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Aylon Y, Furth N, Mallel G, Friedlander G, Nataraj NB, Dong M, Hassin O, Zoabi R, Cohen B, Drendel V, Salame TM, Mukherjee S, Harpaz N, Johnson R, Aulitzky WE, Yarden Y, Shema E, Oren M. Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis. Nat Commun 2022; 13:7199. [PMID: 36443319 PMCID: PMC9705295 DOI: 10.1038/s41467-022-34863-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Abstract
Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a "basal-like" state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed "basal-like" genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.
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Affiliation(s)
- Yael Aylon
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Noa Furth
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Giuseppe Mallel
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gilgi Friedlander
- grid.13992.300000 0004 0604 7563Department of Life Sciences Core Facilities, The Nancy & Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nishanth Belugali Nataraj
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Meng Dong
- grid.502798.10000 0004 0561 903XDr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology and University of Tuebingen, Stuttgart, Germany
| | - Ori Hassin
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Rawan Zoabi
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Benjamin Cohen
- grid.13992.300000 0004 0604 7563Department of Immunology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Vanessa Drendel
- grid.416008.b0000 0004 0603 4965Department of Pathology, Robert Bosch Hospital, Stuttgart, Germany
| | - Tomer Meir Salame
- grid.13992.300000 0004 0604 7563Flow Cytometry Unit, Department of Life Sciences Core Facilities, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Saptaparna Mukherjee
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nofar Harpaz
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Randy Johnson
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Walter E. Aulitzky
- grid.416008.b0000 0004 0603 4965Department of Hematology, Oncology and Palliative Medicine, Robert Bosch Hospital, Stuttgart, Germany
| | - Yosef Yarden
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Efrat Shema
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Moshe Oren
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
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Yang L, Chen R, Goodison S, Sun Y. An efficient and effective method to identify significantly perturbed subnetworks in cancer. NATURE COMPUTATIONAL SCIENCE 2021; 1:79-88. [PMID: 37346964 PMCID: PMC10284573 DOI: 10.1038/s43588-020-00009-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/02/2020] [Indexed: 06/23/2023]
Abstract
The identification of key functional biological networks from high-dimensional genomics data is pivotal for cancer research. Here, we introduce FDRnet, a method for the detection of molecular subnetworks in cancer, which addresses several challenges in pathway analysis. FDRnet detects key subnetworks by solving a mixed-integer linear programming problem, using a given upper bound of false discovery rate (FDR) as a budget constraint, and minimizing a conductance score to find dense subgraphs around seed genes. A large-scale benchmark study was performed on both simulation and cancer genomics data. FDRnet outperformed other methods in the ability to detect functionally homogeneous subnetworks in a scale-free biological network, to control FDRs of the genes in detected subnetworks, to improve computational efficiency and to integrate multi-omics data. By overcoming the limitations of existing approaches, FDRnet can facilitate the detection of key functional pathways in cancer and other genetic diseases.
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Affiliation(s)
- Le Yang
- Department of Computer Science and Engineering, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Steve Goodison
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Yijun Sun
- Department of Computer Science and Engineering, The State University of New York at Buffalo, Buffalo, NY, USA
- Department of Microbiology and Immunology, The State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, The State University of New York at Buffalo, Buffalo, NY, USA
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3
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Noblejas-López MDM, Morcillo-García S, Nieto-Jiménez C, Nuncia-Cantarero M, Győrffy B, Galan-Moya EM, Pandiella A, Ocaña A. Evaluation of transcriptionally regulated genes identifies NCOR1 in hormone receptor negative breast tumors and lung adenocarcinomas as a potential tumor suppressor gene. PLoS One 2018; 13:e0207776. [PMID: 30485330 PMCID: PMC6261593 DOI: 10.1371/journal.pone.0207776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Regulation of transcription is a key process in cellular homeostasis. It depends on regulators that either repress or stimulate the transcription of genes, therefore controlling different biological functions. The Nuclear Receptor Corepressor 1 (NCOR1) is one of those co-repressors that regulate the transcription by facilitating the recruitment of HDAC1, 2, 3, 4, 5 and 7. In our article, by using an in silico approach, we evaluate the mutational status of NCOR1 in breast and lung tumors. We identified that NORC1 is mutated in more than 3% of breast tumors and lung adenocarcinomas and linked this fact with detrimental outcome in some subtypes, particularly in those that are hormone receptor negative. In addition to these findings, as mutations in this gene are deleterious, we confirmed that high levels of this gene were linked with good prognosis in the same tumor subtypes. Findings in the same direction were identified in lung adenocarcinomas, with mutations associated with detrimental prognosis and high expression with better outcome. In conclusion, hereby we describe the presence and prognostic role of mutations in the NCOR1 gene in hormone receptor negative breast and lung adenocarcinomas, and we also confirm that NCOR1 is a tumor suppressor gene. Further studies should be performed to explore therapeutic mechanisms to restore its function.
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Affiliation(s)
- María del Mar Noblejas-López
- Translational Research Unit, Albacete University Hospital, and CIBERONC, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Sara Morcillo-García
- Translational Research Unit, Albacete University Hospital, and CIBERONC, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Cristina Nieto-Jiménez
- Translational Research Unit, Albacete University Hospital, and CIBERONC, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Miriam Nuncia-Cantarero
- Translational Research Unit, Albacete University Hospital, and CIBERONC, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Balázs Győrffy
- Semmelweis University 2nd Dept. of Pediatrics, Budapest, Hungary
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Eva M. Galan-Moya
- Translational Research Unit, Albacete University Hospital, and CIBERONC, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Albacete, Spain
- * E-mail: (AO); (EMGM)
| | | | - Alberto Ocaña
- Translational Research Unit, Albacete University Hospital, and CIBERONC, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Albacete, Spain
- * E-mail: (AO); (EMGM)
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4
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Gillis NE, Taber TH, Bolf EL, Beaudet CM, Tomczak JA, White JH, Stein JL, Stein GS, Lian JB, Frietze S, Carr FE. Thyroid Hormone Receptor β Suppression of RUNX2 Is Mediated by Brahma-Related Gene 1-Dependent Chromatin Remodeling. Endocrinology 2018; 159:2484-2494. [PMID: 29750276 PMCID: PMC6692870 DOI: 10.1210/en.2018-00128] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/03/2018] [Indexed: 12/18/2022]
Abstract
Thyroid hormone receptor β (TRβ) suppresses tumor growth through regulation of gene expression, yet the associated TRβ-mediated changes in chromatin assembly are not known. The chromatin ATPase brahma-related gene 1 (BRG1; SMARCA4), a key component of chromatin-remodeling complexes, is altered in many cancers, but its role in thyroid tumorigenesis and TRβ-mediated gene expression is unknown. We previously identified the oncogene runt-related transcription factor 2 (RUNX2) as a repressive target of TRβ. Here, we report differential expression of BRG1 in nonmalignant and malignant thyroid cells concordant with TRβ. BRG1 and TRβ have similar nuclear distribution patterns and significant colocalization. BRG1 interacts with TRβ, and together, they are part of the regulatory complex at the RUNX2 promoter. Loss of BRG1 increases RUNX2 levels, whereas reintroduction of TRβ and BRG1 synergistically decreases RUNX2 expression. RUNX2 promoter accessibility corresponded to RUNX2 expression levels. Inhibition of BRG1 activity increased accessibility of the RUNX2 promoter and corresponding expression. Our results reveal a mechanism of TRβ repression of oncogenic gene expression: TRβ recruitment of BRG1 induces chromatin compaction and diminishes RUNX2 expression. Therefore, BRG1-mediated chromatin remodeling may be obligatory for TRβ transcriptional repression and tumor suppressor function in thyroid tumorigenesis.
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Affiliation(s)
- Noelle E Gillis
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Thomas H Taber
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Eric L Bolf
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Caitlin M Beaudet
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Jennifer A Tomczak
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Jeffrey H White
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Janet L Stein
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Gary S Stein
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Jane B Lian
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Seth Frietze
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Department of Medical Laboratory Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont
| | - Frances E Carr
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont
- University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Correspondence: Frances E. Carr, PhD, Department of Pharmacology, Larner College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, Vermont 05405. E-mail:
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Goemann IM, Romitti M, Meyer ELS, Wajner SM, Maia AL. Role of thyroid hormones in the neoplastic process: an overview. Endocr Relat Cancer 2017; 24:R367-R385. [PMID: 28928142 DOI: 10.1530/erc-17-0192] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022]
Abstract
Thyroid hormones (TH) are critical regulators of several physiological processes, which include development, differentiation and growth in virtually all tissues. In past decades, several studies have shown that changes in TH levels caused by thyroid dysfunction, disruption of deiodinases and/or thyroid hormone receptor (TR) expression in tumor cells, influence cell proliferation, differentiation, survival and invasion in a variety of neoplasms in a cell type-specific manner. The function of THs and TRs in neoplastic cell proliferation involves complex mechanisms that seem to be cell specific, exerting effects via genomic and nongenomic pathways, repressing or stimulating transcription factors, influencing angiogenesis and promoting invasiveness. Taken together, these observations indicate an important role of TH status in the pathogenesis and/or development of human neoplasia. Here, we aim to present an updated and comprehensive picture of the accumulated knowledge and the current understanding of the potential role of TH status on the different hallmarks of the neoplastic process.
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Affiliation(s)
- Iuri Martin Goemann
- Thyroid SectionEndocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Mirian Romitti
- Thyroid SectionEndocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Erika L Souza Meyer
- Department of Internal MedicineUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Simone Magagnin Wajner
- Thyroid SectionEndocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Luiza Maia
- Thyroid SectionEndocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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Légaré S, Basik M. Minireview: The Link Between ERα Corepressors and Histone Deacetylases in Tamoxifen Resistance in Breast Cancer. Mol Endocrinol 2016; 30:965-76. [PMID: 27581354 DOI: 10.1210/me.2016-1072] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Approximately 70% of breast cancers express the estrogen receptor (ER)α and are treated with the ERα antagonist, tamoxifen. However, resistance to tamoxifen frequently develops in advanced breast cancer, in part due to a down-regulation of ERα corepressors. Nuclear receptor corepressors function by attenuating hormone responses and have been shown to potentiate tamoxifen action in various biological systems. Recent genomic data on breast cancers has revealed that genetic and/or genomic events target ERα corepressors in the majority of breast tumors, suggesting that the loss of nuclear receptor corepressor activity may represent an important mechanism that contributes to intrinsic and acquired tamoxifen resistance. Here, the biological functions of ERα corepressors are critically reviewed to elucidate their role in modifying endocrine sensitivity in breast cancer. We highlight a mechanism of gene repression common to corepressors previously shown to enhance the antitumorigenic effects of tamoxifen, which involves the recruitment of histone deacetylases (HDACs) to DNA. As an indicator of epigenetic disequilibrium, the loss of ERα corepressors may predispose cancer cells to the cytotoxic effects of HDAC inhibitors, a class of drug that has been shown to effectively reverse tamoxifen resistance in numerous studies. HDAC inhibition thus appears as a promising therapeutic approach that deserves to be further explored as an avenue to restore drug sensitivity in corepressor-deficient and tamoxifen-resistant breast cancers.
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Affiliation(s)
- Stéphanie Légaré
- Division of Experimental Medicine, Department of Oncology and Surgery, Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada H3T 1E2
| | - Mark Basik
- Division of Experimental Medicine, Department of Oncology and Surgery, Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada H3T 1E2
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