Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
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Section: New Results

Axis 4: Human and animal health

Rare disease studies Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations in RNU4ATAC, transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi-Linder (TALS/MOPD1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on a few RFMN patient cells, none have been performed in TALS, and more generally no in-depth transcriptomic analysis of the 700 human genes containing a minor (U12-type) intron had been published as yet. We thus sequenced RNA from cells derived from five skin, three amniotic fluid, and one blood biosamples obtained from seven unrelated TALS cases and from age- and sex-matched controls. This allowed us to describe for the first time the mRNA expression and splicing profile of genes containing U12-type introns, in the context of a functional minor spliceosome. Concerning RNU4ATAC-mutated patients, we showed in [15] that as expected, they display distinct U12-type intron splicing profiles compared to controls, but that rather unexpectedly the mRNA expression levels are mostly unchanged. Furthermore, although U12-type intron missplicing concerns most of the expressed U12 genes, the level of U12-type intron retention is surprisingly low in fibroblasts and amniocytes, and much more pronounced in blood cells. Interestingly, we found several occurrences of introns that can be spliced using either U2, U12, or a combination of both types of splice site consensus sequences, with a shift towards splicing using preferentially U2 sites in TALS patients' cells compared to controls.

This work is part of the PhD of Audric Cologne [1] defended in October 2019.

Cancer studies Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. In [30], we analysed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative (R < 0.2) correlation with the expression level of the linear gene. An In silico analysis showed that only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of CNOT2, CREBBP, and RERE in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumour lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of circCNOT2 was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.

Other cancer studies have concerned the automatic discovery of the 100-miRNA signature for cancer classification [21], an Integrative and comparative genomic analysis to identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids [5], [complete with 2 papers not yet entered in Hal], and finally the investigation of new therapeutic interventions that are needed to increase the immunogenicity of tumours and overcome the resistance to these immuno-therapies [29].

Infection studies Mycoplasma hyopneumoniae is an economically devastating pathogen in the pig farming industry, however little is known about its relation with the swine host. To improve our understanding on this interaction, we infected epithelial cells with M. hyopneumoniae to identify the effects of the infection on the expression of swine genes and miRNAs. In addition, we identified miRNAs differentially expressed (DE) in the extracellular milieu and in exosome-like vesicles released by infected cells. A total of 1,268 genes and 170 miRNAs were DE post-infection (p<0.05). We identified the up-regulation of genes related to redox homeostasis and antioxidant defense, most of them putatively regulated by the transcription factor NRF2. Down-regulated genes were enriched in cytoskeleton and ciliary function, which could partially explain M. hyopneumoniae induced ciliostasis. Our predictions showed that DE miRNAs could be regulating the aforementioned functions, since we detected down-regulation of miRNAs predicted to target antioxidant genes and up-regulation of miRNAs targeting ciliary and cytoskeleton genes. Based on these observations, M. hyopneumoniae seems to elicit an antioxidant response induced by NRF2 in infected cells; in addition, we propose that ciliostasis caused by this pathogen might be related to down-regulation of ciliary genes. The paper presenting these results has been submitted and is in revision.

Others Besides the above, a first step towards deep learning assisted genotype-phenotype association in whole genome-sized data has been explored in the context of predicting amyotrophic lateral sclerosis [34].