PhD Defence: Aashiq Hussain Mirza

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2015-04-17: Structured non-coding RNAs in Autoimmune and Inflammatory Diseases. The defence will take place on April 17th at 14:00 in Medical Museion auditorium, Bredgade 62, 1260 Copenhagen

Everybody is welcome. Registration is not necessary.
After the defence a reception will be held at 16:00 – 18:00,  Reception Hall, Medical Museion.

Assessment Committee
1.     (Chairperson) Professor Torben Hansen
The Novo Nordisk Foundation Center for Basic Metabolic Research
Metabolics Genetics, University of Copenhagen, DK
2.    Professor Jørgen Kjems
Department of Molecular Biology, Aarhus University, DK
3.    Professor Romano Regazzi
Department of Fundamental Neurosciences, University of Lausanne, CH

Professor Flemming Pociot, Copenhagen Diabetes Reserach Center, Herlev University Hospital, University of Copenhagen
Professor Jan Gorodkin, Center for non-coding RNA in Technology and Health, IKVH, KU

Non-coding RNAs, including the long non-coding RNAs (lncRNAs) have recently emerged as important players of gene regulation with their involvement in various cellular and developmental processes. LncRNAs have been found dysregulated in panoply of complex human diseases; however, their role(s) in autoimmune and inflammatory diseases is still poorly understood. Towards this end, the main purpose of this PhD project was to explore the role of annotated lncRNAs as well as novel evolutionary conserved structured RNAs in autoimmune and inflammatory diseases with a particular focus on two main forms of inflammatory bowel disease (IBD): Crohn’s disease (CD) and ulcerative colitis (UC).
Currently, there is limited information and lack of understanding in relation to the role of lncRNAs in autoimmune and inflammatory diseases including IBD and type 1 diabetes (T1D). The transcriptomic landscape of annotated lncRNAs in IBD and their inference to the IBD genetic susceptibility loci has not been explored yet. In addition, attempts to screen for novel evolutionary conserved structured RNAs relevant to the disease associated loci at a genome-wide scale have also been lacking.
In this study, we identified all annotated lncRNAs within IBD and T1D loci and analyzed their sequence and structural features along with their expression patterns across an array of human tissues. Furthermore, we identified a number of disease-associated single nucleotide variations (SNPs) potentially disrupting lncRNA secondary structure. We proposed that these lncRNA structure disruptive SNPs might be regulatory in nature based on their tissue-specific expression signatures, cis-eQTLs signals, ENCODE based regulatory features and evidence of recent positive selection.
In a case-control study setting, we performed a genome-wide transcriptome profiling of annotated lncRNAs and protein-coding genes using colon pinch biopsies from IBD patients. We found hundreds of lncRNAs and protein-coding genes dysregulated in both inflamed and non-inflamed tissues from CD and UC patients compared to the healthy controls. The lncRNA based transcriptional signatures allowed successful stratification of both CD and UC patients from the healthy controls. Specifically, we identified a number of differentially expressed lncRNAs not previously associated with IBD, including multiple isoforms of ANRIL lncRNA. We also found enrichment of differentially expressed lncRNAs and protein-coding genes within the IBD loci. Our data highlights the potential of lncRNA transcriptional signatures associated with clinical parameters as novel biomarkers for IBD.
As a case study, we specifically interrogated the genetic and regulatory architecture of ERBB3 region, a susceptibility locus implicated in multiple autoimmune diseases. We identified evolutionary conserved differentially expressed lncRNAs in array of tissues and multiple CTCF bind sites within the ERBB3 locus. Based on the genotyping results from 984 type 1 diabetes children, our analysis demonstrated that the SNP rs2292239 strongly correlates with residual β-cell function and metabolic control in children diagnosed with type 1 diabetes. We also explored the expression of ERBB3, CTCF and the associated lncRNAs in various tissues, including human islets. We showed that ERBB3, CTCF and NONHSAG011351 antisense ERBB3 locus-associated lncRNA are expressed in human islets and ERBB3 is down-regulated by pro-inflammatory cytokines in human islets and insulin-producing INS-1E cells. Moreover, ERBB3 knockdown decreased CTCF protein expression indicating a potential feedback mechanism. Taken together, these data suggest regulatory role of ERBB3 locus in β-cell function.
Further, we identified novel evolutionary conserved RNA structures (CRSs) based on a genome-wide in-silico screen using CMfinder algorithm. Most of the identified CRSs were conserved by purifying selection and found to be under positive selection. Moreover, we presented multiple lines of evidence for CRSs potential functional implications in the genome. Approximately 50% of the identified CRSs were expressed across a panel of human and mouse tissues and we also explored expression of CRSs in human fetal brain based on our custom-designed capture array based profiling. Additionally, large numbers of CRSs were found to be enriched within disease associated regions including IBD loci indicating potential involvement of conserved CRSs in disease pathogenesis.

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