Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Multi-omic comparative analysis of members of the Akkermansia genus reveals species-specific adaptations to growth in mucin.

ABSTRACTAkkermansia muciniphila is a commensal, mucophilic anaerobic bacterium that influences human host physiology. Although additional prominent Akkermansia species have been identified in humans, their responses to mucin-rich environments remain poorly understood. We conducted a comparative analysis of four representative human isolates: A. muciniphila, A. biwaensis, A. massiliensis, and A. durhamii, focusing on proteins involved in mucin degradation, cell-surface components, and species-specific secreted metabolites during growth in mucin. Our results reveal unique adaptations of A. muciniphila to exploit mucin-rich environments, including higher expression of key mucin-degrading proteins during growth in mucin compared to other Akkermansia species. We also demonstrate that A. muciniphila expresses a significantly greater number of secreted PEPCTERM proteins, which contribute to host colonization. The expression of pili-associated proteins varied across species, with non-muciniphila species producing more predicted pili, suggesting the ability to colonize additional niches. Lastly, we find that small peptides previously linked to host and microbiome modulation in the GI tract are over-represented in the metabolomes of non-muciniphila species. Conversely, A. muciniphila produces more hydroxylated fatty acids, indicating potential mechanisms for modulating host health. These findings highlight genetic and regulatory mechanisms that may explain A. muciniphilas dominance in the human gut.

microbiology↗

bioRxiv2025

Ubiquitin ligase PUB41 modulates root hair development in Arabidopsis via interaction with the auxin polar transporter PIN2

Root hairs are short-lived, elongated tubular extensions of epidermal cells, that increase the surface area improving absorption of water and nutrients. Root hair development is affected by developmental, environmental, and hormonal cues, primarily Auxin. Auxin is synthesized in shoot and root apical transporters. Here, we report that mutants of the Arabidopsis PLANT U-BOX41 (AtPUB41) gene encoding a ubiquitin ligase (E3) develop fewer and shorter root hairs than wild-type (WT) plants. pub41 mutants are not impaired in sensing and responding to exogenous auxin, suggesting that the root hair phenotype may result from a change in auxin levels and/or distribution. Indeed, Auxin enhances the steady-state levels of PUB41 transcript and protein in the roots. A catalytically inactive decoy protein lacking the U-box, PUB41({Delta}U), complements the sparse root hair phenotype of pub41 mutants to the same extent as full-length PUB41. Plants expressing PUB41({Delta}U) are hyperresponsive to auxin-induced root hair development and PUB41({Delta}U) accumulates in the root elongation and differentiation zones, preferentially in trichoblast cells and their root hairs. Furthermore, in these cells, PUB41-eGFP and PUB41({Delta}U)-eGFP are primarily located on the anticlinal faces, as is the auxin PIN2 exporter. We show colocalization of PUB41({Delta}U)-eGFP and PIN2-mCherry, and binding in vitro of PUB41 to the cytoplasmic hydrophilic loop of PIN2. Moreover, PUB41({Delta}U) protein stabilizes PIN2 and enhances its abundance in the roots. Our results indicate that PUB41 modulates root hair development via interaction with PIN2. Significance StatementRoot hairs are extensions of the root epidermal cells, which are crucial for the uptake of water and nutrients from the soil. Root hair development is highly regulated and affected by developmental, environmental, and hormonal cues. In this study, we demonstrate that the auxin-induced ubiquitin ligase, PLANT U-BOX 41 (PUB41), regulates root-hair development by interacting with the auxin polar transporter PIN2 responsible for determining auxin levels.

plant biology↗

bioRxiv2025

Copy Number Variation-Based Molecular Sexing of Ixodes scapularis and Rhipicephalus microplus Immature Stages Using qPCR and ddPCR Approaches

Accurate sex identification of immature ticks is essential for understanding sex-specific ecological dynamics, pathogen transmission, and reproductive biology. However, tick larvae and nymphs lack morphological sexual dimorphisms, limiting the studies. Here, we report the development and validation of copy number variation (CNV)-based molecular sexing approach for two important hard tick species, Ixodes scapularis, a major public health vector of human pathogens, and Rhipicephalus microplus, a pest responsible for significant economic losses in cattle industry. Using newly published chromosomal-level genome assemblies and whole-genome resequencing data, we identified female-enriched CNVs in two genes, calcium/calmodulin-dependent 3,5-cyclic nucleotide phosphodiesterase 1A-like (NPD) and rap guanine nucleotide exchange factor 2-like (RAPGEF2), and developed SYBR-Green based and probe-based qPCR, and droplet digital PCR (ddPCR) assays using DNA extracted non-destructively from a single leg, preserving ticks for continued feeding, molting, and behavioral analysis. In I. scapularis, we were able to assign the sex of 87% of nymphs based on results from at least two molecular tests, and these assignments were confirmed when the nymphs later molted into adults. In R. microplus, two qPCR assays revealed clear, sex-linked differences in gene copy number, despite the species having an XX: XO sex system. Together, these findings indicate that CNV-based markers are a reliable and widely applicable method for sex determination in immature ticks. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/695610v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@14616c5org.highwire.dtl.DTLVardef@80e758org.highwire.dtl.DTLVardef@d46484org.highwire.dtl.DTLVardef@1324e5_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Ewing Sarcoma Breakpoint Region 1 (EWSR1) protein binds to the non-structural protein-2 and the non-coding regions of the Chikungunya virus genome to inhibit the virus replication

Chikungunya virus (CHIKV) is an alphavirus with a single-stranded RNA genome. Conserved sequence elements within the 5'- and 3'-non-coding regions (NCRs) of the CHIKV genome interact with host proteins to regulate viral RNA replication. Electrophoretic mobility shift assays (EMSA) and mass spectrometry identified several host RNA-binding proteins that associate with these conserved NCR elements, among which EWSR1 uniquely bound the 3'-ends of both the plus-sense genomic RNA and the minus-sense replication intermediate RNA. EMSA and biolayer interferometry demonstrated that EWSR1 binds strongly to two RNA elements: a 48-nucleotide region in the plus-strand 3'-NCR (3NCR48) and a 50-nucleotide region at the 3'-end of the minus-strand replication intermediate (5NCR-RC50), which is complementary to the genomes 5'-NCR and its adjacent sequence. RNA immunoprecipitation from CHIKV-infected cells confirmed that EWSR1 binds CHIKV RNA in vivo. Functional analyses revealed that CHIKV infection downregulates EWSR1 expression and causes its cytoplasmic accumulation. Knockdown or knockout of EWSR1 expression increased CHIKV genomic RNA levels and viral titers, whereas its overexpression suppressed both. EWSR1 reduced the synthesis of both plus- and minus-sense CHIKV RNAs in infected cells. Additionally, EWSR1 was found to bind CHIKV nsP2 and inhibit its helicase activity, which is critical for viral genome replication. The antiviral activity of EWSR1 extended to Ross River virus but not to Sindbis virus, consistent with conservation of the 48-nucleotide sequence in their respective 3'-NCRs. Together, these findings identify EWSR1 as a novel host restriction factor that limits CHIKV replication through specific interactions with viral RNA and the nsP2 protein. IMPORTANCEChikungunya virus (CHIKV) poses a significant medical challenge, necessitating the development of novel antiviral strategies. This study demonstrates that the host protein EWSR1 plays a key role in controlling CHIKV replication. By binding to specific regions of viral RNA and interacting with nsP2, a critical viral enzyme, EWSR1 inhibits viral RNA synthesis and reduces viral titers. In the absence of EWSR1, CHIKV replicates more efficiently, underscoring its antiviral function. These findings establish EWSR1 as a novel host restriction factor that limits CHIKV replication. Understanding this interaction enhances our knowledge of host-virus dynamics and may guide the design of new antiviral approaches against CHIKV and related alphaviruses.

microbiology↗

bioRxiv2025

An integrated workflow for structural virology with a 100 keV electron microscope

Cryo-EM has revolutionized structural biology, especially for flexible and heterogeneous samples, although access to high end microscopes that enable these studies remains a bottleneck. While 300 keV microscopes have been the go-to for high-resolution structural determination, they are expensive and restricted to institutional and national facilities needing specialized expertise, with access falling far short of the demand. Here, we present the user-managed operation of a cheaper 100 keV electron microscope within a structural biology laboratory enabling close integration with protein production, biochemical and biophysical studies. We provide details and considerations for the installation of the microscope, its day-to-day maintenance, and operations. Using virus surface glycoproteins as case studies, we illustrate the workflow from grid screening, data collection, and data processing, and provide examples of data quality. This user-administered setup provides a training platform for researchers at all levels, with beginners in cryo-EM achieving proficiency to independently operate the microscope within a month of regular use and training. We have demonstrated routine high-quality low-resolution reconstructions using a Ceta CMOS camera and high-resolution reconstructions enabling building of atomic models using a Falcon C direct detector. While there are several examples of facilities that manage cryo-EM and individual laboratories leveraging cryo-EM, we provide here the first demonstration of a modern group independently doing both successfully, something that has been talked about frequently but rarely seen.

biochemistry↗

bioRxiv2025

Nutrient/TOR signaling controls Mitochondrial transcription factor A (TFAM) to regulate organismal growth in Drosophila

Animals must adapt their growth to fluctuations in nutrient availability to ensure proper development. While nutrient-sensing tissues coordinate organismal growth through inter-organ signaling, the metabolic changes within these tissues that mediate whole-body growth control remain poorly understood. Using Drosophila larvae, we show that TOR (Target-Of-Rapamycin), a conserved nutrient-sensing kinase, controls developmental growth through regulation of the mitochondrial genome transcription factor TFAM, which controls mitochondrial bioenergetic capacity and metabolic state. We find that nutrient/TOR signaling post-transcriptionally suppresses TFAM protein levels. Furthermore, we find that TOR regulation of TFAM in the larval fat body, a key nutrient-sensing tissue, controls developmental growth. These findings establish a molecular mechanism linking nutrient-sensing pathways to mitochondrial metabolic reprogramming, revealing how environmental nutrient availability coordinates organismal growth through tissue-specific metabolic control.

cell biology↗

bioRxiv2025

In situ profiling of nanoscale displacements uncovers mechano-architectural predictors of osteoarthritis emergence

Mechanical and anatomical interplay between the distinct tissues of the knee joint is essential for maintaining functional integrity during healthy ageing and contributes to the mechanisms that drive osteoarthritis (OA). In this study, we investigate how age- and disease-associated alterations in joint anatomy influence load transmission and tissue-level strain distribution. Using full-field synchrotron X-ray computed tomography coupled with digital volume correlation, we hierarchically characterised in situ nanoscale strains generated in response to mechanical loading across the tibial epiphysis. Our findings show that greater compressive strains accumulate in the articular condyle of male OA-prone (STR/Ort) epiphyses. Finite element modelling further demonstrated that these strain concentrations are associated with reduced load-bearing capacity, which arise from architectural differences localised to the subchondral bone plate. By coupling high-resolution imaging with computational modelling, our work provides new insights into how structural-function changes to joint anatomy contribute to the initiation and progression of mechanically driven OA. Our approach offers a means to identify early imaging biomarkers prior to OA diagnosis and has potential for monitoring interventions aimed at preserving joint mechanics while promoting healthy joint ageing.

bioengineering↗

bioRxiv2025

Exposure to immune stimuli reprograms alveolar macrophages to acquire neutrophil-derived antimicrobial molecules to prevent staphylococcal pneumonia

The protective adaptation of innate immune defenses against respiratory pathogens has been linked to previous exposure to immune stimuli; however, the underlying mechanisms of these adaptations are not yet fully understood. Here, we show that pre-exposure to a low dose of non-specific immune stimuli or infection protects against subsequent lethal methicillin-resistant Staphylococcus aureus (MRSA) challenge. This enhanced protection concurs with increased alveolar macrophages (AMs) resulting from a self-renewal process in the lungs. Importantly, these AMs are programmed to acquire neutrophil-released antimicrobial enzymes from the extracellular space to kill MRSA, prevent tissue damage, and rapidly restore lung homeostasis. The gain of AM functions is dependent on differential gene expression, including expression of the efferocytosis receptor MerTK and the anti-apoptotic regulator Bcl-xL. Thus, our data highlight that the acquisition of neutrophil enzymes by AMs is an integral component of innate immune adaptation.

immunology↗

bioRxiv2025

Increased versican and fibrosis in mesenteric lymph nodes disrupts immune surveillance and drives systemic bacterial dissemination in cirrhosis

Background and ObjectiveMesenteric lymph nodes (MLN) are immunological barriers against bacterial translocation (BT). Enhanced gut BT through MLN facilitates bacterial spread and higher mortality in cirrhosis. We aimed to elucidate mechanisms underlying MLN failure to effectively contain BT during advanced cirrhosis. DesignBT and immune cells were analyzed in lymphoid organs and circulation of control and CCl4 models, with and without MLN (MLNx). MLN proteomics identified versican (VCAN) as major upregulated protein in cirrhosis, whose immunomodulatory function was examined in vitro and in vivo in CCl and (Bile duct ligation) BDL models. Plasma VCAN were measured in end-stage cirrhosis patients and analyzed as mortality predictor. ResultsIn control rats, bacteria were confined to MLN, whereas cirrhotics showed BT to MLN, lymph, and portal blood. Compared to control, CCl4 rats had increased activated Th-cells in MLN but reduced in circulation. In control-MLNx rats, activated Th-cells were reduced in circulation vs controls. In BDL models, MLN CFU correlated with VCAN level. In vitro, VCAN enhanced T cell suppression and impaired migration which was reversed by CD44 blockade. In vivo VCAN knockdown reduced fibrosis and bacterial burden in MLN, while restoring Th-cell activation locally and systemically. Clinically, plasma VCAN levels were elevated in advanced cirrhosis patients and remained an independent predictor of 28-day sepsis-related mortality. ConclusionIncreased VCAN impairs T cell activation and migration in MLN, fostering immune suppression and bacterial persistence. Plasma VCAN levels serve as promising biomarker for MLN dysfunction and prognostic factor for predicting sepsis-related mortality in end-stage cirrhosis. What is already known on this topic - Enhanced gut bacterial translocation through mes-enteric lymph nodes (MLN) facilitates systemic bacterial spread and increases mortality in cirrhosis. The mechanisms underlying MLN failure to effectively contain bacterial spread during advanced cirrhosis remain largely unknown. What this study adds - The study unveils a critical role of lymph node fibrosis and elevated versican (VCAN) expression in causing deranged immune responses and bacterial clearance in MLN, increasing systemic bacterial load and immunosuppression. Most importantly, high plasma VCAN emerges as a prognostic biomarker for functional failure of MLN and 28-day mortality predictor in critically ill patients with cirrhosis. How this study might affect research, practice or policy - VCAN, representing enhanced MLN fibrosis and dysfunction, emerges as a predictive biomarker of adverse clinical out-comes in patients with advanced cirrhosis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/690350v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@369f4eorg.highwire.dtl.DTLVardef@14c232org.highwire.dtl.DTLVardef@d99b21org.highwire.dtl.DTLVardef@57ac95_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Comparative metagenomics using pan-metagenomics graphs

Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to complex microbial communities remains challenging due to the scale and complexity of metagenomic data. Existing multi-sample sequence graphs used in these settings are highly complex, computationally expensive, less accurate than single-sample alternatives, and often involve arbitrary coarse-graining. Here, we present copangraph, a multi-sample sequence-graph-based analysis framework for comprehensive comparisons of genomic variation across metagenomes. Copangraph uses a novel homology-based graph, which provides both non-arbitrary, evolutionary-motivated grouping of sequences into the same node as well as flexibility in the scale of variation represented by the graph. Its construction relies on hybrid coassembly, a new coassembly approach in which single-sample graphs are first constructed separately and are then merged to create a multi-sample graph. We also present an algorithm that uses paired-end reads to improve detection of contiguous genomic regions, increasing accuracy. Our results demonstrate that copangraph captures sequence and variant information more accurately than alternative methods, provides graphs that are more suitable for comparative analysis than de Bruijn graphs, and is computationally tractable. We show that copangraph reflects meaningful metagenomic variation across diverse scenarios. Importantly, it enables significantly better performance than other metagenomic representations when predicting the gut colonization trajectories of Vancomycin-resistant Enterococcus. Our results underscore the value of our multi-sample, graph-based framework for comparative metagenomic analyses.

bioinformatics↗

bioRxiv2025

Repurposing ethacridine as a potent MMPL3 Inhibitor for the treatment of tuberculosis

Mycobacterium tuberculosis (Mtb), the pathogen responsible for tuberculosis, remains a major global health threat, particularly with the rise of multidrug-resistant and extensively drug-resistant strains. This has renewed interest in repurposing existing drugs and exploring new cellular targets. The mycobacterial cell envelope is a key barrier to antibiotics and an attractive site for therapeutic intervention. In this study, we identify the FDA-approved drug ethacridine as a strong inhibitor of MmpL3, an essential transporter required for exporting trehalose monomycolate and building the cell wall. Computational docking and molecular dynamics indicate that ethacridine engages the MmpL3 binding pocket at residues also targeted by SQ109. Ethacridine shows potent activity against drug-sensitive and resistant Mtb isolates, with an MIC of 1 g/mL, and remains effective against non-replicating bacteria and intracellular infection. Ethacridine-resistant mutants, overexpression strains, and a spheroplast TMM-flipping assay confirm MmpL3 as the target. The compound also disrupts the membrane potential, and flow-cytometry assays

microbiology↗

bioRxiv2025

The transcription factor BCL11A restores differentiation potential to aged oligodendrocyte progenitor cells

In young animals, oligodendrocyte progenitor cells (OPCs) undergo robust differentiation, progressing through stages to become pre-myelinating oligodendrocytes (Pre-OL) and ultimately myelinating oligodendrocytes (OLs). However, OPCs from aged animals have reduced differentiation ability. This disrupts myelin maintenance in the central nervous system (CNS), leading to a lack of remyelination following demyelinating injury and impaired adaptive myelination as a mechanism of learning. To uncover novel factors essential for restoring resilience in aged OPCs, we employed a data-driven approach involving the development of a computational pipeline, gSWITCH (accessible at: https://altoslabs.shinyapps.io/gSWITCH/), that allows for capture of precise dynamic gene expression patterns to pinpoint potential switch genes during lineage progression. Using gSWITCH to identify potential switch genes crucial for OPCs, we conducted a comparative analysis of gene expression in OPCs isolated from young and aged animals. This revealed a group of transcription factors with decreased expression in aged OPCs. Further analysis of transcription factor binding site enrichment in OPC switches highlighted Bcl11a, a zinc finger transcription factor that could potentially serve as a master regulator of many switch genes. Ectopic overexpression of Bcl11a in aged OPCs did not enhance their proliferation; however, it significantly enhanced their differentiation into OLs. Overexpression of Bcl11a in aged mice, followed by demyelination injury in spinal cord white matter, significantly increased the differentiation of OPCs into OLs within the injury region compared to control aged mice. Furthermore, we found that Bcl11a is absent in invertebrates and has undergone pervasive purifying selection throughout vertebrate evolution, constraining its amino-acid sequence by eliminating deleterious mutations. Our study shows that reversing the age-related decline of this evolutionarily conserved factor in aged OPCs restores their impaired capacity for differentiation.

neuroscience↗

bioRxiv2025

A cytochrome P450 G subfamily member, CYP4G35, is highly expressed in antennae and modulates olfactory response in Aedes aegypti mosquitoes.

The cytochrome P450 enzymes of the CYP4G subfamily are some of the most enigmatic insect P450s. The dipterans with sequenced genomes have two CYP4G paralogs. In Drosophila melanogaster, CYP4G1 is highly expressed in the oenocytes and catalyzes the last enzymatic step in the biosynthesis of cuticular hydrocarbons. In contrast, CYP4G15 is expressed in the brain glial cells, but its function is unknown. The Aedes aegypti genome encodes two CYP4Gs: CYP4G36 (ortholog of DmCYP4G1) and CYP4G35 (ortholog of DmCYP4G15). Here, we show that CYP4G35 is highly expressed in mosquito antennae, and the RNAi knockdown of CYP4G35 results in delayed host-seeking. Ae. aegypti CYP4G knockout lines confirmed delayed host-seeking behavior in CYP4G35 knockout females. Proteomics analysis of CYP4G35 KO females also corroborates the physiological findings and shows upregulation of proteins related to olfaction and other CYP4Gs to compensate for the lack of CYP4G35. Immunohistochemistry and in situ hybridization were used to localize CYP4G35 and demonstrated its expression in the sensilla lymph of the antennae and the tip of the proboscis. CYP4G35 and CYP4G36 fusion proteins with cytochrome P450 reductase demonstrated that, unlike CYP4G36, CYP4G35 lacks an oxidative decarbonylase function. Together, our data support a novel function of CYP4G35 in modulating olfactory response.

molecular biology↗

bioRxiv2025

Chemical Dice Integrator (CDI): A Scalable Framework for Multimodal Molecular Representation Learning

The machine learning landscape for molecular property prediction is fragmented, with numerous Featurizers each capturing a narrow, specialized view of chemical structure. This heterogeneity forces a suboptimal choice of representation a priori, limiting model generalizability. We introduce the Chemical Dice Integrator (CDI), a hierarchical framework that unifies six orthogonal molecular representations, physicochemical (Mordred), topological (GROVER), visual (ImageMol), biological (Signaturizer), quantum-mechanical (MOPAC), and linguistic (ChemBERTa), into a single, coherent embedding. The framework consists of CDI-Basic, a two-tiered autoencoder that fuses these modalities, and CDI-Generalised, a Mamba State-Space Model (SSM) that learns a direct, efficient map from SMILES strings to the unified embedding space. Extensive benchmarking across 23 classification (171 tasks) and 10 regression datasets demonstrates that CDI embeddings consistently achieve superior predictive performance compared to individual Featurizers and standard feature aggregation methods. The CDI-Generalised model achieves this performance with exceptional computational efficiency, outperforming deep learning Featurizers in terms of speed and resource overhead. Furthermore, we demonstrate that the CDI embedding is chemically intuitive, allowing for the sensitive distinction of nuanced structural variants, such as chiral enantiomers and kekulized SMILES forms. By bridging multimodal chemical intelligence with scalable, sequence-based inference, CDI offers a strong foundation for molecular machine learning.

bioinformatics↗

bioRxiv2025

LncRNA YIYA enhances pancreatic cancer proliferation under high-glucose conditions through RAS and PKM2 mediated metabolic reprogramming that reinforces the Warburg phenotype

Diabetes and the resulting hyperglycemia are metabolic complications frequently linked to pancreatic cancer (PC). In this study, we observe that the long non-coding RNA (lncRNA)-YIYA, which resides in a genomic region (1q32), frequently altered in various cancers, is overexpressed under conditions of chronic or intermittent high glucose (HG; 25 mM) compared to normal glucose (NG; 5.5 mM) in pancreatic ductal adenocarcinoma (PDAC) cells. It plays a pivotal role in regulating cellular metabolism-linked proliferation of PDAC cells, both under 2D and 3D conditions. Analysis of clinical datasets suggested that patients with elevated YIYA expression generally experience reduced survival in pancreatic cancer. Mechanistically, YIYA was found to regulate cellular energy metabolism and promote a Warburg phenotype, thereby facilitating the rapid proliferative status of PDAC cells. YIYA-mediated effects were found to be dependent on KRAS. Interestingly, the RIP assay revealed that YIYA interacts not only with KRAS but also with an important enzyme catalyzing the final step of the biochemical process, glycolysis, pyruvate kinase M2 (PKM2). YIYA was found to be predominantly localised in the cytoplasm, protecting the stability of the KRAS protein under a hyperglycaemic state. Importantly, YIYA knockdown enhanced autophagy-mediated degradation of KRAS. Our study is the first to identify YIYA as a glucose-responsive lncRNA in PDAC cells, and to reveal a novel YIYA-mediated connection between oncogenic KRAS signalling and metabolic reprogramming. Targeting YIYA represents a promising therapeutic strategy by disrupting the KRAS-PKM2-Warburg axis, thereby sensitizing PDAC cells. Graphical abstracts figure: Proposed model illustrating the effect of hyperglycemia on lncRNA YIYA-mediated regulation of KRAS signaling and metabolic reprogramming in pancreatic cancerUnder hyperglycemic conditions, elevated glucose uptake through GLUT (Glucose Transporter) enhances glycolytic flux, leading to increased levels of PEP (Phosphoenolpyruvate) and activation of PKM2 (Pyruvate Kinase M2), which results in increased pyruvate flux toward the LDH (Lactate Dehydrogenase) pathway and subsequent increased lactate production, promoting the Warburg effect. Downregulation of MPC (Mitochondrial Pyruvate Carrier) also supports reduced shuttling of pyruvate towards the TCA (Tricarboxylic Acid) cycle. On the other hand, constitutively activated master regulator KRAS activates the downstream proliferative signalling via AKT and other DTs (Downstream targets), which upregulates various genes, including lncRNA YIYA aka LINC00538. YIYA exists in a functional complex with KRAS and PKM2, further reinforcing glycolytic and proliferative signalling. Additionally, YIYA suppresses autophagy-mediated degradation of KRAS. Together, these events contribute to hyperglycemia-driven epigenetic changes, metabolic reprogramming, and tumor progression in pancreatic cancer cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/685546v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@13d271org.highwire.dtl.DTLVardef@15d01fcorg.highwire.dtl.DTLVardef@12d7225org.highwire.dtl.DTLVardef@a11c5e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

The serotonin 1B receptor modulates striatal activity differentially based on behavioral context

The dorsomedial striatum (DMS) is critical for goal-directed behavior and has been implicated in both motivating and inhibiting behavioral responses. The DMS circuitry is complex as it integrates multiple inputs from the cortex, thalamus, and other subcortical structures including midbrain dopamine neurons. Though less studied, serotonin neurons from the dorsal raphe nucleus also richly innervate the DMS, which expresses the majority of the 14 receptor subtypes for serotonin. In particular, slice electrophysiology shows that the serotonin 1B receptor (5-HT1BR) impacts DMS physiology and plasticity, and behavioral experiments show that 5-HT1BR expression modulates impulsivity and other DMS-dependent reward-related behaviors. In these studies, our goal was to investigate the effects of 5-HT1BR on the DMS in vivo during goal-directed behavior in mice. Using a genetic 5-HT1BR loss-of-function model, we examined the calcium activity of individual medium spiny neurons (MSNs) in the DMS during operant tasks of responding and waiting. We found that knockout of 5-HT1BRs resulted in a significant reduction of excitatory calcium responses and an increase in the proportion of cells with inhibitory calcium responses following receipt of a reward. This suggests that serotonin may recruit MSN activity in response to reward via actions at 5-HT1BRs. On the other hand, in a behavioral paradigm designed to test impulsivity, we found that serotonin may inhibit DMS calcium activity through 5-HT1BRs. Specifically, mice lacking 5-HT1BR expression had a larger proportion of cells showing increased calcium responses during the waiting period of the trial, compared to controls. These results point to the importance of in vivo studies to understand the functional role of DMS serotonin in reward-related behavior. Overall our results demonstrate that serotonin can modulate the DMS in a behavioral state-specific manner, potentially providing a mechanism for how serotonin effects on behavior are context-dependent.

neuroscience↗

bioRxiv2025

Wnt7a is a Novel Lymphangiocrine Factor Driving Cholangiocyte Proliferation during Liver Regeneration

The significance of lymphatic vessels (LVs) and lymphatic endothelial cells (LyECs) during liver regeneration remains unexplored. We aimed to characterize contribution of LVs and LyECs in liver regeneration using two-thirds partial hepatectomy (PHx) models. An increased number and diameter of CD31+PDPN+ LVs was observed at day 2 and 5 post-PHx. Proteomic analysis of LyECs and ELISA studies in conditioned media of LyECs revealed that one of the secreted proteins, Wnt7a was uniquely expressed at day 2 post PHx. In vitro studies confirmed that Wnt7a is a potent stimulator of proliferation for both hepatocytes and cholangiocytes. In vivo inhibition of lymphangiogenesis and reduction in Wnt7a led to a decline in the percentage of CK19+ cholangiocytes and bile ducts. Western blot analysis showed that Wnt7a activated the downstream Frizzled 7 receptor and non-canonical planar-cell-polarity pathway to drive the proliferation of cholangiocytes. In vivo, Wnt7a loss-of-function experiments in zebrafish along with inhibitor studies in rat models of PHx further re-iterated clear links between Wnt7a and proliferation of bile ducts. Pro-regenerative effects of Wnt7a were demonstrated in a model of small-for-size syndrome (80% PHx), where administering recombinant Wnt7a enhanced both cholangiocyte and hepatocyte proliferation. Elevated Wnt7a levels were seen in donors of liver transplant patients at day 1 and 2 post-hepatectomy and Wnt7a also facilitated growth of human cholangiocyte organoids in vitro. Our findings uncover the novel role of Wnt7 as one of the key lymphangiocrine signals that facilitates proliferation of cholangiocytes during liver regeneration. HighlightsO_LINumber of functional lymphatic Vessels (LVs) and lymphangiogenesis is enhanced between day 2 and day 5 after partial hepatectomy (PHx) in rat models and liver transplant donors. C_LIO_LIWnt7a released from lymphatic endothelial cells (LyECs) acts as a potent lymphangiocrine factor, stimulating proliferation of hepatocytes and cholangiocytes in vitro, across both rodent and human models. C_LIO_LIInhibition of lymphagiogenesis during PHx transiently reduces number of cholangiocytes during early liver regeneration. C_LIO_LIWnt7a signals through Frizzled 7 receptor to activate p-AKT, p-JAK1 and p-STAT3 proteins in cholangiocytes. C_LIO_LIAdministration of recombinant Wnt7a in 80% PHx models induces proliferation of hepatocytes and bile ducts. C_LI

physiology↗

bioRxiv2025

REST elevation-dependent chromatin remodeling and alternative Grk6 transcript synthesis hyperactivates Cxcr4-Sdf1 signaling in cerebellar granule cell progenitors

RE1 Silencing Transcription Factor (REST) is a repressor of transcriptional initiation of genes involved in neurogenesis. Here, we show that conditional REST elevation in cerebellar granule cell progenitors (CGNPs) of RESTTG mice perturbed foliation, increased cell migration, and sustained C-X-C motif receptor 4 (Cxcr4) signaling, a pathway key to postnatal CGNP migration. Mechanistic studies uncovered a novel role for REST in controlling transcript diversity and exon skipping in CGNPs. Alternative transcript expression was detected in known Cxcr4 signaling regulator, G-protein-coupled receptor kinase-6 (Grk6). Further analysis of Grk6s isoform expression revealed an upregulation of a transcript lacking exon 10a (Grk6-207) in RESTTG CGNPs. Grk6-207 expression in wildtype CGNPs hyperactivated Cxcr4 signaling and increased chemotaxis. Structural modeling of Grk6-207 predicted changes in active site conformation and interactions with Cxcr4 and {beta}-Arrestin-1, supporting impairment of Cxcr4 signaling desensitization. Interestingly, REST elevation promoted increased chromatin accessibility at the exon10a-10b junction and exon 10a exclusion. Integrated multiomic analyses identified the enhancer of zeste (Ezh2) as a potential mediator of alternative transcript generation which demonstrated increased occupancy at the exon10a-10b locus in RESTTG CGNPs. Pharmacological inhibition of Ezh2 downregulated Grk6-207, confirming a role for Ezh2 in Grk6 exon10a exclusion and the increased migration in RESTTG CGNPs. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/682654v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@166db32org.highwire.dtl.DTLVardef@1c0c5e0org.highwire.dtl.DTLVardef@ff2d6borg.highwire.dtl.DTLVardef@fed170_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗