The first part of my work was to measure the extent of isoform diversity in immune cells using RNA sequencing data obtained across a cohort of 200 individuals and in response to 4 different stimuli. This work quantified 16,173 frequent splicing events occurring in innate immune cells and identified 1,919 genes with altered splicing in response to immune stimuli, including essential regulators of the immune response. I further analysed the regulatory networks governing splicing regulation and identified several splicing factors associated to strong variation in splicing during immune response, highlighting key regulators of the immune splicing response.
Next, I studied the genetic determinants of splicing and identified 1,271 loci associated to changes in isoform levels, 157 of which were previously associated to human phenotypes, including several auto-immune disorders. I further showed that while the effect of most splicing-altering variants is independent of the stimulation state, some genetic variants act in a stimulation-dependent manner. In total, I identified 274 such variants and analysed their neighbouring DNA sequences to identify specific motifs enriched in their surroundings. I thus highlighted both motifs of known splicing factors and novel regulatory motifs, contributing to regulate splicing of immune cells at basal state and in response to immune stimulation.
Finally, to understand the impact of natural selection on splicing, I searched for splicing differences between human populations, and identified 515 genes showing differential splicing between individuals of African and European ancestry. I found that population differences in frequency of splicing altering variants accounted for up to 81% of these differences in splicing. I further identified several splicing altering variants overlapping strong signatures of positive selection (extreme differentiation of allelic frequency between populations, and strong variation of haplotype length between alleles), including loci associated to childhood resistance to tuberculosis and systemic lupus erythematous, suggesting that natural selection has contributed to shape differences in isoform usage, and ultimately in immune responses, of present-day human populations.
--- Exploitation/Dissemination ---
The following measures have been taken to ensure dissemination of the results obtained as part of the MSCA:
* Participation to International conferences
- American Society of Human Genetics meeting, 2016, Vancouver, Canada. Poster
- Biology of Genomes, 2017, Cold Spring Harbor laboratory, NY, USA. Poster
- Keystone symposia “Understanding the function of human genome variation” ,Uppsala, 2016. Poster.
- Symposium: “Computational modeling with functional and evolutionary genomics of infectious diseases”, 2017, Tel Aviv, Israel. Oral presentation
* Publications:
- Quach H*, Rotival M*, et al (2016) Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations. Cell 167(3):643-656 (*equal contributors)
- Rotival M, Quach H, Quintana-Murci L. Increased plasticity of immune splicing shapes auto-immune disease susceptibility. Manuscript in preparation. Submission planned to Nature Communications.
All manuscripts include reference to EU funding.
* Outreach activities:
- UPA Conferences 2015 at the “Museum National d’Histoire Naturelle” organised by the “Union des Professeurs des classes préparatoires aux grandes écoles Agronomiques, biologique géologiques et vétérinaire)”.
- Teaching to master level students at the Institut Pasteur : “Human Population Genetics and Genetic Epidemiology course”.
- Press release and radio interventions were organized following the publication in Cell (Quach et al, 2016) of the work done during the MSC Fellowship.
All communications included reference to EU funding.
