Investigating the role of long non-coding RNA genetically associated with rheumatoid arthritis susceptibility

  • James Ding

Student thesis: Phd


Rheumatoid arthritis (RA) is a chronic, debilitating autoimmune condition. It is highly prevalent and is caused by a combination of environmental and genetic factors; however, how the majority of the > 100 genetic loci associated with RA susceptibility contribute to pathogenesis is largely unknown. Observations have previously been made regarding the overlap between long non-coding RNA (lncRNA) and RA susceptibility loci, however this overlap has not been formally investigated. Here, an enrichment of lncRNA amongst RA susceptibility loci is demonstrated and a focused, functional approach is implemented, aiming to identify one or more lncRNA that are responsible for mediating the increase in disease risk associated with known susceptibility loci. Bioinformatic interrogation of RA susceptibility loci was used to identify and prioritise intergenic loci that overlap long intergenic non-coding RNA (lincRNA). A selection of lincRNA that overlap RA associated regions were subjected to expression analysis in an array of disease relevant cell types, using the NanoString platform. Expression of four lincRNA was detected in primary T helper (TH) cells, which are thought to be one of the most important cell types in RA pathogenesis. These include lnc-IRF8-5, which overlaps the 16q24 RA susceptibility locus. Single cell RNA-sequencing was used to better characterise the response of lnc-IRF8-5 and its putative target, IRF8, to TH cell stimulation. This provided a novel, unbiased perspective on the transcriptional heterogeneity of unstimulated and stimulated TH cells. A genome editing strategy, using Cas9 ribonucleoproteins, was developed in order to investigate the relationship between lnc IRF8 5 and IRF8, in primary TH cells, and is broadly applicable to the study of other intergenic susceptibility loci. Whilst focussed on the role of lncRNA in RA this work bears relevance to the study of intergenic loci in general and demonstrates the multifaceted approach necessary to characterise a locus, using a mixture of publically available resources and laboratory based experimentation.
Date of Award1 Aug 2018
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorStephen Eyre (Supervisor), Jane Worthington (Supervisor) & Annie Yarwood (Supervisor)


  • lncRNA
  • rheumatoid arthritis
  • T helper cells
  • functional genomics

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