This project stems from gaps still present in the etiopathogenesis of MS. A plausible role by the recently described transient RNA s (trRNAs) may contribute to fill these gaps. Regulatory tr-RNA share some features: erratic time dynamics; highly contextual expression (in time and tissues); propensity to respond to non-genetic `cues¿ converging on DNA regulatory regions. The transient transcriptome has a half-life of minutes, compared to stable RNA (mRNAs, long-noncoding RNAs, and micro-RNAs) that last at least hours. Transient transcriptomes include enhancer RNAs (eRNA), short intergenic non-coding RNAs (sincRNA - promoter-associated RNAs within 10 Kbp of a GENCODE mRNA transcription start site) and antisense RNAs.
Our working hypothesis is that genomic regions coding for trRNA are significantly enriched of genetic variants associated to MS, and significantly enriched of binding motifs for non-genetic `drivers¿ capable of tuning the regulation exerted by trRNA physiologically or with a pathogenic outcome, as it may be in MS. The research plan will include the following steps:
-Implementing maps of genomic regions coding for trRNA, with special reference to eRNA and sincRNA, from as many tissues as possible;
-Matching between genomic regions coding trRNA (categorized according to their tissue expression) and genomic regions resulting from genomewide association studies on MS;
-Verifying whether the genomic regions coding for trRNA are significantly enriched of DNA-binding sites for ¿transductors¿ of adaptive/pathogenic cues such as vitamin D receptor, activation-induced cytidine deaminase, aryl hydrocarbon receptor, and Epstein Barr virus nuclear antigens (EBNA2 and EBNA3C).
The availability of advanced genomic annotations and bioinformatics tools, as well as the recent published TT-seq protocol to map the human transient transcriptome, make the working hypothesis testable in silico (the present project) and, if confirmed, in ex-vivo experiments in MS patients.
Current gene regulatory models help only in part to fully detail which disease-associated SNP signals coming from GWAS are causal, and by which exact mechanisms they are causal. We hypothesize that genomic regions coding for trRNA are significantly enriched of GWAS variants associated to MS, as well as significantly enriched of binding motifs for non-genetic `drivers¿ capable of tuning the regulation of the gene expression exerted by trRNA. No data are currently available in MS and other autoimmune disease on this topic. The availability of advanced genomic annotations and bioinformatics tools for biomedical research, as well as the recent published method to map the human transient transcriptome (the TT-seq proptocol) make the working hypothesis testable in silico and, if confirmed, in ex-vivo experiments.
GWAS have recently identified more than 200 MS-associated loci across the human genome (27). Technological advances, adequate sample sizes, and improved statistical approaches have contributed to a progress in the definition of the MS genetic architecture (limited to the role of human histocompatibility haplotypes until 15 years ago). However, at least two challenges remain. First, the definition of a comprehensive etiological model is still lacking, to better understand the plausible causal effects for many of the susceptibility regions identified and the relevant impact of non-genetic factors, demonstrated also by twin studies (approximately one identical pairs out of ten is MS-concordant in a nationwide Italian study; 28). Second, the clinical translation of genomic data needs a progress: it may exploit the relevance of pathogenic pathways with therapeutics already available in clinical practice, or may drive the discovery of new druggable targets.
The present project proposes a unifying hypothesis to interpret the interplay between genetic and non-genetic etiologic factors underpinning MS development. We plan to demonstrate that genomic regions coding trRNAs are special sites of interaction between genetic and non-genetic factors, and their transcripts (in particular sincRNA and eRNA) are highly likely to show different expression profiles between patients and controls, also zeroing the genetic components, as in disease-discordant identical twins, for future ex-vivo studies.
A better understand of the meaning of genomic regions associated to MS, and their possible prioritization for a plausible causal role, may pave the way for etiologic treatments, that are still in their infancy (29) in the landscape of disease-modifying therapies. Moreover, the working hypothesis of our project will hopefully contribute to understand the interaction between genetic and non-genetic causal factors, thus making possible attacks against both sides of the etiologic loop. Two main outcomes may be anticipated for the possible clinical translations of the GWAS data reworking that we propose: a repurposing approach, if therapeutics approved for other indications should proved to be repositionable for new MS pathogenic pathways; the discovery of new druggable targets, by applying systematic approaches, such as chemogenomics, chemoinformatics, or phenotypic screenings.
27. Cotsapas C, Mitrovic M. Clin Transl Immunol 2018; 7(6):e1018.
28. Ristori G, Cannoni S, Stazi MA, et al. Ann Neurol 2006;59(1):27-34.
29. Pender MP, Csurhes PA, Smith C, et al. JCI Insight. 2018;3(22). pii: 12471.