Biology subjects

Singh, A. K.

Publications and source records attributed to Singh, A. K..

At least 19 recordsLinked to original sources

bioRxiv2026

Sphingosine-1-Phosphate Restrains Foamy Macrophage Formation and Modulates Inflammation in Multidrug-Resistant Tuberculosis

The high abundance of lipid loaded foamy macrophages in the granulomatous lesions is a key hallmark of advanced pulmonary tuberculosis. These macrophages serve as lipid-rich intracellular hiding niches that provides Mycobacterium tuberculosis (M.tb) survival and persistence during prolonged anti-tubercular treatment. Persistent infection and dysregulated inflammatory responses further complicate disease control, particularly in multidrug-resistant tuberculosis (MDR-TB), highlighting the need for host-directed therapeutic strategies. Our previous preclinical study demonstrated the therapeutic potential of the host sphingolipid sphingosine-1-phosphate (S1P) in reducing the mycobacterial burden in M.tb-infected animals, accompanied by enhanced pulmonary macrophage activation. To explore its translational potential, we investigated whether S1P modulates foamy macrophage formation in CD14 monocyte-derived macrophages from healthy donors and patients with MDR-TB. Notably, macrophages derived from patients with MDR-TB exhibited greater intracellular lipid droplet accumulation than those derived from healthy donors. This phenotype was further characterized by increased nitric oxide production and quantitative RT-PCR analysis of genes associated with immune regulation and lipid metabolism, including APOE, LDLR1, CLEC4E, CLEC7A, GP96, IL4, and IL13, which suggested a Th2-associated immunological bias in foamy macrophages. Collectively, these findings highlight the potential role of host sphingolipids in modulating foamy macrophage phenotypes and associated immunometabolic dysregulation, supporting further investigation of S1P as a host-directed therapeutic strategy against MDR-TB.

immunology↗

bioRxiv2026

Whole-Genome Metagenomics Insights Revealed a Uranium Bio-remediating Cross-Domain Microbiome in the Dhala Impact Structure, India

Meteorite impact structures on earth represent unique terrestrial analogues of extreme planetary environments where fractured lithologies, hydrothermal alteration, elevated concentrations of radionuclides, and prolonged water-rock interactions create ecological niches for specialized microbial communities. The Palaeoproterozoic Dhala impact structure in north-central India is characterized by uranium-bearing impactites and possesses a very high concentration of Uranium (up to 99.5 ppm) that makes it a unique natural laboratory to investigate microbial adaptation to radioactive and metal-rich geological environments. In addition, the Dhala structure harbors specialized radiotoxic hydrothermal mineral phases such as coffinite and pitchblende, which show a globally distinct and biologically unexplored niche. The present investigation is the first in-depth, whole-genome metagenomic study of soil and water samples of uranium-rich sites from the Dhala structure, exploring the whole microbial community (Bacteria, Archaea, Eukaryotes, and Viruses) up to the species level present in the samples. The cross-domain metagenomics analysis identified a highly unique and resilient microbiome that consists of bacteria, archaea, eukaryotes, and viruses, coevolved under prolonged radiological and multiple metal stress. Functional metagenomic analysis revealed numerous metabolic adaptations responsible for their survival, homeostasis, and biomineralization in situ. The deep sequencing method further enabled the identification of 58 functional genes directly involved in uranium bioremediation. Furthermore, this study revealed important pathways for radionuclide reduction, cellular efflux, and biotransformation. Novel findings of the present study point out the in-depth evolutionary relations of biosphere-geosphere interaction within an ancient hypervelocity impact-generated ecosystem. In a nutshell, the Dhala extremophiles with novel genetic makeup present an untapped and promising reservoir for the development of eco-friendly, next-generation microbial bioremediation strategies to efficiently tackle the global anthropogenic contamination of uranium and the challenges of nuclear waste management. Thus, the present study establishes Dhala structure as an unparalleled site for environmental geomicrobiology, microbial evolution, and astrobiology.

genomics↗

bioRxiv2026

Transcription factor co-occupancy shapes the somatic mutational landscapes across regulatory regions in liver cancer

Both global and local chromatin structure influence the heterogeneous distribution of somatic mutations across the cancer genome. For instance, at the local scale, DNA regions bound by transcription factors (TF) and other chromatin-associated proteins display elevated somatic mutation rates, due to variable DNA damage and repair at these protein-bound sites. However, the contribution of TF co-binding towards the variations in somatic mutation rates remains largely unexplored. Here, we combine somatic mutations from whole-genome sequencing of liver cancers with ChIP-seq profiles for over 150 TFs and chromatin-associated proteins in the human liver cancer cell line HepG2, to systematically examine how TF co-occupancy shapes local mutational landscapes. We show that somatic mutation rates at binding sites vary substantially across distinct TFs and co-binding combinations. Furthermore, the magnitude and spatial distribution of somatic mutation rates at TF binding sites differ across promoters and enhancers, likely influenced by the local chromatin accessibility and architecture. Finally, we identify NFIA (Nuclear Factor IA) as a distinct exception, maintaining elevated mutation rates across its binding sites independent of local co-binding context. Together, these findings reveal that combinatorial TF co-occupancy and local chromatin architecture are associated with differences in somatic mutation rates across regulatory regions in liver cancer.

genomics↗

bioRxiv2026

L-Serine potentiates the efficacy of Isoniazid, and Rifampicin as host-directed adjunctive treatment for Mycobacterium tuberculosis.

Host-directed therapies (HDTs) have acquired paramount importance for management of tuberculosis (TB). L-Serine is an important metabolite and immunomodulatory biomolecule with promising role in managing infections, and autoimmune diseases. However, the role of L-Serine as host directed therapeutic against Mycobacterium tuberculosis (M.tb) remains unexplored. Therefore, we adopted de novo-based approach and employed L-Serine and palmitoyl CoA precursors for enhancing sphingolipid in host and accessed their anti-tubercular potential. In this study, we investigated whether L-Serine could modulate the antibiotics efficacy against M.tb. L-Serine particularly in combination with palmitic acid, rifampicin and isoniazid showed enhanced intracellular bacterial clearance in a dose- and time-dependent manner in murine and human macrophages. This synergistic effect was accompanied by increased nitric oxide production and modulation of the host immune response. We identified elevated levels of pro-inflammatory cytokine TNF- and reduced anti-inflammatory IL-10 expression. Furthermore, L-Serine supplementation demonstrated antimicrobial activity in isolated primary CD14 monocytes from TB patients. Similarly, the metabolic supplementation of L-Serine in combination with isoniazid, rifampicin, and palmitic acid significantly reduced bacterial burden in the lungs and spleen, while improving tissue architecture in murine infection model. Our observations suggest that L-Serine and palmitic acid in combination with isoniazid and rifampicin contributes to the observed therapeutic effects. Collectively, this study concludes that L-Serine and palmitic acid acts as a promising host-directed therapeutic adjunct, which enhances antimicrobial immunity and potentiating antibiotic efficacy, providing a potential strategy for improving tuberculosis treatment outcomes.

microbiology↗

bioRxiv2026

Aberrant expression of stress-related Hsrω-n lncRNA contributes to CGG repeat-mediated toxicity in a Drosophila model of FXTAS

Fragile X-associated tremor/ataxia syndrome (FXTAS) is an adult-onset neurodegenerative disease associated with carriers of premutation (PM) alleles of the fragile X messenger ribonucleoprotein 1 (FMR1) gene. Expanded CGG repeats in the PM alleles are sufficient to cause cellular stress and toxicity in animal and cellular models of FXTAS. Here, we show that in a Drosophila transgenic model of FXTAS, expanded CGG repeats result in the overexpression of heat shock RNA omega-nuclear (Hsr{omega}-n), a stress-related long non-coding RNA (lncRNA) that dominantly enhances expanded CGG-induced neurotoxicity, whereas its reduction suppresses CGG-induced neurotoxicity. Furthermore, overexpression of Hsr{omega}-n lncRNA concomitantly resulted in a significant enhancement in its association with Hrb87F, the fly ortholog of one of the previously identified CGG repeat RNA-binding proteins, hnRNP A2/B1, and with the imitation switch (ISWI) protein, a chromatin remodeling factor. We extended the findings of Hsr{omega}-n to show that the mammalian stress-related lncRNAs SatIII and Neat1 are elevated in cells expressing expanded CGG repeats. Together, these findings highlight the critical roles of stress-related lncRNAs in CGG repeat-mediated toxicity and support a model in which the total steady-state levels of stress-related lncRNAs increase in the presence of expanded CGG repeats as part of the normal regulatory response to combat stress. However, the effects of chronic expanded CGG repeat expression in post-mitotic neurons may result in altered distribution and/or sequestration of specific RNA-binding proteins or chromatin remodeling factors associated with stress-related lncRNAs. This could contribute to the altered cellular homeostasis and genomic instability associated with FXTAS. SignificanceIndividuals carrying the FMR1 allele with expanded CGG repeats (55-200) in the 5' untranslated region are predisposed to fragile X-associated tremor/ataxia syndrome (FXTAS), a late-onset neurodegenerative disorder. FXTAS demonstrates incomplete penetrance, suggesting the possible involvement of genetic modifiers in its pathogenesis. We used a transgenic Drosophila FXTAS model to conduct genetic, molecular, and biochemical analyses. Our findings revealed that the expression of expanded CGG repeats aberrantly activates stress-related Hsr{omega}-n lncRNA in Drosophila melanogaster. Overexpression of this lncRNA exacerbates CGG-mediated neurodegeneration, whereas its repression alleviates this effect. Extending these findings to mammalian systems, we observed the upregulation of SATIII and Neat I, functional homologs of Hsr{omega}-n lncRNA, in cells expressing expanded CGG repeats. Collectively, these findings identify stress-related lncRNAs as key mediators of CGG-mediated toxicity and underscore their potential as therapeutic targets for FXTAS.

genetics↗

bioRxiv2026

Specific F1 ATP synthase inhibition delivers transient mitochondrial stress for selective targeting of acute myeloid leukemia

Targeting oxidative phosphorylation (OXPHOS) represents an attractive therapeutic strategy in acute myeloid leukemia, which exhibits exceptional dependence on mitochondrial respiration compared to normal hematopoietic cells. However, clinical attempts to exploit this vulnerability have been limited by on-target toxicity to healthy tissue. Here, we comprehensively compare the cellular consequences of inhibiting distinct nodes of the electron transport chain in AML. We demonstrate that selective inhibition of the F1 subunit of ATP synthase with EB2023 (ammocidin A) delivers an energetic stress to AML cells without the profound redox stress that characterizes complex I inhibition, preventing NAD/NADH imbalance and allowing continued TCA cycling. Further, the duration of OXPHOS inhibition is transient in nature in vivo, a finding revealed through pharmacokinetic and serial pharmacodynamic monitoring of AMPK phosphorylation accompanied by OPA1-mediated mitochondrial structural remodeling that primes AML cells for BCL2 inhibitor synergy. EB2023 in combination with venetoclax demonstrates potent anti-AML activity across cell lines and patient-derived xenograft models at doses that spare normal hematopoietic progenitors and avoid the neuropathy and sustained detrimental systemic metabolic rewiring in healthy tissues associated with prior efforts to target OXPHOS. These findings establish F1-selective ATP synthase inhibition as a clinically actionable therapeutic strategy in AML and establish the duration of OXPHOS inhibition as a critical and previously underappreciated determinant of therapeutic index.

cancer biology↗

bioRxiv2026

MTB-LysB1: A Novel Endolysin Against Multidrug-resistant Mycobacterium tuberculosis

The phenotypic plasticity, slow replication, and complex, hydrophobic cell envelope of Mycobacterium tuberculosis contribute to its successful survival as a pathogen and its drug tolerance. Consequently, the global threat of multidrug-resistant Tuberculosis (MDR-TB), coupled with lengthy and highly toxic treatment regimens, necessitates the development of innovative treatment solutions. Mycobacteriophages are natural viruses of mycobacteria that typically encode two endolysins, which cooperatively facilitate host cell lysis at the end of the lytic life cycle: LysA, a peptidoglycan hydrolase, and LysB, a lipolytic enzyme, targeting the mycolylarabinogalactan-peptidoglycan complex. Their precise and efficient lytic activity, along with their low propensity to induce resistance, make them, particularly LysBs, promising candidates for new treatment solutions. In this study, we report MTB-LysB1, a novel LysB enzyme from an F1 sub-cluster mycobacteriophage isolated from our laboratory collection. While studying its structural features by comparing the modelled structure with representative mycobacteriophage LysB homologues, we found that the /{beta}-hydrolase fold and key motifs are conserved. Also, we identified putative membrane-interaction motifs that may play a role in LysB1s cell permeation. Significantly, we found MTB-LysB1 to be active against both drug-susceptible and multidrug-resistant (MDR) M. tuberculosis strains at nanomolar concentrations, comparable to the well-characterised D29 LysB reference enzyme. Beyond its standalone activity, MTB-LysB1 exhibits an additive effect when combined with the TB drugs rifampicin and moxifloxacin, and co-administration reduces the drugs minimum inhibitory concentrations (MICs), which holds clinical significance. By structurally damaging the mycobacterial cell wall, the enzyme appears to act as a permeability enhancer for the chemotherapeutic drugs, thereby improving antibiotic efficacy. Collectively, our findings position the enzyme not only as a novel antimycobacterial agent but also provide a structural framework for its rational engineering as a promising next-generation adjunct to TB drug regimens. HighlightsO_LIA novel F1 sub-cluster phage-derived LysB is discovered and characterised using integrated computational, biochemical and microbiological methods. C_LIO_LIAlphaFold2 modelling, molecular dynamics simulations and comparative structural analyses revealed an /{beta}-hydrolase fold with conserved catalytic and membrane-interaction features. C_LIO_LIThe enzyme exhibited high esterase activity, thermal stability and potent lytic activity against Mycobacterium tuberculosis. C_LIO_LIAn additive effect with TB drugs rifampicin and moxifloxacin highlights MTB-LysB1s potential as an adjunct therapeutic. C_LI

microbiology↗

bioRxiv2026

HERC4 limits oxidative stress-induced DNA damage during bacterial and viral-bacterial infection

Respiratory (co-)infections caused by influenza viruses and Streptococcus pneumoniae represent significant threats to global health. In our analysis of host cell ubiquitination, we identified reactive oxygen species (ROS) produced by S. pneumoniae as critical effectors in reducing the amount of intracellular polyubiquitinated proteins. Together with reduced ubiquitination we observed a downregulation of the E3 ligase HERC4 upon infection with S. pneumoniae in human alveolar epithelial and macrophage-like cells as well as in samples obtained from S. pneumoniae infected humans and mice. This was further aggravated in the viral-bacterial coinfection with influenza A. CRISPR-Cas9 deletion of HERC4 prior bacterial infection resulted in increased ROS-induced DNA damage, enhanced host cell apoptosis and reduced Histone 2B ubiquitination. In contrast, HERC4 overexpression diminished DNA damage indicating a role of HERC4 in DNA-damage-repair upon infection. By establishing a link between HERC4 expression and ROS-induced DNA damage and repair, we identified a potential marker for predicting the outcome of viral and bacterial (co-)infections. Targeting HERC4 expression defines a novel strategy to protect host cells from S. pneumoniae (co-)infection attenuating infection exacerbation.

microbiology↗

bioRxiv2026

The KN domain of KANK proteins contains separable talin-binding and intramolecular interaction modules

KANK proteins link integrin adhesions to the cortical microtubule stabilising complex (CMSC) through interactions with the adhesion adaptor talin. However, how KANK proteins are regulated remains unclear. Here we show that the KN domain of KANK proteins contains separable regions that mediate talin binding and a conserved intramolecular interaction. Using fluorescence polarisation, NMR spectroscopy and structural analysis, we map an interaction between the N-terminal KN domain and the C-terminal ankyrin repeat domain and identify residues 60-68 of the KN domain as required for this intramolecular interaction. In contrast, the canonical LD motif within residues 30-60 mediates binding to talin. Deletion of residues 60-68 disrupts the intramolecular interaction while preserving talin binding, demonstrating that the KN domain contains distinct modules for talin engagement and intramolecular regulation. This regulatory architecture is conserved across the KANK family, although sequence variation modulates the strength of the intramolecular interaction. Together, these findings identify a modular organisation within the KANK KN domain that separates talin recognition from intramolecular regulation and is consistent with an autoinhibitory mechanism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/731086v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@e2dd22org.highwire.dtl.DTLVardef@240996org.highwire.dtl.DTLVardef@1f1926borg.highwire.dtl.DTLVardef@c3e523_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO The KN domain of KANK proteins contains separable talin-binding and intramolecular interaction modules.The LD motif (blue) mediates binding to the talin R7 domain, whereas residues 60-68 (yellow) are required for interaction with the C-terminal ankyrin repeat domain. An AlphaFold model is shown as a structural interpretation of the intramolecular KN-ankyrin repeat interaction identified in this study. C_FIG

biochemistry↗

bioRxiv2026

Mycobacteriophage D29-Derived LysB Enhances Anti-Tubercular Therapy in Experimental Pulmonary Tuberculosis

Adjunctive therapies that enhance the efficacy of existing antitubercular drugs are needed for drug-resistant tuberculosis. We evaluated the efficacy of intranasally administered recombinant D29 LysB, a mycobacteriophage-derived mycolylarabinogalactan esterase, in murine and guinea pig models of pulmonary tuberculosis. BALB/c mice and guinea pigs were aerosol-infected with Mycobacterium tuberculosis H37Rv and treated for 4 weeks with LysB alone or with standard antitubercular therapy (ATT: rifampicin, isoniazid, pyrazinamide). Outcomes included pulmonary and extrapulmonary bacterial burden (CFU), lung and spleen histopathology, cytokine profiling, and humoral immune responses. LysB monotherapy produced modest pulmonary CFU reductions. When given adjunctively with ATT, LysB produced an additional 0.6-0.7 log10 reduction in lung CFU compared with ATT alone and decreased splenic dissemination in both species. Combination therapy improved tissue pathology, reducing granulomatous involvement and preserving pulmonary architecture. LysB treatment increased TNF- with a moderate rise in IL-10, a profile consistent with enhanced antibacterial immunity without excessive inflammatory damage. Repeated intranasal administration was well tolerated; no IgE-mediated hypersensitivity was detected. LysB-specific IgG developed but did not diminish therapeutic efficacy. These results show that intranasal D29 LysB augments the bactericidal and histopathological effects of standard ATT in vivo and support further development of inhaled phage-derived lysins as adjunctive therapies for drug-resistant tuberculosis. ImportanceTuberculosis remains a major cause of infectious mortality worldwide, and the increasing burden of multidrug-resistant and extensively drug-resistant disease continues to challenge effective treatment. New therapeutic approaches that complement conventional antibiotics are urgently needed. In this study, intranasally delivered recombinant mycobacteriophage-derived LysB was well tolerated and enhanced treatment efficacy in experimental pulmonary tuberculosis. Adjunctive LysB improved bacterial clearance, reduced tissue pathology, and modulated host immune responses in both murine and guinea pig models. These findings highlight phage-derived endolysins as promising inhalable adjunctive therapeutics for drug-resistant tuberculosis.

microbiology↗

bioRxiv2026

XRRA1 acts as a molecular brake on radiation-induced DNA damage signaling and immunogenic cell death in tumor cells.

Radiotherapy kills cancer cells by inducing DNA damage, but adaptive responses that buffer injury and limit immunogenic signaling remain incompletely understood. Although ionizing radiation can activate cytosolic DNA sensing and immunogenic cell death, the tumor-intrinsic regulators linking these processes to radioresistance are not well defined. Here, we show that XRRA1 is a stress-adaptive determinant of radioresponse identified by integrating discovery proteomics into chronic myeloid leukemia with clinical tissue validation and functional studies across multiple tumor models. In peripheral-blood proteomes, XRRA1 was quantitatively reduced in chronic myeloid leukemia yet associated with a favorable prognosis and with networks enriched for RNA regulation, apoptosis, and DNA-repair biology. In human biopsy specimens, XRRA1 protein abundance was increased in radiation-exposed tissues, and in cultured cells, ionizing radiation induced XRRA1 more strongly and persistently in normal cells than in cancer cells. Silencing XRRA1 had little effect on basal growth but markedly enhanced radiation-induced loss of viability, apoptosis, spheroid disruption, and clonogenic failure, while increasing {gamma}H2AX- and DNA-PK-associated damage signaling and linking XRRA1 to non-homologous end joining factors. XRRA1 depletion also amplified cGAS-STING-TBK1-IRF3 activation, interferon-stimulated gene expression, extracellular ATP release, and cell-surface calreticulin exposure. These findings identify XRRA1 as a molecular brake that limits the conversion of radiation-induced DNA damage into immunogenic stress responses. XRRA1, therefore, represents a candidate biomarker of radioadaptive stress and a potential target for radiosensitization and radiotherapy-immunotherapy combinations.

cancer biology↗

bioRxiv2026

Chemotherapy-Induced Oral Mucosal Injury Is Defined by p53 Activation, Cell Cycle Arrest and Diverse Epithelial Progenitor Dynamics

Chemotherapy-induced oral mucositis is a common and debilitating complication, yet the mechanisms underlying oral mucosa injury and repair remain poorly defined. Using a mouse model of 5-fluorouracil (5-FU)-induced mucositis, we define gene networks and oral mucosal cellular landscape dynamics in response to chemotoxic stress. We show that 5-FU-induced epithelial atrophy is driven primarily by cell cycle arrest rather than apoptosis, despite concurrent activation of p53-dependent transcriptional programs linked to both cell fates within individual cells. Relative to intestine, the recovering oral mucosa exhibits a more effective cell cycle checkpoint response and uniquely undergoes metabolic reprogramming toward lipid oxidation. Single-cell RNA sequencing revealed putative epithelial progenitor populations with distinct responses to chemotherapy, including chemoresistant cells with a p53- and AP-1 complex gene signature, reminiscent of lung transitional cell states. These findings define diverse progenitor dynamics and p53-driven responses as key determinants of oral mucosal injury and repair following chemotherapy.

cell biology↗

bioRxiv2026

Transferrin receptor 1 binds human parvovirus B19 VP1u to facilitate entry

Human parvovirus B19 (B19V) exhibits a strict tropism for erythroid progenitor cells, which is governed by the VP1 unique region (VP1u). This region mediates cell-specific uptake by interacting with an unknown cellular receptor, termed VP1uR. Proximity labeling in permissive erythroid cells identified transferrin receptor 1 (TfR1/CD71) as the predominant membrane protein associated with VP1u. VP1u constructs colocalized with TfR1 at the cell surface of erythroid cells. Incubation with anti-TfR1 antibody OKT9 abolished binding and uptake of recombinant VP1u. While OKT9 efficiently inhibited B19V uptake and infection, it did not block virus binding to host cells. Direct binding assays confirmed interaction of VP1u to human TfR1. Using cryoEM we solved the 2.4 [A] structure of the TfR1-VP1u complex, mapping the binding site and identifying the specific interactions. These findings establish TfR1 as the previously unknown receptor, VP1uR, required for B19V uptake.

microbiology↗

bioRxiv2026

Topological Regulation of the Mammalian Genome by Positive DNA Supercoiling

DNA supercoiling is a fundamental aspect of genome topology characterizing all DNA transactions. While negative supercoiling has been extensively characterized, positive supercoiling remains poorly understood. Using a quantitative GapR profiling system, we establish comprehensive maps of positive supercoiling across interphase and mitosis. We show that positive super-coils accumulate not only at gene ends but prominently at promoters, enhancers, insulators and loop anchors, where they are resolved by Topoisomerases. Biochemical and functional assays reveal the main sources of positive torsion: transcription generates genic supercoils, while R-loops and Cohesin drive accumulation at regulatory elements, topologically associating domains and their boundaries. During mitotic chromosomal compaction, Condensins establish a global wave of positive supercoiling that largely homogenizes the genome, yet promoters with rapid post-mitotic reactivation retain elevated torsion and R-loops. These findings establish positive DNA supercoiling as a form of topological memory that links DNA mechanics to transcriptional control, genome architecture and epigenetic inheritance.

molecular biology↗

bioRxiv2026

Fasting primes small intestinal regeneration after damage via a microbiome metabolite chromatin axis

Fasting enhances small intestinal regeneration after radiation but the contribution of the gut microbiome to this process remains uncharacterized. We identify Akkermansia muciniphila (AKK) as a key mediator of this response. AKK was enriched in fasted mice and its antibiotic depletion abrogated radioprotection whereas reintroduction restored both organismal survival and intestinal integrity. Fasting elevated propionic acid, consistent with AKKs metabolic output. AKK-conditioned medium and propionate induced histone H3 acetylation in intestinal stem cell cultures while in vivo fasting induced AKK-dependent H3K27ac and H3K9ac, remodeling promoter-enhancer landscapes in crypt epithelial cells. Epigenetic profiling revealed a rewired core regulatory program enriched for pioneer transcription factors (Foxa, Gata, Klf), architectural organizers (Ctcf, Boris), and lineage-defining and metabolic regulators (Cdx2, Hnf4). This program supports expansion of a population of persister stem cells characterized by open chromatin accessibility at key stem and regenerative-associated loci including Clu, Olfm4, Lgr5, Ascl2, Lrig1, Sox9, Rnf43, and Axin2. These findings define a fasting-induced microbiome-metabolite-chromatin axis that epigenetically primes highly plastic persister stem cells for rapid regeneration of the intestinal epithelium following radiation-induced injury. Significance StatementFasting changes the gut microbiome, but how these changes help the body recover from damage is not well understood. We found that fasting increases a helpful bacterium, Akkermansia muciniphila, which produces propionate, which drives epigenetic changes by modifying histones and regulating gene activity. These changes promote the expansion of persister stem cells that help the intestine recover after radiation. This study shows how fasting and gut bacteria work together to protect healthy tissue and suggests that diet or microbial treatments could help reduce side effects of cancer radiotherapy.

cell biology↗

bioRxiv2026

Unique pore architecture underlies constitutive gating of human retinalTRPM1

Transient receptor potential melastatin 1 (TRPM1), a Ca{superscript 2}-permeable nonselective cation channel essential for retinal ON bipolar cell signaling and night vision, and implicated in congenital night blindness, has remained structurally and functionally poorly characterized. Here we report the first cryo-electron microscopy structure of human TRPM1 in conducting state. Although the channel assembles as a tetramer, it adopts an unexpected clockwise domain-swapped pore module with rotational geometry inverse to that observed in previously characterized 6-TM tetrameric channels. This inverted topology is accompanied by extensive remodeling of the S5-P-S6 module, dilation of the selectivity filter, expansion of the central cavity, and splaying of S6 to form a wide intracellular gate. Single-channel recordings reveal constitutive activity consistent with the conductive state captured. Together, these findings uncover a new 6-TM fold in tetrameric channel and provide a framework for understanding TRPM1 gating and disease-associated dysfunction.

biochemistry↗

bioRxiv2025

Improvement in Orchard Nutrient Status and Productivity Through Integrated Nutrient Management in Mango (Mangifera indica L.) Under Medium-Density Planting

AbstractBalanced nutrient management is essential for sustaining productivity and soil health in perennial fruit crops. A two-year field study (2022-2024) was conducted to evaluate the effects of integrating soil and foliar micronutrient applications with reduced recommended doses of fertilizers (RDF) on vegetative growth, nutrient status, yield, fruit quality, and economic performance of mango (Mangifera indica L.) cv. Dashehari under medium-density planting. Nine nutrient modules combining 25-100% RDF with soil- and foliar-applied Fe, Zn, B, Cu, and Ca were compared using ANOVA, PCA, and PLS-SEM. Integrated treatments significantly enhanced canopy height, spread, and volume, with the 75% RDF + two foliar micronutrient sprays producing the greatest vegetative growth. Yield attributes, fruit size, retention, and shelf life improved markedly under micronutrient-enriched treatments. The highest fruit yield and benefit-cost ratio was obtained with 75% RDF + two foliar sprays, outperforming the conventional 100% RDF. Soil pH and EC were moderated, and organic carbon improved slightly under integrated nutrient management. Soil and leaf macro- and micronutrient concentrations were consistently higher with combined soil-foliar approaches. PCA clustered high-performing nutrient modules with yield and canopy variables, while PLS-SEM identified plant nutrient status as the strongest predictor of fruit yield. Overall, integrating micronutrient supplementation with 75% RDF improved nutrient-use efficiency, productivity, and economic returns while reducing dependence on full-dose fertilizers. The study highlights 75% RDF + foliar micronutrient sprays as an effective and sustainable nutrient management strategy for enhancing yield and orchard performance in mango. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/697138v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@227e25org.highwire.dtl.DTLVardef@87b769org.highwire.dtl.DTLVardef@1a73b2org.highwire.dtl.DTLVardef@a1cf12_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

Silylation of hydroxychloroquine enhances autophagy inhibition and antiproliferative activity in breast and pancreatic cancer cells

IntroductionAutophagy is a key survival mechanism in cancer, and chloroquine (CQ) and hydroxychloroquine (HCQ) are widely used late-stage autophagy inhibitors. However, their low potency and the need for high doses limit antitumor efficacy and raise concerns about off-target toxicity. We therefore designed hydroxychloroquine silyl derivatives based on the hypothesis that increasing lipophilicity at the terminal 2-hydroxyethyl moiety enhances lysosomal accumulation and autophagy inhibition while preserving the 4-aminoquinoline pharmacophore. MethodsThree HCQ silyl ethers-OTBS (2), OTIPS (3), and ODPS (4) have been synthesized by silylating the terminal hydroxyl of HCQ. Antiproliferative activity and autophagic flux along with apoptosis have been assessed for LC3B-II, p62/SQSTM1, and caspase-3-mediated PARP-1 cleavage. Results and DiscussionThe HCQ silyl derivatives retain the core pharmacophore and display improved or comparable antiproliferative activity relative to HCQ, achieving low-micromolar IC50 values. Candidate compounds 2 and 3 strongly induce LC3B-II and p62 accumulation than HCQ, consistent with enhanced blockade of autophagic flux. This autophagy disruption is accompanied by increased PARP-1 cleavage, particularly in aggressive 4T1 and MIAPaCa-2 cells, linking reinforced lysosomal/autophagy inhibition to apoptotic signaling. ConclusionThese findings show that silylation of HCQ enhances autophagy inhibition and pro-apoptotic activity while maintaining pharmacology, identifying HCQ silyl derivatives as promising leads for autophagy-targeting antitumor agents.

cancer biology↗