1
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Jagust P, Powell AM, Ola M, Watson L, de Pablos-Aragoneses A, García-Gómez P, Fallon R, Bane F, Heiland M, Morris G, Cavanagh B, McGrath J, Ottaviani D, Hegarty A, Cocchiglia S, Sweeney KJ, MacNally S, Brett FM, Cryan J, Beausang A, Morris P, Valiente M, Hill ADK, Varešlija D, Young LS. RET overexpression leads to increased brain metastatic competency in luminal breast cancer. J Natl Cancer Inst 2024:djae091. [PMID: 38852945 DOI: 10.1093/jnci/djae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/22/2023] [Accepted: 04/14/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Breast cancer brain metastasis is a rising occurrence, necessitating a better understanding of the mechanisms involved for effective management. Breast cancer brain metastases diverge notably from the primary tumor, with gains in kinase and concomitant losses of steroid signaling observed. In this study, we explored the role of the kinase receptor RET in promoting breast cancer brain metastases and provide a rationale for targeting this receptor. METHODS RET expression was characterized in a cohort of patients with primary and brain metastatic tumors. RET functionality was assessed using pharmacological inhibition and gene silencing in patient-derived brain metastatic tumor explants and in vivo models, organoid models, and brain organotypic cultures. RNA sequencing was used to uncover novel brain metastatic relevant RET mechanisms of action. RESULTS A statistically significant enrichment of RET in brain metastases was observed in estrogen receptor-positive breast cancer, where it played a role in promoting cancer cell adhesion, survival, and outgrowth in the brain. In vivo, RET overexpression enhanced brain metastatic competency in patient-derived models. At a mechanistic level, RET overexpression was found to enhance the activation of gene programs involved in cell adhesion, requiring EGFR cooperation to deliver a pro-brain metastatic phenotype. CONCLUSION Our results illustrate, for the first time, the role of RET in regulating colonization and outgrowth of breast cancer brain metastasis and provide data to support the use of RET inhibitors in the management strategy for patients with breast cancer brain metastases.
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Affiliation(s)
- Petra Jagust
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Aoibhin M Powell
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Mihaela Ola
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Louise Watson
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | | | | | - Ramón Fallon
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Fiona Bane
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Mona Heiland
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Gareth Morris
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Brenton Cavanagh
- Cellular and Molecular Imaging Core, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Jason McGrath
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Daniela Ottaviani
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Aisling Hegarty
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Sinéad Cocchiglia
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Kieron J Sweeney
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Stephen MacNally
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | | | - Jane Cryan
- Department of Neuropathology, National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Patrick Morris
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
| | | | - Arnold D K Hill
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Damir Varešlija
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
| | - Leonie S Young
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
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2
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Lavaud M, Tesfaye R, Lassous L, Brounais B, Baud'huin M, Verrecchia F, Lamoureux F, Georges S, Ory B. Super-enhancers: drivers of cells' identities and cells' debacles. Epigenomics 2024; 16:681-700. [PMID: 38587919 PMCID: PMC11160454 DOI: 10.2217/epi-2023-0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Precise spatiotemporal regulations of gene expression are essential for determining cells' fates and functions. Enhancers are cis-acting DNA elements that act as periodic transcriptional thrusters and their activities are cell type specific. Clusters of enhancers, called super-enhancers, are more densely occupied by transcriptional activators than enhancers, driving stronger expression of their target genes, which have prominent roles in establishing and maintaining cellular identities. Here we review the current knowledge on the composition and structure of super-enhancers to understand how they robustly stimulate the expression of cellular identity genes. We also review their involvement in the development of various cell types and both noncancerous and cancerous disorders, implying the therapeutic interest of targeting them to fight against various diseases.
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Affiliation(s)
- Mélanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Robel Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Léa Lassous
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Bénédicte Brounais
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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3
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Richter S, Bechmann N. Patient Sex and Origin Influence Distribution of Driver Genes and Clinical Presentation of Paraganglioma. J Endocr Soc 2024; 8:bvae038. [PMID: 38481600 PMCID: PMC10928507 DOI: 10.1210/jendso/bvae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Indexed: 04/07/2024] Open
Abstract
Context Sexual and ancestral differences in driver gene prevalence have been described in many cancers but have not yet been investigated in pheochromocytoma and paraganglioma (PPGL). Objective This study aims to assess whether sex and ancestry influence prevalence of PPGL driver genes and clinical presentation. Methods We conducted a retrospective analysis of patients with PPGL considering studies from 2010 onwards that included minimal data of type of disease, sex, mutated gene, and country of origin. Additional features were recorded when available (age, tumor location, bilateral or multifocal, somatic or germline, and metastatic disease). Results We included 2162 patients: 877 in Europe and 757 in Asia. Males presented more often with germline pathogenic variants (PVs) in genes activating hypoxia pathways (P = .0006) and had more often sympathetic paragangliomas (P = .0005) and metastasis (P = .0039). On the other hand, females with PPGLs due to MAX PVs were diagnosed later than males (P = .0378) and more often developed metastasis (P = .0497). European but not Asian females presented more often with PPGLs due to PVs in genes related to kinase signaling (P = .0052), particularly RET and TMEM127. Contrary to experiences from Europe, Asian patients with PPGL due to PVs in kinase signaling genes NF1, HRAS, and FGFR1 showed a high proportion of sympathetic tumors, while European patients almost exclusively had adrenal tumors (P < .005). Conclusion Personalized management of patients with PPGL might benefit from considering sexual and ancestral differences. Further studies with better clinically aligned cohorts from various origins are required to better dissect ancestral influences on PPGL development.
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Affiliation(s)
- Susan Richter
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Nicole Bechmann
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
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4
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Frett B, Stephens KE, Koss B, Melnyk S, Farrar J, Saha D, Roy Choudhury S. Enhancer-activated RET confers protection against oxidative stress to KMT2A-rearranged acute myeloid leukemia. Cancer Sci 2024; 115:963-973. [PMID: 38226414 PMCID: PMC10920984 DOI: 10.1111/cas.16069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/19/2023] [Accepted: 12/30/2023] [Indexed: 01/17/2024] Open
Abstract
Ectopic activation of rearranged during transfection (RET) has been reported to facilitate lineage differentiation and cell proliferation in different cytogenetic subtypes of acute myeloid leukemia (AML). Herein, we demonstrate that RET is significantly (p < 0.01) upregulated in AML subtypes containing rearrangements of the lysine methyltransferase 2A gene (KMT2A), commonly referred to as KMT2A-rearranged (KMT2A-r) AML. Integrating multi-epigenomics data, we show that the KMT2A-MLLT3 fusion induces the development of CCCTC-binding (CTCF)-guided de novo extrusion enhancer loop to upregulate RET expression in KMT2A-r AML. Based on the finding that RET expression is tightly correlated with the selective chromatin remodeler and mediator (MED) proteins, we used a small-molecule inhibitor having dual inhibition against RET and MED12-associated cyclin-dependent kinase 8 (CDK8) in KMT2A-r AML cells. Dual inhibition of RET and CDK8 restricted cell proliferation by producing multimodal oxidative stress responses in treated cells. Our data suggest that epigenetically enhanced RET protects KMT2A-r AML cells from oxidative stresses, which could be exploited as a potential therapeutic strategy.
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Affiliation(s)
- Brendan Frett
- Department of Pharmaceutical SciencesUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Kimberly E. Stephens
- Arkansas Children's Research InstituteLittle RockArkansasUSA
- Division of Infectious Diseases, Department of PediatricsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Brian Koss
- Department of Biochemistry & Molecular BiologyUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Stepan Melnyk
- Arkansas Children's Research InstituteLittle RockArkansasUSA
| | - Jason Farrar
- Arkansas Children's Research InstituteLittle RockArkansasUSA
- Division of Hematology/Oncology, Department of PediatricsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Debasmita Saha
- Sanford Burnham Presbys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Samrat Roy Choudhury
- Arkansas Children's Research InstituteLittle RockArkansasUSA
- Division of Hematology/Oncology, Department of PediatricsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
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5
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Gou X, Kim BJ, Anurag M, Lei JT, Young MN, Holt MV, Fandino D, Vollert CT, Singh P, Alzubi MA, Malovannaya A, Dobrolecki LE, Lewis MT, Li S, Foulds CE, Ellis MJ. Kinome Reprogramming Is a Targetable Vulnerability in ESR1 Fusion-Driven Breast Cancer. Cancer Res 2023; 83:3237-3251. [PMID: 37071495 PMCID: PMC10543968 DOI: 10.1158/0008-5472.can-22-3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/20/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Transcriptionally active ESR1 fusions (ESR1-TAF) are a potent cause of breast cancer endocrine therapy (ET) resistance. ESR1-TAFs are not directly druggable because the C-terminal estrogen/anti-estrogen-binding domain is replaced with translocated in-frame partner gene sequences that confer constitutive transactivation. To discover alternative treatments, a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) was deployed to identify druggable kinases that are upregulated by diverse ESR1-TAFs. Subsequent explorations of drug sensitivity validated RET kinase as a common therapeutic vulnerability despite remarkable ESR1-TAF C-terminal sequence and structural diversity. Organoids and xenografts from a pan-ET-resistant patient-derived xenograft model that harbors the ESR1-e6>YAP1 TAF were concordantly inhibited by the selective RET inhibitor pralsetinib to a similar extent as the CDK4/6 inhibitor palbociclib. Together, these findings provide preclinical rationale for clinical evaluation of RET inhibition for the treatment of ESR1-TAF-driven ET-resistant breast cancer. SIGNIFICANCE Kinome analysis of ESR1 translocated and mutated breast tumors using drug bead-based mass spectrometry followed by drug-sensitivity studies nominates RET as a therapeutic target. See related commentary by Wu and Subbiah, p. 3159.
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Affiliation(s)
- Xuxu Gou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston Texas
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jonathan T. Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Meggie N. Young
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Matthew V. Holt
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Diana Fandino
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Craig T. Vollert
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Employee of Adrienne Helis Malvin Medical Research Foundation, New Orleans, Los Angeles
| | - Purba Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Mohammad A. Alzubi
- Employee of Adrienne Helis Malvin Medical Research Foundation, New Orleans, Los Angeles
| | - Anna Malovannaya
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lacey E. Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Michael T. Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Radiology, Baylor College of Medicine, Houston, Texas
| | - Shunqiang Li
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Charles E. Foulds
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Matthew J. Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
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6
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Jin C, Luo Y, Liang Z, Li X, Kołat D, Zhao L, Xiong W. Crucial role of the transcription factors family activator protein 2 in cancer: current clue and views. J Transl Med 2023; 21:371. [PMID: 37291585 PMCID: PMC10249218 DOI: 10.1186/s12967-023-04189-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
The transcription factor family activator protein 2 (TFAP2) is vital for regulating both embryonic and oncogenic development. The TFAP2 family consists of five DNA-binding proteins, including TFAP2A, TFAP2B, TFAP2C, TFAP2D and TFAP2E. The importance of TFAP2 in tumor biology is becoming more widely recognized. While TFAP2D is not well studied, here, we mainly focus on the other four TFAP2 members. As a transcription factor, TFAP2 regulates the downstream targets directly by binding to their regulatory region. In addition, the regulation of downstream targets by epigenetic modification, posttranslational regulation, and interaction with noncoding RNA have also been identified. According to the pathways in which the downstream targets are involved in, the regulatory effects of TFAP2 on tumorigenesis are generally summarized as follows: stemness and EMT, interaction between TFAP2 and tumor microenvironment, cell cycle and DNA damage repair, ER- and ERBB2-related signaling pathway, ferroptosis and therapeutic response. Moreover, the factors that affect TFAP2 expression in oncogenesis are also summarized. Here, we review and discuss the most recent studies on TFAP2 and its effects on carcinogenesis and regulatory mechanisms.
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Affiliation(s)
- Chen Jin
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxiao Luo
- University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Zhu Liang
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Chinese Academy for Medical Sciences Oxford Institute, Oxford, UK
| | - Xi Li
- Department of Urology, Churchill Hospital, Oxford University Hospitals NHS Foundation, Oxford, UK
| | - Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, Lodz, Poland
| | - Linyong Zhao
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Weixi Xiong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China.
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Chengdu, China.
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7
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Pecar G, Liu S, Hooda J, Atkinson JM, Oesterreich S, Lee AV. RET signaling in breast cancer therapeutic resistance and metastasis. Breast Cancer Res 2023; 25:26. [PMID: 36918928 PMCID: PMC10015789 DOI: 10.1186/s13058-023-01622-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 02/16/2023] [Indexed: 03/15/2023] Open
Abstract
RET, a single-pass receptor tyrosine kinase encoded on human chromosome 10, is well known to the field of developmental biology for its role in the ontogenesis of the central and enteric nervous systems and the kidney. In adults, RET alterations have been characterized as drivers of non-small cell lung cancer and multiple neuroendocrine neoplasms. In breast cancer, RET signaling networks have been shown to influence diverse functions including tumor development, metastasis, and therapeutic resistance. While RET is known to drive the development and progression of multiple solid tumors, therapeutic agents selectively targeting RET are relatively new, though multiple multi-kinase inhibitors have shown promise as RET inhibitors in the past; further, RET has been historically neglected as a potential therapeutic co-target in endocrine-refractory breast cancers despite mounting evidence for a key pathologic role and repeated description of a bi-directional relationship with the estrogen receptor, the principal driver of most breast tumors. Additionally, the recent discovery of RET enrichment in breast cancer brain metastases suggests a role for RET inhibition specific to advanced disease. This review assesses the status of research on RET in breast cancer and evaluates the therapeutic potential of RET-selective kinase inhibitors across major breast cancer subtypes.
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Affiliation(s)
- Geoffrey Pecar
- Women's Cancer Research Center, UPMC Hillman Cancer Center and Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, The Assembly, Room 2051, 5051 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Simeng Liu
- Women's Cancer Research Center, UPMC Hillman Cancer Center and Magee-Womens Research Institute, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jagmohan Hooda
- Women's Cancer Research Center, UPMC Hillman Cancer Center and Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, The Assembly, Room 2051, 5051 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Jennifer M Atkinson
- Women's Cancer Research Center, UPMC Hillman Cancer Center and Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, The Assembly, Room 2051, 5051 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Steffi Oesterreich
- Women's Cancer Research Center, UPMC Hillman Cancer Center and Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, The Assembly, Room 2051, 5051 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Adrian V Lee
- Women's Cancer Research Center, UPMC Hillman Cancer Center and Magee-Womens Research Institute, Pittsburgh, PA, USA.
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, The Assembly, Room 2051, 5051 Centre Avenue, Pittsburgh, PA, 15213, USA.
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8
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Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022; 31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Every cell in the human body inherits a copy of the same genetic information. The three billion base pairs of DNA in the human genome, and the roughly 50 000 coding and non-coding genes they contain, must thus encode all the complexity of human development and cell and tissue type diversity. Differences in gene regulation, or the modulation of gene expression, enable individual cells to interpret the genome differently to carry out their specific functions. Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize the regulatory roles of all sequences in a genome. Many researchers and consortia have identified such regulatory elements using functional assays and evolutionary analyses; we discuss the results, strengths and shortcomings of their approaches. We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness.
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Affiliation(s)
- Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
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9
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Zheng ZZ, Xia L, Hu GS, Liu JY, Hu YH, Chen YJ, Peng JY, Zhang WJ, Liu W. Super-enhancer-controlled positive feedback loop BRD4/ERα-RET-ERα promotes ERα-positive breast cancer. Nucleic Acids Res 2022; 50:10230-10248. [PMID: 36124682 PMCID: PMC9561272 DOI: 10.1093/nar/gkac778] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 12/22/2022] Open
Abstract
Estrogen and estrogen receptor alpha (ERα)-induced gene transcription is tightly associated with ERα-positive breast carcinogenesis. ERα-occupied enhancers, particularly super-enhancers, have been suggested to play a vital role in regulating such transcriptional events. However, the landscape of ERα-occupied super-enhancers (ERSEs) as well as key ERα-induced target genes associated with ERSEs remain to be fully characterized. Here, we defined the landscape of ERSEs in ERα-positive breast cancer cell lines, and demonstrated that bromodomain protein BRD4 is a master regulator of the transcriptional activation of ERSEs and cognate ERα target genes. RET, a member of the tyrosine protein kinase family of proteins, was identified to be a key ERα target gene of BRD4-regulated ERSEs, which, in turn, is vital for ERα-induced gene transcriptional activation and malignant phenotypes through activating the RAS/RAF/MEK2/ERK/p90RSK/ERα phosphorylation cascade. Combination therapy with BRD4 and RET inhibitors exhibited additive effects on suppressing ERα-positive breast cancer both in vitro and in vivo, comparable with that of standard endocrine therapy tamoxifen. Furthermore, combination therapy re-sensitized a tamoxifen-resistant ERα-positive breast cancer cell line to tamoxifen treatment. Taken together, our data uncovered the critical role of a super-enhancer-associated positive feedback loop constituting BRD4/ERα–RET–ERα in ERα-positive breast cancer, and suggested that targeting components in this loop would provide a new therapeutic avenue for treating ERα-positive breast cancer in the clinic.
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Affiliation(s)
- Zao-Zao Zheng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Lin Xia
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Guo-Sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jun-Yi Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Ya-Hong Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yu-Jie Chen
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jia-Yin Peng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Wen-Juan Zhang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, No. 23, Qingnian Road, Ganzhou, Jiangxi 341000, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
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10
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Regua AT, Najjar M, Lo HW. RET signaling pathway and RET inhibitors in human cancer. Front Oncol 2022; 12:932353. [PMID: 35957881 PMCID: PMC9359433 DOI: 10.3389/fonc.2022.932353] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Rearranged during transfection (RET) receptor tyrosine kinase was first identified over thirty years ago as a novel transforming gene. Since its discovery and subsequent pathway characterization, RET alterations have been identified in numerous cancer types and are most prevalent in thyroid carcinomas and non-small cell lung cancer (NSCLC). In other tumor types such as breast cancer and salivary gland carcinomas, RET alterations can be found at lower frequencies. Aberrant RET activity is associated with poor prognosis of thyroid and lung carcinoma patients, and is strongly correlated with increased risk of distant metastases. RET aberrations encompass a variety of genomic or proteomic alterations, most of which confer constitutive activation of RET. Activating RET alterations, such as point mutations or gene fusions, enhance activity of signaling pathways downstream of RET, namely PI3K/AKT, RAS/RAF, MAPK, and PLCγ pathways, to promote cell proliferation, growth, and survival. Given the important role that mutant RET plays in metastatic cancers, significant efforts have been made in developing inhibitors against RET kinase activity. These efforts have led to FDA approval of Selpercatinib and Pralsetinib for NSCLC, as well as, additional selective RET inhibitors in preclinical and clinical testing. This review covers the current biological understanding of RET signaling, the impact of RET hyperactivity on tumor progression in multiple tumor types, and RET inhibitors with promising preclinical and clinical efficacy.
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Affiliation(s)
- Angelina T. Regua
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Mariana Najjar
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Hui-Wen Lo
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States
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11
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Das P, Gupta A, Desai KV. JMJD6 orchestrates a transcriptional program in favor of endocrine resistance in ER+ breast cancer cells. Front Endocrinol (Lausanne) 2022; 13:1028616. [PMID: 36419768 PMCID: PMC9678079 DOI: 10.3389/fendo.2022.1028616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
High expression of Jumonji domain containing protein 6 (JMJD6) is strongly associated with poor prognosis in estrogen receptor positive (ER+) breast cancer. We overexpressed JMJD6 in MCF7 cells (JOE cells) and performed RNA-seq analysis. 76% of differentially expressed genes (DEGs) overlapped with ER target genes. Pathway analysis revealed that JMJD6 upregulated a larger subset of genes related to cell proliferation as compared to ER. Interestingly, JOE cells showed a decrease in ER target gene expression prompting us to check ER levels. Indeed, JOE cells showed a significant decrease in both ESR1 and ER levels and JMJD6 siRNA transfection increased the expression of both. Additionally, JOE cells showed increased RET and ERK1 expression, events associated with resistance to endocrine therapy. Accordingly, JOE cells displayed lower sensitivity and survived better at higher doses of 4-hydroxy tamoxifen (Tam) as compared to parental MCF-7 cells. Conversely, LTED-I and TAM R that resist Tam induced death, showed high expression of JMJD6. Further, JMJD6 siRNA treatment decreased growth and improved Tam sensitivity in TAM R. Comparison of JOE DEGs with known Tam signature genes showed a substantial overlap. Overall, these data suggest that blocking ER alone in patients may not eradicate proliferation of JMJD6 expressing ER+ cells and JMJD6 may predispose and sustain endocrine therapy resistance. We propose that immunostaining for JMJD6 could be developed as a potential marker for predicting endocrine therapy resistance. Further, antagonizing JMJD6 action in women expressing higher amounts of this protein, may offer a greater clinical benefit than endocrine therapy.
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12
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Choi J, Lysakovskaia K, Stik G, Demel C, Söding J, Tian TV, Graf T, Cramer P. Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 2021; 10:e65381. [PMID: 33770473 PMCID: PMC8004103 DOI: 10.7554/elife.65381] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/14/2021] [Indexed: 12/18/2022] Open
Abstract
Enhancer activity drives cell differentiation and cell fate determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human leukemia B-cells to macrophages. Putative enhancers are established by binding of the pioneer factor C/EBPα followed by chromatin opening and enhancer RNA (eRNA) synthesis from H3K4-monomethylated regions. Using eRNA synthesis as a proxy for enhancer activity, we find that most putative enhancers cooperate in an additive way to regulate transcription of assigned target genes. However, transcription from 136 target genes depends exponentially on the summed activity of its putative paired enhancers, indicating that these enhancers cooperate synergistically. The target genes are cell type-specific, suggesting that enhancer synergy can contribute to cell fate determination. Enhancer synergy appears to depend on cell type-specific transcription factors, and such interacting enhancers are not predicted from occupancy or accessibility data that are used to detect superenhancers.
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Affiliation(s)
- Jinmi Choi
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Kseniia Lysakovskaia
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Gregoire Stik
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Carina Demel
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Johannes Söding
- Max Planck Institute for Biophysical Chemistry, Quantitative Biology and BioinformaticsGöttingenGermany
| | - Tian V Tian
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
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13
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Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells. Nat Genet 2020; 52:1227-1238. [PMID: 33020665 DOI: 10.1038/s41588-020-0709-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 09/01/2020] [Indexed: 12/20/2022]
Abstract
Adipocyte differentiation is driven by waves of transcriptional regulators that reprogram the enhancer landscape and change the wiring of the promoter interactome. Here, we use high-throughput chromosome conformation enhancer capture to interrogate the role of enhancer-to-enhancer interactions during differentiation of human mesenchymal stem cells. We find that enhancers form an elaborate network that is dynamic during differentiation and coupled with changes in enhancer activity. Transcription factors (TFs) at baited enhancers amplify TF binding at target enhancers, a phenomenon we term cross-interaction stabilization of TFs. Moreover, highly interconnected enhancers (HICE) act as integration hubs orchestrating differentiation by the formation of three-dimensional enhancer communities, inside which, HICE, and other enhancers, converge on phenotypically important gene promoters. Collectively, these results indicate that enhancer interactions play a key role in the regulation of enhancer function, and that HICE are important for both signal integration and compartmentalization of the genome.
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14
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Elhasnaoui J, Miano V, Ferrero G, Doria E, Leon AE, Fabricio ASC, Annaratone L, Castellano I, Sapino A, De Bortoli M. DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage. Cancers (Basel) 2020; 12:cancers12061453. [PMID: 32503257 PMCID: PMC7352480 DOI: 10.3390/cancers12061453] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022] Open
Abstract
DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.
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Affiliation(s)
- Jamal Elhasnaoui
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Valentina Miano
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Giulio Ferrero
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Department of Computer Science, University of Turin, 10149 Turin, Italy
| | - Elena Doria
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Antonette E. Leon
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Aline S. C. Fabricio
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Isabella Castellano
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Turin, Italy
| | - Michele De Bortoli
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Correspondence: ; Tel.: +39-0116-7050-58
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15
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Gattelli A, Hynes NE, Schor IE, Vallone SA. Ret Receptor Has Distinct Alterations and Functions in Breast Cancer. J Mammary Gland Biol Neoplasia 2020; 25:13-26. [PMID: 32080788 DOI: 10.1007/s10911-020-09445-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/06/2020] [Indexed: 12/15/2022] Open
Abstract
Ret receptor tyrosine kinase is a proto-oncogene that participates in development of various cancers. Several independent studies have recently identified Ret as a key player in breast cancer. Although Ret overexpression and function have been under investigation, mainly in estrogen receptor positive breast cancer, a more comprehensive analysis of the impact of recurring Ret alterations in breast cancer is needed. This review consolidates the current knowledge of Ret alterations and their potential effects in breast cancer. We discuss and integrate data on Ret changes in different breast cancer subtypes and potential function in progression, as well as the participation of distinct Ret network signaling partners in these processes. We propose that it will be essential to define a shared molecular feature of tumors with alteration in Ret receptor, be this at the genetic level or via overexpression in order to design effective therapies to target the Ret pathway. Here we review experimental evidence from basic research and pre-clinical studies concentrating on Ret alterations as potential biomarkers for recurrence, and we discuss the possibility that targeting the Ret pathway might in the future become a treatment for breast cancer.
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Affiliation(s)
- Albana Gattelli
- CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Ciudad Universitaria, C1428EGA CABA, Buenos Aires, Argentina.
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria C1428EGA CABA, Buenos Aires, Argentina.
| | - Nancy E Hynes
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, CH-4058, Basel, Switzerland
- University of Basel, CH-4002, Basel, Switzerland
| | - Ignacio E Schor
- CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Ciudad Universitaria, C1428EGA CABA, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Ciudad Universitaria, C1428EGA, CABA, Argentina
| | - Sabrina A Vallone
- CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Ciudad Universitaria, C1428EGA CABA, Buenos Aires, Argentina
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria C1428EGA CABA, Buenos Aires, Argentina
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16
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Mulligan LM. GDNF and the RET Receptor in Cancer: New Insights and Therapeutic Potential. Front Physiol 2019; 9:1873. [PMID: 30666215 PMCID: PMC6330338 DOI: 10.3389/fphys.2018.01873] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
The Glial cell line-derived neurotrophic Family Ligands (GFL) are soluble neurotrophic factors that are required for development of multiple human tissues, but which are also important contributors to human cancers. GFL signaling occurs through the transmembrane RET receptor tyrosine kinase, a well-characterized oncogene. GFL-independent RET activation, through rearrangement or point mutations occurs in thyroid and lung cancers. However, GFL-mediated activation of wildtype RET is an increasingly recognized mechanism promoting tumor growth and dissemination of a much broader group of cancers. RET and GFL expression have been implicated in metastasis or invasion in diverse human cancers including breast, pancreatic, and prostate tumors, where they are linked to poorer patient prognosis. In addition to directly inducing tumor growth in these diseases, GFL-RET signaling promotes changes in the tumor microenvironment that alter the surrounding stroma and cellular composition to enhance tumor invasion and metastasis. As such, GFL RET signaling is an important target for novel therapeutic approaches to limit tumor growth and spread and improve disease outcomes.
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Affiliation(s)
- Lois M. Mulligan
- Division of Cancer Biology and Genetics, Department of Pathology and Molecular Medicine, Cancer Research Institute, Queen’s University, Kingston, ON, Canada
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17
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Horibata S, Rice EJ, Mukai C, Marks BA, Sams K, Zheng H, Anguish LJ, Coonrod SA, Danko CG. ER-positive breast cancer cells are poised for RET-mediated endocrine resistance. PLoS One 2018; 13:e0194023. [PMID: 29608602 PMCID: PMC5880349 DOI: 10.1371/journal.pone.0194023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/22/2018] [Indexed: 01/13/2023] Open
Abstract
The RET tyrosine kinase signaling pathway is involved in the development of endocrine resistant ER+ breast cancer. However, we know little about how ER+ cells activate RET signaling and initiate an endocrine resistant phenotype. Here we show that both ER+ endocrine resistant and sensitive breast cancers have a functional RET tyrosine kinase signaling pathway, but that endocrine sensitive breast cancer cells lack RET ligands that are necessary to drive endocrine resistance. Transcription of one RET ligand, GDNF, is necessary and sufficient to confer resistance in the ER+ MCF-7 cell line. Endogenous GDNF produced by endocrine resistant cells is translated, secreted into the media, and activates RET signaling in nearby cells. In patients, RET ligand expression predicts responsiveness to endocrine therapies and correlates with survival. Collectively, our findings show that ER+ tumor cells are "poised" for RET mediated endocrine resistance, expressing all components of the RET signaling pathway, but endocrine sensitive cells lack high expression of RET ligands that are necessary to initiate the resistance phenotype.
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Affiliation(s)
- Sachi Horibata
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Edward J. Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Chinatsu Mukai
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Brooke A. Marks
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Kelly Sams
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Hui Zheng
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Lynne J. Anguish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Scott A. Coonrod
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Charles G. Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
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18
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Carleton JB, Berrett KC, Gertz J. Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers. Cell Syst 2017; 5:333-344.e5. [PMID: 28964699 DOI: 10.1016/j.cels.2017.08.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/13/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022]
Abstract
Multiple regulatory regions have the potential to regulate a single gene, yet how these elements combine to affect gene expression remains unclear. To uncover the combinatorial relationships between enhancers, we developed Enhancer-interference (Enhancer-i), a CRISPR interference-based approach that uses 2 different repressive domains, KRAB and SID, to prevent enhancer activation simultaneously at multiple regulatory regions. We applied Enhancer-i to promoter-distal estrogen receptor α binding sites (ERBS), which cluster around estradiol-responsive genes and therefore may collaborate to regulate gene expression. Targeting individual sites revealed predominant ERBS that are completely required for the transcriptional response, indicating a lack of redundancy. Simultaneous interference of different ERBS combinations identified supportive ERBS that contribute only when predominant sites are active. Using mathematical modeling, we find strong evidence for collaboration between predominant and supportive ERBS. Overall, our findings expose a complex functional hierarchy of enhancers, where multiple loci bound by the same transcription factor combine to fine-tune the expression of target genes.
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Affiliation(s)
- Julia B Carleton
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Kristofer C Berrett
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
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19
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Role of Estrogens in the Size of Neuronal Somata of Paravaginal Ganglia in Ovariectomized Rabbits. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2089645. [PMID: 28316975 PMCID: PMC5339489 DOI: 10.1155/2017/2089645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/18/2016] [Accepted: 01/15/2017] [Indexed: 01/07/2023]
Abstract
We aimed to determine the role of estrogens in modulating the size of neuronal somata of paravaginal ganglia. Rabbits were allocated into control (C), ovariectomized (OVX), and OVX treated with estradiol benzoate (OVX + EB) groups to evaluate the neuronal soma area; total serum estradiol (E2) and testosterone (T) levels; the percentage of immunoreactive (ir) neurons anti-aromatase, anti-estrogen receptor (ERα, ERβ) and anti-androgen receptor (AR); the intensity of the immunostaining anti-glial cell line-derived neurotrophic factor (GDNF) and the GDNF family receptor alpha type 1 (GFRα1); and the number of satellite glial cells (SGCs) per neuron. There was a decrease in the neuronal soma size for the OVX group, which was associated with low T, high percentages of aromatase-ir and neuritic AR-ir neurons, and a strong immunostaining anti-GDNF and anti-GFRα1. The decrease in the neuronal soma size was prevented by the EB treatment that increased the E2 without affecting the T levels. Moreover, there was a high percentage of neuritic AR-ir neurons, a strong GDNF immunostaining in the SGC, and an increase in the SGCs per neuron. Present findings show that estrogens modulate the soma size of neurons of the paravaginal ganglia, likely involving the participation of the SGC.
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20
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Long HK, Prescott SL, Wysocka J. Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution. Cell 2016; 167:1170-1187. [PMID: 27863239 PMCID: PMC5123704 DOI: 10.1016/j.cell.2016.09.018] [Citation(s) in RCA: 564] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/24/2016] [Accepted: 09/07/2016] [Indexed: 12/27/2022]
Abstract
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating spatiotemporally precise gene-expression programs during development. Consequently, divergence in enhancer sequence and activity is thought to be an important mediator of inter- and intra-species phenotypic variation. Here, we give an overview of emerging principles of enhancer function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution, and the influence of three-dimensional genome organization on long-range gene regulation. We discuss intricate relationships between distinct elements within complex regulatory landscapes and consider their potential impact on specificity and robustness of transcriptional regulation.
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Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sara L Prescott
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA.
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21
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Griseri P, Garrone O, Lo Sardo A, Monteverde M, Rusmini M, Tonissi F, Merlano M, Bruzzi P, Lo Nigro C, Ceccherini I. Genetic and epigenetic factors affect RET gene expression in breast cancer cell lines and influence survival in patients. Oncotarget 2016; 7:26465-79. [PMID: 27034161 PMCID: PMC5041993 DOI: 10.18632/oncotarget.8417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 03/04/2016] [Indexed: 12/14/2022] Open
Abstract
Germline and somatic mutations play a crucial role in breast cancer (BC), driving the initiation, progression, response to therapy and outcome of the disease. Hormonal therapy is limited to patients with tumors expressing steroid hormone receptors, such as estrogen receptor (ER), nevertheless resistance often limits its success.The RET gene is known to be involved in neurocristopathies such as Hirschsprung disease and Multiple Endocrine Neoplasia type 2, in the presence of loss-of-function and gain-of-function mutations, respectively. More recently, RET over-expression has emerged as a new player in ER-positive (ER+) BC, and as a potential target to enhance sensitivity and avoid resistance to tamoxifen therapy.Therefore, targeting the RET pathway may lead to new therapies in ER+ BC. To this end, we have investigated the molecular mechanisms which underlie RET overexpression and its possible modulation in two BC cell lines, MCF7 and T47D, showing different RET expression levels. Moreover, we have carried out a pilot association study in 93 ER+ BC patients. Consistent with the adverse role of RET over-expression in BC, increased overall survival was observed in carriers of the variant allele of SNP rs2435357, a RET polymorphism already known to be associated with reduced RET expression.
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Affiliation(s)
- Paola Griseri
- UOC Medical Genetics, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Ornella Garrone
- Unit of Medical Oncology, Department of Oncology, S. Croce & Carle Teaching Hospital, Cuneo, Italy
| | | | - Martino Monteverde
- Laboratory of Cancer Genetics and Translational Oncology, Department of Oncology, S. Croce & Carle Teaching Hospital, Cuneo, Italy
| | - Marta Rusmini
- UOC Medical Genetics, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Federica Tonissi
- Laboratory of Cancer Genetics and Translational Oncology, Department of Oncology, S. Croce & Carle Teaching Hospital, Cuneo, Italy
| | - Marco Merlano
- Unit of Medical Oncology, Department of Oncology, S. Croce & Carle Teaching Hospital, Cuneo, Italy
| | - Paolo Bruzzi
- Clinical Epidemiology, IRCCS AUO San Martino IST, Genoa, Italy
| | - Cristiana Lo Nigro
- Laboratory of Cancer Genetics and Translational Oncology, Department of Oncology, S. Croce & Carle Teaching Hospital, Cuneo, Italy
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22
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De Andrade JP, Park JM, Gu VW, Woodfield GW, Kulak MV, Lorenzen AW, Wu VT, Van Dorin SE, Spanheimer PM, Weigel RJ. EGFR Is Regulated by TFAP2C in Luminal Breast Cancer and Is a Target for Vandetanib. Mol Cancer Ther 2016; 15:503-11. [PMID: 26832794 DOI: 10.1158/1535-7163.mct-15-0548-t] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/27/2015] [Indexed: 12/20/2022]
Abstract
Expression of TFAP2C in luminal breast cancer is associated with reduced survival and hormone resistance, partially explained through regulation of RET. TFAP2C also regulates EGFR in HER2 breast cancer. We sought to elucidate the regulation and functional role of EGFR in luminal breast cancer. We used gene knockdown (KD) and treatment with a tyrosine kinase inhibitor (TKI) in cell lines and primary cancer isolates to determine the role of RET and EGFR in regulation of p-ERK and tumorigenesis. KD of TFAP2C decreased expression of EGFR in a panel of luminal breast cancers, and chromatin immunoprecipitation sequencing (ChIP-seq) confirmed that TFAP2C targets the EGFR gene. Stable KD of TFAP2C significantly decreased cell proliferation and tumor growth, mediated in part through EGFR. While KD of RET or EGFR reduced proliferation (31% and 34%, P < 0.01), combined KD reduced proliferation greater than either alone (52% reduction, P < 0.01). The effect of the TKI vandetanib on proliferation and tumor growth response of MCF-7 cells was dependent upon expression of TFAP2C, and dual KD of RET and EGFR eliminated the effects of vandetanib. The response of primary luminal breast cancers to TKIs assessed by ERK activation established a correlation with expression of RET and EGFR. We conclude that TFAP2C regulates EGFR in luminal breast cancer. Response to vandetanib was mediated through the TFAP2C target genes EGFR and RET. Vandetanib may provide a therapeutic effect in luminal breast cancer, and RET and EGFR can serve as molecular markers for response.
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Affiliation(s)
| | - Jung M Park
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | - Vivian W Gu
- Department of Surgery, University of Iowa, Iowa City, Iowa
| | | | | | | | - Vincent T Wu
- Department of Surgery, University of Iowa, Iowa City, Iowa
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23
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Spanheimer PM, Lorenzen AW, De Andrade JP, Kulak MV, Carr JC, Woodfield GW, Sugg SL, Weigel RJ. Receptor Tyrosine Kinase Expression Predicts Response to Sunitinib in Breast Cancer. Ann Surg Oncol 2015; 22:4287-94. [PMID: 25971960 DOI: 10.1245/s10434-015-4597-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND Preliminary data indicate that tyrosine kinase inhibitors (TKIs) function through rearranged during transfection (RET) in breast cancer. However, TKIs are not specific and can block several receptor tyrosine kinases (RTKs). This study used cell lines and primary breast cancer specimens to determine factors associated with TKI response. METHODS Proliferation was assessed after short interfering RNA knockdown with or without sunitinib in breast cancer cell lines by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide). Breast cancer tissue and matched normal breast was obtained from 30 women with invasive breast carcinoma. Gene expression was assessed by reverse transcriptase-polymerase chain reaction. Fresh tissue was treated in vitro with sunitinib or control media for 30 min, and response was assessed by phosphorylation-specific western blot. RESULTS The RTKs including epidermal growth factor receptor (EGFR), vascular endothelial growth factor receptor (VEGFR1-3), platelet-derived growth factor receptor (PDGFRa/b), and Kit were overexpressed in triple-negative breast tumors relative to HER2- and estrogen receptor-alpha (ERα)-positive tumors and normal breast tissue. Knockdown of EGFR reduced in vitro proliferation in MCF-7 and MDA-MB-231 but not in SKBR-3 or ZR-75-1 breast cancer cells. With the exception of RET, response to sunitinib was independent of RTK expression in all four cell lines. Both ERα-positive and low-EGFR-expressing tumors had an increased in vitro sunitinib response, as determined by alteration of Erk activation. Expression of other RTKs and additional clinical factors were not associated with response. CONCLUSION Triple-negative breast cancers overexpress RTKs but have decreased in vitro response to the TKI sunitinib. In addition to RET, TKIs that block EGFR may increase the therapeutic efficacy of TKIs in breast cancer.
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Affiliation(s)
| | | | | | - Mikhail V Kulak
- Department of Surgery, University of Iowa, Iowa City, IA, USA
| | - Jennifer C Carr
- Department of Surgery, University of Iowa, Iowa City, IA, USA
| | | | - Sonia L Sugg
- Department of Surgery, University of Iowa, Iowa City, IA, USA
| | - Ronald J Weigel
- Department of Surgery, University of Iowa, Iowa City, IA, USA.
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24
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Nagalakshmi VK, Yu J. The ureteric bud epithelium: morphogenesis and roles in metanephric kidney patterning. Mol Reprod Dev 2015; 82:151-66. [PMID: 25783232 DOI: 10.1002/mrd.22462] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/12/2015] [Indexed: 01/03/2023]
Abstract
The mammalian metanephric kidney is composed of two epithelial components, the collecting duct system and the nephron epithelium, that differentiate from two different tissues -the ureteric bud epithelium and the nephron progenitors, respectively-of intermediate mesoderm origin. The collecting duct system is generated through reiterative ureteric bud branching morphogenesis, whereas the nephron epithelium is formed in a process termed nephrogenesis, which is initiated with the mesenchymal-epithelial transition of the nephron progenitors. Ureteric bud branching morphogenesis is regulated by nephron progenitors, and in return, the ureteric bud epithelium regulates nephrogenesis. The metanephric kidney is physiologically divided along the corticomedullary axis into subcompartments that are enriched with specific segments of these two epithelial structures. Here, we provide an overview of the major molecular and cellular processes underlying the morphogenesis and patterning of the ureteric bud epithelium and its roles in the cortico-medullary patterning of the metanephric kidney.
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Affiliation(s)
- Vidya K Nagalakshmi
- Department of Cell Biology and Division of Center of Immunity, Inflammation and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
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25
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Rusmini M, Griseri P, Matera I, Pontarini E, Ravazzolo R, Mavilio D, Ceccherini I. Expression Variability and Function of the RET Gene in Adult Peripheral Blood Mononuclear Cells. J Cell Physiol 2014; 229:2027-37. [DOI: 10.1002/jcp.24660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 04/25/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Marta Rusmini
- U.O.C. Genetica Medica; Istituto Giannina Gaslini; Genova Italy
| | - Paola Griseri
- U.O.C. Genetica Medica; Istituto Giannina Gaslini; Genova Italy
| | - Ivana Matera
- U.O.C. Genetica Medica; Istituto Giannina Gaslini; Genova Italy
| | - Elena Pontarini
- Unit of Clinical and Experimental Immunology; Humanitas Clinical and Research Center; Rozzano Milan Italy
| | - Roberto Ravazzolo
- U.O.C. Genetica Medica; Istituto Giannina Gaslini; Genova Italy
- Dipartimento di Neuroscienze, Oftalmologia, Genetica e Materno Infantile (DINOGMI); Università di Genova; Genova Italy
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology; Humanitas Clinical and Research Center; Rozzano Milan Italy
- Department of Medical Biotechnologies and Translational Medicine; University of Milan; Milan Italy
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26
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Distinct pathways regulated by RET and estrogen receptor in luminal breast cancer demonstrate the biological basis for combination therapy. Ann Surg 2014; 259:793-9. [PMID: 24045439 DOI: 10.1097/sla.0b013e3182a6f552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVE We investigated directed therapy based on TFAP2C-regulated pathways to inform new therapeutic approaches for treatment of luminal breast cancer. BACKGROUND TFAP2C regulates the expression of genes characterizing the luminal phenotype including ESR1 and RET, but pathway cross talk and potential for distinct elements have not been characterized. METHODS Activation of extracellular signal-regulated kinases (ERK) and AKT was assessed using phosphorylation-specific Western blot. Cell proliferation was measured with MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] after siRNA (small interfering RNA) gene knockdown or drug treatment. Cell cycle, Ki-67, and cleaved caspase 3 were measured by fluorescence-activated cell sorting. Tumorigenesis was assessed in mice xenografts. RESULTS Knockdown of TFAP2C or RET inhibited GDNF (glial cell line-derived neurotrophic factor)-mediated activation of ERK and AKT in MCF-7 cells. Similarly, sunitinib, a small-molecule inhibitor of RET, blocked GDNF-mediated activation of ERK and AKT. Inhibition of RET either by gene knockdown or by treatment with sunitinib or vandetanib reduced RET-dependent growth of luminal breast cancer cells. Interestingly, knockdown of TFAP2C, which controls both ER (estrogen receptor) and RET, demonstrated a greater effect on cell growth than either RET or ER alone. Parallel experiments using treatment with tamoxifen and sunitinib confirmed the increased effectiveness of dual inhibition of the ER and RET pathways in regulating cell growth. Whereas targeting the ER pathway altered cell proliferation, as measured by Ki-67 and S-phase, anti-RET primarily increased apoptosis, as demonstrated by cleaved caspase 3 and increased TUNEL (terminal deoxyneucleotidyl transferase dUTP nick end labeling) expression in xenografts. CONCLUSIONS ER and RET primarily function through distinct pathways regulating proliferation and cell survival, respectively. The findings inform a therapeutic approach based on combination therapy with antiestrogen and anti-RET in luminal breast cancer.
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27
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Spanheimer PM, Park JM, Askeland RW, Kulak MV, Woodfield GW, De Andrade JP, Cyr AR, Sugg SL, Thomas A, Weigel RJ. Inhibition of RET increases the efficacy of antiestrogen and is a novel treatment strategy for luminal breast cancer. Clin Cancer Res 2014; 20:2115-25. [PMID: 24526731 DOI: 10.1158/1078-0432.ccr-13-2221] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE Recent findings suggest that combination treatment with antiestrogen and anti-RET may offer a novel treatment strategy in a subset of patients with breast cancer. We investigated the role of RET in potentiating the effects of antiestrogen response and examined whether RET expression predicted the ability for tyrosine kinase inhibitor (TKI) to affect extracellular signal-regulated kinase 1/2 (ERK1/2) activation in primary breast cancer. EXPERIMENTAL DESIGN Growth response, ERK1/2 activation, Ki-67, and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling were assessed in breast cancer cell lines in vitro and in xenografts with vandetanib and/or tamoxifen. Thirty tumors with matched normal breast tissue were evaluated for RET expression and response to TKI treatment. RESULTS Vandetanib potentiated the inhibitory effect of tamoxifen in hormone responsive (P = 0.01) and hormone insensitive (P < 0.001) estrogen receptor α (ERα)-positive breast cancer cells. Vandetanib significantly repressed tumorigenesis of MCF-7 xenografts (P < 0.001), which displayed decreased activation of ERK1/2 and AKT. Vandetanib and tamoxifen reduced the growth of established tumors with a greater effect of dual therapy compared with single agent (P = 0.003), with tamoxifen-reducing proliferative index and vandetanib-inducing apoptosis. In primary breast cancers, RET expression correlated with the ERα-positive subtype. Relative decrease in ERK1/2 phosphorylation with TKI treatment was 42% (P < 0.001) in RET-positive tumors versus 14% (P = ns) in RET-negative tumors. CONCLUSIONS Vandetanib potentiated the antigrowth effects of tamoxifen in breast cancer, which was mediated through RET activation. RET predicted response to TKI therapy with minimal effects on ERK1/2 activation in RET-negative tumors. The preclinical data support evaluation of antiestrogen in combination with TKI as a potential treatment strategy for RET-positive luminal breast cancer.
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Affiliation(s)
- Philip M Spanheimer
- Authors' Affiliations: Departments of Surgery, Pathology, Internal Medicine, and Biochemistry, University of Iowa, Iowa City, Iowa
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Paroly SS, Wang F, Spraggon L, Merregaert J, Batourina E, Tycko B, Schmidt-Ott KM, Grimmond S, Little M, Mendelsohn C. Stromal protein Ecm1 regulates ureteric bud patterning and branching. PLoS One 2013; 8:e84155. [PMID: 24391906 PMCID: PMC3877229 DOI: 10.1371/journal.pone.0084155] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/12/2013] [Indexed: 01/28/2023] Open
Abstract
The interactions between the nephrogenic mesenchyme and the ureteric bud during kidney development are well documented. While recent studies have shed some light on the importance of the stroma during renal development, many of the signals generated in the stroma, the genetic pathways and interaction networks involving the stroma are yet to be identified. Our previous studies demonstrate that retinoids are crucial for branching of the ureteric bud and for patterning of the cortical stroma. In the present study we demonstrate that autocrine retinoic acid (RA) signaling in stromal cells is critical for their survival and patterning, and show that Extracellular matrix 1, Ecm1, a gene that in humans causes irritable bowel syndrome and lipoid proteinosis, is a novel RA-regulated target in the developing kidney, which is secreted from the cortical stromal cells surrounding the cap mesenchyme and ureteric bud. Our studies suggest that Ecm1 is required in the ureteric bud for regulating the distribution of Ret which is normally restricted to the tips, as inhibition of Ecm1 results in an expanded domain of Ret expression and reduced numbers of branches. We propose a model in which retinoid signaling in the stroma activates expression of Ecm1, which in turn down-regulates Ret expression in the ureteric bud cleft, where bifurcation normally occurs and normal branching progresses.
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Affiliation(s)
- Suneeta S. Paroly
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
- * E-mail:
| | - Fengwei Wang
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
| | - Lee Spraggon
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
| | - Joseph Merregaert
- Laboratory of Molecular Biotechnology, Department of Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - Ekatherina Batourina
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
| | - Benjamin Tycko
- Institute for Cancer Genetics & Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York, United States of America
| | - Kai M. Schmidt-Ott
- Max-Delbrueck Center for Molecular Medicine Robert-Roessle-Str. Berlin, Germany
| | - Sean Grimmond
- Institute for Molecular Bioscience, The University of Queensland St Lucia QLD, Australia
| | - Melissa Little
- Institute for Molecular Bioscience, The University of Queensland St Lucia QLD, Australia
| | - Cathy Mendelsohn
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
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29
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Shirakihara T, Kawasaki T, Fukagawa A, Semba K, Sakai R, Miyazono K, Miyazawa K, Saitoh M. Identification of integrin α3 as a molecular marker of cells undergoing epithelial-mesenchymal transition and of cancer cells with aggressive phenotypes. Cancer Sci 2013; 104:1189-97. [PMID: 23786209 DOI: 10.1111/cas.12220] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 06/05/2013] [Accepted: 06/15/2013] [Indexed: 01/28/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a crucial event in wound healing, tissue repair, and cancer progression in adult tissues. Transforming growth factor (TGF)-β induces EMT in mouse epithelial cells. During prolonged treatment, TGF-β successively induces myofibroblastic differentiation with increased expression of myofibroblast marker proteins, including smooth muscle α actin and calponin. We recently showed that fibroblast growth factor-2 prevented myofibroblastic differentiation induced by TGF-β, and transdifferentiated the cells to those with much more aggressive characteristics (enhanced EMT). To identify the molecular markers specifically expressed in cells undergoing enhanced EMT induced by the combination of TGF-β and fibroblast growth factor-2, we carried out a microarray-based analysis and found that integrin α3 (ITGA3) and Ret were upregulated. Intriguingly, ITGA3 was also overexpressed in breast cancer cells with aggressive phenotypes and its expression was correlated with that of δEF-1, a key regulator of EMT. Moreover, the expression of both genes was downregulated by U0126, a MEK 1/2 inhibitor. Therefore, ITGA3 is a potential marker protein for cells undergoing enhanced EMT and for cancer cells with aggressive phenotypes, which is positively regulated by δEF-1 and the MEK-ERK pathway.
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Affiliation(s)
- Takuya Shirakihara
- Division of Metastasis and Invasion Signaling, National Cancer Center Research Institute, Tokyo, Japan
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30
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Morandi A, Martin LA, Gao Q, Pancholi S, Mackay A, Robertson D, Zvelebil M, Dowsett M, Plaza-Menacho I, Isacke CM. GDNF-RET signaling in ER-positive breast cancers is a key determinant of response and resistance to aromatase inhibitors. Cancer Res 2013; 73:3783-95. [PMID: 23650283 DOI: 10.1158/0008-5472.can-12-4265] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Most breast cancers at diagnosis are estrogen receptor-positive (ER(+)) and depend on estrogen for growth and survival. Blocking estrogen biosynthesis by aromatase inhibitors has therefore become a first-line endocrine therapy for postmenopausal women with ER(+) breast cancers. Despite providing substantial improvements in patient outcome, aromatase inhibitor resistance remains a major clinical challenge. The receptor tyrosine kinase, RET, and its coreceptor, GFRα1, are upregulated in a subset of ER(+) breast cancers, and the RET ligand, glial-derived neurotrophic factor (GDNF) is upregulated by inflammatory cytokines. Here, we report the findings of a multidisciplinary strategy to address the impact of GDNF-RET signaling in the response to aromatase inhibitor treatment. In breast cancer cells in two-dimensional and three-dimensional culture, GDNF-mediated RET signaling is enhanced in a model of aromatase inhibitor resistance. Furthermore, GDNF-RET signaling promoted the survival of aromatase inhibitor-resistant cells and elicited resistance in aromatase inhibitor-sensitive cells. Both these effects were selectively reverted by the RET kinase inhibitor, NVP-BBT594. Gene expression profiling in ER(+) cancers defined a proliferation-independent GDNF response signature that prognosed poor patient outcome and, more importantly, predicted poor response to aromatase inhibitor treatment with the development of resistance. We validated these findings by showing increased RET protein expression levels in an independent cohort of aromatase inhibitor-resistant patient specimens. Together, our results establish GDNF-RET signaling as a rational therapeutic target to combat or delay the onset of aromatase inhibitor resistance in breast cancer.
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Affiliation(s)
- Andrea Morandi
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, Department of Academic Biochemistry, The Royal Marsden Hospital; and London Research Institute, Cancer Research UK, London, United Kingdom
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31
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Jannot AS, Pelet A, Henrion-Caude A, Chaoui A, Masse-Morel M, Arnold S, Sanlaville D, Ceccherini I, Borrego S, Hofstra RMW, Munnich A, Bondurand N, Chakravarti A, Clerget-Darpoux F, Amiel J, Lyonnet S. Chromosome 21 scan in Down syndrome reveals DSCAM as a predisposing locus in Hirschsprung disease. PLoS One 2013; 8:e62519. [PMID: 23671607 PMCID: PMC3646051 DOI: 10.1371/journal.pone.0062519] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/20/2013] [Indexed: 12/19/2022] Open
Abstract
Hirschsprung disease (HSCR) genetics is a paradigm for the study and understanding of multigenic disorders. Association between Down syndrome and HSCR suggests that genetic factors that predispose to HSCR map to chromosome 21. To identify these additional factors, we performed a dose-dependent association study on chromosome 21 in Down syndrome patients with HSCR. Assessing 10,895 SNPs in 26 Caucasian cases and their parents led to identify two associated SNPs (rs2837770 and rs8134673) at chromosome-wide level. Those SNPs, which were located in intron 3 of the DSCAM gene within a 19 kb-linkage disequilibrium block region were in complete association and are consistent with DSCAM expression during enteric nervous system development. We replicated the association of HSCR with this region in an independent sample of 220 non-syndromic HSCR Caucasian patients and their parents. At last, we provide the functional rationale to the involvement of DSCAM by network analysis and assessment of SOX10 regulation. Our results reveal the involvement of DSCAM as a HSCR susceptibility locus, both in Down syndrome and HSCR isolated cases. This study further ascertains the chromosome-scan dose-dependent methodology used herein as a mean to map the genetic bases of other sub-phenotypes both in Down syndrome and other aneuploidies.
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Affiliation(s)
- Anne-Sophie Jannot
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
| | - Anna Pelet
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
| | - Alexandra Henrion-Caude
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
| | | | - Marine Masse-Morel
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
| | - Stacey Arnold
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Damien Sanlaville
- HCL, Service de génétique, Bron, France
- INSERM U-1028, CNRS UMR5292, Université Claude Bernard Lyon 1, Equipe TIGER, Lyon, France
| | | | - Salud Borrego
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- CIBER de Enfermedades Raras, ISCIII, Sevilla, Spain
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, ErasmusMC, University of Rotterdam, Rotterdam, The Netherlands
| | - Arnold Munnich
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
| | | | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Françoise Clerget-Darpoux
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
| | - Jeanne Amiel
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
| | - Stanislas Lyonnet
- INSERM U-781, AP-HP Hôpital Necker-Enfants Malades, Paris, France
- Département de Génétique, Université Paris Descartes, Faculté de Médecine, Paris, France
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Betts JA, French JD, Brown MA, Edwards SL. Long-range transcriptional regulation of breast cancer genes. Genes Chromosomes Cancer 2012; 52:113-25. [PMID: 23077082 DOI: 10.1002/gcc.22020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is a major health problem and understanding the genetic basis of this disease is crucial for predicting risk and developing effective targeted therapeutics. Several breast cancer predisposing genes have been identified, but mutations in the coding regions of these genes only accounts for a small proportion of risk. Research now suggests that combinations of multiple non-coding changes in breast cancer susceptibility genes, which cause moderate alterations in gene expression, will be responsible for the remaining inherited risk. These non-coding changes will include variants in proximal and distal transcriptional and post-transcriptional regulatory elements and may affect the levels and function of trans-acting factors, including proteins and RNAs, which act on these elements. Somatic changes in such elements and factors have also been associated with breast cancer progression. With the recent advent of techniques allowing the detection of long-range DNA interactions spanning the human genome, it has become increasingly clear that long-range regulatory elements constitute an important mechanism for gene regulation. Recent studies have identified several such elements that are important for regulating genes involved in breast cancer, raising the possibility that defects in these sequences may contribute to breast cancer predisposition and progression. In this review, we discuss the emerging functions of cis-regulatory elements and a subset of trans-acting factors in breast tumorigenesis. We also discuss some recent progress in our understanding of how dysregulation in these transcriptional components may contribute to breast cancer, and the potential implications for molecular diagnosis, prognosis prediction, and the treatment of this disease.
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Affiliation(s)
- Joshua A Betts
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
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Spanheimer PM, Woodfield GW, Cyr AR, Kulak MV, White-Baer LS, Bair TB, Weigel RJ. Expression of the RET proto-oncogene is regulated by TFAP2C in breast cancer independent of the estrogen receptor. Ann Surg Oncol 2012; 20:2204-12. [PMID: 22878616 DOI: 10.1245/s10434-012-2570-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Indexed: 01/16/2023]
Abstract
BACKGROUND The RET proto-oncogene is expressed as part of the estrogen receptor (ER) cluster in breast cancer. We sought to determine if TFAP2C regulates Ret expression directly or indirectly through ER. METHODS Chromatin immunoprecipitation sequencing (ChIP-Seq) and gel-shift assay were used to identify TFAP2C binding sites in the RET promoter in four breast cancer cell lines. Ret mRNA and protein levels were evaluated in ER-positive and ER-negative breast cancer cell lines after knockdown of TFAP2C. Luciferase expression assay was performed to assess expression from two of the identified sites. RESULTS ChIP-Seq identified five main binding peaks for TFAP2C in the RET promoter at -101.5 kb, -50.7 kb, -32.5 kb, +5.0 kb, and +33.6 from the RET transcriptional start site. Binding at three of the AP-2 sites was conserved across all four cell lines, whereas the RET -101.5 and RET +33.6 sites were each found to be unbound by TFAP2C in one cell line. A TFAP2C consensus element was confirmed for all five sites. Knockdown of TFAP2C by siRNA in ER-positive MCF-7 cells resulted in significant down regulation of Ret mRNA compared to nontargeting (NT) siRNA (0.09 vs. 1.0, P < 0.001). Knockdown of TFAP2C in ER-negative MDA-MB-453 cells also led to a significant reduction in Ret mRNA compared to NT siRNA (0.16 vs. 1.0, P < 0.001). In MCF-7 cells, knockdown of TFAP2C abrogated Ret protein expression (0.02 vs. 1.0, P < 0.001) before reduction in ER. CONCLUSIONS TFAP2C regulates expression of the RET proto-oncogene through five AP-2 regulatory sites in the RET promoter. Regulation of Ret by TFAP2C occurs independently of ER expression in breast carcinoma.
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