TGFβ promotes low IL10-producing ILC2 with profibrotic ability involved in skin fibrosis in systemic sclerosis

Objective : Innate lymphoid cells-2 (ILC2) were shown to be involved in the development of lung or hepatic fibrosis. We sought to explore the functional and phenotypic heterogeneity of ILC2 in skin fibrosis within systemic sclerosis (SSc). Methods : Blood samples and skin biopsies from healthy donor or patients with SSc were analysed by immunostaining techniques. The fibrotic role of sorted ILC2 was studied in vitro on dermal fibroblast and further explored by transcriptomic approach. Finally, the efficacy of a new treatment against fibrosis was assessed with a mouse model of SSc. Results : We found that ILC2 numbers were increased in the skin of patients with SSc and correlated with the extent of skin fibrosis. In SSc skin, KLRG1− ILC2 (natural ILC2) were dominating over KLRG1+ ILC2 (inflammatory ILC2). The cytokine transforming growth factor-β (TGFβ), whose activity is increased in SSc, favoured the expansion of KLRG1- ILC2 simultaneously decreasing their production of interleukin 10 (IL10), which regulates negatively collagen production by dermal fibroblasts. TGFβ-stimulated ILC2 also increased myofibroblast differentiation. Thus, human KLRG1- ILC2 had an enhanced profibrotic activity. In a mouse model of SSc, therapeutic intervention-combining pirfenidone with the administration of IL10 was required to reduce the numbers of skin infiltrating ILC2, enhancing their expression of KLRG1 and strongly alleviating skin fibrosis. Conclusion : Our results demonstrate a novel role for natural ILC2 and highlight their inter-relationships with TGFβ and IL10 in the development of skin fibrosis, thereby opening up new therapeutic approaches in SSc

Utilisation d'une Grille de Calcul (GRISBI) pour le Traitement de Données NGS

International audienc

Utilisation d'une Grille de Calcul (GRISBI) pour le Traitement de Données NGS (New Generation Sequencing)

International audienceUtilisation d'une Grille de Calcul (GRISBI) pour le Traitement de Données NGS (New Generation Sequencing

Finishing bacterial genome assemblies with Mix

National audienceMotivation: Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase. Methods: In this paper we address these two aspects by developing Mix, a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length. Results: We evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects. Availability: Mix is implemented in Python and is available at https://github.com/cbib/MIX, novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

International audienceCost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different setups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inocu-lum in a suspension culture resulted in an impoverishment of putative cellulase-and hemi-cellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of ligno-cellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment setup can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity

Targeting CAMKK2 and SOC Channels as a Novel Therapeutic Approach for Sensitizing Acute Promyelocytic Leukemia Cells to All-Trans Retinoic Acid

International audienceCalcium ions (Ca2+) play important and diverse roles in the regulation of autophagy, cell death and differentiation. Here, we investigated the impact of Ca2+ in regulating acute promyelocytic leukemia (APL) cell fate in response to the anti-cancer agent all-trans retinoic acid (ATRA). We observed that ATRA promotes calcium entry through store-operated calcium (SOC) channels into acute promyelocytic leukemia (APL) cells. This response is associated with changes in the expression profiles of ORAI1 and STIM1, two proteins involved in SOC channels activation, as well as with a significant upregulation of several key proteins associated to calcium signaling. Moreover, ATRA treatment of APL cells led to a significant activation of calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) and its downstream effector AMP-activated protein kinase (AMPK), linking Ca2+ signaling to autophagy. Pharmacological inhibition of SOC channels and CAMKK2 enhanced ATRA-induced cell differentiation and death. Altogether, our results unravel an ATRA-elicited signaling pathway that involves SOC channels/CAMKK2 activation, induction of autophagy, inhibition of cellular differentiation and suppression of cell death. We suggest that SOC channels and CAMKK2 may constitute novel drug targets for potentiating the anti-cancer effect of ATRA in APL patients

Gross Dissection Time Values of Pathologists\u27 Assistants Using Standardized Metrics.

OBJECTIVES: A validated and objective method to quantify the gross dissection time of pathologists\u27 assistants (PAs) does not exist. We propose a method to calculate standardized work units (dissection time values [DTVs]) to monitor PA productivity. METHODS: The Current Procedural Terminology system specifies six levels of specimen complexity encompassing 176 unique specimen types. Using our institutional dictionary, we designated all specimen types into a priori five levels of complexity based on expected dissection time. We hypothesized that expected time could be matched prospectively with the actual measured dissection time for all specimens. Dissection time data were collected prospectively for 12,775 specimens at two tertiary academic medical centers, and work effort was converted to a numeric DTV equivalent (number of minutes to dissect single specimen/420 minutes in a working day). RESULTS: For 44 of 155 specimen types, measured dissection time for the five levels was lower than expected dissection (P \u3c .0001). Accordingly, those 44 specimen types were reclassified to a lower level. CONCLUSIONS: A numeric standard of the work effort for dissection time for 155 specimen types was developed, validated, and then used prospectively to monitor grossing efficiency of PA workforce

Insights into genome plasticity of the wine-making bacterium Oenococcus oeni strain ATCC BAA-1163 by decryption of its whole genome.

International audienceStudying genomes of O. oeni strains having opposite oenological aptitudes is important for understanding why this lactic acid bacterium involved in malolactic fermentation is so well adapted to wine. Here, the genome of a strain ATCC BAA-1163, is described and compared with the recently reported genome of the better wine-adapted strain PSU-1. The BAA-1163 genome (8X) was obtained by shotgun sequencing and Phrap assembling. Compact and 62% AT-rich, it consists of a circular 1,792,103-bp chromosome and a 3,948-bp plasmid. It was analysed through a CAAT-Box annotation platform and manually inspected. A total of 51 RNA genes were detected, including two rRNA operons (the second resulting from a duplication of the original one) and 43 tRNAs genes scattered throughout the chromosome. A total of 1,756 ORFs were predicted of which 73% were functionally classified, revealing a specialized metabolic repertoire. The genomic distribution, genetic environment and phylogenetic origin of detected pseudogenes and mobile genetic elements (MGEs) were analyzed. The conservation of gene repertoire and genomic organization were investigated through intra- and inter-species genomic comparisons. BAA-1163 genome was 11.6-kb longer than its PSU-1 counterpart, with macroscopic (i.e. a 674-kb chromosomal inversion between the rRNA operons), and microscopic/small-range rearrangements (local gain/loss of genetic objects). The latter event appeared to affect loci of key metabolic functions presumably involved in wine adaptation, all of them sharing unusual GC-content and abundance of MGEs. These results point up the role of horizontal gene tranfert and MGEs in O. oeni genome plasticity, and give us clues of the genetic origin of its oenological aptitudes. A previous draft has already been released, the complete genome will become available to the scientific community later