Biology subjects

Klatzmann, D.

Publications and source records attributed to Klatzmann, D..

4 recordsLinked to original sources

bioRxiv2018

Clinical data specification and coding for cross-analyses with omics data in autoimmune disease trials

ObjectivesAutoimmune and inflammatory diseases (AIDs) form a continuum of autoimmune and inflammatory diseases, yet AIDs nosology is based on syndromic classification. The TRANSIMMUNOM trial (NCT02466217) was designed to re-evaluate AIDs nosology through clinic-biological and multi-omics investigations of patients with one of 19 selected AIDs. To allow cross-analyses of clinic-biological data together with omics data, we needed to integrate clinical data in a harmonized database.\n\nMaterials and MethodsWe assembled a clinical expert consortium (CEC) to select relevant clinic-biological features to be collected for all patients and a cohort management team comprising biologists, clinicians and computer scientists to design an electronic case report form (eCRF). The eCRF design and implementation has been done on OpenClinica, an open-source CFR-part 11 compliant electronic data capture system.\n\nResultsThe CEC selected 865 clinical and biological parameters. The CMT selected coded the items using CDISC standards into 5835 coded values organized in 28 structured eCRFs. Examples of such coding are check boxes for clinical investigation, numerical values with units, disease scores as a result of an automated calculations, and coding of possible treatment formulas, doses and dosage regimens per disease.\n\nDiscussion21 CRFs were designed using OpenClinica v3.14 capturing the 5835 coded values per patients. Technical adjustment have been implemented to allow data entry and extraction of this amount of data, rarely achieved in classical eCRFs designs.\n\nConclusionsA multidisciplinary endeavour offers complete and harmonized CRFs for AID clinical investigations that are used in TRANSIMMUNOM and will benefit translational research team.

clinical trials↗

bioRxiv2018

Representativeness and robustness of TCR repertoire diversity assessment by high-throughput sequencing

High-throughput sequencing (HTS) has the potential to decipher the diversity of T cell repertoires and their dynamics during immune responses. Applied to T cell subsets such as T effector and T regulatory cells, it should help identify novel biomarkers of diseases. However, given the extreme diversity of TCR repertoires, understanding how the sequencing conditions, including cell numbers, biological and technical sampling and sequencing depth, impact the experimental outcome is critical to properly use of these data. Here we assessed the representativeness and robustness of TCR repertoire diversity assessment according to experimental conditions. By comparative analyses of experimental datasets and computer simulations, we found that (i) for small samples, the number of clonotypes recovered is often higher than the number of cells per sample, even after removing the singletons; (ii) high sequencing depth for small samples alters the clonotype distributions, which can be corrected by filtering the datasets using Shannon entropy as a threshold; (iii) a single sequencing run at high depth does not ensure a good coverage of the clonotype richness in highly polyclonal populations, which can be better covered using multiple sequencing. Altogether, our results warrant better understanding and awareness of the limitation of TCR diversity analyses by HTS and justify the development of novel computational tools for improved modelling of the highly complex nature of TCR repertoires.

immunology↗

bioRxiv2017

High-resolution repertoire analysis of Tfr and Tfh cells reveals unexpectedly high diversities indicating a bystander activation of follicular T cells

T follicular helper (Tfh) and regulatory (Tfr) cells regulate B cell activation and ultimately antibody production. While concordant results show that Tfh cells are specific for the immunizing antigens, limited and even controversial results have been reported regarding the specificity of Tfr cells. Here we used high-throughput T cell receptor (TCR) sequencing to address this issue. We observed that although the Tfh- and Tfr-cell repertoires are less diverse than those of effector (Teff) and regulatory T (Treg) cells, they still represent thousands of clonotypes after immunization with a single antigen. T-cell receptor beta variable (TRBV) gene usage distinguishes both follicular T cells (Tfol) from non-Tfol cells, as well as helper (Teff and Tfh) vs. regulatory (Treg and Tfr) cells. Analysis of the sharing of clonotypes between samples revealed that a specific response to the immunizing antigen can only be detected in Tfh cells immunized with a non-self-antigen and Tfr cells immunized with a self-antigen. Finally, the Tfr TCR repertoire is more similar to that of Tregs than to that of Tfh or Teff cells. Altogether, our results highlight a bystander Tfol-cell activation during antigenic response in the germinal centres and support the Treg cell origin of Tfr cells.\n\nSignificance StatementFollicular helper T (Tfh) cells promote high-affinity antibody production by B cells while follicular regulatory T (Tfr) cells represses it. The question of the specificity of follicular T (Tfol) cells is of utmost importance in the understanding of the antibody response specificity and our work is the first to analysed the global Tfol TCR repertoire in wild type mice. This allowed us not only to portray the overall global structure of these repertoires, but also to substantiate the fact that Tfr cells respond to self-antigen while Tfh cells respond to non self-antigen, a still controversial issue. Importantly, our work revealed an unexpected bystander activation of Tfol cells. We think and discuss that it has a general significance in immune responses and possibly immunopathologies.

immunology↗

bioRxiv2017

The early pregnancy human placenta shares hypomethylation patterns characteristic of solid tumors

BackgroundThe placenta relies on phenotypes that are characteristic of cancer to successfully implant the embryo in the uterus during early pregnancy. Notably, it has to invade its host tissues, promote angiogenesis, while surviving hypoxia, and escape the immune system. Similarities in DNA methylation patterns between the placenta and cancers suggest that common epigenetic mechanisms may be involved in regulating these behaviors.\n\nResultsWe show here that megabase-scale patterns of hypomethylation distinguish first from third trimester chorionic villi in the placenta, and that these patterns mirror those that distinguish many tumors from corresponding normal tissues. We confirmed these findings in villous cytotrophoblasts isolated from the placenta and identified a time window at the end of the first trimester, when these cells come into contact with maternal blood as the likely time period for the methylome alterations. Furthermore, the large genomic regions affected by these patterns of hypomethylation encompass genes involved in pathways related to epithelial-mesenchymal transition (EMT), immune response and inflammation. Analyses of expression profiles corresponding to genes in these hypomethylated regions in colon adenocarcinoma tumors point to networks of differentially expressed genes previously implicated in carcinogenesis and placentogenesis, where nuclear factor kappa B (NF-kB) is a key hub.\n\nConclusionTaken together, our results suggest the existence of epigenetic switches involving large-scale changes of methylation in the placenta during pregnancy and in tumors during neoplastic transformation. The characterization of such epigenetic switches might lead to the identification of biomarkers and drug targets in oncology as well as in obstetrics and gynecology.

genomics↗