1
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Zhang N, Tang W, Torres L, Wang X, Ajaj Y, Zhu L, Luan Y, Zhou H, Wang Y, Zhang D, Kurbatov V, Khan SA, Kumar P, Hidalgo A, Wu D, Lu J. Cell surface RNAs control neutrophil recruitment. Cell 2024; 187:846-860.e17. [PMID: 38262409 PMCID: PMC10922858 DOI: 10.1016/j.cell.2023.12.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/30/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
RNAs localizing to the outer cell surface have been recently identified in mammalian cells, including RNAs with glycan modifications known as glycoRNAs. However, the functional significance of cell surface RNAs and their production are poorly known. We report that cell surface RNAs are critical for neutrophil recruitment and that the mammalian homologs of the sid-1 RNA transporter are required for glycoRNA expression. Cell surface RNAs can be readily detected in murine neutrophils, the elimination of which substantially impairs neutrophil recruitment to inflammatory sites in vivo and reduces neutrophils' adhesion to and migration through endothelial cells. Neutrophil glycoRNAs are predominantly on cell surface, important for neutrophil-endothelial interactions, and can be recognized by P-selectin (Selp). Knockdown of the murine Sidt genes abolishes neutrophil glycoRNAs and functionally mimics the loss of cell surface RNAs. Our data demonstrate the biological importance of cell surface glycoRNAs and highlight a noncanonical dimension of RNA-mediated cellular functions.
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Affiliation(s)
- Ningning Zhang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wenwen Tang
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Lidiane Torres
- Department of Cell Biology and Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Xujun Wang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yasmeen Ajaj
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Li Zhu
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven CT 06511
| | - Yi Luan
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Hongyue Zhou
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yadong Wang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cooperative Center of Excellence in Hematology, New Haven, CT 12208, USA
| | - Dingyao Zhang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Computational Biology and Bioinformatics Graduate Program, Yale University, New Haven, CT 06520, USA
| | - Vadim Kurbatov
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Surgery, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Sajid A Khan
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven CT 06511
| | - Andres Hidalgo
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Dianqing Wu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA; Yale Cancer Center, New Haven, CT 06520, USA.
| | - Jun Lu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cooperative Center of Excellence in Hematology, New Haven, CT 12208, USA; Yale Cancer Center, New Haven, CT 06520, USA; Yale Center for RNA Science and Medicine, New Haven, CT 06520, USA.
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2
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Xie J, Du Y, Liu D, Wu J, Yang K, He X, Zhao J, Hong P, Liao K, Zhang H, Hong Y, Teijaro JR, Kang SG, Xiao C, Liu WH. The miR-17∼92 miRNAs promote plasma cell differentiation by suppressing SOCS3-mediated NIK degradation. Cell Rep 2023; 42:112968. [PMID: 37578862 DOI: 10.1016/j.celrep.2023.112968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
The miR-17∼92 family microRNAs (miRNAs) play a key role in germinal center (GC) reaction through promoting T follicular helper (TFH) cell differentiation. It remains unclear whether they also have intrinsic functions in B cell differentiation and function. Here we show that mice with B cell-specific deletion of the miR-17∼92 family exhibit impaired GC reaction, plasma cell differentiation, and antibody production in response to protein antigen immunization and chronic viral infection. Employing CRISPR-mediated functional screening, we identify Socs3 as a key functional target of miR-17∼92 in regulating plasma cell differentiation. Mechanistically, SOCS3, whose expression is elevated in miR-17∼92 family-deficient B cells, interacts with NIK and promotes its ubiquitination and degradation, thereby impairing NF-κB signaling and plasma cell differentiation. This moderate increase in SOCS3 expression has little effect on IL-21-STAT3 signaling. Our study demonstrates differential sensitivity of two key signaling pathways to alterations in the protein level of an miRNA target gene.
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Affiliation(s)
- Jun Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Ying Du
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Dewang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Kang Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaoyu He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiayi Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Peicheng Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Kunyu Liao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Huanrong Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yazhen Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Seung Goo Kang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Division of Biomedical Convergence/Institute of Bioscience and Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
| | - Changchun Xiao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
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3
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Ma F, Zhan Y, Bartolomé-Cabrero R, Ying W, Asano M, Huang Z, Xiao C, González-Martín A. Analysis of a miR-148a Targetome in B Cell Central Tolerance. Front Immunol 2022; 13:861655. [PMID: 35634349 PMCID: PMC9134011 DOI: 10.3389/fimmu.2022.861655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/15/2022] [Indexed: 12/31/2022] Open
Abstract
A microRNA (miRNA) often regulates the expression of hundreds of target genes. A fundamental question in the field of miRNA research is whether a miRNA exerts its biological function through regulating a small number of key targets or through small changes in the expression of hundreds of target genes. We addressed this issue by performing functional analysis of target genes regulated by miR-148a. We previously identified miR-148a as a critical regulator of B cell central tolerance and found 119 target genes that may mediate its function. We selected 4 of them for validation and demonstrated a regulatory role for Bim, Pten, and Gadd45a in this process. In this study, we performed functional analysis of the other miR-148a target genes in in vitro and in vivo models of B cell central tolerance. Our results show that those additional target genes play a minimal role, if any, in miR-148a-mediated control of B cell central tolerance, suggesting that the function of miRNAs is mediated by a few key target genes. These findings have advanced our understanding of molecular mechanisms underlying miRNA regulation of gene expression and B cell central tolerance.
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Affiliation(s)
- Fengge Ma
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yating Zhan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rocío Bartolomé-Cabrero
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Wei Ying
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Zhe Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Changchun Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- *Correspondence: Alicia González-Martín, ; Changchun Xiao,
| | - Alicia González-Martín
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
- *Correspondence: Alicia González-Martín, ; Changchun Xiao,
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4
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Yadav M, Liu J, Song F, Mo X, Jacob NR, Xu-Welliver M, Chakravarti A, Jacob NK. Utility of circulating microRNA-150 for rapid evaluation of bone marrow depletion after radiation, and efficiency of bone marrow reconstitution. Int J Radiat Oncol Biol Phys 2021; 112:964-974. [PMID: 34767935 DOI: 10.1016/j.ijrobp.2021.10.150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Total body irradiation (TBI) is a common myeloablative preparative regimen used in acute myeloid and lymphoblastic leukemia patients prior to allogenic hematopoietic stem cell transplantation (HSCT). The inefficient clearance of tumor cells and radiation-induced toxicity to normal tissues is attributed to relapse and morbidity in a significant fraction of patients. Developing biomarkers that provide an individual's physiological response to radiation will allow personalized treatment and follow-up. We investigated the utility of circulating microRNA150-5p (miR150) for evaluation of radiation dose response. MATERIALS AND METHODS Age-, gender-, and strain-matched wild type and miR150 null (knock out, KO) mice were subjected to TBI and evaluated for the impact of circulating miR150 expression on survival and hematological endpoints. Dose- and time-dependent changes of the miR150 level in bone marrow were assessed using flow cytometry. The functional roles of miR150 in cellular response to radiation were evaluated using apoptosis assay. miR150 expression in leukemic cell lines and in blood collected from leukemia patients with diverse outcomes were evaluated by quantitative RT-PCR. RESULTS Absence of miR150 in mice conferred resistance to radiation injury and resulted in accelerated recovery of lymphoid and myeloid cells after ablative or partially ablative TBI in mice. Overexpression of miR150 resulted in a higher percentage of cells at G2/M phases of cell cycle which is associated with increased sensitivity and susceptibility to apoptotic cell death after radiation. Levels of circulating miR150 were found to be decreased after radiation in leukemia patients and exhibited an inverse correlation with recurrence. CONCLUSION Current study demonstrates the utility of a miR150-based blood test for rapid evaluation of the efficiency of marrow ablation and recovery following radiation and HSCT. The internally controlled blood test will potentially provide near real-time evaluation of functional marrow that will allow optimal dosing based on an individual's physiological response to radiation.
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Affiliation(s)
- Marshleen Yadav
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Joseph Liu
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Feifei Song
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Xiaokui Mo
- Center for Biostatistics, Ohio State University, Columbus, Ohio
| | - Nitya R Jacob
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Meng Xu-Welliver
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Department of Radiation Oncology, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Arnab Chakravarti
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Department of Radiation Oncology, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Naduparambil K Jacob
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Department of Radiation Oncology, Ohio State University Wexner Medical Center, Columbus, Ohio.
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5
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Borch Jensen M, Marblestone A. In vivo Pooled Screening: A Scalable Tool to Study the Complexity of Aging and Age-Related Disease. FRONTIERS IN AGING 2021; 2:714926. [PMID: 35822038 PMCID: PMC9261400 DOI: 10.3389/fragi.2021.714926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Biological aging, and the diseases of aging, occur in a complex in vivo environment, driven by multiple interacting processes. A convergence of recently developed technologies has enabled in vivo pooled screening: direct administration of a library of different perturbations to a living animal, with a subsequent readout that distinguishes the identity of each perturbation and its effect on individual cells within the animal. Such screens hold promise for efficiently applying functional genomics to aging processes in the full richness of the in vivo setting. In this review, we describe the technologies behind in vivo pooled screening, including a range of options for delivery, perturbation and readout methods, and outline their potential application to aging and age-related disease. We then suggest how in vivo pooled screening, together with emerging innovations in each of its technological underpinnings, could be extended to shed light on key open questions in aging biology, including the mechanisms and limits of epigenetic reprogramming and identifying cellular mediators of systemic signals in aging.
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Affiliation(s)
- Martin Borch Jensen
- Gordian Biotechnology, San Francisco, CA, United States
- *Correspondence: Martin Borch Jensen, ; Adam Marblestone,
| | - Adam Marblestone
- Astera Institute, San Francisco, CA, United States
- Federation of American Scientists, Washington D.C., CA, United States
- *Correspondence: Martin Borch Jensen, ; Adam Marblestone,
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6
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Gutmann C, Joshi A, Zampetaki A, Mayr M. The Landscape of Coding and Noncoding RNAs in Platelets. Antioxid Redox Signal 2021; 34:1200-1216. [PMID: 32460515 DOI: 10.1089/ars.2020.8139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Levels of platelet noncoding RNAs (ncRNAs) are altered by disease, and ncRNAs may exert functions inside and outside of platelets. Their role in physiologic hemostasis and pathologic thrombosis remains to be explored. Recent Advances: The number of RNA classes identified in platelets has been growing since the past decade. Apart from coding messenger RNAs, the RNA landscape in platelets comprises ncRNAs such as microRNAs, circular RNAs, long ncRNAs, YRNAs, and potentially environmentally derived exogenous ncRNAs. Recent research has focused on the function of platelet RNAs beyond platelets, mediated through protective RNA shuttles or even cellular uptake of entire platelets. Multiple studies have also explored the potential of platelet RNAs as novel biomarkers. Critical Issues: Platelet preparations can contain contaminating leukocytes. Even few leukocytes may contribute a substantial amount of RNA. As biomarkers, platelet RNAs have shown associations with platelet activation, but it remains to be seen whether their measurements could improve diagnostics. It also needs to be clarified whether platelet RNAs influence processes beyond platelets. Future Directions: Technological advances such as single-cell RNA-sequencing might help to identify hyperreactive platelet subpopulations on a single-platelet level, avoid the common problem of leukocyte contamination in platelet preparations, and allow simultaneous profiling of native megakaryocytes and their platelet progeny to clarify to what extent the platelet RNA content reflects their megakaryocyte precursors or changes in the circulation. Antioxid. Redox Signal. 34, 1200-1216.
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Affiliation(s)
- Clemens Gutmann
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Abhishek Joshi
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
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7
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Circulatory miR-155 correlation with platelet and neutrophil recovery after autologous hematopoietic stem cell transplantation, a multivariate analysis. Int J Hematol 2021; 114:235-245. [PMID: 33895969 DOI: 10.1007/s12185-021-03154-2] [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: 01/14/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
The involvement of microRNAs in the regulation of hematopoietic stem cells paves the way for their use in the management of autologous HSC transplantation (AHSCT). We aimed to evaluate the predictive value of circulatory microRNAs in extracellular vesicles (EVs) and plasma in platelet and neutrophil engraftment. Circulatory miR-125b, mir-126, miR-150, and miR-155 expression was assessed in isolated EVs and plasma in samples collected from AHSCT candidates. Multivariate analysis, COX models, and ROC assessment were performed to evaluate the predictive values of these microRNAs in platelet and neutrophil engraftment. miR-155 expression following conditioning with other clinical factors such as chemotherapy courses after diagnosis was the most significant predictors of platelet/neutrophil engraftment. A CD34+ cell count ≥ 3.5 × 106/kg combined with miR-155 could be used as an engraftment predictor; however, in cases where the CD34+ cell count was < 3.5 × 106/kg, this parameter lost its predictive value for engraftment and could be replaced by miR-155. The correlation between miR-155 and platelet/neutrophil engraftment even with lower numbers of CD34+ cells suggests the importance of this microRNA in the prediction of AHSCT outcome. Moreover, miR-155 could be utilized in therapeutic approaches to provide a better outcome for patients undergoing AHSCT.
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8
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Tian J, Zhang D, Kurbatov V, Wang Q, Wang Y, Fang D, Wu L, Bosenberg M, Muzumdar MD, Khan S, Lu Q, Yan Q, Lu J. 5-Fluorouracil efficacy requires anti-tumor immunity triggered by cancer-cell-intrinsic STING. EMBO J 2021; 40:e106065. [PMID: 33615517 DOI: 10.15252/embj.2020106065] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/02/2021] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug, but the mechanisms underlying 5-FU efficacy in immunocompetent hosts in vivo remain largely elusive. Through modeling 5-FU response of murine colon and melanoma tumors, we report that effective reduction of tumor burden by 5-FU is dependent on anti-tumor immunity triggered by the activation of cancer-cell-intrinsic STING. While the loss of STING does not induce 5-FU resistance in vitro, effective 5-FU responsiveness in vivo requires cancer-cell-intrinsic cGAS, STING, and subsequent type I interferon (IFN) production, as well as IFN-sensing by bone-marrow-derived cells. In the absence of cancer-cell-intrinsic STING, a much higher dose of 5-FU is needed to reduce tumor burden. 5-FU treatment leads to increased intratumoral T cells, and T-cell depletion significantly reduces the efficacy of 5-FU in vivo. In human colorectal specimens, higher STING expression is associated with better survival and responsiveness to chemotherapy. Our results support a model in which 5-FU triggers cancer-cell-initiated anti-tumor immunity to reduce tumor burden, and our findings could be harnessed to improve therapeutic effectiveness and toxicity for colon and other cancers.
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Affiliation(s)
- Jingru Tian
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Yale Stem Cell Center, New Haven, CT, USA.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Dingyao Zhang
- Yale Stem Cell Center, New Haven, CT, USA.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Vadim Kurbatov
- Yale Stem Cell Center, New Haven, CT, USA.,Yale Cancer Center, New Haven, CT, USA.,Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Qinrong Wang
- Yale Stem Cell Center, New Haven, CT, USA.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Yadong Wang
- Yale Stem Cell Center, New Haven, CT, USA.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Dorthy Fang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Lizhen Wu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Mandar D Muzumdar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, New Haven, CT, USA.,Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Sajid Khan
- Yale Cancer Center, New Haven, CT, USA.,Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hospital of Skin Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qin Yan
- Yale Cancer Center, New Haven, CT, USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jun Lu
- Yale Stem Cell Center, New Haven, CT, USA.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, New Haven, CT, USA.,Yale Center for RNA Science and Medicine, New Haven, CT, USA.,Yale Cooperative Center of Excellence in Hematology, New Haven, CT, USA
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9
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Zhao R, Zhang H, Zhang Y, Li D, Huang C, Li F. In vivo Screen Identifies Zdhhc2 as a Critical Regulator of Germinal Center B Cell Differentiation. Front Immunol 2020; 11:1025. [PMID: 32587588 PMCID: PMC7297983 DOI: 10.3389/fimmu.2020.01025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/28/2020] [Indexed: 12/23/2022] Open
Abstract
Germinal center (GC) B cell differentiation is critical for the production of affinity-matured pathogen-specific antibodies, the dysregulation of which may lead to humoral immunodeficiency or autoimmunity. The development of an in vivo screening system for factors regulating GC B cell differentiation has been a challenge. Here we describe a small-scale in vivo screening system with NP-specific B1-8hi cells and a retroviral shRNA library targeting 78 candidate genes to search for B cell-intrinsic factors that specifically regulate GC B cell differentiation. Zdhhc2, a gene encoding palmitoyltransferase ZDHHC2 and highly expressed in GC B cells, is identified as a strong positive regulator of GC B cell differentiation. B1-8hi cells transduced with Zdhhc2-shRNA are severely compromised in differentiating into GC B cells. A further analysis of in vitro differentiated B cells transduced with Zdhhc2-shRNA shows that Zdhhc2 is critical for the proliferation and the survival of B cells stimulated by CD40L, BAFF, and IL-21 and consequently impacts on their differentiation into GC B cells and post-GC B cells. These studies not only identify Zdhhc2 as a novel regulator of GC B cell differentiation but also represent a proof of concept of in vivo screen for regulators of GC B cell differentiation.
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Affiliation(s)
- Rongqing Zhao
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huihui Zhang
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Zhang
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Li
- Boston Consulting Group, Shenzhen, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fubin Li
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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10
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Wünsche P, Eckert ESP, Holland-Letz T, Paruzynski A, Hotz-Wagenblatt A, Fronza R, Rath T, Gil-Farina I, Schmidt M, von Kalle C, Klein C, Ball CR, Herbst F, Glimm H. Mapping Active Gene-Regulatory Regions in Human Repopulating Long-Term HSCs. Cell Stem Cell 2019; 23:132-146.e9. [PMID: 29979988 DOI: 10.1016/j.stem.2018.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 04/03/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022]
Abstract
Genes that regulate hematopoietic stem cell (HSC) self-renewal, proliferation, and differentiation are tightly controlled by regulatory regions. However, mapping such regions relies on surface markers and immunophenotypic definition of HSCs. Here, we use γ-retroviral integration sites (γRV ISs) from a gene therapy trial for 10 patients with Wiskott-Aldrich syndrome to mark active enhancers and promoters in functionally defined long-term repopulating HSCs. Integration site clusters showed the highest ATAC-seq signals at HSC-specific peaks and strongly correlated with hematopoietic risk variants. Tagged genes were significantly enriched for HSC gene sets. We were able to map over 3,000 HSC regulatory regions in late-contributing HSCs, and we used these data to identify miR-10a and miR-335 as two miRNAs regulating early hematopoiesis. In this study, we show that viral insertion sites can be used as molecular tags to assess chromatin conformation on functionally defined cell populations, thereby providing a genome-wide resource for regulatory regions in human repopulating long-term HSCs.
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Affiliation(s)
- Peer Wünsche
- Department of Translational and Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Elias S P Eckert
- Department of Translational and Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Tim Holland-Letz
- Department of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Agnes Hotz-Wagenblatt
- Core Facility Omics IT and Data Management, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raffaele Fronza
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Rath
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irene Gil-Farina
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; GeneWerk GmbH, Heidelberg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, NCT-Dresden, University Hospital, Carl Gustav Carus, Technische Universität Dresden, Dresden and DKFZ, Heidelberg, Germany
| | - Friederike Herbst
- Department of Translational and Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational and Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Translational Medical Oncology, NCT-Dresden, University Hospital, Carl Gustav Carus, Technische Universität Dresden, Dresden and DKFZ, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany.
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11
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Biomarker Potential of Plasma MicroRNA-150-5p in Prostate Cancer. ACTA ACUST UNITED AC 2019; 55:medicina55090564. [PMID: 31484346 PMCID: PMC6780076 DOI: 10.3390/medicina55090564] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Background and Objectives: Over decades, prostate cancer (PCa) has become one of the leading causes of cancer mortality in men. Extensive evidence exists that microRNAs (miRNAs or miRs) are key players in PCa and a new class of non-invasive cancer biomarkers. Materials and Methods: We performed miRNA profiling in plasma and tissues of PCa patients and attempted the validation of candidate individual miRs as biomarkers. Results: The comparison of tissue and plasma profiling results revealed five commonly dysregulated miRs, namely, miR-130a-3p, miR-145-5p, miR-148a-3p, miR-150-5p, and miR-365a-3p, of which only three show concordant changes—miR-130a-3p and miR-150-5p were downregulated and miR-148a-3p was upregulated in both tissue and plasma samples, respectively. MiR-150-5p was validated as significantly downregulated in both plasma and tissue cancer samples, with a fold change of −2.697 (p < 0.001), and −1.693 (p = 0.035), respectively. ROC analysis showed an area under the curve (AUC) of 0.817 (95% CI: 0.680–0.995) for plasma samples and 0.809 (95% CI: 0.616–1.001) for tissue samples. Conclusions: We provide data indicating that miR-150-5p plasma variations in PCa patients are associated with concordant changes in prostate cancer tissues; however, given the heterogeneous nature of previous findings of miR-150-5p expression in PCa cells, additional future studies of a larger sample size are warranted in order to confirm the biomarker potential and role of miRNA-150-5p in PCa biology.
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12
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Nazimek K, Bustos-Morán E, Blas-Rus N, Nowak B, Ptak W, Askenase PW, Sánchez-Madrid F, Bryniarski K. Syngeneic red blood cell-induced extracellular vesicles suppress delayed-type hypersensitivity to self-antigens in mice. Clin Exp Allergy 2019; 49:1487-1499. [PMID: 31365154 DOI: 10.1111/cea.13475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND At present, the role of autologous cells as antigen carriers inducing immune tolerance is appreciated. Accordingly, intravenous administration of haptenated syngeneic mouse red blood cells (sMRBC) leads to hapten-specific suppression of contact hypersensitivity (CHS) in mice, mediated by light chain-coated extracellular vesicles (EVs). Subsequent studies suggested that mice intravenously administered with sMRBC alone may also generate regulatory EVs, revealing the possible self-tolerogenic potential of autologous erythrocytes. OBJECTIVES The current study investigated the immune effects induced by mere intravenous administration of a high dose of sMRBC in mice. METHODS The self-tolerogenic potential of EVs was determined in a newly developed mouse model of delayed-type hypersensitivity (DTH) to sMRBC. The effects of EV's action on DTH effector cells were evaluated cytometrically. The suppressive activity of EVs, after coating with anti-hapten antibody light chains, was assessed in hapten-induced CHS in wild-type or miRNA-150-/- mice. RESULTS Intravenous administration of sMRBC led to the generation of CD9 + CD81+ EVs that suppressed sMRBC-induced DTH in a miRNA-150-dependent manner. Furthermore, the treatment of DTH effector cells with sMRBC-induced EVs decreased the activation of T cells but enhanced their apoptosis. Finally, EVs coated with antibody light chains inhibited hapten-induced CHS. CONCLUSIONS AND CLINICAL RELEVANCE The current study describes a newly discovered mechanism of self-tolerance induced by the intravenous delivery of a high dose of sMRBC that is mediated by EVs in a miRNA-150-dependent manner. This mechanism implies the concept of naturally occurring immune tolerance, presumably activated by overloading of the organism with altered self-antigens.
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Affiliation(s)
- Katarzyna Nazimek
- Department of Immunology, Jagiellonian University Medical College, Krakow, Poland.,Department of Immunology, Health Research Institute of Princesa Hospital (ISS-IP), Hospital de la Princesa, Autonomous University of Madrid, Madrid, Spain.,Section of Rheumatology, Allergy and Clinical Immunology, Yale University School of Medicine, New Haven, CT, USA
| | - Eugenio Bustos-Morán
- Department of Immunology, Health Research Institute of Princesa Hospital (ISS-IP), Hospital de la Princesa, Autonomous University of Madrid, Madrid, Spain
| | - Noelia Blas-Rus
- Department of Immunology, Health Research Institute of Princesa Hospital (ISS-IP), Hospital de la Princesa, Autonomous University of Madrid, Madrid, Spain
| | - Bernadeta Nowak
- Department of Immunology, Jagiellonian University Medical College, Krakow, Poland
| | - Włodzimierz Ptak
- Department of Immunology, Jagiellonian University Medical College, Krakow, Poland
| | - Philip W Askenase
- Section of Rheumatology, Allergy and Clinical Immunology, Yale University School of Medicine, New Haven, CT, USA
| | - Francisco Sánchez-Madrid
- Department of Immunology, Health Research Institute of Princesa Hospital (ISS-IP), Hospital de la Princesa, Autonomous University of Madrid, Madrid, Spain
| | - Krzysztof Bryniarski
- Department of Immunology, Jagiellonian University Medical College, Krakow, Poland.,Section of Rheumatology, Allergy and Clinical Immunology, Yale University School of Medicine, New Haven, CT, USA
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13
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A stemness screen reveals C3orf54/INKA1 as a promoter of human leukemia stem cell latency. Blood 2019; 133:2198-2211. [DOI: 10.1182/blood-2018-10-881441] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/18/2019] [Indexed: 12/17/2022] Open
Abstract
Abstract
There is a growing body of evidence that the molecular properties of leukemia stem cells (LSCs) are associated with clinical outcomes in acute myeloid leukemia (AML), and LSCs have been linked to therapy failure and relapse. Thus, a better understanding of the molecular mechanisms that contribute to the persistence and regenerative potential of LSCs is expected to result in the development of more effective therapies. We therefore interrogated functionally validated data sets of LSC-specific genes together with their known protein interactors and selected 64 candidates for a competitive in vivo gain-of-function screen to identify genes that enhanced stemness in human cord blood hematopoietic stem and progenitor cells. A consistent effect observed for the top hits was the ability to restrain early repopulation kinetics while preserving regenerative potential. Overexpression (OE) of the most promising candidate, the orphan gene C3orf54/INKA1, in a patient-derived AML model (8227) promoted the retention of LSCs in a primitive state manifested by relative expansion of CD34+ cells, accumulation of cells in G0, and reduced output of differentiated progeny. Despite delayed early repopulation, at later times, INKA1-OE resulted in the expansion of self-renewing LSCs. In contrast, INKA1 silencing in primary AML reduced regenerative potential. Mechanistically, our multidimensional confocal analysis found that INKA1 regulates G0 exit by interfering with nuclear localization of its target PAK4, with concomitant reduction of global H4K16ac levels. These data identify INKA1 as a novel regulator of LSC latency and reveal a link between the regulation of stem cell kinetics and pool size during regeneration.
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14
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Huang R, Hu Z, Cao Y, Li H, Zhang H, Su W, Xu Y, Liang L, Melgiri ND, Jiang L. MiR-652-3p inhibition enhances endothelial repair and reduces atherosclerosis by promoting Cyclin D2 expression. EBioMedicine 2019; 40:685-694. [PMID: 30674440 PMCID: PMC6413686 DOI: 10.1016/j.ebiom.2019.01.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Atherosclerosis is a hyperlipidemia-induced condition affecting the arterial wall that damages healthy endothelial cell (EC) function, leading to enhanced risk of atherothrombotic events. Certain microRNAs regulate EC dysfunction in response to hyperlipidemia and may be suitable therapeutic targets to combat atherosclerosis. METHODS miRNA expression in human ECs was analyzed under various conditions to identify key microRNAs. High-cholesterol diet (HCD)-fed Mir652-/-Apoe-/- (Mir652-/-) mice and matching Mir652+/+Apoe-/- (Mir652+/+) mice were subjected to carotid injury to analyze the effects of miR-652 knockdown on endothelial repair. In silico analysis followed by in vitro and in vivo experiments were applied to identify miR-652's target gene Ccnd2 and investigate the pair's effects on ECs. miR-652-5p and miR-652-3p antagomir therapies were tested in Mir652+/+ mice under normal and HCD diet to assess their effect on endothelial repair. FINDINGS miR-652-3p, which is upregulated in human and murine atherosclerotic plaques, suppresses expression of the endothelial repair gene Ccnd2, thereby enhancing atherosclerotic lesion formation. Post-denudation recovery of ECs was promoted in Mir652-/- mice due to enhanced EC proliferation attributable to de-repression of miR-652-3p's (but not miR-652-5p's) regulation of Ccnd2 expression. Under hyperlipidemic conditions at non-predilection sites, miR-652-3p produces anti-proliferative effects in ECs, such that Mir652-/- mice display reduced atherosclerotic progression. In contrast, neither miR-652-3p nor Ccnd2 displayed significant effects on the endothelium at predilection sites or under disturbed flow conditions. Administration of a miR-652-3p antagomir rescued the proliferation of ECs in vivo, thereby limiting atherosclerotic development. INTERPRETATION miR-652-3p blockade may be a potential therapeutic strategy against atherosclerosis.
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Affiliation(s)
- Rongzhong Huang
- Department of Cardiothoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Zicheng Hu
- Department of Neurology, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yu Cao
- Department of Cardiothoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Hongrong Li
- Department of Cardiothoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Hong Zhang
- Department of Cardiology, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Wenhua Su
- Department of Cardiology, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Yu Xu
- Statistical Laboratory, Chuangxu Institute of Lifescience, Chongqing, China
| | - Liwen Liang
- Department of Cardiology, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - N D Melgiri
- Impactys Foundation for Biomedical Research, San Diego, CA, USA.
| | - Lihong Jiang
- Department of Cardiothoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.
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15
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A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset. Nat Commun 2018; 9:5455. [PMID: 30575719 PMCID: PMC6303340 DOI: 10.1038/s41467-018-07801-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/19/2018] [Indexed: 12/30/2022] Open
Abstract
Non-classical monocyte subsets may derive from classical monocyte differentiation and the proportion of each subset is tightly controlled. Deregulation of this repartition is observed in diverse human diseases, including chronic myelomonocytic leukemia (CMML) in which non-classical monocyte numbers are significantly decreased relative to healthy controls. Here, we identify a down-regulation of hsa-miR-150 through methylation of a lineage-specific promoter in CMML monocytes. Mir150 knock-out mice demonstrate a cell-autonomous defect in non-classical monocytes. Our pulldown experiments point to Ten-Eleven-Translocation-3 (TET3) mRNA as a hsa-miR-150 target in classical human monocytes. We show that Tet3 knockout mice generate an increased number of non-classical monocytes. Our results identify the miR-150/TET3 axis as being involved in the generation of non-classical monocytes.
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16
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Raghuwanshi S, Dahariya S, Musvi SS, Gutti U, Kandi R, Undi RB, Sahu I, Gautam DK, Paddibhatla I, Gutti RK. MicroRNA function in megakaryocytes. Platelets 2018; 30:809-816. [DOI: 10.1080/09537104.2018.1528343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sanjeev Raghuwanshi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Swati Dahariya
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Syed Shahid Musvi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Usha Gutti
- Department of Biotechnology, GITAM Institute of Science, GITAM University, Visakhapatnam, AP, India
| | - Ravinder Kandi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Ram Babu Undi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Itishri Sahu
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Dushyant Kumar Gautam
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Indira Paddibhatla
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Ravi Kumar Gutti
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
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17
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Kim TH, Jeong JY, Park JY, Kim SW, Heo JH, Kang H, Kim G, An HJ. miR-150 enhances apoptotic and anti-tumor effects of paclitaxel in paclitaxel-resistant ovarian cancer cells by targeting Notch3. Oncotarget 2017; 8:72788-72800. [PMID: 29069826 PMCID: PMC5641169 DOI: 10.18632/oncotarget.20348] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 07/19/2017] [Indexed: 01/08/2023] Open
Abstract
Tumor recurrence by obtaining chemoresistance is a major obstacle to treating ovarian cancer. By TargetScan database and a luciferase reporter assay, we identified miR-150 directly targets Notch3, which is a key oncogene in ovarian cancer. We, therefore, investigated the role of miR-150 in ovarian cancer cells, and the usefulness of miR-150 as a therapeutic target in chemoresistant ovarian cancer, through examining miR-150 expression by qRT-PCR in ovarian cancer cell lines and tissues, and assessing the gain-of-function effect by WST, colony forming, TUNEL, wound healing and angiogenesis assays. Western blotting was performed to evaluate its downstream targets. The miR-150 expression was significantly downregulated in ovarian cancers. Treatment with pre-miR-150 significantly inhibited cancer cell proliferation, and induced apoptosis in PTX (paclitaxel) -resistant SKpac cells, which was not seen by PTX only treatment. On spheroid forming assay, an additional pre-miR-150 treatment with PTX decreased cancer stem cell activation in PTX-resistant SKpac cells. An experimental upregulation of miR-150 also decreased cancer cell migration and angiogenesis in SKpac cells. The Notch3 downstream proteins(NICD3 and HEY2), and cell cycle-related proteins (cyclinD3, pS6, and NF-kB), and apoptosis-related proteins (BCL-2 and BCL-W) were significantly downregulated by pre-miR-150 transfection. Taken together, miR-150 is related with PTX-resistance in ovarian cancer, and treatment with pre-miR-150 resensitizes cancer cells to PTX. Therefore, it may be a promising treatment strategy in chemoresistant and recurrent ovarian cancer.
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Affiliation(s)
- Tae Hoen Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
| | - Ju-Yeon Jeong
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
| | - Ju-Yeon Park
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
| | - Se-Wha Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
| | - Jin Hyung Heo
- Department of Pathology, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
| | - Haeyoun Kang
- Department of Pathology, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
| | - Gwangil Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
| | - Hee Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Gyeonggi-do, Korea
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18
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Roden C, Gaillard J, Kanoria S, Rennie W, Barish S, Cheng J, Pan W, Liu J, Cotsapas C, Ding Y, Lu J. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Genome Res 2017; 27:374-384. [PMID: 28087842 PMCID: PMC5340965 DOI: 10.1101/gr.208900.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 01/06/2017] [Indexed: 12/26/2022]
Abstract
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36 ± 3 nt is optimal for pri-miRNA processing. We identify two bulge-depleted regions on the miRNA stem, located ∼16-21 nt and ∼28-32 nt from the base of the stem, that are less tolerant of unpaired bases. We further show that the CNNC primary sequence motif selectively enhances the processing of optimal-length hairpins. We predict that a small but significant fraction of human single-nucleotide polymorphisms (SNPs) alter pri-miRNA processing, and confirm several predictions experimentally including a disease-causing mutation. Our study enhances the rules governing mammalian pri-miRNA processing and suggests a diverse impact of human genetic variation on miRNA biogenesis.
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Affiliation(s)
- Christine Roden
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.,Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA.,Graduate Program in Biological and Biomedical Sciences, Yale University, New Haven, Connecticut 06510, USA
| | - Jonathan Gaillard
- Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.,School of Medicine, Yale University, New Haven, Connecticut 06510, USA
| | - Shaveta Kanoria
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
| | - William Rennie
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
| | - Syndi Barish
- Graduate Program in Biological and Biomedical Sciences, Yale University, New Haven, Connecticut 06510, USA
| | - Jijun Cheng
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.,Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA
| | - Wen Pan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.,Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA
| | - Jun Liu
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.,Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA
| | - Chris Cotsapas
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06511, USA
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.,Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA.,Yale Cooperative Center of Excellence in Hematology, Yale University, New Haven, Connecticut 06520, USA
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19
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miR-125b promotes MLL-AF9-driven murine acute myeloid leukemia involving a VEGFA-mediated non-cell-intrinsic mechanism. Blood 2017; 129:1491-1502. [PMID: 28053194 DOI: 10.1182/blood-2016-06-721027] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/28/2016] [Indexed: 12/14/2022] Open
Abstract
The hematopoietic stem cell-enriched miR-125 family microRNAs (miRNAs) are critical regulators of hematopoiesis. Overexpression of miR-125a or miR-125b is frequent in human acute myeloid leukemia (AML), and the overexpression of these miRNAs in mice leads to expansion of hematopoietic stem cells accompanied by perturbed hematopoiesis with mostly myeloproliferative phenotypes. However, whether and how miR-125 family miRNAs cooperate with known AML oncogenes in vivo, and how the resultant leukemia is dependent on miR-125 overexpression, are not well understood. We modeled the frequent co-occurrence of miR-125b overexpression and MLL translocations by examining functional cooperation between miR-125b and MLL-AF9 By generating a knock-in mouse model in which miR-125b overexpression is controlled by doxycycline induction, we demonstrated that miR-125b significantly enhances MLL-AF9-driven AML in vivo, and the resultant leukemia is partially dependent on continued overexpression of miR-125b Surprisingly, miR-125b promotes AML cell expansion and suppresses apoptosis involving a non-cell-intrinsic mechanism. MiR-125b expression enhances VEGFA expression and production from leukemia cells, in part by suppressing TET2 Recombinant VEGFA recapitulates the leukemia-promoting effects of miR-125b, whereas knockdown of VEGFA or inhibition of VEGF receptor 2 abolishes the effects of miR-125b In addition, significant correlation between miR-125b and VEGFA expression is observed in human AMLs. Our data reveal cooperative and dependent relationships between miR-125b and the MLL oncogene in AML leukemogenesis, and demonstrate a miR-125b-TET2-VEGFA pathway in mediating non-cell-intrinsic leukemia-promoting effects by an oncogenic miRNA.
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Menon N, Rogers CJ, Lukaszewicz AI, Axtelle J, Yadav M, Song F, Chakravarti A, Jacob NK. Detection of Acute Radiation Sickness: A Feasibility Study in Non-Human Primates Circulating miRNAs for Triage in Radiological Events. PLoS One 2016; 11:e0167333. [PMID: 27907140 PMCID: PMC5132176 DOI: 10.1371/journal.pone.0167333] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/11/2016] [Indexed: 11/19/2022] Open
Abstract
Development of biomarkers capable of estimating absorbed dose is critical for effective triage of affected individuals after radiological events. Levels of cell-free circulating miRNAs in plasma were compared for dose-response analysis in non-human primates (NHP) exposed to lethal (6.5 Gy) and sub-lethal (1 and 3 Gy) doses over a 7 day period. The doses and test time points were selected to mimic triage needs in the event of a mass casualty radiological event. Changes in miRNA abundance in irradiated animals were compared to a non-irradiated cohort and a cohort experiencing acute inflammation response from exposure to lipopolysaccharide (LPS). An amplification-free, hybridization-based direct digital counting method was used for evaluation of changes in microRNAs in plasma from all animals. Consistent with previous murine studies, circulating levels of miR-150-5p exhibited a dose- and time-dependent decrease in plasma. Furthermore, plasma miR-150-5p levels were found to correlate well with lymphocyte and neutrophil depletion kinetics. Additionally, plasma levels of several other evolutionarily and functionally conserved miRNAs were found altered as a function of dose and time. Interestingly, miR-574-5p exhibited a distinct, dose-dependent increase 24 h post irradiation in NHPs with lethal versus sub-lethal exposure before returning to the baseline level by day 3. This particular miRNA response was not detected in previous murine studies but was observed in animals exposed to LPS, indicating distinct molecular and inflammatory responses. Furthermore, an increase in low-abundant miR-126, miR-144, and miR-21 as well as high-abundant miR-1-3p and miR-206 was observed in irradiated animals on day 3 and/or day 7. The data from this study could be used to develop a multi-marker panel with known tissue-specific origin that could be used for developing rapid assays for dose assessment and evaluation of radiation injury on multiple organs. Furthermore this approach may be utilized to screen for tissue toxicity in patients who receive myeloablative and therapeutic radiation.
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Affiliation(s)
- Naresh Menon
- ChromoLogic LLC, Monrovia, California, United States of America
| | | | | | - James Axtelle
- ChromoLogic LLC, Monrovia, California, United States of America
| | - Marshleen Yadav
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center Columbus, Ohio, United States of America
| | - Feifei Song
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center Columbus, Ohio, United States of America
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center Columbus, Ohio, United States of America
| | - Naduparambil K. Jacob
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center Columbus, Ohio, United States of America
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Roden C, Lu J. MicroRNAs in Control of Stem Cells in Normal and Malignant Hematopoiesis. CURRENT STEM CELL REPORTS 2016; 2:183-196. [PMID: 27547713 PMCID: PMC4988405 DOI: 10.1007/s40778-016-0057-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Studies on hematopoietic stem cells (HSCs) and leukemia stem cells (LSCs) have helped to establish the paradigms of normal and cancer stem cell concepts. For both HSCs and LSCs, specific gene expression programs endowed by their epigenome functionally distinguish them from their differentiated progenies. MicroRNAs (miRNAs), as a class of small non-coding RNAs, act to control post-transcriptional gene expression. Research in the past decade has yielded exciting findings elucidating the roles of miRNAs in control of multiple facets of HSC and LSC biology. Here we review recent progresses on the functions of miRNAs in HSC emergence during development, HSC switch from a fetal/neonatal program to an adult program, HSC self-renewal and quiescence, HSC aging, HSC niche, and malignant stem cells. While multiple different miRNAs regulate a diverse array of targets, two common themes emerge in HSC and LSC biology: miRNA mediated regulation of epigenetic machinery and cell signaling pathways. In addition, we propose that miRNAs themselves behave like epigenetic regulators, as they possess key biochemical and biological properties that can provide both stability and alterability to the epigenetic program. Overall, the studies of miRNAs in stem cells in the hematologic contexts not only provide key understandings to post-transcriptional gene regulation mechanisms in HSCs and LSCs, but also will lend key insights for other stem cell fields.
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Affiliation(s)
- Christine Roden
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut, 06520, USA
- Graduate Program in Biological and Biomedical Sciences, Yale University, New Haven, Connecticut 06510, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut, 06520, USA
- Yale Center for RNA Science and Medicine, New Haven, Connecticut, 06520, USA
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Dinh TKT, Fendler W, Chałubińska-Fendler J, Acharya SS, O’Leary C, Deraska PV, D’Andrea AD, Chowdhury D, Kozono D. Circulating miR-29a and miR-150 correlate with delivered dose during thoracic radiation therapy for non-small cell lung cancer. Radiat Oncol 2016; 11:61. [PMID: 27117590 PMCID: PMC4847218 DOI: 10.1186/s13014-016-0636-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/14/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Risk of normal tissue toxicity limits the amount of thoracic radiation therapy (RT) that can be routinely prescribed to treat non-small cell lung cancer (NSCLC). An early biomarker of response to thoracic RT may provide a way to predict eventual toxicities-such as radiation pneumonitis-during treatment, thereby enabling dose adjustment before the symptomatic onset of late effects. MicroRNAs (miRNAs) were studied as potential serological biomarkers for thoracic RT. As a first step, we sought to identify miRNAs that correlate with delivered dose and standard dosimetric factors. METHODS We performed miRNA profiling of plasma samples obtained from five patients with Stage IIIA NSCLC at five dose-points each during radical thoracic RT. Candidate miRNAs were then assessed in samples from a separate cohort of 21 NSCLC patients receiving radical thoracic RT. To identify a cellular source of circulating miRNAs, we quantified in vitro miRNA expression intracellularly and within secreted exosomes in five NSCLC and stromal cell lines. RESULTS miRNA profiling of the discovery cohort identified ten circulating miRNAs that correlated with delivered RT dose as well as other dosimetric parameters such as lung V20. In the validation cohort, miR-29a-3p and miR-150-5p were reproducibly shown to decrease with increasing radiation dose. Expression of miR-29a-3p and miR-150-5p in secreted exosomes decreased with radiation. This was concomitant with an increase in intracellular levels, suggesting that exosomal export of these miRNAs may be downregulated in both NSCLC and stromal cells in response to radiation. CONCLUSIONS miR-29a-3p and miR-150-5p were identified as circulating biomarkers that correlated with delivered RT dose. miR-150 has been reported to decrease in the circulation of mammals exposed to radiation while miR-29a has been associated with fibrosis in the human heart, lungs, and kidneys. One may therefore hypothesize that outlier levels of circulating miR-29a-3p and miR-150-5p may eventually help predict unexpected responses to radiation therapy, such as toxicity.
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Affiliation(s)
- Tru-Khang T. Dinh
- />Harvard Medical School, 25 Shattuck St, Boston, MA 02115 USA
- />Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
| | - Wojciech Fendler
- />Department of Biostatistics and Translational Medicine, Medical University of Łódź, Al. Kościuszki 4, 90-419 Łódź, Poland
| | | | - Sanket S. Acharya
- />Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
| | - Colin O’Leary
- />Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
| | - Peter V. Deraska
- />Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
| | - Alan D. D’Andrea
- />Harvard Medical School, 25 Shattuck St, Boston, MA 02115 USA
- />Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
- />Center for DNA Damage and Repair, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
| | - Dipanjan Chowdhury
- />Harvard Medical School, 25 Shattuck St, Boston, MA 02115 USA
- />Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
| | - David Kozono
- />Harvard Medical School, 25 Shattuck St, Boston, MA 02115 USA
- />Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215 USA
- />Department of Radiation Oncology, Brigham and Women’s Hospital, 75 Francis St, Boston, MA 02115 USA
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23
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Cheng J, Roden CA, Pan W, Zhu S, Baccei A, Pan X, Jiang T, Kluger Y, Weissman SM, Guo S, Flavell RA, Ding Y, Lu J. A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions. Nat Commun 2016; 7:11178. [PMID: 27025950 PMCID: PMC4820989 DOI: 10.1038/ncomms11178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/26/2016] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly-interspaced palindromic repeats (CRISPR)-based genetic screens using single-guide-RNA (sgRNA) libraries have proven powerful to identify genetic regulators. Applying CRISPR screens to interrogate functional elements in noncoding regions requires generating sgRNA libraries that are densely covering, and ideally inexpensive, easy to implement and flexible for customization. Here we present a Molecular Chipper technology for generating dense sgRNA libraries for genomic regions of interest, and a proof-of-principle screen that identifies novel cis-regulatory domains for miR-142 biogenesis. The Molecular Chipper approach utilizes a combination of random fragmentation and a type III restriction enzyme to derive a densely covering sgRNA library from input DNA. Applying this approach to 17 microRNAs and their flanking regions and with a reporter for miR-142 activity, we identify both the pre-miR-142 region and two previously unrecognized cis-domains important for miR-142 biogenesis, with the latter regulating miR-142 processing. This strategy will be useful for identifying functional noncoding elements in mammalian genomes.
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Affiliation(s)
- Jijun Cheng
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut 06520, USA
| | - Christine A. Roden
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut 06520, USA
- Graduate Program in Biological and Biomedical Sciences, Yale University, New Haven, Connecticut 06510, USA
| | - Wen Pan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut 06520, USA
| | - Shu Zhu
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Anna Baccei
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Xinghua Pan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Tingting Jiang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
| | - Sherman M. Weissman
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Shangqin Guo
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, Connecticut 06520, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
- Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA
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The microRNA miR-148a functions as a critical regulator of B cell tolerance and autoimmunity. Nat Immunol 2016; 17:433-40. [PMID: 26901150 PMCID: PMC4803625 DOI: 10.1038/ni.3385] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/18/2015] [Indexed: 12/14/2022]
Abstract
Autoreactive B cells have critical roles in a large diversity of autoimmune diseases, but the molecular pathways that control these cells remain poorly understood. We performed an in vivo functional screen of a lymphocyte-expressed microRNA library and identified miR-148a as a potent regulator of B cell tolerance. Elevated miR-148a expression impaired B cell tolerance by promoting the survival of immature B cells after engagement of the B cell antigen receptor by suppressing the expression of the autoimmune suppressor Gadd45α, the tumor suppressor PTEN and the pro-apoptotic protein Bim. Furthermore, increased expression of miR-148a, which occurs frequently in patients with lupus and lupus-prone mice, facilitated the development of lethal autoimmune disease in a mouse model of lupus. Our studies demonstrate a function for miR-148a as a regulator of B cell tolerance and autoimmunity.
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25
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Bystrykh LV, Belderbos ME. Clonal Analysis of Cells with Cellular Barcoding: When Numbers and Sizes Matter. Methods Mol Biol 2016; 1516:57-89. [PMID: 27044044 DOI: 10.1007/7651_2016_343] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cellular barcoding is a recently rediscovered tool to trace the clonal output of individual cells with genetically distinct and heritable DNA sequences. Each year a few dozens of papers are published using the cellular barcoding technique. Those publications largely focus on mutually related issues, namely: counting cells capable of clonal proliferation and expansion, monitoring clonal dynamics in time, tracing the origin of differentiated cells, characterizing the differentiation potential of stem cells and similar topics. Apart from their biological content, claims and conclusions, these studies show remarkable diversity in technical aspects of the barcoding method and sometimes in major conclusions. Although a diversity of approaches is quite usual in data analysis, deviant handling of barcode data might directly affect experimental results and their biological interpretation. Here, we will describe typical challenges and caveats in cellular barcoding publications available so far.
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Affiliation(s)
- Leonid V Bystrykh
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Building 3226, Groningen, 9713, AV, The Netherlands.
| | - Mirjam E Belderbos
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Building 3226, Groningen, 9713, AV, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
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26
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MiR-150 impairs inflammatory cytokine production by targeting ARRB-2 after blocking CD28/B7 costimulatory pathway. Immunol Lett 2015; 172:1-10. [PMID: 26549736 DOI: 10.1016/j.imlet.2015.11.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022]
Abstract
MiR-150, a major modulator negatively regulating the development and differentiation of various immune cells, is widely involved in orchestrating inflammation. In transplantation immunity, miR-150 can effectively induce immune tolerance, although the underlying mechanisms have not been fully elucidated. In the current study, we found that miR-150 is elevated after blocking CD28/B7 co-stimulatory signaling pathway and impaired IL-2 production by targeting ARRB2. Further investigation suggested that miR-150 not only repressed the level of ARRB2/PDE4 directly but also prevented AKT/ARRB2/PDE4 trimer recruitment into the lipid raft by inhibiting the activities of PI3K and AKT through the cAMP-PKA-Csk signaling pathway. This leads to the interruption of cAMP degradation and subsequently results in inhibition of the NF-kB pathway and reduced production of both IL-2 and TNF. In conclusion, our study demonstrated that miR-150 can effectively prevent CD28/B7 co-stimulatory signaling transduction, decrease production of inflammatory cytokines, such as IL-2 and TNF, and elicit the induction of immune tolerance. Therefore, miR-150 could become a novel potential therapeutic target in transplantation immunology.
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Ranganathan P, Jayakumar C, Tang Y, Park KM, Teoh JP, Su H, Li J, Kim IM, Ramesh G. MicroRNA-150 deletion in mice protects kidney from myocardial infarction-induced acute kidney injury. Am J Physiol Renal Physiol 2015; 309:F551-8. [PMID: 26109086 DOI: 10.1152/ajprenal.00076.2015] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/18/2015] [Indexed: 11/22/2022] Open
Abstract
Despite greater understanding of acute kidney injury (AKI) in animal models, many of the preclinical studies are not translatable. Most of the data were derived from a bilateral renal pedicle clamping model with warm ischemia. However, ischemic injury of the kidney in humans is distinctly different and does not involve clamping of renal vessel. Permanent ligation of the left anterior descending coronary artery model was used to test the role of microRNA (miR)-150 in AKI. Myocardial infarction in this model causes AKI which is similar to human cardiac bypass surgery. Moreover, the time course of serum creatinine and biomarker elevation were also similar to human ischemic injury. Deletion of miR-150 suppressed AKI which was associated with suppression of inflammation and interstitial cell apoptosis. Immunofluorescence staining with endothelial marker and marker of apoptosis suggested that dying cells are mostly endothelial cells with minimal epithelial cell apoptosis in this model. Interestingly, deletion of miR-150 also suppressed interstitial fibrosis. Consistent with protection, miR-150 deletion causes induction of its target gene insulin-like growth factor-1 receptor (IGF-1R) and overexpression of miR-150 in endothelial cells downregulated IGF-1R, suggesting miR-150 may mediate its detrimental effects through suppression of IGF-1R pathways.
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Affiliation(s)
- Punithavathi Ranganathan
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Calpurnia Jayakumar
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Yaoping Tang
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Kyoung-mi Park
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Jian-peng Teoh
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Huabo Su
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Jie Li
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Il-man Kim
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
| | - Ganesan Ramesh
- Department of Medicine and Vascular Biology Center, Georgia Regents University, Augusta, Georgia
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Testa U, Pelosi E. MicroRNAs expressed in hematopoietic stem/progenitor cells are deregulated in acute myeloid leukemias. Leuk Lymphoma 2015; 56:1466-74. [PMID: 25242094 DOI: 10.3109/10428194.2014.955019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MicroRNAs are key regulators of hematopoiesis, specifically involved in regulating the maintenance of stemness of primitive hematopoietic progenitor cells (HPCs) and the early and late stages of hematopoietic differentiation. Some microRNAs have been found to be expressed in hematopoietic stem cells (HSCs) and primitive HPCs, and play a relevant role in regulation of the early steps of hematopoietic cell differentiation. Notable examples of these microRNAs are given by miR-22, miR-29, miR-125 and miR-126. These HSC/HPC-regulating microRNAs are often deregulated in some subsets of acute myeloid leukemia (AML), with pathogenic, diagnostic and prognostic implications. Therefore, elucidation of the pattern of microRNA expression at the level of the early stages of hematopoietic cell differentiation has essential implications, not only for elucidation of the molecular bases of the early stages of hematopoietic differentiation, but also for a better understanding of the pathogenic mechanisms underlying AML.
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Affiliation(s)
- Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità , Rome , Italy
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29
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Palagani A, Op de Beeck K, Naulaerts S, Diddens J, Sekhar Chirumamilla C, Van Camp G, Laukens K, Heyninck K, Gerlo S, Mestdagh P, Vandesompele J, Berghe WV. Ectopic microRNA-150-5p transcription sensitizes glucocorticoid therapy response in MM1S multiple myeloma cells but fails to overcome hormone therapy resistance in MM1R cells. PLoS One 2014; 9:e113842. [PMID: 25474406 PMCID: PMC4256227 DOI: 10.1371/journal.pone.0113842] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 11/01/2014] [Indexed: 11/18/2022] Open
Abstract
Glucocorticoids (GCs) selectively trigger cell death in the multiple myeloma cell line MM1S which express NR3C1/Glucocorticoid Receptor (GR) protein, but fail to kill MM1R cells which lack GR protein. Given recent demonstrations of altered microRNA profiles in a diverse range of haematological malignancies and drug resistance, we characterized GC inducible mRNA and microRNA transcription profiles in GC sensitive MM1S as compared to GC resistant MM1R cells. Transcriptome analysis revealed that GCs regulate expression of multiple genes involved in cell cycle control, cell organization, cell death and immunological disease in MM1S cells, which remain unaffected in MM1R cells. With respect to microRNAs, mir-150-5p was identified as the most time persistent GC regulated microRNA, out of 5 QPCR validated microRNAs (mir-26b, mir-125a-5p, mir-146-5p, mir-150-5p, and mir-184), which are GC inducible in MM1S but not in MM1R cells. Functional studies further revealed that ectopic transfection of a synthetic mir-150-5p mimics GR dependent gene expression changes involved in cell death and cell proliferation pathways. Remarkably, despite the gene expression changes observed, overexpression of mir-150-5p in absence of GCs did not trigger significant cytotoxicity in MM1S or MM1R cells. This suggests the requirement of additional steps in GC induced cell death, which can not be mimicked by mir-150-5p overexpression alone. Interestingly, a combination of mir-150-5p transfection with low doses GC in MM1S cells was found to sensitize therapy response, whereas opposite effects could be observed with a mir-150-5p specific antagomir. Although mir-150-5p overexpression did not substantially change GR expression levels, it was found that mir-150-5p evokes GR specific effects through indirect mRNA regulation of GR interacting transcription factors and hormone receptors, GR chaperones, as well as various effectors of unfolded protein stress and chemokine signalling. Altogether GC-inducible mir-150-5p adds another level of regulation to GC specific therapeutic responses in multiple myeloma.
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Affiliation(s)
- Ajay Palagani
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
- Laboratory of Eukaryotic Gene Expression and Signal Transduction (LEGEST), Department of Physiology, Ghent University, Ghent, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Laboratory of Cancer Research and Clinical Oncology, Department of Medical Oncology, University of Antwerp/Antwerp University Hospital, Antwerp, Belgium
| | - Stefan Naulaerts
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp & University Hospital Antwerp, Antwerp, Belgium
- Advanced Database Research and Modelling (ADReM), Department of Mathematics & Computer sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Jolien Diddens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Chandra Sekhar Chirumamilla
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp & University Hospital Antwerp, Antwerp, Belgium
- Advanced Database Research and Modelling (ADReM), Department of Mathematics & Computer sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Karen Heyninck
- Laboratory of Eukaryotic Gene Expression and Signal Transduction (LEGEST), Department of Physiology, Ghent University, Ghent, Belgium
| | - Sarah Gerlo
- VIB-UGent Department of Medical Protein Research, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Joke Vandesompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
- Laboratory of Eukaryotic Gene Expression and Signal Transduction (LEGEST), Department of Physiology, Ghent University, Ghent, Belgium
- * E-mail:
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Hu K, Xu C, Ni H, Xu Z, Wang Y, Xu S, Ji K, Xiong J, Liu H. Mir-218 contributes to the transformation of 5-Aza/GF induced umbilical cord mesenchymal stem cells into hematopoietic cells through the MITF pathway. Mol Biol Rep 2014; 41:4803-16. [DOI: 10.1007/s11033-014-3351-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
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Montagner S, Dehó L, Monticelli S. MicroRNAs in hematopoietic development. BMC Immunol 2014; 15:14. [PMID: 24678908 PMCID: PMC4000146 DOI: 10.1186/1471-2172-15-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/26/2014] [Indexed: 02/08/2023] Open
Abstract
Background MicroRNAs (miRNAs) are short non-coding RNAs involved in the posttranscriptional regulation of a wide range of biological processes. By binding to complementary sequences on target messenger RNAs, they trigger translational repression and degradation of the target, eventually resulting in reduced protein output. MiRNA-dependent regulation of protein translation is a very widespread and evolutionarily conserved mechanism of posttranscriptional control of gene expression. Accordingly, a high proportion of mammalian genes are likely to be regulated by miRNAs. In the hematopoietic system, both transcriptional and posttranscriptional regulation of gene expression ensure proper differentiation and function of stem cells, committed progenitors as well as mature cells. Results In recent years, miRNA expression profiling of various cell types in the hematopoietic system, as well as gene-targeting approaches to assess the function of individual miRNAs, revealed the importance of this type of regulation in the development of both innate and acquired immunity. Conclusions We discuss the general role of miRNA biogenesis in the development of hematopoietic cells, as well as specific functions of individual miRNAs in stem cells as well as in mature immune cells.
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Affiliation(s)
| | | | - Silvia Monticelli
- Institute for Research in Biomedicine, Via Vincenzo Vela 6, Bellinzona CH-6500, Switzerland.
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Abstract
As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in miRNA-related research demands global miRNA expression profiling on large numbers of samples. We describe here a robust protocol that supports high-throughput sample labeling and detection on hundreds of samples simultaneously. This method employs 96-well-based miRNA capturing from total RNA samples and on-site biochemical reactions, coupled with bead-based detection in 96-well format for hundreds of miRNAs per sample. With low-cost, high-throughput, high detection specificity, and flexibility to profile both small and large numbers of samples, this protocol can be adapted in a wide range of laboratory settings.
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Affiliation(s)
- Yanwen Guo
- Department of Genetics, Yale Stem Cell Center, Yale University, 10 Amistad Street, New Haven, CT, 06520-8005, USA
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33
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Cheng J, Guo S, Chen S, Mastriano SJ, Liu C, D’Alessio AC, Hysolli E, Guo Y, Yao H, Megyola CM, Li D, Liu J, Pan W, Roden CA, Zhou XL, Heydari K, Chen J, Park IH, Ding Y, Zhang Y, Lu J. An extensive network of TET2-targeting MicroRNAs regulates malignant hematopoiesis. Cell Rep 2013; 5:471-81. [PMID: 24120864 PMCID: PMC3834864 DOI: 10.1016/j.celrep.2013.08.050] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/30/2013] [Accepted: 08/29/2013] [Indexed: 02/05/2023] Open
Abstract
The Ten-Eleven-Translocation 2 (TET2) gene, which oxidates 5-methylcytosine in DNA to 5-hydroxylmethylcytosine (5hmC), is a key tumor suppressor frequently mutated in hematopoietic malignancies. However, the molecular regulation of TET2 expression is poorly understood. We show that TET2 is under extensive microRNA (miRNA) regulation, and such TET2 targeting is an important pathogenic mechanism in hematopoietic malignancies. Using a high-throughput 3' UTR activity screen, we identify >30 miRNAs that inhibit TET2 expression and cellular 5hmC. Forced expression of TET2-targeting miRNAs in vivo disrupts normal hematopoiesis, leading to hematopoietic expansion and/or myeloid differentiation bias, whereas coexpression of TET2 corrects these phenotypes. Importantly, several TET2-targeting miRNAs, including miR-125b, miR-29b, miR-29c, miR-101, and miR-7, are preferentially overexpressed in TET2-wild-type acute myeloid leukemia. Our results demonstrate the extensive roles of miRNAs in functionally regulating TET2 and cellular 5hmC and reveal miRNAs with previously unrecognized oncogenic potential. Our work suggests that TET2-targeting miRNAs might be exploited in cancer diagnosis.
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Affiliation(s)
- Jijun Cheng
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Shangqin Guo
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Department of Cell Biology, Yale University, New Haven, CT 06520, USA
| | - Suning Chen
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Stephen J. Mastriano
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Chaochun Liu
- Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12201, USA
| | - Ana C. D’Alessio
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Eriona Hysolli
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Yanwen Guo
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Hong Yao
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Cynthia M. Megyola
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Dan Li
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Jun Liu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Wen Pan
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Christine A. Roden
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Xiao-Ling Zhou
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Department of Cell Biology and Genetics, Shantou University Medical College, Guangdong 515041, China
| | - Kartoosh Heydari
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Jianjun Chen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - In-Hyun Park
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12201, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Lu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
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34
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The role of miR-150 in normal and malignant hematopoiesis. Oncogene 2013; 33:3887-93. [PMID: 23955084 DOI: 10.1038/onc.2013.346] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/24/2013] [Accepted: 06/24/2013] [Indexed: 12/18/2022]
Abstract
MicroRNAs are a class of small non-coding RNAs that have been implicated to mediate gene regulation in virtually all important biological processes. Recently there is accumulating evidence showing that miR-150 has essential regulatory roles in both normal and malignant hematopoiesis and holds great potential as a therapeutic target in treating various types of hematopoietic malignancies. The purpose of this review is to summarize our current knowledge about the expression patterns, biological functions and regulatory mechanisms of miR-150 in normal and malignant hematopoiesis, and to highlight the important questions to be answered in this burgeoning field.
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35
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Cheng WC, Kingsbury TJ, Wheelan SJ, Civin CI. A simple high-throughput technology enables gain-of-function screening of human microRNAs. Biotechniques 2013; 54:77-86. [PMID: 23384178 DOI: 10.2144/000113991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/14/2013] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRs) regulate cellular processes by modulating gene expression. Although transcriptomic studies have identified numerous miRs differentially expressed in diseased versus normal cells, expression analysis alone cannot distinguish miRs driving a disease phenotype from those merely associated with the disease. To address this limitation, we developed miR-HTS, a method for unbiased high-throughput screening of the miRNome to identify functionally relevant miRs. Herein, we applied miR-HTS to simultaneously analyze the effects of 578 lentivirally transduced human miRs or miR clusters on growth of the IMR90 human lung fibroblast cell line. Growth-regulatory miRs were identified by quantitating the representation (i.e., relative abundance) of cells overexpressing each miR over a one-month culture of IMR90, using a panel of custom-designed quantitative real-time PCR (qPCR) assays specific for each transduced miR expression cassette. The miR-HTS identified 4 miRs previously reported to inhibit the growth of human lung-derived cell lines and 55 novel growth-inhibitory miR candidates. Nine of 12 (75%) selected candidate miRs were validated and shown to inhibit IMR90 cell growth. Thus, this novel lentiviral library- and qPCR-based miR-HTS technology provides a sensitive platform for functional screening that is straightforward and relatively inexpensive.
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Affiliation(s)
- Wen-Chih Cheng
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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36
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miR-150 promotes the proliferation of lung cancer cells by targeting P53. FEBS Lett 2013; 587:2346-51. [PMID: 23747308 DOI: 10.1016/j.febslet.2013.05.059] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 05/28/2013] [Indexed: 12/16/2022]
Abstract
Lung cancer is one of the most common causes for cancer-related death. Previous studies suggested that uncontrolled cell proliferation induced by activation of pro-cancer genes or inhibition of cancer suppressor genes plays an important role in the pathogenesis of lung cancer. Here, we demonstrate that miR-150 is aberrantly upregulated in lung cancer tissue and negatively correlates with the expression of the proapoptotic gene p53 but not EGR2. We show that miR-150 specifically targets the 3'-UTR of p53 and regulates its expression. Inhibition of miR-150 effectively delays cell proliferation and promotes apoptosis, accompanied by increased p53 protein expression. Our data reveals the mechanisms underlying miR-150 regulated lung cancer pathogenesis, which might be beneficial for lung cancer therapy.
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37
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Edelstein LC, McKenzie SE, Shaw C, Holinstat MA, Kunapuli SP, Bray PF. MicroRNAs in platelet production and activation. J Thromb Haemost 2013; 11 Suppl 1:340-50. [PMID: 23809137 DOI: 10.1111/jth.12214] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent work by the Encyclopedia of DNA Elements project showed that non-protein-coding RNAs account for an unexpectedly large proportion of the human genome. Among these non-coding RNAs are microRNAs (miRNAs), which are small RNA molecules that modulate protein expression by degrading mRNA or repressing mRNA translation. MiRNAs have been shown to play important roles in hematopoiesis including embryonic stem cell differentiation, erythropoiesis, granulocytopoiesis/monocytopoiesis, lymphopoiesis, and megakaryocytopoiesis. Additionally, disordered miRNA biogenesis and quantitative or qualitative alterations in miRNAs and their targets are associated with hematological pathologies. Platelets contain machinery to process pre-miRNAs into mature miRNAs, and specific platelet miRNA levels have been found to correlate with platelet reactivity. This review summarizes the current state of knowledge of miRNAs in megakaryocytes and platelets, and the exciting possibilities for future megakaryocyte-platelet transcriptome research.
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Affiliation(s)
- L C Edelstein
- The Cardeza Foundation for Hematologic Research and Department of Medicine, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
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38
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Jacob NK, Cooley JV, Yee TN, Jacob J, Alder H, Wickramasinghe P, Maclean KH, Chakravarti A. Identification of sensitive serum microRNA biomarkers for radiation biodosimetry. PLoS One 2013; 8:e57603. [PMID: 23451251 PMCID: PMC3581493 DOI: 10.1371/journal.pone.0057603] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/22/2013] [Indexed: 12/13/2022] Open
Abstract
Exposure to ionizing radiation through environmental, occupational or a nuclear reactor accident such as the recent Fukushima Daiichi incident often results in major consequences to human health. The injury caused by radiation can manifest as acute radiation syndromes within weeks in organs with proliferating cells such as hematopoietic and gastrointestinal systems. Cancers, fibrosis and degenerative diseases are also reported in organs with differentiated cells, months or years later. Studies conducted on atom bomb survivors, nuclear reactor workers and animal models have shown a direct correlation of these effects with the absorbed dose. Physical dosimeters and the available radio-responsive biologics in body fluids, whose responses are rather indirect, have limitations to accurately evaluate the extent of post exposure damage. We have used an amplification-free, hybridization based quantitative assay utilizing the nCounter multiplex platform developed by nanoString Technologies to compare the levels of over 600 miRNAs in serum from mice irradiated at a range of 1 to 12 Gy at 24 and 48 hr time points. Development of a novel normalization strategy using multiple spike-in oligonucleotides allowed accurate measurement of radiation dose and time dependent changes in serum miRNAs. The response of several evolutionarily conserved miRNAs abundant in serum, were found to be robust and sensitive in the dose range relevant for medical triage and in patients who receive total body radiation as preparative regimen for bone marrow transplantation. Notably, miRNA-150, abundant in lymphocytes, exhibited a dose and time dependent decrease in serum, which we propose as a sensitive marker indicative of lymphocyte depletion and bone marrow damage. Our study has identified several markers useful for evaluation of an individual's response by minimally invasive methods, relevant to triage in case of a radiation accident and evaluation of toxicity and response during and after therapeutic radiation.
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Affiliation(s)
- Naduparambil Korah Jacob
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America.
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