25
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Shackney SE, Chowdhury SA, Schwartz R. A Novel Subset of Human Tumors That Simultaneously Overexpress Multiple E2F-responsive Genes Found in Breast, Ovarian, and Prostate Cancers. Cancer Inform 2014; 13:89-100. [PMID: 25392696 PMCID: PMC4221091 DOI: 10.4137/cin.s14062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/08/2014] [Accepted: 09/15/2014] [Indexed: 01/14/2023] Open
Abstract
Reasoning that overexpression of multiple E2F-responsive genes might be a useful marker for RB1 dysfunction, we compiled a list of E2F-responsive genes from the literature and evaluated their expression in publicly available gene expression microarray data of patients with breast cancer, serous ovarian cancer, and prostate cancer. In breast cancer, a group of tumors was identified, each of which simultaneously overexpressed multiple E2F-responsive genes. Seventy percent of these genes were concerned with cell cycle progression, DNA repair, or mitosis. These E2F-responsive gene overexpressing (ERGO) tumors frequently exhibited additional evidence of Rb/E2F axis dysfunction, were mostly triple negative, and preferentially overexpressed multiple basal cytokeratins, suggesting that they overlapped substantially with the basal-like tumor subset. ERGO tumors were also identified in serous ovarian cancer and prostate cancer. In these cancer types, there was no evidence for a tumor subset comparable to the breast cancer basal-like subset. A core group of about 30 E2F-responsive genes were overexpressed in all three cancer types. Thus, it appears that disorders of the Rb/E2F axis can arise at multiple organ sites and produce tumors that simultaneously overexpress multiple E2F-responsive genes.
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Affiliation(s)
- Stanley E Shackney
- President and CEO, Intelligent Oncotherapeutics Incorporated, Pittsburgh, PA, USA
| | - Salim Akhter Chowdhury
- Graduate student of Computational Biology, Lane Center for Computational Biology and Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Russell Schwartz
- Professor of Biological Sciences and Computational Biology, Department of Biological Sciences and Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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26
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Larsen MJ, Thomassen M, Gerdes AM, Kruse TA. Hereditary breast cancer: clinical, pathological and molecular characteristics. BREAST CANCER-BASIC AND CLINICAL RESEARCH 2014; 8:145-55. [PMID: 25368521 PMCID: PMC4213954 DOI: 10.4137/bcbcr.s18715] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/02/2023]
Abstract
Pathogenic mutations in BRCA1 or BRCA2 are only detected in 25% of families with a strong history of breast cancer, though hereditary factors are expected to be involved in the remaining families with no recognized mutation. Molecular characterization is expected to provide new insight into the tumor biology to guide the search of new high-risk alleles and provide better classification of the growing number of BRCA1/2 variants of unknown significance (VUS). In this review, we provide an overview of hereditary breast cancer, its genetic background, and clinical implications, before focusing on the pathologically and molecular features associated with the disease. Recent transcriptome and genome profiling studies of tumor series from BRCA1/2 mutation carriers as well as familial non-BRCA1/2 will be discussed. Special attention is paid to its association with molecular breast cancer subtypes as well as the latest advances in predicting BRCA1/2 involvement (BRCAness) using molecular signatures, for improved diagnostics and selection of patients sensitive to targeted therapeutics.
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Affiliation(s)
- Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
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27
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Bai F, Chan HL, Scott A, Smith MD, Fan C, Herschkowitz JI, Perou CM, Livingstone AS, Robbins DJ, Capobianco AJ, Pei XH. BRCA1 suppresses epithelial-to-mesenchymal transition and stem cell dedifferentiation during mammary and tumor development. Cancer Res 2014; 74:6161-72. [PMID: 25239453 DOI: 10.1158/0008-5472.can-14-1119] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BRCA1 mutation carriers are predisposed to developing basal-like breast cancers with high metastasis and poor prognosis. Yet, how BRCA1 suppresses formation of basal-like breast cancers is still obscure. Deletion of p18(Ink4c) (p18), an inhibitor of CDK4 and CDK6, functionally inactivates the RB pathway, stimulates mammary luminal stem cell (LSC) proliferation, and leads to spontaneous luminal tumor development. Alternately, germline mutation of Brca1 shifts the fate of luminal cells to cause luminal-to-basal mammary tumor transformation. Here, we report that disrupting Brca1 by either germline or epithelium-specific mutation in p18-deficient mice activates epithelial-to-mesenchymal transition (EMT) and induces dedifferentiation of LSCs, which associate closely with expansion of basal and cancer stem cells and formation of basal-like tumors. Mechanistically, BRCA1 bound to the TWIST promoter, suppressing its activity and inhibiting EMT in mammary tumor cells. In human luminal cancer cells, BRCA1 silencing was sufficient to activate TWIST and EMT and increase tumor formation. In parallel, TWIST expression and EMT features correlated inversely with BRCA1 expression in human breast cancers. Together, our findings showed that BRCA1 suppressed TWIST and EMT, inhibited LSC dedifferentiation, and repressed expansion of basal stem cells and basal-like tumors. Thus, our work offers the first genetic evidence that Brca1 directly suppresses EMT and LSC dedifferentiation during breast tumorigenesis.
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Affiliation(s)
- Feng Bai
- Molecular Oncology Program, Department of Surgery and
| | - Ho Lam Chan
- Molecular Oncology Program, Department of Surgery and
| | | | - Matthew D Smith
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cheng Fan
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jason I Herschkowitz
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Charles M Perou
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - David J Robbins
- Molecular Oncology Program, Department of Surgery and Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Anthony J Capobianco
- Molecular Oncology Program, Department of Surgery and Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Xin-Hai Pei
- Molecular Oncology Program, Department of Surgery and Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida.
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28
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Melchor L, Molyneux G, Mackay A, Magnay FA, Atienza M, Kendrick H, Nava-Rodrigues D, López-García MÁ, Milanezi F, Greenow K, Robertson D, Palacios J, Reis-Filho JS, Smalley MJ. Identification of cellular and genetic drivers of breast cancer heterogeneity in genetically engineered mouse tumour models. J Pathol 2014; 233:124-37. [PMID: 24615332 DOI: 10.1002/path.4345] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 01/24/2014] [Accepted: 02/26/2014] [Indexed: 11/08/2022]
Abstract
The heterogeneous nature of mammary tumours may arise from different initiating genetic lesions occurring in distinct cells of origin. Here, we generated mice in which Brca2, Pten and p53 were depleted in either basal mammary epithelial cells or luminal oestrogen receptor (ER)-negative cells. Basal cell-origin tumours displayed similar histological phenotypes, regardless of the depleted gene. In contrast, luminal ER-negative cells gave rise to diverse phenotypes, depending on the initiating lesions, including both ER-negative and, strikingly, ER-positive invasive ductal carcinomas. Molecular profiling demonstrated that luminal ER-negative cell-origin tumours resembled a range of the molecular subtypes of human breast cancer, including basal-like, luminal B and 'normal-like'. Furthermore, a subset of these tumours resembled the 'claudin-low' tumour subtype. These findings demonstrate that not only do mammary tumour phenotypes depend on the interactions between cell of origin and driver genetic aberrations, but also multiple mammary tumour subtypes, including both ER-positive and -negative disease, can originate from a single epithelial cell type. This is a fundamental advance in our understanding of tumour aetiology.
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MESH Headings
- Animals
- BRCA2 Protein/deficiency
- BRCA2 Protein/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Claudins/metabolism
- Disease Models, Animal
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Humans
- Mammary Glands, Animal/metabolism
- Mammary Glands, Animal/pathology
- Mice
- Mice, Knockout
- PTEN Phosphohydrolase/deficiency
- PTEN Phosphohydrolase/genetics
- Phenotype
- Receptors, Estrogen/metabolism
- Time Factors
- Tumor Suppressor Protein p53/deficiency
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Lorenzo Melchor
- Division of Breast Cancer Research, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
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29
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De Summa S, Pinto R, Sambiasi D, Petriella D, Paradiso V, Paradiso A, Tommasi S. BRCAness: a deeper insight into basal-like breast tumors. Ann Oncol 2014; 24 Suppl 8:viii13-viii21. [PMID: 24131964 DOI: 10.1093/annonc/mdt306] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The molecular scenario of breast cancer has become more complex in the last few years. Distinguishing between BRCA-associated, sporadic, HER2-enriched and triple-negative tumors is not sufficient to allow effective clinical management. Basal-like breast cancer, a subtype of triple-negative breast cancer, differs from others grouped under this heading. Commonalities between BRCA-related tumors and basal-like breast cancers (BRCAness phenotype) are highly relevant to ongoing clinical trials, in particular those investigating targeted therapies (e.g. PARP inhibitors) in sporadic breast tumors. The 'gold standard' to identify basal-like phenotype is DNA microarray, but integrated results could provide a panel of biomarkers helpful in identifying 'BRCAness' tumors (e.g. copy number aberrations, abnormal protein localization and altered transcriptional levels) and other molecular targets, such as APE1,the inhibition of which is emerging as an attractive breast cancer treatment in certain therapeutic settings.
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Affiliation(s)
- S De Summa
- NCRC Istituto Tumori 'Giovanni Paolo II', Bari, Italy
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30
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Feigin ME, Akshinthala SD, Araki K, Rosenberg AZ, Muthuswamy LB, Martin B, Lehmann BD, Berman HK, Pietenpol JA, Cardiff RD, Muthuswamy SK. Mislocalization of the cell polarity protein scribble promotes mammary tumorigenesis and is associated with basal breast cancer. Cancer Res 2014; 74:3180-94. [PMID: 24662921 DOI: 10.1158/0008-5472.can-13-3415] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Scribble (SCRIB) localizes to cell-cell junctions and regulates establishment of epithelial cell polarity. Loss of expression of SCRIB functions as a tumor suppressor in Drosophila and mammals; conversely, overexpression of SCRIB promotes epithelial differentiation in mammals. Here, we report that SCRIB is frequently amplified, mRNA overexpressed, and protein is mislocalized from cell-cell junctions in human breast cancers. High levels of SCRIB mRNA are associated with poor clinical prognosis, identifying an unexpected role for SCRIB in breast cancer. We find that transgenic mice expressing a SCRIB mutant [Pro 305 to Leu (P305L)] that fails to localize to cell-cell junctions, under the control of the mouse mammary tumor virus long terminal repeat promoter, develop multifocal hyperplasia that progresses to highly pleomorphic and poorly differentiated tumors with basal characteristics. SCRIB interacts with phosphatase and tensin homolog (PTEN) and the expression of P305L, but not wild-type SCRIB, promotes an increase in PTEN levels in the cytosol. Overexpression of P305L, but not wild-type SCRIB, activates the Akt/mTOR/S6K signaling pathway. Human breast tumors overexpressing SCRIB have high levels of S6K but do not harbor mutations in PTEN or PIK3CA, identifying SCRIB amplification as a mechanism of activating PI3K signaling in tumors without mutations in PIK3CA or PTEN. Thus, we demonstrate that high levels of mislocalized SCRIB functions as a neomorph to promote mammary tumorigenesis by affecting subcellular localization of PTEN and activating an Akt/mTOR/S6kinase signaling pathway.
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Affiliation(s)
- Michael E Feigin
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - S Dipikaa Akshinthala
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Kiyomi Araki
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Avi Z Rosenberg
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Lakshmi B Muthuswamy
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Bernard Martin
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Brian D Lehmann
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Hal K Berman
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Jennifer A Pietenpol
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Robert D Cardiff
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Senthil K Muthuswamy
- Authors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, TennesseeAuthors' Affiliations: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Princess Margaret Cancer Center, Campbell Family Institute for Breast Cancer Research, Department of Medical Biophysics, University of Toronto; Ontario Institute for Cancer Research, Ontario, Canada; Center for Comparative Medicine, University of California, Davis, Davis, California; and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
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31
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Weigelt B, Reis-Filho JS. Epistatic interactions and drug response. J Pathol 2014; 232:255-63. [PMID: 24105606 DOI: 10.1002/path.4265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 02/06/2023]
Abstract
The advent of massively parallel sequencing has allowed for an unprecedented genetic characterization of cancers, which has revealed not only the complexity of cancer genomes, but also the fact that tumours from the same anatomical site or even of the same histological and/or molecular subtype display distinct constellations of somatic genetic aberrations. Epistatic interactions (ie the interplay between genetic aberrations) are likely to play pivotal roles not only in terms of tumourigenesis and disease progression, but also in response to therapeutic interventions. In this review, we discuss the challenges posed by the complexity of tumour genomes and epistatic interactions, and approaches for harnessing the wealth of genetic information on human cancers for the implementation of precision medicine.
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Affiliation(s)
- Britta Weigelt
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
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32
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Larsen MJ, Thomassen M, Tan Q, Lænkholm AV, Bak M, Sørensen KP, Andersen MK, Kruse TA, Gerdes AM. RNA profiling reveals familial aggregation of molecular subtypes in non-BRCA1/2 breast cancer families. BMC Med Genomics 2014; 7:9. [PMID: 24479546 PMCID: PMC3909442 DOI: 10.1186/1755-8794-7-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/24/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND In more than 70% of families with a strong history of breast and ovarian cancers, pathogenic mutation in BRCA1 or BRCA2 cannot be identified, even though hereditary factors are expected to be involved. It has been proposed that tumors with similar molecular phenotypes also share similar underlying pathophysiological mechanisms. In the current study, the aim was to investigate if global RNA profiling can be used to identify functional subgroups within breast tumors from families tested negative for BRCA1/2 germline mutations and how these subgroupings relate to different breast cancer patients within the same family. METHODS In the current study we analyzed a collection of 70 frozen breast tumor biopsies from a total of 58 families by global RNA profiling and promoter methylation analysis. RESULTS We show that distinct functional subgroupings, similar to the intrinsic molecular breast cancer subtypes, exist among non-BRCA1/2 breast cancers. The distribution of subtypes was markedly different from the distribution found among BRCA1/2 mutation carriers. From 11 breast cancer families, breast tumor biopsies from more than one affected family member were included in the study. Notably, in 8 of these families we found that patients from the same family shared the same tumor subtype, showing a tendency of familial aggregation of tumor subtypes (p-value = 1.7e-3). Using our previously developed BRCA1/2-signatures, we identified 7 non-BRCA1/2 tumors with a BRCA1-like molecular phenotype and provide evidence for epigenetic inactivation of BRCA1 in three of the tumors. In addition, 7 BRCA2-like tumors were found. CONCLUSIONS Our finding indicates involvement of hereditary factors in non-BRCA1/2 breast cancer families in which family members may carry genetic susceptibility not just to breast cancer but to a particular subtype of breast cancer. This is the first study to provide a biological link between breast cancers from family members of high-risk non-BRCA1/2 families in a systematic manner, suggesting that future genetic analysis may benefit from subgrouping families into molecularly homogeneous subtypes in order to search for new high penetrance susceptibility genes.
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Affiliation(s)
- Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Sdr, Boulevard 29, Odense 5000, Denmark.
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33
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Stefansson OA, Esteller M. Epigenetic Modifications in Breast Cancer and Their Role in Personalized Medicine. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:1052-1063. [DOI: 10.1016/j.ajpath.2013.04.033] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/04/2013] [Accepted: 04/29/2013] [Indexed: 12/14/2022]
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34
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Gorrini C, Baniasadi PS, Harris IS, Silvester J, Inoue S, Snow B, Joshi PA, Wakeham A, Molyneux SD, Martin B, Bouwman P, Cescon DW, Elia AJ, Winterton-Perks Z, Cruickshank J, Brenner D, Tseng A, Musgrave M, Berman HK, Khokha R, Jonkers J, Mak TW, Gauthier ML. BRCA1 interacts with Nrf2 to regulate antioxidant signaling and cell survival. ACTA ACUST UNITED AC 2013; 210:1529-44. [PMID: 23857982 PMCID: PMC3727320 DOI: 10.1084/jem.20121337] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BRCA1 deficiency results in impaired Nrf2-mediated antioxidant responses followed by cell death, with estradiol rescuing the effect by inducing Nrf2 stabilization. Oxidative stress plays an important role in cancer development and treatment. Recent data implicate the tumor suppressor BRCA1 in regulating oxidative stress, but the molecular mechanism and the impact in BRCA1-associated tumorigenesis remain unclear. Here, we show that BRCA1 regulates Nrf2-dependent antioxidant signaling by physically interacting with Nrf2 and promoting its stability and activation. BRCA1-deficient mouse primary mammary epithelial cells show low expression of Nrf2-regulated antioxidant enzymes and accumulate reactive oxygen species (ROS) that impair survival in vivo. Increased Nrf2 activation rescues survival and ROS levels in BRCA1-null cells. Interestingly, 53BP1 inactivation, which has been shown to alleviate several defects associated with BRCA1 loss, rescues survival of BRCA1-null cells without restoring ROS levels. We demonstrate that estrogen treatment partially restores Nrf2 levels in the absence of BRCA1. Our data suggest that Nrf2-regulated antioxidant response plays a crucial role in controlling survival downstream of BRCA1 loss. The ability of estrogen to induce Nrf2 posits an involvement of an estrogen-Nrf2 connection in BRCA1 tumor suppression. Lastly, BRCA1-mutated tumors retain a defective antioxidant response that increases the sensitivity to oxidative stress. In conclusion, the role of BRCA1 in regulating Nrf2 activity suggests important implications for both the etiology and treatment of BRCA1-related cancers.
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Affiliation(s)
- Chiara Gorrini
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario M5G 2M9, Canada
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35
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Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis. J Transl Med 2013; 93:701-10. [PMID: 23568031 DOI: 10.1038/labinvest.2013.54] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples. Owing to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromized, which means obtaining informative data regarding epigenetic, genomic, and expression alterations can be challenging. Here, we have investigated the utility of repairing damaged DNA derived from FFPE tumors prior to single-nucleotide polymorphism (SNP) arrays for whole-genome DNA copy number analysis. DNA was extracted from FFPE samples spanning five decades, involving tumor material obtained from surgical specimens and postmortems. Various aspects of the protocol were assessed, including the method of DNA extraction, the role of Quality Control quantitative PCR (qPCR) in predicting sample success, and the effect of DNA restoration on assay performance, data quality, and the prediction of copy number aberrations (CNAs). DNA that had undergone the repair process yielded higher SNP call rates, reduced log R ratio variance, and improved calling of CNAs compared with matched FFPE DNA not subjected to repair. Reproducible mapping of genomic break points and detection of focal CNAs representing high-level gains and homozygous deletions (HD) were possible, even on autopsy material obtained in 1974. For example, DNA amplifications at the ERBB2 and EGFR gene loci and a HD mapping to 13q14.2 were validated using immunohistochemistry, in situ hybridization, and qPCR. The power of SNP arrays lies in the detection of allele-specific aberrations; however, this aspect of the analysis remains challenging, particularly in the distinction between loss of heterozygosity (LOH) and copy neutral LOH. In summary, attempting to repair DNA that is damaged during fixation and storage may be a useful pretreatment step for genomic studies of large archival FFPE cohorts with long-term follow-up or for understanding rare cancer types, where fresh frozen material is scarce.
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36
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Reynisdottir I, Arason A, Einarsdottir BO, Gunnarsson H, Staaf J, Vallon-Christersson J, Jonsson G, Ringnér M, Agnarsson BA, Olafsdottir K, Fagerholm R, Einarsdottir T, Johannesdottir G, Johannsson OT, Nevanlinna H, Borg A, Barkardottir RB. High expression of ZNF703 independent of amplification indicates worse prognosis in patients with luminal B breast cancer. Cancer Med 2013; 2:437-46. [PMID: 24156016 PMCID: PMC3799278 DOI: 10.1002/cam4.88] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 12/31/2022] Open
Abstract
Amplification of 8p12-p11 is relatively common in breast cancer and several genes within the region have been suggested to affect breast tumor progression. The aim of the study was to map the amplified 8p12-p11 region in a large set of breast tumors in an effort to identify the genetic driver and to explore its impact on tumor progression and prognosis. Copy number alterations (CNAs) were mapped in 359 tumors, and gene expression data from 577 tumors (359 tumors included) were correlated with CNA, clinical–pathological factors, and protein expression (39 tumors). 8p12-p11 was amplified in 11.4% of tumors. The smallest region of amplification harbored one full-length gene, ZNF703. ZNF703 mRNA expression was significantly higher in estrogen receptor (ER)-positive than ER-negative tumors (P = 2 × 10−16), a reflection of high expression in luminal tumors. Forty-eight percent of tumors with ZNF703 amplification were luminal B tumors in which the best correlation between DNA copy number and mRNA was seen (P = 1.2 × 10−7) as well as correlation between mRNA and protein expression (P = 0.02). High ZNF703 mRNA correlated with poor survival in patients with ER-positive luminal B tumors (log rank P = 0.04). Furthermore, high ZNF703 mRNA expression correlated with poor outcome in patients with ZNF703 copy number neutral, ER-positive, luminal B tumors (log rank P = 0.004). The results support ZNF703 as the driver gene of the 8p12 amplification and suggest that independent of amplification, high expression of the gene affects prognosis in luminal B tumors. Our mapping of 8p12-p11 and analyses of ZNF703 mRNA and protein expression in breast tumors support ZNF703 as an oncogene in luminal B tumors. High ZNF703 expression, independent of the amplification, correlated with worse prognosis for the breast cancer patients with ER-positive luminal tumors, particularly of the luminal B subtype.
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Affiliation(s)
- Inga Reynisdottir
- Department of Pathology, Landspitali-University Hospital 101, Reykjavik, Iceland
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37
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Larsen MJ, Kruse TA, Tan Q, Lænkholm AV, Bak M, Lykkesfeldt AE, Sørensen KP, Hansen TVO, Ejlertsen B, Gerdes AM, Thomassen M. Classifications within molecular subtypes enables identification of BRCA1/BRCA2 mutation carriers by RNA tumor profiling. PLoS One 2013; 8:e64268. [PMID: 23704984 PMCID: PMC3660328 DOI: 10.1371/journal.pone.0064268] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 04/11/2013] [Indexed: 12/30/2022] Open
Abstract
Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants of unclear pathogen significance are found in the families, constituting an increasing clinical challenge. New methods are therefore needed to improve the detection rate and aid the interpretation of the clinically uncertain variants. In this study we analyzed a series of 33 BRCA1, 22 BRCA2, and 128 sporadic tumors by RNA profiling to investigate the classification potential of RNA profiles to predict BRCA1/2 mutation status. We found that breast tumors from BRCA1 and BRCA2 mutation carriers display characteristic RNA expression patterns, allowing them to be distinguished from sporadic tumors. The majority of BRCA1 tumors were basal-like while BRCA2 tumors were mainly luminal B. Using RNA profiles, we were able to distinguish BRCA1 tumors from sporadic tumors among basal-like tumors with 83% accuracy and BRCA2 from sporadic tumors among luminal B tumors with 89% accuracy. Furthermore, subtype-specific BRCA1/2 gene signatures were successfully validated in two independent data sets with high accuracies. Although additional validation studies are required, indication of BRCA1/2 involvement (“BRCAness”) by RNA profiling could potentially be valuable as a tool for distinguishing pathogenic mutations from benign variants, for identification of undetected mutation carriers, and for selecting patients sensitive to new therapeutics such as PARP inhibitors.
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Affiliation(s)
- Martin J. Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
- * E-mail:
| | - Torben A. Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | | | - Martin Bak
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Anne E. Lykkesfeldt
- Breast Cancer Group, Unit of Cell Death and Metabolism, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Kristina P. Sørensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Thomas v. O. Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bent Ejlertsen
- Danish Breast Cancer Cooperative Group Statistical Center, Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
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38
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The complex genetic landscape of familial breast cancer. Hum Genet 2013; 132:845-63. [PMID: 23552954 DOI: 10.1007/s00439-013-1299-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/21/2013] [Indexed: 01/19/2023]
Abstract
Familial breast cancer represents a minor percentage of all human breast cancers. Mutations in two high susceptibility genes BRCA1 and BRCA2 explain around 25 % of familial breast cancers, while other high, moderate and low susceptibility genes explain up to 20 % more of breast cancer families. Thus, it is important to decipher the genetic architecture of families that show no mutations to improve genetic counselling. The comprehensive description of familial breast cancer using different techniques and platforms has shown to be very valuable for better patient diagnosis, tumour surveillance, and ultimately patient treatment. This review focuses on the complex landscape of pathological, protein, genetic and genomic features associated with BRCA1-, BRCA2-, and non-BRCA1/BRCA2-related cancers described up to date. Special emphasis deserves the coexistence of distinct molecular breast cancer subtypes, the development of tumour classifiers to predict BRCA1/2 mutations, and the last insights from recent whole genome sequencing studies and miRNA profiling.
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Holm K, Grabau D, Lövgren K, Aradottir S, Gruvberger-Saal S, Howlin J, Saal LH, Ethier SP, Bendahl PO, Stål O, Malmström P, Fernö M, Rydén L, Hegardt C, Borg Å, Ringnér M. Global H3K27 trimethylation and EZH2 abundance in breast tumor subtypes. Mol Oncol 2012; 6:494-506. [PMID: 22766277 DOI: 10.1016/j.molonc.2012.06.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/11/2012] [Accepted: 06/12/2012] [Indexed: 01/03/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) and its core member enhancer of zeste homolog 2 (EZH2) mediate the epigenetic gene silencing mark: trimethylation of lysine 27 on histone 3 (H3K27me3). H3K27me3 is characteristic of the chromatin at genes involved in developmental regulation in undifferentiated cells. Overexpression of EZH2 has been found in several cancer types such as breast, prostate, melanoma and bladder cancer. Moreover, overexpression is associated with highly proliferative and aggressive types of breast and prostate tumors. We have analyzed the abundance of EZH2 and H3K27me3 using immunohistochemistry in two large and well-characterized breast tumor data sets encompassing more than 400 tumors. The results have been analyzed in relation to the molecular subtypes of breast tumors (basal-like, luminal A, luminal B, HER2-enriched and normal-like), as well as in subtypes defined by clinical markers (triple negative, ER+/HER2-/Ki67low, ER+/HER2-/Ki67high and HER2+), and were validated in representative breast cancer cell lines by western blot. We found significantly different expression of both EZH2 and H3K27me3 across all subtypes with high abundance of EZH2 in basal-like, triple negative and HER2-enriched tumors, and high H3K27me3 in luminal A, HER2-enriched and normal-like tumors. Intriguingly, the two markers show an inverse correlation, particularly for the basal-like and triple negative tumors. Consequently, high expression of EZH2 was associated with poor distant disease-free survival whereas high expression of H3K27me3 was associated with better survival. Additionally, none of 182 breast tumors was found to carry a previously described EZH2 mutation affecting Tyr641. Our observation that increased expression of EZH2 does not necessarily correlate with increased abundance of H3K27me3 supports the idea that EZH2 can have effects beyond epigenetic silencing of target genes in breast cancer.
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Affiliation(s)
- Karolina Holm
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, SE-221 85 Lund, Sweden.
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