Literature DB >> 31000790

Insights into rheumatic diseases from next-generation sequencing.

Laura T Donlin1,2,3, Sung-Ho Park1,2, Eugenia Giannopoulou1,2,4, Aleksandra Ivovic5, Kyung-Hyun Park-Min1,2,3, Richard M Siegel5, Lionel B Ivashkiv6,7,8,9.   

Abstract

Rheumatic diseases have complex aetiologies that are not fully understood, which makes the study of pathogenic mechanisms in these diseases a challenge for researchers. Next-generation sequencing (NGS) and related omics technologies, such as transcriptomics, epigenomics and genomics, provide an unprecedented genome-wide view of gene expression, environmentally responsive epigenetic changes and genetic variation. The integrated application of NGS technologies to samples from carefully phenotyped clinical cohorts of patients has the potential to solve remaining mysteries in the pathogenesis of several rheumatic diseases, to identify new therapeutic targets and to underpin a precision medicine approach to the diagnosis and treatment of rheumatic diseases. This Review provides an overview of the NGS technologies available, showcases important advances in rheumatic disease research already powered by these technologies and highlights NGS approaches that hold particular promise for generating new insights and advancing the field.

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Year:  2019        PMID: 31000790      PMCID: PMC6673602          DOI: 10.1038/s41584-019-0217-7

Source DB:  PubMed          Journal:  Nat Rev Rheumatol        ISSN: 1759-4790            Impact factor:   20.543


  98 in total

Review 1.  Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics.

Authors:  Romain Banchereau; Alma-Martina Cepika; Jacques Banchereau; Virginia Pascual
Journal:  Annu Rev Immunol       Date:  2017-01-30       Impact factor: 28.527

2.  Effects of cold application on maximal isometric contraction.

Authors:  H L McGown
Journal:  Phys Ther       Date:  1967-03

Review 3.  Immune cell profiling to guide therapeutic decisions in rheumatic diseases.

Authors:  Joerg Ermann; Deepak A Rao; Nikola C Teslovich; Michael B Brenner; Soumya Raychaudhuri
Journal:  Nat Rev Rheumatol       Date:  2015-06-02       Impact factor: 20.543

4.  Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients.

Authors:  Romain Banchereau; Seunghee Hong; Brandi Cantarel; Nicole Baldwin; Jeanine Baisch; Michelle Edens; Alma-Martina Cepika; Peter Acs; Jacob Turner; Esperanza Anguiano; Parvathi Vinod; Shaheen Khan; Gerlinde Obermoser; Derek Blankenship; Edward Wakeland; Lorien Nassi; Alisa Gotte; Marilynn Punaro; Yong-Jun Liu; Jacques Banchereau; Jose Rossello-Urgell; Tracey Wright; Virginia Pascual
Journal:  Cell       Date:  2016-06-02       Impact factor: 41.582

Review 5.  Rebooting Human Immunology.

Authors:  Mark M Davis; Petter Brodin
Journal:  Annu Rev Immunol       Date:  2018-02-28       Impact factor: 28.527

6.  Transcriptome Sequencing (RNAseq) Enables Utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development.

Authors:  Oystein Eikrem; Christian Beisland; Karin Hjelle; Arnar Flatberg; Andreas Scherer; Lea Landolt; Trude Skogstrand; Sabine Leh; Vidar Beisvag; Hans-Peter Marti
Journal:  PLoS One       Date:  2016-02-22       Impact factor: 3.240

Review 7.  RNA-Seq differential expression analysis: An extended review and a software tool.

Authors:  Juliana Costa-Silva; Douglas Domingues; Fabricio Martins Lopes
Journal:  PLoS One       Date:  2017-12-21       Impact factor: 3.240

8.  Three-dimensional intact-tissue sequencing of single-cell transcriptional states.

Authors:  Xiao Wang; William E Allen; Matthew A Wright; Emily L Sylwestrak; Nikolay Samusik; Sam Vesuna; Kathryn Evans; Cindy Liu; Charu Ramakrishnan; Jia Liu; Garry P Nolan; Felice-Alessio Bava; Karl Deisseroth
Journal:  Science       Date:  2018-06-21       Impact factor: 47.728

9.  Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics.

Authors:  Glynn Dennis; Cécile T J Holweg; Sarah K Kummerfeld; David F Choy; A Francesca Setiadi; Jason A Hackney; Peter M Haverty; Houston Gilbert; Wei Yu Lin; Lauri Diehl; S Fischer; An Song; David Musselman; Micki Klearman; Cem Gabay; Arthur Kavanaugh; Judith Endres; David A Fox; Flavius Martin; Michael J Townsend
Journal:  Arthritis Res Ther       Date:  2014-04-30       Impact factor: 5.156

Review 10.  Translating RNA sequencing into clinical diagnostics: opportunities and challenges.

Authors:  Sara A Byron; Kendall R Van Keuren-Jensen; David M Engelthaler; John D Carpten; David W Craig
Journal:  Nat Rev Genet       Date:  2016-03-21       Impact factor: 53.242

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  11 in total

Review 1.  Synovial Tissue: Cellular and Molecular Phenotyping.

Authors:  Sara Shanaj; Laura T Donlin
Journal:  Curr Rheumatol Rep       Date:  2019-08-29       Impact factor: 4.592

Review 2.  Peptide-Based Vaccination Therapy for Rheumatic Diseases.

Authors:  Bin Wang; Shiju Chen; Qing Zheng; Yuan Liu; Guixiu Shi
Journal:  J Immunol Res       Date:  2020-03-18       Impact factor: 4.818

3.  Longitudinal profiling of the gut microbiome in patients with psoriatic arthritis and ankylosing spondylitis: a multicentre, prospective, observational study.

Authors:  Jesus Miguens Blanco; Federica Borghese; Neil McHugh; Peter Kelleher; Raj Sengupta; Julian R Marchesi; Sonya Abraham
Journal:  BMC Rheumatol       Date:  2020-11-10

4.  Heritability of Oral Microbiota and Immune Responses to Oral Bacteria.

Authors:  Anders Esberg; Simon Haworth; Ralf Kuja-Halkola; Patrik K E Magnusson; Ingegerd Johansson
Journal:  Microorganisms       Date:  2020-07-27

5.  Epigenetic control of ion channel expression and cell-specific splicing in nociceptors: Chronic pain mechanisms and potential therapeutic targets.

Authors:  Diane Lipscombe; E Javier Lopez-Soto
Journal:  Channels (Austin)       Date:  2021-12       Impact factor: 2.581

Review 6.  Current status of use of high throughput nucleotide sequencing in rheumatology.

Authors:  Sebastian Boegel; John C Castle; Andreas Schwarting
Journal:  RMD Open       Date:  2021-01

Review 7.  Nutrition and Rheumatoid Arthritis in the 'Omics' Era.

Authors:  Manuela Cassotta; Tamara Y Forbes-Hernandez; Danila Cianciosi; Maria Elexpuru Zabaleta; Sandra Sumalla Cano; Irma Dominguez; Beatriz Bullon; Lucia Regolo; Josè Miguel Alvarez-Suarez; Francesca Giampieri; Maurizio Battino
Journal:  Nutrients       Date:  2021-02-26       Impact factor: 5.717

8.  CD127 imprints functional heterogeneity to diversify monocyte responses in inflammatory diseases.

Authors:  Bin Zhang; Yuan Zhang; Lei Xiong; Yuzhe Li; Yunliang Zhang; Jiuliang Zhao; Hui Jiang; Can Li; Yunqi Liu; Xindong Liu; Haofei Liu; Yi-Fang Ping; Qiangfeng Cliff Zhang; Zheng Zhang; Xiu-Wu Bian; Yan Zhao; Xiaoyu Hu
Journal:  J Exp Med       Date:  2022-01-11       Impact factor: 17.579

9.  Genetic Factors of Predisposition and Clinical Characteristics of Rheumatoid Arthritis in Russian Patients.

Authors:  Ekaterina A Vetchinkina; Dmitry S Mikhaylenko; Ekaterina B Kuznetsova; Tatiana A Deryagina; Ekaterina A Alekseeva; Irina V Bure; Andrey A Zamyatnin; Marina V Nemtsova
Journal:  J Pers Med       Date:  2021-05-25

10.  Dialogue: High-throughput studies in rheumatology: time for unsupervised clustering?

Authors:  George Bertsias
Journal:  Lupus Sci Med       Date:  2021-12
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