Biology subjects

Singh, R. R.

Publications and source records attributed to Singh, R. R..

5 recordsLinked to original sources

bioRxiv2026

Metabolism of trichloroethylene following inhalation exposure in mice

Trichloroethylene (TCE) is a pervasive environmental pollutant associated with elevated risk of developing Parkinson's disease (PD). Studies characterizing TCE metabolism in humans indicate that 40 - 75% of the absorbed dose is metabolized, suggesting that TCE toxicity may be attributable to its metabolites. However, there is limited knowledge of TCE metabolite neurotoxicity. We conducted a TCE inhalation study in mice followed by high-resolution mass spectrometry (HRMS) on brain, liver, and blood to identify which TCE metabolites were present following human-relevant TCE exposure. Mice were exposed to 100 ppm TCE for 4 hours. Plasma, brain, and liver were collected from each animal up to 24 hours after exposure. We developed a method capable of detecting TCE metabolites trichloroacetic acid (TCA), dichloroacetic acid (DCA), monochloroacetic acid (MCA), trichloroethanol (TCEOH), trichloroethanol glucuronide (TCEOH-gluc), S-(1,2-dichlorovinyl)glutathione (DCVG), S-(1,2-dichlorovinyl)-L-cysteine (DCVC), N-acetyl-S-(1,2-dichlorovinyl)-L-cysteine (NAcDCVC), and untargeted metabolites using a single extraction protocol on a liquid chromatography-based mass spectrometry system (LC-MS/MS). Targeted analysis of TCE-exposed biological samples identified DCA, TCA, and TCEOH-gluc. Untargeted analysis of TCE-exposed mouse brain revealed previously established and novel pathway perturbations associated with TCE exposure. Together, these findings indicate that DCA, TCA, and TCEOH-gluc are the most prevalent TCE metabolites in mice. The novel pathways perturbed by TCE exposure warrant further exploration to better understand the mechanisms underlying the toxicity of TCE and its metabolites

pharmacology and toxicology↗

bioRxiv2026

PIEZO1 mediates mechanosensing and myofibroblastic activation of synovial fibroblasts in post-traumatic osteoarthritis

Fibrosis and inflammation of the synovium are common pathological features of joint diseases. In osteoarthritis (OA), extensive evidence supports that synovial pathology drives symptoms and disease progression, yet the mechanisms underpinning pathological synovial remodeling, including fibrosis, remain unclear. Here, we identify the mechanosensitive ion channel PIEZO1 as a critical regulator of myofibroblast-like activation of synovial fibroblasts (SFs) in post-traumatic osteoarthritis (PTOA). Using multi-omic assessments in human and murine synovium, a murine model of joint injury, histopathology, and functional in vitro phenotyping, we demonstrate that joint injury triggers expansion of myofibroblast-like SFs concurrent with fibrotic remodeling and mechanical stiffening of the synovium. Myofibroblastic commitment of synovial progenitors was associated with activation of the YAP1 regulon, and PIEZO1 agonism drove nuclear accumulation of YAP1 in SFs. PIEZO1 was enriched in synovia of injured joints, and in cultured SFs pharmacologic PIEZO1 activation promoted SMA enrichment and increased matrix contraction, which were both ablated by YAP1 inhibition. PIEZO1 silencing abrogated TGF-{beta}-induced contractility and markedly altered the transcriptomic response to mechanical loading in vitro, including ECM production and neuroinflammatory programs. In vivo, acute intra-articular pharmacologic PIEZO1 activation induced a pro-fibrotic, pro-inflammatory, and anti-adipogenic transcriptomic program in synovium. Collectively, these findings establish PIEZO1 as a key mediator of the pathogenic activation of SFs and identify aberrant mechanosensing as a mechanism underlying synovial fibrosis in PTOA.

cell biology↗

bioRxiv2023

First complete genome characterization of an Indian pigeon pox virus directly from a clinical sample

Avian pox disease is a highly contagious infection caused by pox virus and has serious consequences on avian species with regards to economic and conservation aspects. This viral genus named as Avipox virus (APV) that infects nearly 300 bird species and lack of enough complete genome information creates hindrance to infer this virus biology. Thus in this study, we have revealed the first complete genome of an Indian pigeon pox virus that belongs to the genus APV followed by comparative genomics analysis. The entire genome of present isolate (PPV/Pur-Od-4b/01/Ind) having 280058 bp nucleotide sequences with the GC content 29.51%. The unique feature of this complete genome revealed the presence of 270 open reading frames (ORFs) circumscribed by inverted terminal repeats (ITRs) of 4,689 bp at each end and lack of recombination events. The concatenated amino acid phylogenetic tree deciphered the present isolate closely related with Feral Pigeon pox virus derived from Africa. The molecular markers, such as microsatellites were ubiquitously distributed throughout the genome and more prevalent within the functional genes.

evolutionary biology↗

bioRxiv2023

The Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution

Advanced urothelial cancer is a frequently lethal disease characterized by marked genetic heterogeneity. In this study, we investigate the evolution of the genomic signatures caused by endogenous and external mutagenic stimuli and their interplay with complex structural variants. We superimposed mutational signatures and phylogenetic analyses of matched serial tumors from patients with urothelial cancer to define the evolutionary patterns of these processes. We show that APOBEC3-induced mutations are clonal and early, whereas mutational bursts comprising hundreds of late subclonal mutations are induced by chemotherapy. Using a novel genome graph computational paradigm, we observed frequent circular high copy-number amplicons characteristic of extrachromosomal DNA (ecDNA) involving double-minutes, breakage-fusion-bridge, and tyfonas events. We characterized the distinct temporal patterns of APOBEC3 mutations and chemotherapy-induced mutations within ecDNA, gaining new insights into the timing of these events relative to ecDNA biogenesis. Finally, we discovered that most CCND1 amplifications in urothelial cancer arise within circular ecDNA amplicons. These CCND1 ecDNA amplification events persisted and increased in complexity incorporating additional DNA segments potentially contributing selective fitness advantage to the evolution of treatment resistance. Our findings define fundamental mechanisms driving urothelial cancer evolution and have therapeutic implications for treating this disease.

genomics↗

bioRxiv2023

CLN3 deficiency leads to neurological and metabolic perturbations during early development

Juvenile Neuronal Ceroid Lipofuscinosis (or Batten disease) is an autosomal recessive, rare neurodegenerative disorder that affects mainly children above the age of 5 years and is most commonly caused by mutations in the highly conserved CLN3 gene. Here, we generated cln3 morphants and stable mutant lines in zebrafish. Although neither morphant nor mutant cln3 larvae showed any obvious developmental or morphological defects, behavioral phenotyping of the mutant larvae revealed higher basal activity, hyposensitivity to abrupt light changes and hypersensitivity to pro-convulsive drugs. Importantly, in-depth metabolomics and lipidomics analyses revealed significant accumulation of several glycerophosphodiesters (GPDs) and a global decrease of bis(monoacylglycero)phosphate (BMP) species, two classes of molecules previously proposed as potential biomarkers for CLN3 disease based on independent studies in other organisms. We could also demonstrate GPD accumulation in human-induced pluripotent stem cell-derived cerebral organoids carrying a pathogenic variant for CLN3. Our models revealed that GPDs accumulate at very early stages of life in the absence of functional CLN3 and highlight glycerophosphoinositol and BMP as promising biomarker candidates for pre-symptomatic CLN3 disease.

molecular biology↗