Biology subjects

Thapa, K.

Publications and source records attributed to Thapa, K..

7 recordsLinked to original sources

bioRxiv2026

An Ovol1 Variant in Endothelial Cells Regulates Slug and is Essential for Pathological Angiogenesis

During development, the blood vasculature expands by sprouting angiogenesis, but the programs that guide this process can become dysregulated in the pathological angiogenesis of neovascular diseases leading to excessive disorganized blood vessels. We previously reported that in endothelial cells, the pro-mesenchymal transcription factor Slug critically regulates angiogenesis through a partial and reversible endothelial-to-mesenchymal transition (pEndoMT); however, the upstream regulators that activate Slug and may contribute to pathological activation of the pEndoMT pathway in disease are still poorly understood. Here, we show that endothelial cells express an unusual low molecular weight variant of Ovol1 - a zinc-finger transcription factor that regulates mesenchymal transition in epithelial cells. Ovol1 and Slug are co-expressed in angiogenic endothelial cells, and using ChIP, we confirm direct Ovol1 binding to the endogenous Slug gene at a species-conserved binding motif. Whereas Ovol1 is typically a transcriptional repressor in epithelial cells, we find using a combination of silencing RNA and lentiviral overexpression constructs that the endothelial Ovol1 variant upregulates Slug, and is sufficient to drive pEndoMT marker expression and enhance endothelial cell migratory capacity. Silencing of Ovol1 abolished sprouting angiogenesis in a 3D in vitro sprouting angiogenesis assay, whereas constitutive overexpression of Ovol1 produced overaggressive and disorganized hypersprouting that depends upon Slug. We generated Ovol1 or Slug endothelial-specific knockout mice (Ovol1ECKO and SlugECKO) and found that healthy developmental angiogenesis of the neonatal mouse retina proceeds relatively normally in knockout animals. By contrast, Ovol1 was reduced in established post-natal blood vessels but became strongly re-expressed in tumor endothelial cells, and we found that colorectal cancer syngraft growth was significantly reduced in both Ovol1ECKO and SlugECKO mice alongside a failure of tumor angiogenesis. Lastly, neovascularization in the oxygen-induced retinopathy (OIR) model was also reduced in SlugECKO mice. In conclusion, we report that an endothelial Ovol1 variant upregulates Slug and drives a mesenchymal-like state, and that this Ovol1-Slug pEndoMT signaling axis is essential for pathological angiogenesis in neovascular disease models.

cell biology↗

bioRxiv2026

Shared and Divergent Features of Cardiac Transcriptome and Glucose Metabolism Markers in Human and Mouse HFpEF

Heart Failure with Preserved Ejection Fraction (HFpEF) is more prevalent in females and is associated with altered cardiac glucose metabolism. However, whether these metabolic alterations are conserved across sexes and between humans and widely used cardiometabolic mouse model of HFpEF remains unclear. We investigated species-, sex-, and ventricle-specific conserved and divergent features of HFpEF. Cardiometabolic HFpEF was induced in mice using the 'two-hit' model (high-fat diet + L-NAME), followed by assessment of cardiac function, RNA sequencing, and protein expression in the right (RV) and left (LV) ventricles. Published human HFpEF RV and LV RNA-seq datasets were reanalyzed and compared with our mouse data. Only male HFpEF mice recapitulated human phenotype of increased RV GLUT1 protein. In contrast, mouse GLUT1 was downregulated in RV of females and in the LV of both sexes, whereas GLUT4 protein remained unchanged. Cardiac PDK4 transcript and protein levels increased in the RV and LV of mice. Conversely, human PDK4 mRNA levels were reduced in the RV with HFpEF and unchanged in LV. Cardiac transcriptome analysis in mice revealed extensive alterations in LV, particularly in females, with enrichment of inflammatory pathways. Cross-species analysis demonstrated greater conservation of HFpEF-associated signatures in the RV than the LV. Furthermore, number of differentially expressed transcripts in human LV increased substantially after excluding patients with atrial fibrillation or diabetes. Overall, the RV of the 'two-hit' model more closely resembles human HFpEF. The cardiac transcriptome reflects sexual dimorphism, and conserved signatures are primarily associated with metabolic alteration, mitochondrial dysfunction, and cellular stress.

physiology↗

bioRxiv2026

Phenological Plasticity without Directional Change: Tropical Hornbills Track Temperature but Maintain Reproductive Stability

Climate change is altering breeding phenology in birds worldwide, yet tropical systems remain understudied despite harbouring the greatest avian diversity. We drew upon 26 years (1998-2024) of breeding phenology and reproductive success data on three sympatric Asian hornbill species (Great Hornbill Buceros bicornis, Wreathed Hornbill Rhyticeros undulatus, Oriental Pied Hornbill Anthracoceros albirostris) from a tropical forest in northeast India to examine whether trends in long-term breeding parameters reflect directional climate change or interannual variability. Over the study period, we found no significant directional trends in nest entry timing, occupancy, or breeding success over 26 years, despite modest regional warming. However, breeding parameters showed sensitivity to interannual temperature variation, with pre-breeding temperature (January-February) explaining 36-70% of variance in nest timing. Temperature sensitivity differed among species, with Wreathed Hornbill showing the strongest response (-15.9 days/{degrees}C), followed by Great Hornbill (-9.8 days/{degrees}C), and Oriental Pied Hornbill showing the weakest (-4.8 days/{degrees}C), consistent with predictions that larger, frugivorous species with extended breeding cycles would exhibit greater climatic sensitivity. The underlying mechanism appears related to a body size-phenology-thermal exposure interaction: Oriental Pied Hornbills nest later (mid-April) with shorter breeding cycles ([~]90 days), completing reproduction before peak monsoon heat (June), whereas both larger species nest earlier (mid-February) but endure thermal stress throughout extended breeding cycles ([~]130+ days) into August. Notably, annual occupancy and breeding success remained stable across years despite strong phenological responses to temperature, suggesting that phenological plasticity may help maintain reproductive performance under current climatic variation. These findings indicate that tropical cavity-nesting frugivores exhibit phenological plasticity coupled with demographic stability, though the mechanisms underlying this apparent buffering remain incompletely understood, and body size-dependent differences in thermal exposure suggest heterogeneous vulnerabilities to future warming scenarios.

ecology↗

bioRxiv2026

Chromatoid body integrates piRNA, SMG6 and m⁶A pathways to control mRNAs in the male germline

Spermatogenesis requires tightly controlled transcriptome regulation, supported by the PIWI-interacting RNA (piRNA) and nonsense-mediated decay (NMD) pathways, both concentrated in the chromatoid body (CB) of haploid spermatids. We previously showed that the NMD endonuclease SMG6 interacts with the piRNA-binding protein PIWIL1, and that loss of either factor results in overlapping mRNA dysregulation, suggesting functional cooperation. Here, we demonstrate that SMG6 and PIWIL1 assemble with shared RNA-regulatory proteins and bind common mRNA targets in the testis. Functional experiments in GC-2spd cells revealed cooperative regulation of selected transcripts, including Ccny and Taf1d, and established that SMG6 is required for piRNA-guided degradation of these targets, implicating its endonuclease activity in the piRNA pathway. Target mRNAs were mA-methylated, and this modification shaped their expression levels, SMG6 binding, and CB localization. Moreover, intact target mRNAs accumulated in CBs isolated from Smg6-cKO testes, indicating defective CB-associated decay. Together, these findings uncover a key role for the CB in mRNA regulation through coordinated action of the NMD and piRNA pathways.

cell biology↗

bioRxiv2024

Patterns of leaf, flower and fruit phenology and environmental relationships in a seasonal tropical forest in the Indian Eastern Himalaya

Tree phenology plays an important role in determining the structure and function of tropical forest communities. However, there are few long-term studies on tree phenology from South Asia. We monitored 716 trees of 54 species monthly from 2011 to 2023 for leaf flush, flowering, and fruiting in Pakke Tiger Reserve, Arunachal Pradesh, India. We examined monthly patterns in the percentage of species and trees in leaf flush, flower and fruit and characterized phenological seasonality using circular statistics. Flowering periodicity was classified using Fourier analysis and we examined the relationships between phenological activity and temperature, rainfall, solar radiation and daylength using GAMLSS. Leaf flush and flowering were moderately seasonal, peaking in the warm dry season months of March to May. Fruiting patterns and their seasonality differed among dispersal modes. At the community level and for bird-dispersed species, fruiting was bimodal and relatively aseasonal, peaking in April and October. The highly seasonal fruiting of mammal-dispersed species peaked in October, while that of mechanically-dispersed species was bimodal and concentrated in the dry season months. The majority of species (78.13%) and trees (51.17%) flowered annually. Daylength, solar radiation and minimum temperature had significant nonlinear effects on phenology. This indicated the existence of narrow ranges of optimal climatic conditions for phenology, which could be affected by climate change. Our study emphasizes the need for long-term monitoring to rigorously quantify phenological patterns, particularly in the context of rapid global change.

plant biology↗

bioRxiv2023

A prognostic matrix code defines functional glioblastoma phenotypes and niches.

Interactions among tumor, immune and vascular niches play major roles in driving glioblastoma (GBM) malignancy and treatment responses. The composition, heterogeneity, and localization of extracellular core matrix proteins (CMPs) that mediate such interactions, however, are not well understood. Here, we characterize functional and clinical relevance of genes encoding CMPs in GBM at bulk, single cell, and spatial anatomical resolution. We identify a "matrix code" for genes encoding CMPs whose expression levels categorize GBM tumors into matrisome-high and matrisome-low groups that correlate with worse and better survival, respectively, of patients. The matrisome enrichment is associated with specific driver oncogenic alterations, mesenchymal state, infiltration of pro-tumor immune cells and immune checkpoint gene expression. Anatomical and single cell transcriptome analyses indicate that matrisome gene expression is enriched in vascular and leading edge/infiltrative anatomic structures that are known to harbor glioma stem cells driving GBM progression. Finally, we identified a 17-gene matrisome signature that retains and further refines the prognostic value of genes encoding CMPs and, importantly, potentially predicts responses to PD1 blockade in clinical trials for GBM. The matrisome gene expression profiles may provide biomarkers of functionally relevant GBM niches that contribute to mesenchymal-immune cross talk and patient stratification to optimize treatment responses.

cancer biology↗

bioRxiv2022

Melanocortin 1 receptor regulates cholesterol and bile acid metabolism in the liver

Melanocortin 1 receptor (MC1-R) is widely expressed in melanocytes and leukocytes, and is thus strongly implicated in the regulation of skin pigmentation and inflammation. MC1-R mRNA has also been found in the rat and human liver, but its functional role has remained elusive. We hypothesized that MC1-R is functionally active in the liver and involved in the regulation of cholesterol and bile acid metabolism. We generated hepatocyte-specific MC1-R knock-out (L-Mc1r-/-) mice and phenotyped the mouse model for lipid profiles, liver histology and bile acid levels. L-Mc1r-/- mice had significantly increased liver weight, which was accompanied by elevated levels of total cholesterol and triglycerides in the liver as well as in the plasma. These mice demonstrated also enhanced liver fibrosis and a disturbance in bile acid metabolism as evidenced by markedly reduced bile acid levels in the plasma and feces. Mechanistically, using HepG2 cells as an in vitro model, we found that selective activation of MC1-R in HepG2 cells reduced cellular cholesterol content and enhanced uptake of low- and high-density lipoprotein particles via a cAMP-independent mechanism. In conclusion, the present results demonstrate that MC1-R signaling in hepatocytes regulates cholesterol and bile acid metabolism and its deficiency leads to hypercholesterolemia and enhanced lipid accumulation and fibrosis in the liver.

physiology↗