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Vattathil SM, Gerasimov ES, Canon SM, Lori A, Tan SSM, Kim PJ, Liu Y, Lai EC, Bennett DA, Wingo TS, Wingo AP. Genetic regulation of microRNAs in the older adult brain and their contribution to neuropsychiatric conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.610174. [PMID: 39314369 PMCID: PMC11419020 DOI: 10.1101/2024.09.10.610174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
MicroRNAs are essential post-transcriptional regulators of gene expression and involved in many biological processes; however, our understanding of their genetic regulation and role in brain illnesses is limited. Here, we mapped brain microRNA expression quantitative trait loci (miR-QTLs) using genome-wide small RNA sequencing profiles from dorsolateral prefrontal cortex (dlPFC) samples of 604 older adult donors of European ancestry. miR-QTLs were identified for 224 miRNAs (48% of 470 tested miRNAs) at false discovery rate < 1%. We found that miR-QTLs were enriched in brain promoters and enhancers, and that intragenic miRNAs often did not share QTLs with their host gene. Additionally, we integrated the brain miR-QTLs with results from 16 GWAS of psychiatric and neurodegenerative diseases using multiple independent integration approaches and identified four miRNAs that contribute to the pathogenesis of bipolar disorder, major depression, post-traumatic stress disorder, schizophrenia, and Parkinson's disease. This study provides novel insights into the contribution of miRNAs to the complex biological networks that link genetic variation to disease.
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Affiliation(s)
- Selina M Vattathil
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | | | - Se Min Canon
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriana Lori
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Sze Min Tan
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul J Kim
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yue Liu
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Thomas S Wingo
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
- Alzheimer's Disease Research Center, University of California, Davis, Sacramento, CA, USA
| | - Aliza P Wingo
- Department of Psychiatry, University of California, Davis, Sacramento, CA, USA
- Veterans Affairs Northern California Health Care System, Sacramento, CA, USA
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2
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Wang Y, Tang X, Lu J. Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biol Rev Camb Philos Soc 2024; 99:525-545. [PMID: 37987240 DOI: 10.1111/brv.13033] [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: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA-mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage-specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth-death evolutionary pattern aligning with the 'out-of-the-testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA-mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species.
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Affiliation(s)
- Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
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3
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Diener C, Keller A, Meese E. The miRNA-target interactions: An underestimated intricacy. Nucleic Acids Res 2024; 52:1544-1557. [PMID: 38033323 PMCID: PMC10899768 DOI: 10.1093/nar/gkad1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. Their cellular regulatory impact is determined not solely by their sheer number, which likely amounts to >2000 individual miRNAs in human, than by the regulatory effectiveness of single miRNAs. Although, one begins to develop an understanding of the complex mechanisms underlying miRNA-target interactions (MTIs), the overall knowledge of MTI functionality is still rather patchy. In this critical review, we summarize key features of mammalian MTIs. We especially highlight latest insights on (i) the dynamic make-up of miRNA binding sites including non-canonical binding sites, (ii) the cooperativity between miRNA binding sites, (iii) the adaptivity of MTIs through sequence modifications, (iv) the bearing of intra-cellular miRNA localization changes and (v) the role of cell type and cell status specific miRNA interaction partners. The MTI biology is discussed against the background of state-of-the-art approaches with particular emphasis on experimental strategies for evaluating miRNA functionality.
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Affiliation(s)
- Caroline Diener
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
| | - Andreas Keller
- Saarland University (USAAR), Chair for Clinical Bioinformatics, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
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4
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Fromm B, Sorger T. Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy. iScience 2024; 27:108740. [PMID: 38327773 PMCID: PMC10847693 DOI: 10.1016/j.isci.2023.108740] [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: 11/28/2022] [Revised: 09/13/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024] Open
Abstract
The metabolic efficiency of mammalian cells depends on the attenuation of intrinsic translation noise by microRNAs. We devised a metric of cellular metabolic rate (cMR), rMR/Mexp optimally fit to the number of microRNA families (mirFam), that is robust to variation in mass and sensitive to body temperature (Tb), consistent with the heat dissipation limit theory of Speakman and Król (2010). Using mirFam as predictor, an Ornstein-Uhlenbeck process of stabilizing selection, with an adaptive shift at the divergence of Boreoeutheria, accounted for 95% of the variation in cMR across mammals. Branchwise rates of evolution of cMR, mirFam and Tb concurrently increased 6- to 7-fold at the divergence of Boreoeutheria, independent of mass. Cellular MR variation across placental mammals was also predicted by the sum of model conserved microRNA-target interactions, revealing an unexpected degree of integration of the microRNA-target apparatus into the energy economy of the mammalian cell.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Thomas Sorger
- Department of Biology, Roger Williams University, Bristol, RI 02809, USA
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5
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Wagner V, Kern F, Hahn O, Schaum N, Ludwig N, Fehlmann T, Engel A, Henn D, Rishik S, Isakova A, Tan M, Sit R, Neff N, Hart M, Meese E, Quake S, Wyss-Coray T, Keller A. Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues. Nat Biotechnol 2024; 42:109-118. [PMID: 37106037 DOI: 10.1038/s41587-023-01751-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.
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Affiliation(s)
- Viktoria Wagner
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Dominic Henn
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shusruto Rishik
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michelle Tan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rene Sit
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Norma Neff
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Martin Hart
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Steve Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany.
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6
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Umu SU, Paynter VM, Trondsen H, Buschmann T, Rounge TB, Peterson KJ, Fromm B. Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. CELL GENOMICS 2023; 3:100348. [PMID: 37601971 PMCID: PMC10435380 DOI: 10.1016/j.xgen.2023.100348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 08/22/2023]
Abstract
The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
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Affiliation(s)
- Sinan Uğur Umu
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vanessa M. Paynter
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Håvard Trondsen
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
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7
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Hammond RK, Gupta P, Patel P, Meyers BC. miRador: a fast and precise tool for the prediction of plant miRNAs. PLANT PHYSIOLOGY 2023; 191:894-903. [PMID: 36437740 PMCID: PMC9922418 DOI: 10.1093/plphys/kiac538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Plant microRNAs (miRNAs) are short, noncoding RNA molecules that restrict gene expression via posttranscriptional regulation and function in several essential pathways, including development, growth, and stress responses. Accurately identifying miRNAs in populations of small RNA sequencing libraries is a computationally intensive process that has resulted in the misidentification of inaccurately annotated miRNA sequences. In recent years, criteria for miRNA annotation have been refined with the aim to reduce these misannotations. Here, we describe miRador, a miRNA identification tool that utilizes the most up-to-date, community-established criteria for accurate identification of miRNAs in plants. We combined target prediction and Parallel Analysis of RNA Ends (PARE) data to assess the precision of the miRNAs identified by miRador. We compared miRador to other commonly used miRNA prediction tools and found that miRador is at least as precise as other prediction tools while being substantially faster than other tools. miRador should be broadly useful for the plant community to identify and annotate miRNAs in plant genomes.
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Affiliation(s)
- Reza K Hammond
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19714, USA
| | - Pallavi Gupta
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Columbia, Missouri 65211, USA
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19714, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, 52 Agriculture Lab, Columbia, Missouri 65211, USA
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8
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Johnson NR, Larrondo LF, Álvarez JM, Vidal EA. Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links. eLife 2022; 11:e83691. [PMID: 36484778 PMCID: PMC9757828 DOI: 10.7554/elife.83691] [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: 09/24/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
RNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technologies. Despite this relevant source of information, relatively little is known about mi/milRNA features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/milRNA characteristics and annotation confidence, we searched for publications describing mi/milRNA loci and re-assessed the annotations for 41 fungal species. We extracted and normalized the annotation data for 1727 reported mi/milRNA loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 25 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying more than 150 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms.
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Affiliation(s)
- Nathan R Johnson
- Millennium Science Initiative - Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad MayorSantiagoChile
| | - Luis F Larrondo
- Millennium Science Initiative - Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiagoChile
| | - José M Álvarez
- Millennium Science Initiative - Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad MayorSantiagoChile
- Centro de Biotecnología Vegetal, Facultad de Ciencias, Universidad Andrés BelloSantiagoChile
| | - Elena A Vidal
- Millennium Science Initiative - Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad MayorSantiagoChile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad MayorSantiagoChile
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9
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Hauschild AC, Pastrello C, Ekaputeri G, Bethune-Waddell D, Abovsky M, Ahmed Z, Kotlyar M, Lu R, Jurisica I. MirDIP 5.2: tissue context annotation and novel microRNA curation. Nucleic Acids Res 2022; 51:D217-D225. [PMID: 36453996 PMCID: PMC9825511 DOI: 10.1093/nar/gkac1070] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/16/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
MirDIP is a well-established database that aggregates microRNA-gene human interactions from multiple databases to increase coverage, reduce bias, and improve usability by providing an integrated score proportional to the probability of the interaction occurring. In version 5.2, we removed eight outdated resources, added a new resource (miRNATIP), and ran five prediction algorithms for miRBase and mirGeneDB. In total, mirDIP 5.2 includes 46 364 047 predictions for 27 936 genes and 2734 microRNAs, making it the first database to provide interactions using data from mirGeneDB. Moreover, we curated and integrated 32 497 novel microRNAs from 14 publications to accelerate the use of these novel data. In this release, we also extend the content and functionality of mirDIP by associating contexts with microRNAs, genes, and microRNA-gene interactions. We collected and processed microRNA and gene expression data from 20 resources and acquired information on 330 tissue and disease contexts for 2657 microRNAs, 27 576 genes and 123 651 910 gene-microRNA-tissue interactions. Finally, we improved the usability of mirDIP by enabling the user to search the database using precursor IDs, and we integrated miRAnno, a network-based tool for identifying pathways linked to specific microRNAs. We also provide a mirDIP API to facilitate access to its integrated predictions. Updated mirDIP is available at https://ophid.utoronto.ca/mirDIP.
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Affiliation(s)
| | | | - Gitta Kirana Anindya Ekaputeri
- Department of Medical Informatics, University Medical Center Göttingen, Georg-August University, Göttingen, Lower Saxony 37075, Germany
| | - Dylan Bethune-Waddell
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Mark Abovsky
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Zuhaib Ahmed
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Richard Lu
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Igor Jurisica
- To whom correspondence should be addressed. Tel: +1 416 581 7437;
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10
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Genetic Variants of MIR27A, MIR196A2 May Impact the Risk for the Onset of Coronary Artery Disease in the Pakistani Population. Genes (Basel) 2022; 13:genes13050747. [PMID: 35627132 PMCID: PMC9141586 DOI: 10.3390/genes13050747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Genetic variants in microRNA genes have a detrimental effect on miRNA-mediated regulation of gene expression and may contribute to coronary artery disease (CAD). CAD is the primary cause of mortality worldwide. Several environmental, genetic, and epigenetic factors are responsible for CAD susceptibility. The contribution of protein-coding genes is extensively studied. However, the role of microRNA genes in CAD is at infancy. The study is aimed to investigate the impact of rs895819, rs11614913, and rs2168518 variants in MIR27A, MIR196A2, and MIR4513, respectively, in CAD using allele-specific PCR. Results: For variant rs11614913, significant distribution of the genotypes among the cases and controls was determined by co-dominant [χ2 = 54.4; p value ≤ 0.0001], dominant (C/C vs. C/T + T/T) [OR = 0.257 (0.133-0.496); p value ≤ 0.0001], recessive (T/T vs. C/T + C/C) [OR = 1.56 (0.677-0.632); p value = 0.398], and additive models [OR = 0.421 (0.262-0.675); p value = 0.0004]. Similarly, a significant association of rs895819 was determined by co-dominant [χ2 = 9.669; p value ≤ 0.008], dominant (A/A vs. A/G + G/G) [OR = 0.285 (0.1242-0.6575); p value ≤ 0.0034], recessive (G/G vs. A/G + A/A) [OR = 0.900 (0.3202-3.519); p value = 1.000], and additive models [OR = 0.604 (0.3640-1.002); p value = 0.05] while no significant association of rs2168518 with CAD was found. Conclusion: The variants rs895819 and rs11614913 are the susceptibility factors for CAD.
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11
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Meng Y, Ma X, Li J, Shao C. Creating and maintaining a high-confidence microRNA repository for crop research: A brief review and re-examination of the current crop microRNA registries. JOURNAL OF PLANT PHYSIOLOGY 2022; 270:153636. [PMID: 35124290 DOI: 10.1016/j.jplph.2022.153636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
miRBase was established as an authoritative microRNA (miRNA) database with a uniform nomenclature system and a searchable web interface. Recent popularization of the next-generation sequencing technology in small RNA cloning led to an explosive growth of the miRNA repository. Although a specific definition system has been proposed for the plant miRNAs, the quality of the plant miRNA registries deposited in miRBase is largely dependent on the submitters. With the growing concerns over the annotation quality, a set of criteria for identification of the high-confidence (HC) miRNAs was recently developed by miRBase. Since miRNAs could serve as a powerful tool for crop genetic improvement and breeding, we present a brief overview of the miRBase-registered crop miRNAs in this study. A total of 54 plants were identified from the 82 Viridiplantae species in the current version of miRBase, and were regarded as the crops. A total of 6316 precursors encoding 7422 mature miRNAs (miRBase release 22.1) were included in our survey. Based on the HC annotation criteria, we performed structure- and sequencing data-based analyses of the confidence of the crop miRNAs. According to the results, we propose suggestions for improvements of the HC annotation system and, moreover, discuss strategies for creating and maintaining an HC miRNA repository of crops. Finally, we hope that this study inspires more efforts devoted to HC miRNA discoveries for crop research.
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Affiliation(s)
- Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China; School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jie Li
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou, 313000, China
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12
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Veryaskina YA, Titov SE, Ivanov MK, Ruzankin PS, Tarasenko AS, Shevchenko SP, Kovynev IB, Stupak EV, Pospelova TI, Zhimulev IF. Selection of reference genes for quantitative analysis of microRNA expression in three different types of cancer. PLoS One 2022; 17:e0254304. [PMID: 35176014 PMCID: PMC8853544 DOI: 10.1371/journal.pone.0254304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 01/30/2022] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are promising biomarkers in cancer research. Quantitative PCR (qPCR), also known as real-time PCR, is the most frequently used technique for measuring miRNA expression levels. The use of this technique, however, requires that expression data be normalized against reference genes. The problem is that a universal internal control for quantitative analysis of miRNA expression by qPCR has yet to be known. The aim of this work was to find the miRNAs with stable expression in the thyroid gland, brain and bone marrow according to NanoString nCounter miRNA quantification data. As a results, the most stably expressed miRNAs were as follows: miR-361-3p, -151a-3p and -29b-3p in the thyroid gland; miR-15a-5p, -194-5p and -532-5p in the brain; miR-140-5p, -148b-3p and -362-5p in bone marrow; and miR-423-5p, -28-5p and -532-5p, no matter what tissue type. These miRNAs represent promising reference genes for miRNA quantification by qPCR.
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Affiliation(s)
- Yuliya A. Veryaskina
- Laboratory of Gene Engineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
| | - Sergei E. Titov
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- AO Vector-Best, Novosibirsk, Russia
| | | | - Pavel S. Ruzankin
- Sobolev Institute of Mathematics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, Novosibirsk, Russia
| | - Anton S. Tarasenko
- Sobolev Institute of Mathematics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, Novosibirsk, Russia
| | | | - Igor B. Kovynev
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, Novosibirsk, Russia
| | - Evgenij V. Stupak
- Department of Neurosurgery, Ya.L. Tsivyan Novosibirsk Research Institute of Traumatology and Orthopedics, Novosibirsk, Russia
| | - Tatiana I. Pospelova
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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13
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Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Res 2021; 50:D204-D210. [PMID: 34850127 PMCID: PMC8728216 DOI: 10.1093/nar/gkab1101] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 11/23/2021] [Indexed: 12/03/2022] Open
Abstract
We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Xiangfu Zhong
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Ernesto Aparicio-Puerta
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Vladimir Ovchinnikov
- Computational and Molecular Evolutionary Biology Research Group, School of life sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Sinan U Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Peter J Chabot
- Department of Biological Sciences, Dartmouth College, Hanover, USA
| | - Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | | | - Morten Johansen
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Hackenberg
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, USA
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14
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Kolanska K, Sbeih M, Canlorbe G, Mekinian A, Varinot J, Capmas P, Koskas M, Aractingi S, Daraï E, Chabbert-Buffet N. Ulipristal Acetate Modifies miRNA Expression in Both Superficial and Basal Layers of the Human Endometrium. J Clin Med 2021; 10:jcm10194442. [PMID: 34640460 PMCID: PMC8509688 DOI: 10.3390/jcm10194442] [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: 09/04/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/05/2022] Open
Abstract
(1) Background: Ulipristal acetate (UPA) is a selective progesterone receptor modulator (SPRM) widely used for emergency contraception and mid- to long-term leiomyoma treatment. The aim of this study was to identify modifications of miRNA expression in superficial and basal layers of the human endometrium at the end of the UPA treatment for at least 3 months. (2) Methods: Microarray miRNA analysis of formalin-fixed, paraffin-embedded hysterectomy tissue samples was conducted, followed by an Ingenuity Pathway Analysis. Samples were divided into three groups: women having had 3 months of UPA treatment (n = 7); and two control groups of UPA-naïve women in the proliferative (n = 8) or secretory (n = 6) phase. (3) Results: The UPA modified the expression of 59 miRNAs involved in the processes of cell cycle, carcinogenesis, and inflammation. Their expression profiles were different in the basal and superficial layers. Most of the processes influenced by the UPA in the basal layer were connected to the cell cycle and immune regulation. (4) Conclusion: Specific changes were observed in both layers of the endometrium in the UPA group. However, the miRNA expression in the basal layer was not consistent with that in the superficial layer. Other large studies analysing the long-term impact of SPRM on endometrial miRNA expression are necessary.
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Affiliation(s)
- Kamila Kolanska
- INSERM UMRS 938, Sorbonne Université, Site Saint-Antoine, 27 rue Chaligny, CEDEX 12, 75571 Paris, France; (M.S.); (G.C.); (M.K.); (S.A.); (E.D.); (N.C.-B.)
- Service de Gynécologie Sestertius et Médecine de la Reproduction, AP-HP Sorbonne Université Site Tenon, 4 rue de la Chine, 75020 Paris, France
- Correspondence:
| | - Maria Sbeih
- INSERM UMRS 938, Sorbonne Université, Site Saint-Antoine, 27 rue Chaligny, CEDEX 12, 75571 Paris, France; (M.S.); (G.C.); (M.K.); (S.A.); (E.D.); (N.C.-B.)
| | - Geoffroy Canlorbe
- INSERM UMRS 938, Sorbonne Université, Site Saint-Antoine, 27 rue Chaligny, CEDEX 12, 75571 Paris, France; (M.S.); (G.C.); (M.K.); (S.A.); (E.D.); (N.C.-B.)
- Department of Gynecological and Breast Surgery and Oncology, Pitié-Salpêtrière University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), 75013 Paris, France
| | - Arsène Mekinian
- Service de Médecine Interne, AP-HP Sorbonne Université Site St Antoine, 184 rue du Faubourg Saint Antoine, 75012 Paris, France;
| | - Justine Varinot
- Service d’Anatomopathologie, AP HP Sorbonne Université Site Tenon, 4 rue de la Chine, 75020 Paris, France;
| | - Perrine Capmas
- Department of Gynecology and Obstetrics, University Paris Saclay, 78 rue du Général Leclerc, 94270 Le Kremlin-Bicêtre, France;
- Inserm, Centre of Research in Epidemiology and Population Health (CESP), U1018, 94276 Le Kremlin-Bicêtre, France
| | - Martin Koskas
- INSERM UMRS 938, Sorbonne Université, Site Saint-Antoine, 27 rue Chaligny, CEDEX 12, 75571 Paris, France; (M.S.); (G.C.); (M.K.); (S.A.); (E.D.); (N.C.-B.)
- Department of Obstetrics and Gynecology, AP-HP Bichat University Hospital, 75018 Paris, France
- Institut de Recherche en Santé de la Femme, Equipe d’accueil 7285, Universite de Versailles Saint-Quentin-en-Yvelines, 78180 Montigny-le-Bretonneux, France
| | - Selim Aractingi
- INSERM UMRS 938, Sorbonne Université, Site Saint-Antoine, 27 rue Chaligny, CEDEX 12, 75571 Paris, France; (M.S.); (G.C.); (M.K.); (S.A.); (E.D.); (N.C.-B.)
| | - Emile Daraï
- INSERM UMRS 938, Sorbonne Université, Site Saint-Antoine, 27 rue Chaligny, CEDEX 12, 75571 Paris, France; (M.S.); (G.C.); (M.K.); (S.A.); (E.D.); (N.C.-B.)
- Service de Gynécologie Sestertius et Médecine de la Reproduction, AP-HP Sorbonne Université Site Tenon, 4 rue de la Chine, 75020 Paris, France
| | - Nathalie Chabbert-Buffet
- INSERM UMRS 938, Sorbonne Université, Site Saint-Antoine, 27 rue Chaligny, CEDEX 12, 75571 Paris, France; (M.S.); (G.C.); (M.K.); (S.A.); (E.D.); (N.C.-B.)
- Service de Gynécologie Sestertius et Médecine de la Reproduction, AP-HP Sorbonne Université Site Tenon, 4 rue de la Chine, 75020 Paris, France
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15
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Keller A, Gröger L, Tschernig T, Solomon J, Laham O, Schaum N, Wagner V, Kern F, Schmartz GP, Li Y, Borcherding A, Meier C, Wyss-Coray T, Meese E, Fehlmann T, Ludwig N. miRNATissueAtlas2: an update to the human miRNA tissue atlas. Nucleic Acids Res 2021; 50:D211-D221. [PMID: 34570238 PMCID: PMC8728130 DOI: 10.1093/nar/gkab808] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing the expression of miRNAs across organs in the human body. Here, we present an updated resource containing sequencing data of 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling the organs from the same bodies minimizes intra-individual variability and facilitates the making of a precise high-resolution body map of the non-coding transcriptome. The data allow shedding light on the organ- and organ system-specificity of piwi-interacting RNAs (piRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs) and other non-coding RNAs. As use case of our resource, we describe the identification of highly specific ncRNAs in different organs. The update also contains 58 samples from six tissues of the Tabula Muris collection, allowing to check if the tissue specificity is evolutionary conserved between Homo sapiens and Mus musculus. The updated resource of 87 252 non-coding RNAs from nine non-coding RNA classes for all organs and organ systems is available online without any restrictions (https://www.ccb.uni-saarland.de/tissueatlas2).
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Affiliation(s)
- Andreas Keller
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurobiology, Stanford University, CA 94305, USA
| | - Laura Gröger
- Center for Human and Molecular Biology, Junior Research Group Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Thomas Tschernig
- Institute for Anatomy, Saarland University, 66421 Homburg, Germany
| | - Jeffrey Solomon
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Omar Laham
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nicholas Schaum
- Department of Neurology and Neurobiology, Stanford University, CA 94305, USA
| | - Viktoria Wagner
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Georges Pierre Schmartz
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Yongping Li
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Carola Meier
- Institute for Anatomy, Saarland University, 66421 Homburg, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurobiology, Stanford University, CA 94305, USA
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Center for Human and Molecular Biology, Junior Research Group Human Genetics, Saarland University, 66421 Homburg, Germany
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16
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Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson’s disease progression. ACTA ACUST UNITED AC 2021; 1:309-322. [PMID: 37118411 DOI: 10.1038/s43587-021-00042-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Noncoding RNAs have diagnostic and prognostic importance in Parkinson's disease (PD). We studied circulating small noncoding RNAs (sncRNAs) in two large-scale longitudinal PD cohorts (Parkinson's Progression Markers Initiative (PPMI) and Luxembourg Parkinson's Study (NCER-PD)) and modeled their impact on the transcriptome. Sequencing of sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI yielded 323 billion reads, most of which mapped to microRNAs but covered also other RNA classes such as piwi-interacting RNAs, ribosomal RNAs and small nucleolar RNAs. Dysregulated microRNAs associated with disease and disease progression occur in two distinct waves in the third and seventh decade of life. Originating predominantly from immune cells, they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. Profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort validated biomarkers and main findings by an independent technology. Finally, network analysis of sncRNA and transcriptome sequencing from PPMI identified regulatory modules emerging in patients with progressing PD.
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17
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Solomon J, Kern F, Fehlmann T, Meese E, Keller A. HumiR: Web Services, Tools and Databases for Exploring Human microRNA Data. Biomolecules 2020; 10:biom10111576. [PMID: 33233537 PMCID: PMC7699549 DOI: 10.3390/biom10111576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
For many research aspects on small non-coding RNAs, especially microRNAs, computational tools and databases are developed. This includes quantification of miRNAs, piRNAs, tRNAs and tRNA fragments, circRNAs and others. Furthermore, the prediction of new miRNAs, isomiRs, arm switch events, target and target pathway prediction and miRNA pathway enrichment are common tasks. Additionally, databases and resources containing expression profiles, e.g., from different tissues, organs or cell types, are generated. This information in turn leads to improved miRNA repositories. While most of the respective tools are implemented in a species-independent manner, we focused on tools for human small non-coding RNAs. This includes four aspects: (1) miRNA analysis tools (2) databases on miRNAs and variations thereof (3) databases on expression profiles (4) miRNA helper tools facilitating frequent tasks such as naming conversion or reporter assay design. Although dependencies between the tools exist and several tools are jointly used in studies, the interoperability is limited. We present HumiR, a joint web presence for our tools. HumiR facilitates an entry in the world of miRNA research, supports the selection of the right tool for a research task and represents the very first step towards a fully integrated knowledge-base for human small non-coding RNA research. We demonstrate the utility of HumiR by performing a very comprehensive analysis of Alzheimer's miRNAs.
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Affiliation(s)
- Jeffrey Solomon
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
| | - Eckart Meese
- Institute for Human Genetics, Saarland University, 66421 Homburg, Germany;
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Neurobiology, Stanford University, Palo Alto, CA 94305, USA
- Correspondence: ; Tel.: +49-681-30268611
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18
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Kern F, Amand J, Senatorov I, Isakova A, Backes C, Meese E, Keller A, Fehlmann T. miRSwitch: detecting microRNA arm shift and switch events. Nucleic Acids Res 2020; 48:W268-W274. [PMID: 32356893 PMCID: PMC7319450 DOI: 10.1093/nar/gkaa323] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 12/27/2022] Open
Abstract
Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.
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Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeremy Amand
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Ilya Senatorov
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,School of Medicine Office, Stanford University, Stanford, CA 94305, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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19
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Vorozheykin PS, Titov II. Erratum to: How Animal miRNAs Structure Influences Their Biogenesis. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420220019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Res 2020; 48:D132-D141. [PMID: 31598695 PMCID: PMC6943042 DOI: 10.1093/nar/gkz885] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023] Open
Abstract
Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database - MirGeneDB - to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.
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Affiliation(s)
- Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Diana Domanska
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vladimir Ovchinnikov
- School of Life Sciences, Faculty of Health and Life Sciences, University of Nottingham, UK.,Department of Human and Animal Genetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Morten Johansen
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.,Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Hackenberg
- Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
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21
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Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase: from microRNA sequences to function. Nucleic Acids Res 2020; 47:D155-D162. [PMID: 30423142 PMCID: PMC6323917 DOI: 10.1093/nar/gky1141] [Citation(s) in RCA: 2543] [Impact Index Per Article: 635.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/25/2018] [Indexed: 12/13/2022] Open
Abstract
miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: 38 589 hairpin precursors and 48 860 mature microRNAs. We describe improvements to the database and website to provide more information about the quality of microRNA gene annotations, and the cellular functions of their products. We have collected 1493 small RNA deep sequencing datasets and mapped a total of 5.5 billion reads to microRNA sequences. The read mapping patterns provide strong support for the validity of between 20% and 65% of microRNA annotations in different well-studied animal genomes, and evidence for the removal of >200 sequences from the database. To improve the availability of microRNA functional information, we are disseminating Gene Ontology terms annotated against miRBase sequences. We have also used a text-mining approach to search for microRNA gene names in the full-text of open access articles. Over 500 000 sentences from 18 542 papers contain microRNA names. We score these sentences for functional information and link them with 12 519 microRNA entries. The sentences themselves, and word clouds built from them, provide effective summaries of the functional information about specific microRNAs. miRBase is publicly and freely available at http://mirbase.org/.
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Affiliation(s)
- Ana Kozomara
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Maria Birgaoanu
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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22
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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23
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Nersisyan S, Shkurnikov M, Poloznikov A, Turchinovich A, Burwinkel B, Anisimov N, Tonevitsky A. A Post-Processing Algorithm for miRNA Microarray Data. Int J Mol Sci 2020; 21:ijms21041228. [PMID: 32059403 PMCID: PMC7072892 DOI: 10.3390/ijms21041228] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 11/16/2022] Open
Abstract
One of the main disadvantages of using DNA microarrays for miRNA expression profiling is the inability of adequate comparison of expression values across different miRNAs. This leads to a large amount of miRNAs with high scores which are actually not expressed in examined samples, i.e., false positives. We propose a post-processing algorithm which performs scoring of miRNAs in the results of microarray analysis based on expression values, time of discovery of miRNA, and correlation level between the expressions of miRNA and corresponding pre-miRNA in considered samples. The algorithm was successfully validated by the comparison of the results of its application to miRNA microarray breast tumor samples with publicly available miRNA-seq breast tumor data. Additionally, we obtained possible reasons why miRNA can appear as a false positive in microarray study using paired miRNA sequencing and array data. The use of DNA microarrays for estimating miRNA expression profile is limited by several factors. One of them consists of problems with comparing expression values of different miRNAs. In this work, we show that situation can be significantly improved if some additional information is taken into consideration in a comparison.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
- Correspondence:
| | - Maxim Shkurnikov
- P.A. Hertsen Moscow Oncology Research Center, Branch of National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Second Botkinsky lane 3, 125284 Moscow, Russia;
| | - Andrey Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 249036 Obninks, Russia;
- School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia;
| | - Andrey Turchinovich
- Molecular Epidemiology C080, German Cancer Research Center, 69120 Heidelberg, Germany; (A.T.); (B.B.)
- SciBerg e.Kfm, 68309 Mannheim, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology C080, German Cancer Research Center, 69120 Heidelberg, Germany; (A.T.); (B.B.)
- University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Nikita Anisimov
- School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia;
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, 117312 Moscow, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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25
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Mármol-Sánchez E, Cirera S, Quintanilla R, Pla A, Amills M. Discovery and annotation of novel microRNAs in the porcine genome by using a semi-supervised transductive learning approach. Genomics 2019; 112:2107-2118. [PMID: 31816430 DOI: 10.1016/j.ygeno.2019.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/13/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022]
Abstract
Despite the broad variety of available microRNA (miRNA) prediction tools, their application to the discovery and annotation of novel miRNA genes in domestic species is still limited. In this study we designed a comprehensive pipeline (eMIRNA) for miRNA identification in the yet poorly annotated porcine genome and demonstrated the usefulness of implementing a motif search positional refinement strategy for the accurate determination of precursor miRNA boundaries. The small RNA fraction from gluteus medius skeletal muscle of 48 Duroc gilts was sequenced and used for the prediction of novel miRNA loci. Additionally, we selected the human miRNA annotation for a homology-based search of porcine miRNAs with orthologous genes in the human genome. A total of 20 novel expressed miRNAs were identified in the porcine muscle transcriptome and 27 additional novel porcine miRNAs were also detected by homology-based search using the human miRNA annotation. The existence of three selected novel miRNAs (ssc-miR-483, ssc-miR484 and ssc-miR-200a) was further confirmed by reverse transcription quantitative real-time PCR analyses in the muscle and liver tissues of Göttingen minipigs. In summary, the eMIRNA pipeline presented in the current work allowed us to expand the catalogue of porcine miRNAs and showed better performance than other commonly used miRNA prediction approaches. More importantly, the flexibility of our pipeline makes possible its application in other yet poorly annotated non-model species.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Susanna Cirera
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, 2nd Floor, 1870 Frederiksberg C, Denmark
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Albert Pla
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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26
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Ludwig N, Fehlmann T, Kern F, Gogol M, Maetzler W, Deutscher S, Gurlit S, Schulte C, von Thaler AK, Deuschle C, Metzger F, Berg D, Suenkel U, Keller V, Backes C, Lenhof HP, Meese E, Keller A. Machine Learning to Detect Alzheimer's Disease from Circulating Non-coding RNAs. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:430-440. [PMID: 31809862 PMCID: PMC6943763 DOI: 10.1016/j.gpb.2019.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/26/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022]
Abstract
Blood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches are applied to discover biomarker signatures. These have to be validated in larger cohorts and evaluated by adequate statistical learning approaches. Previously, we published high-throughput sequencing based microRNA (miRNA) signatures in Alzheimer’s disease (AD) patients in the United States (US) and Germany. Here, we determined abundance levels of 21 known circulating miRNAs in 465 individuals encompassing AD patients and controls by RT-qPCR. We computed models to assess the relation between miRNA expression and phenotypes, gender, age, or disease severity (Mini-Mental State Examination; MMSE). Of the 21 miRNAs, expression levels of 20 miRNAs were consistently de-regulated in the US and German cohorts. 18 miRNAs were significantly correlated with neurodegeneration (Benjamini-Hochberg adjusted P < 0.05) with highest significance for miR-532-5p (Benjamini-Hochberg adjusted P = 4.8 × 10−30). Machine learning models reached an area under the curve (AUC) value of 87.6% in differentiating AD patients from controls. Further, ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted P = 0.0002). Interestingly, the miRNAs with lower abundance in AD were enriched in monocytes and T-helper cells, while those up-regulated in AD were enriched in serum, exosomes, cytotoxic t-cells, and B-cells. Our study represents the next important step in translational research for a miRNA-based AD test.
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Affiliation(s)
- Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Manfred Gogol
- Institut für Gerontologie, Universität Heidelberg, 69047 Heidelberg, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Stephanie Deutscher
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Simone Gurlit
- Department of Anesthesiology and Intensive Care, St. Franziskus Hospital Muenster, 48145 Muenster, Germany
| | - Claudia Schulte
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Anna-Katharina von Thaler
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Christian Deuschle
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Florian Metzger
- Department of Psychiatry and Psychotherapy, University Hospital Tuebingen, 72016 Tuebingen, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Ulrike Suenkel
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, 66421 Homburg/Saar, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.
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Rojo Arias JE, Busskamp V. Challenges in microRNAs' targetome prediction and validation. Neural Regen Res 2019; 14:1672-1677. [PMID: 31169173 PMCID: PMC6585557 DOI: 10.4103/1673-5374.257514] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/14/2019] [Indexed: 11/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules with important roles in post-transcriptional regulation of gene expression. In recent years, the predicted number of miRNAs has skyrocketed, largely as a consequence of high-throughput sequencing technologies becoming ubiquitous. This dramatic increase in miRNA candidates poses multiple challenges in terms of data deposition, curation, and validation. Although multiple databases containing miRNA annotations and targets have been developed, ensuring data quality by validating miRNA-target interactions requires the efforts of the research community. In order to generate databases containing biologically active miRNAs, it is imperative to overcome a multitude of hurdles, including restricted miRNA expression patterns, distinct miRNA biogenesis machineries, and divergent miRNA-mRNA interaction dynamics. In the present review, we discuss recent advances and limitations in miRNA prediction, identification, and validation. Lastly, we focus on the most enriched neuronal miRNA, miR-124, and its gene regulatory network in human neurons, which has been revealed using a combined computational and experimental approach.
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Affiliation(s)
| | - Volker Busskamp
- Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Dresden, Germany
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28
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Backes C, Fehlmann T, Kern F, Kehl T, Lenhof HP, Meese E, Keller A. miRCarta: a central repository for collecting miRNA candidates. Nucleic Acids Res 2019; 46:D160-D167. [PMID: 29036653 PMCID: PMC5753177 DOI: 10.1093/nar/gkx851] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022] Open
Abstract
The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014. As a result, publications describing new miRNA candidates in the last three to five years might have a substantial overlap of candidates without noticing. With miRCarta we implemented a database to collect novel miRNA candidates and augment the information provided by miRBase. In the first stage, miRCarta is thought to be a highly sensitive collection of potential miRNA candidates with a high degree of analysis functionality, annotations and details on each miRNA. We added-besides the full content of the miRBase-12,857 human miRNA precursors to miRCarta. Users can match their own predictions to the entries of miRCarta to reduce potential redundancies in their studies. miRCarta provides the most comprehensive collection of human miRNAs and miRNA candidates to form a basis for further refinement and validation studies. The database is freely accessible at https://mircarta.cs.uni-saarland.de/.
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Affiliation(s)
- Christina Backes
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Eckart Meese
- Institute for Human Genetics, Medical School, Saarland University, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
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Tu C, Du T, Ye X, Shao C, Xie J, Shen Y. Using miRNAs and circRNAs to estimate PMI in advanced stage. Leg Med (Tokyo) 2019; 38:51-57. [PMID: 30986695 DOI: 10.1016/j.legalmed.2019.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/13/2022]
Abstract
In our previous study, we evaluated the stability of multi-RNA markers in heart, liver and skeletal muscle tissues of mice within 8 days after death and concluded that microRNAs (miRNAs) and circular (circRNAs) were more stable as reference genes in dead bodies than other kinds of RNAs. Based on their tissue-specific expression, we obtained reference genes for three kinds of tissues: miR-122, miR-133a and 18S in heart tissues; LC-Ogdh, circ-AFF1 and miR-122 in liver tissues; and miR-133a, circ-AFF1 in skeletal muscle tissues. For the estimation of post mortem interval (PMI), we also selected suitable biomarkers, which exhibited the best correlation coefficient with PMI. In our stability analysis of multi-RNA markers, Gapdh, Rps18, U6 and β-actin were unstable and selected as candidate target biomarkers. By analyzing the correlation between the expression levels of candidate target biomarkers and PMI, we obtained suitable target biomarkers for the three kinds of tissues, respectively. Finally, we established mathematical models of PMI estimation using the above selected reference genes and target biomarkers. The low estimated error in the validated samples demonstrated that PMI in advanced stage could be accurately predicted by real-time quantitative polymerase chain reaction (qPCR) through systematically selected effective reference genes and target biomarkers. Besides, combining the estimated results of various tissues and multi-biomarkers could improve the accuracy of PMI estimation.
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Affiliation(s)
- Chunyan Tu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China
| | - Tieshuai Du
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China
| | - Xing Ye
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Yiwen Shen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
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30
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Wang Y, Peng M, Wang W, Chen Y, He Z, Cao J, Lin Z, Yang Z, Gong M, Yin Y. Verification of miRNAs in ginseng decoction by high-throughput sequencing and quantitative real-time PCR. Heliyon 2019; 5:e01418. [PMID: 30984884 PMCID: PMC6446053 DOI: 10.1016/j.heliyon.2019.e01418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/13/2019] [Accepted: 03/21/2019] [Indexed: 12/24/2022] Open
Abstract
Panax ginseng C. A. Meyer is a precious traditional Chinese medicine that has been clinically used for over thousands of years. In general, ginseng needs to be prepared to ginseng decoction before taking it. MicroRNAs are a class of small (18–24 nt), single-stranded molecules that regulate gene expression at the post-transcriptional level. Considering that ginseng miRNAs may be bioactive compounds, we used Illumina high-throughput sequencing and quantitative real-time PCR (qRT-PCR) to validate the existence of miRNAs in fresh ginseng decoction which have been boiled at high temperature. Our previous studies have demonstrated that there are several miRNAs in fresh ginseng. The roots of fresh Panax ginseng were prepared according to routine methods, from which miRNAs were extracted and sequenced. A total of 43 miRNAs were identified from water decoction by Illumina high-throughput sequencing, belonging to 71 miRNA families. The target genes of these miRNAs were predicted by sequencing, and were annotated by GO, KEGG and Nr databases. The functions of these target genes mainly included plant hormone signal transduction, transcription regulation, macromolecular metabolism and auxin signaling. Nine highly expressed miRNAs (miR159, miR167, miR396, miR166, miR168, miR156, miR165, miR162 and miR394) were verified by qRT-PCR, and the results of Illumina high-throughput sequencing and qRT-PCR were consistent. Results from this study indicate that miRNAs remained stable in P. ginseng after high-temperature boiling. Additionally, Illumina high-throughput sequencing was superior in the acquisition of higher amount of small RNAs.
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Affiliation(s)
- Yingfang Wang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Engineering & Technology Research Center of Topical Precise Drug Delivery System, Guangzhou 510006, china
- Corresponding author.
| | - Mengyuan Peng
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjuan Wang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yanlin Chen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhihua He
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jingjing Cao
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhiyun Lin
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zemin Yang
- School of Basic Courses, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Mengjuan Gong
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yongqin Yin
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
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31
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Halushka PV, Goodwin AJ, Halushka MK. Opportunities for microRNAs in the Crowded Field of Cardiovascular Biomarkers. ANNUAL REVIEW OF PATHOLOGY 2019; 14:211-238. [PMID: 30332561 PMCID: PMC6442682 DOI: 10.1146/annurev-pathmechdis-012418-012827] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cardiovascular diseases exist across all developed countries. Biomarkers that can predict or diagnose diseases early in their pathogeneses can reduce their morbidity and mortality in afflicted individuals. microRNAs are small regulatory RNAs that modulate translation and have been identified as potential fluid-based biomarkers across numerous maladies. We describe the current state of cardiovascular disease biomarkers across a range of diseases, including myocardial infarction, acute coronary syndrome, myocarditis, hypertension, heart failure, heart transplantation, aortic stenosis, diabetic cardiomyopathy, atrial fibrillation, and sepsis. We present the current understanding of microRNAs as possible biomarkers in these categories and where their best opportunities exist to enter clinical practice.
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Affiliation(s)
- Perry V Halushka
- Department of Pharmacology, South Carolina Clinical and Translational Research Institute, Medical University of South Carolina, Charleston, South Carolina 29425, USA;
- Department of Medicine, South Carolina Clinical and Translational Research Institute, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Andrew J Goodwin
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, USA;
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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32
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Fehlmann T, Laufer T, Backes C, Kahramann M, Alles J, Fischer U, Minet M, Ludwig N, Kern F, Kehl T, Galata V, Düsterloh A, Schrörs H, Kohlhaas J, Bals R, Huwer H, Geffers L, Krüger R, Balling R, Lenhof HP, Meese E, Keller A. Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity. RNA Biol 2018; 16:93-103. [PMID: 30567465 DOI: 10.1080/15476286.2018.1559689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The validation of microRNAs (miRNAs) identified by next generation sequencing involves amplification-free and hybridization-based detection of transcripts as criteria for confirming valid miRNAs. Since respective validation is frequently not performed, miRNA repositories likely still contain a substantial fraction of false positive candidates while true miRNAs are not stored in the repositories yet. Especially if downstream analyses are performed with these candidates (e.g. target or pathway prediction), the results may be misleading. In the present study, we evaluated 558 mature miRNAs from miRBase and 1,709 miRNA candidates from next generation sequencing experiments by amplification-free hybridization and investigated their distributions in patients with various disease conditions. Notably, the most significant miRNAs in diseases are often not contained in the miRBase. However, these candidates are evolutionary highly conserved. From the expression patterns, target gene and pathway analyses and evolutionary conservation analyses, we were able to shed light on the complexity of miRNAs in humans. Our data also highlight that a more thorough validation of miRNAs identified by next generation sequencing is required. The results are available in miRCarta ( https://mircarta.cs.uni-saarland.de ).
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Affiliation(s)
- Tobias Fehlmann
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Thomas Laufer
- b Department of Human Genetics , Saarland University , Homburg , Germany.,c Hummingbird Diagnostics GmbH , Heidelberg , Germany
| | - Christina Backes
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Mustafa Kahramann
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,c Hummingbird Diagnostics GmbH , Heidelberg , Germany
| | - Julia Alles
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Ulrike Fischer
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Marie Minet
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Nicole Ludwig
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Fabian Kern
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Tim Kehl
- d Center for Bioinformatics , Saarland Informatics Campus , Saarbrücken , Germany
| | - Valentina Galata
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | | | | | | | - Robert Bals
- e Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine , Saarland University Hospital , Homburg , Germany
| | - Hanno Huwer
- f Department of Thoracic Surgery , SHG Clinics , Völklingen , Germany
| | - Lars Geffers
- g LCSB, Luxembourg Centre for Systems Biomedicine , University of Luxembourg , Esch-Sur-Alzette , Luxembourg
| | - Rejko Krüger
- g LCSB, Luxembourg Centre for Systems Biomedicine , University of Luxembourg , Esch-Sur-Alzette , Luxembourg
| | - Rudi Balling
- g LCSB, Luxembourg Centre for Systems Biomedicine , University of Luxembourg , Esch-Sur-Alzette , Luxembourg
| | - Hans-Peter Lenhof
- d Center for Bioinformatics , Saarland Informatics Campus , Saarbrücken , Germany
| | - Eckart Meese
- b Department of Human Genetics , Saarland University , Homburg , Germany
| | - Andreas Keller
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,d Center for Bioinformatics , Saarland Informatics Campus , Saarbrücken , Germany
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Ammerlaan W, Trouet J, Sachs MC, Guan P, Carithers L, Lambert P, Frasquilho S, Antunes L, Kofanova O, Rohrer D, Valley DR, Blanski A, Jewell S, Moore H, Betsou F. Small Nucleolar RNA Score: An Assay to Detect Formalin-Overfixed Tissue. Biopreserv Biobank 2018; 16:467-476. [PMID: 30234371 PMCID: PMC6308291 DOI: 10.1089/bio.2018.0042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Although there are millions of formalin-fixed paraffin-embedded (FFPE) tissue blocks potentially available for scientific research, many are of questionable quality, partly due to unknown fixation conditions. We analyzed FFPE tissue biospecimens as part of the NCI Biospecimen Preanalytical Variables (BPV) program to identify microRNA (miRNA) markers for fixation time. miRNA was extracted from kidney and ovary tumor FFPE blocks (19 patients, cold ischemia ≤2 hours) with 6, 12, 24, and 72 hours fixation times, then analyzed using the WaferGen SmartChip platform (miRNA chip with 1036 miRNA targets). For fixation time, principal component analysis of miRNA chip expression data separated 72 hours fixed samples from 6 to 24 hours fixed samples. A set of small nuclear RNA (snRNA) targets was identified that best determines fixation time and was validated using a second independent cohort of seven different tissue types. A customized assay was then developed, based on a set of 24 miRNA and snRNA targets, and a simple “snoRNA score” defined. This score detects FFPE tissue samples with fixation for 72 hours or more, with 79% sensitivity and 80% specificity. It can therefore be used to assess the fitness-for-purpose of FFPE samples for DNA or RNA-based research or clinical assays, which are known to be of limited robustness to formalin overfixation.
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Affiliation(s)
| | | | - Michael C Sachs
- Biostatistics Unit, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Keller A, Fehlmann T, Ludwig N, Kahraman M, Laufer T, Backes C, Vogelmeier C, Diener C, Biertz F, Herr C, Jörres RA, Lenhof HP, Meese E, Bals R. Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:162-171. [PMID: 29981854 PMCID: PMC6076380 DOI: 10.1016/j.gpb.2018.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/22/2018] [Accepted: 06/29/2018] [Indexed: 01/11/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) significantly increases the risk of developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development independent of the tumor type. From 2741 participants of COSYCONET diagnosed with COPD, we selected 534 individuals including 33 patients who developed cancer during the follow-up period of 54 months and 501 patients who did not develop cancer, but had similar age, gender and smoking history. Genome-wide miRNA profiles were generated and evaluated using machine learning techniques. For patients developing cancer we identified nine miRNAs with significantly decreased abundance (two-tailed unpaired t-test adjusted for multiple testing P < 0.05), including members of the miR-320 family. The identified miRNAs regulate different cancer-related pathways including the MAPK pathway (P = 2.3 × 10−5). We also observed the impact of confounding factors on the generated miRNA profiles, underlining the value of our matched analysis. For selected miRNAs, qRT-PCR analysis was applied to validate the results. In conclusion, we identified several miRNAs in blood of COPD patients, which could serve as candidates for biomarkers to help identify COPD patients at risk of developing cancer.
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Affiliation(s)
- Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Thomas Laufer
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany; Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Claus Vogelmeier
- Department of Internal Medicine, Division for Pulmonary Diseases, Philipps University of Marburg, 35043 Marburg, Germany
| | - Caroline Diener
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Frank Biertz
- Institute for Biostatistics, Hannover Medical School, 30625 Hanover, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University Hospital, 66421 Homburg, Germany
| | - Rudolf A Jörres
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Comprehensive Pneumology Center Munich (CPC-M), Ludwig-Maximilians-University Munich, Member of the German Center for Lung Research (DZL), 80539 Munich, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University Hospital, 66421 Homburg, Germany
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Ludwig N, Fehlmann T, Galata V, Franke A, Backes C, Meese E, Keller A. Small ncRNA-Seq Results of Human Tissues: Variations Depending on Sample Integrity. Clin Chem 2018; 64:1074-1084. [PMID: 29691221 DOI: 10.1373/clinchem.2017.285767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/19/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Although mature miRNAs are relatively stable in vivo, RNA degradation can have a substantial influence on small noncoding RNA (sncRNA) profiles. METHODS Using different tissue storage conditions and RNA isolation procedures, we analyzed the integrity and quality of RNA isolates from human lung and heart tissues. We sequenced a total of 64 RNA samples and quantified the effect of RNA degradation, DNA contamination, and other confounding factors on the sncRNA-seq data. Besides microRNAs, other noncoding RNA species (piRNAs, tRNAs, snoRNAs, rRNAs) were investigated. RESULTS Consistent with previous results, we found that the tissue specificity of microRNAs is generally well preserved. The distribution of microRNA isoforms was similar to the distribution of canonical forms. New miRNAs were more frequently discovered in degraded samples. sncRNA Reads generated from degraded samples mapped frequently to piRNAs, tRNAs, snoRNAs, or scaRNAs. Sequencing reads that were depleted of sncRNAs showed an increased mapping frequency to bacterial species. CONCLUSIONS Our data emphasize the importance of sample integrity, especially for next-generation sequencing (NGS)-based high-throughput sncRNA profiles. For the prediction of novel miRNAs in particular, only samples with the highest RNA integrity should be used in order to avoid identification of false "miRNAs."
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Affiliation(s)
- Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Tobias Fehlmann
- Department of Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Valentina Galata
- Department of Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Andre Franke
- Institute for Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Christina Backes
- Department of Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Department of Clinical Bioinformatics, Saarland University, Saarbrücken, Germany;
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