Biology subjects

Joshi, R. S.

Publications and source records attributed to Joshi, R. S..

8 recordsLinked to original sources

bioRxiv2026

A conserved lncRNA regulates trehalose-glucose homeostasis through direct RNA-RNA interactions

Trehalose is a primary circulating sugar in insects and essential for energy homeostasis, yet its non-coding RNA-based regulatory circuitry remains enigmatic. Here, we characterize a conserved long non-coding RNA, lncRNA1, as a post-transcriptional regulator of trehalose-glucose homeostasis in Lepidoptera. lncRNA1 encodes a structurally stable, pseudoknot-containing transcript that is strongly induced upon trehalose pathway perturbation and exhibits a reciprocal developmental expression pattern relative to the trehalose metabolism enzymes. RNAi-mediated silencing of lncRNA1 in Helicoverpa armigera elevates TPS/TPP and Treh transcript abundance, increases enzyme activities, reduces haemolymph trehalose, raises glucose. This drives broad transcriptomic and metabolomic reprogramming of carbohydrate, lipid, and growth-signalling pathways, resulting in accelerated larval growth. Overexpression of lncRNA1 reverses these phenotypes. Mechanistically, lncRNA1 physically associates with TPS/TPP and Treh mRNAs through evolutionarily conserved sequence motifs, modulating their post-transcriptional dynamics. Targeted deletion of these motifs abolishes regulatory activity and disrupts metabolic homeostasis. This regulatory axis is functionally conserved in Spodoptera frugiperda, validated across loss-of-function, gain-of-function, and cell-based systems. Our findings reveal a conserved lncRNA-based layer of post-transcriptional control over insect energy metabolism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/738560v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@eabc51org.highwire.dtl.DTLVardef@f1aaeforg.highwire.dtl.DTLVardef@d64aforg.highwire.dtl.DTLVardef@14d38e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Trehalose metabolism regulates transcriptional control of muscle development in lepidopteran insects

The connection between trehalose metabolism and insect muscle development has long been unclear. Here we demonstrate that trehalose-derived glucose flux is essential for sustaining glycolysis and maintaining cellular energetics during metamorphosis in Helicoverpa armigera. Disruption of trehalose synthesis through silencing of trehalose 6-phosphate synthase/phosphatase (TPS/TPP) or paramyosin (Prm) produced defective eclosion and alike fragmented muscle fibers. Metabolic profiling revealed broad depletion of glycolytic intermediates and cofactors consistent with elevated AMP and activation of energy-stress signalling. Transcriptome analysis also showed downregulation of the transcription factor E2F/Dp, along with reduced expression of cyclin/CDK components, indicative of cell cycle checkpoint dysregulation. E2F/Dp repression resulted in lower expression of Mef2, Prm, MHC, and other sarcomeric components, causing defective muscle development and weakened muscle architecture. Gene set enrichment analysis, gene regulatory network and promotor binding analysis confirmed E2F binding motifs within promoters of trehalose metabolism and myogenic genes, suggesting a potential metabolic-transcriptional connection. Furthermore, dietary trehalose supplementation partially rescued metabolic depletion and restored expression of E2F targets in TPS/TPP- and E2F/Dp-silenced insects. Collectively, our findings establish trehalose metabolism as a metabolic regulator that couples energy homeostasis to cell-cycle transcriptional control and muscle development.

developmental biology↗

bioRxiv2025

Trehalose Transport Dynamics Underpin a Metabolic Trade-Off between Exogenous Uptake and Endogenous Synthesis in Lepidopteran Insects

Trehalose is the major insect hemolymph sugar and plays a diverse role. Its level is regulated endogenously by the dynamics of biosynthesis and distribution by sugar transporters (STs). The metabolic trade-off between trehalose synthesis and uptake remains poorly understood, despite its critical role in homeostasis. Here, we examined the role of a gut-specific trehalose transporter, HaST46, in regulating this metabolic trade-off in Helicoverpa armigera, a Lepidopteran pest model. Integrated transcriptomics analysis and functional analyses revealed that HaST46 acts as a diet-responsive transporter, localised to the posterior midgut, with trehalose preference. Its expression is modulated in response to dietary trehalose availability, enhancing the efficient exogenous trehalose uptake while attenuating its endogenous synthesis and conserving energy. Functional perturbation through overexpression and silencing revealed a feedback-regulated mechanism in which HaST46 expression showed strong correlation with trehalose metabolising enzymes and other HaSTs isoforms to maintain systemic trehalose homeostasis. Overall, our findings reveal a metabolic trade-off between exogenous trehalose uptake and endogenous synthesis mediated by gut-specific sugar transporters.

physiology↗

bioRxiv2022

Cellular and clinical impact of Protein Phosphatase Enzyme epigenetic silencing in multiple cancer tissues.

Protein Phosphatase Enzymes (PPE) and protein kinases simultaneously control phosphorylation mechanisms that tightly regulate intracellular signaling pathways and stimulate cellular responses. In human malignancies, PPE and protein kinases are frequently mutated resulting in uncontrolled kinase activity and PPE suppression, leading to cell proliferation, migration and resistance to anti-cancer therapies. Cancer associated DNA hypermethylation at PPE promoters gives rise to transcriptional silencing (epimutations) and is a hallmark of cancer. Despite recent advances in sequencing technologies, data availability and computational capabilities, only a fraction of PPE have been reported as transcriptionally inactive as a consequence of epimutations. Using the Infinium HumanMethylation450 BeadChip, we compared DNA methylation profiles from 705 cancer patients across 5 major tissues and 3 cancer cell models against a cohort of healthy controls. Here, we report epimutations in PPE (and their interacting proteins or PPEIP) are a frequent occurrence in the cancer genome and manifest independent of transcriptional activity. We observed that different tumors have varying susceptibility to epimutations and identify specific cellular signalling networks that are primarily affected by epimutations. Additionally, RNA-seq analysis showed the negative impact of epimutations on most (not all) Protein Tyrosine Phosphatase transcription. Finally, we detected novel clinical biomarkers that inform on patient mortality and anti-cancer treatment sensitivity. We propose that DNA hypermethylation marks at PPEIP frequently contribute to the pathogenesis of malignancies and within the precision medicine space, hold promise as biomarkers to inform on clinical features such as patient survival and therapeutic response.

cancer biology↗

bioRxiv2020

Molecular Elucidation of Pancreatic Elastase Inhibition by Baicalein

The serine protease, elastase exists in various forms and plays diverse roles in the human body. Pharmacological inhibition of elastase has been investigated for its therapeutic role in managing conditions such as diabetes, pneumonia and arthritis. Sivelestat, a synthetic molecule, is the only elastase inhibitor to have been approved by any major drug regulatory authority (PMDA, in this case) - but still has failed to attain widespread clinical usage owing to its high price, cumbersome administration and obscure long-term safety profile. In order to find a relatively better-suited alternative, screening was conducted using plant flavonoids, which yielded Baicalein - a molecule that showed robust inhibition against Pancreatic Elastase inhibition (IC50: 3.53 M). Other than having an IC50 almost 1/5th of that of sivelestats, baicalein is also cheaper, safer and easier to administer. While Microscale thermophoresis validated baicalein-elastase interaction, enzyme-kinetic studies, molecular docking and molecular dynamic simulation revealed the mode of inhibition to be non-competitive. Baicalein exhibited binding to a distinct allosteric site on the enzyme. The current study demonstrates the elastase inhibition properties of baicalein in an in-vitro and in-silico environment.

biochemistry↗

bioRxiv2019

Diminution of feeding response in Helicoverpa armigera by inhibition or silencing of sugar gustatory receptor

Gustatory receptor (GR) is one of the essential chemosensory molecules in Lepidopteran pests. GR is involved in sensing several canonical tastes which in turn regulate the diverse behavioral and physiological responses of these insects. In this article, we have evaluated the alteration in feeding response of Helicoverpa armigera by blocking and silencing of sugar-sensing gustatory receptor 9 (HarmGr9). Sf9 cells based assay showed that glucose analogue, Miglitol, can bind to the expressed HarmGr9. This binding might lead to an inhibition of receptor activation and downstream signaling, indicated by reduced intracellular Ca2+ fluorescence. Further, the in-vivo study illustrated the feeding rate reduced on a diet containing miglitol as compared to the larvae fed on the artificial diet. Reduction in feeding rate was prolonged in insects fed on the miglitol containing diet even after switching to the control glucose diet. Competitive cell-based assay and feeding assay, using equimolar glucose and miglitol, also showed an inhibitory effect on HarmGr-9 activation and insect feeding rate. We have observed similar feeding rate reduction in HarmGr9 knockdown in H. armigera larvae. We believe this unique approach of H. armigera feeding response inhibition by blocking the sugar receptor can be further used to develop a novel strategy for agricultural pest management.

molecular biology↗

bioRxiv2018

Identification of rare de novo epigenetic variations in congenital disorders

Certain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. With recent dramatic advances in genomic technologies, genome-wide surveys of cohorts of patients with ND/CAs for point mutations and structural variations have greatly advanced our understanding of their genetic etiologies1,2. However, even after whole genome sequencing (WGS), a substantial fraction of such disorders remain unexplained3. In contrast, the possibility that constitutive epigenetic variations (epivariations) might underlie such traits has not been well explored. We hypothesized that some cases of ND/CA are caused by aberrations of DNA methylation that lead to a dysregulation of normal genome function. By comparing DNA methylation profiles from 489 individuals with ND/CAs against 1,534 population controls, we identified epivariations as a frequent occurrence in the human genome. De novo epivariations were significantly enriched in cases when compared to controls. RNAseq data from population studies showed that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detected and replicated an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations. Thus, some epivariations occur secondary to cis-linked mutations in regulatory regions, providing a rationale for interpreting non-coding genetic variation. We propose that epivariations likely represent the causative genomic defect in 5-10% of patients with unexplained ND/CAs. This constitutes a yield comparable to CNV microarrays, and as such has significant diagnostic relevance.

genomics↗

bioRxiv2017

A survey of DNA methylation polymorphism identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome

While studies such as the 1000 Genomes Projects have resulted in detailed maps of genetic variation in humans, to date there are few robust maps of epigenetic variation. We defined sites of common epigenetic variation, termed Variably Methylated Regions (VMRs) in five purified cell types. We observed that VMRs occur preferentially at enhancers and 3 UTRs. While the majority of VMRs have high heritability, a subset of VMRs within the genome show highly correlated variation in trans, forming co-regulated networks that have low heritability, differ between cell types and are enriched for specific transcription factor binding sites and biological pathways of functional relevance to each tissue. For example, in T cells we defined a network of 72 co-regulated VMRs enriched for genes with roles in T-cell activation; in fibroblasts a network of 21 coregulated VMRs comprising all four HOX gene clusters enriched for control of tissue growth; and in neurons a network of 112 VMRs enriched for roles in learning and memory. By culturing genetically-identical fibroblasts under varying conditions of nutrient deprivation and cell density, we experimentally demonstrate that some VMR networks are responsive to environmental conditions, with methylation levels at these loci changing in a coordinated fashion in trans dependent on cellular growth. Intriguingly these environmentally-responsive VMRs showed a strong enrichment for imprinted loci (p<10-94), suggesting that these are particularly sensitive to environmental conditions. Our study provides a detailed map of common epigenetic variation in the human genome, showing that both genetic and environmental causes underlie this variation.

genomics↗