Search bioRxiv⌕ Search

Biology subjects

Mukherjee, P. K.

Publications and source records attributed to Mukherjee, P. K..

4 recordsLinked to original sources

Cdc42 small GTPase is a novel regulator of the fibrogenic activation of human intestinal myofibroblasts

Cell division cycle 42 (Cdc42) is a member of the Rho family of small GTPases, which plays crucial roles in regulating cytoskeletal remodeling, and membrane trafficking. While previous studies implicated Cdc42 in controlling intestinal epithelial homeostasis, the involvement of this small GTPase in the process of intestinal fibrogenesis remains unexplored. Our study was designed to determine whether Cdc42 regulates the fibrogenic activation of intestinal myofibroblasts in vitro. The study was conducted using a CCD-18Co normal human colonic fibroblast cell line, and primary human intestinal myofibroblasts (HIMF) isolated from Crohns disease (CD) patients. CCD-18Co and HIMF cells were stimulated by transforming growth factor-{beta}1 (TGF-{beta}1). Cdc42 was inhibited either genetically, using siRNA-mediated knockdown, or pharmacologically using specific Cdc42 inhibitors, ML141 and CASIN. Genetic and pharmacologic inhibition of Cdc42 markedly reduced TGF-{beta}1 induced expression of the major contractile cytoskeletal proteins, -smooth muscle actin, calponin 1 and L-caldesmon. Furthermore, Cdc42 inhibition significantly attenuated expression of key extracellular matrix (ECM) proteins, fibronectin and collagen I, in activated CCD-18Co cells and HIMF. Interestingly, decreased expression of contractile and ECM proteins in Cdc42-depleted myofibroblasts was not due to downregulation of the TGF-{beta}1 signaling, decreased mRNA transcription or increased lysosomal or proteasomal degradation of these proteins. Such suppressed pro-fibrotic activation of Cdc42-deficient CCD-18Co cells and HIMF involved a selective inhibition of protein translation due to inactivation of the AKT-mammalian target of rapamycin (mTOR) signaling module. These findings highlight Cdc42 as a key regulator of intestinal fibrosis that controls mTOR activation to enhance ECM production and contractile actomyosin cytoskeleton in intestinal myofibroblasts. In briefZafar et al. unravel a novel role of Cdc42 small GTPase in fibrogenic activation of human intestinal myofibroblasts. Genetic and pharmacologic inhibition of Cdc42 markedly reduced TGF-{beta} induced expression of contractile cytoskeletal proteins and extracellular matrix proteins in activated myofibroblasts. The mechanisms underlying such profibrotic activity of Cdc42 involve regulation of de novo protein translation via activation of the AKT-mTOR signaling module. HighlightsO_LICdc42 regulates TGF-{beta} dependent activation of human intestinal myofibroblasts C_LIO_LIProfibrotic activity of Cdc42 involves regulation of de novo protein translation C_LIO_LICdc42 regulates myofibroblast activation via AKT-mTOR signaling pathway C_LIO_LITargeting Cdc42-Akt-mTOR signaling may facilitate the development of novel antifibrotic therapies C_LI

cell biology↗

Whole genome assembly of the Little Millet (Panicum sumatrense) genome: A climate resilient crop species

Little millet (Panicum sumatrense) belongs to one of the largest genera, Panicum comprising of 500 species that are distributed especially in tropical and sub-tropical Asia as well as Africa. This is a climate resilient crop that has the ability to adapt to adverse growing conditions, especially drought. Added to this is the better nutritional profile of little millet, which has higher iron and fibre contents as compared with rice. These characteristics make it an important crop species that would be pivotal for ensuring food security. Generating genomic resources for the species is significant and will have implications in crop improvement. Therefore, in the present study we report the de novo whole genome sequence of P. sumatrense. Long read sequencing and Hi-C based scaffolding resulted in a total of 279 scaffolds with N50 of 7.8Mb. The genome was annotated to predict protein coding genes and orthologous groups were analysed after comparison with various plant genomes. This high-quality genome assembly can be a valuable resource as future reference for genomic studies in this crop and related crop species.

genomics↗

Stricturing Crohn's disease single-cell RNA sequencing reveals fibroblast heterogeneity and intercellular interactions

BackgroundFibroblasts play a key role in stricture formation in Crohns disease (CD) but understanding its pathogenesis requires a systems-level investigation to uncover new treatment targets. We studied full thickness CD tissues to characterize fibroblast heterogeneity and function by generating the first single cell RNA sequencing (scRNAseq) atlas of strictured bowel and providing proof of principle for therapeutic target validation. MethodsWe performed scRNAseq of 13 fresh full thickness CD resections containing non-involved, inflamed non-strictured, and strictured segments as well as 7 normal non-CD bowel segments. Each segment was separated into mucosa/submucosa or muscularis propria and analyzed separately for a total of 99 tissue samples and 409,001 cells. We validated cadherin-11 (CDH11) as a potential therapeutic target by using whole tissues, isolated intestinal cells, NanoString nCounter, next generation sequencing, proteomics and animal models. ResultsOur integrated dataset revealed fibroblast heterogeneity in strictured CD with the majority of stricture-selective changes detected in the mucosa/submucosa, but not the muscle layer. Cell-cell interaction modeling revealed CXCL14+ as well as MMP/WNT5A+ fibroblasts displaying a central signaling role in CD strictures. CDH11, a fibroblast cell-cell adhesion molecule, was broadly expressed and upregulated, and its pro-fibrotic function was validated by NanoString nCounter, RNA sequencing, tissue target expression, in vitro gain- and loss-of-function experiments, proteomics, and two animal models of experimental colitis. ConclusionA full-thickness bowel scRNAseq atlas revealed previously unrecognized fibroblast heterogeneity and interactions in CD strictures and CDH11 was validated as a potential therapeutic target. These results provide a new resource for a better understanding of CD stricture formation and opens potential therapeutic developments.

immunology↗

In Vitro and In Vivo activity of a novel catheter lock solution against bacterial and fungal biofilms

Central line associated bloodstream infections (CLABSIs) are increasingly recognized to be associated with intralumenal microbial biofilms, and effective measures for the prevention and treatment of BSI remain lacking. This report evaluates a new commercially developed antimicrobial catheter lock solution (ACL) containing trimethoprim (5 mg/ml) and ethanol (25%) and CA-EDTA 3% for activity against bacterial and fungal biofilms using in vitro and in vivo (rabbit) catheter biofilm models. Biofilms were formed with bacterial (seven different species including vancomycin-resistant enterococcus, VRE) or fungal (C. albicans) species on catheter materials. Biofilm formation was evaluated by quantitative culture (colony forming units, CFUs) and scanning electron microscopy (SEM). Treatment with ACL inhibited growth of adhesion phase biofilms in vitro after 60 min (VRE) or 15 min (all others), while mature biofilms were eradicated after exposure for 2 or 4 h, compared to control. Similar results were observed for drug-resistant bacteria. In the catheterized rabbit model, when compared against heparinized saline control, ACL lock therapy significantly reduced the catheter bacterial (3.49 {+/-} 0.75 vs. 0.03 {+/-} 0.06 log CFU/catheter, respectively; P = 0.001) and fungal burden (2.48 {+/-} 1.60 vs. 0.55 {+/-} 1.19 log CFU/catheter segment, respectively; P = 0.012). SEM also demonstrated eradication of bacterial and fungal biofilms in vivo on catheters exposed to ACL, while vigorous biofilms were observed on untreated control catheters. Our results demonstrate that ACL was efficacious against both adhesion phase and mature biofilms formed by bacteria and fungi in vitro as well as in vivo.

microbiology↗