Biology subjects

Ghosh, S.

Publications and source records attributed to Ghosh, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Plasma Metabolomic Profiling of COPD Patients Stratified by Smoking Status: A GC-MS- Based Approach

BackgroundChronic obstructive pulmonary disease, primarily caused by exposure to cigarette smoke, is a heterogeneous lung condition characterized by complex metabolic alterations. The metabolic changes associated with smoking status have not been thoroughly investigated. Our study aims to explore the metabolite profile of COPD patients categorised by their smoking habits, including smokers, ex-smokers, and non-smokers. MethodsIn this study, the plasma metabolome of smoking stratified COPD patients were assessed using gas chromatography coupled to mass spectrometry. We applied multivariate and univariate statistical analysis to identify the differentially abundant metabolites. ResultsWe identified 23 altered metabolites in the smokers and 36 in the ex-smokers COPD subgroups. Interestingly, in comparison to the control group, no significant alteration was observed in the plasma of non-smoker COPD patients. Additionally, pathway enrichment analysis revealed top dysregulated metabolic pathways, including biosynthesis of unsaturated fatty acids, galactose metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, and glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The receiver operating characteristic curve screened five metabolites, such as tetradecanoic acid, 2,4-di-tert-butylphenol, chloroxylenol, tetradecanal, and 1-dodecene, with the highest diagnostic performance (AUC > 0.8). ConclusionThis study reveals distinct plasma metabolic signatures across COPD subgroups categorized by cigarette smoking history.

biochemistry↗

bioRxiv2026

A conserved vesicular circuit enables metabolic adaptation and maintains systemic heme homeostasis

Metabolic homeostasis depends on adaptive control of intracellular metabolite flux, yet how such control is reconfigured when canonical transport pathways fail is unknown. Here we define a conserved vesicular circuit that preserves systemic heme balance by rerouting intracellular heme flux. We show that loss of the intestinal heme exporter MRP-5 in Caenorhabditis elegans causes lethal heme sequestration within endolysosomal compartments. This defect is bypassed by disabling the vesicular adaptor AP-3, which stabilizes and reroutes the heme importer HRG-1, restoring heme export without increasing cytosolic heme. Unbiased genetics and transcriptomics identify two previously uncharacterized SLC49A family members, HRG-13 and HRG-14, as heme exporters with distinct affinities that engage in a vesicular importer-exporter handoff. Live imaging reveals heme-enhanced contacts between HRG-1 and SLC49A-containing vesicles, consistent with direct vesicular transfer. This circuitry extends to vertebrates as disruption of the SLC49A3 homolog impairs erythropoiesis in zebrafish and causes intracellular heme overload, premature hemoglobinization and apoptosis in differentiating human erythroid cells. Together, these findings establish SLC49A3 proteins as conserved heme exporters and uncover a general principle of metabolic adaptation in which reprogramming intracellular compartmentalization, rather than increasing nutrient supply, restores systemic homeostasis.

cell biology↗

bioRxiv2026

Microbial diversity and insights into feeding behavior of the two-spot cotton leaf hopper (Amrasca biguttula)

The recent invasion of the two-spot cotton leaf hopper (TSCL) (Amrasca biguttula) into the U.S. now threatens row and vegetable crops as well as ornamentals. TSCL ecology and biology, including microbial diversity, are understudied. Insect-specific microbes could influence host biology and ecology including insect-plant interactions. Here, microbiota (bacteria and viruses) within TSCL along with its feeding behavior were characterized using high throughput sequencing, microscopy, and Electrical penetration graph (EPG). Results revealed low diversity of bacteria dominated by Wolbachia and confirm the absence of obligate (primary) symbionts. Two distinct and differentially abundant Wolbachia strains (B-supergroup) were found co-infecting midgut tissues of 60% of TSCL tested, and the remaining 40% were free of symbionts. Virome analysis uncovered a diverse complex of at least eight dsDNA genomes (12-17 kb) of Adintoviruses (Eupolintoviridae), but no RNA viruses commonly found in other leafhoppers were identified in TSCL. The mesophyll feeding nature of TSCL was identified by observing chlorophyll derived autofluorescence in midguts and higher abundance of chloroplast transcripts (photosystem I, II, Rubisco, cytochrome b6 and ATP synthase complex) in TSCL (whole insects) compared with thrips and aphids. EPG recordings show a cell-rupture style of feeding with differences between adults and nymphs. Lastly, consistent with its cell-rupturing feeding style, no evidence for the presence of plant-pathogenic bacteria or viruses that could induce hopperburn was found. These results overall provide insights into the microbial diversity and feeding pattern of TSCL and lay a foundation for future research. Key messageThis work characterizes the TSCL microbiome and its mesophyll feeding pattern. Symbionts within insects often complement the nutritional deficiencies of its host and can aid insect spread by boosting immunity. The findings of this study lay the foundation for future research on the biology, ecology, and management of this invasive pest.

microbiology↗

bioRxiv2026

Neuropilin-1 functions as a proviral and immunoregulatory host factor during Chikungunya virus infection

Neuropilin-1 (NRP1) is a transmembrane glycoprotein involved in angiogenesis, neurodevelopment, inflammation, cancer driven immune suppression, and immune homeostasis. However, its contribution to virus-induced immune responses is not explored. Chikungunya virus (CHIKV) is a re-emerging arthritogenic alphavirus that causes severe arthralgia, and myalgia, accompanied by heightened inflammatory cytokine responses. The host factors that drive these inflammatory responses, however, remain poorly defined. Here, in this current study, the role of NRP1 in CHIKV infection was investigated using in vitro, and in vivo model systems. Using genetic manipulation, pharmacological, and antibody blockade-mediated approaches in murine and human cellular infection models, it was demonstrated that NRP1 promotes CHIKV infection while restraining the production of proinflammatory cytokines. Furthermore, NRP1 inhibition selectively increased JNK phosphorylation. Hence, inhibiting JNK reduced the elevated cytokine production caused by NRP1 blockade. Moreover, NRP1 interacted with CHIKV-E1 and is involved in multiple phases of CHIKV infection. In addition, it was demonstrated that NRP1 inhibition using EG00229 trifluoroacetate can reduce viral infection in several CHIKV-susceptible cells, human peripheral blood macrophages, and in the in vivo mice model of infection. Together, these findings indicate that NRP1 is an important host factor and a probable therapeutic target during CHIKV infection. IMPORTANCEChikungunya virus (CHIKV) causes acute febrile illness that can progress to debilitating chronic musculoskeletal and occasional neurological complications. The absence of a globally available effective vaccine and the lack of specific antivirals underscore CHIKV as a major burden, especially in endemic tropical regions. There is a growing need to understand host factors that shape CHIKV-driven immune response. The importance of our study lies in understanding the immunoregulatory role of the host receptor Neuropilin-1 (NRP1) during CHIKV infection. We identify NRP1 as a novel host factor of CHIKV infection that also acts as a rheostat to restrict the inflammatory viral immune response. Moreover, we report anti-viral potential of the NRP1 antagonist EG00229 trifluoroacetate in multiple cell lines, primary cells, and mice model. Our findings indicate NRP1 as a probable therapeutic target in CHIKV pathogenesis.

immunology↗

bioRxiv2026

A first-in-class multimodal organomercury compound demonstrates preferential blast reduction with hematopoietic and immune restoration in Acute Lymphoblastic Leukemia

Acute leukemia treatment requires effective blast reduction while improving hematopoietic and immune health. As reported previously, we developed a structurally distinct organomercury derivative of curcumin, -Mercurin, having improved aqueous solubility and intravenous applicability. Here we comprehensively evaluated therapeutic efficacy, pharmacological response, systemic toxicity, blood Hg pharmacokinetics (PK), Hg biodistribution and elimination profile for -Mercurin in a N-nitroso-N-ethylurea (ENU)-induced autochthonous Acute lymphoblastic leukemia (ALL) rat model, comparing with clinical standard cytarabine. Results showed recovery in body-weight, along with longer time-to-humane-endpoint from 13 to 39 days. Treatment successfully reduced immature blast count, while promoting erythroid, myeloid, and megakaryocytic compartments and improving immune mediators across peripheral blood, bone marrow, thymus, spleen, and lymph nodes. Histopathology showed reduced leukemic infiltration with preservation of major organ architecture, while cytarabine produced evident myelosuppression, neurotoxicity, and cardiotoxicity. PK study showed blood Hg reached Tmax at 15 min, followed by urinary and fecal elimination with residual retention in kidney tissue and no detectable Hg in brain. Collectively, -Mercurin demonstrated a promising multimodal therapeutic index, combining cytoreductive activity with improvement in hematopoietic and immune health, along with favorable safety profile for future ALL therapy.

cancer biology↗

bioRxiv2026

Microbiota-sensitive glial and metabolic programs define a critical window in early postnatal brainstem development

Paediatric brain tumours are increasingly recognised as diseases of disrupted development, arising when lineage progression programs, that normally govern neural and glial maturation, become stalled or dysregulated. Diffuse midline glioma (DMG), a highly aggressive paediatric brainstem tumour, emerges during early childhood in the pons, a region undergoing rapid postnatal growth characterized by oligodendrocyte precursor cell (OPC) proliferation and differentiation. However, the environmental factors that shape these developmental trajectories remain poorly defined. Here, using germ-free and conventionally colonized mice, we investigated whether early-life microbiota influences transcriptional and metabolic programs in the developing brainstem during this critical developmental window. Bulk RNA sequencing revealed pronounced microbiota-associated transcriptional differences at postnatal day 2 (P2), but not at P8, identifying a temporally restricted period during which microbial colonization is associated with pathways linked to oligodendrocyte lineage progression, myelination, and neuroimmune signalling. Transcriptional analyses further identified altered expression of genes associated with CD11c microglia, a developmental microglial subtype implicated in regulating oligodendrocyte maturation. Untargeted metabolomic profiling revealed parallel microbiota-associated differences in pathways related to mitochondrial function, redox balance, and methyl-donor metabolism. Integrated multi-omics analyses identified coordinated networks linking glial lineage programs with metabolites involved in cellular metabolism and epigenetic regulation. Notably, several of these transcriptional and metabolic programs overlap with gene signatures reported in diffuse midline glioma, suggesting that microbiota-sensitive developmental pathways intersect with cellular states relevant to paediatric brainstem tumour biology.

neuroscience↗

bioRxiv2026

A Bioengineered Live Biotherapeutic Exploits Inflammation to Restore Gut Liver Brain Axis Function under Diet-Induced Stress

Systemic inflammatory diseases can be influenced by dietary intake, with gastrointestinal dysfunction driving both metabolic and behavioural changes mirroring the altered inflammatory profile. Additionally, the use of live biotherapeutic products (LBPs) shows promise for treating metabolic and inflammatory diseases, but their efficacy is limited by poor persistence in inflamed gut environments. Designed to utilize inflammatory byproducts, the LBP EcN::ttr has proven efficacy in the treatment of acute and chronic colitis, however its effects on the metabolic and behavioural patterns remain uncharacterized. We evaluated the effects of EcN::ttr on mice fed a proinflammatory omega-6 PUFA-rich diet. EcN::ttr-treated mice exhibited notable changes in the gut, including an improved expression of tight junction protein occludin, accompanied by reduced serum lipopolysaccharide (LPS) - binding protein, indicating protection against endotoxemia. EcN::ttr improved insulin sensitivity compared to the parental strain, associated with increased hepatic insulin receptor expression and reduced GSK3{beta} activation and endoplasmic reticulum stress. Secondary bile acids in mice treated with EcN::ttr were more abundant, with increases in those associated with resolving diarrhea and bile acid detoxification. Behavioural assessment highlighted a normalization of long-term memory along with a reduction of stress management behaviours. Altogether, EcN::ttr restores gut-liver-brain axis function through coordinated modulation of inflammation, barrier integrity, and bile acid metabolism. HighlightsO_LILive Biotherapeutic Product EcN::ttr, designed with a fitness advantage to survive inflammation, and provides protection against a proinflammatory omega 6-rich diet C_LIO_LIAdministration of EcN::ttr improved metabolic outcomes including increasing insulin sensitivity C_LIO_LIEcN::ttr increased the abundance of secondary bile acids including those that modulate bile acid detoxification C_LIO_LIBehavioural parameters were normalized in mice given EcN::ttr C_LIO_LIEcN::ttr partially normalizes gut-liver-brain axis through restoring barrier integrity, modulating inflammation and improving secondary bile acid metabolism C_LI

systems biology↗

bioRxiv2026

Mating imperatives drive plasticity of the daily temporal niche via dopamine signaling.

Animals confine their daily activity to distinct diurnal, crepuscular, or nocturnal windows. It remains unclear how hundreds of sympatric species sharing the same temporal niche manage to coexist. To address this, we monitored the daily activity of the twilight-active, species-rich Drosophila genus under naturalistic conditions. Here, we show that intense sociosexual interactions rapidly drive a species-specific reformatting of their canonical crepuscular niche. The dominant sensory modality used for sexual communication predicts niche shift direction: reliance on chemosensation for courtship redirects behavioral activity into the night, while visual reliance shifts it into the day. This temporal plasticity bypasses the circadian clock, instead operating via a conserved dopaminergic pathway that simultaneously inhibits sleep and sustains sexual motivation. Our results reveal how mating imperatives enable conditional colonization of otherwise restricted temporal windows. Ultimately, by driving the divergence of previously overlapping niches, sociosexually induced temporal plasticity provides a powerful mechanism for sympatric coexistence in crowded environments.

neuroscience↗

bioRxiv2026

Distinct Programs of Tissue Adaptation Shape Vitreous CD4+ and CD8+ T-cell States in Chronic Uveitis

Tissue-resident memory (TRM) T-cells are increasingly recognized as key mediators of chronic autoimmune inflammation, yet their organization and functional adaptation within the eye remain poorly understood. We investigated paired vitreous body biopsies and peripheral blood T cells from patients with chronic posterior segment uveitis using multiparameter flow cytometry, antigen-specific stimulation assays, single-cell RNA sequencing, and T-cell receptor sequencing to define the intraocular tissue-adaptive immune states. Vitreous T cells were phenotypically, transcriptionally, and clonally distinct from their circulating counterparts and enriched for canonical TRM markers. However, tissue adaptation differed substantially between CD4+ and CD8+ lineages. Vitreous CD4+ T cells segregated into clonally expanded tissue-adaptive states characterized by greater CXCR6 expression, enhanced antigen-specific cytokine responses, and well-defined transcriptional profiles. In contrast, vitreous CD8+ T cells expressed higher levels of the retention-associated markers CD103 and CD49a yet maintained greater clonal and phenotypic continuity with peripheral blood T cells. Both vitreous CD4+ and CD8+ subsets exhibited a restrained effector profile associated with tissue-adaptive transcriptional programs. Our data reveal that CD4+ and CD8+ T cells in chronic uveitis assume distinct states in the vitreous microenvironment, such that the intraocular immune response relies on both localized tissue retention and active adaptation to the inflammatory niche.

immunology↗

bioRxiv2026

Elucidating the effect of a rationally designed nanostructured form-switching ASO (NaFASO) for targeting long non-coding RNA to alleviate Japanese encephalitis virus infection

RNA therapeutic modalities such as antisense oligonucleotides (ASOs) have emerged as promising tools to target previously "undruggable" targets. Despite their great promise as precision therapeutic agents, their clinical adoption remains limited due to production costs, sequence-length restrictions, limited structural heterogeneity, and the generation of environmentally hazardous waste during synthesis. Biocatalytic synthesis strategies provide a sustainable alternative; however, their reliance on specialized enzymes and precursors often limits sequence diversity and scalability. To address these limitations, we report the design and biocatalytic synthesis of a novel circular ASO: Nanostructured Form-switching Antisense Oligonucleotide (NaFASO) for targeting Japanese Encephalitis Virus (JEV) infection-associated host long non-coding RNA (lncRNA) JINR1 (JEV-induced non-coding RNA1) in SH-SY5Y cells. The novel modular architecture in NaFASO has been designed to have a metastable stem that separates the functional antisense domain from the splint-padlock circularizing region, ensuring both structural integrity and efficient target engagement. The serum- and nuclease-stable NaFASOs achieved knockdown of the lncRNA JINR1 during JEV infection, resulting in a reduction in JEV replication and neuronal cell death. NaFASO-mediated JINR1 depletion also resulted in downregulation of the JEV replication-associated gene GRP78. Together, these findings establish NaFASO as a first-of-its-kind structure-switching circular ASO platform for combating JEV infection, combining stability, efficacy, and environmental sustainability. Beyond the JEV, the generalizability of this design suggests broad applicability for targeting diverse RNA species implicated in genetic disorders, viral infections, and cancer, thus highlighting a promising paradigm for developing next-generation transformational nucleic acid therapeutics.

biochemistry↗

bioRxiv2026

Lamin A/C coordinates nuclear mechanics, chromatin architecture, and transcriptional homeostasis in skeletal muscle in vivo

The nuclear lamina provides mechanical integrity to the eukaryotic nucleus and organizes lamina-associated chromatin domains that are important for chromatin architecture and gene-expression regulation. Lamin A/C, a major component of the nuclear lamina, is disrupted in hereditary laminopathies and has also been implicated in aging-associated nuclear dysfunction. Although the mechanical role of Lamin A/C has been extensively studied in vitro, particularly in monolayer cell culture and isolated nuclei, its role in maintaining nuclear mechanics and chromatin organization in intact tissues remains incompletely understood. Here, we investigated how partial and complete Lamin A/C disruption affects nuclear shape, chromatin architecture, intranuclear mechanics, and gene expression in vivo. Across multiple murine tissues, Lamin A/C deficiency did not cause a generalized collapse of nuclear shape or gross tissue architecture. Instead, Lamin A/C disruption preferentially altered chromatin architecture in mechanically stiff tissues, including skeletal muscle and heart. Using live in vivo deformation microscopy during controlled hindlimb muscle stimulation, we quantified real-time multiscale deformation of skeletal muscle tissue and nuclei. These measurements revealed reduced effective nuclear stiffness and altered load sharing between euchromatin-rich and heterochromatin-rich domains after Lamin A/C loss. Super-resolution imaging further showed that partial and complete Lamin A/C disruption uncoupled H3K9me3 from DAPI-dense heterochromatin, indicating a spatial disruption of repressive chromatin organization. Exploratory ATAC-seq suggested increased chromatin accessibility in heterozygous muscle, whereas RNA-seq showed that complete Lamin A/C loss caused broad myopathic transcriptional dysregulation while partial loss preserved a near-wild-type transcriptomic state. Integrated analysis identified HDAC2 as a candidate mechanosensitive compensatory node that may help buffer gene expression after partial Lamin A/C disruption. Together, these results establish Lamin A/C as an in vivo coordinator of nuclear mechanics, heterochromatin organization, and transcriptional homeostasis in skeletal muscle.

cell biology↗

bioRxiv2026

Targeting lncRNA JINR1 with programmable Circular Active Nano DNAzyme (CANDe) suppresses Japanese Encephalitis Virus infection

Oligonucleotide therapeutics such as antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) enable sequence-specific gene silencing but rely on endogenous cellular machinery and often require extensive chemical modification for stability and efficacy. DNAzymes offer a mechanistically distinct alternative through intrinsic catalytic RNA cleavage; however, their therapeutic translation has been limited by nuclease susceptibility, structural constraints, and synthetic challenges. Here, we report the development of Circular Active Nano DNAzyme (CANDe), an enzymatically synthesized circular DNAzyme platform designed to enhance stability without backbone modification. The therapeutic potential of CANDe constructs was investigated against Japanese Encephalitis Virus (JEV) infection associated host long-noncoding RNA JINR1 (LINC01518). CANDe constructs were generated via splint-assisted ligation and incorporate modular elements, including catalytic cores (8-17 or 10-23), target-binding arms, and structural stems. Circularization conferred marked resistance to exonuclease-mediated degradation compared to linear DNA, maintaining structural integrity under nuclease-rich conditions.,CANDe targeting the lncRNA JINR1 achieved effective JINR1 knockdown in SHSY-5Y with and without JEV infection. This was accompanied by reduced expression JEV RNA and titers. In line with this, CANDe constructs attenuated of virus-induced cytotoxicity and apoptosis. Among the constructs, 10-23-based CANDe targeting the JINR1-1 site exhibited the strongest overall activity. These findings establish CANDe as a modular, modification-free DNAzyme platform that combines catalytic efficiency with enhanced stability, enabling effective host-directed antiviral intervention. This approach highlights topological engineering as a viable alternative to chemical modification for advancing DNAzyme-based therapeutics.

biochemistry↗

bioRxiv2026

Revisiting CPUs for Protein Folding: Xeon-Based Acceleration of AlphaFold2

Protein structure prediction via AlphaFold2 has revolutionized drug discovery, yet its end-to-end execution remains computationally intensive. While GPUs are traditionally favored for deep learning, the AlphaFold2 algorithm consists of heterogeneous phases -- preprocessing with sparse database searches and model inference with low-arithmetic-intensity attention modules -- that present unique architectural challenges. In this work, we address these bottlenecks by introducing Open-Omics-AlphaFold2, a highly optimized implementation for Intel(R) Xeon(R) CPU. By leveraging the CPUs versatility in handling both sparse preprocessing algorithms and dense matrix operations via Intel Advanced Matrix Extensions (AMX), we accelerate the entire pipeline end-to-end. Our optimization strategy employs multi-level parallelism -- spanning multiprocessing, multi-threading, and vectorization -- alongside cacheaware tiling and operator fusion. Our results demonstrate that, on a Xeon CPU, Open-Omics-AlphaFold2 achieves 2 7.58 speedup for preprocessing and 19.8 29.2 speedup for model inference over baseline Deepmind-AlphaFold2. Moreover, for a proteome of 391 proteins, Open-Omics-AlphaFold2 running on a dual-socket Intel Xeon 6980P system achieves a remarkable 76% higher through-put over the state-of-the-art GPU-accelerated solution, FastFold, running on a single-socket Intel Xeon 6980P CPU with an NVIDIA H100 offioad. Code availabilityBaremetal: https://github.com/IntelLabs/open-omics-alphafold Containerized: https://github.com/IntelLabs/Open-Omics-Accelera tion-Framework/tree/main/pipelines/alphafold2-based-protein-folding

genomics↗

bioRxiv2026

Hepatocyte TEAD1 drives epithelial-stromal remodeling during cholestatic liver injury

Background & AimsPrimary sclerosing cholangitis (PSC) is a progressive cholangiopathy characterized by ductular remodeling, inflammation, and periportal fibrosis, for which effective medical therapies remain limited. The Hippo pathway effector TEAD1 has been implicated in liver regeneration and fibrogenesis; however, its role in cholestatic injury remains poorly defined. We investigated whether hepatocyte TEAD1 regulates injury-associated remodeling in a PSC-mimicking model and whether this mechanism is conserved in human PSC liver. MethodsHepatocyte-specific TEAD1 knockout mice (Alb-TEAD1-/-) and littermate controls were subjected to DDC-induced cholestatic injury. Ductular reaction, fibrosis, inflammation, and bile acid-related gene programs were assessed by histology, immunostaining, and gene expression analyses. Translational relevance was evaluated using bulk and single-cell transcriptomic datasets from human PSC liver. ResultsHepatocyte TEAD1 deletion attenuated DDC-induced fibrosis, ductular expansion, and inflammatory cell accumulation, while preserving hepatocyte proliferative responses. TEAD1-deficient livers exhibited reduced expression of profibrotic mediators, including Spp1, Ctgf, and Cyr61, with decreased extracellular matrix deposition. In contrast, canonical transcriptional adaptations to cholestatic stress, including suppression of bile acid uptake, induction of efflux pathways, and repression of bile acid synthesis genes, were preserved in the absence of TEAD1. Analysis of human PSC datasets demonstrated coordinated upregulation of TEAD1 and TEAD-associated target genes. Single-cell transcriptomic analysis further revealed hepatocyte-enriched TEAD1 expression and activation of a TEAD1 target gene program across all hepatic zones in PSC, with effect sizes exceeding those observed in non-parenchymal populations. TEAD1 activation was accompanied by co-expression of profibrotic mediators and downregulation of hepatocyte differentiation markers, consistent with a maladaptive hepatocyte state. ConclusionsHepatocyte TEAD1 drives ductular, inflammatory, and fibrogenic remodeling during cholestatic injury without disrupting bile acid metabolic adaptation. These findings identify TEAD1 as a hepatocyte-intrinsic regulator of epithelial-stromal crosstalk and establish conserved activation of this pathway in human PSC, supporting TEAD-directed signaling as a therapeutic target.

pathology↗

bioRxiv2026

Mitochondrial copper stabilizes lipoylated TCA cycle proteins to sustain metabolism and proliferation

Copper (Cu) is an essential cofactor for mitochondrial cytochrome c oxidase, yet whether it directly regulates mitochondrial metabolism beyond respiration remains unclear. Here we show that mitochondrial Cu, delivered by SLC25A3, is required to maintain the stability of lipoylated TCA cycle proteins. Loss of Slc25a3 or pharmacological Cu depletion selectively destabilized the lipoylated E2 subunits of mitochondrial dehydrogenases and the lipoylation enzymes LIPT1 and LIPT2, an effect not reproduced by acute electron transport chain inhibition. Mechanistically, we find that Cu directly engages the reduced lipoyl moiety using chemical probes and synthetic peptide approaches. Cu depletion impaired PDH and OGDH activity, rewired TCA cycle metabolism, and imposed a dependence on pyruvate carboxylase for anaplerosis. This metabolic defect depleted aspartate, suppressed mTORC1 signaling, and limited proliferation. Conversely, selective delivery of Cu to the mitochondria restored lipoylation, TCA cycle function, and cell growth. Together, these findings identify mitochondrial Cu as a structural regulator of the lipoylation machinery and reveal a direct link between Cu homeostasis and central carbon metabolism.

cell biology↗

bioRxiv2026

Transforming off-the-shelf personal glucose meter into a sustainable and decentralized label-free nucleic acid and NAAT detection platform

In todays world, point-of-care nucleic acid detection still remains extensively constrained and limited by the heavy dependence on centralized urban instrumentation facilities and complex assay workflows. Here, we elucidate a glucometer-based analytical platform that enables label-free detection of nucleic acids and the nucleic acid amplification products through a simple redox-mediated mechanism. The approach leverages the potassium ferricyanide (K3[Fe(CN)6])/ potassium ferrocyanide (K4[Fe(CN)6]), redox system, which is intrinsic to commercial glucometers, complementing with interactions between methylene blue (MB) and nucleic acids. These interactions transduce concentration differences in nucleic acids into quantifiable electrochemical signal readouts. Distinct varied signal outputs are observed between single-stranded and double-stranded DNA, enabling the direct detection as well as integration with nucleic acid amplification tests (NAATs), including polymerase chain reaction, rolling circle amplification, and loop-mediated isothermal amplification. Optimization of reaction parameters and conditions leads to enhancement of the overall signal discrimination and sensitivity across various assay formats. This innovation repurposes widely available off-the-shelf glucometers as a low-cost, portable nucleic acid detectors, thus eliminating the need for any specialized instrumentation. Our results enumerate and establish a generalized and scalable strategy for nucleic acid sensing. The platform thus supports sustainable and environmentally responsible point-of-care testing, thereby enabling improved accessibility and public health monitoring at resource-limited and remote settings.

biochemistry↗

bioRxiv2026

Translation of a four-codon ORF in the 3'UTR of MAP3K10 regulates its expression

Several eukaryotic mRNAs are polycistronic because of translatable open reading frames (ORFs) embedded in their untranslated regions (UTRs), in addition to the primary ORF (i.e., the coding sequence). While 5'UTR upstream ORFs (uORFs) are mechanistically and functionally well studied, 3'UTR downstream ORFs (dORFs) remain poorly understood. Here, we identify and characterize a short, translatable dORF in the 3'UTR of MAP3K10, which encodes a serine/threonine kinase involved in JNK signalling. A stringent computational screen predicted a conserved RNA G-quadruplex (rG4) within the 3'UTR of MAP3K10. Biophysical assays provided more evidence for rG4 formation, which drives translation of a conserved four-codon dORF. Disruption of the rG4 by point mutations or by an rG4-binding ligand reduced dORF translation. Reporter assays using constructs with strategically placed hairpin structures show that translation of the dORF is independent of both the 5 cap and the translation of the canonical ORF. Notably, deletion of the rG4-dORF module, either in exogenous constructs or in CRISPR-edited cells, led to reduced MAP3K10 expression. Together, these results provide evidence for the regulation of MAP3K10 expression by rG4-driven translation of a dORF. Thus, our study contributes to the growing body of evidence suggesting that dORF translation can regulate gene expression.

molecular biology↗

bioRxiv2026

One-Pot NADH-Mediated Physiological Redox-Controlled Synthesis of Papain-Stabilized Copper Nanoclusters with Preserved Bioactivity for Efficient Drug Delivery

Protein-protected copper nanoclusters are promising candidates for bioimaging and therapeutic applications. However, harsh reducing conditions required for their synthesis, compromising the proteins structural integrity and bioactivity. Here, we report a one-pot, physiologically compatible aqueous synthesis for papain-protected copper nanoclusters (Pap-CuNCs) with blue photoluminescence and excellent photostability using nicotinamide adenine dinucleotide (NADH) as a biological reducing agent. The mild conditions (ambient temperature, neutral pH) enable the simultaneous formation of a metallic Cu0 core while stabilizing the helical content of the protein. This approach introduces a physiologically redox-controlled strategy for nanocluster formation, establishing physiological redox chemistry as a governing principle for controlling nanoscale structure and protein conformational stability. Spectroscopic and microscopic studies have demonstrated the presence of crystalline nanoclusters with a protein corona that undergoes -helical stabilization as revealed by circular dichroism. Notably, atomistic simulation studies reveal preferential binding of the copper core in the proteins active site, enhancing the -helical content of papain, consistent with experimental observations. Functionally, the Pap-CuNCs possess biocompatibility and serve as an effective delivery platform for 5-fluorouracil, leading to a 50-fold decrease in IC50 for HeLa cells without causing cytotoxicity to normal cells. This establishes a generalizable framework for bio-integrated nanocluster design under biologically compatible conditions. TOC Text O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC="FIGDIR/small/719779v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1ca9292org.highwire.dtl.DTLVardef@5cd82aorg.highwire.dtl.DTLVardef@173ed2forg.highwire.dtl.DTLVardef@1d8c30c_HPS_FORMAT_FIGEXP M_FIG C_FIG NADH-mediated physiological redox synthesis of papain-stabilized copper nanoclusters with enhanced -helical stability. This bio-integrated nanoplatform facilitates drug loading and delivery, resulting in a [~]50-fold increase in cytotoxicity in cancer cells while maintaining excellent biocompatibility toward normal cells.

bioengineering↗