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Wang H, Chen M, Wei X, Xia R, Pei D, Huang X, Han B. Computational tools for plant genomics and breeding. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2578-6. [PMID: 38676814 DOI: 10.1007/s11427-024-2578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024]
Abstract
Plant genomics and crop breeding are at the intersection of biotechnology and information technology. Driven by a combination of high-throughput sequencing, molecular biology and data science, great advances have been made in omics technologies at every step along the central dogma, especially in genome assembling, genome annotation, epigenomic profiling, and transcriptome profiling. These advances further revolutionized three directions of development. One is genetic dissection of complex traits in crops, along with genomic prediction and selection. The second is comparative genomics and evolution, which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant discovery. The third direction is the development of deep learning approaches for the rational design of biological sequences, especially proteins, for synthetic biology. All three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.
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Affiliation(s)
- Hai Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Mengjiao Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
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2
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Pereira G, Charpigny G, Guo Y, Silva E, Silva MF, Ye T, Lopes-da-Costa L, Humblot P. Characterization of circulating microRNA profiles of postpartum dairy cows with persistent subclinical endometritis. J Dairy Sci 2023; 106:9704-9717. [PMID: 37641364 DOI: 10.3168/jds.2023-23616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/30/2023] [Indexed: 08/31/2023]
Abstract
Subclinical endometritis (SCE) is an unresolved inflammation of the endometrium of postpartum dairy cows, seriously affecting fertility. Current diagnosis, which relies on uterine cytology or even more invasive biopsy sampling, would benefit from the identification of blood-based diagnostic biomarkers. Due to the known role of microRNAs (miRNAs) in other diseases, this case-control study evaluated the cell-free circulating miRNA profiles of SCE cows, and the network of transcripts predicted to interact with those miRNAs, previously identified as differentially expressed genes (DEG) in the endometrium of the same cows. Healthy (H, n = 6) and persistent SCE (n = 11) cows characterized by endometrial cytology and biopsy were blood sampled at 21 and 44 d postpartum (DPP). Following extraction of cell-free plasma miRNAs and RNA-seq analysis, differential abundance analysis of miRNAs was performed with the DESeq2 R package (adjusted p-value of 0.05), and in silico prediction of miRNA-interacting genes on a sequence complementary basis was conducted using the miRWalk database. The principal component analysis showed a clear clustering between groups of uterine health phenotypes (H vs. SCE), although the clustering between groups was less pronounced at 44 DPP than at 21 DPP. No effect of the stage (21 vs. 44 DPP) was observed. A total of 799 known circulating miRNAs were identified, from which 34 demonstrated differential abundance between H and SCE cows (12 less abundant and 22 more abundant in SCE than in H cows). These 34 miRNAs are predicted to interact with 10,104 transcripts, among which 43, 81, and 147 were previously identified as differentially expressed in, respectively, endometrial luminal epithelial, glandular epithelial, and stromal cells of the same cows. This accounts for approximately half of the DEG identified between those H and SCE cows, including genes involved in endometrial cell proliferation, angiogenesis and immune response, whose dysregulation in SCE cows may impair pregnancy establishment. From 219 miRNAs with mean normalized read counts above 100, the presence and abundance of miR-425-3p and miR-2285z had the highest discriminatory level to differentiate SCE from H cows. In conclusion, despite apparent confinement to the endometrium, SCE is associated with a distinct circulating miRNA profile, which may represent a link between the systemic changes associated with disease and the endometrial immune response. The validation of a miRNA panel consisting of circulating cell-free miR-425-3p and miR-2285z may prove a relevant advancement for the noninvasive diagnosis of persistent SCE.
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Affiliation(s)
- Gonçalo Pereira
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Gilles Charpigny
- Université Paris-Saclay, INRAE, ENVA, BREED, 78350, Jouy-en-Josas, France
| | - Yongzhi Guo
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, PO, 750 07 Uppsala, Sweden
| | - Elisabete Silva
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Marta Filipa Silva
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal; Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Centre National de Recherche Scientifique (CNRS) UMR7104, Université de Strasbourg,1 rue Laurent Fries, 67404 Illkirch, France
| | - Luís Lopes-da-Costa
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal.
| | - Patrice Humblot
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, PO, 750 07 Uppsala, Sweden
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Devers EA, Brosnan CA, Sarazin A, Schott G, Lim P, Lehesranta S, Helariutta Y, Voinnet O. In planta dynamics, transport biases, and endogenous functions of mobile siRNAs in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1377-1393. [PMID: 37243897 DOI: 10.1111/tpj.16327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
In RNA interference (RNAi), small interfering RNAs (siRNAs) produced from double-stranded RNA guide ARGONAUTE (AGO) proteins to silence sequence-complementary RNA/DNA. RNAi can propagate locally and systemically in plants, but despite recent advances in our understanding of the underlying mechanisms, basic questions remain unaddressed. For instance, RNAi is inferred to diffuse through plasmodesmata (PDs), yet how its dynamics in planta compares with that of established symplastic diffusion markers remains unknown. Also is why select siRNA species, or size classes thereof, are apparently recovered in RNAi recipient tissues, yet only under some experimental settings. Shootward movement of endogenous RNAi in micro-grafted Arabidopsis is also yet to be achieved, while potential endogenous functions of mobile RNAi remain scarcely documented. Here, we show (i) that temporal, localized PD occlusion in source leaves' companion cells (CCs) suffices to abrogate all systemic manifestations of CC-activated mobile transgene silencing, including in sink leaves; (ii) that the presence or absence of specific AGOs in incipient/traversed/recipient tissues likely explains the apparent siRNA length selectivity observed upon vascular movement; (iii) that stress enhancement allows endo-siRNAs of a single inverted repeat (IR) locus to translocate against the shoot-to-root phloem flow; and (iv) that mobile endo-siRNAs generated from this locus have the potential to regulate hundreds of transcripts. Our results close important knowledge gaps, rationalize previously noted inconsistencies between mobile RNAi settings, and provide a framework for mobile endo-siRNA research.
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Affiliation(s)
- Emanuel A Devers
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Christopher A Brosnan
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Alexis Sarazin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Gregory Schott
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Peiqi Lim
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Satu Lehesranta
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland
| | - Yrjö Helariutta
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), Universitätsstrasse 2, 8092, Zürich, Switzerland
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4
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Brazane M, Dimitrova DG, Pigeon J, Paolantoni C, Ye T, Marchand V, Da Silva B, Schaefer E, Angelova MT, Stark Z, Delatycki M, Dudding-Byth T, Gecz J, Plaçais PY, Teysset L, Préat T, Piton A, Hassan BA, Roignant JY, Motorin Y, Carré C. The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance. Life Sci Alliance 2023; 6:e202201877. [PMID: 36720500 PMCID: PMC9889914 DOI: 10.26508/lsa.202201877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 02/02/2023] Open
Abstract
FTSJ1 is a conserved human 2'-O-methyltransferase (Nm-MTase) that modifies several tRNAs at position 32 and the wobble position 34 in the anticodon loop. Its loss of function has been linked to X-linked intellectual disability (XLID), and more recently to cancers. However, the molecular mechanisms underlying these pathologies are currently unclear. Here, we report a novel FTSJ1 pathogenic variant from an X-linked intellectual disability patient. Using blood cells derived from this patient and other affected individuals carrying FTSJ1 mutations, we performed an unbiased and comprehensive RiboMethSeq analysis to map the ribose methylation on all human tRNAs and identify novel targets. In addition, we performed a transcriptome analysis in these cells and found that several genes previously associated with intellectual disability and cancers were deregulated. We also found changes in the miRNA population that suggest potential cross-regulation of some miRNAs with these key mRNA targets. Finally, we show that differentiation of FTSJ1-depleted human neural progenitor cells into neurons displays long and thin spine neurites compared with control cells. These defects are also observed in Drosophila and are associated with long-term memory deficits. Altogether, our study adds insight into FTSJ1 pathologies in humans and flies by the identification of novel FTSJ1 targets and the defect in neuron morphology.
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Affiliation(s)
- Mira Brazane
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Julien Pigeon
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tao Ye
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, EpiRNASeq Core Facility, UMS2008/US40 IBSLor,Nancy, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Elise Schaefer
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Margarita T Angelova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide; South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Pierre-Yves Plaçais
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Thomas Préat
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Amélie Piton
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Bassem A Hassan
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
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5
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Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 2023; 23:33. [PMID: 36625940 PMCID: PMC9838419 DOI: 10.1007/s10142-022-00947-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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Barman B, Sung BH, Krystofiak E, Ping J, Ramirez M, Millis B, Allen R, Prasad N, Chetyrkin S, Calcutt MW, Vickers K, Patton JG, Liu Q, Weaver AM. VAP-A and its binding partner CERT drive biogenesis of RNA-containing extracellular vesicles at ER membrane contact sites. Dev Cell 2022; 57:974-994.e8. [PMID: 35421371 PMCID: PMC9075344 DOI: 10.1016/j.devcel.2022.03.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
RNA transfer via extracellular vesicles (EVs) influences cell phenotypes; however, lack of information regarding biogenesis of RNA-containing EVs has limited progress in the field. Here, we identify endoplasmic reticulum membrane contact sites (ER MCSs) as platforms for the generation of RNA-containing EVs. We identify a subpopulation of small EVs that is highly enriched in RNA and regulated by the ER MCS linker protein VAP-A. Functionally, VAP-A-regulated EVs are critical for miR-100 transfer between cells and in vivo tumor formation. Lipid analysis of VAP-A-knockdown EVs revealed reductions in the EV biogenesis lipid ceramide. Knockdown of the VAP-A-binding ceramide transfer protein CERT led to similar defects in EV RNA content. Imaging experiments revealed that VAP-A promotes luminal filling of multivesicular bodies (MVBs), CERT localizes to MVBs, and the ceramide-generating enzyme neutral sphingomyelinase 2 colocalizes with VAP-A-positive ER. We propose that ceramide transfer via VAP-A-CERT linkages drives the biogenesis of a select RNA-containing EV population.
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Affiliation(s)
- Bahnisikha Barman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bong Hwan Sung
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Evan Krystofiak
- Vanderbilt University Cell Imaging Shared Resource, Nashville, TN, USA
| | - Jie Ping
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol Ramirez
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bryan Millis
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt Biophotonics Center, Vanderbilt School of Engineering, Nashville, TN, USA
| | - Ryan Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sergei Chetyrkin
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Kasey Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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Diamantopoulos MA, Georgoulia KK, Scorilas A. Identification and expression analysis of ten novel small non-coding RNAs (sncRNAs) in cancer cells using a high-throughput sequencing approach. Gene 2022; 809:146025. [PMID: 34710527 DOI: 10.1016/j.gene.2021.146025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/13/2021] [Accepted: 10/14/2021] [Indexed: 01/18/2023]
Abstract
Non-coding RNAs are characterized as RNA molecules, which lack the capacity to encode protein structures and appear to include a level of internal signals. Moreover, they control various stages of gene expression, thus controlling the cell physiology and development. In this study, we implemented a high-throughput sequencing approach based on the primary semi-conductor technology and computational tools, in order to identity novel small non-coding RNAs. Fourteen human cancer cell lines were cultured, and RNA samples were enriched for small RNAs following semi-conductor next generation sequencing (NGS). Bioinformatics analysis of NGS data revealed the existence of several classes of ncRNAs using the miRDeep* and CPSS 2.0 software. To investigate the existence of the predicted non-coding RNA sequences in cDNA pools of cell lines, a developed qPCR-based assay was implemented. The structure of each novel small ncRNA was visualized, using the RNAfold algorithm. Our results support the existence of twenty (20) putative new small ncRNAs, ten (10) of which have had their expression experimentally validated and presented differential profiles in cancerous and normal cells. A deeper comprehension of the ncRNAs interactive network and its role in cancer can therefore be translated into a wide range of clinical applications. Despite this progress, further scientific research from different perspectives and in different fields is needed, so that the riddle of the human transcriptome can be solved.
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Affiliation(s)
- Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Konstantina K Georgoulia
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
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9
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Bokobza C, Joshi P, Schang AL, Csaba Z, Faivre V, Montané A, Galland A, Benmamar-Badel A, Bosher E, Lebon S, Schwendimann L, Mani S, Dournaud P, Besson V, Fleiss B, Gressens P, Van Steenwinckel J. miR-146b Protects the Perinatal Brain against Microglia-Induced Hypomyelination. Ann Neurol 2021; 91:48-65. [PMID: 34741343 PMCID: PMC9298799 DOI: 10.1002/ana.26263] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022]
Abstract
Objectives In the premature newborn, perinatal inflammation mediated by microglia contributes significantly to neurodevelopmental injuries including white matter injury (WMI). Brain inflammation alters development through neuroinflammatory processes mediated by activation of homeostatic microglia toward a pro‐inflammatory and neurotoxic phenotype. Investigating immune regulators of microglial activation is crucial to find effective strategies to prevent and treat WMI. Methods Ex vivo microglial cultures and a mouse model of WMI induced by perinatal inflammation (interleukin‐1‐beta [IL‐1β] and postnatal days 1–5) were used to uncover and elucidate the role of microRNA‐146b‐5p in microglial activation and WMI. Results A specific reduction in vivo in microglia of Dicer, a protein required for microRNAs maturation, reduces pro‐inflammatory activation of microglia and prevents hypomyelination in our model of WMI. Microglial miRNome analysis in the WMI model identified miRNA‐146b‐5p as a candidate modulator of microglial activation. Ex vivo microglial cell culture treated with the pro‐inflammatory stimulus lipopolysaccharide (LPS) led to overexpression of immunomodulatory miRNA‐146b‐5p but its drastic reduction in the microglial extracellular vesicles (EVs). To increase miRNA‐146b‐5p expression, we used a 3DNA nanocarrier to deliver synthetic miRNA‐146b‐5p specifically to microglia. Enhancing microglial miRNA‐146b‐5p overexpression significantly decreased LPS‐induced activation, downregulated IRAK1, and restored miRNA‐146b‐5p levels in EVs. In our WMI model, 3DNA miRNA‐146b‐5p treatment significantly prevented microglial activation, hypomyelination, and cognitive defect induced by perinatal inflammation. Interpretations These findings support that miRNA‐146b‐5p is a major regulator of microglia phenotype and could be targeted to reduce the incidence and the severity of perinatal brain injuries and their long‐term consequences. ANN NEUROL 2022;91:48–65
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Affiliation(s)
- Cindy Bokobza
- Université de Paris, NeuroDiderot, Inserm, Paris, France
| | - Pooja Joshi
- Université de Paris, NeuroDiderot, Inserm, Paris, France
| | - Anne-Laure Schang
- Université de Paris, Centre de recherche en Epidémiologie et Statistiques, Inserm, Paris, France
| | - Zsolt Csaba
- Université de Paris, NeuroDiderot, Inserm, Paris, France
| | - Valérie Faivre
- Université de Paris, NeuroDiderot, Inserm, Paris, France
| | - Amélie Montané
- Université de Paris, NeuroDiderot, Inserm, Paris, France
| | - Anne Galland
- Université de Paris, NeuroDiderot, Inserm, Paris, France
| | | | | | - Sophie Lebon
- Université de Paris, NeuroDiderot, Inserm, Paris, France
| | | | - Shyamala Mani
- Université de Paris, NeuroDiderot, Inserm, Paris, France.,Curadev Pharma, Pvt. Ltd, Noida, India
| | | | - Valerie Besson
- Université de Paris, Faculté de Pharmacie de Paris, UMR-S1144 Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Bobbi Fleiss
- Université de Paris, NeuroDiderot, Inserm, Paris, France.,School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
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10
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Brioudes F, Jay F, Sarazin A, Grentzinger T, Devers EA, Voinnet O. HASTY, the Arabidopsis EXPORTIN5 ortholog, regulates cell-to-cell and vascular microRNA movement. EMBO J 2021; 40:e107455. [PMID: 34152631 PMCID: PMC8327949 DOI: 10.15252/embj.2020107455] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 01/04/2023] Open
Abstract
Plant microRNAs (miRNAs) guide cytosolic post-transcriptional gene silencing of sequence-complementary transcripts within the producing cells, as well as in distant cells and tissues. Here, we used an artificial miRNA-based system (amiRSUL) in Arabidopsis thaliana to explore the still elusive mechanisms of inter-cellular miRNA movement via forward genetics. This screen identified many mutant alleles of HASTY (HST), the ortholog of mammalian EXPORTIN5 (XPO5) with a recently reported role in miRNA biogenesis in Arabidopsis. In both epidermis-peeling and grafting assays, amiRSUL levels were reduced much more substantially in miRNA-recipient tissues than in silencing-emitting tissues. We ascribe this effect to HST controlling cell-to-cell and phloem-mediated movement of the processed amiRSUL, in addition to regulating its biogenesis. While HST is not required for the movement of free GFP or siRNAs, its cell-autonomous expression in amiRSUL-emitting tissues suffices to restore amiRSUL movement independently of its nucleo-cytosolic shuttling activity. By contrast, HST is dispensable for the movement and activity of amiRSUL within recipient tissues. Finally, HST enables movement of endogenous miRNAs that display mostly unaltered steady-state levels in hst mutant tissues. We discuss a role for HST as a hitherto unrecognized regulator of miRNA movement in relation to its recently assigned nuclear function at the nexus of MIRNA transcription and miRNA processing.
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Affiliation(s)
| | - Florence Jay
- Department of BiologyETH ZürichZürichSwitzerland
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11
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Fiori LM, Kos A, Lin R, Théroux JF, Lopez JP, Kühne C, Eggert C, Holzapfel M, Huettl RE, Mechawar N, Belzung C, Ibrahim EC, Chen A, Turecki G. miR-323a regulates ERBB4 and is involved in depression. Mol Psychiatry 2021; 26:4191-4204. [PMID: 33219358 DOI: 10.1038/s41380-020-00953-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/27/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023]
Abstract
Major depressive disorder (MDD) is a complex and debilitating illness whose etiology remains unclear. Small RNA molecules, such as micro RNAs (miRNAs) have been implicated in MDD, where they display differential expression in the brain and the periphery. In this study, we quantified miRNA expression by small RNA sequencing in the anterior cingulate cortex and habenula of individuals with MDD and psychiatrically-healthy controls. Thirty-two miRNAs showed significantly correlated expression between the two regions (False Discovery Rate < 0.05), of which four, miR-204-5p, miR-320b, miR-323a-3p, and miR-331-3p, displayed upregulated expression in MDD. We assessed the expression of predicted target genes of differentially expressed miRNAs in the brain, and found that the expression of erb-b2 receptor tyrosine kinase 4 (ERBB4), a gene encoding a neuregulin receptor, was downregulated in both regions, and was influenced by miR-323a-3p in vitro. Finally, we assessed the effects of manipulating miRNA expression in the mouse ACC on anxiety- and depressive-like behaviors. Mice in which miR-323-3p was overexpressed or knocked-down displayed increased and decreased emotionality, respectively. Additionally, these mice displayed significantly downregulated and upregulated expression of Erbb4, respectively. Overall, our findings indicate the importance of brain miRNAs in the pathology of MDD, and emphasize the involvement of miR-323a-3p and ERBB4 in this phenotype. Future studies further characterizing miR-323a-3p and neuregulin signaling in depression are warranted.
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Affiliation(s)
- Laura M Fiori
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Aron Kos
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany.,Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Rixing Lin
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Jean-Francois Théroux
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Juan Pablo Lopez
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany.,Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Claudia Kühne
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Carola Eggert
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Maria Holzapfel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Rosa-Eva Huettl
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Naguib Mechawar
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Catherine Belzung
- UMR 1253, iBrain, UFR Sciences et Techniques, Parc Grandmont, Tours, France
| | - El Chérif Ibrahim
- Aix-Marseille Université, CNRS, INT, Institute Neuroscience Timone, Marseille, France
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany. .,Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.
| | - Gustavo Turecki
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada.
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12
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Billa PA, Faulconnier Y, Ye T, Bourdon C, Pires JAA, Leroux C. Nutrigenomic analyses reveal miRNAs and mRNAs affected by feed restriction in the mammary gland of midlactation dairy cows. PLoS One 2021; 16:e0248680. [PMID: 33857151 PMCID: PMC8049318 DOI: 10.1371/journal.pone.0248680] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
The objective of this study was to investigate the effects of feed restriction on mammary miRNAs and coding gene expression in midlactation cows. Five Holstein cows and 6 Montbéliarde cows underwent 6 days of feed restriction, during which feed allowance was reduced to meet 50% of their net energy for lactation requirements. Mammary biopsies were performed before and at the end of the restriction period. Mammary miRNA and mRNA analyses were performed using high-throughput sequencing and microarray analyses, respectively. Feed restriction induced a negative energy balance and decreased milk production and fat and protein yields in both breeds. Feed restriction modified the expression of 27 miRNAs and 374 mRNAs in mammary glands from Holstein cows, whereas no significant miRNA change was observed in Montbéliarde cows. Among the 27 differentially expressed miRNAs, 8 miRNAs were associated with dairy QTL. Analysis of target genes indicate that the 8 most abundantly expressed miRNAs control transcripts related to lipid metabolism, mammary remodeling and stress response. A comparison between the mRNAs targeted by the 8 most strongly expressed miRNAs and 374 differentially expressed mRNAs identified 59 mRNAs in common. The bioinformatic analyses of these 59 mRNAs revealed their implication in lipid metabolism and endothelial cell proliferation. These effects of feed restriction on mammary miRNAs and mRNAs observed in Holstein cows suggest a potential role of miRNAs in mammary structure and lipid biosynthesis that could explain changes in milk production and composition.
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Affiliation(s)
- Pierre-Alexis Billa
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Yannick Faulconnier
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Céline Bourdon
- INRAE, AgroParisTech, Université Paris-Saclay, UMR Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - José A. A. Pires
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Christine Leroux
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
- * E-mail:
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13
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MicroRNAs Regulating Autophagy in Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1208:191-264. [PMID: 34260028 DOI: 10.1007/978-981-16-2830-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Social and economic impacts of neurodegenerative diseases (NDs) become more prominent in our constantly aging population. Currently, due to the lack of knowledge about the aetiology of most NDs, only symptomatic treatment is available for patients. Hence, researchers and clinicians are in need of solid studies on pathological mechanisms of NDs. Autophagy promotes degradation of pathogenic proteins in NDs, while microRNAs post-transcriptionally regulate multiple signalling networks including autophagy. This chapter will critically discuss current research advancements in the area of microRNAs regulating autophagy in NDs. Moreover, we will introduce basic strategies and techniques used in microRNA research. Delineation of the mechanisms contributing to NDs will result in development of better approaches for their early diagnosis and effective treatment.
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14
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Chen SP, Chang YA, Chou CH, Juan CC, Lee HC, Chen LK, Wu PC, Wang YF, Fuh JL, Lirng JF, Ducros A, Huang HD, Wang SJ. Circulating microRNAs Associated With Reversible Cerebral Vasoconstriction Syndrome. Ann Neurol 2020; 89:459-473. [PMID: 33314303 DOI: 10.1002/ana.25965] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The purpose of this study was to investigate the significance of circulating micro RNAs (miRNAs) in the pathogenesis of reversible cerebral vasoconstriction syndrome (RCVS). METHODS We prospectively recruited 3 independent cohorts of patients with RCVS and age-matched and sex-matched controls in a single medical center. Next-generation small RNA sequencing followed by quantitative polymerase chain reaction (PCR) was used to identify and validate differentially expressed miRNAs, which was cross-validated in migraine patients in ictal stage or interictal stage. Computational analysis was used to predict the target genes of miRNAs, followed by in vitro functional analysis. RESULTS We identified a panel of miRNAs including miR-130a-3p, miR-130b-3p, let-7a-5p, let-7b-5p, and let-7f-5p that well differentiated patients with RCVS from controls (area under the receiver operating characteristics curve [AUC] was 0.906, 0.890, and 0.867 in the 3 cohorts, respectively). The abundance of let-7a-5p, let-7b-5p, and let-7f-5p, but not miR-130a-3p nor miR-130b-3p, was significantly higher in patients with ictal migraine compared with that of controls and patients with interictal migraine. Target prediction and pathway enrichment analysis suggested that the transforming growth factor-β signaling pathway and endothelin-1 responsible for vasomotor control might link these miRNAs to RCVS pathogenesis, which was confirmed in vitro by transfecting miRNAs mimics or incubating the patients' cerebrospinal fluid (CSF) in 3 different vascular endothelial cells. Moreover, miR-130a-3p was associated with imaging-proven disruption of the blood-brain barrier (BBB) in patients with RCVS and its overexpression led to reduced transendothelial electrical resistance (ie, increased permeability) in in vitro human BBB model. INTERPRETATION We identified the circulating miRNA signatures associated with RCVS, which may be functionally linked to its headache, BBB integrity, and vasomotor function. ANN NEUROL 2021;89:459-473.
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Affiliation(s)
- Shih-Pin Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-An Chang
- Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan
| | - Chih-Hung Chou
- Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, HsinChu, Taiwan
| | - Chi-Chang Juan
- Institute of Physiology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hsin-Chen Lee
- Department and Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Luen-Kui Chen
- Institute of Physiology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Chun Wu
- Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yen-Feng Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jong-Ling Fuh
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jiing-Feng Lirng
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Radiology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Anne Ducros
- Neurology Department, Montpellier University Hospital, Montpellier, France.,Charles Coulomb Laboratory (L2C), UMR5221CNRS, Montpellier University, Montpellier, France
| | - Hsien-Da Huang
- Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China
| | - Shuu-Jiun Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
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15
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Vivek AT, Kumar S. Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. Brief Bioinform 2020; 22:6041165. [PMID: 33333550 DOI: 10.1093/bib/bbaa322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
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Affiliation(s)
- A T Vivek
- National Institute of Plant Genome Research in New Delhi, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research in New Delhi
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16
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Corral-Jara KF, Cantini L, Poupin N, Ye T, Rigaudière JP, Vincent SDS, Pinel A, Morio B, Capel F. An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids. Nutrients 2020; 12:E3864. [PMID: 33348802 PMCID: PMC7765958 DOI: 10.3390/nu12123864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
Insulin resistance decreases the ability of insulin to inhibit hepatic gluconeogenesis, a key step in the development of metabolic syndrome. Metabolic alterations, fat accumulation, and fibrosis in the liver are closely related and contribute to the progression of comorbidities, such as hypertension, type 2 diabetes, or cancer. Omega 3 (n-3) polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA), were identified as potent positive regulators of insulin sensitivity in vitro and in animal models. In the current study, we explored the effects of a transgenerational supplementation with EPA in mice exposed to an obesogenic diet on the regulation of microRNAs (miRNAs) and gene expression in the liver using high-throughput techniques. We implemented a comprehensive molecular systems biology approach, combining statistical tools, such as MicroRNA Master Regulator Analysis pipeline and Boolean modeling to integrate these biochemical processes. We demonstrated that EPA mediated molecular adaptations, leading to the inhibition of miR-34a-5p, a negative regulator of Irs2 as a master regulatory event leading to the inhibition of gluconeogenesis by insulin during the fasting-feeding transition. Omics data integration provided greater biological insight and a better understanding of the relationships between biological variables. Such an approach may be useful for deriving innovative data-driven hypotheses and for the discovery of molecular-biochemical mechanistic links.
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Affiliation(s)
- Karla Fabiola Corral-Jara
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Laura Cantini
- Computational Systems Biology Team, Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France;
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France;
| | - Tao Ye
- GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries/BP 10142/, 67404 Illkirch, France;
| | - Jean Paul Rigaudière
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Sarah De Saint Vincent
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Alexandre Pinel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Lyon 1, 69310 Pierre Bénite, France;
| | - Frédéric Capel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
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17
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Lin YCD, Huang HY, Shrestha S, Chou CH, Chen YH, Chen CR, Hong HC, Li J, Chang YA, Chiew MY, Huang YR, Tu SJ, Sun TH, Weng SL, Tseng CP, Huang HD. Multi-omics profiling reveals microRNA-mediated insulin signaling networks. BMC Bioinformatics 2020; 21:389. [PMID: 32938376 PMCID: PMC7496206 DOI: 10.1186/s12859-020-03678-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background MicroRNAs (miRNAs) play a key role in mediating the action of insulin on cell growth and the development of diabetes. However, few studies have been conducted to provide a comprehensive overview of the miRNA-mediated signaling network in response to glucose in pancreatic beta cells. In our study, we established a computational framework integrating multi-omics profiles analyses, including RNA sequencing (RNA-seq) and small RNA sequencing (sRNA-seq) data analysis, inverse expression pattern analysis, public data integration, and miRNA targets prediction to illustrate the miRNA-mediated regulatory network at different glucose concentrations in INS-1 pancreatic beta cells (INS-1), which display important characteristics of the pancreatic beta cells. Results We applied our computational framework to the expression profiles of miRNA/mRNA of INS-1, at different glucose concentrations. A total of 1437 differentially expressed genes (DEGs) and 153 differentially expressed miRNAs (DEmiRs) were identified from multi-omics profiles. In particular, 121 DEmiRs putatively regulated a total of 237 DEGs involved in glucose metabolism, fatty acid oxidation, ion channels, exocytosis, homeostasis, and insulin gene regulation. Moreover, Argonaute 2 immunoprecipitation sequencing, qRT-PCR, and luciferase assay identified Crem, Fn1, and Stc1 are direct targets of miR-146b and elucidated that miR-146b acted as a potential regulator and promising target to understand the insulin signaling network. Conclusions In this study, the integration of experimentally verified data with system biology framework extracts the miRNA network for exploring potential insulin-associated miRNA and their target genes. The findings offer a potentially significant effect on the understanding of miRNA-mediated insulin signaling network in the development and progression of pancreatic diabetes.
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Affiliation(s)
- Yang-Chi-Dung Lin
- School of Life and Health Sciences, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China
| | - Hsi-Yuan Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China
| | - Sirjana Shrestha
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yen-Hua Chen
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, 10021, USA
| | - Chi-Ru Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsiao-Chin Hong
- School of Life and Health Sciences, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China
| | - Jing Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China
| | - Yi-An Chang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Men-Yee Chiew
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ya-Rong Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Siang-Jyun Tu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ting-Hsuan Sun
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan
| | - Ching-Ping Tseng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
| | - Hsien-Da Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China. .,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Longgang District, Shenzhen, 518172, Guangdong Province, China. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
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18
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Devers EA, Brosnan CA, Sarazin A, Albertini D, Amsler AC, Brioudes F, Jullien PE, Lim P, Schott G, Voinnet O. Movement and differential consumption of short interfering RNA duplexes underlie mobile RNA interference. NATURE PLANTS 2020; 6:789-799. [PMID: 32632272 DOI: 10.1038/s41477-020-0687-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 05/06/2020] [Indexed: 05/19/2023]
Abstract
In RNA interference (RNAi), the RNase III Dicer processes long double-stranded RNA (dsRNA) into short interfering RNA (siRNA), which, when loaded into ARGONAUTE (AGO) family proteins, execute gene silencing1. Remarkably, RNAi can act non-cell autonomously2,3: it is graft transmissible4-7, and plasmodesmata-associated proteins modulate its cell-to-cell spread8,9. Nonetheless, the molecular mechanisms involved remain ill defined, probably reflecting a disparity of experimental settings. Among other caveats, these almost invariably cause artificially enhanced movement via transitivity, whereby primary RNAi-target transcripts are converted into further dsRNA sources of secondary siRNA5,10,11. Whether siRNA mobility naturally requires transitivity and whether it entails the same or distinct signals for cell-to-cell versus long-distance movement remains unclear, as does the identity of the mobile signalling molecules themselves. Movement of long single-stranded RNA, dsRNA, free/AGO-bound secondary siRNA or primary siRNA have all been advocated12-15; however, an entity necessary and sufficient for all known manifestations of plant mobile RNAi remains to be ascertained. Here, we show that the same primary RNAi signal endows both vasculature-to-epidermis and long-distance silencing movement from three distinct RNAi sources. The mobile entities are AGO-free primary siRNA duplexes spreading length and sequence independently. However, their movement is accompanied by selective siRNA depletion reflecting the AGO repertoires of traversed cell types. Coupling movement with this AGO-mediated consumption process creates qualitatively distinct silencing territories, potentially enabling unlimited spatial gene regulation patterns well beyond those granted by mere gradients.
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Affiliation(s)
| | - Christopher A Brosnan
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | | | | | | | - Pauline E Jullien
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Peiqi Lim
- Department of Biology, ETH Zürich, Zurich, Switzerland
- QIAGEN Singapore, Singapore, Singapore
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19
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Qi B, Fiori LM, Turecki G, Trakadis YJ. Machine Learning Analysis of Blood microRNA Data in Major Depression: A Case-Control Study for Biomarker Discovery. Int J Neuropsychopharmacol 2020; 23:505-510. [PMID: 32365192 PMCID: PMC7689198 DOI: 10.1093/ijnp/pyaa029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/14/2020] [Accepted: 04/26/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND There is a lack of reliable biomarkers for major depressive disorder (MDD) in clinical practice. However, several studies have shown an association between alterations in microRNA levels and MDD, albeit none of them has taken advantage of machine learning (ML). METHOD Supervised and unsupervised ML were applied to blood microRNA expression profiles from a MDD case-control dataset (n = 168) to distinguish between (1) case vs control status, (2) MDD severity levels defined based on the Montgomery-Asberg Depression Rating Scale, and (3) antidepressant responders vs nonresponders. RESULTS MDD cases were distinguishable from healthy controls with an area-under-the receiver-operating characteristic curve (AUC) of 0.97 on testing data. High- vs low-severity cases were distinguishable with an AUC of 0.63. Unsupervised clustering of patients, before supervised ML analysis of each cluster for MDD severity, improved the performance of the classifiers (AUC of 0.70 for cluster 1 and 0.76 for cluster 2). Antidepressant responders could not be successfully separated from nonresponders, even after patient stratification by unsupervised clustering. However, permutation testing of the top microRNA, identified by the ML model trained to distinguish responders vs nonresponders in each of the 2 clusters, showed an association with antidepressant response. Each of these microRNA markers was only significant when comparing responders vs nonresponders of the corresponding cluster, but not using the heterogeneous unclustered patient set. CONCLUSIONS Supervised and unsupervised ML analysis of microRNA may lead to robust biomarkers for monitoring clinical evolution and for more timely assessment of treatment in MDD patients.
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Affiliation(s)
- Bill Qi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Laura M Fiori
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Gustavo Turecki
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Yannis J Trakadis
- Department of Human Genetics, McGill University, Montreal, QC, Canada,Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada,Department of Medical Genetics, McGill University Health Center, Montreal, QC, Canada,Correspondence: Yannis J. Trakadis, MD MSc FRCPC FCCMG, Human Genetics, McGill University Health Centre, Room A04.3140, Montreal Children’s Hospital, 1001 Boul. Décarie, Montreal, Quebec, Canada, H4A 3J1 ()
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20
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Morgado L, Johannes F. Computational tools for plant small RNA detection and categorization. Brief Bioinform 2020; 20:1181-1192. [PMID: 29059285 PMCID: PMC6781577 DOI: 10.1093/bib/bbx136] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/09/2017] [Indexed: 01/06/2023] Open
Abstract
Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches. Although a large number of computational tools have been developed to predict features of sRNA sequences, these tools are mostly dedicated to microRNAs and none integrates the functionalities necessary to describe units from all sRNA pathways thus far discovered in plants. Here, we review the different classes of sRNA found in plants and describe available bioinformatics tools that can help in their detection and categorization.
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Affiliation(s)
- Lionel Morgado
- Corresponding author: Lionel Morgado, Groningen Bioinformatics Centre, University of Groningen, Nijenborgh 25 7, 9747 AG Groningen, The Netherlands. Tel.: +31 685 585 827; E-mail:
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21
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Just J, Yan Y, Farup J, Sieljacks P, Sloth M, Venø M, Gu T, de Paoli FV, Nyengaard JR, Bæk R, Jørgensen MM, Kjems J, Vissing K, Drasbek KR. Blood flow-restricted resistance exercise alters the surface profile, miRNA cargo and functional impact of circulating extracellular vesicles. Sci Rep 2020; 10:5835. [PMID: 32245988 PMCID: PMC7125173 DOI: 10.1038/s41598-020-62456-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/10/2020] [Indexed: 01/12/2023] Open
Abstract
Ischemic exercise conducted as low-load blood flow restricted resistance exercise (BFRE) can lead to muscle remodelling and promote muscle growth, possibly through activation of muscle precursor cells. Cell activation can be triggered by blood borne extracellular vesicles (EVs) as these nano-sized particles are involved in long distance signalling. In this study, EVs isolated from plasma of healthy human subjects performing a single bout of BFRE were investigated for their change in EV surface profiles and miRNA cargos as well as their impact on skeletal muscle precursor cell proliferation. We found that after BFRE, five EV surface markers and 12 miRNAs were significantly altered. Furthermore, target prediction and functional enrichment analysis of the miRNAs revealed several target genes that are associated to biological pathways involved in skeletal muscle protein turnover. Interestingly, EVs from BFRE plasma increased the proliferation of muscle precursor cells. In addition, alterations in surface markers and miRNAs indicated that the combination of exercise and ischemic conditioning during BFRE can stimulate blood cells to release EVs. These results support that BFRE promotes EV release to engage in muscle remodelling and/or growth processes.
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Affiliation(s)
- Jesper Just
- Center of Functionally Integrative Neuroscience, Dept of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Yan Yan
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Jean Farup
- Research laboratory for Biochemical Pathology, Dept of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Dept of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Peter Sieljacks
- Section for Sport Science, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Mette Sloth
- Center of Functionally Integrative Neuroscience, Dept of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Morten Venø
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Tingting Gu
- Center of Functionally Integrative Neuroscience, Dept of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Jens Randel Nyengaard
- Dept of Clinical Medicine, Core Center for Molecular Morphology, Section for Stereology and Microscopy, Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University, Aarhus, Denmark
| | - Rikke Bæk
- Dept of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Malene Møller Jørgensen
- Dept of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark.,Dept of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.,Dept of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kristian Vissing
- Section for Sport Science, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Kim Ryun Drasbek
- Center of Functionally Integrative Neuroscience, Dept of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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22
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Liu Q, Ding C, Lang X, Guo G, Chen J, Su X. Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. Brief Bioinform 2019; 22:463-473. [PMID: 31885040 PMCID: PMC7820841 DOI: 10.1093/bib/bbz151] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 11/01/2019] [Indexed: 02/05/2023] Open
Abstract
Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https://bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Xiaoqiang Lang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Ganggang Guo
- Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China 610041
| | - Jiafei Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Xiaohua Su
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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23
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Yrondi A, Fiori LM, Frey BN, Lam RW, MacQueen GM, Milev R, Müller DJ, Foster JA, Kennedy SH, Turecki G. Association Between Side Effects and Blood microRNA Expression Levels and Their Targeted Pathways in Patients With Major Depressive Disorder Treated by a Selective Serotonin Reuptake Inhibitor, Escitalopram: A CAN-BIND-1 Report. Int J Neuropsychopharmacol 2019; 23:88-95. [PMID: 31819986 PMCID: PMC7093997 DOI: 10.1093/ijnp/pyz066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/06/2019] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION Antidepressant drugs are effective therapies for major depressive disorder; however, they are frequently associated with side effects. Although there is some evidence for a relationship between genetic variation and side effects, little is known regarding the role of dynamic molecular factors as moderators of side effects. The aim of this study was to assess microRNA (miRNA) changes associated with side effects during escitalopram treatment and their downstream effects on target gene expression. METHODS A total 160 patients with major depressive disorder from the CAN-BIND-1 cohort were included. Side effects were assessed with the Toronto Side Effect Scale after 2 weeks of treatment with escitalopram. We assessed the relationship between side effects and changes in peripheral expression of miRNAs between baseline and week 2. For miRNA whose expression changed, we used target prediction algorithms to identify putative messenger RNA (mRNA) targets and assessed their expression. RESULTS Nausea was experienced by 42.5% of patients. We identified 45 miRNAs whose expression changed on initiation of escitalopram treatment, of which 10 displayed a negative association with intensity of nausea (miR15b-5p, miR17-5p, miR20a-5p, miR20b-5p, miR103a-3p, miR103b, miR106a-5p, miR182-5p, miR185-5p, and miR660-5p). Additionally, we found negative associations between 4 microRNAs (miR20a-5p, miR106a-5p, miR185-5p, miR660-5p) and mRNA targets. The expression of the miR185-5p target, CAMK2δ was significantly decreased [log 2 mean = -0.048 (0.233)] between weeks 0 and 2 (P = .01)]. CONCLUSIONS We identified an overexpression of miR185-5p during escitalopram treatment of major depressive disorder, which was negatively associated with intensity of nausea, and identified a potential mRNA target that may mediate this effect.
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Affiliation(s)
- Antoine Yrondi
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Laura M Fiori
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Benicio N Frey
- McMaster University and St Joseph’s Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Raymond W Lam
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Glenda M MacQueen
- University of Calgary Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Roumen Milev
- Providence Care Hospital, Kingston, Ontario, Canada
| | - Daniel J Müller
- Department of Psychiatry, University Health Network, Krembil Research Institute, University of Toronto, Toronto, Ontario, Canada,Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Jane A Foster
- Department of Psychiatry, University Health Network, Krembil Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Sidney H Kennedy
- Department of Psychiatry, University Health Network, Krembil Research Institute, University of Toronto, Toronto, Ontario, Canada,St Michael’s Hospital, Li Ka Shing Knowledge Institute, Centre for Depression and Suicide, Studies, Toronto, Ontario, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada,Correspondence: Gustavo Turecki, MD, PhD, Douglas Mental Health University Institute, Frank B Common Pavilion Room F-3125, 6875 LaSalle Boulevard, Montreal, Quebec, H4H 1R3 Canada ()
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24
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Florian RT, Kraft F, Leitão E, Kaya S, Klebe S, Magnin E, van Rootselaar AF, Buratti J, Kühnel T, Schröder C, Giesselmann S, Tschernoster N, Altmueller J, Lamiral A, Keren B, Nava C, Bouteiller D, Forlani S, Jornea L, Kubica R, Ye T, Plassard D, Jost B, Meyer V, Deleuze JF, Delpu Y, Avarello MDM, Vijfhuizen LS, Rudolf G, Hirsch E, Kroes T, Reif PS, Rosenow F, Ganos C, Vidailhet M, Thivard L, Mathieu A, Bourgeron T, Kurth I, Rafehi H, Steenpass L, Horsthemke B, LeGuern E, Klein KM, Labauge P, Bennett MF, Bahlo M, Gecz J, Corbett MA, Tijssen MAJ, van den Maagdenberg AMJM, Depienne C. Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3. Nat Commun 2019; 10:4919. [PMID: 31664039 PMCID: PMC6820781 DOI: 10.1038/s41467-019-12763-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022] Open
Abstract
Familial Adult Myoclonic Epilepsy (FAME) is a genetically heterogeneous disorder characterized by cortical tremor and seizures. Intronic TTTTA/TTTCA repeat expansions in SAMD12 (FAME1) are the main cause of FAME in Asia. Using genome sequencing and repeat-primed PCR, we identify another site of this repeat expansion, in MARCH6 (FAME3) in four European families. Analysis of single DNA molecules with nanopore sequencing and molecular combing show that expansions range from 3.3 to 14 kb on average. However, we observe considerable variability in expansion length and structure, supporting the existence of multiple expansion configurations in blood cells and fibroblasts of the same individual. Moreover, the largest expansions are associated with micro-rearrangements occurring near the expansion in 20% of cells. This study provides further evidence that FAME is caused by intronic TTTTA/TTTCA expansions in distinct genes and reveals that expansions exhibit an unexpectedly high somatic instability that can ultimately result in genomic rearrangements.
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Affiliation(s)
- Rahel T Florian
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sabine Kaya
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Stephan Klebe
- Department of Neurology, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Eloi Magnin
- Department of Neurology, CHU Jean Minjoz, 25000, Besançon, France
| | - Anne-Fleur van Rootselaar
- Departments of Neurology and Clinical Neurophysiology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Julien Buratti
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Theresa Kühnel
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Christopher Schröder
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sebastian Giesselmann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Nikolai Tschernoster
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Janine Altmueller
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Anaide Lamiral
- Department of Neurology, CHU Jean Minjoz, 25000, Besançon, France
| | - Boris Keren
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Caroline Nava
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Delphine Bouteiller
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Sylvie Forlani
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Ludmila Jornea
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Regina Kubica
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Tao Ye
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Damien Plassard
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Bernard Jost
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Yannick Delpu
- Genomic Vision, 80 Rue des Meuniers, 92220, Bagneux, France
| | | | - Lisanne S Vijfhuizen
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Gabrielle Rudolf
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
- Department of Neurology-centre de référence des epilepsies rares, University Hospital of Strasbourg, 1 Avenue Molière, 67200, Strasbourg, France
| | - Edouard Hirsch
- Department of Neurology-centre de référence des epilepsies rares, University Hospital of Strasbourg, 1 Avenue Molière, 67200, Strasbourg, France
| | - Thessa Kroes
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Philipp S Reif
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
| | - Felix Rosenow
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
| | - Christos Ganos
- Department of Neurology, Charité University Medicine Berlin, 10117, Berlin, Germany
| | - Marie Vidailhet
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
- APHP, Hôpital Pitié-Salpêtrière, Département de Neurologie, 75013, Paris, France
| | - Lionel Thivard
- APHP, Hôpital Pitié-Salpêtrière, Département de Neurologie, 75013, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions, Pasteur Institute, UMR3571 CNRS, Université de Paris, 75015, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Pasteur Institute, UMR3571 CNRS, Université de Paris, 75015, Paris, France
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Eric LeGuern
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Karl Martin Klein
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
- Departments of Clinical Neurosciences, Medical Genetics and Community Health Sciences, Hotchkiss Brain Institute & Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Pierre Labauge
- Department of Neurology, Gui de Chauliac University Hospital, 34295, Montpellier, France
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Jozef Gecz
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
- South Australian Health and Medical Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Mark A Corbett
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Marina A J Tijssen
- Department of Neurology, University Medical Center Groningen, University of Groningen, 9700, AB, Groningen, the Netherlands
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France.
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France.
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25
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Cheng WC, Liao TT, Lin CC, Yuan LTE, Lan HY, Lin HH, Teng HW, Chang HC, Lin CH, Yang CY, Huang SC, Jiang JK, Yang SH, Yang MH, Hwang WL. RAB27B-activated secretion of stem-like tumor exosomes delivers the biomarker microRNA-146a-5p, which promotes tumorigenesis and associates with an immunosuppressive tumor microenvironment in colorectal cancer. Int J Cancer 2019; 145:2209-2224. [PMID: 30980673 DOI: 10.1002/ijc.32338] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/12/2019] [Accepted: 04/02/2019] [Indexed: 12/21/2022]
Abstract
The dynamic cell-cell communication is essential for tissue homeostasis in normal physiological circumstances and contributes to a diversified tumor microenvironment. Although exosomes are extracellular vesicles that actively participate in cell-cell interaction by shutting cellular components, impacts of tumor exosomes in the context of cancer stemness remain elusive. Here, we expand colorectal cancer stem cells (CRCSCs) as cancer spheroids and demonstrate that the β-catenin/Tcf-4-activated RAB27B expression is required for the secretion of CRCSC exosomes. In an exosomal RNA sequencing analysis, a switch of exosomal RNA species from retrotransposons to microRNAs (miRNAs) is identified upon expanding CRCSCs. miRNA-146a-5p (miR-146a) is the major miRNA in CRCSC exosomes and exosomal miR-146a promotes stem-like properties and tumorigenicity by targeting Numb in recipient CRC cells. Among 53 CRC patients, those with abundant exosomal miR-146a expression in serum exhibits higher miR-146aHigh /NumbLow CRCSC traits, an increased number of tumor-filtrating CD66(+) neutrophils and a decreased number of tumor-infiltrating CD8(+) T cells. Our study elucidates a unique mechanism of tumor exosome-mediated stemness expansion.
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Affiliation(s)
- Wei-Chung Cheng
- Graduate Institute of Cancer Biology, China Medical University, Taichung, Taiwan
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan
| | - Tsai-Tsen Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Cancer Progression Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Chi Lin
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Medicine, National Yang-Ming University, Taipei, Taiwan
| | | | - Hsin-Yi Lan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hung-Hsin Lin
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hao-Wei Teng
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsin-Chuan Chang
- Cancer Progression Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Chi-Hung Lin
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Yung Yang
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
| | - Shih-Ching Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jeng-Kai Jiang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shung-Haur Yang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Muh-Hwa Yang
- Cancer Progression Research Center, National Yang-Ming University, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Wei-Lun Hwang
- Cancer Progression Research Center, National Yang-Ming University, Taipei, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
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26
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Marchais A, Chevalier C, Voinnet O. Extensive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including AGO5-dependent pseudogene-derived siRNAs. RNA (NEW YORK, N.Y.) 2019; 25:1098-1117. [PMID: 31138671 PMCID: PMC6800511 DOI: 10.1261/rna.069294.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/07/2019] [Indexed: 05/19/2023]
Abstract
In a reductionist perspective, plant silencing small (s)RNAs are often classified as mediating nuclear transcriptional gene silencing (TGS) or cytosolic posttranscriptional gene silencing (PTGS). Among the PTGS diagnostics is the association of AGOs and their sRNA cargos with the translation apparatus. In Arabidopsis, this is observed for AGO1 loaded with micro(mi)RNAs and, accordingly, translational-repression (TR) is one layer of plant miRNA action. Using AGO1:miRNA-mediated TR as a paradigm, we explored, with two unrelated polysome-isolation methods, which, among the ten Arabidopsis AGOs and numerous sRNA classes, interact with translation. We found that representatives of all three AGO-clades associate with polysomes, including the TGS-effector AGO4 and stereotypical 24-nt sRNAs that normally mediate TGS of transposons/repeats. Strikingly, approximately half of these annotated 24-nt siRNAs displayed unique matches in coding regions/introns of genes, and in pseudogenes, but not in transposons/repeats commonly found in their vicinity. Protein-coding gene-derived 24-nt sRNAs correlate with gene-body methylation. Those derived from pseudogenes belong to two main clusters defined by their parental-gene expression patterns, and are vastly enriched in AGO5, itself found on polysomes. Based on their tight expression pattern in developing and mature siliques, their biogenesis, and genomic/epigenomic features of their loci-of-origin, we discuss potential roles for these hitherto unknown polysome-enriched, pseudogene-derived siRNAs.
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Affiliation(s)
- Antonin Marchais
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Clément Chevalier
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
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27
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Kuksa PP, Amlie-Wolf A, Katanic Ž, Valladares O, Wang LS, Leung YY. SPAR: small RNA-seq portal for analysis of sequencing experiments. Nucleic Acids Res 2019; 46:W36-W42. [PMID: 29733404 PMCID: PMC6030839 DOI: 10.1093/nar/gky330] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/17/2018] [Indexed: 02/01/2023] Open
Abstract
The introduction of new high-throughput small RNA sequencing protocols that generate large-scale genomics datasets along with increasing evidence of the significant regulatory roles of small non-coding RNAs (sncRNAs) have highlighted the urgent need for tools to analyze and interpret large amounts of small RNA sequencing data. However, it remains challenging to systematically and comprehensively discover and characterize sncRNA genes and specifically-processed sncRNA products from these datasets. To fill this gap, we present Small RNA-seq Portal for Analysis of sequencing expeRiments (SPAR), a user-friendly web server for interactive processing, analysis, annotation and visualization of small RNA sequencing data. SPAR supports sequencing data generated from various experimental protocols, including smRNA-seq, short total RNA sequencing, microRNA-seq, and single-cell small RNA-seq. Additionally, SPAR includes publicly available reference sncRNA datasets from our DASHR database and from ENCODE across 185 human tissues and cell types to produce highly informative small RNA annotations across all major small RNA types and other features such as co-localization with various genomic features, precursor transcript cleavage patterns, and conservation. SPAR allows the user to compare the input experiment against reference ENCODE/DASHR datasets. SPAR currently supports analyses of human (hg19, hg38) and mouse (mm10) sequencing data. SPAR is freely available at https://www.lisanwanglab.org/SPAR.
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Affiliation(s)
- Pavel P Kuksa
- Penn Neurodegeneration Genomics Center, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexandre Amlie-Wolf
- Penn Neurodegeneration Genomics Center, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Živadin Katanic
- Penn Neurodegeneration Genomics Center, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute on Aging, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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28
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Billa PA, Faulconnier Y, Ye T, Chervet M, Le Provost F, Pires JAA, Leroux C. Deep RNA-Seq reveals miRNome differences in mammary tissue of lactating Holstein and Montbéliarde cows. BMC Genomics 2019; 20:621. [PMID: 31362707 PMCID: PMC6668132 DOI: 10.1186/s12864-019-5987-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
Background Genetic polymorphisms are known to influence milk production and composition. However, the genomic mechanisms involved in the genetic regulation of milk component synthesis are not completely understood. MicroRNAs (miRNAs) regulate gene expression. Previous research suggests that the high developmental potential of the mammary gland may depend in part on a specific miRNA expression pattern. The objective of the present study was to compare the mammary gland miRNomes of two dairy cow breeds, Holstein and Montbéliarde, which have different mammogenic potentials that are related to differences in dairy performance. Results Milk, fat, protein, and lactose yields were lower in Montbéliarde cows than in Holstein cows. We detected 754 distinct miRNAs in the mammary glands of Holstein (n = 5) and Montbéliarde (n = 6) midlactating cows using RNA-Seq technology, among which 738 were known and 16 were predicted miRNAs. The 25 most abundant miRNAs accounted for 90.6% of the total reads. The comparison of their abundances in the mammary glands of Holstein versus Montbéliarde cows identified 22 differentially expressed miRNAs (Padj ≤ 0.05). Among them, 11 presented a fold change ≥2, and 2 (miR-100 and miR-146b) were highly expressed. Among the most abundant miRNAs, miR-186 is known to inhibit cell proliferation and epithelial-to-mesenchymal transition. Data mining showed that 17 differentially expressed miRNAs with more than 20 reads were involved in the regulation of mammary gland plasticity. Several of them may potentially target mRNAs involved in signaling pathways (such as mTOR) and lipid metabolism, thereby indicating that they could influence milk composition. Conclusion We found differences in the mammary gland miRNomes of two dairy cattle breeds. These differences suggest a potential role for miRNAs in mammary gland plasticity and milk component synthesis, both of which are related to milk production and composition. Further research is warranted on the genetic regulation of miRNAs and their role in milk synthesis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5987-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- P A Billa
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - Y Faulconnier
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - T Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67404, Illkirch, France
| | - M Chervet
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| | - F Le Provost
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, F-78352, France
| | - J A A Pires
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - C Leroux
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France. .,Department of Food Science & Technology, University of California Davis, Davis, CA, USA.
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29
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Kesharwani RK, Chiesa M, Bellazzi R, Colombo GI. CBS-miRSeq: A comprehensive tool for accurate and extensive analyses of microRNA-sequencing data. Comput Biol Med 2019; 110:234-243. [DOI: 10.1016/j.compbiomed.2019.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022]
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30
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Brosnan CA, Sarazin A, Lim P, Bologna NG, Hirsch‐Hoffmann M, Voinnet O. Genome-scale, single-cell-type resolution of microRNA activities within a whole plant organ. EMBO J 2019; 38:e100754. [PMID: 31268601 PMCID: PMC6600646 DOI: 10.15252/embj.2018100754] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 01/27/2023] Open
Abstract
Loaded into ARGONAUTE(AGO) proteins, eukaryotic micro(mi)RNAs regulate gene expression via cleavage, translational repression, and/or accelerated decay of sequence-complementary target transcripts. Despite their importance in development, cell identity maintenance and stress responses, how individual miRNAs contribute to spatial gene regulation within the complex cell mosaics formed in tissues/organs has remained inaccessible in any organism to date. We have developed a non-invasive methodology to examine, at single-cell-type resolution, the AGO-loading and activity patterns of entire miRNA cohorts in intact organs, applied here to the Arabidopsis root tip. A dual miRNAome-targetome analytical interface allowing intuitive data integration/visualization was developed as the basis for in-depth investigations via single-cell-type experimentation. These uncovered an array of so far speculative or hitherto unknown types of spatial miRNA-mediated gene regulation schemes, including via widespread cell-to-cell movement between contiguous layers of distinct identities. This study provides the proof of principle that minimally invasive, genome-scale analysis of miRNA activities within and between single-cell types of whole organs is achievable.
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Affiliation(s)
- Christopher Andrew Brosnan
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Present address:
Queensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Alexis Sarazin
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
| | - PeiQi Lim
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Present address:
QIAGEN Singapore Pte. Ltd.SingaporeSingapore
| | - Nicolas Gerardo Bologna
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Present address:
Center for Research in Agricultural Genomics (CRAG)BarcelonaSpain
| | | | - Olivier Voinnet
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
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31
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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32
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Dørum G, Ingold S, Hanson E, Ballantyne J, Russo G, Aluri S, Snipen L, Haas C. Predicting the origin of stains from whole miRNome massively parallel sequencing data. Forensic Sci Int Genet 2019; 40:131-139. [DOI: 10.1016/j.fsigen.2019.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/24/2018] [Accepted: 02/14/2019] [Indexed: 12/15/2022]
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33
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Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell 2019; 177:1035-1049.e19. [PMID: 31031003 DOI: 10.1016/j.cell.2019.03.030] [Citation(s) in RCA: 407] [Impact Index Per Article: 81.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 11/22/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
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Affiliation(s)
- Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaojing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sara R Savage
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yun Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lisa J Zimmerman
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Therese R Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew C Chambers
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Robbert J C Slebos
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Qianxing Mo
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Ding
- The McDonnell Genome Institute, Washington University in St. Louis, Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108, USA
| | - Matthew Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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Karunanithi S, Simon M, Schulz MH. Automated analysis of small RNA datasets with RAPID. PeerJ 2019; 7:e6710. [PMID: 30993044 PMCID: PMC6462184 DOI: 10.7717/peerj.6710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2.
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Affiliation(s)
- Sivarajan Karunanithi
- Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Universität des Saarlandes, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany
| | - Martin Simon
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Marcel H Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany
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35
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Tumor stem-like cell-derived exosomal RNAs prime neutrophils for facilitating tumorigenesis of colon cancer. J Hematol Oncol 2019; 12:10. [PMID: 30683126 PMCID: PMC6347849 DOI: 10.1186/s13045-019-0699-4] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022] Open
Abstract
Background Cell-cell interactions maintain tissue homeostasis and contribute to dynamic alteration of the tumor microenvironment (TME). Communication between cancer and host cells not only promotes advanced disease aggression but also determines therapeutic response in cancer patients. Despite accumulating evidence supporting the role of tumor-infiltrating immunocytes in modulating tumor immunity, the interplay between heterogeneous tumor subpopulations and immunocytes is elusive. Methods We expanded colorectal cancer stem cells (CRCSCs) as cancer spheroids from the murine colorectal cancer (CRC) cell line CT26 to interrogate tumor-host interactions using a syngeneic tumor model. RNA-sequencing analysis of host cells and tumor exosomes was performed to identify molecular determinants that mediate the crosstalk between CRCSCs and immunocytes. The Cancer Genome Atlas (TCGA) database was used to validate the clinical significance in CRC patients. Results The expanded CT26 cancer spheroids showed increased stemness gene expression, enhanced spheroid and clonogenicity potential, and an elevated tumor-initiating ability, characteristic of CRCSCs. By examining immune cell composition in syngeneic tumor-bearing mice, a systemic increase in CD11b+/Ly6GHigh/Ly6CLow neutrophils was observed in mice bearing CRCSC-derived tumors. An increased secretion of CRCSC exosomes was observed in vitro, and through in vivo tracking, CRCSC exosomes were found to be transported to the bone marrow. Moreover, CRCSC exosomes prolonged the survival of bone marrow-derived neutrophils and engendered a protumoral phenotype in neutrophils. Mechanistically, tumor exosomal tri-phosphate RNAs induced the expression of interleukin-1β (IL-1β) through a pattern recognition-NF-κB signaling axis to sustain neutrophil survival. CRCSC-secreted CXCL1 and CXCL2 then attracted CRCSC-primed neutrophils to promote tumorigenesis of CRC cells via IL-1β. Moreover, neutrophil depletion using a Ly6G-specific antibody (clone 1A8) attenuated the tumorigenicity of CRCSCs. In human specimens, CRC patients exhibiting an active CRCSC signal (Snail+IL8+) showed elevated tumor infiltration of MPO+ neutrophils, and high (in the top 10%) MPO expression predicted poor survival of CRC patients. Conclusions This study elucidates a multistep CRCSC-neutrophil interaction during advanced cancer progression. Strategies targeting aberrant neutrophil activation may be developed for combating CSC-related malignancy. Electronic supplementary material The online version of this article (10.1186/s13045-019-0699-4) contains supplementary material, which is available to authorized users.
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Pain-Associated Transcriptome Changes in Synovium of Knee Osteoarthritis Patients. Genes (Basel) 2018; 9:genes9070338. [PMID: 29973527 PMCID: PMC6070955 DOI: 10.3390/genes9070338] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 06/29/2018] [Indexed: 01/15/2023] Open
Abstract
Joint pain causes significant morbidity in osteoarthritis (OA). The aetiology of joint pain in OA is not well understood. The synovial membrane as an innervated joint structure represents a potential source of peripheral pain in OA. Here we analyse, using a hypothesis-free next generation RNA sequencing, the differences in protein-coding and non-coding transcriptomes in knee synovial tissues from OA patients with high knee pain (n = 5) compared with OA patients with low knee pain (n = 5), as evaluated by visual analogue scale (VAS). We conduct Gene Ontology and pathway analyses on differentially expressed mRNA genes. We identify new protein-coding, long non-coding RNA and microRNA candidates that can be associated with OA joint pain. Top enriched genes in painful OA knees encode neuronal proteins that are known to promote neuronal survival under cellular stress or participate in calcium-dependent synaptic exocytosis and modulation of GABA(γ-aminobutyric acid)ergic activity. Our study uncovers transcriptome changes associated with pain in synovial microenvironment of OA knees. This sets a firm ground for future mechanistic studies and drug discovery to alleviate joint pain in OA.
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Differential Expression of MicroRNAs in Uterine Cervical Cancer and Its Implications in Carcinogenesis; An Integrative Approach. Int J Gynecol Cancer 2018; 28:553-562. [DOI: 10.1097/igc.0000000000001203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
ObjectivesCervical cancer is the second most common cancer in women in developing countries, including India. Recently, microRNAs (miRNAs) are gaining importance in cancer biology because of their involvement in various cellular processes. The present study aimed to profile miRNA expression pattern in cervical cancer, identify their target genes, and understand their role in carcinogenesis.MethodsHuman papillomavirus (HPV) infection statuses in samples were assessed by heminested polymerase chain reaction followed by direct DNA sequencing. Next-generation sequencing and miRNA microarray were used for miRNA profiling in cervical cancer cell lines and tissue samples, respectively. MicroRNA signature was validated by quantitative real-time PCR, and biological significance was elucidated using various in silico analyses.ResultsCervical cancer tissues samples were mostly infected by HPV type 16 (93%). MicroRNA profiling showed that the pattern of miRNA expression differed with respect to HPV positivity in cervical cancer cell lines. However, target and pathway analyses indicated identical involvement of these significantly deregulated miRNAs in HPV-positive cervical cancer cell lines irrespective of type of HPV infected. Microarray profiling identified a set of miRNAs that are differentially deregulated in cervical cancer tissue samples which were validated using quantitative real-time PCR. In silico analyses revealed that the signature miRNAs are mainly involved in PI3K-Akt and mTOR pathways.ConclusionsThe study identified that high-risk HPV induces similar carcinogenic mechanism irrespective of HPV type. The miRNA signature of cervical cancer and their target genes were also elucidated, thereby providing a better insight into the molecular mechanism underlying cervical cancer development.
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Large-Scale Integrative Analysis of Epigenetic Modifications Induced by Isotretinoin, Doxycycline and Metronidazole in Murine Colonic Intestinal Epithelial Cells. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Gangloff S, Achaz G, Francesconi S, Villain A, Miled S, Denis C, Arcangioli B. Quiescence unveils a novel mutational force in fission yeast. eLife 2017; 6. [PMID: 29252184 PMCID: PMC5734874 DOI: 10.7554/elife.27469] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 12/02/2017] [Indexed: 12/18/2022] Open
Abstract
To maintain life across a fluctuating environment, cells alternate between phases of cell division and quiescence. During cell division, the spontaneous mutation rate is expressed as the probability of mutations per generation (Luria and Delbrück, 1943; Lea and Coulson, 1949), whereas during quiescence it will be expressed per unit of time. In this study, we report that during quiescence, the unicellular haploid fission yeast accumulates mutations as a linear function of time. The novel mutational landscape of quiescence is characterized by insertion/deletion (indels) accumulating as fast as single nucleotide variants (SNVs), and elevated amounts of deletions. When we extended the study to 3 months of quiescence, we confirmed the replication-independent mutational spectrum at the whole-genome level of a clonally aged population and uncovered phenotypic variations that subject the cells to natural selection. Thus, our results support the idea that genomes continuously evolve under two alternating phases that will impact on their size and composition.
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Affiliation(s)
- Serge Gangloff
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Guillaume Achaz
- ISYEB UMR7505 CNRS MNHN UPMC EPHE CIRB UMR 7241 CNRS Collège de France INSERM, UPMC, Paris, France
| | - Stefania Francesconi
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | | | - Samia Miled
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Claire Denis
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Benoit Arcangioli
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
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40
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Panero R, Rinaldi A, Memoli D, Nassa G, Ravo M, Rizzo F, Tarallo R, Milanesi L, Weisz A, Giurato G. iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. Bioinformatics 2017; 33:938-940. [PMID: 28057684 DOI: 10.1093/bioinformatics/btw734] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/15/2016] [Indexed: 11/13/2022] Open
Abstract
Summary The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data. Availability and Implementation iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password). Contact aweisz@unisa.it or ggiurato@unisa.it. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Riccardo Panero
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza 52, Torino, Italy
| | - Antonio Rinaldi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Genomix4Life, University of Salerno, Baronissi, SA, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Luciano Milanesi
- Institute for Biomedical Technologies, National Research Council, Segrate, MI, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Genomix4Life, University of Salerno, Baronissi, SA, Italy
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Lu Y, Zhao X, Liu Q, Li C, Graves-Deal R, Cao Z, Singh B, Franklin JL, Wang J, Hu H, Wei T, Yang M, Yeatman TJ, Lee E, Saito-Diaz K, Hinger S, Patton JG, Chung CH, Emmrich S, Klusmann JH, Fan D, Coffey RJ. lncRNA MIR100HG-derived miR-100 and miR-125b mediate cetuximab resistance via Wnt/β-catenin signaling. Nat Med 2017; 23:1331-1341. [PMID: 29035371 PMCID: PMC5961502 DOI: 10.1038/nm.4424] [Citation(s) in RCA: 297] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/08/2017] [Indexed: 12/11/2022]
Abstract
De novo and acquired resistance, which are largely attributed to genetic alterations, are barriers to effective anti-epidermal-growth-factor-receptor (EGFR) therapy. To generate cetuximab-resistant cells, we exposed cetuximab-sensitive colorectal cancer cells to cetuximab in three-dimensional culture. Using whole-exome sequencing and transcriptional profiling, we found that the long non-coding RNA MIR100HG and two embedded microRNAs, miR-100 and miR-125b, were overexpressed in the absence of known genetic events linked to cetuximab resistance. MIR100HG, miR-100 and miR-125b overexpression was also observed in cetuximab-resistant colorectal cancer and head and neck squamous cell cancer cell lines and in tumors from colorectal cancer patients that progressed on cetuximab. miR-100 and miR-125b coordinately repressed five Wnt/β-catenin negative regulators, resulting in increased Wnt signaling, and Wnt inhibition in cetuximab-resistant cells restored cetuximab responsiveness. Our results describe a double-negative feedback loop between MIR100HG and the transcription factor GATA6, whereby GATA6 represses MIR100HG, but this repression is relieved by miR-125b targeting of GATA6. These findings identify a clinically actionable, epigenetic cause of cetuximab resistance.
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Affiliation(s)
- Yuanyuan Lu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Xiaodi Zhao
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Qi Liu
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cunxi Li
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Ramona Graves-Deal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Zheng Cao
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bhuminder Singh
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeffrey L Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jing Wang
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Huaying Hu
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Tianying Wei
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Mingli Yang
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, USA
| | - Timothy J Yeatman
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology and Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kenyi Saito-Diaz
- Department of Cell and Developmental Biology and Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Scott Hinger
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Stephan Emmrich
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | | | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Robert J Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
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Engelmann I, Alidjinou EK, Bertin A, Bossu J, Villenet C, Figeac M, Sane F, Hober D. Persistent coxsackievirus B4 infection induces microRNA dysregulation in human pancreatic cells. Cell Mol Life Sci 2017; 74:3851-3861. [PMID: 28601984 PMCID: PMC11107484 DOI: 10.1007/s00018-017-2567-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/16/2017] [Accepted: 06/06/2017] [Indexed: 12/15/2022]
Abstract
Enterovirus infections are implicated in the development of type 1 diabetes (T1D). MicroRNAs as regulators of gene expression are involved in many physiological and pathological processes. Given that viral infections dysregulate cellular microRNAs, we investigated the impact of persistent coxsackievirus B4 infection on microRNA expression of human pancreatic cells. Next-generation sequencing was used to determine microRNA expression in PANC-1 cells persistently infected (for several weeks) with coxsackievirus B4 and uninfected control cells. Target prediction restricted to T1D risk genes was performed with miRWalk2.0. Functional annotation analysis was performed with DAVID6.7. Expression of selected microRNAs and T1D risk genes was measured by quantitative reverse-transcription polymerase chain reaction. Eighty-one microRNAs were dysregulated in persistently infected PANC-1 cells. Forty-nine of the known fifty-five T1D risk genes were predicted as putative targets of at least one of the dysregulated microRNAs. Most functional annotation terms that were enriched in these 49 putative target genes were related to the immune response or autoimmunity. mRNA levels of AFF3, BACH2, and IL7R differed significantly between persistently infected cells and uninfected cells. This is the first characterization of the microRNA expression profile changes induced by persistent coxsackievirus B4 infection in pancreatic cells. The predicted targeting of genes involved in the immune response and autoimmunity by the dysregulated microRNAs as well as the dysregulated expression of diabetes risk genes shows that persistent coxsackievirus B4 infection profoundly impacts the host cell. These data support the hypothesis of a possible link between persistent coxsackievirus B4 infection and the development of T1D.
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Affiliation(s)
- Ilka Engelmann
- Univ Lille Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Lille, F-59000, France
| | - Enagnon K Alidjinou
- Univ Lille Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Lille, F-59000, France
| | - Antoine Bertin
- Univ Lille Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Lille, F-59000, France
| | - Johann Bossu
- Univ Lille Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Lille, F-59000, France
| | - Céline Villenet
- CHU Lille, Plate-forme de Génomique Fonctionnelle et Structurale, Lille, F-59000, France
| | - Martin Figeac
- CHU Lille, Plate-forme de Génomique Fonctionnelle et Structurale, Lille, F-59000, France
| | - Famara Sane
- Univ Lille Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Lille, F-59000, France
| | - Didier Hober
- Univ Lille Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Lille, F-59000, France.
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de Felippes FF, Marchais A, Sarazin A, Oberlin S, Voinnet O. A single miR390 targeting event is sufficient for triggering TAS3-tasiRNA biogenesis in Arabidopsis. Nucleic Acids Res 2017; 45:5539-5554. [PMID: 28334969 PMCID: PMC5435969 DOI: 10.1093/nar/gkx119] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023] Open
Abstract
In plants, tasiRNAs form a class of endogenous secondary siRNAs produced through the action of RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) upon microRNA-mediated cleavage of non-coding TAS RNAs. In Arabidopsis thaliana, TAS1, TAS2 and TAS4 tasiRNA production proceeds via a single cleavage event mediated by 22nt-long or/and asymmetric miRNAs in an ARGONAUTE-1 (AGO1)-dependent manner. By contrast, tasiRNA production from TAS3 seems to follow the so-called ‘two-hit’ process, where dual targeting of TAS3, specifically mediated by the 21nt-long, symmetric miR390, initiates AGO7-dependent tasiRNA production. Interestingly, features for TAS3 tasiRNA production differ in other plant species and we show here that such features also enable TAS3 tasiRNA biogenesis in Arabidopsis, and that a single miR390 targeting event is, in fact, sufficient for this process, suggesting that the ‘one-hit’ model underpins all the necessary rudiments of secondary siRNA biogenesis from plant TAS transcripts. Further results suggest that the two-hit configuration likely enhances the fidelity of tasiRNA production and, hence, the accuracy of downstream gene regulation. Finally, we show that a ‘non-cleavable one-hit’ process allows tasiRNA production from both TAS1 and TAS3 transcripts, indicating that RDR6 recruitment does not require miRNA cleavage, nor does the recruitment, as we further show, of SUPRRESSOR-OF-GENE-SILENCING-3, indispensable for tasiRNA generation.
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Affiliation(s)
- Felipe Fenselau de Felippes
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Antonin Marchais
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Alexis Sarazin
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Stefan Oberlin
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Olivier Voinnet
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
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Cottard F, Madi-Berthélémy PO, Erdmann E, Schaff-Wendling F, Keime C, Ye T, Kurtz JE, Céraline J. Dual effects of constitutively active androgen receptor and full-length androgen receptor for N-cadherin regulation in prostate cancer. Oncotarget 2017; 8:72008-72020. [PMID: 29069764 PMCID: PMC5641107 DOI: 10.18632/oncotarget.18270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 05/12/2017] [Indexed: 12/18/2022] Open
Abstract
Constitutively active androgen receptor (AR) variants have been involved in the expression of mesenchymal markers such as N-cadherin in prostate cancer (PCa). However, the underlying molecular mechanisms remain elusive. It remains unclear, whether N-cadherin gene (CDH2) is a direct transcriptional target of AR variants or whether the observed upregulation is due to indirect effects through additional regulatory factors. Moreover, the specific contribution of full-length AR and AR variants in N-cadherin regulation in PCa has never been explored deeply. To investigate this, we artificially mimicked the co-expression of AR variants together with a full-length AR and performed miRNA-seq, RNA-seq and ChIP assays. Our results were in favor of a direct AR variants action on CDH2. Our data also revealed a distinctive mode of action between full-length AR and AR variants to regulate N-cadherin expression. Both wild type AR and AR variants could interact with a regulatory element in intron 1 of CDH2. However, a higher histone H4 acetylation in this genomic region was only observed with AR variants. This suggests that full-length AR may play an occluding function to impede CDH2 upregulation. Our data further highlighted a negative effect of AR variants on the expression of the endogenous full-length AR in LNCaP. These differences in the mode of action of AR variants and full-length AR for the control of one key gene for prostate cancer progression could be worth considering for targeting AR variants in PCa.
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Affiliation(s)
| | | | - Eva Erdmann
- Université de Strasbourg, INSERM, FMTS, Strasbourg, France
| | - Frédérique Schaff-Wendling
- Université de Strasbourg, INSERM, FMTS, Strasbourg, France.,Service d'Onco-Hématologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Céline Keime
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Tao Ye
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Jean-Emmanuel Kurtz
- Université de Strasbourg, INSERM, FMTS, Strasbourg, France.,Service d'Onco-Hématologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jocelyn Céraline
- Université de Strasbourg, INSERM, FMTS, Strasbourg, France.,Service d'Onco-Hématologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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45
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Lopez JP, Fiori LM, Cruceanu C, Lin R, Labonte B, Cates HM, Heller EA, Vialou V, Ku SM, Gerald C, Han MH, Foster J, Frey BN, Soares CN, Müller DJ, Farzan F, Leri F, MacQueen GM, Feilotter H, Tyryshkin K, Evans KR, Giacobbe P, Blier P, Lam RW, Milev R, Parikh SV, Rotzinger S, Strother SC, Lewis CM, Aitchison KJ, Wittenberg GM, Mechawar N, Nestler EJ, Uher R, Kennedy SH, Turecki G. MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes. Nat Commun 2017; 8:15497. [PMID: 28530238 PMCID: PMC5477510 DOI: 10.1038/ncomms15497] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/30/2017] [Indexed: 02/08/2023] Open
Abstract
Antidepressants (ADs) are the most common treatment for major depressive disorder (MDD). However, only ∼30% of patients experience adequate response after a single AD trial, and this variability remains poorly understood. Here, we investigated microRNAs (miRNAs) as biomarkers of AD response using small RNA-sequencing in paired samples from MDD patients enrolled in a large, randomized placebo-controlled trial of duloxetine collected before and 8 weeks after treatment. Our results revealed differential expression of miR-146a-5p, miR-146b-5p, miR-425-3p and miR-24-3p according to treatment response. These results were replicated in two independent clinical trials of MDD, a well-characterized animal model of depression, and post-mortem human brains. Furthermore, using a combination of bioinformatics, mRNA studies and functional in vitro experiments, we showed significant dysregulation of genes involved in MAPK/Wnt signalling pathways. Together, our results indicate that these miRNAs are consistent markers of treatment response and regulators of the MAPK/Wnt systems. Antidepressant drugs are the most common treatment for depressive episodes but only a fraction of patients experience adequate response. Here the authors find dysregulation of miRNAs in peripheral blood samples from depressed patients after antidepressant treatment, and show that the miRNAs are regulators of psychiatrically relevant signalling pathways.
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Affiliation(s)
- Juan Pablo Lopez
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada H4H 1R3
| | - Laura M Fiori
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada H4H 1R3
| | - Cristiana Cruceanu
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada H4H 1R3
| | - Rixing Lin
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada H4H 1R3
| | - Benoit Labonte
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hannah M Cates
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Elizabeth A Heller
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Vincent Vialou
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Stacy M Ku
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Christophe Gerald
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ming-Hu Han
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jane Foster
- Department of Psychiatry, University Health Network, University of Toronto, Toronto, Ontario, Canada M5T 2S8
| | - Benicio N Frey
- McMaster University and St Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada L8S 4L8
| | - Claudio N Soares
- St Michael's Hospital, Toronto, Ontario, Canada M5B 1M4.,Department of Psychiatry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Daniel J Müller
- Department of Psychiatry, University Health Network, University of Toronto, Toronto, Ontario, Canada M5T 2S8.,Centre for Addiction and Mental Health, Toronto, Ontario, Canada M6J 1A8
| | - Faranak Farzan
- Department of Psychiatry, University Health Network, University of Toronto, Toronto, Ontario, Canada M5T 2S8.,Centre for Addiction and Mental Health, Toronto, Ontario, Canada M6J 1A8.,School of Mechatronic Systems Engineering, Surrey, British Columbia, Canada V3T 0A3
| | | | - Glenda M MacQueen
- University of Calgary Hotchkiss Brain Institute, Calgary, Alberta, Canada T2N 1N4
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Kenneth R Evans
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada K7L 3N6.,Indoc Research, Toronto, Ontario, Canada M5A 1N1
| | - Peter Giacobbe
- Department of Psychiatry, University Health Network, University of Toronto, Toronto, Ontario, Canada M5T 2S8
| | - Pierre Blier
- University of Ottawa Institute of Mental Health Research, Ottawa, Ontario, Canada K1Z 7K4
| | - Raymond W Lam
- University of British Columbia and Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada V6T 2A1
| | - Roumen Milev
- Queen's University, Providence Care, Mental Health Services, Kingston, Ontario, Canada K7L 4X3
| | | | - Susan Rotzinger
- Department of Psychiatry, University Health Network, University of Toronto, Toronto, Ontario, Canada M5T 2S8
| | - Steven C Strother
- Rotman Research Institute at Baycrest Centre, Toronto, Ontario, Canada M6A 2E1
| | - Cathryn M Lewis
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology &Neuroscience, King's College London, London SE5 8AF, UK
| | - Katherine J Aitchison
- Departments of Psychiatry and Medical Genetics, University of Alberta, Edmonton, Alberta, Canada T6G 2B7.,Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 2E2
| | | | - Naguib Mechawar
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada H4H 1R3
| | - Eric J Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Rudolf Uher
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology &Neuroscience, King's College London, London SE5 8AF, UK.,Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 2E2
| | - Sidney H Kennedy
- Department of Psychiatry, University Health Network, University of Toronto, Toronto, Ontario, Canada M5T 2S8
| | - Gustavo Turecki
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada H4H 1R3
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46
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Sui X, Zheng Y, Li R, Padmanabhan C, Tian T, Groth-Helms D, Keinath AP, Fei Z, Wu Z, Ling KS. Molecular and Biological Characterization of Tomato mottle mosaic virus and Development of RT-PCR Detection. PLANT DISEASE 2017; 101:704-711. [PMID: 30678578 DOI: 10.1094/pdis-10-16-1504-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tomato mottle mosaic virus (ToMMV) was first identified in 2013 as a novel tobamovirus infecting tomatoes in Mexico. In just a few years, ToMMV has been identified in several countries around the world, including the United States. In the present study, we characterized the molecular, serological, and biological properties of ToMMV and developed a species-specific RT-PCR to detect three tomato-infecting tobamoviruses: Tobacco mosaic virus (TMV), Tomato mosaic virus (ToMV), and ToMMV. Previously, ToMMV has been reported in Florida and New York. In this study, we made two new reports on the occurrences of ToMMV on tomatoes in California and South Carolina. Their complete genome sequences were obtained and their genetic relationships to other tobamoviruses evaluated. In host range studies, some differential responses in host plants were also identified between ToMMV and ToMV. To alleviate cross-serological reactivity among the tomato-infecting tobamoviruses, a new multiplex RT-PCR was developed to allow for species-specific detection and identification of TMV, ToMV, and ToMMV. In addition, we observed resistance breaking by ToMMV on selected tomato cultivars that were resistant to ToMV. This has caused serious concerns to tomato growers worldwide. In conclusion, the characterization in molecular and biological properties of ToMMV would provide us with fundamental knowledge to manage this emerging virus on tomato and other solanaceous crops in the U.S. and around the world.
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Affiliation(s)
- Xuelian Sui
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC, and Department of Plant Protection, Fujian Agriculture and Forest University, Fuzhou, China
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY
| | - Rugang Li
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC
| | | | - Tongyan Tian
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento
| | | | - Anthony P Keinath
- Clemson University, Coastal Research and Education Center, Charleston, SC
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, and USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY
| | - Zujian Wu
- Department of Plant Protection, Fujian Agriculture and Forest University, Fuzhou, China
| | - Kai-Shu Ling
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC
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Frank-Bertoncelj M, Trenkmann M, Klein K, Karouzakis E, Rehrauer H, Bratus A, Kolling C, Armaka M, Filer A, Michel BA, Gay RE, Buckley CD, Kollias G, Gay S, Ospelt C. Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions. Nat Commun 2017; 8:14852. [PMID: 28332497 PMCID: PMC5376654 DOI: 10.1038/ncomms14852] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/02/2017] [Indexed: 01/15/2023] Open
Abstract
A number of human diseases, such as arthritis and atherosclerosis, include characteristic pathology in specific anatomical locations. Here we show transcriptomic differences in synovial fibroblasts from different joint locations and that HOX gene signatures reflect the joint-specific origins of mouse and human synovial fibroblasts and synovial tissues. Alongside DNA methylation and histone modifications, bromodomain and extra-terminal reader proteins regulate joint-specific HOX gene expression. Anatomical transcriptional diversity translates into joint-specific synovial fibroblast phenotypes with distinct adhesive, proliferative, chemotactic and matrix-degrading characteristics and differential responsiveness to TNF, creating a unique microenvironment in each joint. These findings indicate that local stroma might control positional disease patterns not only in arthritis but in any disease with a prominent stromal component. Arthritis affects different joints variably despite systemic inflammatory cues. Here the authors show anatomical differences in the transcriptome, epigenome and function of synovial fibroblasts that might affect susceptibility to site-specific joint diseases.
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Affiliation(s)
- Mojca Frank-Bertoncelj
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Michelle Trenkmann
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Kerstin Klein
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Emmanuel Karouzakis
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anna Bratus
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - Maria Armaka
- Division of Immunology, Biomedical Sciences Research Center 'Alexander Fleming', 34, Fleming Street, 16672 Vari, Attica, Greece
| | - Andrew Filer
- Institute of Inflammation and Ageing (IIA), University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WB, UK
| | - Beat A Michel
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Renate E Gay
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Christopher D Buckley
- Institute of Inflammation and Ageing (IIA), University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WB, UK
| | - George Kollias
- Division of Immunology, Biomedical Sciences Research Center 'Alexander Fleming', 34, Fleming Street, 16672 Vari, Attica, Greece.,Department of Experimental Physiology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Goudi, Athens, Greece
| | - Steffen Gay
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland.,Center of Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Caroline Ospelt
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland.,Center of Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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48
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Tarabay Y, Achour M, Teletin M, Ye T, Teissandier A, Mark M, Bourc'his D, Viville S. Tex19 paralogs are new members of the piRNA pathway controlling retrotransposon suppression. J Cell Sci 2017; 130:1463-1474. [PMID: 28254886 DOI: 10.1242/jcs.188763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 02/27/2017] [Indexed: 01/29/2023] Open
Abstract
Tex19 genes are mammalian specific and duplicated to give Tex19.1 and Tex19.2 in some species, such as the mouse and rat. It has been demonstrated that mutant Tex19.1 males display a variable degree of infertility whereas they all upregulate MMERVK10C transposons in their germ line. In order to study the function of both paralogs in the mouse, we generated and studied Tex19 double knockout (Tex19DKO) mutant mice. Adult Tex19DKO males exhibited a fully penetrant phenotype, similar to the most severe phenotype observed in the single Tex19.1KO mice, with small testes and impaired spermatogenesis, defects in meiotic chromosome synapsis, persistence of DNA double-strand breaks during meiosis, lack of post-meiotic germ cells and upregulation of MMERVK10C expression. The phenotypic similarities to mice with knockouts in the Piwi family genes prompted us to check and then demonstrate, by immunoprecipitation and GST pulldown followed by mass spectrometry analyses, that TEX19 paralogs interact with PIWI proteins and the TEX19 VPTEL domain directly binds Piwi-interacting RNAs (piRNAs) in adult testes. We therefore identified two new members of the postnatal piRNA pathway.
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Affiliation(s)
- Yara Tarabay
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Mayada Achour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Marius Teletin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France.,Service de Biologie de la Reproduction, Centre Hospitalier Universitaire, Strasbourg 67000, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Aurélie Teissandier
- Institut Curie, department of Genetics and Developmental Biology, CNRS UMR3215, INSERM U934, 75005 Paris, France
| | - Manuel Mark
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France.,Service de Biologie de la Reproduction, Centre Hospitalier Universitaire, Strasbourg 67000, France
| | - Déborah Bourc'his
- Institut Curie, department of Genetics and Developmental Biology, CNRS UMR3215, INSERM U934, 75005 Paris, France
| | - Stéphane Viville
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France .,Centre Hospitalier Universitaire, Strasbourg 67000, France
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49
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Alidjinou EK, Engelmann I, Bossu J, Villenet C, Figeac M, Romond MB, Sané F, Hober D. Persistence of Coxsackievirus B4 in pancreatic ductal-like cells results in cellular and viral changes. Virulence 2017; 8:1229-1244. [PMID: 28112573 DOI: 10.1080/21505594.2017.1284735] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Although known as cytolytic viruses, group B coxackieviruses (CVB) are able to establish a persistent infection in vitro and in vivo. Viral persistence has been reported as a key mechanism in the pathogenesis of CVB-associated chronic diseases such as type 1 diabetes (T1D). The impact of CVB4 persistence on human pancreas ductal-like cells was investigated. METHODS A persistent CVB4 infection was established in ductal-like cells. PDX-1 expression, resistance to CVB4-induced lysis and CAR expression were evaluated. The profile of cellular microRNAs (miRNAs) was investigated through miRNA-sequencing. Viral phenotypic changes were examined, and genomic modifications were assessed by sequencing of the viral genome. RESULTS The CVB4 persistence in ductal-like cells was productive, with continuous release of infectious particles. Persistently infected cells displayed a resistance to CVB4-induced lysis upon superinfection and expression of PDX-1 and CAR was decreased. These changes were maintained even after virus clearance. The patterns of cellular miRNA expression in mock-infected and in CVB4-persistently infected ductal-like cells were clearly different. The persistent infection-derived virus (PIDV) was still able to induce cytopathic effect but its plaques were smaller than the parental virus. Several mutations appeared in various PIDV genome regions, but amino acid substitutions did not affect the predicted site of interaction with CAR. CONCLUSION Cellular and viral changes occur during persistent infection of human pancreas ductal-like cells with CVB4. The persistence of cellular changes even after virus clearance supports the hypothesis of a long-lasting impact of persistent CVB infection on the cells.
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Affiliation(s)
- E K Alidjinou
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - I Engelmann
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - J Bossu
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - C Villenet
- b Plate-forme de Génomique Fonctionnelle et Structurale , CHU de Lille , France
| | - M Figeac
- b Plate-forme de Génomique Fonctionnelle et Structurale , CHU de Lille , France
| | - M-B Romond
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - F Sané
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - D Hober
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
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50
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Han Y, He X. Integrating Epigenomics into the Understanding of Biomedical Insight. Bioinform Biol Insights 2016; 10:267-289. [PMID: 27980397 PMCID: PMC5138066 DOI: 10.4137/bbi.s38427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/01/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research. Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets. In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources and integrative analysis approaches, and finally outline the challenges and future directions in computational epigenomics.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.; Present address: Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ximiao He
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.; Present address: Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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