Biology subjects

Sharma, R.

Publications and source records attributed to Sharma, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

EnSEMBLE: a framework for enhancer-anchored pathway analysis that locks in enhancer-corroborated pathways from transcriptome sequencing data for biological validation

Background Pathway discovery methods for transcriptome sequencing return tens to hundreds of redundant gene sets, and biologists often subjectively select the pathways fitting biological expectations. What is missing is not another statistical method, but a way to corroborate each candidate pathway against an independent, mechanistic line of evidence. Results We introduce EnSEMBLE (Enhancer-Set Enrichment & Mechanism-Based Linked Evidence), a tool that corroborates gene-level pathway enrichment with an orthogonal enhancer layer drawn from the same transcriptome sequencing data: active enhancers transcribe enhancer RNAs already present in standard RNA-seq, so a pathway's regulatory state can be scored from the very run that produced the gene-level signal, at no added cost. EnSEMBLE pairs pathway enrichments with Enhancer-Program Enrichment Analysis (EPEA), collapses redundant gene sets into process-level Themes, and retains only those that a concordant enhancer program corroborates. This dual-evidence requirement reduced reported signatures by >97% (hundreds of gene sets to 3-18 claims) across four datasets spanning cancer perturbations and iPSC-to-neuron differentiation. Surviving claims recovered expected biology--mesenchymal-program collapse upon SNAI1 knockout, regulatory convergence during neuronal differentiation--and named mechanisms pathway enrichments missed, including an mTOR-MYC-SPT5 elongation axis in rapamycin-treated PANC1 cells. A language AI agent performs narrative synthesis over deterministic statistics, with reproducibility enforced by temperature-zero inference and three-run consensus. We further provide enhancer over-representation analysis (eORA), mapping non-coding GWAS variants to the same programs to recover cell-type-selective trait associations. Conclusions EnSEMBLE shifts transcriptomic interpretation from enumerating possibilities to adjudicating evidence, yielding a compact, traceable set of enhancer-corroborated claims that identify the regulatory programs driving cellular change and prioritize them for experimental validation.

bioinformatics↗

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

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

The sequence-dependent mechanical landscapes of double-stranded nucleic acid (dsNA) remain largely unexplored beyond canonical dsDNA. We describe cgNA+, a coarse-grained predictive model of the mechanics of dsRNA, DNA:RNA hybrids, and epigenetically modified dsDNA, all parameterised from 1.26 milliseconds of atomistic simulations. cgNA+ predicts non-local sequence-dependent equilibrium shape and stiffness with errors an order of magnitude smaller than sequence-variability, while enabling exploration of numbers of sequences inaccessible to atomistic simulation. We show that dsNA equilibrium shape is strongly influenced by flanking sequence up to octamer context, with flexible dimer-steps more context-sensitive. CpG-modification alters equilibrium shape comparable to changes caused by single-nucleotide polymorphisms. Groove width analysis across dsNA decamers reveals strong sequence dependence, reflecting the differing characteristic helical geometry of dsDNA and dsRNA, whereas DRHs exhibit mixed behaviour depending on DNA-strand pyrimidine content. CTCF binding sites exhibit a distinct groove width signature. Persistence-length spectra from [~] 9 million sequences indicate that dsRNA is stiffer than dsDNA, whereas DRH exhibit intermediate stiffness modulated by DNA strand pyrimidine content. Persistence length increases upon CpG-modification, but decreases on hypermodification. Overall, the cgNA+ model enables a first, highly accurate, very large-scale, comparative study of sequence-dependent mechanics both within and across dsNA classes, demonstrating previously hidden regulatory layers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/740023v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1a430edorg.highwire.dtl.DTLVardef@88469borg.highwire.dtl.DTLVardef@d3a7eforg.highwire.dtl.DTLVardef@1b65a15_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Asthma Exacerbations: Integrative Analysis of miRNA Activity Using Single-Cell Transcriptomics

BackgroundAsthma exacerbations are caused by dysregulated cellular interactions between airway and immune cell populations. Circulating microRNAs (miRNAs) are potential biomarkers for asthma exacerbations; however, their target airway cells remain poorly defined. ObjectiveTo identify the cell types that are regulated by the circulating microRNAs linked to asthma exacerbations and the extent to which the cells are regulated by miRNAs. MethodsWe integrated a curated panel of exacerbation-associated circulating miRNAs with single-cell RNA sequencing (scRNA-seq) profiles from induced sputum of 16 asthma patients and 8 healthy controls. Experimentally validated miRNA-target interactions were combined with cell-type-specific differential expression. Elastic Net regression and SHAP analysis quantified gene-level regulatory contributions, yielding a composite Regulation Strength metric. Findings were validated against four independent GEO datasets. ResultsImmune cells, including monocytes, dendritic cells, and macrophages, demonstrated the strongest statistically significant miRNA regulatory signals, in contrast to airway epithelial cells.hsa-miR-222-3p showed opposing regulatory effects in mature versus alveolar macrophages, indicating differentiation-state-dependent activity, while B_Plasma cells showed no detectable regulatory effect from any miRNA tested. Independent GEO validation confirmed higher expression of protective miRNAs (hsa-miR-126-3p, hsa-miR-146b-5p) in healthy individuals, consistent with prior CAMP cohort associations. ConclusionCirculating miRNAs show cell-type-specific regulatory activity, strongest in monocytes, dendritic cells, and macrophages. hsa-miR-222-3p showed opposing regulatory directions between macrophage subtypes, while B_Plasma cells showed no effect, validated across independent GEO cohorts.

bioinformatics↗

bioRxiv2026

Glomerular-Targeted Delivery of Low-Dose Prednisolone Attenuates Established Lupus Nephritis in MRL/lpr Mice.

BackgroundLupus nephritis remains a major cause of chronic kidney disease and kidney failure in systemic lupus erythematosus. Glucocorticoids are central to treatment but are limited by systemic toxicity. We evaluated whether a previously characterized collagen IV 3-targeted liposomal nanoparticle formulation carrying low-dose prednisolone could attenuate established lupus nephritis in MRL/lpr mice. MethodsFemale MRL/lpr mice with disease present at treatment initiation and C57BL/6J control mice received saline or collagen IV 3-targeted prednisolone-loaded nanoparticles (Col4-3-Pred-NPs). Renal outcomes were assessed by longitudinal proteinuria, glomerular filtration rate (GFR), survival, kidney histopathology, renal IgG and C3d deposition, dUTP/TUNEL-associated injury staining, and renal cytokine/chemokine profiling. Body weight, food and water intake, and blood glucose were monitored as measures of general condition and preliminary tolerability. ResultsCol4-3-Pred-NPs improved survival in MRL/lpr mice, reduced cumulative proteinuria burden, and attenuated terminal GFR decline compared with saline-treated MRL/lpr controls. Treatment reduced glomerular and tubulointerstitial injury, lowered composite EGTI histopathology scores, decreased terminal kidney enlargement, reduced glomerular IgG deposition and renal dUTP-positive injury signals, and reduced renal signals for IL-28A/B, IL-7, PD-ECGF, IL-11, CCL6/C10, and IL-15. C3d deposition was not significantly altered. Nanoparticle treatment was not associated with sustained treatment-related increases in blood glucose or body-weight loss during the measured study period. ConclusionsCollagen IV 3-targeted liposomal delivery of low-dose prednisolone attenuated established lupus nephritis in MRL/lpr mice and improved renal structural, functional, inflammatory, and survival outcomes. These findings support further evaluation of glomerulus-targeted nanotherapy as a potential strategy to improve the precision and therapeutic index of glucocorticoid treatment in lupus nephritis.

physiology↗

bioRxiv2026

Mapping Enteric Neural Circuits by Anterograde Transsynaptic Tracing

The diverse functions of the enteric nervous system (ENS) arise from communication between molecularly distinct neuronal populations organized into complete circuits. While recent single-cell transcriptomic studies have resolved the molecular identity of enteric neuron classes, methods for defining their synaptic connectivity remain limited. Here, we describe the implementation of mWmC, an anterograde monosynaptic tracer based on a fusion of wheat germ agglutinin (WGA) and mCherry, as a non-toxic, single-component viral tool for mapping neuronal circuits within and beyond the ENS. Following adeno-associated virus (AAV)-mediated expression in enteric neurons, mWmC was efficiently expressed and transmitted selectively to postsynaptic neurons, with no detectable transfer to enteric glia, interstitial cells of Cajal, blood vessels or other mesenchymal cell types. The method also identified postsynaptic neurons in the celiac-superior mesenteric ganglia following tracing of intestinofugal enteric neurons, demonstrating its utility for mapping inter-organ circuits. As proof of principle, we applied mWmC to two genetically defined myenteric interneuron populations and identified preferential postsynaptic targets, revealing selective connectivity with distinct enteric neuron classes. Time-course experiments showed that transsynaptic labeling occurred between 4 and 10 days and reached a plateau thereafter, consistent with monosynaptic transfer. Finally, we developed a dual-reporter version of the system that simultaneously distinguishes input and target neurons within the same tissue. Together, mWmC provides a robust approach for defining circuit architecture in the ENS, linking molecular cell atlases with neuronal connectivity and paving the way for deeper insights into the circuit mechanisms underlying gut physiology. Graphical AbstractSchematics illustrating the implementation and applications of the anterograde monosynaptic tracer mWmC for mapping enteric neuronal circuits. Parts of schematics are generated with Biorender. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=36 SRC="FIGDIR/small/741165v2_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@19635bborg.highwire.dtl.DTLVardef@a18ffborg.highwire.dtl.DTLVardef@f3d011org.highwire.dtl.DTLVardef@e1359c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

IL-1β/IL-6 signaling circuit in the tumor microenvironment drives prostate cancer development

Despite considerable progress in elucidating mechanisms leading to castration-resistant prostate cancer (CRPC), insight into the early stages of prostate cancer initiation and progression remains limited. Genomic drivers of prostate cancer initiation have been defined through patient tumor sequencing, but the subsequent events responsible for local tissue invasion are poorly understood. Here we leverage a well-studied genetically engineered mouse prostate cancer model (Hi-Myc) that, based on robust and reproducible kinetics for transitioning from pre-invasive prostatic intraepithelial neoplasia (PIN) to invasive prostate adenocarcinoma (PCa), provides an ideal system to systematically address this question using single-cell analysis. Surprisingly, the transcriptomic profiles of early PIN lesions are indistinguishable from those of late-stage, highly invasive tumor cells, suggesting that MYC activation at the PIN stage establishes a transcriptional program that is fully capable of driving invasion but is restrained by the local tumor microenvironment (TME). Indeed, we find that progression to PCa is associated with progressive infiltration of IL-1{beta}+ tumor-infiltrating macrophages at the PIN stage that, based on immunodepletion and cytokine neutralization experiments, are required for the PIN-to-PCa transition. Mechanistically, IL-1{beta} from macrophages acts directly on prostate fibroblasts, leading to the release of IL-6, which drives invasion by activating IL-6R in tumor cells. Collectively, these findings identify a pro-tumorigenic IL-1{beta}/IL-6 signaling circuit mediated through local macrophages and fibroblasts that unleashes the full oncogenic potential of a cancer driver (MYC) activated at the PIN stage. We also find evidence of this circuit in other (non-MYC-driven) prostate cancer models as well as human prostate and lung adenocarcinoma, with implications for TME-specific targeted therapeutics in early-stage disease.

cancer biology↗

bioRxiv2026

Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics

Single-cell proteomics (SCP) currently lacks validated benchmarking standards, and cell annotation often relies on transcriptomic proxies. Unsupervised clustering offers a proxy-free alternative, but its success depends on biological signal outweighing technical variation. In homogeneous samples this is achievable, but in heterogeneous populations, where closely related cell types differ only subtly, technical variation can dominate the clustering and obscure the biology needed for annotation. To address this, we developed an integrated experimental and computational pipeline for protein-level cell annotation and applied it to human PBMCs as an immune-cell test case. We isolated T cells, B cells, monocytes, and NK cells by negative-selection sorting to build a high-fidelity reference. In parallel, unsorted PBMCs from the same donor were processed on a cellenONE and acquired using label-free DIA on an Orbitrap Astral Zoom. Using the labeled reference dataset, we systematically benchmarked normalization, imputation, and clustering methods to assess their effect on cell-type separation. Unsupervised analysis resolved functional subpopulations within each lineage, and a probabilistic SCP classifier trained on these annotations identified the corresponding cell types and states in the unsorted PBMC fraction, validating the pipeline on unenriched, heterogeneous samples. Together, this work delivers an analytically benchmarked SCP workflow that resolves immune lineage and cell-state heterogeneity in human PBMCs and provides a classifier-ready, protein-level reference for immune-cell assignment.

bioinformatics↗

bioRxiv2026

Coupling Luciferase Activation and BRET Enables High-Contrast Red-Window Calcium Imaging

Genetically encoded bioluminescent calcium indicators enable excitation-free imaging of Ca2+ dynamics with low background, no photobleaching, and improved tissue penetration. However, many exhibit lower dynamic ranges than their fluorescent counterparts, motivating the development of new sensor configurations, particularly for imaging in the red optical window, where tissue absorption and scattering are reduced. Here, we developed HyBRIC and HyBRIC2, two hybrid indicators that integrate Ca2+-dependent luciferase activation and bioluminescence resonance energy transfer (BRET) within a single molecular architecture. When paired with pyCTZ luciferin, they exhibited an approximately 55-fold Ca2+-dependent signal increase in the red optical window in vitro. Compared with HyBRIC, HyBRIC2 showed improved brightness and responsiveness in mammalian cells. It robustly resolved induced Ca2+ dynamics in HEK293T and HeLa cells, with particularly strong red-window responses. Together, these findings expand the limited repertoire of responsive red-window bioluminescent calcium indicators and establish hybrid multiplicative sensing as a modular strategy for improving biosensor contrast.

biochemistry↗

bioRxiv2026

Altered volume-regulated anion channel activity contributes to depression and anxiety-related molecular and behavioural phenotypes in zebrafish

Major depressive disorder (MDD) is a leading cause of global morbidity and mortality. Unfortunately, a substantial proportion of patients do not respond adequately to currently available therapies, highlighting the need for new therapeutic targets. Here, we investigated the role of volume-regulated anion channel (VRAC) in depression-related phenotypes using zebrafish. Disruption of VRAC function, either by pharmacological inhibition or morpholino-mediated knockdown of lrrc8aa, the zebrafish ortholog of mammalian LRRC8A, the obligatory subunit required for VRAC function, induced anxiety- and depression-like behaviours in zebrafish larvae and altered the expression of genes associated with affective disorders. Transcriptomic analysis of lrrc8aa-deficient larvae revealed dysregulation of pathways involved in neuronal signalling and cellular stress responses. Conversely, pharmacological activation of VRAC with zinc pyrithione (ZPT) improved behavioural abnormalities and partially restored altered gene expression. In adult zebrafish subjected to chronic unpredictable stress, ZPT produced antidepressant- and anxiolytic-like effects comparable to those of imipramine and normalized elevated monoamine oxidase (mao) expression. Together, these findings indicate that reduced VRAC function contributes to depression- and anxiety-related behavioural and molecular phenotypes and identify VRAC as a potential target for the development of novel antidepressant therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/740018v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@d81884org.highwire.dtl.DTLVardef@131b8e9org.highwire.dtl.DTLVardef@162d1d0org.highwire.dtl.DTLVardef@bcdb82_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Integrative synaptosome multi-omics reveals disrupted synapse organization and localized cryptic transcripts in C9ORF72-Frontotemporal Dementia

Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS) are linked neurodegenerative diseases characterized by both synaptic dysfunction and TDP-43 pathology. A hexanucleotide repeat expansion (HRE) in the C9ORF72 (C9) gene represents the most common genetic cause of FTD and ALS, yet the synapse-specific mechanisms underlying disease pathogenesis remain poorly understood. Here, we performed integrated multi-omic profiling of synaptosomes enriched from postmortem frontal cortex and patient-derived induced pluripotent stem cell (iPSC)-derived cortical neurons to define molecular alterations associated with C9-FTD-mediated synaptic dysfunction. Proteomic profiling of frontal cortex-derived synaptosomes identified 1,324 differentially abundant proteins (p<0.05) enriched in pathways regulating synaptic vesicle transport and synapse organization, while synaptosomal RNA sequencing revealed 2,835 differentially expressed protein-coding genes. C9-FTD iPSC-cortical neurons exhibited reductions in excitatory and inhibitory postsynaptic markers, accompanied by progressive impairment of neuronal network activity, supporting both structural and functional deficits. iPSC-derived synaptosomes recapitulated key molecular pathways observed in patient brain, revealing convergent dysregulation of synaptic signaling pathways. Comparative analyses revealed divergence between protein and RNA alterations, consistent with the disruption of regulatory processes that link RNA and protein abundance diseased synapses. Consistent with TDP-43 loss-of-function pathology we identified cryptic exon (CE)-containing transcripts within C9-FTD frontal cortex-derived synaptosomes, including KALRN and STMN2, providing evidence that aberrantly spliced RNAs localize to synaptic compartments. Together, these findings define convergent molecular pathways underlying synapse vulnerability in both C9-FTD model systems and identify synaptic localization of CE-containing transcripts as a previously unrecognized feature of TDP-43 proteinopathy.

neuroscience↗

bioRxiv2026

An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid

The retinal pigment epithelium and choroid are critical for supporting the function and maintaining the homeostasis of the outer retina, and their dysfunction underlies a range of inherited and complex ocular diseases. To comprehensively characterize the cellular, transcriptomic, and epigenomic heterogeneity and dynamics within these tissues, we assembled an integrated multi-omics reference atlas comprising 719,813 single-cell/single-nucleus transcriptomes and 234,007 snATAC-seq profiles from 102 ancestrally diverse donors spanning 0 to 99 years of age, including cells from both the macula and periphery. This atlas resolves 48 distinct cell types or states and catalogs 448,567 open chromatin regions. Specifically, we resolved five distinct RPE subpopulations organized along a central-to-peripheral spatial axis, alongside two distinct stress/senescence states. We reconstructed the transcriptomic and epigenetic zonation of endothelial cells and expanded choroidal stromal heterogeneity by characterizing 11 fibroblast and two pericyte types. Age-associated compositional analysis revealed a significant fractional depletion of melanocytes, PI16+ fibroblasts, and venule endothelial cells with age, alongside a modest relative loss of central RPE and a corresponding increase in far-peripheral RPE. Cell-type-specific aging transcriptomics uncovered shared pathways related to inflammatory responses alongside distinct cell-type-specific signatures. Notably, significant age-associated epigenetic changes concentrated in the macula during the transition from early-to-middle adulthood and remained stable into old age, with transcription factors from the AP-1/bZIP family emerging as the dominant enriched motifs. Finally, integrating this atlas with AMD GWAS data provides novel variant-to-gene evidence implicating LIPG and COL4A3 in AMD pathogenesis. Together, this multi-omics atlas serves as both an invaluable community reference and a powerful discovery engine that translates genetic risk signals into localized target cells and candidate mechanisms, laying a foundation for understanding RPE/choroid biology in health and disease.

genomics↗

bioRxiv2026

Impact of thermal variation on the transcriptome of Plasmodium falciparum infected Anopheles stephensi

Temperature is a key determinant of malaria transmission, influencing both parasite development and mosquito physiology, yet the underlying mechanisms remain poorly understood. Here, we examined how temperature and time modulate gene expression in Anopheles stephensi infected with Plasmodium falciparum. Using RNA-sequencing over 1-19 days post-blood meal and three temperature regimes (20, 24, and 28{degrees}C with diurnal fluctuations of 9{degrees}C), we characterize transcriptome responses to infection with P. falciparum at the site of infection in the midgut, and systemically, in the carcasses. Oocyst prevalence and density declined over the thermal gradient, albeit with distinct, non-linear temporal dynamics in parasite development rates. Although infection contributed minimally to global variation in gene expression relative to temperature and time, infection-associated genes in the midgut showed coordinated transcriptional responses enriched in canonical Plasmodium associated extracellular, proteolytic, immune, and metabolic functions; notably, decline in oocyst infections in the midguts over the thermal gradient was reflected in reduced expression of immune genes known to regulate P. falciparum. Network analysis demonstrated that these genes participate in a significantly interconnected protein-protein interaction network, within which a small number of high betweenness centrality proteins act as bottlenecks linking immune, metabolic, reproductive and behavioral processes. Our results suggest responses to infection may be mediated through coordinated physiological networks rather than large-scale transcriptional changes. Our findings also indicate that differences in thermal conditions may be an important factor when comparing mechanisms of vector- parasite interactions between Plasmodium species. Together, our results highlight the importance of integrating thermal context into mechanistic studies of vector-parasite interactions.

ecology↗

bioRxiv2026

Glomerulus-Targeted Nanotherapy via Collagen IV-α3 Binding Enhances Renal Immunoregulation in Lupus Nephritis

Lupus nephritis requires long-term immunosuppressive therapy, which is often associated with severe systemic side effects. Therefore, new therapeutic strategies that maintain high efficacy while minimizing adverse effects is essential. Although nanomedicine has advanced systemic and kidney-targeted drug delivery, a reliable method for glomerulus-specific delivery is lacking. Collagen IV (Col4)-alpha 3, located in the glomerular basement membrane (GBM) at the blood-tissue interface through fenestrated capillary endothelium, represents an ideal target for glomeruli delivery. Herein, we developed a novel liposomal nanoparticle conjugated with a Col4-alpha 3 binding peptide (Col4-3-NPs) for selective glomerular targeting. Prednisolone-loaded Col4-3-NPs were administered to lupus-prone mice twice weekly for 8 weeks. Kidney injury and function were evaluated biweekly, and renal immune cell populations were analyzed by flow cytometry at study completion. The results show that rhodamine-labeled NPs predominantly accumulate in kidney glomeruli 48 hours after intravenous injection. The Col4-NP system demonstrated stable and prolonged release of the encapsulated drug for over 48 hours. Lupus-prone mice treated with prednisolone-loaded Col4-NPs showed significantly improved renal function and histology, including a 30% increase in glomerular filtration rate (GFR), a 56% reduction in proteinuria, and decreased IgG deposition and fibrosis. Notably, treatment also enhanced renal regulatory T cell (Treg) populations. These findings suggest that glomerulus-targeted Col4-3-NPs hold significant translational promise. This platform may offer an effective, site-specific treatment for lupus nephritis while minimizing systemic side effects and could be adapted for other glomerular diseases requiring targeted therapy.

physiology↗

bioRxiv2026

The basal cell state maintains pancreatic cancers by controlling an immunosuppressive circuit

Intra-tumoral heterogeneity is a cardinal feature of solid tumors, yet how distinct cancer cell states functionally contribute to malignant and stromal diversity in situ remains poorly understood. Using mouse models to lineage-trace or genetically ablate the two predominant cancer cell states in autochthonous pancreatic ductal adenocarcinoma (PDAC), we discover that basal cancer cells are highly plastic, whereas classical cancer cells exhibit limited plasticity. Strikingly, ablation of the basal, but not the classical, state induced rapid and durable tumor collapse, driven by loss of immunosuppressive cancer-associated fibroblasts, macrophage repolarization, and reprogramming of the tumor cytokine milieu, culminating in tumor destruction by cytotoxic lymphocytes. Knockout of a single cytokine, GM-CSF, specifically in basal cells recapitulated macrophage repolarization and lymphocyte recruitment observed upon basal state ablation and shrank tumors. These results reveal the basal cell state controls an immunosuppressive cell circuit critical for PDAC maintenance, motivating therapeutic targeting of the basal cells.

cancer biology↗

bioRxiv2026

Conserved Transcriptomic Signatures of Sirt6 Activity: A Cross-Species RNA-seq Meta-analysis

The NAD+-dependent histone deacetylase Sirt6 regulates transcription of multiple classes of genes, including those involved in metabolism, immune response, oxidative stress response, and development. Defining the Sirt6-regulated transcriptome is relevant to understanding the various important physiological roles of Sirt6, such as extending lifespan, maintaining metabolic health, and tumor suppression. Numerous studies have identified Sirt6 target genes, using both targeted and genome-wide approaches; however, consensus is limited and there has yet to be a systematic analysis of gene expression changes induced by altering Sirt6 levels. In the present study, we conducted a meta-analysis of 19 mammalian RNA-seq datasets in which Sirt6 levels were perturbed (knockout, knockdown, or overexpression). Our analyses included Gene Set Enrichment Analysis, pathway analysis of differentially expressed genes, and identification of individual differentially expressed genes. Our analysis identified consistent gene expression changes associated with lowering Sirt6 levels, including increased expression of immune response and ribosomal protein genes and reduced expression of lipid oxidation and oxidative phosphorylation genes. Extracellular Matrix and E2F target genes also had consistently increased expression upon Sirt6 reduction, highlighting novel regulation by Sirt6. To determine the conservation of gene regulation by Sirt6, we performed additional RNA-Seq meta-analysis on tissues from Drosophila melanogaster with Sirt6 deletion and overexpression. The fly datasets produced similar results to the mammal results, except for lipid oxidation genes, which were found to increase in Sirt6-low conditions. These results provide consensus about conserved and novel pathways transcriptionally regulated by Sirt6.

genomics↗

bioRxiv2026

Far-red timing uncovers cultivar-dependent yield and bolting responses in vertical-farm spinach (Spinacia oleracea L.)

Far-red light (FR; 700-750 nm) is increasingly incorporated into controlled-environment lighting because it can improve photosynthetic efficiency when combined with comparatively shorter wavelengths. In long-day leafy crops such as spinach, however, FR may also promote the transition from vegetative to reproductive growth and thereby reduce marketable yield. Most studies have evaluated FR fraction, intensity or end-of-day exposure, whereas the developmental timing of FR has rarely been tested, particularly in spinach. Here, we evaluated six commercial spinach cultivars (Amador, Harp, Renegade, Responder, Rubino and Santa Cruz) in an indoor vertical farm under a common red-green-blue background (PPFD 260-264 {micro}mol m-{superscript 2} s-{superscript 1}, 12 h photoperiod, 24 {degrees}C) and four FR timing treatments: no FR (Control), FR throughout production (FullFR), FR during early development only (EarlyFR), and FR during late development only (LateFR). LateFR increased marketable fresh weight relative to Control (244 vs 224 g) and reduced flowering incidence, whereas far-red supplied during early development reduced fresh weight (158 g) and increased flowering. The magnitude of the timing response differed among cultivars: switching from EarlyFR to LateFR recovered 0 % fresh weight in Amador but 107 % in Renegade and Rubino, with the largest penalties occurring in otherwise bolt-resistant cultivars. EarlyFR also increased total chlorophyll and reduced the chlorophyll a:b ratio. These results show that FR response in spinach is strongly conditioned by developmental stage and cultivar. Although LateFR received more total far-red than EarlyFR, it behaved like the Control, indicating that the penalty was set by far-red timing rather than dose. Treatment differences in bolting and yield tracked an estimated phytochrome photostationary-state deficit during early development: a phytochrome-deficit model markedly outperformed a cumulative-dose model ({Delta}AIC = 441), and the deficit x cultivar interaction was strong (p < 0.001), with bolt-resistant cultivars losing most yield when far-red coincided with the early developmental window. We therefore propose that FR should be treated as a genotype-dependent management variable rather than as a fixed spectral input, with late application and bolt-resistant cultivars offering the most favourable combination for vertical-farm spinach production. Framed within the breeders equation, the close match between the trial and production environment and the scope for shorter breeding cycles indoors suggest that genotype and far-red timing can be optimised jointly to accelerate genetic gain.

plant biology↗

bioRxiv2026

Molecular and Structural Basis of Cardiac Remodelling in Niemann-Pick Type C

Key Point SummaryNiemann-Pick disease type C (NPC) patients showed a high prevalence of ECG abnormalities, with additional echocardiographic evidence of altered left-ventricular structure and function. Npc1-/- mouse hearts exhibited age-associated glycosphingolipid accumulation accompanied by marked myocardial fibrosis and increased collagen deposition. Ex vivo electrophysiology revealed QT prolongation and atrioventricular conduction defects in Npc1-/- hearts, particularly under {beta}-adrenergic stress. Transcriptomic profiling identified inflammatory and fibrotic pathway activation consistent with the structural and electrophysiological abnormalities observed. Together, these findings demonstrate previously unrecognised cardiac involvement in NPC and support routine cardiac screening to improve clinical management. Niemann-Pick disease type C (NPC) is a rare autosomal recessive neurodegenerative lysosomal storage disease caused by pathogenic variants in NPC1 or NPC2. Sudden death can occur due to seizures, but cardiac involvement has not been well defined. We performed 12-lead electrocardiograms (ECG) in 14 adult NPC patients (8 male, 6 female). Cardiac structure and function were examined in Npc1-/- adult mouse hearts, alongside wild-type controls. Glycosphingolipid accumulation was quantified by high-performance liquid chromatography, fibrosis and collagen deposition were quantified using Massons Trichrome (M&T) and Picrosirius Red (PR) staining. Whole-heart morphology, including chamber size and wall thickness, was assessed. Ex vivo ECG recordings assessed conduction abnormalities and arrhythmias. RNA-seq transcriptomics characterised molecular pathways altered in Npc1-/- hearts. 8/14 patients showed ECG abnormalities including abnormal QRS transitions (N=8), increased QRS amplitude (N=4), fascicular block (N=2), and abnormal T wave inversion (N=1). 13 patients also had transthoracic echocardiograms identifying mildly impaired LV systolic function (N=2) and increased wall thickness/LV mass (N=4). In Npc1-/- mice, age-related glycosphingolipid accumulation was associated with pronounced ventricular fibrotic remodelling. There was a significant increase in stained connective tissue area and connective tissue to cardiac tissue ratio in both M&T and PR staining. ECG from Langendorff-perfused Npc1-/- hearts showed QT prolongation and atrioventricular conduction abnormalities under isoprenaline stress. Transcriptomics revealed major changes in Npc1-/- hearts, consistent with histological fibrosis and linking NPC to inflammation-driven remodelling and arrhythmogenesis. These findings support routine cardiac screening in NPC patients and highlight the need for further studies to improve management and treatment.

physiology↗