Analyse de Données Omiques

@article{pmid36482098,

title = {RNA-Seq comparative study reveals molecular effectors linked to the resistance of Pinna nobilis to Haplosporidium pinnae parasite},

author = {Pauline Salis and Claire Peyran and Titouan Morage and Simon de Bernard and Julien Nourikyan and Stéphane Coupé and Robert Bunet and Serge Planes},

doi = {10.1038/s41598-022-25555-x},

issn = {2045-2322},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {Sci Rep},

volume = {12},

number = {1},

pages = {21229},

abstract = {With the intensification of maritime traffic, recently emerged infectious diseases have become major drivers in the decline and extinction of species. Since 2016, mass mortality events have decimated the endemic Mediterranean Sea bivalve Pinna nobilis, affecting ca. 100% of individuals. These events have largely been driven by Haplosporidium pinnae's infection, an invasive species which was likely introduced by shipping. While monitoring wild populations of P. nobilis, we observed individuals that survived such a mass mortality event during the summer of 2018 (France). We considered these individuals resistant, as they did not show any symptoms of the disease, while the rest of the population in the area was devastated. Furthermore, the parasite was not detected when we conducted a PCR amplification of a species-specific fragment of the small subunit ribosomal DNA. In parallel, the transcriptomic analysis showed evidence of some parasite RNA indicating that the resistant individuals had been exposed to the parasite without proliferating. To understand the underlying mechanisms of resistance in these individuals, we compared their gene expression with that of susceptible individuals. We performed de novo transcriptome assembly and annotated the expressed genes. A comparison of the transcriptomes in resistant and susceptible individuals highlighted a gene expression signature of the resistant phenotype. We found significant differential expressions of genes involved in immunity and cell architecture. This data provides the first insights into how individuals escape the pathogenicity associated with infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36065187,

title = {CD8 memory precursor cell generation is a continuous process},

author = {Helena Todorov and Margaux Prieux and Daphne Laubreton and Matteo Bouvier and Shaoying Wang and Simon de Bernard and Christophe Arpin and Robrecht Cannoodt and Wouter Saelens and Arnaud Bonnaffoux and Olivier Gandrillon and Fabien Crauste and Yvan Saeys and Jacqueline Marvel},

doi = {10.1016/j.isci.2022.104927},

issn = {2589-0042},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {iScience},

volume = {25},

number = {9},

pages = {104927},

abstract = {In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T cells collected during the postinfection expansion phase. We used different tools to reconstruct the developmental trajectory that CD8 T cells followed after activation. Cells that exhibited a memory precursor signature were identified and positioned on this trajectory. We found that these memory precursors are generated continuously with increasing numbers arising over time. Similarly, expression of genes associated with effector functions was also found to be raised in memory precursors at later time points. The ability of cells to enter quiescence and differentiate into memory cells was confirmed by BrdU pulse-chase experiment . Analysis of cell counts indicates that the vast majority of memory cells are generated at later time points from cells that have extensively divided.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35184302,

title = {Gene profiling reveals a contact allergy signature in most positive Amerchol L-101 patch test reactions},

author = {Linda Ljungberg Silic and Marine-Alexia Lefevre and Ola Bergendorff and Simon De Bernard and Julien Nourikyan and Laurent Buffat and Audrey Nosbaum and Magnus Bruze and Jean-François Nicolas and Cecilia Svedman and Marc Vocanson},

doi = {10.1111/cod.14077},

issn = {1600-0536},

year  = {2022},

date = {2022-07-01},

urldate = {2022-07-01},

journal = {Contact Dermatitis},

volume = {87},

number = {1},

pages = {40--52},

abstract = {BACKGROUND: Diagnosis of contact allergy (CA) to Amerchol L-101 (AL-101), a marker for lanolin allergy, is problematic. Positive patch test reactions are frequently doubtful or weakly positive and difficult to associate with clinical relevance.



OBJECTIVE: To gain further insight on the allergic or irritant nature of skin reactions induced by AL-101 patch test.



METHODS: We re-tested in a dose-response fashion, 10 subjects with AL-101 CA and performed comprehensive transcriptomic analysis (gene arrays, quantitative real-time polymerase chain reaction [qRT-PCR]) of samples of their skin reactions.



RESULTS: Eight of the 10 CA subjects reacted positively upon re-test, whereas two did not react. Most of AL-101 positive patch tests expressed an allergy signature with strong activation of gene modules associated with adaptive immunity and downregulation of cornification pathway genes. In addition, the breadth of gene modulation correlated with the magnitude of patch test reactions and the concentration of AL-101 applied. However, we observed that some of the positive patch test reactions to AL-101 expressed no/few allergy biomarkers, suggesting the induction of an irritant skin inflammation in these samples.



CONCLUSIONS: This study confirms that AL-101 is an allergen that can cause both contact allergy and contact irritation. Our results also highlight that molecular profiling might help to strengthen clinical diagnosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}