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Zou Y, Carbonetto P, Xie D, Wang G, Stephens M. Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.14.536893. [PMID: 37425935 PMCID: PMC10327118 DOI: 10.1101/2023.04.14.536893] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
We introduce mvSuSiE, a multi-trait fine-mapping method for identifying putative causal variants from genetic association data (individual-level or summary data). mvSuSiE learns patterns of shared genetic effects from data, and exploits these patterns to improve power to identify causal SNPs. Comparisons on simulated data show that mvSuSiE is competitive in speed, power and precision with existing multi-trait methods, and uniformly improves on single-trait fine-mapping (SuSiE) in each trait separately. We applied mvSuSiE to jointly fine-map 16 blood cell traits using data from the UK Biobank. By jointly analyzing the traits and modeling heterogeneous effect sharing patterns, we discovered a much larger number of causal SNPs (>3,000) compared with single-trait fine-mapping, and with narrower credible sets. mvSuSiE also more comprehensively characterized the ways in which the genetic variants affect one or more blood cell traits; 68% of causal SNPs showed significant effects in more than one blood cell type.
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Affiliation(s)
- Yuxin Zou
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Dongyue Xie
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Gao Wang
- Gertrude. H. Sergievsky Center, Department of Neurology, Columbia University, New York, NY, USA
| | - Matthew Stephens
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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2
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Ajore R, Mattsson J, Pertesi M, Ekdahl L, Ali Z, Hansson M, Nilsson B. Genome-wide CRISPR/Cas9 screen identifies regulators of BCMA expression on multiple myeloma cells. Blood Cancer J 2024; 14:21. [PMID: 38272874 PMCID: PMC10811322 DOI: 10.1038/s41408-024-00986-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Affiliation(s)
- Ram Ajore
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden
| | - Jenny Mattsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden
- BioInvent International AB, Ideongatan 1, 223 70, Lund, Sweden
| | - Maroulio Pertesi
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden
| | - Ludvig Ekdahl
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden
| | - Zain Ali
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden
| | - Markus Hansson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy, Göteborg University, 41346, Göteborg, Sweden
| | - Björn Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden.
- Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden.
- Broad Institute, Cambridge, MA, 02142, USA.
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3
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Kim H, Ahn HS, Hwang N, Huh Y, Bu S, Seo KJ, Kwon SH, Lee HK, Kim JW, Yoon BK, Fang S. Epigenomic landscape exhibits interferon signaling suppression in the patient of myocarditis after BNT162b2 vaccination. Sci Rep 2023; 13:8926. [PMID: 37264110 DOI: 10.1038/s41598-023-36070-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023] Open
Abstract
After the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, a novel mRNA vaccine (BNT162b2) was developed at an unprecedented speed. Although most countries have achieved widespread immunity from vaccines and infections, yet people, even who have recovered from SARS-CoV-2 infection, are recommended to receive vaccination due to their effectiveness in lowering the risk of recurrent infection. However, the BNT162b2 vaccine has been reported to increase the risk of myocarditis. To our knowledge, for the first time in this study, we tracked changes in the chromatin dynamics of peripheral blood mononuclear cells (PBMCs) in the patient who underwent myocarditis after BNT162b2 vaccination. A longitudinal study of chromatin accessibility using concurrent analysis of single-cell assays for transposase-accessible chromatin with sequencing and single-cell RNA sequencing showed downregulation of interferon signaling and upregulated RUNX2/3 activity in PBMCs. Considering BNT162b2 vaccination increases the level of interferon-α/γ in serum, our data highlight the immune responses different from the conventional responses to the vaccination, which is possibly the key to understanding the side effects of BNT162b2 vaccination.
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Affiliation(s)
- Hyeonhui Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Hyo-Suk Ahn
- Division of Cardiology, Department of Internal Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, 06591, Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Nahee Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Yune Huh
- Department of Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seonghyeon Bu
- Division of Cardiology, Department of Internal Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, 06591, Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Kyung Jin Seo
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, South Korea
| | - Se Hwan Kwon
- Department of Radiology, Kyung Hee University Medical Center, Seoul, South Korea
| | - Hae-Kyung Lee
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jae-Woo Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Bo Kyung Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea.
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea.
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea.
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Zhou J, Toh SHM, Tan TK, Balan K, Lim JQ, Tan TZ, Xiong S, Jia Y, Ng SB, Peng Y, Jeyasekharan AD, Fan S, Lim ST, Ong CAJ, Ong CK, Sanda T, Chng WJ. Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma. Mol Cancer 2023; 22:69. [PMID: 37032358 PMCID: PMC10084643 DOI: 10.1186/s12943-023-01767-1] [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: 05/23/2022] [Accepted: 03/24/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Extranodal natural killer/T-cell lymphoma (NKTL) is an aggressive type of non-Hodgkin lymphoma with dismal outcome. A better understanding of disease biology and key oncogenic process is necessary for the development of targeted therapy. Super-enhancers (SEs) have been shown to drive pivotal oncogenes in various malignancies. However, the landscape of SEs and SE-associated oncogenes remain elusive in NKTL. METHODS We used Nano-ChIP-seq of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs NKTL primary tumor samples. Integrative analysis of RNA-seq and survival data further pinned down high value, novel SE oncogenes. We utilized shRNA knockdown, CRISPR-dCas9, luciferase reporter assay, ChIP-PCR to investigate the regulation of transcription factor (TF) on SE oncogenes. Multi-color immunofluorescence (mIF) staining was performed on an independent cohort of clinical samples. Various function experiments were performed to evaluate the effects of TOX2 on the malignancy of NKTL in vitro and in vivo. RESULTS SE landscape was substantially different in NKTL samples in comparison with normal tonsils. Several SEs at key transcriptional factor (TF) genes, including TOX2, TBX21(T-bet), EOMES, RUNX2, and ID2, were identified. We confirmed that TOX2 was aberrantly overexpressed in NKTL relative to normal NK cells and high expression of TOX2 was associated with worse survival. Modulation of TOX2 expression by shRNA, CRISPR-dCas9 interference of SE function impacted on cell proliferation, survival and colony formation ability of NKTL cells. Mechanistically, we found that RUNX3 regulates TOX2 transcription by binding to the active elements of its SE. Silencing TOX2 also impaired tumor formation of NKTL cells in vivo. Metastasis-associated phosphatase PRL-3 has been identified and validated as a key downstream effector of TOX2-mediated oncogenesis. CONCLUSIONS Our integrative SE profiling strategy revealed the landscape of SEs, novel targets and insights into molecular pathogenesis of NKTL. The RUNX3-TOX2-SE-TOX2-PRL-3 regulatory pathway may represent a hallmark of NKTL biology. Targeting TOX2 could be a valuable therapeutic intervene for NKTL patients and warrants further study in clinic.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Kalpnaa Balan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Tuan Zea Tan
- Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Yunlu Jia
- Department of Medical Oncology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Soon Thye Lim
- Director's office, National Cancer Centre, Singapore, 168583, Singapore
- Office of Education, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore, 168583, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, 168583, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673, Singapore
| | - Choon Kiat Ong
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Singapore.
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5
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Antonova DV, Gnatenko DA, Kotova ES, Pleshkan VV, Kuzmich AI, Didych DA, Sverdlov ED, Alekseenko IV. Cell-specific expression of the FAP gene is regulated by enhancer elements. Front Mol Biosci 2023; 10:1111511. [PMID: 36825204 PMCID: PMC9941708 DOI: 10.3389/fmolb.2023.1111511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
Fibroblast activation protein (FAP) is an integral membrane serine protease that acts as both dipeptidyl peptidase and collagenase. In recent years, FAP has attracted considerable attention due to its specific upregulation in multiple types of tumor cell populations, including cancer cells in various cancer types, making FAP a potential target for therapy. However, relatively few papers pay attention to the mechanisms driving the cell-specific expression of the FAP gene. We found no correlation between the activities of the two FAP promoter variants (short and long) and the endogenous FAP mRNA expression level in several cell lines with different FAP expression levels. This suggested that other mechanisms may be responsible for specific transcriptional regulation of the FAP gene. We analyzed the distribution of known epigenetic and structural chromatin marks in FAP-positive and FAP-negative cell lines and identified two potential enhancer-like elements (E1 and E2) in the FAP gene locus. We confirmed the specific enrichment of H3K27ac in the putative enhancer regions in FAP-expressing cells. Both the elements exhibited enhancer activity independently of each other in the functional test by increasing the activity of the FAP promoter variants to a greater extent in FAP-expressing cell lines than in FAP-negative cell lines. The transcription factors AP-1, CEBPB, and STAT3 may be involved in FAP activation in the tumors. We hypothesized the existence of a positive feedback loop between FAP and STAT3, which may have implications for developing new approaches in cancer therapy.
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Affiliation(s)
- Dina V. Antonova
- Gene Immunooncotherapy Group, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Department of Genomics and Postgenomic Technologies, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Gnatenko
- Gene Immunooncotherapy Group, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Department of Genomics and Postgenomic Technologies, Russian Academy of Sciences, Moscow, Russia
| | - Elena S. Kotova
- Laboratory of Human Molecular Genetics, FSBI Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Victor V. Pleshkan
- Gene Immunooncotherapy Group, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Department of Genomics and Postgenomic Technologies, Russian Academy of Sciences, Moscow, Russia,Gene Oncotherapy Sector, Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Alexey I. Kuzmich
- Gene Immunooncotherapy Group, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Department of Genomics and Postgenomic Technologies, Russian Academy of Sciences, Moscow, Russia,Gene Oncotherapy Sector, Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Dmitry A. Didych
- Gene Immunooncotherapy Group, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Department of Genomics and Postgenomic Technologies, Russian Academy of Sciences, Moscow, Russia,*Correspondence: Dmitry A. Didych,
| | - Eugene D. Sverdlov
- Kurchatov Center for Genome Research, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Irina V. Alekseenko
- Gene Immunooncotherapy Group, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Department of Genomics and Postgenomic Technologies, Russian Academy of Sciences, Moscow, Russia,Gene Oncotherapy Sector, Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow, Russia,Laboratory of Epigenetics, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov, Ministry of Healthcare of Russian Federation, Moscow, Russia
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6
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Sanders TR, Kelley MW. Specification of neuronal subtypes in the spiral ganglion begins prior to birth in the mouse. Proc Natl Acad Sci U S A 2022; 119:e2203935119. [PMID: 36409884 PMCID: PMC9860252 DOI: 10.1073/pnas.2203935119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
The afferent innervation of the cochlea is comprised of spiral ganglion neurons (SGNs), which are characterized into four subtypes (Type 1A, B, and C and Type 2). However, little is known about the factors and/or processes that determine each subtype. Here, we present a transcriptional analysis of approximately 5,500 single murine SGNs collected across four developmental time points. All four subtypes are transcriptionally identifiable prior to the onset of coordinated spontaneous activity, indicating that the initial specification process is under genetic control. Trajectory analysis indicates that SGNs initially split into two precursor types (Type 1A/2 and Type 1B/C), followed by subsequent splits to give rise to four transcriptionally distinct subtypes. Differential gene expression, pseudotime, and regulon analyses were used to identify candidate transcription factors which may regulate the subtypes specification process. These results provide insights into SGN development and comprise a transcriptional atlas of SGN maturation across the prenatal period.
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Affiliation(s)
- Tessa R. Sanders
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD20892
| | - Matthew W. Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD20892
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7
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Zhao H, Chen Y, Shen P, Gong L. Prognostic value and immune characteristics of RUNX gene family in human cancers: a pan-cancer analysis. Aging (Albany NY) 2022; 14:4014-4035. [PMID: 35522574 PMCID: PMC9134966 DOI: 10.18632/aging.204065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/23/2022] [Indexed: 11/25/2022]
Abstract
Background: Runt-related transcription factors (RUNX) are involved in numerous fundamental biological processes and play crucial parts in tumorigenesis and metastasis both directly and indirectly. However, the pan-cancer evidence of the RUNX gene family is not available. Methods: In this study, we analyzed the potential association between RUNX gene family expression and patient’s prognosis, immune cell infiltration, drug response, and genetic mutation data across different types of tumors using based on The Cancer Genome Atlas, Gene Expression Omnibus, and Oncomine database. Results: The results showed that the expression of the RUNX gene family varied among different cancer types, revealing its heterogeneity in cancers and that expression of RUNX2 was lower than that of RUNX1 and RUNX3 across all cancer types. RUNX gene family gene expression was related to prognosis in several cancers. Furthermore, our study revealed a clear association between RUNX gene family expression and ESTIMATE score, RNA stemness, and DNA stemness scores. Compared with RUNX1 and RUNX2, RUNX3 showed relatively low levels of genetic alterations. RUNX gene family genes had clear associations with immune infiltrate subtypes, and their expression was positively related to immune checkpoint genes and drug sensitivity in most cases. Two immunotherapy cohorts confirm that the expression of RUNX was correlated with the clinical response of immunotherapy. Conclusions: These findings will help to elucidate the potential oncogenic roles of RUNX gene family genes in different types of cancer and it can function as a prognostic marker in various malignant tumors.
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Affiliation(s)
- Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, Shanghai, China.,Laboratory of Myopia, NHC Key Laboratory of Myopia, Fudan University, Chinese Academy of Medical Sciences, Shanghai 200000, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, Shanghai, China
| | - Yun Chen
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Peijun Shen
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, Henan, China
| | - Lan Gong
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, Shanghai, China.,Laboratory of Myopia, NHC Key Laboratory of Myopia, Fudan University, Chinese Academy of Medical Sciences, Shanghai 200000, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, Shanghai, China
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8
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Menezes AC, Dixon C, Scholz A, Nicholson R, Leckenby A, Azevedo A, Baker S, Gilkes AF, Davies S, Darley RL, Tonks A. RUNX3 overexpression inhibits normal human erythroid development. Sci Rep 2022; 12:1243. [PMID: 35075235 PMCID: PMC8786893 DOI: 10.1038/s41598-022-05371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
RUNX proteins belong to a family of transcription factors essential for cellular proliferation, differentiation, and apoptosis with emerging data implicating RUNX3 in haematopoiesis and haematological malignancies. Here we show that RUNX3 plays an important regulatory role in normal human erythropoiesis. The impact of altering RUNX3 expression on erythropoiesis was determined by transducing human CD34+ cells with RUNX3 overexpression or shRNA knockdown vectors. Analysis of RUNX3 mRNA expression showed that RUNX3 levels decreased during erythropoiesis. Functionally, RUNX3 overexpression had a modest impact on early erythroid growth and development. However, in late-stage erythroid development, RUNX3 promoted growth and inhibited terminal differentiation with RUNX3 overexpressing cells exhibiting lower expression of glycophorin A, greater cell size and less differentiated morphology. These results suggest that suppression of RUNX3 is required for normal erythropoiesis. Overexpression of RUNX3 increased colony formation in liquid culture whilst, corresponding RUNX3 knockdown suppressed colony formation but otherwise had little impact. This study demonstrates that the downregulation of RUNX3 observed in normal human erythropoiesis is important in promoting the terminal stages of erythroid development and may further our understanding of the role of this transcription factor in haematological malignancies.
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Affiliation(s)
- Ana Catarina Menezes
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Christabel Dixon
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Anna Scholz
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Rachael Nicholson
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Adam Leckenby
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Aleksandra Azevedo
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Sarah Baker
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK.,Cardiff Experimental Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Amanda F Gilkes
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK.,Cardiff Experimental Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sara Davies
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Richard L Darley
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Alex Tonks
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK.
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9
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Yokomizo-Nakano T, Sashida G. Two faces of RUNX3 in myeloid transformation. Exp Hematol 2021; 97:14-20. [PMID: 33600870 DOI: 10.1016/j.exphem.2021.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/01/2021] [Accepted: 02/10/2021] [Indexed: 01/09/2023]
Abstract
RUNX3, a transcription factor, has been implicated as a tumor suppressor in various cancers, including hematological malignancies; however, recent studies revealed an oncogenic function of RUNX3 in the pathogenesis of myeloid malignancies, such as myelodysplastic syndrome and acute myeloid leukemia. In contrast to the high frequency of mutations in the RUNX1 gene, deletion of and loss-of-function mutations in RUNX3 are rarely detected in patients with hematopoietic malignancies. Although RUNX3 is expressed in normal hematopoietic stem and progenitor cells, its expression decreases with aging in humans. The loss of Runx3 did not result in the development of lethal hematological diseases in mice despite the expansion of myeloid cells. Therefore, RUNX3 does not appear to initiate the transformation of normal hematopoietic stem cells. However, the overexpression of RUNX3 inhibits the expression and transcriptional function of the RUNX1 gene, but activates the expression of key oncogenic pathways, such as MYC, resulting in the transformation of premalignant stem cells harboring a driver genetic mutation. We herein discuss the mechanisms by which RUNX3 is activated and how RUNX3 exerts oncogenic effects on the cellular function of and transcriptional program in premalignant stem cells to drive myeloid transformation.
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Affiliation(s)
- Takako Yokomizo-Nakano
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
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10
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Dybska E, Adams AT, Duclaux-Loras R, Walkowiak J, Nowak JK. Waiting in the wings: RUNX3 reveals hidden depths of immune regulation with potential implications for inflammatory bowel disease. Scand J Immunol 2021; 93:e13025. [PMID: 33528856 DOI: 10.1111/sji.13025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Complex interactions between the environment and the mucosal immune system underlie inflammatory bowel disease (IBD). The involved cytokine signalling pathways are modulated by a number of transcription factors, one of which is runt-related transcription factor 3 (RUNX3). OBJECTIVE To systematically review the immune roles of RUNX3 in immune regulation, with a focus on the context of IBD. METHODS Relevant articles and reviews were identified through a Scopus search in April 2020. Information was categorized by immune cell types, analysed and synthesized. IBD transcriptome data sets and FANTOM5 regulatory networks were processed in order to complement the literature review. RESULTS The available evidence on the immune roles of RUNX3 allowed for its description in twelve cell types: intraepithelial lymphocyte, Th1, Th2, Th17, Treg, double-positive T, cytotoxic T, B, dendritic, innate lymphoid, natural killer and macrophages. In the gut, the activity of RUNX3 is multifaceted and context-dependent: it may promote homeostasis or exacerbated reactions via cytokine signalling and regulation of receptor expression. RUNX3 is mostly engaged in pathways involving ThPOK, T-bet, IFN-γ, TGF-β/IL-2Rβ, GATA/CBF-β, SMAD/p300 and a number of miRNAs. RUNX3 targets relevant to IBD may include RAG1, OSM and IL-17B. Moreover, in IBD RUNX3 expression correlates positively with GZMM, and negatively with IFNAR1, whereas in controls, it strongly associates with TGFBR3. CONCLUSIONS Dysregulation of RUNX3, mostly in the form of deficiency, likely contributes to IBD pathogenesis. More clinical research is needed to examine RUNX3 in IBD.
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Affiliation(s)
- Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Rémi Duclaux-Loras
- INSERM U1111, Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Lyon, France
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
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11
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Mevel R, Draper JE, Lie-A-Ling M, Kouskoff V, Lacaud G. RUNX transcription factors: orchestrators of development. Development 2019; 146:dev148296. [PMID: 31488508 DOI: 10.1242/dev.148296] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RUNX transcription factors orchestrate many different aspects of biology, including basic cellular and developmental processes, stem cell biology and tumorigenesis. In this Primer, we introduce the molecular hallmarks of the three mammalian RUNX genes, RUNX1, RUNX2 and RUNX3, and discuss the regulation of their activities and their mechanisms of action. We then review their crucial roles in the specification and maintenance of a wide array of tissues during embryonic development and adult homeostasis.
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Affiliation(s)
- Renaud Mevel
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
| | - Julia E Draper
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
| | - Michael Lie-A-Ling
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
| | - Valerie Kouskoff
- Division of Developmental Biology & Medicine, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Georges Lacaud
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
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12
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Wang J, Van Den Berg D, Hwang AE, Weisenberger D, Triche T, Nathwani BN, Conti DV, Siegmund K, Mack TM, Horvath S, Cozen W. DNA methylation patterns of adult survivors of adolescent/young adult Hodgkin lymphoma compared to their unaffected monozygotic twin. Leuk Lymphoma 2019; 60:1429-1437. [PMID: 30668190 DOI: 10.1080/10428194.2018.1533128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA methylation (DNAm) silences gene expression and may play a role in immune dysregulation that is characteristic of adolescent/young adult Hodgkin lymphoma (AYAHL). We used the Infinium HumanMethylation27 BeadChip to quantify DNAm in blood (N = 9 pairs, mean age 57.4 y) or saliva (N = 36 pairs, mean age 50.0 y) from long-term AYAHL survivors and their unaffected co-twins. Epigenetic aging (DNAm age) was calculated using previously described methods and compared between survivors and co-twins using paired t-tests and analyses were stratified by sample type, histology, sex, age at sample collection and time since diagnosis. Differences in blood DNAm age were observed between survivors and unaffected co-twins (64.1 vs. 61.3 years, respectively, p = .04), especially in females (p = .01); no differences in saliva DNAm age were observed. Survivors and co-twins had 74 (in blood DNA) and 6 (in saliva DNA) differentially methylated loci. Our results suggest persistent epigenetic aging in AYAHL survivors long after HL cure.
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Affiliation(s)
- Jun Wang
- a Department of Preventive Medicine , University of Southern California , Los Angeles , CA , USA
| | - David Van Den Berg
- a Department of Preventive Medicine , University of Southern California , Los Angeles , CA , USA
| | - Amie E Hwang
- a Department of Preventive Medicine , University of Southern California , Los Angeles , CA , USA
| | - Daniel Weisenberger
- b Norris Comprehensive Cancer Center , University of Southern California , Los Angeles , CA , USA
| | - Timothy Triche
- c Department of Translational Genomics , University of Southern California , Los Angeles , CA , USA.,d Center for Epigenetics, Van Andel Research Institute , Grand Rapids , MI , USA
| | - Bharat N Nathwani
- e Department of Pathology , City of Hope National Medical Center , Duarte , CA , USA
| | - David V Conti
- a Department of Preventive Medicine , University of Southern California , Los Angeles , CA , USA
| | - Kim Siegmund
- a Department of Preventive Medicine , University of Southern California , Los Angeles , CA , USA
| | - Thomas M Mack
- a Department of Preventive Medicine , University of Southern California , Los Angeles , CA , USA.,f Department of Pathology , University of Southern California , Los Angeles , CA , USA
| | - Steve Horvath
- g Department of Biostatistics , University of California at Los Angeles , Los Angeles , CA , USA
| | - Wendy Cozen
- a Department of Preventive Medicine , University of Southern California , Los Angeles , CA , USA.,f Department of Pathology , University of Southern California , Los Angeles , CA , USA
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13
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Leung A, Trac C, Kato H, Costello KR, Chen Z, Natarajan R, Schones DE. LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome. Genome Res 2018; 28:1791-1798. [PMID: 30381291 PMCID: PMC6280761 DOI: 10.1101/gr.233585.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 10/24/2018] [Indexed: 12/13/2022]
Abstract
Endogenous retroviruses (ERVs) are ancient viral elements that have accumulated in the genome through retrotransposition events. Although they have lost their ability to transpose, many of the long terminal repeats (LTRs) that originally flanked full-length ERVs maintain the ability to regulate transcription. While these elements are typically repressed in somatic cells, they can function as transcriptional enhancers and promoters when this repression is lost. Epstein-Barr virus (EBV), which transforms primary B cells into continuously proliferating cells, is a tumor virus associated with lymphomas. We report here that transformation of primary B cells by EBV leads to genome-wide activation of LTR enhancers and promoters. The activation of LTRs coincides with local DNA hypomethylation and binding by transcription factors such as RUNX3, EBF1, and EBNA2. The set of activated LTRs is unique to transformed B cells compared with other cell lines known to have activated LTRs. Furthermore, we found that LTR activation impacts the B cell transcriptome by up-regulating transcripts driven by cryptic LTR promoters. These transcripts include genes important to oncogenesis of Hodgkin lymphoma and other cancers, such as HUWE1/HECTH9 These data suggest that the activation of LTRs by EBV-induced transformation is important to the pathology of EBV-associated cancers. Altogether, our results indicate that EBV-induced transformation of B cells alters endogenous retroviral element activity, thereby impacting host gene regulatory networks and oncogenic potential.
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Affiliation(s)
- Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Candi Trac
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Hiroyuki Kato
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Kevin R Costello
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
| | - Zhaoxia Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
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14
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Martínez-Bueno M, Oparina N, Dozmorov MG, Marion MC, Comeau ME, Gilkeson G, Kamen D, Weisman M, Salmon J, McCune JW, Harley JB, Kimberly R, James JA, Merrill J, Montgomery C, Langefeld CD, Alarcón-Riquelme ME. Trans-Ethnic Mapping of BANK1 Identifies Two Independent SLE-Risk Linkage Groups Enriched for Co-Transcriptional Splicing Marks. Int J Mol Sci 2018; 19:ijms19082331. [PMID: 30096841 PMCID: PMC6121630 DOI: 10.3390/ijms19082331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 11/17/2022] Open
Abstract
BANK1 is a susceptibility gene for several systemic autoimmune diseases in several populations. Using the genome-wide association study (GWAS) data from Europeans (EUR) and African Americans (AA), we performed an extensive fine mapping of ankyrin repeats 1 (BANK1). To increase the SNP density, we used imputation followed by univariate and conditional analysis, combined with a haplotypic and expression quantitative trait locus (eQTL) analysis. The data from Europeans showed that the associated region was restricted to a minimal and dependent set of SNPs covering introns two and three, and exon two. In AA, the signal found in the Europeans was split into two independent effects. All of the major risk associated SNPs were eQTLs, and the risks were associated with an increased BANK1 gene expression. Functional annotation analysis revealed the enrichment of repressive B cell epigenomic marks (EZH2 and H3K27me3) and a strong enrichment of splice junctions. Furthermore, one eQTL located in intron two, rs13106926, was found within the binding site for RUNX3, a transcriptional activator. These results connect the local genome topography, chromatin structure, and the regulatory landscape of BANK1 with co-transcriptional splicing of exon two. Our data defines a minimal set of risk associated eQTLs predicted to be involved in the expression of BANK1 modulated through epigenetic regulation and splicing. These findings allow us to suggest that the increased expression of BANK1 will have an impact on B-cell mediated disease pathways.
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Affiliation(s)
- Manuel Martínez-Bueno
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Government, PTS, 18016 Granada, Spain.
| | - Nina Oparina
- Unit of Chronic Inflammatory Diseases, Institute for Environmental Medicine, Karolinska Institutet, 171 67 Solna, Sweden.
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Miranda C Marion
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Mary E Comeau
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Gary Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Diane Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Michael Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Jane Salmon
- Hospital for Special Surgery, New York, NY 10021, USA.
| | - Joseph W McCune
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, OH and US Department of Veterans Affairs Medical Center, Cincinnati, OH 45229, USA.
| | - Robert Kimberly
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35205, USA.
| | - Judith A James
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
| | - Joan Merrill
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
| | - Courtney Montgomery
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Marta E Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Government, PTS, 18016 Granada, Spain.
- Unit of Chronic Inflammatory Diseases, Institute for Environmental Medicine, Karolinska Institutet, 171 67 Solna, Sweden.
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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15
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Sud A, Thomsen H, Law PJ, Försti A, Filho MIDS, Holroyd A, Broderick P, Orlando G, Lenive O, Wright L, Cooke R, Easton D, Pharoah P, Dunning A, Peto J, Canzian F, Eeles R, Kote-Jarai ZS, Muir K, Pashayan N, Hoffmann P, Nöthen MM, Jöckel KH, Strandmann EPV, Lightfoot T, Kane E, Roman E, Lake A, Montgomery D, Jarrett RF, Swerdlow AJ, Engert A, Orr N, Hemminki K, Houlston RS. Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility. Nat Commun 2017; 8:1892. [PMID: 29196614 PMCID: PMC5711884 DOI: 10.1038/s41467-017-00320-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/20/2017] [Indexed: 02/08/2023] Open
Abstract
Several susceptibility loci for classical Hodgkin lymphoma have been reported. However, much of the heritable risk is unknown. Here, we perform a meta-analysis of two existing genome-wide association studies, a new genome-wide association study, and replication totalling 5,314 cases and 16,749 controls. We identify risk loci for all classical Hodgkin lymphoma at 6q22.33 (rs9482849, P = 1.52 × 10-8) and for nodular sclerosis Hodgkin lymphoma at 3q28 (rs4459895, P = 9.43 × 10-17), 6q23.3 (rs6928977, P = 4.62 × 10-11), 10p14 (rs3781093, P = 9.49 × 10-13), 13q34 (rs112998813, P = 4.58 × 10-8) and 16p13.13 (rs34972832, P = 2.12 × 10-8). Additionally, independent loci within the HLA region are observed for nodular sclerosis Hodgkin lymphoma (rs9269081, HLA-DPB1*03:01, Val86 in HLA-DRB1) and mixed cellularity Hodgkin lymphoma (rs1633096, rs13196329, Val86 in HLA-DRB1). The new and established risk loci localise to areas of active chromatin and show an over-representation of transcription factor binding for determinants of B-cell development and immune response.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Lauren Wright
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SM2 5NG, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M1 3BB, UK
- Division of Health Sciences, Warwick Medical School, Warwick University, Warwick, CV4 7AL, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Per Hoffmann
- Department of Biomedicine, Division of Medical Genetics, University of Basel, Basel, 4031, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | | | | | - Tracy Lightfoot
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Annette Lake
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Dorothy Montgomery
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Ruth F Jarrett
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, 50937, Germany
| | - Nick Orr
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK.
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16
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Ryan RJH, Petrovic J, Rausch DM, Zhou Y, Lareau CA, Kluk MJ, Christie AL, Lee WY, Tarjan DR, Guo B, Donohue LKH, Gillespie SM, Nardi V, Hochberg EP, Blacklow SC, Weinstock DM, Faryabi RB, Bernstein BE, Aster JC, Pear WS. A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Rep 2017; 21:784-797. [PMID: 29045844 PMCID: PMC5687286 DOI: 10.1016/j.celrep.2017.09.066] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/26/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022] Open
Abstract
Gain-of-function Notch mutations are recurrent in mature small B cell lymphomas such as mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL), but the Notch target genes that contribute to B cell oncogenesis are largely unknown. We performed integrative analysis of Notch-regulated transcripts, genomic binding of Notch transcription complexes, and genome conformation data to identify direct Notch target genes in MCL cell lines. This B cell Notch regulome is largely controlled through Notch-bound distal enhancers and includes genes involved in B cell receptor and cytokine signaling and the oncogene MYC, which sustains proliferation of Notch-dependent MCL cell lines via a Notch-regulated lineage-restricted enhancer complex. Expression of direct Notch target genes is associated with Notch activity in an MCL xenograft model and in CLL lymph node biopsies. Our findings provide key insights into the role of Notch in MCL and other B cell malignancies and have important implications for therapeutic targeting of Notch-dependent oncogenic pathways.
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Affiliation(s)
- Russell J H Ryan
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dylan M Rausch
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caleb A Lareau
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Michael J Kluk
- Department of Pathology, Weill Cornell School of Medicine, New York, NY 10065, USA
| | - Amanda L Christie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Winston Y Lee
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Daniel R Tarjan
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Bingqian Guo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Laura K H Donohue
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Shawn M Gillespie
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ephraim P Hochberg
- Department of Medicine, MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02140, USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Chromatin reorganisation in Epstein-Barr virus-infected cells and its role in cancer development. Curr Opin Virol 2017; 26:149-155. [DOI: 10.1016/j.coviro.2017.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/07/2017] [Accepted: 08/17/2017] [Indexed: 11/23/2022]
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18
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Chen JB, Zhang J, Hu HZ, Xue M, Jin YJ. Polymorphisms of TGFB1, TLE4 and MUC22 are associated with childhood asthma in Chinese population. Allergol Immunopathol (Madr) 2017; 45:432-438. [PMID: 28262390 DOI: 10.1016/j.aller.2016.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/31/2016] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To investigate whether the genetic variants of TGFB1, TLE4, MUC22 and IKZF3 are associated with the development of asthma in Chinese children. METHODS 572 adolescent asthma patients and 590 age-matched healthy controls were included in this study. A total of four SNPs were genotyped, including rs2241715 of TGFB1, rs2378383 of TLE4, rs2523924 of MUC22, and rs907092 of IKZF3. Allele frequencies of the patients and the control group were compared by the Chi-square test. The Student t test was used to analyse the relationship between genotypes and clinical feature of the patients. RESULTS Patients were found to have significantly different frequencies of allele A of rs2241715, allele G of rs2378383 and allele A of rs2523924 as compared with the controls (40.4% vs. 45.9%, p=0.01 for rs2241715; 17.2% vs. 13.4%, p=0.01 for rs2378383; 15.3% vs. 11.9%, p=0.02 for rs2523924). For patients with severe asthma, those with genotype AA/AG of rs2241715 had remarkably higher FEV1% as compared with those with genotype GG (59.1±4.3% vs. 55.4±3.7%, p<0.001). Moreover, those with genotype GG/GA of rs2378383 had remarkably lower FEV1% as compared with those with genotype AA (54.6±2.9% vs. 58.6±4.1%, p<0.001). CONCLUSIONS Genes TGFB1, TLE4 and MUC22 are associated with the risk of childhood asthma in Chinese population. Our results associating TGFB1 and TLE4 with clinical features of asthma suggest potential application of these parameters in the management of asthma children.
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Affiliation(s)
- J B Chen
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - J Zhang
- Department of Gastroenterology, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - H Z Hu
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - M Xue
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - Y J Jin
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China.
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Paschos K, Bazot Q, Ho G, Parker GA, Lees J, Barton G, Allday MJ. Core binding factor (CBF) is required for Epstein-Barr virus EBNA3 proteins to regulate target gene expression. Nucleic Acids Res 2017; 45:2368-2383. [PMID: 27903901 PMCID: PMC5389572 DOI: 10.1093/nar/gkw1167] [Citation(s) in RCA: 14] [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: 08/02/2016] [Revised: 10/14/2016] [Accepted: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
ChIP-seq performed on lymphoblastoid cell lines (LCLs), expressing epitope-tagged EBNA3A, EBNA3B or EBNA3C from EBV-recombinants, revealed important principles of EBNA3 binding to chromatin. When combined with global chromatin looping data, EBNA3-bound loci were found to have a singular character, each directly associating with either EBNA3-repressed or EBNA3-activated genes, but not with both. EBNA3A and EBNA3C showed significant association with repressed and activated genes. Significant direct association for EBNA3B loci could only be shown with EBNA3B-repressed genes. A comparison of EBNA3 binding sites with known transcription factor binding sites in LCL GM12878 revealed substantial co-localization of EBNA3s with RUNX3-a protein induced by EBV during B cell transformation. The beta-subunit of core binding factor (CBFβ), that heterodimerizes with RUNX3, could co-immunoprecipitate robustly EBNA3B and EBNA3C, but only weakly EBNA3A. Depletion of either RUNX3 or CBFβ with lentivirus-delivered shRNA impaired epitope-tagged EBNA3B and EBNA3C binding at multiple regulated gene loci, indicating a requirement for CBF heterodimers in EBNA3 recruitment during target-gene regulation. ShRNA-mediated depletion of CBFβ in an EBNA3C-conditional LCL confirmed the role of CBF in the regulation of EBNA3C-induced and -repressed genes. These results reveal an important role for RUNX3/CBF during B cell transformation and EBV latency that was hitherto unexplored.
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Affiliation(s)
- Kostas Paschos
- Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Quentin Bazot
- Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Guiyi Ho
- Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Gillian A. Parker
- Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Jonathan Lees
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Geraint Barton
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK
| | - Martin J. Allday
- Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK
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20
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West MJ, Farrell PJ. Roles of RUNX in B Cell Immortalisation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:283-298. [PMID: 28299664 DOI: 10.1007/978-981-10-3233-2_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RUNX1 and RUNX3 are the main RUNX genes expressed in B lymphocytes. Both are expressed throughout B-cell development and play key roles at certain key developmental transitions. The tumour-associated Epstein-Barr virus (EBV) has potent B-cell transforming ability and manipulates RUNX3 and RUNX1 transcription through novel mechanisms to control B cell growth. In contrast to resting mature B cells where RUNX1 expression is high, in EBV-infected cells RUNX1 levels are low and RUNX3 levels are high. Downregulation of RUNX1 in these cells results from cross-regulation by RUNX3 and serves to relieve RUNX1-mediated growth repression. RUNX3 is upregulated by the EBV transcription factor (TF) EBNA2 and represses RUNX1 transcription through RUNX sites in the RUNX1 P1 promoter. Recent analysis revealed that EBNA2 activates RUNX3 transcription through an 18 kb upstream super-enhancer in a manner dependent on the EBNA2 and Notch DNA-binding partner RBP-J. This super-enhancer also directs RUNX3 activation by two further RBP-J-associated EBV TFs, EBNA3B and 3C. Counter-intuitively, EBNA2 also hijacks RBP-J to target a super-enhancer region upstream of RUNX1 to maintain some RUNX1 expression in certain cell backgrounds, although the dual functioning EBNA3B and 3C proteins limit this activation. Interestingly, the B-cell genome binding sites of EBV TFs overlap extensively with RUNX3 binding sites and show enrichment for RUNX motifs. Therefore in addition to B-cell growth manipulation through the long-range control of RUNX transcription, EBV may also use RUNX proteins as co-factors to deregulate the transcription of many B cell genes during immortalisation.
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Affiliation(s)
- Michelle J West
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK.
| | - Paul J Farrell
- Section of Virology, Faculty of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK
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Abstract
In this chapter we summarize the pros and cons of the notion that Runx3 is a major tumor suppressor gene (TSG). Inactivation of TSGs in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago it was suggested that RUNX3 is involved in gastric cancer development, a postulate extended later to other epithelial cancers portraying RUNX3 as a major TSG. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. In contrast, RUNX3 is overexpressed in a significant fraction of tumor cells in various human epithelial cancers and its overexpression in pancreatic cancer cells promotes their migration, anchorage-independent growth and metastatic potential. Moreover, recent high-throughput quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models have unequivocally demonstrated that RUNX3 is not a bona fide cell-autonomous TSG. Importantly, accumulating data demonstrated that RUNX3 functions in control of immunity and inflammation, thereby indirectly influencing epithelial tumor development.
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Neil JC, Gilroy K, Borland G, Hay J, Terry A, Kilbey A. The RUNX Genes as Conditional Oncogenes: Insights from Retroviral Targeting and Mouse Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:247-264. [PMID: 28299662 DOI: 10.1007/978-981-10-3233-2_16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The observation that the Runx genes act as targets for transcriptional activation by retroviral insertion identified a new family of dominant oncogenes. However, it is now clear that Runx genes are 'conditional' oncogenes whose over-expression is growth inhibitory unless accompanied by another event such as concomitant over-expression of MYC or loss of p53 function. Remarkably, while the oncogenic activities of either MYC or RUNX over-expression are suppressed while p53 is intact, the combination of both neutralises p53 tumour suppression in vivo by as yet unknown mechanisms. Moreover, there is emerging evidence that endogenous, basal RUNX activity is important to maintain the viability and proliferation of MYC-driven lymphoma cells. There is also growing evidence that the human RUNX genes play a similar conditional oncogenic role and are selected for over-expression in end-stage cancers of multiple types. Paradoxically, reduced RUNX activity can also predispose to cell immortalisation and transformation, particularly by mutant Ras. These apparently conflicting observations may be reconciled in a stage-specific model of RUNX involvement in cancer. A question that has yet to be fully addressed is the extent to which the three Runx genes are functionally redundant in cancer promotion and suppression.
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Affiliation(s)
- James C Neil
- Molecular Oncology Laboratory, Centre for Virus Research, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK.
| | - Kathryn Gilroy
- Molecular Oncology Laboratory, Centre for Virus Research, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Gillian Borland
- Molecular Oncology Laboratory, Centre for Virus Research, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Jodie Hay
- Molecular Oncology Laboratory, Centre for Virus Research, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Anne Terry
- Molecular Oncology Laboratory, Centre for Virus Research, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Anna Kilbey
- Molecular Oncology Laboratory, Centre for Virus Research, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
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Voon DCC, Hor YT, Ito Y. The RUNX complex: reaching beyond haematopoiesis into immunity. Immunology 2015; 146:523-36. [PMID: 26399680 DOI: 10.1111/imm.12535] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/13/2015] [Accepted: 07/15/2015] [Indexed: 12/24/2022] Open
Abstract
Among their diverse roles as transcriptional regulators during development and cell fate specification, the RUNX transcription factors are best known for the parts they play in haematopoiesis. RUNX proteins are expressed throughout all haematopoietic lineages, being necessary for the emergence of the first haematopoietic stem cells to their terminal differentiation. Although much progress has been made since their discoveries almost two decades ago, current appreciation of RUNX in haematopoiesis is largely grounded in their lineage-specifying roles. In contrast, the importance of RUNX to immunity has been mostly obscured for historic, technical and conceptual reasons. However, this paradigm is likely to shift over time, as a primary purpose of haematopoiesis is to resource the immune system. Furthermore, recent evidence suggests a role for RUNX in the innate immunity of non-haematopoietic cells. This review takes a haematopoiesis-centric approach to collate what is known of RUNX's contribution to the overall mammalian immune system and discuss their growing prominence in areas such as autoimmunity, inflammatory diseases and mucosal immunity.
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Affiliation(s)
- Dominic Chih-Cheng Voon
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan.,Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | | | - Yoshiaki Ito
- Cancer Biology Programme, Cancer Science Institute of Singapore, Singapore
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Estécio MRH, Maddipoti S, Bueso-Ramos C, DiNardo CD, Yang H, Wei Y, Kondo K, Fang Z, Stevenson W, Chang KS, Pierce SA, Bohannan Z, Borthakur G, Kantarjian H, Garcia-Manero G. RUNX3 promoter hypermethylation is frequent in leukaemia cell lines and associated with acute myeloid leukaemia inv(16) subtype. Br J Haematol 2015; 169:344-51. [PMID: 25612675 DOI: 10.1111/bjh.13299] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/08/2014] [Indexed: 01/15/2023]
Abstract
Correlative and functional studies support the involvement of the RUNX gene family in haematological malignancies. To elucidate the role of epigenetics in RUNX inactivation, we evaluated promoter DNA methylation of RUNX1, 2, and 3 in 23 leukaemia cell lines and samples from acute myeloid leukaemia (AML), acute lymphocytic leukaemia (ALL) and myelodysplatic syndromes (MDS) patients. RUNX1 and RUNX2 gene promoters were mostly unmethylated in cell lines and clinical samples. Hypermethylation of RUNX3 was frequent among cell lines (74%) and highly variable among patient samples, with clear association to cytogenetic status. High frequency of RUNX3 hypermethylation (85% of the 20 studied cases) was found in AML patients with inv(16)(p13.1q22) compared to other AML subtypes (31% of the other 49 cases). RUNX3 hypermethylation was also frequent in ALL (100% of the six cases) but low in MDS (21%). In support of a functional role, hypermethylation of RUNX3 was correlated with low levels of protein, and treatment of cell lines with the DNA demethylating agent, decitabine, resulted in mRNA re-expression. Furthermore, relapse-free survival of non-inv(16)(p13.1q22) AML patients without RUNX3 methylation was significantly better (P = 0·016) than that of methylated cases. These results suggest that RUNX3 silencing is an important event in inv(16)(p13.1q22) leukaemias.
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Affiliation(s)
- Marcos R H Estécio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Abstract
B cell maturation antigen (BCMA) is a tumor necrosis family receptor (TNFR) member that is predominantly expressed on terminally differentiated B cells and, upon binding to its ligands B cell activator of the TNF family (BAFF) and a proliferation inducing ligand (APRIL), delivers pro-survival cell signals. Thus, BCMA is mostly known for its functional activity in mediating the survival of plasma cells that maintain long-term humoral immunity. The expression of BCMA has also been linked to a number of cancers, autoimmune disorders, and infectious diseases that suggest additional roles for BCMA activity. Despite recent advances in our understanding of the roles for the related TNFR members BAFF-R and transmembrane activator and calcium-modulator and cyclophilin ligand interactor (TACI), the signaling pathway used by BCMA for mediating plasma cell survival as well as its putative function in certain disease states are not well understood. By examining the expression, regulation, and signaling targets of BCMA, we may gain further insight into this receptor and how it operates within cells in both health and disease. This information is important for identifying new therapeutic targets that may be relevant in treating diseases that involve the BAFF/APRIL cytokine network.
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Affiliation(s)
- Christine M Coquery
- Department of Microbiology, Immunology, & Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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26
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Chimge NO, Frenkel B. The RUNX family in breast cancer: relationships with estrogen signaling. Oncogene 2013; 32:2121-30. [PMID: 23045283 PMCID: PMC5770236 DOI: 10.1038/onc.2012.328] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/20/2012] [Accepted: 06/20/2012] [Indexed: 12/22/2022]
Abstract
The three RUNX family members are lineage specific master regulators, which also have important, context-dependent roles in carcinogenesis as either tumor suppressors or oncogenes. Here we review evidence for such roles in breast cancer (BCa). RUNX1, the predominant RUNX family member in breast epithelial cells, has a tumor suppressor role reflected by many somatic mutations found in primary tumor biopsies. The classical tumor suppressor gene RUNX3 does not consist of such a mutation hot spot, but it too seems to inhibit BCa; it is often inactivated in human BCa tumors and its haploinsufficiency in mice leads to spontaneous BCa development. The tumor suppressor activities of RUNX1 and RUNX3 are mediated in part by antagonism of estrogen signaling, a feature recently attributed to RUNX2 as well. Paradoxically, however RUNX2, a master osteoblast regulator, has been implicated in various aspects of metastasis in general and bone metastasis in particular. Reciprocating the anti-estrogenic tumor suppressor activity of RUNX proteins, inhibition of RUNX2 by estrogens may help explain their context-dependent anti-metastatic roles. Such roles are reserved to non-osseous metastasis, because ERα is associated with increased, not decreased skeletal dissemination of BCa cells. Finally, based on diverse expression patterns in BCa subtypes, the successful use of future RUNX-based therapies will most likely require careful patient selection.
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Affiliation(s)
- N-O Chimge
- Department of Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - B Frenkel
- Departments of Orthopaedic Surgery and Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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Lotem J, Levanon D, Negreanu V, Groner Y. The False Paradigm of RUNX3 Function as Tumor Suppressor in Gastric Cancer. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jct.2013.41a003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Chuang LSH, Ito K, Ito Y. RUNX family: Regulation and diversification of roles through interacting proteins. Int J Cancer 2012. [PMID: 23180629 DOI: 10.1002/ijc.27964] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Runt-related transcription factors (RUNX) belong to an ancient family of metazoan genes involved in developmental processes. Through multiple protein-interacting partners, RUNX proteins have been implicated in diverse signaling pathways and cellular processes. The frequent inactivation of RUNX genes in cancer indicates crucial roles for RUNX in tumor suppression. This review discusses the abilities of RUNX proteins, in particular RUNX3, to integrate oncogenic signals or environmental cues and to initiate appropriate tumor suppressive responses.
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Brady G, Elgueta Karstegl C, Farrell PJ. Novel function of the unique N-terminal region of RUNX1c in B cell growth regulation. Nucleic Acids Res 2012; 41:1555-68. [PMID: 23254331 PMCID: PMC3561965 DOI: 10.1093/nar/gks1273] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RUNX family proteins are expressed from alternate promoters, giving rise to different N-terminal forms, but the functional difference of these isoforms is not understood. Here, we show that growth of a human B lymphoblastoid cell line infected with Epstein-Barr virus is inhibited by RUNX1c but not by RUNX1b. This gives a novel functional assay for the unique N-terminus of RUNX1c, and amino acids of RUNX1c required for the effect have been identified. Primary resting B cells contain RUNX1c, consistent with the growth inhibitory effect in B cells. The oncogene TEL-RUNX1 lacks the N-terminus of RUNX1c because of the TEL fusion and does not inhibit B cell growth. Mouse Runx1c lacks some of the sequences required for human RUNX1c to inhibit B cell growth, indicating that this aspect of human B cell growth control may differ in mice. Remarkably, a cell-penetrating peptide containing the N-terminal sequence of RUNX1c specifically antagonizes the growth inhibitory effect in B lymphoblastoid cells and might be used to modulate the function of human RUNX1c.
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Affiliation(s)
- Gareth Brady
- Section of Virology, Imperial College Faculty of Medicine, Norfolk Place, London W2 1PG, UK
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Park ES, Park J, Franceschi RT, Jo M. The role for runt related transcription factor 2 (RUNX2) as a transcriptional repressor in luteinizing granulosa cells. Mol Cell Endocrinol 2012; 362:165-75. [PMID: 22713854 PMCID: PMC3864655 DOI: 10.1016/j.mce.2012.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 05/08/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
Abstract
Transcription factors induced by the LH surge play a vital role in reprogramming the gene expression in periovulatory follicles. The present study investigated the role of RUNX2 transcription factor in regulating the expression of Runx1, Ptgs2, and Tnfaip6 using cultured granulosa cells isolated from PMSG-primed immature rats. hCG or forskolin+PMA induced the transient increase in Runx1, Ptgs2, and Tnfaip6 expression, while the expression of Runx2 continued to increase until 48 h. The knockdown of the agonist-stimulated Runx2 expression increased Runx1, Ptgs2, and Tnfaip6 expression and PGE(2) levels in luteinizing granulosa cells. Conversely, the over-expression of RUNX2 inhibited the expression of these genes and PGE(2) levels. The mutation of RUNX binding motifs in the Runx1 promoter enhanced transcriptional activity of the Runx1 promoter. The knockdown and overexpression of Runx2 increased and decreased Runx1 promoter activity, respectively. ChIP assays revealed the binding of RUNX2 in the Runx1 and Ptgs2 promoters. Together, these novel findings provide support for the role of RUNX2 in down-regulation of Runx1, Ptgs2, and Tnfaip6 during the late ovulatory period to support proper ovulation and/or luteinization.
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Affiliation(s)
- Eun-Sil Park
- Department of Obstetrics and Gynecology, Chandler Medical Center, University of Kentucky, Lexington, Kentucky 40536-0298, USA
- Department of Molecular and Biomedical Pharmacology, Chandler Medical Center, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Jiyeon Park
- Department of Obstetrics and Gynecology, Chandler Medical Center, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Renny T. Franceschi
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, 1011N University Ave. Ann Arbor, MI 48109-1078, USA
- Department of Biological Chemistry, School of Medicine, University of Michigan, 1011N University Ave. Ann Arbor, MI 48109-1078, USA
| | - Misung Jo
- Department of Obstetrics and Gynecology, Chandler Medical Center, University of Kentucky, Lexington, Kentucky 40536-0298, USA
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Varshney B, Agnihotram S, Tan YJ, Baric R, Lal SK. SARS coronavirus 3b accessory protein modulates transcriptional activity of RUNX1b. PLoS One 2012; 7:e29542. [PMID: 22253733 PMCID: PMC3257236 DOI: 10.1371/journal.pone.0029542] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/30/2011] [Indexed: 12/12/2022] Open
Abstract
Background The causative agent of severe acute respiratory syndrome, SARS coronavirus (SARS-CoV) genome encodes several unique group specific accessory proteins with unknown functions. Among them, accessory protein 3b (also known as ORF4) was lately identified as one of the viral interferon antagonist. Recently our lab uncovered a new role for 3b in upregulation of AP-1 transcriptional activity and its downstream genes. Thus, we believe that 3b might play an important role in SARS-CoV pathogenesis and therefore is of considerable interest. The current study aims at identifying novel host cellular interactors of the 3b protein. Methodology/Principal Findings In this study, using yeast two-hybrid and co-immunoprecipitation techniques, we have identified a host transcription factor RUNX1b (Runt related transcription factor, isoform b) as a novel interacting partner for SARS-CoV 3b protein. Chromatin immunoprecipitaion (ChIP) and reporter gene assays in 3b expressing jurkat cells showed recruitment of 3b on the RUNX1 binding element that led to an increase in RUNX1b transactivation potential on the IL2 promoter. Kinase assay and pharmacological inhibitor treatment implied that 3b also affect RUNX1b transcriptional activity by regulating its ERK dependent phosphorylation levels. Additionally, mRNA levels of MIP-1α, a RUNX1b target gene upregulated in SARS-CoV infected monocyte-derived dendritic cells, were found to be elevated in 3b expressing U937 monocyte cells. Conclusions/Significance These results unveil a novel interaction of SARS-CoV 3b with the host factor, RUNX1b, and speculate its physiological relevance in upregulating cytokines and chemokine levels in state of SARS virus infection.
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Affiliation(s)
- Bhavna Varshney
- Virology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sudhakar Agnihotram
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yee-Joo Tan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sunil K. Lal
- Virology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- * E-mail:
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Upregulation of the cell-cycle regulator RGC-32 in Epstein-Barr virus-immortalized cells. PLoS One 2011; 6:e28638. [PMID: 22163048 PMCID: PMC3232240 DOI: 10.1371/journal.pone.0028638] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 11/11/2011] [Indexed: 12/19/2022] Open
Abstract
Epstein-Barr virus (EBV) is implicated in the pathogenesis of multiple human tumours of lymphoid and epithelial origin. The virus infects and immortalizes B cells establishing a persistent latent infection characterized by varying patterns of EBV latent gene expression (latency 0, I, II and III). The CDK1 activator, Response Gene to Complement-32 (RGC-32, C13ORF15), is overexpressed in colon, breast and ovarian cancer tissues and we have detected selective high-level RGC-32 protein expression in EBV-immortalized latency III cells. Significantly, we show that overexpression of RGC-32 in B cells is sufficient to disrupt G2 cell-cycle arrest consistent with activation of CDK1, implicating RGC-32 in the EBV transformation process. Surprisingly, RGC-32 mRNA is expressed at high levels in latency I Burkitt's lymphoma (BL) cells and in some EBV-negative BL cell-lines, although RGC-32 protein expression is not detectable. We show that RGC-32 mRNA expression is elevated in latency I cells due to transcriptional activation by high levels of the differentially expressed RUNX1c transcription factor. We found that proteosomal degradation or blocked cytoplasmic export of the RGC-32 message were not responsible for the lack of RGC-32 protein expression in latency I cells. Significantly, analysis of the ribosomal association of the RGC-32 mRNA in latency I and latency III cells revealed that RGC-32 transcripts were associated with multiple ribosomes in both cell-types implicating post-initiation translational repression mechanisms in the block to RGC-32 protein production in latency I cells. In summary, our results are the first to demonstrate RGC-32 protein upregulation in cells transformed by a human tumour virus and to identify post-initiation translational mechanisms as an expression control point for this key cell-cycle regulator.
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Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proc Natl Acad Sci U S A 2011; 108:14902-7. [PMID: 21746931 DOI: 10.1073/pnas.1108892108] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Epstein-Barr virus nuclear antigen 2 (EBNA2) regulation of transcription through the cell transcription factor RBPJ is essential for resting B-lymphocyte (RBL) conversion to immortal lymphoblast cell lines (LCLs). ChIP-seq of EBNA2 and RBPJ sites in LCL DNA found EBNA2 at 5,151 and RBPJ at 10,529 sites. EBNA2 sites were enriched for RBPJ (78%), early B-cell factor (EBF, 39%), RUNX (43%), ETS (39%), NFκB (22%), and PU.1 (22%) motifs. These motif associations were confirmed by LCL RBPJ ChIP-seq finding 72% RBPJ occupancy and Encyclopedia Of DNA Elements LCL ChIP-seq finding EBF, NFκB RELA, and PU.1 at 54%, 31%, and 17% of EBNA2 sites. EBNA2 and RBPJ were predominantly at intergene and intron sites and only 14% at promoter sites. K-means clustering of EBNA2 site transcription factors identified RELA-ETS, EBF-RUNX, EBF, ETS, RBPJ, and repressive RUNX clusters, which ranked from highest to lowest in H3K4me1 signals and nucleosome depletion, indicative of active chromatin. Surprisingly, although quantitatively less, the same genome sites in RBLs exhibited similar high-level H3K4me1 signals and nucleosome depletion. The EBV genome also had an LMP1 promoter EBF site, which proved critical for EBNA2 activation. LCL HiC data mapped intergenic EBNA2 sites to EBNA2 up-regulated genes. FISH and chromatin conformation capture linked EBNA2/RBPJ enhancers 428 kb 5' of MYC to MYC. These data indicate that EBNA2 evolved to target RBL H3K4me1 modified, nucleosome-depleted, nonpromoter sites to drive B-lymphocyte proliferation in primary human infection. The primed RBL program likely supports antigen-induced proliferation.
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Guo C, Ahmad T, Beckly J, Cummings JRF, Hancock L, Geremia A, Cooney R, Pathan S, Jewell DP. Association of caspase-9 and RUNX3 with inflammatory bowel disease. ACTA ACUST UNITED AC 2010; 77:23-9. [DOI: 10.1111/j.1399-0039.2010.01569.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Zhao F, Chen Y, Zeng L, Li R, Zeng R, Wen L, Liu Y, Zhang C. Role of triptolide in cell proliferation, cell cycle arrest, apoptosis and histone methylation in multiple myeloma U266 cells. Eur J Pharmacol 2010; 646:1-11. [PMID: 20547150 DOI: 10.1016/j.ejphar.2010.05.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 04/28/2010] [Accepted: 05/25/2010] [Indexed: 10/19/2022]
Abstract
Multiple myeloma is an incurable hematological malignancy. Different studies demonstrated the occurrence of genetic and epigenetic alterations in multiple myeloma. Histone lysine methylation has emerged as a central epigenetic change in the organization of eukaryotic chromatin with far-reaching implications for the regulation of cell proliferation, cell-type differentiation, gene expression, genome stability, overall development, and genesis of cancer. Triptolide is the principal active ingredient in extracts from the Chinese herb Tripterygium wilfordii Hook.F (TwHF), and numerous studies have elucidated its antitumor property. Our experiments discovered that triptolide inhibited the proliferation of multiple myeloma cell line U266 in a time- and dose-dependent manner, induced G2/M cell cycle arrest and caspase-dependent apoptosis. Triptolide could decrease the expression of histone H3K4, H3K27 and H3K36 trimethylation in parallel with histone methyltransferases SMYD3, EZH2 and NSD1 respectively, which possibly was the anti-myeloma mechanism of triptolide.
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Affiliation(s)
- Fei Zhao
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Chromatin immunoprecipitation and association study revealed a possible role of Runt-related transcription factor 3 in the ulcerative colitis of Chinese population. Clin Immunol 2010; 135:483-9. [PMID: 20392673 DOI: 10.1016/j.clim.2010.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 01/06/2023]
Abstract
RUNX3 was recently found to be associated with ulcerative colitis. In this study, downstream target genes of RUNX3 were identified by chromatin immunoprecipitation and promoter sequence microarray chips. Polymorphisms of RUNX3 and its 2 putative downstream (OCTN1 and PPAR-gamma) target genes were genotyped by PCR-SSP and sequencing in 144 Chinese UC patients and 151 healthy controls. Expression of RUNX3 in colonic mucosa of UC patients was detected by immunohistochemical staining. Twelve genes involved in IBD were identified as the downstream target genes of RUNX3. The RUNX3 rs2236851 CT genotype was associated significantly with UC susceptibility and risk of early onset in Chinese population. No association of OCTN1 and PPAR-gamma with UC susceptibility or subphenotypes was identified. RUNX3 expression was significantly increased in UC mucosa. Therefore, RUNX3 might be involved in UC pathogenesis by regulating the expression of genes related with immune response.
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Chuang LSH, Ito Y. RUNX3 is multifunctional in carcinogenesis of multiple solid tumors. Oncogene 2010; 29:2605-15. [DOI: 10.1038/onc.2010.88] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Zhao F, Chen Y, Li R, Liu Y, Wen L, Zhang C. Triptolide alters histone H3K9 and H3K27 methylation state and induces G0/G1 arrest and caspase-dependent apoptosis in multiple myeloma in vitro. Toxicology 2010; 267:70-9. [DOI: 10.1016/j.tox.2009.10.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Revised: 10/17/2009] [Accepted: 10/19/2009] [Indexed: 12/15/2022]
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Hancock DB, Romieu I, Shi M, Sienra-Monge JJ, Wu H, Chiu GY, Li H, del Rio-Navarro BE, Willis-Owens SAG, Weiss ST, Raby BA, Gao H, Eng C, Chapela R, Burchard EG, Tang H, Sullivan PF, London SJ. Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children. PLoS Genet 2009; 5:e1000623. [PMID: 19714205 PMCID: PMC2722731 DOI: 10.1371/journal.pgen.1000623] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 07/30/2009] [Indexed: 01/07/2023] Open
Abstract
Many candidate genes have been studied for asthma, but replication has varied. Novel candidate genes have been identified for various complex diseases using genome-wide association studies (GWASs). We conducted a GWAS in 492 Mexican children with asthma, predominantly atopic by skin prick test, and their parents using the Illumina HumanHap 550 K BeadChip to identify novel genetic variation for childhood asthma. The 520,767 autosomal single nucleotide polymorphisms (SNPs) passing quality control were tested for association with childhood asthma using log-linear regression with a log-additive risk model. Eleven of the most significantly associated GWAS SNPs were tested for replication in an independent study of 177 Mexican case-parent trios with childhood-onset asthma and atopy using log-linear analysis. The chromosome 9q21.31 SNP rs2378383 (p = 7.10x10(-6) in the GWAS), located upstream of transducin-like enhancer of split 4 (TLE4), gave a p-value of 0.03 and the same direction and magnitude of association in the replication study (combined p = 6.79x10(-7)). Ancestry analysis on chromosome 9q supported an inverse association between the rs2378383 minor allele (G) and childhood asthma. This work identifies chromosome 9q21.31 as a novel susceptibility locus for childhood asthma in Mexicans. Further, analysis of genome-wide expression data in 51 human tissues from the Novartis Research Foundation showed that median GWAS significance levels for SNPs in genes expressed in the lung differed most significantly from genes not expressed in the lung when compared to 50 other tissues, supporting the biological plausibility of our overall GWAS findings and the multigenic etiology of childhood asthma.
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Affiliation(s)
- Dana B. Hancock
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | | | - Min Shi
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | | | - Hao Wu
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Grace Y. Chiu
- Westat, Research Triangle Park, North Carolina, United States of America
| | - Huiling Li
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | | | | | - Scott T. Weiss
- Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin A. Raby
- Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hong Gao
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Celeste Eng
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Rocio Chapela
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Esteban G. Burchard
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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