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      Osteoarthritis year in review: genetics, genomics, epigenetics

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          Summary

          Objective

          In this review, we have highlighted the advances over the past year in genetics, genomics and epigenetics in the field of osteoarthritis (OA).

          Methods

          A literature search of PubMed was performed using the criteria: “osteoarthritis” and one of the following terms “genetic(s), genomic(s), epigenetic(s), polymorphism, noncoding ribonucleic acid (RNA), microRNA, long noncoding RNA, lncRNA, circular RNA, RNA sequencing (RNA-seq), single cell sequencing, transcriptomics, or deoxyribonucleic acid (DNA) methylation between April 01, 2020 and April 30, 2021.

          Results

          In total we identified 765 unique publications, which eventually reduced to 380 of relevance to the field as judged by two assessors. Many of these studies included multiple search terms. We summarised advances relating to genetics, functional genetics, genomics and epigenetics, focusing on our personal key papers during the year.

          Conclusions

          This year few studies have identified new genetic variants contributing to OA susceptibility, but a focus has been on refining risk loci or their functional validation. The use of new technologies together with investigating the cross-talk between multiple tissue types, greater sample sizes and/or better patient classification (OA subtypes) will continue to increase our knowledge of disease mechanisms and progress towards understanding and treating OA.

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          Most cited references73

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          UpSetR: an R package for the visualization of intersecting sets and their properties

          Abstract Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability and implementation: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/. Contact: nils@hms.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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            Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

            Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.
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              Endogenous microRNA sponges: evidence and controversy.

              The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.
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                Author and article information

                Contributors
                Journal
                Osteoarthritis Cartilage
                Osteoarthritis Cartilage
                Osteoarthritis and Cartilage
                W.B. Saunders For The Osteoarthritis Research Society
                1063-4584
                1522-9653
                1 February 2022
                February 2022
                : 30
                : 2
                : 216-225
                Affiliations
                [1]Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
                Author notes
                []Address correspondence and reprint requests to: D.A. Young, Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK. Tel.: 44-191-2418831. d.a.young@ 123456ncl.ac.uk
                Article
                S1063-4584(21)00963-8
                10.1016/j.joca.2021.11.004
                8811265
                34774787
                b023590c-2440-4286-98df-f820145b4fde
                © 2021 The Author(s)

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 14 September 2021
                : 2 November 2021
                Categories
                Review

                Rheumatology
                osteoarthritis,genetics,genomics,epigenetics,microrna,circrna,lncrna
                Rheumatology
                osteoarthritis, genetics, genomics, epigenetics, microrna, circrna, lncrna

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