51
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Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells. Nat Commun 2021; 12:4316. [PMID: 34262050 PMCID: PMC8280203 DOI: 10.1038/s41467-021-24611-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs. Second, we analyze MCF7 single cell equivalents of the eight best protocols. Third, we sequence single cells from eight different cell lines and 67 circulating tumor cells (CTCs) from seven SCLC patients. Altogether, we analyze 244 different samples. We observe high reproducibility within protocols and reads covered a broad spectrum of RNAs. For the 67 CTCs, we detect a median of 68 miRNAs, with 10 miRNAs being expressed in 90% of tested cells. Enrichment analysis suggested the lung as the most likely organ of origin and enrichment of cancer-related categories. Even the identification of non-annotated candidate miRNAs was feasible, underlining the potential of single cell small RNA sequencing. Technologies for small non-coding RNA sequencing at the single-cell level are less mature than for sequencing mRNAs. Here the authors evaluate available protocols for analysis of circulating lung cancer tumour cells.
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52
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Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD. A microRNA expression and regulatory element activity atlas of the mouse immune system. Nat Immunol 2021; 22:914-927. [PMID: 34099919 PMCID: PMC8480231 DOI: 10.1038/s41590-021-00944-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
To better define the control of immune system regulation, we generated an atlas of microRNA (miRNA) expression from 63 mouse immune cell populations and connected these signatures with assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation followed by sequencing (ChIP-seq) and nascent RNA profiles to establish a map of miRNA promoter and enhancer usage in immune cells. miRNA complexity was relatively low, with >90% of the miRNA compartment of each population comprising <75 miRNAs; however, each cell type had a unique miRNA signature. Integration of miRNA expression with chromatin accessibility revealed putative regulatory elements for differentially expressed miRNAs, including miR-21a, miR-146a and miR-223. The integrated maps suggest that many miRNAs utilize multiple promoters to reach high abundance and identified dominant and divergent miRNA regulatory elements between lineages and during development that may be used by clustered miRNAs, such as miR-99a/let-7c/miR-125b, to achieve distinct expression. These studies, with web-accessible data, help delineate the cis-regulatory elements controlling miRNA signatures of the immune system.
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Affiliation(s)
- Samuel A Rose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksandra Wroblewska
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maxime Dhainaut
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | - Anela Bektesevic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Ben-Zvi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Rhoads
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Edy Y Kim
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bingfei Yu
- Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Yonit Lavin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian D Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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53
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Carol S Ringelberg
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Holly S Stevenson
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shipra Gupta
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Julie Koeman
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - Kara L Pivarski
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Xinkun Wang
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, USA
| | - Tania E Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Thomas L Volkert
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jennifer A Love
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA
| | - Jun Wang
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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54
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Benesova S, Kubista M, Valihrach L. Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Diagnostics (Basel) 2021; 11:964. [PMID: 34071824 PMCID: PMC8229417 DOI: 10.3390/diagnostics11060964] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol's performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research.
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Affiliation(s)
- Sarka Benesova
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
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55
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Chorley BN, Atabakhsh E, Doran G, Gautier JC, Ellinger-Ziegelbauer H, Jackson D, Sharapova T, Yuen PST, Church RJ, Couttet P, Froetschl R, McDuffie J, Martinez V, Pande P, Peel L, Rafferty C, Simutis FJ, Harrill AH. Methodological considerations for measuring biofluid-based microRNA biomarkers. Crit Rev Toxicol 2021; 51:264-282. [PMID: 34038674 DOI: 10.1080/10408444.2021.1907530] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA that regulate the expression of messenger RNA and are implicated in almost all cellular processes. Importantly, miRNAs can be released extracellularly and are stable in these matrices where they may serve as indicators of organ or cell-specific toxicity, disease, and biological status. There has thus been great enthusiasm for developing miRNAs as biomarkers of adverse outcomes for scientific, regulatory, and clinical purposes. Despite advances in measurement capabilities for miRNAs, miRNAs are still not routinely employed as noninvasive biomarkers. This is in part due to the lack of standard approaches for sample preparation and miRNA measurement and uncertainty in their biological interpretation. Members of the microRNA Biomarkers Workgroup within the Health and Environmental Sciences Institute's (HESI) Committee on Emerging Systems Toxicology for the Assessment of Risk (eSTAR) are a consortium of private- and public-sector scientists dedicated to developing miRNAs as applied biomarkers. Here, we explore major impediments to routine acceptance and use of miRNA biomarkers and case examples of successes and deficiencies in development. Finally, we provide insight on miRNA measurement, collection, and analysis tools to provide solid footing for addressing knowledge gaps toward routine biomarker use.
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Affiliation(s)
- Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | | | | | | | - David Jackson
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Peter S T Yuen
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rachel J Church
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | | - Lauren Peel
- Health and Environmental Sciences Institute, Washington, DC, USA
| | | | | | - Alison H Harrill
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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56
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Zamith-Miranda D, Peres da Silva R, Couvillion SP, Bredeweg EL, Burnet MC, Coelho C, Camacho E, Nimrichter L, Puccia R, Almeida IC, Casadevall A, Rodrigues ML, Alves LR, Nosanchuk JD, Nakayasu ES. Omics Approaches for Understanding Biogenesis, Composition and Functions of Fungal Extracellular Vesicles. Front Genet 2021; 12:648524. [PMID: 34012462 PMCID: PMC8126698 DOI: 10.3389/fgene.2021.648524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all kingdoms of life. The diverse biogenesis pathways of EVs result in a wide variety of physical properties and functions across different organisms. Fungal EVs were first described in 2007 and different omics approaches have been fundamental to understand their composition, biogenesis, and function. In this review, we discuss the role of omics in elucidating fungal EVs biology. Transcriptomics, proteomics, metabolomics, and lipidomics have each enabled the molecular characterization of fungal EVs, providing evidence that these structures serve a wide array of functions, ranging from key carriers of cell wall biosynthetic machinery to virulence factors. Omics in combination with genetic approaches have been instrumental in determining both biogenesis and cargo loading into EVs. We also discuss how omics technologies are being employed to elucidate the role of EVs in antifungal resistance, disease biomarkers, and their potential use as vaccines. Finally, we review recent advances in analytical technology and multi-omic integration tools, which will help to address key knowledge gaps in EVs biology and translate basic research information into urgently needed clinical applications such as diagnostics, and immuno- and chemotherapies to fungal infections.
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Affiliation(s)
- Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erin L. Bredeweg
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Meagan C. Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carolina Coelho
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Emma Camacho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Leonardo Nimrichter
- Laboratório de Glicobiologia de Eucariotos, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Igor C. Almeida
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Marcio L. Rodrigues
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lysangela R. Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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57
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Wang H, Huang R, Li L, Zhu J, Li Z, Peng C, Zhuang X, Lin H, Shi S, Huang P. CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini. Cell Discov 2021; 7:25. [PMID: 33867522 PMCID: PMC8053708 DOI: 10.1038/s41421-021-00265-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
High-throughput sequencing reveals the complex landscape of small noncoding RNAs (sRNAs). However, it is limited by requiring 5'-monophosphate and 3'-hydroxyl in RNAs for adapter ligation and hindered by methylated nucleosides that interfere with reverse transcription. Here we develop Cap-Clip acid pyrophosphatase (Cap-Clip), T4 polynucleotide kinase (PNK) and AlkB/AlkB(D135S)-facilitated small ncRNA sequencing (CPA-seq) to detect and quantify sRNAs with terminus multiplicities and nucleoside methylations. CPA-seq identified a large number of previously undetected sRNAs. Comparison of sRNAs with or without AlkB/AlkB(D135S) treatment reveals nucleoside methylations on sRNAs. Using CPA-seq, we profiled the sRNA transcriptomes (sRNomes) of nine mouse tissues and reported the extensive tissue-specific differences of sRNAs. We also observed the transition of sRNomes during hepatic reprogramming. Knockdown of mesenchymal stem cell-enriched U1-5' snsRNA promoted hepatic reprogramming. CPA-seq is a powerful tool with high sensitivity and specificity for profiling sRNAs with methylated nucleosides and diverse termini.
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Affiliation(s)
- Heming Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ling Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Junjin Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhihong Li
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Xuran Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Shuo Shi
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, 201210, China.
| | - Pengyu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
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58
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Roy JW, Taylor CA, Beauregard AP, Dhadi SR, Ayre DC, Fry S, Chacko S, Wajnberg G, Joy AP, Mai-Thi NN, Crapoulet N, Barnett DA, Ghosh A, Lewis SM, Ouellette RJ. A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling. Sci Rep 2021; 11:8085. [PMID: 33850235 PMCID: PMC8044196 DOI: 10.1038/s41598-021-87526-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) have been recognized as a rich material for the analysis of DNA, RNA, and protein biomarkers. A remaining challenge for the deployment of EV-based diagnostic and prognostic assays in liquid biopsy testing is the development of an EV isolation method that is amenable to a clinical diagnostic lab setting and is compatible with multiple types of biomarker analyses. We have previously designed a synthetic peptide, known as Vn96 (ME kit), which efficiently isolates EVs from multiple biofluids in a short timeframe without the use of specialized lab equipment. Moreover, it has recently been shown that Vn96 also facilitates the co-isolation of cell-free DNA (cfDNA) along with EVs. Herein we describe an optimized method for Vn96 affinity-based EV and cfDNA isolation from plasma samples and have developed a multiparametric extraction protocol for the sequential isolation of DNA, RNA, and protein from the same plasma EV and cfDNA sample. We are able to isolate sufficient material by the multiparametric extraction protocol for use in downstream analyses, including ddPCR (DNA) and 'omic profiling by both small RNA sequencing (RNA) and mass spectrometry (protein), from a minimum volume (4 mL) of plasma. This multiparametric extraction protocol should improve the ability to analyse multiple biomarker materials (DNA, RNA and protein) from the same limited starting material, which may improve the sensitivity and specificity of liquid biopsy tests that exploit EV-based and cfDNA biomarkers for disease detection and monitoring.
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Affiliation(s)
- Jeremy W Roy
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Catherine A Taylor
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Annie P Beauregard
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
- Fisheries and Oceans Canada, Aquatic Animal Health, Moncton, NB, Canada
| | - Surendar R Dhadi
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - D Craig Ayre
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
- Immunology, Genetics and Molecular Sciences, University of Medicine and Health Sciences, Basseterre, St. Kitts and Nevis
| | - Sheena Fry
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
- Specialized Health Services Directorate, Health Canada, Ottawa, ON, Canada
| | - Simi Chacko
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Gabriel Wajnberg
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Andrew P Joy
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Ngoc-Nu Mai-Thi
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Nicolas Crapoulet
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - David A Barnett
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
| | - Anirban Ghosh
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Rodney J Ouellette
- Atlantic Cancer Research Institute, 35 Providence St., Moncton, NB, E1C 8X3, Canada.
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.
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59
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Kupsco A, Prada D, Valvi D, Hu L, Petersen MS, Coull B, Grandjean P, Weihe P, Baccarelli AA. Human milk extracellular vesicle miRNA expression and associations with maternal characteristics in a population-based cohort from the Faroe Islands. Sci Rep 2021; 11:5840. [PMID: 33712635 PMCID: PMC7970999 DOI: 10.1038/s41598-021-84809-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
Human milk plays a critical role in infant development and health, particularly in cognitive, immune, and cardiometabolic functions. Milk contains extracellular vesicles (EVs) that can transport biologically relevant cargo from mother to infant, including microRNAs (miRNAs). We aimed to characterize milk EV-miRNA profiles in a human population cohort, assess potential pathways and ontology, and investigate associations with maternal characteristics. We conducted the first study to describe the EV miRNA profile of human milk in 364 mothers from a population-based mother-infant cohort in the Faroe Islands using small RNA sequencing. We detected 1523 miRNAs with ≥ one read in 70% of samples. Using hierarchical clustering, we determined five EV-miRNA clusters, the top three consisting of 15, 27 and 67 miRNAs. Correlation coefficients indicated that the expression of many miRNAs within the top three clusters was highly correlated. Top-cluster human milk EV-miRNAs were involved in pathways enriched for the endocrine system, cellular community, neurodevelopment, and cancers. miRNA expression was associated with time to milk collection post-delivery, maternal body mass index, and maternal smoking, but not maternal parity. Future studies investigating determinants of human EV-miRNAs and associated health outcomes are needed to elucidate the role of human milk EV-miRNAs in health and disease.
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Affiliation(s)
- Allison Kupsco
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA.
| | - Diddier Prada
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA
- Unit for Biomedical Research in Cancer, Instituto Nacional de Cancerologia, Universidad Nacional Autonoma de Mexico, 14080, Mexico City, Mexico
| | - Damaskini Valvi
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa Hu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA
| | - Maria Skaalum Petersen
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Brent Coull
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Philippe Grandjean
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Environmental Medicine, University of Southern Denmark, Odense C, Denmark
| | - Pal Weihe
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA
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60
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Ibing S, Michels BE, Mosdzien M, Meyer HR, Feuerbach L, Körner C. On the impact of batch effect correction in TCGA isomiR expression data. NAR Cancer 2021; 3:zcab007. [PMID: 34316700 PMCID: PMC8210273 DOI: 10.1093/narcan/zcab007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/30/2021] [Accepted: 02/18/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with diverse functions in post-transcriptional regulation of gene expression. Sequence and length variants of miRNAs are called isomiRs and can exert different functions compared to their canonical counterparts. The Cancer Genome Atlas (TCGA) provides isomiR-level expression data for patients of various cancer entities collected in a multi-center approach over several years. However, the impact of batch effects within individual cohorts has not been systematically investigated and corrected for before. Therefore, the aim of this study was to identify relevant cohort-specific batch variables and generate batch-corrected isomiR expression data for 16 TCGA cohorts. The main batch variables included sequencing platform, plate, sample purity and sequencing depth. Platform bias was related to certain length and sequence features of individual recurrently affected isomiRs. Furthermore, significant downregulation of reported tumor suppressive isomiRs in lung tumor tissue compared to normal samples was only observed after batch correction, highlighting the importance of working with corrected data. Batch-corrected datasets for all cohorts including quality control are provided as supplement. In summary, this study reveals that batch effects present in the TCGA dataset might mask biologically relevant effects and provides a valuable resource for research on isomiRs in cancer (accessible through GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164767).
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Affiliation(s)
- Susanne Ibing
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Berliner Straße 41, 69120 Heidelberg, Germany
| | - Birgitta E Michels
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Moritz Mosdzien
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Helen R Meyer
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Berliner Straße 41, 69120 Heidelberg, Germany
| | - Cindy Körner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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61
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Siddiqui S, Johansson K, Joo A, Bonser LR, Koh KD, Le Tonqueze O, Bolourchi S, Bautista RA, Zlock L, Roth TL, Marson A, Bhakta NR, Ansel KM, Finkbeiner WE, Erle DJ, Woodruff PG. Epithelial miR-141 regulates IL-13-induced airway mucus production. JCI Insight 2021; 6:139019. [PMID: 33682796 PMCID: PMC8021117 DOI: 10.1172/jci.insight.139019] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
IL-13-induced goblet cell metaplasia contributes to airway remodeling and pathological mucus hypersecretion in asthma. miRNAs are potent modulators of cellular responses, but their role in mucus regulation is largely unexplored. We hypothesized that airway epithelial miRNAs play roles in IL-13-induced mucus regulation. miR-141 is highly expressed in human and mouse airway epithelium, is altered in bronchial brushings from asthmatic subjects at baseline, and is induced shortly after airway allergen exposure. We established a CRISPR/Cas9-based protocol to target miR-141 in primary human bronchial epithelial cells that were differentiated at air-liquid-interface, and goblet cell hyperplasia was induced by IL-13 stimulation. miR-141 disruption resulted in decreased goblet cell frequency, intracellular MUC5AC, and total secreted mucus. These effects correlated with a reduction in a goblet cell gene expression signature and enrichment of a basal cell gene expression signature defined by single cell RNA sequencing. Furthermore, intranasal administration of a sequence-specific mmu-miR-141-3p inhibitor in mice decreased Aspergillus-induced secreted mucus and mucus-producing cells in the lung and reduced airway hyperresponsiveness without affecting cellular inflammation. In conclusion, we have identified a miRNA that regulates pathological airway mucus production and is amenable to therapeutic manipulation through an inhaled route.
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Affiliation(s)
- Sana Siddiqui
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Sandler Asthma Basic Research Center
| | - Kristina Johansson
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Sandler Asthma Basic Research Center
- Department of Microbiology and Immunology
| | - Alex Joo
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Sandler Asthma Basic Research Center
| | | | - Kyung Duk Koh
- Lung Biology Center
- Cardiovascular Research Institute
| | | | - Samaneh Bolourchi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Sandler Asthma Basic Research Center
| | - Rodriel A. Bautista
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Sandler Asthma Basic Research Center
| | | | - Theodore L. Roth
- Department of Microbiology and Immunology
- Biomedical Sciences Graduate Program, and
- Diabetes Center, UCSF, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Alexander Marson
- Department of Microbiology and Immunology
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- J. David Gladstone Institutes, San Francisco, California, USA
- Department of Medicine, Division of Infectious Diseases, UCSF, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Nirav R. Bhakta
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - K. Mark Ansel
- Sandler Asthma Basic Research Center
- Department of Microbiology and Immunology
| | | | - David J. Erle
- Lung Biology Center
- Cardiovascular Research Institute
| | - Prescott G. Woodruff
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Sandler Asthma Basic Research Center
- Cardiovascular Research Institute
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62
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Yan Y, Tang R, Li B, Cheng L, Ye S, Yang T, Han YC, Liu C, Dong Y, Qu LH, Lui KO, Yang JH, Huang ZP. The cardiac translational landscape reveals that micropeptides are new players involved in cardiomyocyte hypertrophy. Mol Ther 2021; 29:2253-2267. [PMID: 33677093 PMCID: PMC8261087 DOI: 10.1016/j.ymthe.2021.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/11/2020] [Accepted: 03/02/2021] [Indexed: 11/27/2022] Open
Abstract
Hypertrophic growth of cardiomyocytes is one of the major compensatory responses in the heart after physiological or pathological stimulation. Protein synthesis enhancement, which is mediated by the translation of messenger RNAs, is one of the main features of cardiomyocyte hypertrophy. Although the transcriptome shift caused by cardiac hypertrophy induced by different stimuli has been extensively investigated, translatome dynamics in this cellular process has been less studied. Here, we generated a nucleotide-resolution translatome as well as transcriptome data from isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORFs) were detected from the deep sequencing of ribosome-protected fragments (Ribo-seq), which orchestrated the shift of the translatome in hypertrophied cardiomyocytes. Our data suggest that rather than increase the translational rate of ribosomes, the increased efficiency of protein synthesis in cardiomyocyte hypertrophy was attributable to an increased quantity of ribosomes. In addition, more than 100 uncharacterized short ORFs (sORFs) were detected in long noncoding RNA genes from Ribo-seq with potential of micropeptide coding. In a random test of 15 candidates, the coding potential of 11 sORFs was experimentally supported. Three micropeptides were identified to regulate cardiomyocyte hypertrophy by modulating the activities of oxidative phosphorylation, the calcium signaling pathway, and the mitogen-activated protein kinase (MAPK) pathway. Our study provides a genome-wide overview of the translational controls behind cardiomyocyte hypertrophy and demonstrates an unrecognized role of micropeptides in cardiomyocyte biology.
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Affiliation(s)
- Youchen Yan
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Rong Tang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Bin Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liangping Cheng
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Shangmei Ye
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Tiqun Yang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan-Chuang Han
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Chen Liu
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Yugang Dong
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR 999077, China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China.
| | - Zhan-Peng Huang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, Guangzhou 510080, China.
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63
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Systematic evaluation of multiple qPCR platforms, NanoString and miRNA-Seq for microRNA biomarker discovery in human biofluids. Sci Rep 2021; 11:4435. [PMID: 33627690 PMCID: PMC7904811 DOI: 10.1038/s41598-021-83365-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
Aberrant miRNA expression has been associated with many diseases, and extracellular miRNAs that circulate in the bloodstream are remarkably stable. Recently, there has been growing interest in identifying cell-free circulating miRNAs that can serve as non-invasive biomarkers for early detection of disease or selection of treatment options. However, quantifying miRNA levels in biofluids is technically challenging due to their low abundance. Using reference samples, we performed a cross-platform evaluation in which miRNA profiling was performed on four different qPCR platforms (MiRXES, Qiagen, Applied Biosystems, Exiqon), nCounter technology (NanoString), and miRNA-Seq. Overall, our results suggest that using miRNA-Seq for discovery and targeted qPCR for validation is a rational strategy for miRNA biomarker development in clinical samples that involve limited amounts of biofluids.
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64
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Bergo V, Trompouki E. New tools for 'ZEBRA-FISHING'. Brief Funct Genomics 2021:elab001. [PMID: 33605988 DOI: 10.1093/bfgp/elab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 11/14/2022] Open
Abstract
Zebrafish has been established as a classical model for developmental studies, yet in the past years, with the explosion of novel technological methods, the use of zebrafish as a model has expanded. One of the prominent fields that took advantage of zebrafish as a model organism early on is hematopoiesis, the process of blood cell generation from hematopoietic stem and progenitor cells (HSPCs). In zebrafish, HSPCs are born early during development in the aorta-gonad-mesonephros region and then translocate to the caudal hematopoietic tissue, where they expand and finally take residence in the kidney marrow. This journey is tightly regulated at multiple levels from extracellular signals to chromatin. In order to delineate the mechanistic underpinnings of this process, next-generation sequencing techniques could be an important ally. Here, we describe genome-wide approaches that have been undertaken to delineate zebrafish hematopoiesis.
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65
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Measurements Methods for the Development of MicroRNA-Based Tests for Cancer Diagnosis. Int J Mol Sci 2021; 22:ijms22031176. [PMID: 33503982 PMCID: PMC7865473 DOI: 10.3390/ijms22031176] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/19/2022] Open
Abstract
Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.
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66
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Hou G, Harley ITW, Lu X, Zhou T, Xu N, Yao C, Qin Y, Ouyang Y, Ma J, Zhu X, Yu X, Xu H, Dai D, Ding H, Yin Z, Ye Z, Deng J, Zhou M, Tang Y, Namjou B, Guo Y, Weirauch MT, Kottyan LC, Harley JB, Shen N. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nat Commun 2021; 12:135. [PMID: 33420081 PMCID: PMC7794586 DOI: 10.1038/s41467-020-20460-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Since most variants that impact polygenic disease phenotypes localize to non-coding genomic regions, understanding the consequences of regulatory element variants will advance understanding of human disease mechanisms. Here, we report that the systemic lupus erythematosus (SLE) risk variant rs2431697 as likely causal for SLE through disruption of a regulatory element, modulating miR-146a expression. Using epigenomic analysis, genome-editing and 3D chromatin structure analysis, we show that rs2431697 tags a cell-type dependent distal enhancer specific for miR-146a that physically interacts with the miR-146a promoter. NF-kB binds the disease protective allele in a sequence-specific manner, increasing expression of this immunoregulatory microRNA. Finally, CRISPR activation-based modulation of this enhancer in the PBMCs of SLE patients attenuates type I interferon pathway activation by increasing miR-146a expression. Our work provides a strategy to define non-coding RNA functional regulatory elements using disease-associated variants and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.
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Affiliation(s)
- Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Isaac T W Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Rheumatology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ning Xu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Chao Yao
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences(SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031, China
| | - Yuting Qin
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ye Ouyang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xinyi Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Hong Xu
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
- Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
| | - Dai Dai
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Jun Deng
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Mi Zhou
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Ya Guo
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Leah C Kottyan
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - John B Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, 45229, USA
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China.
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China.
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA.
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67
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Tosar JP, Witwer K, Cayota A. Revisiting Extracellular RNA Release, Processing, and Function. Trends Biochem Sci 2021; 46:438-445. [PMID: 33413996 DOI: 10.1016/j.tibs.2020.12.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/26/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
It is assumed that RNAs enriched in extracellular samples were selected for release by their parental cells. However, recent descriptions of extracellular RNA (exRNA) biogenesis and their differential stabilities question this assumption, as they could produce identical outcomes. Here, we share our opinion about the importance of considering both selective and nonselective mechanisms for RNA release into the extracellular environment. In doing so, we provide new perspectives on RNA-mediated intercellular communication, including an analogy to communication through social media. We also argue that technical limitations have restricted the study of some of the most abundant exRNAs, both inside and outside extracellular vesicles (EVs). These RNAs may be better positioned to induce a response in recipient cells compared with low abundance miRNAs.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, School of Science, Universidad de la República, Montevideo, Uruguay; Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay; Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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68
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Mechanisms and biomarkers of cancer-associated thrombosis. Transl Res 2020; 225:33-53. [PMID: 32645431 PMCID: PMC8020882 DOI: 10.1016/j.trsl.2020.06.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
Cancer-associated thrombosis is a leading cause of non-cancer death in cancer patients and is comprised of both arterial and venous thromboembolism (VTE). There are multiple risk factors for developing VTE, including cancer type, stage, treatment, and other medical comorbidities, which suggests that the etiology of thrombosis is multifactorial. While cancer-associated thrombosis can be treated with anticoagulation, benefits of therapy must be balanced with the increased bleeding risks seen in patients with cancer. Although risk models exist for primary and recurrent VTE, additional predictors are needed to improve model performance and discrimination of high-risk patients. This review will outline the diverse mechanisms driving thrombosis in cancer patients, as well as provide an overview of biomarkers studied in thrombosis risk and important considerations when selecting candidate biomarkers.
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O'Brien K, Breyne K, Ughetto S, Laurent LC, Breakefield XO. RNA delivery by extracellular vesicles in mammalian cells and its applications. Nat Rev Mol Cell Biol 2020; 21:585-606. [PMID: 32457507 PMCID: PMC7249041 DOI: 10.1038/s41580-020-0251-y] [Citation(s) in RCA: 962] [Impact Index Per Article: 240.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
The term 'extracellular vesicles' refers to a heterogeneous population of vesicular bodies of cellular origin that derive either from the endosomal compartment (exosomes) or as a result of shedding from the plasma membrane (microvesicles, oncosomes and apoptotic bodies). Extracellular vesicles carry a variety of cargo, including RNAs, proteins, lipids and DNA, which can be taken up by other cells, both in the direct vicinity of the source cell and at distant sites in the body via biofluids, and elicit a variety of phenotypic responses. Owing to their unique biology and roles in cell-cell communication, extracellular vesicles have attracted strong interest, which is further enhanced by their potential clinical utility. Because extracellular vesicles derive their cargo from the contents of the cells that produce them, they are attractive sources of biomarkers for a variety of diseases. Furthermore, studies demonstrating phenotypic effects of specific extracellular vesicle-associated cargo on target cells have stoked interest in extracellular vesicles as therapeutic vehicles. There is particularly strong evidence that the RNA cargo of extracellular vesicles can alter recipient cell gene expression and function. During the past decade, extracellular vesicles and their RNA cargo have become better defined, but many aspects of extracellular vesicle biology remain to be elucidated. These include selective cargo loading resulting in substantial differences between the composition of extracellular vesicles and source cells; heterogeneity in extracellular vesicle size and composition; and undefined mechanisms for the uptake of extracellular vesicles into recipient cells and the fates of their cargo. Further progress in unravelling the basic mechanisms of extracellular vesicle biogenesis, transport, and cargo delivery and function is needed for successful clinical implementation. This Review focuses on the current state of knowledge pertaining to packaging, transport and function of RNAs in extracellular vesicles and outlines the progress made thus far towards their clinical applications.
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Affiliation(s)
- Killian O'Brien
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefano Ughetto
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Oncology, University of Turin, Candiolo, Italy
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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Comparison of Reproducibility, Accuracy, Sensitivity, and Specificity of miRNA Quantification Platforms. Cell Rep 2020; 29:4212-4222.e5. [PMID: 31851944 PMCID: PMC7499898 DOI: 10.1016/j.celrep.2019.11.078] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 01/08/2023] Open
Abstract
Given the increasing interest in their use as disease biomarkers, the establishment of reproducible, accurate, sensitive, and specific platforms for microRNA (miRNA) quantification in biofluids is of high priority. We compare four platforms for these characteristics: small RNA sequencing (RNA-seq), FirePlex, EdgeSeq, and nCounter. For a pool of synthetic miRNAs, coefficients of variation for technical replicates are lower for EdgeSeq (6.9%) and RNA-seq (8.2%) than for FirePlex (22.4%); nCounter replicates are not performed. Receiver operating characteristic analysis for distinguishing present versus absent miRNAs shows small RNA-seq (area under curve 0.99) is superior to EdgeSeq (0.97), nCounter (0.94), and FirePlex (0.81). Expected differences in expression of placenta-associated miRNAs in plasma from pregnant and non-pregnant women are observed with RNA-seq and EdgeSeq, but not FirePlex or nCounter. These results indicate that differences in performance among miRNA profiling platforms impact ability to detect biological differences among samples and thus their relative utility for research and clinical use. Using pools of synthetic RNA oligonucleotides and standardized extracellular RNA samples, Godoy et al. compare small RNA sequencing to three targeted miRNA quantification platforms to evaluate reproducibility, bias, specificity and sensitivity, and accuracy. Each platform has strengths and limitations important to consider for biomarker discovery, clinical validation, and broad clinical use.
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Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Bofill-De Ros X, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano L. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics 2020; 36:698-703. [PMID: 31504201 DOI: 10.1093/bioinformatics/btz675] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/17/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION MicroRNAs (miRNAs) are small RNA molecules (∼22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. RESULTS To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification. AVAILABILITY AND IMPLEMENTATION https://github.com/miRTop/mirGFF3/ and https://github.com/miRTop/mirtop. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Karen Eilbeck
- University of Utah, Biomedical Informatics, Salt Lake City, UT 84108, USA
| | - Jeffery Ma
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Gianvito Urgese
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10129, Italy
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 114 18, Sweden
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ernesto Aparicio-Puerta
- Computational Epigenomics Laboratory, Genetics Department and Biotechnology Institute and Biosanitary Institute, University of Granada, Granada 18002, Spain
| | - Victor Barrera
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Roderic Espín
- Universitat Oberta de Catalunya, Barcelona 08018, Spain
| | - Florian Thibord
- Sorbonne Université, Pierre Louis Doctoral School of Public Health, Paris 75006, France.,Institut National pour la Santé et la Recherche Médicale (INSERM) Unité Mixte de Recherche en Santé (UMR_S), University of Bordeaux, Bordeaux 33076, France
| | - Xavier Bofill-De Ros
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Eric Londin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10129, Italy
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 114 18, Sweden
| | | | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Michael Hackenberg
- Computational Epigenomics Laboratory, Genetics Department and Biotechnology Institute and Biosanitary Institute, University of Granada, Granada 18002, Spain
| | - Ioannis S Vlachos
- Non-coding Research Lab, Department of Pathology, Cancer Research Institute, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lorena Pantano
- Bioinformatics Core, The Picower Institute for Learning and Memory, Cambridge, MA 02139, USA
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Cao J, Cowan DB, Wang DZ. tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy. Front Pharmacol 2020; 11:572941. [PMID: 33041815 PMCID: PMC7527594 DOI: 10.3389/fphar.2020.572941] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/28/2020] [Indexed: 12/21/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundantly expressed, small non-coding RNAs that have long been recognized as essential components of the protein translation machinery. The tRNA-derived small RNAs (tsRNAs), including tRNA halves (tiRNAs), and tRNA fragments (tRFs), were unexpectedly discovered and have been implicated in a variety of important biological functions such as cell proliferation, cell differentiation, and apoptosis. Mechanistically, tsRNAs regulate mRNA destabilization and translation, as well as retro-element reverse transcriptional and post-transcriptional processes. Emerging evidence has shown that tsRNAs are expressed in the heart, and their expression can be induced by pathological stress, such as hypertrophy. Interestingly, cardiac pathophysiological conditions, such as oxidative stress, aging, and metabolic disorders can be viewed as inducers of tsRNA biogenesis, which further highlights the potential involvement of tsRNAs in these conditions. There is increasing enthusiasm for investigating the molecular and biological functions of tsRNAs in the heart and their role in cardiovascular disease. It is anticipated that this new class of small non-coding RNAs will offer new perspectives in understanding disease mechanisms and may provide new therapeutic targets to treat cardiovascular disease.
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Affiliation(s)
- Jun Cao
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Douglas B Cowan
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AY, T. Flåm S, Leithaug M, Dalland M, Rayner S, Lie BA, Gilfillan GD. An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biol 2020; 17:1284-1292. [PMID: 32436772 PMCID: PMC7549702 DOI: 10.1080/15476286.2020.1761081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 11/12/2022] Open
Abstract
High-throughput sequencing has emerged as the favoured method to study microRNA (miRNA) expression, but biases introduced during library preparation have been reported. We recently compared the performance (sensitivity, reliability, titration response and differential expression) of six commercially-available kits on synthetic miRNAs and human RNA, where library preparation was performed by the vendors. We hereby supplement this study with data from two further commonly used kits (NEBNext, NEXTflex) whose manufacturers initially declined to participate. NEXTflex demonstrated the highest sensitivity, which may reflect its use of partially-randomized adapter sequences, but overall performance was lower than the QIAseq and TailorMix kits. NEBNext showed intermediate performance. We reaffirm that biases are kit specific, complicating the comparison of miRNA datasets generated using different kits.
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Affiliation(s)
- Fatima Heinicke
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Xiangfu Zhong
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Manuela Zucknick
- Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
| | - Johannes Breidenbach
- National Forest Inventory, Norwegian Institute for Bioeconomy Research, Ås, Norway
| | - Arvind Y.M. Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Siri T. Flåm
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marianne Dalland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Benedicte A. Lie
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Gregor D. Gilfillan
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
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74
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Sun YM, Chen YQ. Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application. J Hematol Oncol 2020; 13:109. [PMID: 32778133 PMCID: PMC7416809 DOI: 10.1186/s13045-020-00945-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of innovative technologies, an increasing number of novel ncRNAs have been uncovered; information about their prominent tissue-specific expression patterns, various interaction networks, and subcellular locations will undoubtedly enhance our understanding of their potential functions. Here, we summarized the principles and innovative methods for identifications of novel ncRNAs that have potential functional roles in cancer biology. Moreover, this review also provides alternative ncRNA databases based on high-throughput sequencing or experimental validation, and it briefly describes the current strategy for the clinical translation of cancer-associated ncRNAs to be used in diagnosis.
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Affiliation(s)
- Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
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75
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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76
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Gámbaro F, Li Calzi M, Fagúndez P, Costa B, Greif G, Mallick E, Lyons S, Ivanov P, Witwer K, Cayota A, Tosar JP. Stable tRNA halves can be sorted into extracellular vesicles and delivered to recipient cells in a concentration-dependent manner. RNA Biol 2020; 17:1168-1182. [PMID: 31885318 PMCID: PMC7549683 DOI: 10.1080/15476286.2019.1708548] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/22/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) are cell-derived nanoparticles that act as natural carriers of nucleic acids between cells. They offer advantages as delivery vehicles for therapeutic nucleic acids such as small RNAs. Loading of desired nucleic acids into EVs can be achieved by electroporation or transfection once purified. An attractive alternative is to transfect cells with the desired small RNAs and harness the cellular machinery for RNA sorting into the EVs. This possibility has been less explored because cells are believed to secrete only specific RNAs. However, we hypothesized that, even in the presence of selective secretion, concentration-driven RNA sorting to EVs would still be feasible. To show this, we transfected cells with glycine 5' tRNA halves, which we have previously shown to better resist RNases. We then measured their levels in EVs and in recipient cells and found that, in contrast to unstable RNAs of random sequence, these tRNA halves were present in vesicles and in recipient cells in amounts proportional to the concentration of RNA used for transfection. Similar efficiencies were obtained with other stable oligonucleotides of random sequence. Our results demonstrate that RNA stability is a key factor needed to maintain high intracellular concentrations, a prerequisite for efficient non-selective RNA sorting to EVs and delivery to cells. Given that glycine 5' tRNA halves belong to the group of stress-induced tRNA fragments frequently detected in extracellular space and biofluids, we propose that upregulation of extracellular tRNA fragments is consequential to cellular stress and might be involved in intercellular signalling.
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Affiliation(s)
- Fabiana Gámbaro
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Molecular Virology Laboratory, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Marco Li Calzi
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Fagúndez
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Bruno Costa
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Greif
- Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Emily Mallick
- Molecular and Comparative Pathobiology, and Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shawn Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry, and The Genome Science Institute, Boston University School of Medicine, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and M.I.T., Cambridge, MA, USA
| | - Kenneth Witwer
- Molecular and Comparative Pathobiology, and Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, Faculty of Medicine, Universidad de la República, Montevideo, Uruguay
| | - Juan Pablo Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
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Abstract
Exosomes are small, single-membrane, secreted organelles of ∼30 to ∼200 nm in diameter that have the same topology as the cell and are enriched in selected proteins, lipids, nucleic acids, and glycoconjugates. Exosomes contain an array of membrane-associated, high-order oligomeric protein complexes, display pronounced molecular heterogeneity, and are created by budding at both plasma and endosome membranes. Exosome biogenesis is a mechanism of protein quality control, and once released, exosomes have activities as diverse as remodeling the extracellular matrix and transmitting signals and molecules to other cells. This pathway of intercellular vesicle traffic plays important roles in many aspects of human health and disease, including development, immunity, tissue homeostasis, cancer, and neurodegenerative diseases. In addition, viruses co-opt exosome biogenesis pathways both for assembling infectious particles and for establishing host permissiveness. On the basis of these and other properties, exosomes are being developed as therapeutic agents in multiple disease models.
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Affiliation(s)
- D Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Stephen J Gould
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA;
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Hu H, Zhang Q, Chen W, Wu T, Liu S, Li X, Luo B, Zhang T, Yan G, Lu H, Lu Z. MicroRNA-301a promotes pancreatic cancer invasion and metastasis through the JAK/STAT3 signaling pathway by targeting SOCS5. Carcinogenesis 2020; 41:502-514. [PMID: 31233116 DOI: 10.1093/carcin/bgz121] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/10/2019] [Accepted: 06/20/2019] [Indexed: 12/17/2022] Open
Abstract
Pancreatic cancer is one of the most lethal digestive malignant tumors. We had previously found that microRNA-301a (miR-301a) is a oncogenic microRNA whose recognized conduce to nuclear factor-kappa B (NF-κB) activation in pancreatic cancer, yet the underlying mechanisms of miR-301a in promoting pancreatic cancer invasion and migration is obscure. In this work we found that high expression of miR-301a in human pancreatic cancer patients is related to poor survival. Overexpression of miR-301a enhances pancreatic cancer cell invasion, angiogenesis and migration, whereas inhibition of miR-301a suppresses pancreatic cancer cell invasion and reduces orthotopic pancreatic tumor growth and metastasis. Furthermore, suppressor of cytokine signaling 5 (SOCS5) is identified as a target gene of miR-301a. We found that miR-301a suppressed the expression of SOCS5 leads to janus kinase/signal transducer and activator of transcription 3 (JAK/STAT3) activation and is related to poor overall survival of pancreatic cancer patients. Taken together, our data show for the first time that the feedback loop between miR-301a and JAK/STAT3 pathway may play a significant role in pancreatic cancer invasion and metastasis. Targeting the loop may prove beneficial to prevent metastasis and provide a more effective therapeutic strategy for pancreatic cancer.
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Affiliation(s)
- Hui Hu
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Zhang
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Weiqun Chen
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Research Institute of Wuhan, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory for Molecular Diagnosis of Hubei Province, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tangwei Wu
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiyi Liu
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Research Institute of Wuhan, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyi Li
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Luo
- Department of Pathology, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tianzhu Zhang
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Ge Yan
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Hongda Lu
- Cancer Research Institute of Wuhan, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Oncology, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongxin Lu
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
- Cancer Research Institute of Wuhan, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory for Molecular Diagnosis of Hubei Province, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Aparicio-Puerta E, Jáspez D, Lebrón R, Koppers-Lalic D, Marchal JA, Hackenberg M. liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies. Nucleic Acids Res 2020; 47:D113-D120. [PMID: 30357370 PMCID: PMC6323997 DOI: 10.1093/nar/gky981] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/18/2018] [Indexed: 12/25/2022] Open
Abstract
MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction and processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation. LiqDB is available at http://bioinfo5.ugr.es/liqdb.
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Affiliation(s)
- Ernesto Aparicio-Puerta
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento.,Department of Human Anatomy and Embryology, Institute of Biopathology and Regenerative Medicine, Excellence Research Unit "Modeling Nature" (MNat), University of Granada, Granada, Spain.,Biohealth Research Institute in Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Spain; Conocimiento s/n, 18100 Granada, Spain
| | - David Jáspez
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento
| | - Ricardo Lebrón
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento
| | | | - Juan A Marchal
- Department of Human Anatomy and Embryology, Institute of Biopathology and Regenerative Medicine, Excellence Research Unit "Modeling Nature" (MNat), University of Granada, Granada, Spain.,Biohealth Research Institute in Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Spain; Conocimiento s/n, 18100 Granada, Spain
| | - Michael Hackenberg
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento.,Biohealth Research Institute in Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Spain; Conocimiento s/n, 18100 Granada, Spain
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80
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Babayan A, Neumann MHD, Herdean A, Shaffer JM, Janning M, Kobus F, Loges S, Di Pasquale F, Kubista M, Schlumpberger M, Lampignano R, Krahn T, Schlange T, Sprenger-Haussels M, Pantel K, Kloten V. Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis. Cancers (Basel) 2020; 12:cancers12051166. [PMID: 32380788 PMCID: PMC7281602 DOI: 10.3390/cancers12051166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background: Among emerging circulating biomarkers, miRNA has the potential to detect lung cancer and follow the course of the disease. However, miRNA analysis deserves further standardization before implementation into clinical trials or practice. Here, we performed international ring experiments to explore (pre)-analytical factors relevant to the outcome of miRNA blood tests in the context of the EU network CANCER-ID. Methods: Cell-free (cfmiRNA) and extracellular vesicle-derived miRNA (EVmiRNA) were extracted using the miRNeasy Serum/Plasma Advanced, and the ExoRNeasy Maxi kit, respectively, in a plasma cohort of 27 NSCLC patients and 20 healthy individuals. Extracted miRNA was investigated using small RNA sequencing and hybridization platforms. Validation of the identified miRNA candidates was performed using quantitative PCR. Results: We demonstrate the highest read counts in healthy individuals and NSCLC patients using QIAseq. Moreover, QIAseq showed 15.9% and 162.9% more cfmiRNA and EVmiRNA miRNA counts, respectively, in NSCLC patients compared to healthy control samples. However, a systematic comparison of selected miRNAs revealed little agreement between high-throughput platforms, thus some miRNAs are detected with one technology, but not with the other. Adding to this, 35% (9 of 26) of selected miRNAs in the cfmiRNA and 42% (11 of 26) in the EVmiRNA fraction were differentially expressed by at least one qPCR platform; about half of the miRNAs (54%) were concordant for both platforms. Conclusions: Changing of (pre)-analytical methods of miRNA analysis has a significant impact on blood test results and is therefore a major confounding factor. In addition, to confirm miRNA biomarker candidates screening studies should be followed by targeted validation using an independent platform or technology.
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Affiliation(s)
- Anna Babayan
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
| | | | - Andrei Herdean
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden; (A.H.); (M.K.)
| | | | - Melanie Janning
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Franca Kobus
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sonja Loges
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, 68167 Mannheim, Germany
| | | | - Mikael Kubista
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden; (A.H.); (M.K.)
| | | | - Rita Lampignano
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
| | - Thomas Krahn
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
| | - Thomas Schlange
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
| | | | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
| | - Vera Kloten
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
- Correspondence:
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81
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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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82
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Bermúdez-Barrientos JR, Ramírez-Sánchez O, Chow FWN, Buck AH, Abreu-Goodger C. Disentangling sRNA-Seq data to study RNA communication between species. Nucleic Acids Res 2020; 48:e21. [PMID: 31879784 PMCID: PMC7038986 DOI: 10.1093/nar/gkz1198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/23/2019] [Accepted: 12/18/2019] [Indexed: 12/28/2022] Open
Abstract
Many organisms exchange small RNAs (sRNAs) during their interactions, that can target or bolster defense strategies in host-pathogen systems. Current sRNA-Seq technology can determine the sRNAs present in any symbiotic system, but there are very few bioinformatic tools available to interpret the results. We show that one of the biggest challenges comes from sequences that map equally well to the genomes of both interacting organisms. This arises due to the small size of the sRNAs compared to large genomes, and because a large portion of sequenced sRNAs come from genomic regions that encode highly conserved miRNAs, rRNAs or tRNAs. Here, we present strategies to disentangle sRNA-Seq data from samples of communicating organisms, developed using diverse plant and animal species that are known to receive or exchange RNA with their symbionts. We show that sequence assembly, both de novo and genome-guided, can be used for these sRNA-Seq data, greatly reducing the ambiguity of mapping reads. Even confidently mapped sequences can be misleading, so we further demonstrate the use of differential expression strategies to determine true parasite-derived sRNAs within host cells. We validate our methods on new experiments designed to probe the nature of the extracellular vesicle sRNAs from the parasitic nematode Heligmosomoides bakeri that get into mouse intestinal epithelial cells.
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Affiliation(s)
- José Roberto Bermúdez-Barrientos
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato 36824, México
| | - Obed Ramírez-Sánchez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato 36824, México
| | - Franklin Wang-Ngai Chow
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Amy H Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Cei Abreu-Goodger
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato 36824, México
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83
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Weiser DA, West-Szymanski DC, Fraint E, Weiner S, Rivas MA, Zhao CWT, He C, Applebaum MA. Progress toward liquid biopsies in pediatric solid tumors. Cancer Metastasis Rev 2020; 38:553-571. [PMID: 31836951 DOI: 10.1007/s10555-019-09825-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pediatric solid tumors have long been known to shed tumor cells, DNA, RNA, and proteins into the blood. Recent technological advances have allowed for improved capture and analysis of these typically scant circulating materials. Efforts are ongoing to develop "liquid biopsy" assays as minimally invasive tools to address diagnostic, prognostic, and disease monitoring needs in childhood cancer care. Applying these highly sensitive technologies to serial liquid biopsies is expected to advance understanding of tumor biology, heterogeneity, and evolution over the course of therapy, thus opening new avenues for personalized therapy. In this review, we outline the latest technologies available for liquid biopsies and describe the methods, pitfalls, and benefits of the assays that are being developed for children with extracranial solid tumors. We discuss what has been learned in several of the most common pediatric solid tumors including neuroblastoma, sarcoma, Wilms tumor, and hepatoblastoma and highlight promising future directions for the field.
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Affiliation(s)
- Daniel A Weiser
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Ellen Fraint
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | - Shoshana Weiner
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
| | - Marco A Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Mark A Applebaum
- Department of Pediatrics, The University of Chicago, 900 E. 57th St., KCBD 5116, Chicago, IL, 60637, USA.
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84
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Babatunde KA, Yesodha Subramanian B, Ahouidi AD, Martinez Murillo P, Walch M, Mantel PY. Role of Extracellular Vesicles in Cellular Cross Talk in Malaria. Front Immunol 2020; 11:22. [PMID: 32082312 PMCID: PMC7005784 DOI: 10.3389/fimmu.2020.00022] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/07/2020] [Indexed: 12/13/2022] Open
Abstract
Malaria infection caused by the Plasmodium species is a complex disease in which a fine balance between host and parasite factors determine the disease severity. While in some individuals, the infection will trigger only a mild and uncomplicated disease, other individuals will develop severe complications which lead to death. Extracellular vesicles (EVs) secreted by infected red blood cells (iRBCs), as well as other host cells, are important regulators of the balance that determines the disease outcome. In addition, EVs constitute a robust mode of cell-to-cell communication by transferring signaling cargoes between parasites, and between parasites and host, without requiring cellular contact. The transfer of membrane and cytosolic proteins, lipids, DNA, and RNA through EVs not only modulate the immune response, it also mediates cellular communication between parasites to synchronize the transmission stage. Here, we review the recent progress in understanding EV roles during malaria.
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Affiliation(s)
- Kehinde Adebayo Babatunde
- Center for Engineering in Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States.,Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland
| | | | - Ambroise Dioum Ahouidi
- Laboratory of Bacteriology and Virology, Le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal.,Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | | | - Michael Walch
- Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland
| | - Pierre-Yves Mantel
- Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland
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85
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Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. Cell 2020; 177:446-462.e16. [PMID: 30951671 DOI: 10.1016/j.cell.2019.03.024] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/29/2018] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.
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86
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The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research. Cell 2020; 177:231-242. [PMID: 30951667 DOI: 10.1016/j.cell.2019.03.023] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Extracellular RNA Communication Consortium (ERCC) was launched to accelerate progress in the new field of extracellular RNA (exRNA) biology and to establish whether exRNAs and their carriers, including extracellular vesicles (EVs), can mediate intercellular communication and be utilized for clinical applications. Phase 1 of the ERCC focused on exRNA/EV biogenesis and function, discovery of exRNA biomarkers, development of exRNA/EV-based therapeutics, and construction of a robust set of reference exRNA profiles for a variety of biofluids. Here, we present progress by ERCC investigators in these areas, and we discuss collaborative projects directed at development of robust methods for EV/exRNA isolation and analysis and tools for sharing and computational analysis of exRNA profiling data.
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87
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Kalani MYS, Alsop E, Meechoovet B, Beecroft T, Agrawal K, Whitsett TG, Huentelman MJ, Spetzler RF, Nakaji P, Kim S, Van Keuren-Jensen K. Extracellular microRNAs in blood differentiate between ischaemic and haemorrhagic stroke subtypes. J Extracell Vesicles 2020; 9:1713540. [PMID: 32128071 PMCID: PMC7034450 DOI: 10.1080/20013078.2020.1713540] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
Rapid identification of patients suffering from cerebral ischaemia, while excluding intracerebral haemorrhage, can assist with patient triage and expand patient access to chemical and mechanical revascularization. We sought to identify blood-based, extracellular microRNAs 15 (ex-miRNAs) derived from extracellular vesicles associated with major stroke subtypes using clinical samples from subjects with spontaneous intraparenchymal haemorrhage (IPH), aneurysmal subarachnoid haemorrhage (SAH) and ischaemic stroke due to cerebral vessel occlusion. We collected blood from patients presenting with IPH (n = 19), SAH (n = 17) and ischaemic stroke (n = 21). We isolated extracellular vesicles from plasma, extracted RNA cargo, 20 sequenced the small RNAs and performed bioinformatic analyses to identify ex-miRNA biomarkers predictive of the stroke subtypes. Sixty-seven miRNAs were significantly variant across the stroke subtypes. A subset of exmiRNAs differed between haemorrhagic and ischaemic strokes, and LASSO analysis could distinguish SAH from the other subtypes with an accuracy of 0.972 ± 0.002. Further analyses predicted 25 miRNA classifiers that stratify IPH from ischaemic stroke with an accuracy of 0.811 ± 0.004 and distinguish haemorrhagic from ischaemic stroke with an accuracy of 0.813 ± 0.003. Blood-based, ex-miRNAs have predictive value, and could be capable of distinguishing between major stroke subtypes with refinement and validation. Such a biomarker could one day aid in the triage of patients to expand the pool eligible for effective treatment.
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Affiliation(s)
- M Yashar S Kalani
- Departments of Neurological Surgery and Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Bessie Meechoovet
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Taylor Beecroft
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Komal Agrawal
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Matthew J Huentelman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Robert F Spetzler
- Department of Neurological Surgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Peter Nakaji
- Department of Neurosurgery, Banner Heath and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Seungchan Kim
- Center for Computational Systems Biology, Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A & M University, Prairie View, TX, USA
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88
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Correia de Sousa M, Gjorgjieva M, Dolicka D, Sobolewski C, Foti M. Deciphering miRNAs' Action through miRNA Editing. Int J Mol Sci 2019; 20:E6249. [PMID: 31835747 PMCID: PMC6941098 DOI: 10.3390/ijms20246249] [Citation(s) in RCA: 514] [Impact Index Per Article: 102.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with the capability of modulating gene expression at the post-transcriptional level either by inhibiting messenger RNA (mRNA) translation or by promoting mRNA degradation. The outcome of a myriad of physiological processes and pathologies, including cancer, cardiovascular and metabolic diseases, relies highly on miRNAs. However, deciphering the precise roles of specific miRNAs in these pathophysiological contexts is challenging due to the high levels of complexity of their actions. Indeed, regulation of mRNA expression by miRNAs is frequently cell/organ specific; highly dependent on the stress and metabolic status of the organism; and often poorly correlated with miRNA expression levels. Such biological features of miRNAs suggest that various regulatory mechanisms control not only their expression, but also their activity and/or bioavailability. Several mechanisms have been described to modulate miRNA action, including genetic polymorphisms, methylation of miRNA promoters, asymmetric miRNA strand selection, interactions with RNA-binding proteins (RBPs) or other coding/non-coding RNAs. Moreover, nucleotide modifications (A-to-I or C-to-U) within the miRNA sequences at different stages of their maturation are also critical for their functionality. This regulatory mechanism called "RNA editing" involves specific enzymes of the adenosine/cytidine deaminase family, which trigger single nucleotide changes in primary miRNAs. These nucleotide modifications greatly influence a miRNA's stability, maturation and activity by changing its specificity towards target mRNAs. Understanding how editing events impact miRNA's ability to regulate stress responses in cells and organs, or the development of specific pathologies, e.g., metabolic diseases or cancer, should not only deepen our knowledge of molecular mechanisms underlying complex diseases, but can also facilitate the design of new therapeutic approaches based on miRNA targeting. Herein, we will discuss the current knowledge on miRNA editing and how this mechanism regulates miRNA biogenesis and activity.
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Affiliation(s)
| | | | | | | | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (M.C.d.S.); (M.G.); (D.D.); (C.S.)
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89
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Srinivasan S, Duval MX, Kaimal V, Cuff C, Clarke SH. Assessment of methods for serum extracellular vesicle small RNA sequencing to support biomarker development. J Extracell Vesicles 2019; 8:1684425. [PMID: 31741724 PMCID: PMC6844434 DOI: 10.1080/20013078.2019.1684425] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) have great potential as a source for clinically relevant biomarkers since they can be readily isolated from biofluids and carry microRNA (miRNA), mRNA, and proteins that can reflect disease status. However, the biological and technical variability of EV content is unknown making comparisons between healthy subjects and patients difficult to interpret. In this study, we sought to establish a laboratory and bioinformatics analysis pipeline to analyse the small RNA content within EVs from patient serum that could serve as biomarkers and to assess the biological and technical variability of EV RNA content in healthy individuals. We sequenced EV small RNA from multiple individuals (biological replicates) and sequenced multiple replicates per individual (technical replicates) using the Illumina Truseq protocol. We observed that the replicates of samples clustered by subject indicating that the biological variability (~95%) was greater than the technical variability (~0.50%). We observed that ~30% of the sequencing reads were miRNAs. We evaluated the technical parameters of sequencing by spiking the EV RNA preparation with a mix of synthetic small RNA and demonstrated a disconnect between input concentration of the spike-in RNA and sequencing read frequencies indicating that bias was introduced during library preparation. To determine whether there are differences between library preparation platforms, we compared the Truseq with the Nextflex protocol that had been designed to reduce bias in library preparation. While both methods were technically robust, the Nextflex protocol reduced the bias and exhibited a linear range across input concentrations of the synthetic spike-ins. Altogether, our results indicate that technical variability is much smaller than biological variability supporting the use of EV small RNAs as potential biomarkers. Our findings also indicate that the choice of library preparation method leads to artificial differences in the datasets generated invalidating the comparability of sequencing data across library preparation platforms.
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Affiliation(s)
- Swetha Srinivasan
- Transalational Immunology, AbbVie Bioresearch Center, Worcester, MA, USA
| | - Manuel X. Duval
- Transalational Immunology, AbbVie Bioresearch Center, Worcester, MA, USA
| | - Vivek Kaimal
- Transalational Immunology, AbbVie Bioresearch Center, Worcester, MA, USA
| | - Carolyn Cuff
- Transalational Immunology, AbbVie Bioresearch Center, Worcester, MA, USA
| | - Stephen H. Clarke
- Transalational Immunology, AbbVie Bioresearch Center, Worcester, MA, USA
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90
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Kim H, Kim J, Kim K, Chang H, You K, Kim VN. Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification. Nucleic Acids Res 2019; 47:2630-2640. [PMID: 30605524 PMCID: PMC6411932 DOI: 10.1093/nar/gky1293] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/07/2018] [Accepted: 12/15/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) modulate diverse biological and pathological processes via post-transcriptional gene silencing. High-throughput small RNA sequencing (sRNA-seq) has been widely adopted to investigate the functions and regulatory mechanisms of miRNAs. However, accurate quantification of miRNAs has been limited owing to the severe ligation bias in conventional sRNA-seq methods. Here, we quantify miRNAs and their variants (known as isomiRs) by an improved sRNA-seq protocol, termed AQ-seq (accurate quantification by sequencing), that utilizes adapters with terminal degenerate sequences and a high concentration of polyethylene glycol (PEG), which minimize the ligation bias during library preparation. Measurement using AQ-seq allows us to correct the previously misannotated 5' end usage and strand preference in public databases. Importantly, the analysis of 5' terminal heterogeneity reveals widespread alternative processing events which have been underestimated. We also identify highly uridylated miRNAs originating from the 3p strands, indicating regulations mediated by terminal uridylyl transferases at the pre-miRNA stage. Taken together, our study reveals the complexity of the miRNA isoform landscape, allowing us to refine miRNA annotation and to advance our understanding of miRNA regulation. Furthermore, AQ-seq can be adopted to improve other ligation-based sequencing methods including crosslinking-immunoprecipitation-sequencing (CLIP-seq) and ribosome profiling (Ribo-seq).
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Affiliation(s)
- Haedong Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jimi Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kwontae You
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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91
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Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AYM, T Flåm S, Leithaug M, Dalland M, Farmer A, Henderson JM, Hussong MA, Moll P, Nguyen L, McNulty A, Shaffer JM, Shore S, Yip HK, Vitkovska J, Rayner S, Lie BA, Gilfillan GD. Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biol 2019; 17:75-86. [PMID: 31559901 PMCID: PMC6948978 DOI: 10.1080/15476286.2019.1667741] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
High-throughput sequencing is increasingly favoured to assay the presence and abundance of microRNAs (miRNAs) in biological samples, even from low RNA amounts, and a number of commercial vendors now offer kits that allow miRNA sequencing from sub-nanogram (ng) inputs. Although biases introduced during library preparation have been documented, the relative performance of current reagent kits has not been investigated in detail. Here, six commercial kits capable of handling <100ng total RNA input were used for library preparation, performed by kit manufactures, on synthetic miRNAs of known quantities and human total RNA samples. We compared the performance of miRNA detection sensitivity, reliability, titration response and the ability to detect differentially expressed miRNAs. In addition, we assessed the use of unique molecular identifiers (UMI) sequence tags in one kit. We observed differences in detection sensitivity and ability to identify differentially expressed miRNAs between the kits, but none were able to detect the full repertoire of synthetic miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the relative levels of the majority of miRNAs. UMI tags, at least within the input ranges tested, offered little advantage to improve data utility. In conclusion, biases in miRNA abundance are heavily influenced by the kit used for library preparation, suggesting that comparisons of datasets prepared by different procedures should be made with caution. This article is intended to assist researchers select the most appropriate kit for their experimental conditions.
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Affiliation(s)
- Fatima Heinicke
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Xiangfu Zhong
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Manuela Zucknick
- Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
| | - Johannes Breidenbach
- Norwegian Institute for Bioeconomy Research, National Forest Inventory, Ås, Norway
| | - Arvind Y M Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Siri T Flåm
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marianne Dalland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | | | | | | | | | | | | | | | | | | | | | - Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Gregor D Gilfillan
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
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92
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Extracellular RNA in a single droplet of human serum reflects physiologic and disease states. Proc Natl Acad Sci U S A 2019; 116:19200-19208. [PMID: 31481608 PMCID: PMC6754586 DOI: 10.1073/pnas.1908252116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Extracellular RNAs (exRNAs) are present in human serum. It remains unclear to what extent these circulating exRNAs may reflect human physiologic and disease states. Here, we developed SILVER-seq (Small Input Liquid Volume Extracellular RNA Sequencing) to efficiently sequence both integral and fragmented exRNAs from a small droplet (5 μL to 7 μL) of liquid biopsy. We calibrated SILVER-seq in reference to other RNA sequencing methods based on milliliters of input serum and quantified droplet-to-droplet and donor-to-donor variations. We carried out SILVER-seq on more than 150 serum droplets from male and female donors ranging from 18 y to 48 y of age. SILVER-seq detected exRNAs from more than a quarter of the human genes, including small RNAs and fragments of mRNAs and long noncoding RNAs (lncRNAs). The detected exRNAs included those derived from genes with tissue (e.g., brain)-specific expression. The exRNA expression levels separated the male and female samples and were correlated with chronological age. Noncancer and breast cancer donors exhibited pronounced differences, whereas donors with or without cancer recurrence exhibited moderate differences in exRNA expression patterns. Even without using differentially expressed exRNAs as features, nearly all cancer and noncancer samples and a large portion of the recurrence and nonrecurrence samples could be correctly classified by exRNA expression values. These data suggest the potential of using exRNAs in a single droplet of serum for liquid biopsy-based diagnostics.
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93
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Hardigan AA, Roberts BS, Moore DE, Ramaker RC, Jones AL, Myers RM. CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries. Nucleic Acids Res 2019; 47:e84. [PMID: 31165880 PMCID: PMC6698666 DOI: 10.1093/nar/gkz425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/19/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adapter dimer ligation products that, unless removed by gel-separation, comprise most of the library. Here, we have adapted and modified recently described methods for CRISPR/Cas9-based Depletion of Abundant Species by Hybridization ('DASH') to smRNA-seq, which we have termed miRNA and Adapter Dimer-DASH (MAD-DASH). In MAD-DASH, Cas9 is complexed with single guide RNAs (sgRNAs) targeting adapter dimer ligation products, alongside highly expressed tissue-specific smRNAs, for cleavage in vitro. This process dramatically reduces adapter dimer and targeted smRNA sequences, can be multiplexed, shows minimal off-target effects, improves the quantification of lowly expressed miRNAs from human plasma and tissue derived RNA, and obviates the need for gel-separation, greatly increasing sample throughput. Additionally, the method is fully customizable to other smRNA-seq preparation methods. Like depletion of ribosomal RNA for mRNA-seq and mitochondrial DNA for ATAC-seq, our method allows for greater proportional read-depth of non-targeted sequences.
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Affiliation(s)
- Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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94
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Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet 2019; 20:631-656. [DOI: 10.1038/s41576-019-0150-2] [Citation(s) in RCA: 679] [Impact Index Per Article: 135.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2019] [Indexed: 12/12/2022]
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95
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Gholamalipour Y, Karunanayake Mudiyanselage A, Martin CT. 3' end additions by T7 RNA polymerase are RNA self-templated, distributive and diverse in character-RNA-Seq analyses. Nucleic Acids Res 2019; 46:9253-9263. [PMID: 30219859 PMCID: PMC6182178 DOI: 10.1093/nar/gky796] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 11/13/2022] Open
Abstract
Synthetic RNA is widely used in basic science, nanotechnology and therapeutics research. The vast majority of this RNA is synthesized in vitro by T7 RNA polymerase or one of its close family members. However, the desired RNA is generally contaminated with products longer and shorter than the DNA-encoded product. To better understand these undesired byproducts and the processes that generate them, we analyze in vitro transcription reactions using RNA-Seq as a tool. The results unambiguously confirm that product RNA rebinds to the polymerase and self-primes (in cis) generation of a hairpin duplex, a process that favorably competes with promoter driven synthesis under high yield reaction conditions. While certain priming modes can be favored, the process is heterogeneous, both in initial priming and in the extent of priming, and already extended products can rebind for further extension, in a distributive process. Furthermore, addition of one or a few nucleotides, previously termed 'nontemplated addition,' also occurs via templated primer extension. At last, this work demonstrates the utility of RNA-Seq as a tool for in vitro mechanistic studies, providing information far beyond that provided by traditional gel electrophoresis.
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Affiliation(s)
- Yasaman Gholamalipour
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | - Craig T Martin
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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96
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Wright C, Rajpurohit A, Burke EE, Williams C, Collado-Torres L, Kimos M, Brandon NJ, Cross AJ, Jaffe AE, Weinberger DR, Shin JH. Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. BMC Genomics 2019; 20:513. [PMID: 31226924 PMCID: PMC6588940 DOI: 10.1186/s12864-019-5870-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias. Furthermore, evaluations of the quantification of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited. No study had yet evaluated the quantification of isomiRs of altered length or compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases. RESULTS All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency. CONCLUSIONS Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
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Affiliation(s)
- Carrie Wright
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,AstraZeneca Postdoc Program, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Anandita Rajpurohit
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Emily E Burke
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Courtney Williams
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Martha Kimos
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Nicholas J Brandon
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Alan J Cross
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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97
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Giraldez MD, Spengler RM, Etheridge A, Goicochea AJ, Tuck M, Choi SW, Galas DJ, Tewari M. Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma. EMBO J 2019; 38:e101695. [PMID: 31053596 PMCID: PMC6545557 DOI: 10.15252/embj.2019101695] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/25/2022] Open
Abstract
Extracellular RNAs (exRNAs) in biofluids have attracted great interest as potential biomarkers. Although extracellular microRNAs in blood plasma are extensively characterized, extracellular messenger RNA (mRNA) and long non-coding RNA (lncRNA) studies are limited. We report that plasma contains fragmented mRNAs and lncRNAs that are missed by standard small RNA-seq protocols due to lack of 5' phosphate or presence of 3' phosphate. These fragments were revealed using a modified protocol ("phospho-RNA-seq") incorporating RNA treatment with T4-polynucleotide kinase, which we compared with standard small RNA-seq for sequencing synthetic RNAs with varied 5' and 3' ends, as well as human plasma exRNA Analyzing phospho-RNA-seq data using a custom, high-stringency bioinformatic pipeline, we identified mRNA/lncRNA transcriptome fingerprints in plasma, including tissue-specific gene sets. In a longitudinal study of hematopoietic stem cell transplant patients, bone marrow- and liver-enriched exRNA genes were tracked with bone marrow recovery and liver injury, respectively, providing proof-of-concept validation as a biomarker approach. By enabling access to an unexplored realm of mRNA and lncRNA fragments, phospho-RNA-seq opens up new possibilities for plasma transcriptomic biomarker development.
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Affiliation(s)
- Maria D Giraldez
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
- Institute of Biomedicine of Seville (IBiS), Seville, Spain
- Unit of Digestive Diseases, Virgen del Rocio University Hospital, Seville, Spain
| | - Ryan M Spengler
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | | | - Annika J Goicochea
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | - Missy Tuck
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | - Sung Won Choi
- Department of Pediatrics, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | - David J Galas
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Muneesh Tewari
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
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98
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Wong RK, MacMahon M, Woodside JV, Simpson DA. A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma. BMC Genomics 2019; 20:446. [PMID: 31159762 PMCID: PMC6547578 DOI: 10.1186/s12864-019-5826-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circulating microRNAs (miRNAs) are attractive non-invasive biomarkers for a variety of conditions due to their stability and altered pathophysiological expression levels. Reliable detection of global expression profiles is required to maximise miRNA biomarker discovery. Although developments in small RNA-Seq technology have improved detection of plasma-based miRNAs, the low RNA content and sequencing bias introduced during library preparation remain challenging. In this study we compare commercially available RNA extraction methods using MagnaZol (Bioo Scientific) or miRNeasy (QIAGEN) and three library preparation methods - CleanTag (TriLink), NEXTflex (Bioo Scientific) and QIAseq (QIAGEN) - which aim to address one or both of these issues. RESULTS Different RNA extractions and library preparation protocols result in differential detection of miRNAs. A greater proportion of reads mapped to miRNAs in libraries prepared with MagnaZol RNA than with miRNeasy RNA. Libraries prepared using QIAseq demonstrated the greatest miRNA diversity with many more very low abundance miRNAs detected (~ 2-3 fold more with < 10 reads), whilst CleanTag detected the fewest individual miRNAs and considerably over-represented miR-486-5p. Libraries prepared with QIAseq had the strongest correlation with RT-qPCR quantification. Analysis of unique molecular indices (UMIs) incorporated in the QIAseq protocol indicate that little PCR bias is introduced during small RNA library preparation. CONCLUSIONS Small RNAs were consistently detected using all RNA extraction and library preparation protocols tested, but with some miRNAs at significantly different levels. Choice of the most suitable protocol should be informed by the relative importance of minimising the total sequencing required, detection of rare miRNAs or absolute quantification.
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Affiliation(s)
- Ryan K.Y. Wong
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL UK
| | - Meabh MacMahon
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL UK
| | - Jayne V. Woodside
- Nutrition Group, Institute for Global Food Security (Centre for Public Health), School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Institute of Clinical Science A (First Floor), Grosvenor Road, Belfast, BT12 6BJ UK
| | - David A. Simpson
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL UK
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99
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Zhou W, Liu T, Saren G, Liao L, Fang W, Zhao H. Comprehensive analysis of differentially expressed long non-coding RNAs in non-small cell lung cancer. Oncol Lett 2019; 18:1145-1156. [PMID: 31423174 PMCID: PMC6607379 DOI: 10.3892/ol.2019.10414] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the primary subtype of lung cancer. Long non-coding RNAs (lncRNAs) have been reported to serve prominent roles in cancer progression. However, the expression patterns and potential roles of lncRNAs in NSCLC remain to be elucidated. In the present study, four public datasets were analyzed to identify differentially expressed lncRNAs (DElncs) in NSCLC. A further dataset, GSE19188, was analyzed to validate the findings. A total of 38 upregulated and 31 downregulated lncRNAs were identified in NSCLC, compared with samples from healthy controls. Among these, 12 lncRNAs were associated with the progression of NSCLC, and dysregulated between high grade (stage III and IV) and low grade (stage II) NSCLC samples. Moreover, dysregulation of lncRNA-SIGLEC17P, GGTA1P, A2M-AS1, LINC00938, GVINP1, LINC00667 and TMPO-AS1 was associated with overall survival time in patients with NSCLC. Co-expression analyses, combined with the construction of protein-protein interaction networks, were performed to reveal the potential roles of key lncRNAs in NSCLC. The present study revealed a series of lncRNAs involved in the progression of NSCLS, which may serve as novel biomarkers for the disease.
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Affiliation(s)
- Wenyong Zhou
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Tao Liu
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Gaowa Saren
- Department of Intensive Care, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Li Liao
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Heng Zhao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
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100
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Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction. Sci Rep 2019; 9:7953. [PMID: 31138886 PMCID: PMC6538698 DOI: 10.1038/s41598-019-44457-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/17/2019] [Indexed: 02/08/2023] Open
Abstract
Thermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by rationally designing RNA-seq adapters that minimize adapter dimer formation. Additionally, we developed biochemical and computational methods for remediating 5′- and 3′-end biases, the latter based on a random forest regression model that provides insight into the contribution of different factors to these biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5′- and 3′-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.
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