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Chen Y, Kincaid RP, Bastin K, Fachko DN, Skalsky RL. MicroRNA-focused CRISPR/Cas9 screen identifies miR-142 as a key regulator of Epstein-Barr virus reactivation. PLoS Pathog 2024; 20:e1011970. [PMID: 38885264 PMCID: PMC11213311 DOI: 10.1371/journal.ppat.1011970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/28/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024] Open
Abstract
Reactivation from latency plays a significant role in maintaining persistent lifelong Epstein-Barr virus (EBV) infection. Mechanisms governing successful activation and progression of the EBV lytic phase are not fully understood. EBV expresses multiple viral microRNAs (miRNAs) and manipulates several cellular miRNAs to support viral infection. To gain insight into the host miRNAs regulating transitions from EBV latency into the lytic stage, we conducted a CRISPR/Cas9-based screen in EBV+ Burkitt lymphoma (BL) cells using anti-Ig antibodies to crosslink the B cell receptor (BCR) and induce reactivation. Using a gRNA library against >1500 annotated human miRNAs, we identified miR-142 as a key regulator of EBV reactivation. Genetic ablation of miR-142 enhanced levels of immediate early and early lytic gene products in infected BL cells. Ago2-PAR-CLIP experiments with reactivated cells revealed miR-142 targets related to Erk/MAPK signaling, including components directly downstream of the B cell receptor (BCR). Consistent with these findings, disruption of miR-142 enhanced SOS1 levels and Mek phosphorylation in response to surface Ig cross-linking. Effects could be rescued by inhibitors of Mek (cobimetinib) or Raf (dabrafenib). Taken together, these results show that miR-142 functionally regulates SOS1/Ras/Raf/Mek/Erk signaling initiated through the BCR and consequently, restricts EBV entry into the lytic cycle.
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Affiliation(s)
- Yan Chen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Rodney P. Kincaid
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Kelley Bastin
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Devin N. Fachko
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Rebecca L. Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
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2
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Chandra Jena B, Flaherty DP, O'Brien VP, Watts VJ. Biochemical pharmacology of adenylyl cyclases in cancer. Biochem Pharmacol 2024:116160. [PMID: 38522554 DOI: 10.1016/j.bcp.2024.116160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/11/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Globally, despite extensive research and pharmacological advancement, cancer remains one of the most common causes of mortality. Understanding the signaling pathways involved in cancer progression is essential for the discovery of new drug targets. The adenylyl cyclase (AC) superfamily comprises glycoproteins that regulate intracellular signaling and convert ATP into cyclic AMP, an important second messenger. The present review highlights the involvement of ACs in cancer progression and suppression, broken down for each specific mammalian AC isoform. The precise mechanisms by which ACs contribute to cancer cell proliferation and invasion are not well understood and are variable among cancer types; however, AC overactivation, along with that of downstream regulators, presents a potential target for novel anticancer therapies. The expression patterns of ACs in numerous cancers are discussed. In addition, we highlight inhibitors of AC-related signaling that are currently under investigation, with a focus on possible anti-cancer strategies. Recent discoveries with small molecules regarding more direct modulation AC activity are also discussed in detail. A more comprehensive understanding of different components in AC-related signaling could potentially lead to the development of novel therapeutic strategies for personalized oncology and might enhance the efficacy of chemoimmunotherapy in the treatment of various cancers.
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Affiliation(s)
- Bikash Chandra Jena
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Valerie P O'Brien
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Val J Watts
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA.
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3
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Geleta U, Prajapati P, Bachstetter A, Nelson PT, Wang WX. Sex-Biased Expression and Response of microRNAs in Neurological Diseases and Neurotrauma. Int J Mol Sci 2024; 25:2648. [PMID: 38473893 PMCID: PMC10931569 DOI: 10.3390/ijms25052648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Neurological diseases and neurotrauma manifest significant sex differences in prevalence, progression, outcome, and therapeutic responses. Genetic predisposition, sex hormones, inflammation, and environmental exposures are among many physiological and pathological factors that impact the sex disparity in neurological diseases. MicroRNAs (miRNAs) are a powerful class of gene expression regulator that are extensively involved in mediating biological pathways. Emerging evidence demonstrates that miRNAs play a crucial role in the sex dimorphism observed in various human diseases, including neurological diseases. Understanding the sex differences in miRNA expression and response is believed to have important implications for assessing the risk of neurological disease, defining therapeutic intervention strategies, and advancing both basic research and clinical investigations. However, there is limited research exploring the extent to which miRNAs contribute to the sex disparities observed in various neurological diseases. Here, we review the current state of knowledge related to the sexual dimorphism in miRNAs in neurological diseases and neurotrauma research. We also discuss how sex chromosomes may contribute to the miRNA sexual dimorphism phenomenon. We attempt to emphasize the significance of sexual dimorphism in miRNA biology in human diseases and to advocate a gender/sex-balanced science.
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Affiliation(s)
- Urim Geleta
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
| | - Paresh Prajapati
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
| | - Adam Bachstetter
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Neuroscience, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Wang-Xia Wang
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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4
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Huang W, Paul D, Calin GA, Bayraktar R. miR-142: A Master Regulator in Hematological Malignancies and Therapeutic Opportunities. Cells 2023; 13:84. [PMID: 38201290 PMCID: PMC10778542 DOI: 10.3390/cells13010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
MicroRNAs (miRNAs) are a type of non-coding RNA whose dysregulation is frequently associated with the onset and progression of human cancers. miR-142, an ultra-conserved miRNA with both active -3p and -5p mature strands and wide-ranging physiological targets, has been the subject of countless studies over the years. Due to its preferential expression in hematopoietic cells, miR-142 has been found to be associated with numerous types of lymphomas and leukemias. This review elucidates the multifaceted role of miR-142 in human physiology, its influence on hematopoiesis and hematopoietic cells, and its intriguing involvement in exosome-mediated miR-142 transport. Moreover, we offer a comprehensive exploration of the genetic and molecular landscape of the miR-142 genomic locus, highlighting its mutations and dysregulation within hematological malignancies. Finally, we discuss potential avenues for harnessing the therapeutic potential of miR-142 in the context of hematological malignancies.
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Affiliation(s)
- Wilson Huang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (W.H.); (G.A.C.)
| | - Doru Paul
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA;
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (W.H.); (G.A.C.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Recep Bayraktar
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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5
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Pohlers M, Gies S, Taenzer T, Stroeder R, Theobald L, Ludwig N, Kim YJ, Bohle RM, Solomayer EF, Meese E, Hart M, Walch-Rückheim B. Th17 cells target the metabolic miR-142-5p-succinate dehydrogenase subunit C/D (SDHC/SDHD) axis, promoting invasiveness and progression of cervical cancers. Mol Oncol 2023. [PMID: 37899663 DOI: 10.1002/1878-0261.13546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/19/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023] Open
Abstract
During cervical carcinogenesis, T-helper (Th)-17 cells accumulate in the peripheral blood and tumor tissues of cancer patients. We previously demonstrated that Th17 cells are associated with therapy resistance as well as cervical cancer metastases and relapse; however, the underlying Th17-driven mechanisms are not fully understood. Here, using microarrays, we found that Th17 cells induced an epithelial-to-mesenchymal transition (EMT) phenotype of cervical cancer cells and promoted migration and invasion of 2D cultures and 3D spheroids via induction of microRNA miR-142-5p. As the responsible mechanism, we identified the subunits C and D of the succinate dehydrogenase (SDH) complex as new targets of miR-142-5p and provided evidence that Th17-miR-142-5p-dependent reduced expression of SDHC and SDHD mediated enhanced migration and invasion of cancer cells using small interfering RNAs (siRNAs) for SDHC and SDHD, and miR-142-5p inhibitors. Consistently, patients exhibited high levels of succinate in their serum associated with lymph node metastases and diminished expression of SDHD in patient biopsies correlated with increased numbers of Th17 cells. Correspondingly, a combination of weak or negative SDHD expression and a ratio of Th17/CD4+ T cells > 43.90% in situ was associated with reduced recurrence-free survival. In summary, we unraveled a previously unknown molecular mechanism by which Th17 cells promote cervical cancer progression and suggest evaluation of Th17 cells as a potential target for immunotherapy in cervical cancer.
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Affiliation(s)
- Maike Pohlers
- Center of Human and Molecular Biology (ZHMB), Institute of Virology, Saarland University, Homburg/Saar, Germany
| | - Selina Gies
- Center of Human and Molecular Biology (ZHMB), Institute of Virology, Saarland University, Homburg/Saar, Germany
| | - Tanja Taenzer
- Center of Human and Molecular Biology (ZHMB), Institute of Virology, Saarland University, Homburg/Saar, Germany
| | - Russalina Stroeder
- Department of Obstetrics and Gynecology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Laura Theobald
- Center of Human and Molecular Biology (ZHMB), Institute of Virology, Saarland University, Homburg/Saar, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, Homburg/Saar, Germany
| | - Yoo-Jin Kim
- Institute of Pathology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Rainer Maria Bohle
- Institute of Pathology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Erich Franz Solomayer
- Department of Obstetrics and Gynecology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, Homburg/Saar, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, Homburg/Saar, Germany
| | - Barbara Walch-Rückheim
- Center of Human and Molecular Biology (ZHMB), Institute of Virology, Saarland University, Homburg/Saar, Germany
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Zhang B, Zhao D, Chen F, Frankhouser D, Wang H, Pathak KV, Dong L, Torres A, Garcia-Mansfield K, Zhang Y, Hoang DH, Chen MH, Tao S, Cho H, Liang Y, Perrotti D, Branciamore S, Rockne R, Wu X, Ghoda L, Li L, Jin J, Chen J, Yu J, Caligiuri MA, Kuo YH, Boldin M, Su R, Swiderski P, Kortylewski M, Pirrotte P, Nguyen LXT, Marcucci G. Acquired miR-142 deficit in leukemic stem cells suffices to drive chronic myeloid leukemia into blast crisis. Nat Commun 2023; 14:5325. [PMID: 37658085 PMCID: PMC10474062 DOI: 10.1038/s41467-023-41167-z] [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: 11/07/2022] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
The mechanisms underlying the transformation of chronic myeloid leukemia (CML) from chronic phase (CP) to blast crisis (BC) are not fully elucidated. Here, we show lower levels of miR-142 in CD34+CD38- blasts from BC CML patients than in those from CP CML patients, suggesting that miR-142 deficit is implicated in BC evolution. Thus, we create miR-142 knockout CML (i.e., miR-142-/-BCR-ABL) mice, which develop BC and die sooner than miR-142 wt CML (i.e., miR-142+/+BCR-ABL) mice, which instead remain in CP CML. Leukemic stem cells (LSCs) from miR-142-/-BCR-ABL mice recapitulate the BC phenotype in congenic recipients, supporting LSC transformation by miR-142 deficit. State-transition and mutual information analyses of "bulk" and single cell RNA-seq data, metabolomic profiling and functional metabolic assays identify enhanced fatty acid β-oxidation, oxidative phosphorylation and mitochondrial fusion in LSCs as key steps in miR-142-driven BC evolution. A synthetic CpG-miR-142 mimic oligodeoxynucleotide rescues the BC phenotype in miR-142-/-BCR-ABL mice and patient-derived xenografts.
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Affiliation(s)
- Bin Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA.
| | - Dandan Zhao
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Fang Chen
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - David Frankhouser
- Department of Computational and Quantitative Medicine, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Huafeng Wang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Khyatiben V Pathak
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Anakaren Torres
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Krystine Garcia-Mansfield
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Yi Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Dinh Hoa Hoang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Min-Hsuan Chen
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Shu Tao
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Hyejin Cho
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Yong Liang
- DNA/RNA Peptide Shared Resources, Beckman Research Institute, Duarte, CA, USA
| | - Danilo Perrotti
- Department of Medicine and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine Baltimore, Baltimore, MD, USA
- Department of Immunology and Inflammation, Centre of Hematology, Imperial College of London, London, UK
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Russell Rockne
- Department of Computational and Quantitative Medicine, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Xiwei Wu
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Lucy Ghoda
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Jie Jin
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Michael A Caligiuri
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Mark Boldin
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Piotr Swiderski
- DNA/RNA Peptide Shared Resources, Beckman Research Institute, Duarte, CA, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, Beckman Research Institute, Duarte, CA, USA
| | - Patrick Pirrotte
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Le Xuan Truong Nguyen
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA.
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA.
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Wang X, Zhang C, Song H, Yuan J, Zhang X, Yuan Y, Zhang L, He J. Characterization of LIMA1 and its emerging roles and potential therapeutic prospects in cancers. Front Oncol 2023; 13:1115943. [PMID: 37274282 PMCID: PMC10235525 DOI: 10.3389/fonc.2023.1115943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
Actin is the most abundant and highly conserved cytoskeletal protein present in all eukaryotic cells. Remodeling of the actin cytoskeleton is controlled by a variety of actin-binding proteins that are extensively involved in biological processes such as cell motility and maintenance of cell shape. LIM domain and actin-binding protein 1 (LIMA1), as an important actin cytoskeletal regulator, was initially thought to be a tumor suppressor frequently downregulated in epithelial tumors. Importantly, the deficiency of LIMA1 may be responsible for dysregulated cytoskeletal dynamics, altered cell motility and disrupted cell-cell adhesion, which promote tumor proliferation, invasion and migration. As research progresses, the roles of LIMA1 extend from cytoskeletal dynamics and cell motility to cell division, gene regulation, apical extrusion, angiogenesis, cellular metabolism and lipid metabolism. However, the expression of LIMA1 in malignant tumors and its mechanism of action have not yet been elucidated, and many problems and challenges remain to be addressed. Therefore, this review systematically describes the structure and biological functions of LIMA1 and explores its expression and regulatory mechanism in malignant tumors, and further discusses its clinical value and therapeutic prospects.
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Affiliation(s)
- Xiaoxiao Wang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Chao Zhang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Huangqin Song
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Junlong Yuan
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Xiaomin Zhang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Yiran Yuan
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Lei Zhang
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- Hepatic Surgery Center, Institute of Hepato-Pancreato-Biliary Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiefeng He
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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8
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Consequences of genetic variants in miRNA genes. Comput Struct Biotechnol J 2022; 20:6443-6457. [DOI: 10.1016/j.csbj.2022.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022] Open
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9
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Menegatti J, Nakel J, Stepanov YK, Caban KM, Ludwig N, Nord R, Pfitzner T, Yazdani M, Vilimova M, Kehl T, Lenhof HP, Philipp SE, Meese E, Fröhlich T, Grässer FA, Hart M. Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse Large B-Cell Lymphoma. Cancers (Basel) 2022; 14:cancers14205031. [PMID: 36291816 PMCID: PMC9600116 DOI: 10.3390/cancers14205031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary The gene of the human tumor suppressive microRNA-142 (miR-142) carries mutations in about 20% of cases of diffuse large B-cell lymphoma (DLBCL). Because microRNAs post-transcriptionally regulate the protein expression of their cognate messenger RNA (mRNAs) targets, we determined the effect of miR-142 knockout on protein expression in two cell lines derived from DLBCL. We found a significant up-regulation of 52 proteins but also a down-regulation of 41 proteins upon miR-142 deletion. Knockout of a miRNA may be used to identify novel targets, and seed-sequence mutants of a miRNA unable to bind to their targets can be used to confirm potential novel targets. With this approach, we identify AKT1S1, CCNB1, LIMA1 and TFRC as novel targets of miR-142. As miR-142 is highly present in the miRNA processing RISC complexes, the deletion of this miRNA might result in its replacement by other miRNAs, thus introducing an additional layer of complexity regarding gene regulation. Abstract Background: As microRNA-142 (miR-142) is the only human microRNA gene where mutations have consistently been found in about 20% of all cases of diffuse large B-cell lymphoma (DLBCL), we wanted to determine the impact of miR-142 inactivation on protein expression of DLBCL cell lines. Methods: miR-142 was deleted by CRISPR/Cas9 knockout in cell lines from DLBCL. Results: By proteome analyses, miR-142 knockout resulted in a consistent up-regulation of 52 but also down-regulation of 41 proteins in GC-DLBCL lines BJAB and SUDHL4. Various mitochondrial ribosomal proteins were up-regulated in line with their pro-tumorigenic properties, while proteins necessary for MHC-I presentation were down-regulated in accordance with the finding that miR-142 knockout mice have a defective immune response. CFL2, CLIC4, STAU1, and TWF1 are known targets of miR-142, and we could additionally confirm AKT1S1, CCNB1, LIMA1, and TFRC as new targets of miR-142-3p or -5p. Conclusions: Seed-sequence mutants of miR-142 confirmed potential targets and novel targets of miRNAs can be identified in miRNA knockout cell lines. Due to the complex contribution of miRNAs within cellular regulatory networks, in particular when miRNAs highly present in RISC complexes are replaced by other miRNAs, primary effects on gene expression may be covered by secondary layers of regulation.
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Affiliation(s)
- Jennifer Menegatti
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Jacqueline Nakel
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Youli K. Stepanov
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Karolina M. Caban
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Ruth Nord
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Thomas Pfitzner
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Maryam Yazdani
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Monika Vilimova
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Stephan E. Philipp
- Experimental and Clinical Pharmacology and Toxicology, Saarland University Medical School, 66421 Homburg, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Friedrich A. Grässer
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
- Correspondence: (F.A.G.); (M.H.)
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
- Correspondence: (F.A.G.); (M.H.)
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10
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Galka-Marciniak P, Kanduła Z, Tire A, Wegorek W, Gwozdz-Bak K, Handschuh L, Giefing M, Lewandowski K, Kozlowski P. Mutations in the miR-142 gene are not common in myeloproliferative neoplasms. Sci Rep 2022; 12:10924. [PMID: 35764886 PMCID: PMC9240003 DOI: 10.1038/s41598-022-15162-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Recent data indicate that MIR142 is the most frequently mutated miRNA gene and one of the most frequently mutated noncoding elements in all cancers, with mutations occurring predominantly in blood cancers, especially diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma. Functional analyses show that the MIR142 alterations have profound consequences for lympho- and myelopoiesis. Furthermore, one of the targets downregulated by miR-142-5p is CD274, which encodes PD-L1 that is elevated in many cancer types, including myeloproliferative neoplasms (MPNs). To extend knowledge about the occurrence of MIR142 mutations, we sequenced the gene in a large panel of MPNs [~ 700 samples, including polycythemia vera, essential thrombocythemia, primary myelofibrosis (PMF), and chronic myeloid leukemia], neoplasm types in which such mutations have never been tested, and in panels of acute myeloid leukemia (AML), and chronic lymphocytic leukemia (CLL). We identified 3 mutations (one in a PMF sample and two others in one CLL sample), indicating that MIR142 mutations are rare in MPNs. In summary, mutations in MIR142 are rare in MPNs; however, in specific subtypes, such as PMF, their frequency may be comparable to that observed in CLL or AML.
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Affiliation(s)
| | - Zuzanna Kanduła
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Adrian Tire
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wladyslaw Wegorek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Kinga Gwozdz-Bak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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11
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Elucidating miRNA Function in Cancer Biology via the Molecular Genetics’ Toolbox. Biomedicines 2022; 10:biomedicines10040915. [PMID: 35453665 PMCID: PMC9029477 DOI: 10.3390/biomedicines10040915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Micro-RNA (miRNAs) are short non-coding RNAs of about 18–20 nucleotides in length and are implicated in many cellular processes including proliferation, development, differentiation, apoptosis and cell signaling. Furthermore, it is well known that miRNA expression is frequently dysregulated in many cancers. Therefore, this review will highlight the various mechanisms by which microRNAs are dysregulated in cancer. Further highlights include the abundance of molecular genetics tools that are currently available to study miRNA function as well as their advantages and disadvantages with a special focus on various CRISPR/Cas systems This review provides general workflows and some practical considerations when studying miRNA function thus enabling researchers to make informed decisions in regards to the appropriate molecular genetics tool to be utilized for their experiments.
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12
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Abstract
Since their first discovery more than 20 years ago, miRNAs have been subject to deliberate research and analysis for revealing their physiological or pathological involvement. Regulatory roles of miRNAs in signal transduction, gene expression, and cellular processes in development, differentiation, proliferation, apoptosis, and homeostasis also imply their critical role in disease pathogenesis. Their roles in cancer, neurodegenerative diseases, and other systemic diseases have been studied broadly. In these regulatory pathways, their mutations and target sequence variations play critical roles to determine their functional repertoire. In this chapter, we summarize studies that investigated the role of mutations, polymorphisms, and other variations of miRNAs in respect to pathological processes.
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13
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Li H, Liu Y, Liu J, Sun Y, Wu J, Xiong Z, Zhang Y, Li B, Jin T. Assessment of ADCY9 polymorphisms and colorectal cancer risk in the Chinese Han population. J Gene Med 2021; 23:e3298. [PMID: 33232543 DOI: 10.1002/jgm.3298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/24/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Recently, ADCY9 has been found to be highly expressed in colon cancer, and high ADCY9 expressionis a poor prognostic factor of colon cancer. However, no study has reported on the relationship between single nucleotide polymorphisms (SNPs) of ADCY9 and colorectal cancer risk in the Chinese Han population. METHODS To evaluate the association between four ADCY9 SNPs and colorectal cancer risk, we performed a case-control study including 511 colorectal cancer patients and 511 healthy controls. SNPs were genotyped using the Agena MassARRAY platform (Agena Bioscience, San Diego, CA, USA). The distributions of alleles and genotypes frequencies between the case and control groups were compared using chi-squared. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression adjusted for age and gender to assess the association between SNPs and colorectal cancer risk. RESULTS The overall analysis found that rs2230742 was associated with an increased risk of colorectal cancer (AA versus GG: OR = 3.54, 95% CI = 1.16-10.86, p = 0.027; recessive model: OR = 3.55, 95% CI = 1.16-10.85, p = 0.027). Stratification analysis showed that rs2230742 was associated with an increased rectal cancer risk; rs11076810 was associated with a reduced colorectal cancer risk for age > 59 years. No association was observed between other two SNPs and colorectal cancer risk. CONCLUSIONS Our findings suggest that ADCY9 polymorphisms (rs2230742 and rs11076810) have an effect on colorectal cancer risk in the Chinese Han population. Future association and functional studies are required to confirm our findings and explore the mechanism of ADCY2 in colorectal cancer.
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Affiliation(s)
- Haiyue Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China
| | - Yuanwei Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China
| | - Jianfeng Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China
| | - Yao Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China
| | - Jiamin Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China
| | - Zichao Xiong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China
| | - Yi Zhang
- Department of Life Science, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Bin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi, China.,The 21st Century Biotechnology Co., Ltd, Xi'an, Shaanxi, China
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14
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Abstract
PURPOSE OF REVIEW MiRNAs are critical regulators for gene expression. Numerous studies have revealed how miRNAs contribute to the pathogenesis of hematologic malignancies. RECENT FINDINGS The identification of novel miRNA regulatory factors and pathways crucial for miRNA dysregulation has been linked to hematologic malignancies. miRNA expression profiling has shown their potential to predict outcomes and treatment responses. Recently, targeting miRNA biogenesis or pathways has become a promising therapeutic strategy with recent miRNA-therapeutics being developed. SUMMARY We provide a comprehensive overview of the role of miRNAs for diagnosis, prognosis, and therapeutic potential in hematologic malignancies.
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15
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Shi Y, Ding D, Qu R, Tang Y, Hao S. Non-Coding RNAs in Diffuse Large B-Cell Lymphoma. Onco Targets Ther 2020; 13:12097-12112. [PMID: 33262609 PMCID: PMC7699984 DOI: 10.2147/ott.s281810] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma worldwide. The molecular mechanisms underlying DLBCL have not been fully elucidated, and approximately 40% of patients who undergo standard chemoimmunotherapy still present with primary refractory disease or relapse. Non-coding RNAs (ncRNAs), a group of biomolecules functioning at the RNA level, are increasingly recognized as vital components of molecular biology. With the development of RNA-sequencing (RNA-Seq) technology, accumulating evidence shows that ncRNAs are important mediators of diverse biological processes such as cell proliferation, differentiation, and apoptosis. They are also considered promising biomarkers and better candidates than proteins and genes for the early recognition of disease onset, as they are associated with relative stability, specificity, and reproducibility. In this review, we provide the first comprehensive description of the current knowledge regarding three groups of ncRNAs—microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs)—focusing on their characteristics, molecular functions, as well as diagnostic and therapeutic potential in DLBCL. This review provides an exhaustive account for researchers to explore novel biomarkers for the diagnosis and prognosis of DLBCL and therapeutic targets.
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Affiliation(s)
- Yan Shi
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Daihong Ding
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Rongfeng Qu
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yan Tang
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuhong Hao
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
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16
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Mir142 loss unlocks IDH2 R140-dependent leukemogenesis through antagonistic regulation of HOX genes. Sci Rep 2020; 10:19390. [PMID: 33173219 PMCID: PMC7656267 DOI: 10.1038/s41598-020-76218-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
AML is a genetically heterogeneous disease and understanding how different co-occurring mutations cooperate to drive leukemogenesis will be crucial for improving diagnostic and therapeutic options for patients. MIR142 mutations have been recurrently detected in IDH-mutated AML samples. Here, we have used a mouse model to investigate the interaction between these two mutations and demonstrate a striking synergy between Mir142 loss-of-function and IDH2R140Q, with only recipients of double mutant cells succumbing to leukemia. Transcriptomic analysis of the non-leukemic single and leukemic double mutant progenitors, isolated from these mice, suggested a novel mechanism of cooperation whereby Mir142 loss-of-function counteracts aberrant silencing of Hoxa cluster genes by IDH2R140Q. Our analysis suggests that IDH2R140Q is an incoherent oncogene, with both positive and negative impacts on leukemogenesis, which requires the action of cooperating mutations to alleviate repression of Hoxa genes in order to advance to leukemia. This model, therefore, provides a compelling rationale for understanding how different mutations cooperate to drive leukemogenesis and the context-dependent effects of oncogenic mutations.
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17
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Li J, Zou J, Wan X, Sun C, Peng F, Chu Z, Hu Y. The Role of Noncoding RNAs in B-Cell Lymphoma. Front Oncol 2020; 10:577890. [PMID: 33194698 PMCID: PMC7645065 DOI: 10.3389/fonc.2020.577890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years, emerging evidence has suggested that noncoding RNAs (ncRNAs) participate in nearly every aspect of biological processes and play a crucial role in the genesis and progression of numerous tumors, including B-cell lymphoma. The exploration of ncRNA dysregulations and their functions in B-cell lymphoma provides new insights into lymphoma pathogenesis and is essential for indicating future clinical trials and optimizing the diagnostic and therapeutic strategies. In this review, we summarize the role of ncRNAs in B-cell lymphoma and discuss their potential in clinical applications.
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Affiliation(s)
- Jingwen Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Zou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyue Wan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangbo Chu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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18
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Urbanek-Trzeciak MO, Galka-Marciniak P, Nawrocka PM, Kowal E, Szwec S, Giefing M, Kozlowski P. Pan-cancer analysis of somatic mutations in miRNA genes. EBioMedicine 2020; 61:103051. [PMID: 33038763 PMCID: PMC7648123 DOI: 10.1016/j.ebiom.2020.103051] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background miRNAs are considered important players in oncogenesis, serving either as oncomiRs or suppressormiRs. Although the accumulation of somatic alterations is an intrinsic aspect of cancer development and many important cancer-driving mutations have been identified in protein-coding genes, the area of functional somatic mutations in miRNA genes is heavily understudied. Methods Here, based on the analysis of large genomic datasets, mostly the whole-exome sequencing of over 10,000 cancer/normal sample pairs deposited within the TCGA repository, we undertook an analysis of somatic mutations in miRNA genes. Findings We identified and characterized over 10,000 somatic mutations and showed that some of the miRNA genes are overmutated in Pan-Cancer and/or specific cancers. Nonrandom occurrence of the identified mutations was confirmed by a strong association of overmutated miRNA genes with KEGG pathways, most of which were related to specific cancer types or cancer-related processes. Additionally, we showed that mutations in some of the overmutated genes correlate with miRNA expression, cancer staging, and patient survival. Interpretation Our study is the first comprehensive Pan-Cancer study of cancer somatic mutations in miRNA genes. It may help to understand the consequences of mutations in miRNA genes and the identification of miRNA functional mutations. The results may also be the first step (form the basis and provide the resources) in the development of computational and/or statistical approaches/tools dedicated to the identification of cancer-driver miRNA genes. Funding This work was supported by research grants from the Polish National Science Centre 2016/22/A/NZ2/00184 and 2015/17/N/NZ3/03629.
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Affiliation(s)
| | | | - Paulina M Nawrocka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ewelina Kowal
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Sylwia Szwec
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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19
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Wu W, Shang Y, Dai S, Yu C, Wang J. Downregulation of miR‑142‑5p inhibits human aortic smooth muscle cell proliferation and migration by targeting MKL2. Mol Med Rep 2020; 22:277-285. [PMID: 32626937 PMCID: PMC7248461 DOI: 10.3892/mmr.2020.11093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
The increased proliferation and migration of vascular smooth muscle cells (VSMCs) are critical in the progression of atherosclerosis (AS). Platelet‑derived growth factor type BB (PDGF‑BB) may induce VSMC proliferation and migration. miR‑142‑5p plays a critical role in various biological processes, including tumorigenesis, angiogenesis and inflammation. However, whether miR‑142‑5p is involved in regulating the pathological process of arteriosclerosis remains to be elucidated. Therefore, in this study, the role of miR‑142‑5p in PDGF‑BB‑induced human aortic smooth muscle cell (HSAMC) proliferation and migration was investigated. The results revealed that the expression level of miR‑142‑5p was enhanced in the serum of patients with AS, while that of its target gene, myocardin‑like protein 2 (MKL2) was decreased, compared with that in healthy volunteers. Moreover, there was a negative correlation between miR‑142‑5p and MKL2 expression in the serum of patients with AS. Furthermore, the downregulation of miR‑142‑5p inhibited PDGF‑BB‑induced HASMC proliferation and migration; however, the inhibition of HASMC proliferation and migration was reversed by co‑transfection with small interfering RNA (siRNA) against MKL2 (siRNA‑MKL2). In addition, transfection with miR‑142‑5p inhibitor significantly increased the expression levels of MKL2, and decreased those of matrix metalloproteinase (MMP)2 and 9, and these effects were reversed by transfection with siRNA‑MKL2. Finally, MKL2 was proven to be a target of miR‑142‑5p. On the whole, the findings of the present study demonstrate that the downregulation of miR‑142‑5p inhibits human aortic smooth muscle cell (HSAMC) proliferation and migration possibly by targeting MKL2. Hence, miR‑142‑5p may prove to be a novel therapeutic target in the treatment of AS.
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Affiliation(s)
- Wei Wu
- Department of Cardiothoracic Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
| | - Yuqiang Shang
- Department of Cardiothoracic Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
| | - Shiling Dai
- Department of Cardiothoracic Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
| | - Chunjun Yu
- Department of Cardiothoracic Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
| | - Jie Wang
- Department of Cardiothoracic Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
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20
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The chilling of adenylyl cyclase 9 and its translational potential. Cell Signal 2020; 70:109589. [PMID: 32105777 DOI: 10.1016/j.cellsig.2020.109589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 12/26/2022]
Abstract
A recent break-through paper has revealed for the first time the high-resolution, three-dimensional structure of a mammalian trans-membrane adenylyl cyclase (tmAC) obtained by cryo-electronmicroscopy (cryo-EM). Reporting the structure of adenylyl cyclase 9 (AC9) in complex with activated Gsα, the cryo-EM study revealed that AC9 has three functionally interlinked, yet structurally distinct domains. The array of the twelve transmembrane helices is connected to the cytosolic catalytic core by two helical segments that are stabilized through the formation of a parallel coiled-coil. Surprisingly, in the presence of Gsα, the isoform-specific carboxyl-terminal tail of AC9 occludes the forskolin- as well as the active substrate-sites, resulting in marked autoinhibition of the enzyme. As AC9 has the lowest primary sequence homology with the eight further mammalian tmAC paralogues, it appears to be the best candidate for selective pharmacologic targeting. This is now closer to reality as the structural insight provided by the cryo-EM study indicates that all of the three structural domains are potential targets for bioactive agents. The present paper summarizes for molecular physiologists and pharmacologists what is known about the biological role of AC9, considers the potential modes of physiologic regulation, as well as pharmacologic targeting on the basis of the high-resolution cryo-EM structure. The translational potential of AC9 is considered upon highlighting the current state of genome-wide association screens, and the corresponding experimental evidence. Overall, whilst the high- resolution structure presents unique opportunities for the full understanding of the control of AC9, the data on the biological role of the enzyme and its translational potential are far from complete, and require extensive further study.
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21
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de Carvalho JB, de Morais GL, Vieira TCDS, Rabelo NC, Llerena JC, Gonzalez SMDC, de Vasconcelos ATR. miRNA Genetic Variants Alter Their Secondary Structure and Expression in Patients With RASopathies Syndromes. Front Genet 2019; 10:1144. [PMID: 31798637 PMCID: PMC6863982 DOI: 10.3389/fgene.2019.01144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/21/2019] [Indexed: 12/22/2022] Open
Abstract
RASopathies are a group of rare genetic diseases caused by germline mutations in genes involved in the RAS–mitogen-activated protein kinase (RAS-MAPK) pathway. Whole-exome sequencing (WES) is a powerful approach for identifying new variants in coding and noncoding DNA sequences, including miRNAs. miRNAs are fine-tuning negative regulators of gene expression. The presence of variants in miRNAs could lead to malfunctions of regulation, resulting in diseases. Here, we identified 41 variants in mature miRNAs through WES analysis in five patients with previous clinical diagnosis of RASopathies syndromes. The pathways, biological processes, and diseases that were over-represented among the target genes of the mature miRNAs harboring variants included the RAS, MAPK, RAP1, and PIK3-Akt signaling pathways, neuronal differentiation, neurogenesis and nervous system development, congenital cardiac defects (hypertrophic cardiomyopathy, dilated cardiomyopathy, and arrhythmogenic right ventricular cardiomyopathy), and the phenotypes and syndromes of RASopathies (Noonan syndrome, Legius syndrome, Costello syndrome, Cafe au lait spots multiple, subaortic stenosis, pulmonary valve stenosis, and LEOPARD syndrome). Furthermore, eight selected variants in nine mature miRNAs (hsa-miR-1304, hsa-miR-146a, hsa-miR-196a2, hsa-miR-499a/hsa-miR-499b, hsa-miR-449b, hsa-miR-548l, hsa-miR-575, and hsa-miR-593) may have caused alterations in the secondary structures of miRNA precursor. Selected miRNAs containing variants such as hsa-miR-146a-3p, hsa-miR-196a-3p, hsa-miR-548l, hsa-miR-449b-5p, hsa-miR-575, and hsa-miR499a-3p could regulate classical genes associated with Rasopathies and RAS-MAPK pathways, contributing to modify the expression pattern of miRNAs in patients. RT-qPCR expression analysis revealed four differentially expressed miRNAs that were downregulated: miRNA-146a-3p in P1, P2, P3, P4, and P5, miR-1304-3p in P2, P3, P4, and P5, miR-196a2-3p in P3, and miR-499b-5p in P1. miR-499a-3p was upregulated in P1, P3, and P5. These results indicate that miRNAs show different expression patterns when these variants are present in patients. Therefore, this study characterized the role of miRNAs harboring variants related to RASopathies for the first time and indicated the possible implications of these variants for phenotypes of RASopathies such as congenital cardiac defects and cardio-cerebrovascular diseases. The expression and existence of miRNA variants may be used in the study of biomarkers of the RASopathies.
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Affiliation(s)
- Joseane Biso de Carvalho
- Bioinformatics Laboratory (LABINFO), National Laboratory for Scientific Computing (LNCC), Petrópolis, Brazil
| | - Guilherme Loss de Morais
- Bioinformatics Laboratory (LABINFO), National Laboratory for Scientific Computing (LNCC), Petrópolis, Brazil
| | - Thays Cristine Dos Santos Vieira
- Laboratory of Genomic Medicine, National Institute of Women, Children and Adolescents Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, Brazil
| | - Natana Chaves Rabelo
- Laboratory of Genomic Medicine, National Institute of Women, Children and Adolescents Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, Brazil
| | - Juan Clinton Llerena
- Department of Medical Genetics, National Institute of Women, Children and Adolescents Health Fernades Figueira, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Sayonara Maria de Carvalho Gonzalez
- Laboratory of Genomic Medicine, National Institute of Women, Children and Adolescents Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, Brazil
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22
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Somatic Mutations in miRNA Genes in Lung Cancer-Potential Functional Consequences of Non-Coding Sequence Variants. Cancers (Basel) 2019; 11:cancers11060793. [PMID: 31181801 PMCID: PMC6627760 DOI: 10.3390/cancers11060793] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023] Open
Abstract
A growing body of evidence indicates that miRNAs may either drive or suppress oncogenesis. However, little is known about somatic mutations in miRNA genes. To determine the frequency and potential consequences of miRNA gene mutations, we analyzed whole exome sequencing datasets of 569 lung adenocarcinoma (LUAD) and 597 lung squamous cell carcinoma (LUSC) samples generated in The Cancer Genome Atlas (TCGA) project. Altogether, we identified 1091 somatic sequence variants affecting 522 different miRNA genes and showed that half of all cancers had at least one such somatic variant/mutation. These sequence variants occurred in most crucial parts of miRNA precursors, including mature miRNA and seed sequences. Due to our findings, we hypothesize that seed mutations may affect miRNA:target interactions, drastically changing the pool of predicted targets. Mutations may also affect miRNA biogenesis by changing the structure of miRNA precursors, DROSHA and DICER cleavage sites, and regulatory sequence/structure motifs. We identified 10 significantly overmutated hotspot miRNA genes, including the miR-379 gene in LUAD enriched in mutations in the mature miRNA and regulatory sequences. The occurrence of mutations in the hotspot miRNA genes was also shown experimentally. We present a comprehensive analysis of somatic variants in miRNA genes and show that some of these genes are mutational hotspots, suggesting their potential role in cancer.
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Epstein-Barr Virus Infection of Cell Lines Derived from Diffuse Large B-Cell Lymphomas Alters MicroRNA Loading of the Ago2 Complex. J Virol 2019; 93:JVI.01297-18. [PMID: 30429351 DOI: 10.1128/jvi.01297-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/05/2018] [Indexed: 12/15/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid tumor which is occasionally Epstein-Barr virus (EBV) positive and is further subtyped as activated B-cell DLBCL (ABC-DLBCL) and germinal center B-cell DLBCL (GCB-DLBCL), which has implications for prognosis and treatment. We performed Ago2 RNA immunoprecipitation followed by high-throughput RNA sequencing (Ago2-RIP-seq) to capture functionally active microRNAs (miRNAs) in EBV-negative ABC-DLBCL and GCB-DLBCL cell lines and their EBV-infected counterparts. In parallel, total miRNA profiles of these cells were determined to capture the cellular miRNA profile for comparison with the functionally active profile. Selected miRNAs with differential abundances were validated using real-time quantitative PCR (RT-qPCR) and Northern blotting. We found 6 miRNAs with differential abundances (2 upregulated and 4 downregulated miRNAs) between EBV-negative and -positive ABC-DLBCL cells and 12 miRNAs with differential abundances (3 upregulated and 9 downregulated miRNAs) between EBV-negative and -positive GCB-DLBCL cells. Eight and twelve miRNAs were confirmed using RT-qPCR in ABC-DLBCL and GCB-DLBCL cells, respectively. Selected miRNAs were analyzed in additional type I/II versus type III EBV latency DLBCL cell lines. Furthermore, upregulation of miR-221-3p and downregulation of let7c-5p in ABC-DLBCL cells and upregulation of miR-363-3p and downregulation of miR-423-5p in GCB-DLBCL cells were verified using RIP-Northern blotting. Our comprehensive sequence analysis of the DLBCL miRNA profiles identified sets of deregulated miRNAs by Ago2-RIP-seq. Our Ago2-IP-seq miRNA profile could be considered an important data set for the detection of deregulated functionally active miRNAs in DLBCLs and could possibly lead to the identification of miRNAs as biomarkers for the classification of DLBCLs or even as targets for personalized targeted treatment.IMPORTANCE Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive tumor of lymphoid origin which is occasionally Epstein-Barr virus (EBV) positive. MicroRNAs are found in most multicellular organisms and even in viruses such as EBV. They regulate the synthesis of proteins by binding to their cognate mRNA. MicroRNAs are tethered to their target mRNAs by "Argonaute" proteins. Here we compared the overall miRNA content of the Ago2 complex by differential loading to the overall content of miRNAs in two DLBCL cell lines and their EBV-converted counterparts. In all cell lines, the Ago2 load was different from the overall expression of miRNAs. In addition, the loading of the Ago2 complex was changed upon infection with EBV. This indicates that the virus not only changes the overall content of miRNAs but also influences the expression of proteins by affecting the Ago complexes.
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Oak N, Ghosh R, Huang KL, Wheeler DA, Ding L, Plon SE. Framework for microRNA variant annotation and prioritization using human population and disease datasets. Hum Mutat 2018; 40:73-89. [PMID: 30302893 DOI: 10.1002/humu.23668] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022]
Abstract
MicroRNA (miRNA) expression is frequently deregulated in human disease, in contrast, disease-associated miRNA mutations are understudied. We developed Annotative Database of miRNA Elements, ADmiRE, which combines multiple existing and new biological annotations to aid prioritization of causal miRNA variation. We annotated 10,206 mature (3,257 within seed region) miRNA variants from multiple large sequencing datasets including gnomAD (15,496 genomes; 123,136 exomes). The pattern of miRNA variation closely resembles protein-coding exonic regions, with no difference between intragenic and intergenic miRNAs (P = 0.56), and high confidence miRNAs demonstrate higher sequence constraint (P < 0.001). Conservation analysis across 100 vertebrates identified 765 highly conserved miRNAs that also have limited genetic variation in gnomAD. We applied ADmiRE to the TCGA PanCancerAtlas WES dataset containing over 10,000 individuals across 33 adult cancers and annotated 1,267 germline (rare in gnomAD) and 1,492 somatic miRNA variants. Several miRNA families with deregulated gene expression in cancer have low levels of both somatic and germline variants, e.g., let-7 and miR-10. In addition to known somatic miR-142 mutations in hematologic cancers, we describe novel somatic miR-21 mutations in esophageal cancers impacting downstream miRNA targets. Through the development of ADmiRE, we present a framework for annotation and prioritization of miRNA variation in disease datasets.
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Affiliation(s)
- Ninad Oak
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Rajarshi Ghosh
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030
| | - Kuan-Lin Huang
- Department of Medicine, Washington University in St. Louis, MO 63108.,McDonnel Genome Institute, Washington University in St. Louis, MO 63108
| | - David A Wheeler
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, MO 63108.,McDonnel Genome Institute, Washington University in St. Louis, MO 63108.,Department of Genetics, Washington University in St. Louis, MO 63108.,Siteman Cancer Center, Washington University in St. Louis, MO 63108
| | - Sharon E Plon
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030
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25
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Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun 2018; 9:4001. [PMID: 30275490 PMCID: PMC6167379 DOI: 10.1038/s41467-018-06354-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/31/2018] [Indexed: 11/26/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3′ UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics. The driver mutations for the two main molecular subgroups of diffuse large B-cell lymphoma (DLBCL) are poorly defined. Here, an integrative genomics analysis identifies 3′ UTR NFKBIZ mutations within the activated B-cell DLBCL subgroup and small FCGR2B amplifications in the germinal centre B-cell DLBCL subgroup.
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26
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miR-150 downregulation contributes to the high-grade transformation of follicular lymphoma by upregulating FOXP1 levels. Blood 2018; 132:2389-2400. [PMID: 30213873 DOI: 10.1182/blood-2018-06-855502] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Follicular lymphoma (FL) is a common indolent B-cell malignancy with a variable clinical course. An unfavorable event in its course is histological transformation to a high-grade lymphoma, typically diffuse large B-cell lymphoma. Recent studies show that genetic aberrations of MYC or its overexpression are associated with FL transformation (tFL). However, the precise molecular mechanisms underlying tFL are unclear. Here we performed the first profiling of expression of microRNAs (miRNAs) in paired samples of FL and tFL and identified 5 miRNAs as being differentially expressed. We focused on one of these miRNAs, namely miR-150, which was uniformly downmodulated in all examined tFLs (∼3.5-fold), and observed that high levels of MYC are responsible for repressing miR-150 in tFL by binding in its upstream region. This MYC-mediated repression of miR-150 in B cells is not dependent on LIN28A/B proteins, which influence the maturation of miR-150 precursor (pri-miR-150) in myeloid cells. We also demonstrated that low miR-150 levels in tFL lead to upregulation of its target, namely FOXP1 protein, which is a known positive regulator of cell survival, as well as B-cell receptor and NF-κB signaling in malignant B cells. We revealed that low levels of miR-150 and high levels of its target, FOXP1, are associated with shorter overall survival in FL and suggest that miR-150 could serve as a good biomarker measurable in formalin-fixed paraffin-embedded tissue. Overall, our study demonstrates the role of the MYC/miR-150/FOXP1 axis in malignant B cells as a determinant of FL aggressiveness and its high-grade transformation.
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27
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Trissal MC, Wong TN, Yao JC, Ramaswamy R, Kuo I, Baty J, Sun Y, Jih G, Parikh N, Berrien-Elliott MM, Fehniger TA, Ley TJ, Maillard I, Reddy PR, Link DC. MIR142 Loss-of-Function Mutations Derepress ASH1L to Increase HOXA Gene Expression and Promote Leukemogenesis. Cancer Res 2018; 78:3510-3521. [PMID: 29724719 PMCID: PMC6030481 DOI: 10.1158/0008-5472.can-17-3592] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/12/2018] [Accepted: 04/23/2018] [Indexed: 12/22/2022]
Abstract
Point mutations in the seed sequence of miR-142-3p are present in a subset of acute myelogenous leukemia (AML) and in several subtypes of B-cell lymphoma. Here, we show that mutations associated with AML result both in loss of miR-142-3p function and in decreased miR-142-5p expression. Mir142 loss altered the hematopoietic differentiation of multipotent hematopoietic progenitors, enhancing their myeloid potential while suppressing their lymphoid potential. During hematopoietic maturation, loss of Mir142 increased ASH1L protein expression and consequently resulted in the aberrant maintenance of Hoxa gene expression in myeloid-committed hematopoietic progenitors. Mir142 loss also enhanced the disease-initiating activity of IDH2-mutant hematopoietic cells in mice. Together these data suggest a novel model in which miR-142, through repression of ASH1L activity, plays a key role in suppressing HOXA9/A10 expression during normal myeloid differentiation. AML-associated loss-of-function mutations of MIR142 disrupt this negative signaling pathway, resulting in sustained HOXA9/A10 expression in myeloid progenitors/myeloblasts and ultimately contributing to leukemic transformation.Significance: These findings provide mechanistic insights into the role of miRNAs in leukemogenesis and hematopoietic stem cell function. Cancer Res; 78(13); 3510-21. ©2018 AACR.
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Affiliation(s)
- Maria C Trissal
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Terrence N Wong
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Juo-Chin Yao
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Rahul Ramaswamy
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Iris Kuo
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Jack Baty
- Division of Biostatistics, Washington University, St. Louis, Missouri
| | - Yaping Sun
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Gloria Jih
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Nishi Parikh
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | | | - Todd A Fehniger
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Timothy J Ley
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Ivan Maillard
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Pavan R Reddy
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Daniel C Link
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri.
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28
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Yi H, Wang K, Jin JF, Jin H, Yang L, Zou Y, Du B, Liu X. Elevated Adenylyl Cyclase 9 Expression Is a Potential Prognostic Biomarker for Patients with Colon Cancer. Med Sci Monit 2018; 24:19-25. [PMID: 29292367 PMCID: PMC5759510 DOI: 10.12659/msm.906002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Adenylyl cyclase 9 (ADCY9) is an enzyme that modulates signal transduction by producing the second messenger, cyclic adenosine monophosphate (cAMP). The aim of the present study was to investigate the association of ADCY9 expression with clinicopathological features and disease-free survival of colon cancer patients. Material/Methods Immunohistochemistry staining with ADCY9 antibody was performed on a tissue microarray. Immunoreactivity scores (IRS) were recorded and applied for association analysis. ADCY9 mRNA expression and clinicopathological information were also extracted from the TCGA colon cancer dataset and analyzed using univariate and multivariate Cox proportional hazards models. Results ADCY9 IRS was significantly higher (P=0.002) in tumor tissues (6.40±1.26, n=200) than in adjacent normal samples (4.13±0.83, n=8). The IRS and mRNA expression of ADCY9 were correlated to colon cancer TNM staging. Longer disease-free survival was observed in patients with lower ADCY9 expression (P=0.001). In the multivariate models, ADCY9 expression level (hazard ratio [HR] 5.495, 95% confidence interval [CI] 1.753–17.227, P=0.003), and distant metastasis (HR 4.329, 95% CI 1.374–13.636, P=0.012) were still associated with disease-free survival. Conclusions High ADCY9 expression is a poor prognostic factor for disease-free survival in colon cancer.
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Affiliation(s)
- Hua Yi
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China (mainland)
| | - Kun Wang
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China (mainland)
| | - Jun-Feng Jin
- Department of Pathology, Zunyi Medical College, Zhuhai Campus, Zhuhai, Guangdou, China (mainland)
| | - He Jin
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China (mainland)
| | - Lihua Yang
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China (mainland)
| | - Yidan Zou
- The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China (mainland)
| | - Biaoyan Du
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China (mainland)
| | - Xiaodong Liu
- Department of Anaesthesiology and Intensive Care, The Chinese University of Hong Kong, Hong Kong SAR, China (mainland)
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29
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Kuriyama K, Enomoto Y, Suzuki R, Watanuki J, Hosoi H, Yamashita Y, Murata S, Mushino T, Tamura S, Hanaoka N, Dyer M, Siebert R, Kiyonari H, Nakakuma H, Kitamura T, Sonoki T. Enforced expression of MIR142, a target of chromosome translocation in human B-cell tumors, results in B-cell depletion. Int J Hematol 2017; 107:345-354. [PMID: 29071477 DOI: 10.1007/s12185-017-2360-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/22/2022]
Abstract
MicroRNA142 (MIR142) is a target of chromosome translocations and mutations in human B-cell lymphomas. We analyzed an aggressive B-cell lymphoma carrying t(8;17)(q24;q22) and t(6;14)(p21;q32), and sought to explore the role(s) of MIR142 in lymphomagenesis. t(8;17)(q24;q22) involved MYC on 8q24 and pri-MIR142 on 17q22. MYC was activated by a promoter substitution by t(8;17)(q24;q22). t(8;17)(q24;q22) was an additional event after t(6;14) (p21;q32), which caused the over-expression of CCND3. Southern blot analyses revealed that the MIR142 locus was deleted from the affected allele, whereas Northern analyses showed over-expression of MIR142 in tumor cells. Although previous studies reported an over-expression of mutations in MIR142 in B-cell lymphomas, limited information is available on the functions of MIR142 in lymphomagenesis. Therefore, we generated bone marrow transplantation (BMT) and transgenic (Eμ/mir142) mice, which showed enforced expression in hematopoietic progenitor cells and B cells, respectively. BMT mice showed decreased numbers of all lineage-positive cells, particularly B cells, in peripheral blood. Eμ/mir142 mice showed decreased numbers of IgM-positive splenocytes, and exhibited altered B-cell phenotypic changes induced by lipopolysaccharide. Our results suggest that over-expression of MIR142 alters B-cell differentiation, implying multi-step lymphomagenesis together with MYC activation and CCND3 over-expression.
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Affiliation(s)
- Kodai Kuriyama
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Yutaka Enomoto
- Division of Cellular Therapy and Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Ritsuro Suzuki
- Hematology and Oncology, Shimane Medical University, Shimane, Japan
| | - Jyuri Watanuki
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Hiroki Hosoi
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Yusuke Yamashita
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Shogo Murata
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Toshiki Mushino
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Shinobu Tamura
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Nobuyoshi Hanaoka
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Martin Dyer
- Department of Cancer Studies and Molecular Medicine, Leicester Medical School, University of Leicester, Leicester, UK
| | - Reiner Siebert
- Institute of Human Genetics, Christian Albrechts University Kiel, Kiel, Germany.,Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Hiroshi Kiyonari
- Animal Resource Development Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe, Japan
| | - Hideki Nakakuma
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy and Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takashi Sonoki
- Hematology/Oncology, Wakayama Medical University, 811-1 Kimi-idera, Wakayama, 641-8510, Japan.
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30
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Alles J, Ludwig N, Rheinheimer S, Leidinger P, Grässer FA, Keller A, Meese E. MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins. Oncotarget 2017; 8:56417-56427. [PMID: 28915601 PMCID: PMC5593572 DOI: 10.18632/oncotarget.17662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 12/12/2022] Open
Abstract
Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3′UTR of either SOS1 or SOS2. Each of the 3′UTRs of SOS1 and SOS2 contained two binding sites for miR-148a both of which were necessary for the decreased luciferase activity. MiR-148a overexpression in HEK-293T lead to significantly reduced levels of both endogenous SOS1 and SOS2 proteins. Likewise, reduced levels of SOS proteins were found in two B cell lines that were transfected with miR-148a. The level of ERK1/2 phosphorylation as one of the most relevant downstream members of the Ras/ERK signaling pathway was also reduced in cells with miR-148a overexpression. The data show that miR-148a impairs the Ras/ERK signaling pathway via SOS1 and SOS2 proteins in B cells.
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Affiliation(s)
- Julia Alles
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Petra Leidinger
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
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31
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Lefebure M, Tothill RW, Kruse E, Hawkins ED, Shortt J, Matthews GM, Gregory GP, Martin BP, Kelly MJ, Todorovski I, Doyle MA, Lupat R, Li J, Schroeder J, Wall M, Craig S, Poortinga G, Cameron D, Bywater M, Kats L, Gearhart MD, Bardwell VJ, Dickins RA, Hannan RD, Papenfuss AT, Johnstone RW. Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene. Nat Commun 2017; 8:14581. [PMID: 28262675 PMCID: PMC5343491 DOI: 10.1038/ncomms14581] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 01/12/2017] [Indexed: 01/05/2023] Open
Abstract
The Eμ-Myc mouse is an extensively used model of MYC driven malignancy; however to date there has only been partial characterization of MYC co-operative mutations leading to spontaneous lymphomagenesis. Here we sequence spontaneously arising Eμ-Myc lymphomas to define transgene architecture, somatic mutations, and structural alterations. We identify frequent disruptive mutations in the PRC1-like component and BCL6-corepressor gene Bcor. Moreover, we find unexpected concomitant multigenic lesions involving Cdkn2a loss and other cancer genes including Nras, Kras and Bcor. These findings challenge the assumed two-hit model of Eμ-Myc lymphoma and demonstrate a functional in vivo role for Bcor in suppressing tumorigenesis. The Eμ-Myc lymphoma mouse model has been invaluable in the study of this disease. Here, the authors use multiple sequencing strategies to analyse the tumours in these mice and find recurrent inactivating mutations in Bcor, suggesting that this gene has a negative role in Myc signalling.
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Affiliation(s)
- Marcus Lefebure
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Elizabeth Kruse
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Edwin D Hawkins
- The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Jake Shortt
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing &Health Sciences, Clayton, Victoria 3168, Australia
| | | | - Gareth P Gregory
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Benjamin P Martin
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Madison J Kelly
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | | | - Maria A Doyle
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Richard Lupat
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Jason Li
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Jan Schroeder
- The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital, Fitzroy, Victoria 3065, Australia.,Department of Medicine, St Vincent's Hospital, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Stuart Craig
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | | | - Don Cameron
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Megan Bywater
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Lev Kats
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Micah D Gearhart
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Vivian J Bardwell
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, AMREP Building, Commercial Road, The Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - Ross D Hannan
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,Cancer Biology and Therapeutics Department, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Anthony T Papenfuss
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia.,The Walter Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia
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32
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Germline mutations predisposing to diffuse large B-cell lymphoma. Blood Cancer J 2017; 7:e532. [PMID: 28211887 PMCID: PMC5386333 DOI: 10.1038/bcj.2017.15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 12/21/2022] Open
Abstract
Genetic studies of diffuse large B-cell lymphomas (DLBCLs) in humans have revealed numerous targets of somatic mutations and an increasing number of potentially relevant germline alterations. The latter often affect genes involved in DNA repair and/or immune function. In general, defects in these genes also predispose to other conditions. Knowledge of these mutations can lead to disease-preventing measures in the patient and relatives thereof. Conceivably, these germline mutations will be taken into account in future therapy of the lymphoma. In other hematological malignancies, mutations originally found as somatic aberrations have also been shown to confer predisposition to these diseases, when occurring in the germline. Further interrogations of the genome in DLBCL patients are therefore expected to reveal additional hereditary predisposition genes. Our review shows that germline mutations have already been described in over one-third of the genes that are somatically mutated in DLBCL. Whether such germline mutations predispose carriers to DLBCL is an open question. Symptoms of the inherited syndromes associated with these genes range from anatomical malformations to intellectual disability, immunodeficiencies and malignancies other than DLBCL. Inherited or de novo alterations in protein-coding and non-coding genes are envisioned to underlie this lymphoma.
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Bouska A, Zhang W, Gong Q, Iqbal J, Scuto A, Vose J, Ludvigsen M, Fu K, Weisenburger DD, Greiner TC, Gascoyne RD, Rosenwald A, Ott G, Campo E, Rimsza LM, Delabie J, Jaffe ES, Braziel RM, Connors JM, Wu CI, Staudt LM, D'Amore F, McKeithan TW, Chan WC. Combined copy number and mutation analysis identifies oncogenic pathways associated with transformation of follicular lymphoma. Leukemia 2017; 31:83-91. [PMID: 27389057 PMCID: PMC5214175 DOI: 10.1038/leu.2016.175] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 12/31/2022]
Abstract
Follicular lymphoma (FL) is typically an indolent disease, but 30-40% of FL cases transform into an aggressive lymphoma (tFL) with a poor prognosis. To identify the genetic changes that drive this transformation, we sequenced the exomes of 12 cases with paired FL and tFL biopsies and identified 45 recurrently mutated genes in the FL-tFL data set and 39 in the tFL cases. We selected 496 genes of potential importance in transformation and sequenced them in 23 additional tFL cases. Integration of the mutation data with copy-number abnormality (CNA) data provided complementary information. We found recurrent mutations of miR-142, which has not been previously been reported to be mutated in FL/tFL. The genes most frequently mutated in tFL included KMT2D (MLL2), CREBBP, EZH2, BCL2 and MEF2B. Many recurrently mutated genes are involved in epigenetic regulation, the Janus-activated kinase-signal transducer and activator of transcription (STAT) or the nuclear factor-κB pathways, immune surveillance and cell cycle regulation or are TFs involved in B-cell development. Of particular interest are mutations and CNAs affecting S1P-activated pathways through S1PR1 or S1PR2, which likely regulate lymphoma cell migration and survival outside of follicles. Our custom gene enrichment panel provides high depth of coverage for the study of clonal evolution or divergence.
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Affiliation(s)
- Alyssa Bouska
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Weiwei Zhang
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Qiang Gong
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Javeed Iqbal
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Anna Scuto
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Julie Vose
- Division of Hematology and Oncology, University of Nebraska Medical Center, Omaha, NE
| | | | - Kai Fu
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | | | - Timothy C. Greiner
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Randy D. Gascoyne
- Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Elias Campo
- Hematopathology Unit, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Lisa M. Rimsza
- Department of Pathology, University of Arizona, Tucson, AZ
| | - Jan Delabie
- Department of Pathology, University of Toronto, Toronto, Canada
| | - Elaine S. Jaffe
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | - Joseph M. Connors
- Division of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Chung-I Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Louis M. Staudt
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | | | - Wing C. Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
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34
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Bradshaw G, Sutherland HG, Haupt LM, Griffiths LR. Dysregulated MicroRNA Expression Profiles and Potential Cellular, Circulating and Polymorphic Biomarkers in Non-Hodgkin Lymphoma. Genes (Basel) 2016; 7:genes7120130. [PMID: 27999330 PMCID: PMC5192506 DOI: 10.3390/genes7120130] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023] Open
Abstract
A large number of studies have focused on identifying molecular biomarkers, including microRNAs (miRNAs) to aid in the diagnosis and prognosis of the most common subtypes of non-Hodgkin lymphoma (NHL), Diffuse Large B-cell Lymphoma and Follicular Lymphoma. NHL is difficult to diagnose and treat with many cases becoming resistant to chemotherapy, hence the need to identify improved biomarkers to aid in both diagnosis and treatment modalities. This review summarises more recent research on the dysregulated miRNA expression profiles found in NHL, as well as the regulatory role and biomarker potential of cellular and circulating miRNAs found in tissue and serum, respectively. In addition, the emerging field of research focusing on miRNA single nucleotide polymorphisms (miRSNPs) in genes of the miRNA biogenesis pathway, in miRNA genes themselves, and in their target sites may provide new insights on gene expression changes in these genes. These miRSNPs may impact miRNA networks and have been shown to play a role in a host of different cancer types including haematological malignancies. With respect to NHL, a number of SNPs in miRNA-binding sites in target genes have been shown to be associated with overall survival.
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Affiliation(s)
- Gabrielle Bradshaw
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
| | - Heidi G Sutherland
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
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35
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Hezaveh K, Kloetgen A, Bernhart SH, Mahapatra KD, Lenze D, Richter J, Haake A, Bergmann AK, Brors B, Burkhardt B, Claviez A, Drexler HG, Eils R, Haas S, Hoffmann S, Karsch D, Klapper W, Kleinheinz K, Korbel J, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Leich E, Loeffler M, Mantovani-Loeffler L, López C, McHardy AC, Möller P, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schlesner M, Scholz I, Stadler PF, Stilgenbauer S, Sungalee S, Szczepanowski M, Trümper L, Weniger MA, Siebert R, Borkhardt A, Hummel M, Hoell JI. Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica 2016; 101:1380-1389. [PMID: 27390358 DOI: 10.3324/haematol.2016.143891] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNA are well-established players in post-transcriptional gene regulation. However, information on the effects of microRNA deregulation mainly relies on bioinformatic prediction of potential targets, whereas proof of the direct physical microRNA/target messenger RNA interaction is mostly lacking. Within the International Cancer Genome Consortium Project "Determining Molecular Mechanisms in Malignant Lymphoma by Sequencing", we performed miRnome sequencing from 16 Burkitt lymphomas, 19 diffuse large B-cell lymphomas, and 21 follicular lymphomas. Twenty-two miRNA separated Burkitt lymphomas from diffuse large B-cell lymphomas/follicular lymphomas, of which 13 have shown regulation by MYC. Moreover, we found expression of three hitherto unreported microRNA. Additionally, we detected recurrent mutations of hsa-miR-142 in diffuse large B-cell lymphomas and follicular lymphomas, and editing of the hsa-miR-376 cluster, providing evidence for microRNA editing in lymphomagenesis. To interrogate the direct physical interactions of microRNA with messenger RNA, we performed Argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation experiments. MicroRNA directly targeted 208 messsenger RNA in the Burkitt lymphomas and 328 messenger RNA in the non-Burkitt lymphoma models. This integrative analysis discovered several regulatory pathways of relevance in lymphomagenesis including Ras, PI3K-Akt and MAPK signaling pathways, also recurrently deregulated in lymphomas by mutations. Our dataset reveals that messenger RNA deregulation through microRNA is a highly relevant mechanism in lymphomagenesis.
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Affiliation(s)
- Kebria Hezaveh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Andreas Kloetgen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany.,Department of Algorithmic Bioinformatics, Heinrich-Heine University, Duesseldorf, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
| | - Kunal Das Mahapatra
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Dido Lenze
- Institute of Pathology, Charité - University Medicine Berlin, Germany
| | - Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Andrea Haake
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Anke K Bergmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Benedikt Brors
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Birgit Burkhardt
- Department of Pediatric Hematology and Oncology, University Hospital Münster, Germany
| | - Alexander Claviez
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Cultures, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology and Bioquant, Heidelberg University, Germany
| | - Siegfried Haas
- Friedrich-Ebert Hospital Neumünster, Clinics for Hematology, Oncology and Nephrology, Neumünster, Germany
| | - Steve Hoffmann
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
| | - Dennis Karsch
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre, Campus Kiel, Germany
| | - Wolfram Klapper
- Hematopathology Section, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- EMBL Heidelberg, Genome Biology, Heidelberg, Germany
| | - Helene Kretzmer
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Chris Lawerenz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ellen Leich
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Markus Loeffler
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | | | - Cristina López
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich-Heine University, Duesseldorf, Germany.,Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Peter Möller
- Institute of Pathology, Medical Faculty of the Ulm University, Germany
| | - Marius Rohde
- Department of Pediatric Hematology and Oncology University Hospital Giessen, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Markus Schilhabel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingrid Scholz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter F Stadler
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany.,RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany.,Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany.,Santa Fe Institute, NM, USA
| | | | | | - Monika Szczepanowski
- Hematopathology Section, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - University Medicine Berlin, Germany
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Tamaddon G, Geramizadeh B, Karimi MH, Mowla SJ, Abroun S. miR-4284 and miR-4484 as Putative Biomarkers for Diffuse Large B-Cell Lymphoma. IRANIAN JOURNAL OF MEDICAL SCIENCES 2016; 41:334-9. [PMID: 27365556 PMCID: PMC4912653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Diffuse large B-cell lymphoma is the most common type of non-Hodgkin lymphoma. MicroRNAs (miRNAs) are endogenous small RNA, which can regulate gene expression at the post-transcriptional level. MiRNA profiling has shown a great potential as novel diagnostic and prognostic biomarkers. The present study was performed at the Nemazee Teaching Hospital (Shiraz, Iran) from 2011 to 2013. The aim of this study was to assess the deregulation of miRNAs profiles in DLBL against hyperplasic reactive lymph node as a normal. This could serve as a biomarker for DLBL. The miRCURY LNA™ microarray was used on the total RNA, which was extracted from formalin-fixed paraffin-embedded tissue of 24 de novo diffuse large B-cell lymphoma patients and 14 normal lymph nodes. The greatest changes were detected in miR-4284 and miR-4484 level in patient's lymphoma samples. These miRNAs can act as a diagnostic biomarker for DLBL.
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Affiliation(s)
- Gholamhossein Tamaddon
- Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bita Geramizadeh
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Karimi
- Transplant Research Center, Nemazee Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Javad Mowla
- Department of Genetics, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran
| | - Said Abroun
- Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran,Correspondence: Said Abroun, PhD; Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran Tel/Fax: +98 21 82884507
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37
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Diederichs S, Bartsch L, Berkmann JC, Fröse K, Heitmann J, Hoppe C, Iggena D, Jazmati D, Karschnia P, Linsenmeier M, Maulhardt T, Möhrmann L, Morstein J, Paffenholz SV, Röpenack P, Rückert T, Sandig L, Schell M, Steinmann A, Voss G, Wasmuth J, Weinberger ME, Wullenkord R. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med 2016; 8:442-57. [PMID: 26992833 PMCID: PMC5126213 DOI: 10.15252/emmm.201506055] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor‐specific mutations not only in protein‐coding sequences but also in non‐coding sequences. Although 98% of the genome is not translated into proteins, most studies have neglected the information hidden in this “dark matter” of the genome. Malignancy‐driving mutations can occur in all genetic elements outside the coding region, namely in enhancer, silencer, insulator, and promoter as well as in 5′‐UTR and 3′‐UTR. Intron or splice site mutations can alter the splicing pattern. Moreover, cancer genomes contain mutations within non‐coding RNA, such as microRNA, lncRNA, and lincRNA. A synonymous mutation changes the coding region in the DNA and RNA but not the protein sequence. Importantly, oncogenes such as TERT or miR‐21 as well as tumor suppressor genes such as TP53/p53,APC,BRCA1, or RB1 can be affected by these alterations. In summary, coding‐independent mutations can affect gene regulation from transcription, splicing, mRNA stability to translation, and hence, this largely neglected area needs functional studies to elucidate the mechanisms underlying tumorigenesis. This review will focus on the important role and novel mechanisms of these non‐coding or allegedly silent mutations in tumorigenesis.
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Affiliation(s)
- Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany Division of RNA Biology & Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany German Cancer Consortium (DKTK), Freiburg, Germany
| | - Lorenz Bartsch
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Julia C Berkmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Karin Fröse
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jana Heitmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Caroline Hoppe
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Deetje Iggena
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Danny Jazmati
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Philipp Karschnia
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Miriam Linsenmeier
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Thomas Maulhardt
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Lino Möhrmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Johannes Morstein
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Stella V Paffenholz
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Paula Röpenack
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Timo Rückert
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ludger Sandig
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maximilian Schell
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Anna Steinmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Gjendine Voss
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jacqueline Wasmuth
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maria E Weinberger
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ramona Wullenkord
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
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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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39
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Nair S. Current insights into the molecular systems pharmacology of lncRNA-miRNA regulatory interactions and implications in cancer translational medicine. AIMS MOLECULAR SCIENCE 2016. [DOI: 10.3934/molsci.2016.2.104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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40
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Shimono Y, Mukohyama J, Nakamura SI, Minami H. MicroRNA Regulation of Human Breast Cancer Stem Cells. J Clin Med 2015; 5:jcm5010002. [PMID: 26712794 PMCID: PMC4730127 DOI: 10.3390/jcm5010002] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/01/2015] [Accepted: 12/21/2015] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in virtually all biological processes, including stem cell maintenance, differentiation, and development. The dysregulation of miRNAs is associated with many human diseases including cancer. We have identified a set of miRNAs differentially expressed between human breast cancer stem cells (CSCs) and non-tumorigenic cancer cells. In addition, these miRNAs are similarly upregulated or downregulated in normal mammary stem/progenitor cells. In this review, we mainly describe the miRNAs that are dysregulated in human breast CSCs directly isolated from clinical specimens. The miRNAs and their clusters, such as the miR-200 clusters, miR-183 cluster, miR-221-222 cluster, let-7, miR-142 and miR-214, target the genes and pathways important for stem cell maintenance, such as the self-renewal gene BMI1, apoptosis, Wnt signaling, Notch signaling, and epithelial-to-mesenchymal transition. In addition, the current evidence shows that metastatic breast CSCs acquire a phenotype that is different from the CSCs in a primary site. Thus, clarifying the miRNA regulation of the metastatic breast CSCs will further advance our understanding of the roles of human breast CSCs in tumor progression.
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Affiliation(s)
- Yohei Shimono
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
- Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
| | - Junko Mukohyama
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
| | - Shun-Ichi Nakamura
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
- Division of Biochemistry, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
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Tuna M, Machado AS, Calin GA. Genetic and epigenetic alterations of microRNAs and implications for human cancers and other diseases. Genes Chromosomes Cancer 2015; 55:193-214. [PMID: 26651018 DOI: 10.1002/gcc.22332] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are a well-studied group of noncoding RNAs that control gene expression by interacting mainly with messenger RNA. It is known that miRNAs and their biogenesis regulatory machineries have crucial roles in multiple cell processes; thus, alterations in these genes often lead to disease, such as cancer. Disruption of these genes can occur through epigenetic and genetic alterations, resulting in aberrant expression of miRNAs and subsequently of their target genes. This review focuses on the disruption of miRNAs and their key regulatory machineries by genetic alterations, with emphasis on mutations and epigenetic changes in cancer and other diseases.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Andreia S Machado
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX
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Mishra S, Yadav T, Rani V. Exploring miRNA based approaches in cancer diagnostics and therapeutics. Crit Rev Oncol Hematol 2015; 98:12-23. [PMID: 26481951 DOI: 10.1016/j.critrevonc.2015.10.003] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 08/06/2015] [Accepted: 10/01/2015] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs), a highly conserved class of tissue specific, small non-protein coding RNAs maintain cell homeostasis by negative gene regulation. Proper controlling of miRNA expression is required for a balanced physiological environment, as these small molecules influence almost every genetic pathway from cell cycle checkpoint, cell proliferation to apoptosis, with a wide range of target genes. Deregulation in miRNAs expression correlates with various cancers by acting as tumor suppressors and oncogenes. Although promising therapies exist to control tumor development and progression, there is a lack of efficient diagnostic and therapeutic approaches for delineating various types of cancer. The molecularly different tumors can be differentiated by specific miRNA profiling as their phenotypic signatures, which can hence be exploited to surmount the diagnostic and therapeutic challenges. Present review discusses the involvement of miRNAs in oncogenesis with the analysis of patented research available on miRNAs.
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Affiliation(s)
- Shivangi Mishra
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida 201307, Uttar Pradesh, India
| | - Tanuja Yadav
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida 201307, Uttar Pradesh, India
| | - Vibha Rani
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida 201307, Uttar Pradesh, India.
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43
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Li J, Drubay D, Michiels S, Gautheret D. Mining the coding and non-coding genome for cancer drivers. Cancer Lett 2015; 369:307-15. [PMID: 26433158 DOI: 10.1016/j.canlet.2015.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 12/20/2022]
Abstract
Progress in next-generation sequencing provides unprecedented opportunities to fully characterize the spectrum of somatic mutations of cancer genomes. Given the large number of somatic mutations identified by such technologies, the prioritization of cancer-driving events is a consistent bottleneck. Most bioinformatics tools concentrate on driver mutations in the coding fraction of the genome, those causing changes in protein products. As more non-coding pathogenic variants are identified and characterized, the development of computational approaches to effectively prioritize cancer-driving variants within the non-coding fraction of human genome is becoming critical. After a short summary of methods for coding variant prioritization, we here review the highly diverse non-coding elements that may act as cancer drivers and describe recent methods that attempt to evaluate the deleteriousness of sequence variation in these elements. With such tools, the prioritization and identification of cancer-implicated regulatory elements and non-coding RNAs is becoming a reality.
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Affiliation(s)
- Jia Li
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Damien Drubay
- Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Villejuif, France; INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Stefan Michiels
- Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Villejuif, France; INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France.
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Alles J, Hasler D, Kazmi SMA, Tesson M, Hamilton A, Schlegel L, Marx S, Eichner N, Reinhardt R, Meister G, Wilson JB, Grässer FA. Epstein-Barr Virus EBER Transcripts Affect miRNA-Mediated Regulation of Specific Targets and Are Processed to Small RNA Species. Noncoding RNA 2015; 1:170-191. [PMID: 29861423 PMCID: PMC5932547 DOI: 10.3390/ncrna1030170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/22/2015] [Accepted: 09/22/2015] [Indexed: 12/11/2022] Open
Abstract
The oncogenic Epstein-Barr virus (EBV) expresses 44 mature microRNAs and two non-coding EBER RNAs of 167 (EBER1) and 172 (EBER2) nt length. MiRNA profiling of NK/T cell lines and primary cells and Northern blotting of EBV-infected cell lines and primary tumors revealed processing of EBER1 to short 5′-derived RNAs of approximately 23, 52 and 70 nt (EBER123, EBER152, and EBER170) and of EBER2 to 3′ fragments. The biogenesis of these species is independent of Dicer, and EBER123 does not act like a miRNA to target its complementary sequence. EBER1, EBER2 and EBER123 were bound by the lupus antigen (La), a nuclear and cytoplasmic protein that facilitates RNAi. Consistent with this, the EBERs affect regulation of interleukin 1alpha (IL1α) and RAC1 reporters harboring miR target sequences, targets of miR-142-3p. However, the EBERs have no effect upon another target of miR-142-3p, ADCY9, nor on TOMM22, a target of ebv-miR-BART16, indicative of selective modulation of gene expression by the EBERs.
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Affiliation(s)
- Julia Alles
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, Homburg/Saar D-66421, Germany.
| | - Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, Regensburg D-93053, Germany.
| | - Syed Mohammad Ali Kazmi
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Mathias Tesson
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Andrew Hamilton
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Linda Schlegel
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, Homburg/Saar D-66421, Germany.
| | - Stefanie Marx
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, Homburg/Saar D-66421, Germany.
| | - Norbert Eichner
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, Regensburg D-93053, Germany.
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, Cologne D-50829, Germany.
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, Regensburg D-93053, Germany.
| | - Joanna B Wilson
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, Homburg/Saar D-66421, Germany.
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Manzano M, Forte E, Raja AN, Schipma MJ, Gottwein E. Divergent target recognition by coexpressed 5'-isomiRs of miR-142-3p and selective viral mimicry. RNA (NEW YORK, N.Y.) 2015; 21:1606-20. [PMID: 26137849 PMCID: PMC4536321 DOI: 10.1261/rna.048876.114] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/08/2015] [Indexed: 05/28/2023]
Abstract
Sequence heterogeneity at the ends of mature microRNAs (miRNAs) is well documented, but its effects on miRNA function are largely unexplored. Here we studied the impact of miRNA 5'-heterogeneity, which affects the seed region critical for target recognition. Using the example of miR-142-3p, an emerging regulator of the hematopoietic lineage in vertebrates, we show that naturally coexpressed 5'-variants (5'-isomiRs) can recognize largely distinct sets of binding sites. Despite this, both miR-142-3p isomiRs regulate exclusive and shared targets involved in actin dynamics. Thus, 5'-heterogeneity can substantially broaden and enhance regulation of one pathway. Other 5'-isomiRs, in contrast, recognize largely overlapping sets of binding sites. This is exemplified by two herpesviral 5'-isomiRs that selectively mimic one of the miR-142-3p 5'-isomiRs. We hypothesize that other cellular and viral 5'-isomiRs can similarly be grouped into those with divergent or convergent target repertoires, based on 5'-sequence features. Taken together, our results provide a detailed characterization of target recognition by miR-142-3p and its 5'-isomiR-specific viral mimic. We furthermore demonstrate that miRNA 5'-end variation leads to differential targeting and can thus broaden the target range of miRNAs.
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Affiliation(s)
- Mark Manzano
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Eleonora Forte
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Archana N Raja
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Matthew J Schipma
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Eva Gottwein
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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46
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Human genetic variation and its effect on miRNA biogenesis, activity and function. Biochem Soc Trans 2015; 42:1184-9. [PMID: 25110023 DOI: 10.1042/bst20140055] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
miRNAs are small non-coding regulators of gene expression that are estimated to regulate over 60% of all human genes. Each miRNA can target multiple mRNA targets and as such, miRNAs are responsible for some of the 'fine tuning' of gene expression and are implicated in regulation of all cellular processes. miRNAs bind to target genes by sequence complementarity, resulting in target degradation or translational blocking and usually a reduction in target gene expression. Like mRNA, miRNAs are transcribed from genomic DNA and are processed in several steps that are heavily reliant on correct secondary and tertiary structure. Secondary structure is determined by RNA sequence, which is in turn determined by the sequence of the genome. The human genome, however, like most eukaryotes is variable. Large numbers of SNPs (single nucleotide polymorphisms), small insertions and deletions (indels) and CNVs (copy number variants) have been described in our genome. Should this genetic variation occur in regions critical for the correct secondary structure or target binding, it may interfere with normal gene regulation and cause disease. In this review, we outline the consequences of genetic variation involving different aspects of miRNA biosynthesis, processing and regulation, with selected examples of incidences when this has potential to affect human disease.
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47
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Altered lymphopoiesis and immunodeficiency in miR-142 null mice. Blood 2015; 125:3720-30. [PMID: 25931583 DOI: 10.1182/blood-2014-10-603951] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/15/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of powerful posttranscriptional regulators implicated in the control of diverse biological processes, including regulation of hematopoiesis and the immune response. To define the biological functions of miR-142, which is preferentially and abundantly expressed in immune cells, we created a mouse line with a targeted deletion of this gene. Our analysis of miR-142(-/-) mice revealed a critical role for this miRNA in the development and homeostasis of lymphocytes. Marginal zone B cells expand in the knockout spleen, whereas the number of T and B1 B cells in the periphery is reduced. Abnormal development of hematopoietic lineages in miR-142(-/-) animals is accompanied by a profound immunodeficiency, manifested by hypoimmunoglobulinemia and failure to mount a productive immune response to soluble antigens and virus. miR-142(-/-) B cells express elevated levels of B-cell-activating factor (BAFF) receptor (BAFF-R) and as a result proliferate more robustly in response to BAFF stimulation. Lowering the BAFF-R gene dose in miR-142(-/-) mice rescues the B-cell expansion defect, suggesting that BAFF-R is a bona fide miR-142 target through which it controls B-cell homeostasis. Collectively, our results uncover miR-142 as an essential regulator of lymphopoiesis, and suggest that lesions in this miRNA gene may lead to primary immunodeficiency.
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48
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Ruvolo PP. The Interplay between PP2A and microRNAs in Leukemia. Front Oncol 2015; 5:43. [PMID: 25750899 PMCID: PMC4335100 DOI: 10.3389/fonc.2015.00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/05/2015] [Indexed: 12/19/2022] Open
Abstract
Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase family whose members have been implicated in tumor suppression in many cancer models. In many cancers, loss of PP2A activity has been associated with tumorigenesis and drug resistance. Loss of PP2A results in failure to turn off survival signaling cascades that drive drug resistance such as those regulated by protein kinase B. PP2A is responsible for modulating function and controlling expression of tumor suppressors such as p53 and oncogenes such as BCL2 and MYC. Thus, PP2A has diverse functions regulating cell survival. The importance of microRNAs (miRs) is emerging in cancer biology. A role for miR regulation of PP2A is not well understood; however, recent studies suggest a number of clinically significant miRs such as miR-155 and miR-19 may include PP2A targets. We have recently found that a PP2A B subunit (B55α) can regulate a number of miRs in acute myeloid leukemia cells. The identification of a miR/PP2A axis represents a novel regulatory pathway in cellular homeostasis. The ability of miRs to suppress specific PP2A targets and for PP2A to control such miRs can add an extra level of control in signaling that could be used as a rheostat for many signaling cascades that maintain cellular homeostasis. As such, loss of PP2A or expression of miRs relevant for PP2A function could promote tumorigenesis or at least result in drug resistance. In this review, we will cover the current state of miR regulation of PP2A with a focus on leukemia. We will also briefly discuss what is known of PP2A regulation of miR expression.
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Affiliation(s)
- Peter P Ruvolo
- Department of Leukemia, University of Texas MD Anderson Cancer Center , Houston, TX , USA
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49
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Lim EL, Trinh DL, Scott DW, Chu A, Krzywinski M, Zhao Y, Robertson AG, Mungall AJ, Schein J, Boyle M, Mottok A, Ennishi D, Johnson NA, Steidl C, Connors JM, Morin RD, Gascoyne RD, Marra MA. Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients. Genome Biol 2015; 16:18. [PMID: 25723320 PMCID: PMC4308918 DOI: 10.1186/s13059-014-0568-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/11/2014] [Indexed: 12/26/2022] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue samples for validation. Results We identify known and candidate novel miRNAs, 25 of which are associated with survival independently of cell-of-origin and International Prognostic Index scores, which are established indicators of outcome. Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort. Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome. Comparison of DLBCL miRNA-seq expression profiles with those from other cancer types identifies miRNAs that were more abundant in B-cell contexts. Unsupervised clustering of miRNAs identifies two clusters of patients that have distinct differences in their outcomes. Our integrative miRNA and mRNA expression analyses reveal that miRNAs increased in abundance in DLBCL appear to regulate the expression of genes involved in metabolism, cell cycle, and protein modification. Additionally, these miRNAs, including one candidate novel miRNA, miR-10393-3p, appear to target chromatin modification genes that are frequent targets of somatic mutation in non-Hodgkin lymphomas. Conclusions Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0568-y) contains supplementary material, which is available to authorized users.
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50
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Xu R, Bi C, Song J, Wang L, Ge C, Liu X, Zhang M. Upregulation of miR-142-5p in atherosclerotic plaques and regulation of oxidized low-density lipoprotein-induced apoptosis in macrophages. Mol Med Rep 2015; 11:3229-34. [PMID: 25586666 PMCID: PMC4368070 DOI: 10.3892/mmr.2015.3191] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 09/18/2014] [Indexed: 01/25/2023] Open
Abstract
MicroRNA (miR)-142-5p is a member of the miR-142 family, which have been shown to be associated with tumors, stem cells and disorders of the immune system. However, the role of miR-142-5p in atherosclerosis has yet to be investigated. In the present study, an atherosclerotic apolipoprotein E-deficient (apoE−/−) mouse model was constructed and fed a high-fat diet. The expression levels of miR-142-5p in the murine atherosclerotic plaques were detected by gene microarray analysis. In addition, an in vitro assay was used to determine the expression levels of miR-142-5p in human endothelial cells, smooth muscle cells and macrophages, which were treated with oxidized low-density lipoprotein (ox-LDL). Furthermore, a miR-142-5p inhibitor and mimic was transfected into cultured human macrophages, in order to observe the effects on transforming growth factor-β2 (TGF-β2) expression. The effects of co-transfection of the miR-142-5p inhibitor or mimic with TGF-β2, in human macrophages, on the rate of apoptosis was analyzed. The expression levels of miR-142-5p were 6.84-fold higher in mice with stable atherosclerotic plaques, and 2.69-fold higher in mice with vulnerable atherosclerotic plaques, as compared with the controls. Furthermore, the expression levels of miR-142-5p were upregulated in the cultured human macrophages. The percentage of apoptotic cells was lowest in the macrophages transfected with both TGF-β2 and miR-142-5p inhibitors and treated with ox-LDL. The expression levels of miR-142-5p were upregulated in the atherosclerotic plaques of the apoE−/− mice. The findings of the present study have shown that the upregulation of miR-142-5p expression may regulate apoptosis in human macrophages by targeting TGF-β2. This effect may have an important role in the progression of atherosclerosis.
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Affiliation(s)
- Ruijin Xu
- Key Laboratory of Cardiovascular Remodeling and Function Research, Department of Cardiology, Chinese Ministries of Education and Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chenglong Bi
- Key Laboratory of Cardiovascular Remodeling and Function Research, Department of Cardiology, Chinese Ministries of Education and Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Jiantao Song
- Key Laboratory of Cardiovascular Remodeling and Function Research, Department of Cardiology, Chinese Ministries of Education and Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Lin Wang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Department of Cardiology, Chinese Ministries of Education and Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Cheng Ge
- Key Laboratory of Cardiovascular Remodeling and Function Research, Department of Cardiology, Chinese Ministries of Education and Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Xinxin Liu
- Key Laboratory of Cardiovascular Remodeling and Function Research, Department of Cardiology, Chinese Ministries of Education and Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Mei Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Department of Cardiology, Chinese Ministries of Education and Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
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