Pilot_experiment_on_functional_genomics_in_osteoarthritis_RNA

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Dataset ID	Description	Technology	Samples
EGAD00001001331	The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.	Illumina HiSeq 2000	24

Publications	Citations
Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis. Steinberg J, Ritchie GRS, Roumeliotis TI, Jayasuriya RL, Clark MJ, Brooks RA, Binch ALA, Shah KM, Coyle R, Pardo M, Le Maitre CL, Ramos YFM, Nelissen RGHH, Meulenbelt I, McCaskie AW, Choudhary JS, Wilkinson JM, Zeggini E. Sci Rep 7: 2017 8935	64
Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis. Zengini E, Hatzikotoulas K, Tachmazidou I, Steinberg J, Hartwig FP, Southam L, Hackinger S, Boer CG, Styrkarsdottir U, Gilly A, Suveges D, Killian B, Ingvarsson T, Jonsson H, Babis GC, McCaskie A, Uitterlinden AG, van Meurs JBJ, Thorsteinsdottir U, Stefansson K, Davey Smith G, Wilkinson JM, Zeggini E. Nat Genet 50: 2018 549-558	154
Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data. Tachmazidou I, Hatzikotoulas K, Southam L, Esparza-Gordillo J, Haberland V, Zheng J, Johnson T, Koprulu M, Zengini E, Steinberg J, Wilkinson JM, Bhatnagar S, Hoffman JD, Buchan N, Süveges D, arcOGEN Consortium, Yerges-Armstrong L, Smith GD, Gaunt TR, Scott RA, McCarthy LC, Zeggini E. Nat Genet 51: 2019 230-236	247
Accelerating functional gene discovery in osteoarthritis. Butterfield NC, Curry KF, Steinberg J, Dewhurst H, Komla-Ebri D, Mannan NS, Adoum AT, Leitch VD, Logan JG, Waung JA, Ghirardello E, Southam L, Youlten SE, Wilkinson JM, McAninch EA, Vancollie VE, Kussy F, White JK, Lelliott CJ, Adams DJ, Jacques R, Bianco AC, Boyde A, Zeggini E, Croucher PI, Williams GR, Bassett JHD. Nat Commun 12: 2021 467	26
A molecular quantitative trait locus map for osteoarthritis. Steinberg J, Southam L, Roumeliotis TI, Clark MJ, Jayasuriya RL, Swift D, Shah KM, Butterfield NC, Brooks RA, McCaskie AW, Bassett JHD, Williams GR, Choudhary JS, Wilkinson JM, Zeggini E. Nat Commun 12: 2021 1309	39
Linking chondrocyte and synovial transcriptional profile to clinical phenotype in osteoarthritis. Steinberg J, Southam L, Fontalis A, Clark MJ, Jayasuriya RL, Swift D, Shah KM, Brooks RA, McCaskie AW, Wilkinson JM, Zeggini E. Ann Rheum Dis 80: 2021 1070-1074	22
A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis. Katsoula G, Steinberg J, Tuerlings M, Coutinho de Almeida R, Southam L, Swift D, Meulenbelt I, Wilkinson JM, Zeggini E. Hum Mol Genet 31: 2022 2090-2105	11
Identification of therapeutic targets in osteoarthritis by combining heterogeneous transcriptional datasets, drug-induced expression profiles, and known drug-target interactions. Costa MC, Angelini C, Franzese M, Iside C, Salvatore M, Laezza L, Napolitano F, Ceccarelli M. J Transl Med 22: 2024 281	2
Primary cartilage transcriptional signatures reflect cell-type-specific molecular pathways underpinning osteoarthritis. Katsoula G, Lawrence JEG, Arruda AL, Tutino M, Balogh P, Southam L, Swift D, Behjati S, Teichmann SA, Wilkinson JM, Zeggini E. Am J Hum Genet 111: 2024 2735-2755	0