A transcriptional signature of fatigue derived from patients with primary Sjogren's Syndrome

Katherine James, Shereen Al-Ali, Jessica Tarn, Simon J. Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin T. Pease, Paul Emery, Peter Lanyon, John A. Hunter, Monica Gupta, Michele Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren & 91 others Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, Frances Hall, Elalaine C. Bacabac, Kuntal Chadravarty, Shamin Lamabadusuriya, Rashidat Adeniba, John Hamburger, Andrea Richards, Saaeha Rauz, Sue Brailsford, Joanne Logan, Diarmuid Mulherin, Jacqueline Andrews, Alison McManus, Alison Booth, Theodoros Dimitroulas, Lucy Kadiki, Daljit Kaur, George Kitas, Mark Lloyd, Lisa Moore, Esther Gordon, Cathy Lawson, Lesley Stirton, Gill Ortiz, Gavin Clunie, Ginny Rose, Sue Cuckow, Susan Knight, Deborah Symmons, Beverley Jones, Andrew Carr, Katherine Collins, Ian Corbett, Christine Downie, Suzanne Edgar, Marco Carrozzo, Francisco Figuereido, Heather Foggo, Katie Hackett, Iain Macleod, Philip Mawson, Andini Natasari, Philip Stocks, Adrian Jones, Alice Muir, Paula White, Susan Pugmire, Marianne Watkins, Anne Field, Stephen Kaye, Devesh Mewar, Patricia Medcalf, Pamela Tomlinson, Debbie Whiteside, John Pauling, Julie James, Nike Olaitan, Jayne McDermott, Olivia Godia, Elizabeth Kidd, Lynne Palmer, Victoria Katsande, Pamela Long, Charles Li, Usha Chandra, Kirsten MacKay, Stefano Fedele, Ada Ferenkeh-Koroma, Helena Maconnell, Stephen Porter, Paul Allcoat, Anil Wipat, Julia Newton, David E. Jones, John Isaacs, Jennifer Hallinan, Wan Fai Ng, UK Primary Sjögren's Syndrome Registry

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Abstract

Background: Fatigue is a debilitating condition with a significant impact on patients' quality of life. Fatigue is frequently reported by patients suffering from primary Sjögren's Syndrome (pSS), a chronic autoimmune condition characterised by dryness of the eyes and the mouth. However, although fatigue is common in pSS, it does not manifest in all sufferers, providing an excellent model with which to explore the potential underpinning biological mechanisms. Methods: Whole blood samples from 133 fully-phenotyped pSS patients stratified for the presence of fatigue, collected by the UK primary Sjögren's Syndrome Registry, were used for whole genome microarray. The resulting data were analysed both on a gene by gene basis and using pre-defined groups of genes. Finally, gene set enrichment analysis (GSEA) was used as a feature selection technique for input into a support vector machine (SVM) classifier. Classification was assessed using area under curve (AUC) of receiver operator characteristic and standard error of Wilcoxon statistic, SE(W). Results: Although no genes were individually found to be associated with fatigue, 19 metabolic pathways were enriched in the high fatigue patient group using GSEA. Analysis revealed that these enrichments arose from the presence of a subset of 55 genes. A radial kernel SVM classifier with this subset of genes as input displayed significantly improved performance over classifiers using all pathway genes as input. The classifiers had AUCs of 0.866 (SE(W) 0.002) and 0.525 (SE(W) 0.006), respectively. Conclusions: Systematic analysis of gene expression data from pSS patients discordant for fatigue identified 55 genes which are predictive of fatigue level using SVM classification. This list represents the first step in understanding the underlying pathophysiological mechanisms of fatigue in patients with pSS.

Original languageEnglish
Article numbere0143970
Pages (from-to)1-21
Number of pages21
JournalPLoS ONE
Volume10
Issue number12
DOIs
Publication statusPublished - 22 Dec 2015
Externally publishedYes

Bibliographical note

Copyright the Author(s) 2015. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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    James, K., Al-Ali, S., Tarn, J., Cockell, S. J., Gillespie, C. S., Hindmarsh, V., ... UK Primary Sjögren's Syndrome Registry (2015). A transcriptional signature of fatigue derived from patients with primary Sjogren's Syndrome. PLoS ONE, 10(12), 1-21. [e0143970]. https://doi.org/10.1371/journal.pone.0143970