Biology subjects

Singh, S.

Publications and source records attributed to Singh, S..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Comparative clinical transcriptome of pir genes in severe Plasmodium vivax malaria

vir genes, a multigene family in Plasmodium vivax that are a part of a larger superfamily of genes called the pir (Plasmodium interspersed repeat) genes, have been reported earlier to be potentially involved in cyto-adherence and evasion of splenic clearance. Plasmodium vivax, historically characterised as a "benign" malaria parasite, has been associated with clinical outcomes including hepatic dysfunction, renal failure, and cerebral malaria in India and several global regions. It constitutes an economic burden and presents a public health challenge alongside other Plasmodium species. Here, we present a part of global transcriptomic studies using custom-designed microarrays that compare the transcriptome of the parasite responsible for severe Plasmodium vivax manifestations, specifically hepatic dysfunction and cerebral malaria from India, with an emphasis on the pir genes, some of which are reported to play a role in cyto-adherence. The RNA of the parasite isolated from 23 patients (uncomplicated group = 6, hepatic dysfunction group = 12, and cerebral malaria group = 5) was subjected to microarray hybridisation, and the data obtained showed a wide range of pir subfamilies to have been differentially expressed. We report the upregulation of 24 pir genes in the cerebral malaria group (n = 5) and 28 pir genes in the hepatic dysfunction group (n = 12), which belong to different subfamilies in at least 50% of the severe malaria patients group. Out of the upregulated pir genes in the cerebral malaria group, members of vir subfamily E (n=8 genes) and the pvpir subfamily H (n=6 genes) are expressed in a higher proportion compared to the hepatic dysfunction group, where members of vir subfamily E (n=9) and C (n=6) are expressed in a major proportion. Author SummaryPlasmodium vivax, considered to cause benign infections, has been reported over the past couple of decades as manifesting with severe symptoms like cerebral malaria, hepatic dysfunction, and others. This paper reports the analysis of a selected pir gene repertoire from microarray hybridisation performed with custom-designed 15K microarrays. Differences between pir genes, which are specifically upregulated in either hepatic dysfunction or cerebral malaria, the two manifestations considered in addition to uncomplicated vivax malaria samples, are highlighted. The latter provided the control values for comparison with the disease groups. The data presented in this study show differentially upregulated pir genes, some of which are also common to both manifestations. Literature has reported one of the VIR proteins, encoded by vir14 C gene, to be involved in adhesion to ICAM-1. The future scope of this work includes validation with a larger sample size and characterising the products of the pir gene, as depicted with reference to their role in cytoadherence or other mechanisms that could lead to severe disease. It would be possible to devise strategies based on this data that could lead to the use of some of these molecules as potential biomarkers or for therapeutic intervention.

genomics↗

bioRxiv2025

Coordinated regulation of trichome morphogenesis and flavonoid pathway by a MYB HDZIP JAZ module in banana (Musa sp.)

O_LITrichomes are epidermal structures that function in defence against biotic and abiotic stresses. The developmental and metabolic aspects of trichomes have not been studied in banana (Musa acuminata). In the present study, we report that banana cultivars with AAA genome contain trichomes on inflorescence stalk. C_LIO_LITranscriptome analysis of epidermal tissues of trichome-rich and trichome-free banana cultivars suggested that genes concerning defence response and specialized metabolism are differentially regulated. Based on the gene expression and phylogenetic analysis, two transcription factors, MaTFR (trichome and flavonol related R2R3-MYB) and MaHDZIV6 (HDZIP-IV), were identified as candidate regulators of trichome development. C_LIO_LIBoth genes partially complemented the glabrous phenotype of trichome-related mutants of Arabidopsis. Transient overexpression and silencing in banana embryogenic cells (ECS) suggested that both MaTFR and MaHDZIV6 regulate the transcription of flavonol biosynthesis genes and modulate flavonoids content. Furthermore, MaTFR was found to directly activate the expression of MaHDZIV6. C_LIO_LITrichome-enriched cultivars have enhanced active JA content compared to trichome-free cultivar suggesting the involvement of JA signalling in regulating trichome development. Two JAZ repressors, MaJAZ5 and MaJAZ8 interacted with MaTFR and attenuated the flavonoid biosynthesis. Our study concludes that the MYB, HDZIP-IV, and JAZ module fine-tunes the flavonoid biosynthesis and the trichome development in banana. C_LI

plant biology↗

bioRxiv2025

Targeting the amino acid metabolism in Lung Sarcopenia: A Systems Engineering Approach

Non-small cell lung cancer (NSCLC) is the most prevalent subtype of lung cancer and a leading cause of cancer-related mortality worldwide. Literature evidences indicates a strong association between systemic inflammation, driven by cytokines such as Interleukin-6 (IL-6), and the development of NSCLC-associated sarcopenia. However, the immuno-metabolic underpinnings that link tumor-derived IL-6 signaling to skeletal muscle degradation remain incompletely understood. We developed a comprehensive immuno-metabolic mathematical model to investigate how IL-6 signaling influences branched-chain amino acids (BCAA) metabolism and redox homeostasis in the context of NSCLC-induced sarcopenia by understanding two key causes of sarcopenia which are malnutrition and redox homeostasis. Our model integrates IL-6-mediated activation of the Janus Kinase (JAK)/Signal transducer and activator of transcription 3 (STAT3) pathway, highlighting the differential roles of STAT3 phosphorylation at S727 (mitochondrial electron transport chain (ETC) activation) and Y705 (nuclear translocation and transcriptional regulation of oncogenes Hypoxia-Inducible Factor 1, alpha (HIF-1) and cellular Myc (c-Myc). These transcription factors reprogram tumor metabolism by upregulating glucose and amino acid transporters, including those specific to BCAAs. In skeletal muscle, elevated IL-6 disrupts insulin signaling via Suppressor of cytokine signaling 3 (SOCS3), suppresses Mechanistic Target of Rapamycin Complex 1 (mTORC1) activation, and enhances oxidative stress, collectively contributing to impaired protein synthesis, increased proteolysis, and muscle wasting. BCAA dysregulation further impairs metabolic balance and exacerbates sarcopenia through defective Tricarboxylic Acid Cycle (TCA) input and epigenetic modulation via acetyl coenzyme A (acetyl-CoA) and S-Adenosylmethionine (SAM). Our model reveals a central role for IL-6-driven metabolic rewiring, particularly BCAA utilization and redox imbalance, in promoting NSCLC-induced sarcopenia. These findings underscore the dual impact of IL-6 on tumor progression and systemic muscle degradation, and provide a framework for evaluating therapeutic strategies that target IL-6/STAT3 signaling and amino acid metabolism via STAT3 and acetyl-CoA cross talk to mitigate NSCLC-induced sarcopenia. Authors SummaryLung cancer is the leading cause of cancer-related deaths worldwide, and NSCLC accounts for approximately 85% of all cases. Beyond its direct effects, NSCLC can induce systemic conditions such as sarcopenia which is a condition leading to progressive loss of skeletal muscle mass and function through chronic inflammation. A key player in this process is IL-6, a cytokine overexpressed and secreted by tumor cells and cells in the tumor microenvironment. In this study, we developed a systems-level mathematical model to explore how IL-6 contributes to NSCLC-induced sarcopenia by disrupting the metabolism of BCAAs, which are essential for muscle protein synthesis and energy homeostasis. Our model shows that IL-6 activates the JAK/STAT3 signaling pathway in cancer cells, promoting tumor survival and metabolic reprogramming which may simultaneously impair nutritional uptake in muscle cells. IL-6 expressed by Tumor micro environment (TME) may disrupt BCAA uptake and utilization, inhibit anabolic signaling, and increase oxidative stress in muscle tissue, thereby accelerating muscle atrophy. By highlighting the interlinked roles of IL-6 signaling and BCAA metabolism in tumor progression and metabolic reprogramming by cancer cells, our findings offer new insights into the metabolic basis of NSCLC-induced sarcopenia and potential intervention points for therapy.

systems biology↗

bioRxiv2025

Lumbar spinal Shox2 interneurons receive monosynaptic excitatory input from the lateral paragigantocellular nucleus in the adult mouse

Locomotor output in vertebrates is generated in the spinal cord but is initiated and controlled by descending projections from supraspinal structures. Spinal interneurons involved in locomotion have been revealed through manipulation of genetically identified interneurons in transgenic mouse lines. Lumbar spinal interneurons expressing the transcription factor Shox2 include putative locomotor rhythm generating neurons in mice. The direct connection between supraspinal and lumbar spinal locomotor-related interneurons is comprised of reticulospinal neurons which are thought to directly provide drive to spinal rhythm generating interneurons that receive descending input and convert it to a rhythmic output. Excitatory neurons in the lateral paragigantocellular nucleus (LPGi) within the medulla have been shown to provide this descending drive in the context of forward locomotor initiation. However, a direct connection between excitatory LPGi neurons and identified spinal rhythm generating neurons has yet to be demonstrated. Here, we performed viral tracing and electrophysiological recordings to test for direct connections between the LPGi and lumbar Shox2 interneurons in adult mice. Using both monosynaptic-restricted transsynaptic rabies and anterograde AAV tracing, we show that excitatory neurons from the LPGi make direct putative excitatory synaptic contacts onto lumbar spinal Shox2 interneurons. A monosynaptic connection was confirmed via recordings of excitatory postsynaptic potentials in Shox2 interneurons in lumbar spinal slices evoked by optogenetic activation of LPGi terminals. These results demonstrate that at least a subset of lumbar spinal Shox2 interneurons receive monosynaptic excitatory input from the LPGi in the medulla, a connection which may provide the substrate for the initiation of locomotion.

neuroscience↗

bioRxiv2025

Phosphorylation-inducing chimera rewires oncogenic kinase to trigger apoptosis

The active sites electric field is integral to enzymatic catalysis (e.g., substrate recognition) and nature employs charge-altering post-translational modifications (e.g., phosphorylation) to perturb this electric field and regulate enzymes. A chromosomal translocation converts Abelson kinase (ABL) to BCR-ABL, whose hyperactivity drives several cancers. Here, we developed a small molecule, BRD8833, that induces BCR-ABL phosphorylation, which perturbs its active sites electric field with loss of hyperactivity. Unlike "occupancy-driven" inhibitors that require stoichiometric concentrations, BRD8833 operates through an event-driven, substoichiometric mechanism by inducing proximity between two BCR-ABL molecules to trigger the inhibitory phosphorylation and selective apoptosis of BCR-ABL-dependent cancer cells. Furthermore, BRD8833 is effective against other oncogenic ABL fusions or clinically observed resistance mutations, including those to occupancy-driven drugs with the same binding site as BRD8833, suggesting differences in their resistance mechanisms. These studies lay the foundation for electric-field and "event-driven" modalities to control hyperactive enzymes with orthogonal resistance mechanisms to occupancy-driven drugs. GRAPHICAL ABSTRACT (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/659082v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1607a40org.highwire.dtl.DTLVardef@fa10deorg.highwire.dtl.DTLVardef@1698232org.highwire.dtl.DTLVardef@1e2e0f1_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

ALOX12B overexpression in the skin drives inflammasome/Th17 signaling axis to promote inflammation in the mouse model and human patients

Inflammation plays a pivotal role in the etiopathogenesis of chronic inflammatory skin diseases. However, the underlying mechanism remains unclear. Here, we employed Gene expression meta-analysis and clinical validation strategy to dissect the global architecture of immune dysregulation responsible for inflammatory conditions in the skin. Using such approaches, we identified a gene signature comprising of ALOX12B, which is significantly upregulated in psoriatic and atopic dermatitis patient skin samples, and correlates with increased levels of pathological IL-1{beta} and Th17 responses. Surprisingly, ALOX12B is predominantly expressed in the skin. Furthermore, skin-specific overexpression of human ALOX12B in transgenic mice resulted in psoriasis-like inflammatory symptoms, including epidermal hyperplasia, immune cell infiltration, and elevated IL-1{beta}/Th17 responses. ALOX12B is a non-heme iron-containing enzyme that catalyses the production of 12R-HETE from polyunsaturated fatty acids such as arachidonic acid. Mechanistically, we found that ALOX12B/12R-HETE accumulation in the skin acts as an intrinsic danger signal that triggers enhanced IL-1{beta} processing and secretion via ROS generation and NLRP3 inflammasome activation. Increased IL-1{beta} levels in turn drive IL-17 producing T-cell polarization. We further designed a novel first-in-class, potent ALOX12B inhibitor, 6a, which exhibited favorable topical pharmacokinetic and safety profiles. The topical application of 6a reduced inflammation-associated pathologies in Tg-hALOX12B mice by suppressing 12R-HETE-induced IL-1{beta} production and ROS generation. These findings revealed a novel mechanism mediated by ALOX12B/12R-HETE overexpression that controls skin inflammation, thereby providing a promising therapeutic target for treating inflammatory skin diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/658245v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@13cdf3forg.highwire.dtl.DTLVardef@164cac3org.highwire.dtl.DTLVardef@3c0364org.highwire.dtl.DTLVardef@2ca91_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO The proposed mechanism through which ALOX12B modulates the inflammatory pathway in psoriasiform-like inflammatory conditions in the skin. The study provides insight into the role of ALOX12B in skin inflammation. Increased levels of ALOX12B expression in the skin result in 12R-HETE accumulation, which subsequently triggers the IL-1/Th17 inflammatory cascade through ROS generation and inflammasome activation. IL-1 produced by the activated inflammasome leads to the polarization of naive T-cells to activated IL-17 producing CD4+ T-cells, which are involved in the skin-inflammation related pathologies such as keratinocyte proliferation, and cellular infiltration. Hence, we propose ALOX12B as a novel potential therapeutic target for psoriasis-like inflammatory skin disorders. Additionally, we designed a novel first-in-class ALOX12B inhibitor, 6a; which shows a substantial alleviation in ALOX12B enzymatic activity, thereby reducing cellular ROS, which in turn results in reduced levels of IL-1, as a result inhibiting IL-1/Th17 inflammatory pathway and subsequent reduction in pathological inflammatory skin conditions. A portion of the image was created using Biorender.com C_FIG HighlightsO_LIALOX12B is a key gene upregulated in the skin during psoriasis and atopic dermatitis. C_LIO_LITransgenic mice overexpressing ALOX12B in the skin developed Psoriasis-like inflammatory symptoms. C_LIO_LIMechanistically, ALOX12B, through 12R-HETE, enhanced IL-1{beta} production via ROS generation and NLRP3 inflammasome activation. Further elevated IL-1{beta} production promotes Th17 cell polarization. C_LIO_LINovel first-in-class ALOX12B inhibitor alleviates inflammatory symptoms in a transgenic mouse model. C_LIO_LIStudy reveals a crucial ALOX12B/12R-HETE-inflammasome-IL-17 axis involvement in inflammatory skin diseases. C_LI

immunology↗

bioRxiv2025

Isolation of a nanobody specific to the PstS-1 protein and evaluation of its immunoreactivity with structural components of Mycobacterium tuberculosis granuloma

M. tuberculosis (Mtb) causes infectious granulomatous disease tuberculosis (TB). Within TB granuloma, foci of Mtb secreted antigens anchored on the surface of either bacilli or host cells may serve as targetable biomarkers for antibody based molecular imaging of TB. Nanobody is better suited over conventional antibody or its fragment derivatives for molecular imaging due to its quick localization in target tissue and rapid clearance from off-target organs. Here, we report the production of a high affinity nanobody against PstS-1 protein of Mtb which helps bacilli in phosphate uptake as well as host cell adhesion. C8 nanobody was isolated from a phage display library displaying nanobodies which was constructed from a camel immunized with secretory proteins of Mtb. C8 Nb was characterized in vitro and in vivo for its immunoreactivity against PstS-1 protein. Ability of C8 Nb to bind PstS-1 protein present on the surface of Mtb bacilli or adhered on macrophages and its localization around BCG cells injected intramuscularly in mice demonstrate its potential in the development of molecular imaging for tuberculosis.

microbiology↗

bioRxiv2025

Galectin-3 C-epitope, ANP, PPIA, and albumin function as drug-responsive panel biomarkers and therapeutic targets in aging and pressure overload-induced cardiac hypertrophy

Biological aging (BA) and pressure overload-induced cardiac hypertrophy (PO-CH) are marked by myocardial thickening, fibrosis, and functional decline, culminating in an increased risk of heart failure. Effective clinical management requires biomarkers that not only track disease progression but also monitor therapeutic response. Using Amalaki Rasayana (AR), a cardioprotective nutraceutical-based medicine, in rat models of BA and PO-CH, we identified a panel of serum biomarkers whose treatment-induced decline was associated with disease regression. Among them, galectin-3 emerged in both full-length and oligomeric C-epitope cleaved forms, with the latter closely linked to pathological surface remodeling. Treatment with AR and its bioactive component gallic acid (GA) suppressed extracellular galectin-3 C-epitope oligomer accumulation by inhibiting full-length galectin-3 secretion through phosphorylation-dependent mechanisms and promotion of intracellular retention. Concurrently, serum levels of atrial natriuretic peptide (ANP), cyclophilin A (PPIA), and albumin (ALB) were consistently modulated by therapy. Validation in sera from elderly individuals and cardiac hypertrophy patients responding to conventional treatments supported the translational relevance of this biomarker panel. These findings establish a novel, mechanistically grounded biomarker set--galectin-3 C-epitope, ANP, PPIA, and ALB--for monitoring therapeutic response in cardiac hypertrophy, and position AR as a promising medicinal intervention against age- and pressure-induced cardiac pathology. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/657024v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@2498d8org.highwire.dtl.DTLVardef@aeb4fcorg.highwire.dtl.DTLVardef@1ec2f9eorg.highwire.dtl.DTLVardef@12a4392_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIGalectin-3 C-epitope, ANP, PPIA, and ALB are elevated in aging and pressure overload driven left ventricular hypertrophy. C_LIO_LIAmalaki rasayana (AR) and Gallic Acid (GA) reduce these markers in cardiac tissue and circulation. C_LIO_LIAR and GA inhibit galectin-3 secretion and oligomeric binding to cardiomyocyte surfaces. C_LIO_LIAR and GA regulation predominantly occurs via phosphorylation-dependent cytoplasmic retention of galectin-3. C_LIO_LIThese markers serve as potential therapeutic targets and diagnostic biomarkers. C_LI

pathology↗

bioRxiv2025

Complex I inhibition shifts mitochondrial dynamics and regulates cancer cell survival, providing a synthetic lethal interaction

Mitochondrial remodeling has emerged as a key regulator of cancer cell metabolism, cell stemness, development of drug resistance, and induction of apoptosis. Metformin, a clinically approved inhibitor of mitochondrial complex I, has shown variable antitumor activity in preclinical and clinical settings, implying that adaptive mitochondrial responses can buffer its cytotoxic effects. Here, we show that metformin reprograms mitochondrial dynamics in liver and colorectal cancer cells, increases mitochondrial biomass, alters fusion-fission balance, and enhances biogenesis in a cell type-dependent manner. These adaptations preserve mitochondrial function and support survival under metformin-induced energetic stress. Notably, the targeted disruption of these mitochondrial adaptations induces cell death in metformin-treated cancer cells and suppresses tumor growth. Overall, the study identifies metformin-driven mitochondrial remodeling as a central adaptive axis to complex I inhibition and provides a rationale for co-targeting mitochondrial dynamics and metabolism to enhance the anticancer efficacy of metformin.

cancer biology↗

bioRxiv2025

A Temporal Single-Cell Multi-Omics Atlas of Murine Pancreatic Islet Remodeling During Hyperglycaemia Progression

Pancreatic islets undergo coordinated cellular remodeling during obesity-induced insulin resistance (IR). However, the associated molecular changes across endocrine and non-endocrine compartments remain largely unexplored. Here, using longitudinal single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) on islets from C57BL/6 mice subjected to high-fat diet (HFD) feeding for 8, 16, and 24 weeks, along with age-matched controls on regular chow, we mapped dynamic changes in islet cell composition and transcriptional states. Beta cells demonstrated pronounced stress-induced reprogramming, with the emergence of proliferative and dysfunctional subsets. Alpha and delta cell fractions declined under HFD, despite increased polyhormonal biosynthesis, suggesting functional rather than numerical adaptation. Immune profiling showed robust expansion of proinflammatory M1 macrophages and upregulation of NF-{kappa}B and chemotaxis pathways, particularly at 16 weeks. Notably, cell-cell communication analyses revealed diet-specific disruption in signaling networks. Under HFD conditions, intercellular communication among beta cells, macrophages, and delta cells was markedly altered, leading to the disruption of key signaling pathways such as the gastric inhibitory polypeptide receptor (GIPR) and major histocompatibility complex-I (MHC-I). Notably, C-C motif chemokine ligand 27A (Ccl27a) expression and chromatin accessibility were significantly altered in a distinct subpopulation of beta cells under HFD condition, indicative of a niche-specific regulatory mechanism. Integration with human islet datasets from obese and type 2 diabetes (T2D) donors confirmed conserved shifts in beta cell identity and immune activation. This study presents a comprehensive high-resolution atlas of islet remodeling under metabolic stress, identifying key communication nodes and transcriptional programs pertinent to T2D pathogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/656754v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@64aee0org.highwire.dtl.DTLVardef@150beborg.highwire.dtl.DTLVardef@1c19c6dorg.highwire.dtl.DTLVardef@4d1a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Host adaptation and genome evolution of the broad host range fungal rust pathogen, Austropuccinia psidii

Rust diseases on plants are caused by fungi in the order Pucciniales. Typically, rust fungi have narrow host specificity however the pandemic biotype of Austropuccinia psidii has an unusually broad host range causing disease on over 480 myrtaceous species globally. We assembled and analysed a fully phased chromosome-level genome for the pandemic A. psidii and addressed key outstanding questions of its infection biology. Our research revealed a conserved rust fungal karyotype of 18 haploid chromosomes, in line with fungi for distantly related cereal rusts. We observed chromosomal re-assortment between the two nuclei, with one nucleus carrying 19 and the other 17 chromosomes. The synteny of universal single-copy orthologs is mostly maintained with the distantly related rust fungus Puccinia graminis f. sp. tritici. In contrast, nucleotide composition and methylation profiles of A. psidii are distinct compared to rust fungi with smaller genome sizes that have not undergone massive transposable element expansions. Our analysis of mating type loci supports a tetrapolar mating system for A. psidii with a novel finding of expanded numbers of pheromone peptide precursors. We show that infection dynamics of A. psidii are consistent on four different susceptible host species separated by 65 mya of evolution and that transcriptional regulation during infection reveals two distinct waves of gene expression in early and late infection, including allele-specific expression of candidate effectors. Together, these findings enhance the understanding of the genome biology and pathology of A. psidii, while also providing a valuable resource for future research on this serious rust pathogen.

microbiology↗

bioRxiv2025

Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes

BackgroundKidney transplantation is the preferred treatment strategy for end-stage kidney disease. Deceased donor kidneys usually undergo cold storage until kidney transplantation, leading to cold ischemia injury that may contribute to poor graft outcomes. However, the molecular characterization of potential mechanisms of cold ischemia injury remains incomplete. ResultsTo bridge this knowledge gap, we leveraged the 10x Visium spatial transcriptomic technology to perform full transcriptome profiling of murine kidneys subject to varying durations of cold ischemia typical in a deceased donor kidney transplant setting. We developed a computational workflow to identify and compare spatiotemporal transcriptomic changes that accompany the injury pathophysiology in a tissue compartment-specific manner. We identified proportional enrichment of oxidative phosphorylation (OXPHOS) genes with increasing duration of cold ischemia injury within the oxygen-lean inner medulla region, suggestive of atypical metabolic presentation. This was distinct in cold ischemia injury tissue compared to warm ischemia-reperfusion kidney injury tissue. Spatiotemporal trends were validated by qPCR and immunofluorescence in a larger cohort of mice. We provide an interactive online browser at https://jef.works/CellCarto-ColdIschemia/ to facilitate exploration of our results by the broader scientific and clinical community. ConclusionsAltogether, our spatiotemporal transcriptomic analysis identified coordinated molecular changes within metabolic pathways such as OXPHOS deep within the cold ischemic kidney, highlighting the need for increased attention to the inner medulla and potential opportunities for new insights beyond those available from superficial biopsy-focused tissue examinations.

bioinformatics↗

bioRxiv2025

Selective targeting of Plasmodium falciparum hexose transporter by phytochemical Ginsenoside Rg1 disrupts glucose metabolism and block development of parasite

The emergence of resistance to first-line antimalarial therapies highlights the critical need for next-generation drugs that target distinct molecular pathways and employ novel mechanisms of action. Notably, the intra-erythrocytic parasite development is highly dependent on a sustained glucose supply as their fundamental energy source. Therefore, exploiting a "selective starvation" strategy, by targeting the parasites reliance on glucose metabolism, particularly through the Plasmodium falciparum hexose transporter (PfHT1), which is critical for parasite survival can serve as a promising therapeutic approach to combat multidrug-resistant Plasmodium parasites. Through molecular docking and structure-based drug design approach, we identified a natural compound, Ginsenoside Rg1 (G-Rg1) from drug bank database library, as a potential PfHT1 inhibitor. The PfHT1 specificity of G-Rg1 was validated using yeast complementation model. Subsequently, to investigate the role of PfHT1 in drug resistant Pf parasites we investigated the stage-specific expression of PfHT1 in both artemisinin (ART)-sensitive and resistant Pf parasites and reported its elevated expression in resistant parasites, predicting its role in their survival. Notably, in vitro growth inhibition studies demonstrated that G-Rg1 effectively suppressed the growth of both ART-sensitive and resistant Pf parasites. Additionally, G-Rg1 potentiated the efficacy of dihydroartemisinin in combination and ring survival assays, indicating its potential to circumvent resistance mechanisms. G-Rg1 administration alone and in combination with ART, in P. berghei ANKA-infected mice reduced parasite multiplication and increased mean survival time. Our findings support G-Rg1 as a promising candidate for drug development against malaria, highlighting the potential of targeting PfHT1 to combat drug-resistant malaria.

pharmacology and toxicology↗

bioRxiv2025

Conformal Bioprinting of Bi-phasic Jammed Bioinks, Independent of Gravity, Orientation, and Curvature

Rapid in situ bioprinting on complex, human-scale anatomical surfaces remain a key challenge for clinical translation. Here, we present a gravity-independent, conformal bioprinting strategy using bi-phasic granular bioink and multinozzle printheads capable of adapting to arbitrary surface curvatures. The bioink comprised of jammed gelatin microgels suspended in a fibrinogen matrix exhibits yield-stress behavior to maintain shape fidelity after extrusion while supporting cell viability and proliferation. Two monolithic multinozzle printhead architectures with identical bioink delivery networks were evaluated: (1) a rigid configuration for handheld bioprinting and (2) a soft robotic variant capable of real-time curvature adaptation via pneumatic actuation. Microgravity experiments aboard a parabolic flight confirmed successful bioink deposition under [~]0 g conditions. A ladder-rung microfluidic architecture ensured uniform bioink delivery across printhead nozzles, improving deposition consistency. In situ bioprinting on anatomical facial phantoms confirmed conformal, high-throughput (deposition at 20 mm{middle dot}s-1) deposition of bioink over physiologically relevant curvatures, both with and without cells. Cell-laden constructs retained >85% cell viability post-printing and supported proliferation. This work introduces a scalable bioprinting platform suitable for clinical, remote, and deep-space environments, enabling autonomous tissue fabrication. The curvature-adaptive printhead advances current in situ bioprinting capabilities, facilitating the generation of personalized grafts with complex anatomical geometries.

bioengineering↗

bioRxiv2025

Epstein-Barr virus and Helicobacter pylori Coinfection Drives Gut and Brain Barrier Dysfunction

Biological barriers, including blood-brain barrier (BBB) and gut epithelial barrier, are essential to maintain homeostasis and provide protection against pathogenic stress. Here, we investigated the impact of Helicobacter pylori-Epstein Barr Virus coinfection on gut-brain axis integrity. Our results demonstrate that coinfection induces significant disruptions in tight and adherens junction (TJ and AJ respectively) proteins in gastric epithelial cells, including downregulation of ZO-1 and E-cadherin. The secretome from these coinfected cells significantly compromises the integrity of BBB-derived endothelial cells, including cleavage of VE-cadherin, loss of TJ proteins such as Claudin-5, and enhanced permeability. Furthermore, the sole exposure of mice to coinfected secretome lead to the loss of cerebral VE-cadherin and ZO-1 and the induction of neuroinflammation, characterized by elevated pro-inflammatory cytokines, TNF-, amyloidogenic accumulation, and neurocognitive deficits. The secretome driving such forces potentially carries pathogenic metabolites, host inflammatory cytokines and metabolites that might contribute to disease pathogenesis as observed in this study. Together, our current study provides novel insights into how coinfections contribute to gut-brain axis dysregulation and neurological pathogenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/655045v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@138ca23org.highwire.dtl.DTLVardef@15eccc4org.highwire.dtl.DTLVardef@d588c6org.highwire.dtl.DTLVardef@106a485_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

microbiology↗

bioRxiv2025

Orthogonal resistance mechanisms of classical- and induced-proximity inhibitors

Resistance development is an inevitable failure mode of many drugs, pointing to the need to develop agents with orthogonal resistance mechanisms. Induced-proximity modalities, an emergent class of therapeutics, operate by forming a ternary complex with the protein-of-interest (POI) and effectors, unlike classical inhibitors that form binary complexes with the POI. Using KRAS as a model system, we employed base editor tiling mutagenesis screening to show that induced-proximity inhibitors exhibit orthogonal resistance mechanisms to classical inhibitors despite overlapping binding sites, offering an opportunity to circumvent resistance mechanisms of classical inhibitors. These findings highlight the use of base editor mutagenesis screens to prioritize inhibitors with orthogonal resistance mechanisms and the potential of induced-proximity inhibitors to overcome the drug resistance of classical inhibitors.

biochemistry↗

bioRxiv2025

Phosphorylation-inducing molecules for regulating dynamic cellular processes

Dynamic cellular processes often employ protein phosphorylation for rapid information transfer within and between cells. Phosphorylation-inducing chimeric small molecules (PHICS) have been developed for targeted protein phosphorylation by on-demand inducing a kinase-protein pairing. However, widespread application of PHICS has been limited as previously reported PHICS that recruited AMP-activated protein kinase (AMPK) required serum starvation and target protein overexpression, recruited only a few of the potential AMPK complexes, and exhibited poor dose- and temporal control. Herein, we report an AMPK PHICS platform that operates under physiological conditions (i.e., no serum starvation or target overexpression), recruits multiple AMPK complexes, and can induce target protein phosphorylation with dose and temporal control. We demonstrated the utility of this platform for controlling phosphorylations that underlie two dynamic cellular processes, namely oncogenic signaling and phase separation. An AMPK PHICS directed against Brutons Tyrosine Kinase (BTK), which is a driver of several B cell malignancies, was effective at inducing the death of drug-resistant cancer cells. Here, PHICS induced inhibitory phosphorylations on BTK and attenuated its oncogenic pathway. Phosphorylation of Liprin-3 induces phase separation in neurons and is critical for neurotransmitter release. Using AMPK PHICS that phosphorylated Liprin-3, we induced Liprin-3 phase separation with dose and temporal control. We envision this PHICS platform to find utility in inducing and controlling protein phosphorylations for basic research and biomedicine. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/652895v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@16bbb20org.highwire.dtl.DTLVardef@1ca5267org.highwire.dtl.DTLVardef@1e805d5org.highwire.dtl.DTLVardef@1d6ec22_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Drug screen reveals new potent host-targeted antivirals against Mpox virus

Mpox virus (MPXV), a re-emerging zoonotic threat, has caused outbreaks in non-endemic regions through respiratory, sexual, and close-contact transmission. The increased transmissibility of Clade IIb fueled the 2022 global outbreak, with 2024 Clade Ib spread in the Democratic Republic of Congo further escalating concern. Both outbreaks were declared public health emergencies by the WHO. Although tecovirimat (TPOXX) has been used off-label for Mpox, its limited effectiveness highlights the critical need for newer antivirals for MPXV. We conducted high- throughput antiviral drug screening using a host-directed kinase inhibitor library composed of 2,750 compounds against 2022 Clade IIb MPXV. Our primary screen identified 138 compounds preventing MPXV cytopathic effects, including multiple inhibitors of EGFR, PI3K-mTOR, and Ras/Raf, as well as apoptosis and autophagy regulators. Secondary and tertiary screenings yielded a shortlist of potent, nontoxic antiviral compounds that inhibited MPXV replication. Three selected compounds, IRAK4-IN-6, SM-7368, and KRAS inhibitor-10, reduced MPXV-induced cell death in primary human epidermal keratinocytes. IRAK4-IN-6 and SM-7368 were also found to modulate NF-{kappa}B and STING signaling. Furthermore, these compounds were found effective in reducing skin lesions and viral burden in a mouse model of MPXV skin infection. Together, our study reveals new classes of antiviral compounds against MPXV, offering promising candidates for future clinical development.

microbiology↗