Biology subjects

Chiaroni, J.

Publications and source records attributed to Chiaroni, J..

4 recordsLinked to original sources

bioRxiv2025

Deep learning analyses of DNA sequences resolve the retention of the Duffy-null resistance to Plasmodium vivax malaria in Africa

P. vivax, the most geographically widespread human malaria parasite with millions of clinical cases per year, is however quasi absent in sub-Saharan Africa. Positive selection targeting the rs2814778 protective mutation, also known as the Duffy-null allele, may explain the absence (or quasi absence) of vivax in sub-Saharan Africa by a progressive purge of the pathogen due to a quasi-fixation of the Duffy-null allele and the resulting high rates of protected carriers in western, central and eastern populations. Yet, while positive selection has been clearly evidenced in admixed populations coexisting with vivax, the selection model currently admitted poorly explains the lack of the Duffy-null allele in Europe, or in Asia where the pathogen is mainly observed. In this article, several validated Deep Learning methods applied to high coverage sequence data obtained in 589 African individuals resolved this retention of the Duffy-null resistance to vivax in Africa. The CNN and GAN algorithms implemented in this study also predict a rise in frequency of the Duffy-null mutation due to selection 25-35 kya years ago in the western part of Africa, a geographical region and a time frame overlapping with the rise of another protective mutation, {beta}S, the sickle-cell mutation protective at heterozygous state against the malaria caused by P. falciparum. In addition, the pattern of Duffy-null haplotypes highlights a quick spread of the Duffy-null allele in sub-Saharan Africa due to post-admixture selection events following the road of the recent Bantu expansion. Independent lines of evidence describing malaria as a life-threatening disease in West Africa from [~]30 kya, together with a rise in frequency followed by recent disseminations of the Duffy-null resistance, open new perspectives about both the history of malaria as a major human disease and the history of the main protective mutations in Africa.

evolutionary biology↗

bioRxiv2023

Low prevalence of HLA-G antibodies in lung transplant patients detected by MAIPA adapted protocol

Lung transplantation is often complicated by acute and/or chronic rejection leading to graft function loss. In addition to the HLA donor-specific antibodies (HLA-DSA), a few autoantibodies are correlated with the occurrence of these complications. Recently, antibodies directed against non-classical HLA molecules, HLA-G, -E, and -F have been detected in autoimmune diseases, like systemic lupus erythematosus. Non-classical HLA molecules are crucial in the immunological acceptance of the lung graft, and some of their isoforms, like HLA-G*01:04 and -G*01:06, are associated with a negative clinical outcome. The aim of this study is to determine the frequency of detection of HLA-G antibodies in lung transplant recipients (LTRs) and their impact on the occurrence of clinical complications. After incubating the cell lines SPI-801, with and without 3 different HLA-G isoforms expression, with sera from 90 healthy blood donors and 35 LTRs (before and after transplantation), HLA-G reactivity was revealed by using reagents from commercial monoclonal antibody immobilization of platelet antigen assay (MAIPA ApDIA(R)). Only one serum from one blood donor had specific reactivity against the HLA-G transduced lines. Non-specific reactivity in many sera from LTRs was observed with transduced and wild type cell lines, which may suggest recognition of an autoantigen expressed by the SPI-801 cell line. In conclusion, this study allowed the development of a specific detection tool for non-denatured HLA-G antibodies. These antibodies seem uncommon, both in healthy subjects and in complicated LTRs. This study should be extended to patients suffering from autoimmune diseases as well as kidney and heart transplant recipients.

immunology↗

bioRxiv2020

ABO blood group, glycosyltransferase activity and risk of Venous Thrombosis

IntroductionABO blood group influence the risk of venous thrombosis (VT) by modifying A and B glycosyltransferases (AGT and BGT) activities that further modulates Factor VIII (FVIII) and von Willebrand Factor (VWF) plasma levels. The aim of this work was to evaluate the association of plasma GTs activities with VWF/FVIII plasma levels and VT risk in a case-control study. Materials and Methods420 cases were matched with 420 controls for age and ABO blood group. GT activities in plasma were measured using the quantitative transfer of tritiated N-acetylgalactosamine or galactose to the 2-fucosyl-lactose and expressed in disintegration per minute/30{micro}L of plasma and 2 hours of reaction (dpm/30{micro}L/2H). FVIII and VWF plasma levels were respectively measured using human FVIII-deficient plasma in a 1-stage factor assay and STA LIATEST VWF (Diagnostica Stago). ResultsA and B GT activities were significantly lower in cases than in controls (8119{+/-}4027 vs 9682{+/-}4177 dpm/30{micro}L/2H, p=2.03 x 10-5, and 4931{+/-}2305 vs 5524{+/-}2096 dpm/30{micro}L/2H, p=0.043 respectively). This association was observed whatever the ABO blood groups. The ABO A1 blood group was found to explain[~]80% of AGT activity. After adjusting for ABO blood groups, AGT activity was not correlated to VWF/FVIII plasma levels. Conversely, there was a moderate correlation ({rho}[~]0.30) between BGT activity and VWF/ FVIII plasma levels in B blood group carriers. ConclusionThis work showed, for the first time, that GT activities were decreased in VT patients in comparison to controls with the same ABO blood group. The biological mechanisms responsible for this association remained to be determined.

pathology↗

bioRxiv2019

Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy

Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.

genomics↗