Biology subjects

Shah, A.

Publications and source records attributed to Shah, A..

At least 19 recordsLinked to original sources

bioRxiv2026

40S Ribosome Remodeling Triggers 18S rRNA U-tailing and DIS3L2-dependent Decay

Eliminating defective ribosomes through quality control is essential for accurate protein synthesis. However, the mechanisms that commit ribosomal subunits to decay remain poorly defined. Here, we identify a tandem mechanism in which ubiquitin-mediated ribosome remodeling and 18S rRNA uridylation lead to 40S ribosomal subunit decay. Specifically, we use an in vitro reconstitution system to show that the atypical kinase RIOK3 displaces the ribosomal protein eS26 from 40S subunits, exposing the 3 end of 18S rRNA. Nanopore direct RNA sequencing and motif analyses reveal that this remodeling event promotes oligo-uridylation, generating uridylated 18S rRNA decay intermediates. We further show that this uridylated 18S rRNA is selectively degraded by the 3-5 exoribonuclease DIS3L2. Moreover, DIS3L2-mediated exoribonucleolytic cleavage triggers endoribonucleolytic decay of the 18S rRNA, amplifying turnover. Together, our findings define a stepwise mechanism in which ribosome remodeling and RNA tailing commit defective 40S subunits to elimination, establishing a mechanistic framework for ribosome surveillance in mammalian cells.

molecular biology↗

bioRxiv2026

Sex-Specific Remodeling Phenotypes of the Tricuspid Valve Leaflets in an Ovine Model of Functional Tricuspid Regurgitation

BackgroundModerate to severe tricuspid regurgitation (TR) affects approximately 1.6 million Americans, yet more than 90% of patients with significant TR remain untreated. Women exhibit higher TR prevalence and more rapid disease progression than men, but the valve-intrinsic mechanisms underlying these sex disparities remain unclear. We hypothesized that sex and circulating testosterone influence tricuspid leaflet remodeling during right-sided pressure overload. MethodsFemale, castrated male (C-Male), and non-castrated male (NC-Male) adult Dorset sheep (n = 45) underwent pulmonary artery banding (PAB) and were followed for 13 {+/-} 1.5 weeks. Tricuspid leaflets were evaluated using morphometry, 3D profilometry, biaxial mechanical testing, histology, and bulk RNA sequencing. Sex-stratified differential gene expression was performed, and pathway enrichment of key biological processes were compared between sexes. ResultsPAB produced a uniform hemodynamic stimulus and equivalent moderate-to-severe TR across sex groups. Despite similar TR burden, leaflet remodeling diverged substantially by sex and castration status. C-Males developed the broadest remodeling phenotype, characterized by diffuse multi-leaflet growth, thickening, increased nuclei count, and low-strain stiffening. Females demonstrated more restricted leaflet and region-specific structural and cellular changes, along with circumferential low-strain stiffening. NC-Males exhibited preferential septal remodeling characterized by growth, thickening, increased nuclei count, and radial high-strain stiffening. Transcriptomic analysis revealed that females upregulated a focused matricellular remodeling program enriched for extracellular space organization (67 DEGs; FDR=0.025), whereas C-Males activated coordinated extracellular matrix and apoptosis-regulatory programs (388 DEGs; FDR=0.009). In contrast, NC-Males exhibited broad transcriptional response (406 DEGs) without significant pathway enrichment. ConclusionsTricuspid leaflet maladaptation during pressure overload is sex-dependent and testosterone-sensitive, involving distinct structural, mechanical, and transcriptional remodeling programs. These findings identify sex and testosterone status as previously under-recognized modulators of tricuspid valve remodeling and may help explain clinical sex disparities in TR progression. NOVELTY AND SIGNIFICANCE What is known?O_LIPulmonary hypertension and right ventricular pressure overload are linked to tricuspid leaflet remodeling through leaflet thickening, enlargement, and altered mechanical properties. C_LIO_LISex and sex-steroid hormones regulate fibrosis and extracellular matrix remodeling in cardiovascular tissues, but their role in tricuspid leaflet remodeling remains poorly understood. C_LI What new information does this article contribute?O_LISex and circulating testosterone status influence the magnitude, spatial distribution, biomechanical behavior, and transcriptional organization of tricuspid leaflet remodeling during pressure overload. C_LIO_LIFemales, castrated males, and non-castrated males develop distinct remodeling programs characterized by focused matricellular remodeling, coordinated extracellular matrix/apoptosis signaling, and diffuse transcriptional activation, respectively. C_LIO_LIThese findings identify sex and hormonal status as biological regulators of tricuspid valve maladaptation during functional tricuspid regurgitation. C_LI SummarySex differences in tricuspid regurgitation progression are recognized clinically, yet the mechanobiological basis underlying these disparities remains poorly understood. Using a controlled ovine model of pressure overload-induced secondary tricuspid regurgitation, we demonstrated that tricuspid leaflet maladaptation is a sex-specific and testosterone-sensitive process spanning structural, mechanical, and transcriptional scales. Under comparable hemodynamic overload, all animals developed significant tricuspid regurgitation, but leaflet remodeling patterns diverged substantially across sexes. Castrated male sheep exhibited the broadest maladaptive phenotype, characterized by diffuse multi-leaflet growth and thickening, increased low-stretch stiffness, and coordinated extracellular matrix and apoptosis-regulatory transcriptional programs. Female sheep developed more spatially restricted remodeling accompanied by a focused matricellular and extracellular matrix secretory response, whereas non-castrated male sheep demonstrated selective leaflet remodeling with broad, but less coordinated, transcriptional activation. Different remodeling patterns emerged in females and castrated males despite comparable testosterone levels, suggesting that testosterone depletion alone does not fully explain these tricuspid valve remodeling phenotypes. These findings establish sex and testosterone status as previously underrecognized biological regulators of tricuspid leaflet maladaptation and support the emerging view that valve leaflets are active, mechanobiologically responsive, participants in functional tricuspid regurgitation progression.

bioengineering↗

bioRxiv2026

Dynamics of the α2-chimaerin-Rac1 interface in Duane retraction syndrome and computational design of candidate probes

Duane retraction syndrome (DRS) is an eye movement disorder caused by gain-of-function mutations in CHN1, which encodes 2-chimaerin. Mutations in CHN1 cause excessive Rac1 suppression during axon guidance, but the dynamics of the 2-chimaerin-Rac1 interaction remain largely uncharacterized. We simulated the CHN1- Rac1 complex with all-atom molecular dynamics to characterize this interface. An Ile420-Arg445 hydrophobic ridge is the persistent core, while the 304-310 patch carrying the catalytic arginine finger scores lower and varies more between replicates. We screened the BioGRID partners of CHN1 with AlphaFold3 and ipSAE; only Rac1, NCK1, and NCK2 gave high-confidence predicted complexes. Rac1 and NCK1 stayed bound in every replicate, and NCK2 in two of three. The MM-GBSA interface {Delta}G for Rac1 was -20 {+/-} 10 kcal/mol. We also explored how the surface could be probed by small molecules and peptides. To identify candidate chemical probes, we sampled natural products from COCONUT, refined top hits through CReM fragment growth, and generated peptides with BoltzGen. Prioritized ligands were evaluated with molecular dynamics and MM-PBSA endpoint free-energy calculations. Across 6 {micro}s of cumulative simulation, the contact network defining the CHN1-Rac1 interface matched ligand and peptide engagement. These results define the key residues of the CHN1-Rac1 interface and identify candidate chemical probes for testing their role experimentally.

biophysics↗

bioRxiv2026

A metabolic checkpoint coordinates bacterial cell envelope biosynthesis and c-di-GMP signaling

The bacterial second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) drives the transition from motile to biofilm lifestyles, yet the mechanisms by which bacteria couple cell envelope stress to c-di-GMP signaling remain poorly understood. Here, we show that sub-inhibitory concentrations of antibiotics targeting early cytoplasmic steps of peptidoglycan (PG) biosynthesis, but not inhibitors of PG polymerization, membrane integrity, or other intracellular processes, specifically elevate intracellular c-di-GMP levels in Pseudomonas aeruginosa. Using live-cell imaging and in vitro enzymatic assays, we demonstrate that this elevation results from reduced phosphodiesterase (PDE) activity rather than increased diguanylate cyclase (DGC) activity, with multiple PDEs contributing to the response. A screen of the complete P. aeruginosa DGC/PDE mutant library identified DipA, BifA, RocR, and RmcA as the primary PDEs mediating this effect. Strikingly, we find that acetyl-CoA, a central metabolite consumed during cell envelope precursor biosynthesis, directly inhibits PDE activity by competing for the conserved EAL domain active site, as supported by biochemical assays with purified RocR and molecular docking analysis. Because EAL domain residues that contact acetyl-CoA are broadly conserved across bacterial species, this mechanism may represent a widespread strategy for sensing metabolic perturbations of cell envelope synthesis. Together, these findings reveal that P. aeruginosa monitors the metabolic status of cell envelope biogenesis through acetyl-CoA-mediated allosteric inhibition of c-di-GMP PDEs, linking envelope biosynthetic flux to adaptive biofilm formation.

microbiology↗

bioRxiv2026

Age Dependent Immunopathology Drives Pneumonia-Associated Cardiac Dysfunction During Streptococcus pneumoniae Infection

Aging is a major risk factor for severe Streptococcus pneumoniae (Spn) infection and pneumonia-associated - major adverse cardiac events (PA-MACE), yet underlying mechanisms remain unclear. Using young and aged murine models, we show that aging exacerbates bacterial burden, mortality, and cardiac dysfunction following Spn infection, associated with impaired macrophage bacterial killing. Single-cell RNA sequencing infected hearts revealed extensive age-dependent remodeling across immune and stromal compartments. Aged mice exhibited heightened pro-inflammatory myeloid responses, with increased neutrophil infiltration characterized by elevated S100A8/9 and LCN2 and reduced antimicrobial programs. Macrophages displayed defective efferocytosis, including disruption of the GAS6-AXL axis. Aging also drove expansion of an infection-responsive fibroblast population with inflammatory signatures and reduced extracellular matrix gene expression. These changes were linked to oxidative stress and impaired glucose oxidation. Notably, anti-inflammatory treatment rescued cardiac dysfunction, implicating excessive inflammation as a central driver of PA-MACE. Together, these findings define mechanisms linking aging to pneumococcal cardiac complications and identify potential therapeutic targets.

immunology↗

bioRxiv2026

Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth

Defining mechanisms used by gut microbiota to control anti-tumor immunity may offer novel therapeutic modalities. Here, we demonstrate that Bacteroides rodentium and closely related Bacteroides uniformis species induce anti-tumor immunity and limit melanoma development when colonized in either germ-free (GF) mice, mice with a complex microbiome, or WT mice. Enhanced CD8+ T cell infiltration seen in tumors of mice harboring B. rodentium coincided with increased expression of immune-stimulating pathways and activation of bone marrow-derived dendritic cells that were co-cultured with the B. rodentium secretome. Metabolomic analyses of cecal samples from GF mice colonized with Altered Shedlar Flora (ASF) plus B. rodentium revealed lower tryptophan levels than in ASF-colonized controls, and WT mice fed a tryptophan-deficient diet exhibited inhibition of melanoma development. In silico genomic reconstruction of metabolic pathways revealed that both B. rodentium and B. uniformis harbor tryptophanase A (TnaA) and aromatic amino transferase (ArAT) genes, both of which function in tryptophan degradation. Administration of a B. uniformis harboring TnaA mutant failed to inhibit melanoma growth in gnotobiotic mice. Notably, administration of indoles, but not kynurenines, also effectively inhibited melanoma development, increasing immune cell infiltration into the tumors. Correspondingly, levels of bacterially encoded tryptophan-degrading enzymes were higher in cohorts of melanoma patients responding to immune checkpoint blockade. These findings highlight a novel mechanism of anti-tumor immunity and tumor growth inhibition dependent on the tryptophan degradation products, indoles, produced by intestinal Bacteroides species.

cancer biology↗

bioRxiv2026

Imatinib Reduces Right Ventricular Systolic Pressure Independent of Arterial or Venous Remodeling in an Inflammatory Murine Model of Pulmonary Hypertension

Pulmonary arterial hypertension is a progressive, fatal disease driven by pathologic vascular remodeling including arterial medial hypertrophy, occlusive neointimal lesion formation, and venous muscularization. Current vasodilatory therapies improve hemodynamics but do not reverse established remodeling. Imatinib mesylate, a tyrosine kinase inhibitor targeting the PDGF-PDGFR signaling axis, has been proposed as an anti-remodeling therapy for pulmonary arterial hypertension and has demonstrated hemodynamic benefit in both preclinical models and clinical trials. However, prior preclinical models lack the neointimal lesions characteristic of human disease, effects on venous remodeling have not been examined, and direct histologic assessment in human trials is precluded by the invasiveness of serial lung biopsy. Here, leveraging the house dust mite mouse model of pulmonary hypertension, which recapitulates medial thickening, neointimal lesion formation, and venous muscularization, we rigorously evaluate the anti-remodeling and hemodynamic effects of imatinib during two defined remodeling stages: neointimal lesion growth and neointimal lesion maintenance. Imatinib treatment significantly reduced right ventricular systolic pressure at both stages. Despite this hemodynamic improvement, quantitative vessel-level analysis of over 1,700 arteries and 1,200 veins revealed no significant effect of imatinib on arterial medial thickness, neointimal lesion growth, neointimal lesion maintenance, or venous muscularization across any vessel size class. These findings dissociate imatinibs hemodynamic benefit from structural vascular remodeling and suggest that imatinib functions primarily as a pulmonary vasodilator rather than an anti-remodeling agent.

physiology↗

bioRxiv2026

Lysine specific demethylase 1 (LSD1) regulates host alpha-ketoglutarate levels to modulate lipid peroxidation during Mycobacterium tuberculosis infection

Mycobacterium tuberculosis (Mtb) subverts host immune responses via modulation of host epigenome and metabolism. In this study, we underscore a role for the epigenetic modifier, Lysine Specific Demethylase 1 (LSD1), in regulating macrophage metabolism to support mycobacterial pathogenesis. In ex vivo and in vivo infection models, LSD1 inhibition reduced mycobacterial CFU alleviating lung pathology. Metabolomic analysis of Mtb infected, LSD1 deficient macrophages revealed increased levels of alpha-ketoglutarate (AKG), a crucial TCA cycle metabolite via regulating genes implicated in glutamine breakdown. Moreover, exogenous addition of AKG resulted in reduced oxidative stress and attenuated lipid peroxidation (LPO) with a consequent decrease in Mtb survival. Blocking glutamine breakdown in LSD1 deficient macrophages failed to reduce LPO and promoted Mtb intracellular survival, highlighting the role of LSD1-AKG axis in this immunomodulation. Dietary supplementation of AKG to Mtb infected mice improved lung pathology, limited Mtb dissemination and reduced the levels of oxidative Malondialdehyde adducts. Therefore, we highlight a host protective role of AKG during Mtb pathogenesis through suppression of lipid peroxidation and uncover an epigenetic-metabolic axis exploited by Mtb, thereby positing dietary supplementation of AKG as a potential therapeutic strategy against Tuberculosis.

immunology↗

bioRxiv2026

The inner nuclear membrane protein SUN1 regulates cullin-3 neddylation to maintain insulin signaling

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease and strongly linked to obesity and insulin resistance. We previously reported that the common nuclear envelope variant rs6461378 (g.842031C>T; SUN1 H118Y) associated with MASLD and related traits including insulin resistance. To gain insight into how wild-type (WT) and H118Y SUN1 might differentially impact insulin signaling, we performed affinity purification-mass spectrometry (AP-MS) in human liver-derived cells stably expressing WT or H118Y SUN1. Unbiased AP-MS revealed a novel SUN1-CUL3 interaction, with comparative analysis showing that WT SUN1 interacted robustly with CUL3, while CUL3 interaction was markedly diminished with H118Y SUN1. Cells in which SUN1 was silenced via siRNA, or in which H118Y SUN1 was ectopically expressed, showed increased CUL3 neddylation, which is required for cullin RING ligase (CRL)-mediated ubiquitination of insulin receptor substrate (IRS) proteins. Inhibition of neddylation restored IRS-1 levels and insulin signaling in H118Y SUN1-expressing cells. Together, our findings provide a potential mechanism of H118Y SUN1-driven insulin resistance and a viable therapeutic approach for its reversal.

physiology↗

bioRxiv2026

Increased expression of a subset of genes within reduced copy number regions across multiple cancer types

The TGIF1 transcription factor gene is present on chromosome 18, which is subject to whole chromosome copy number reduction in colon cancer. Despite this, TGIF1 expression is significantly higher in cancer than in normal. In mice complete deletion of Tgif1 reduced tumor burden in an Apc mutant model of intestinal cancer. Here we show that reducing TGIF1 expression in a human colon cancer cell line slows proliferation and reduces growth of orthotopic xenografts. To ask if additional genes with copy number loss are more highly expressed in tumors we identified chromosomal regions subject to copy number reductions from ten TCGA cancer datasets. Within these regions a small proportion of genes, generally less than 10%, are expressed at higher levels in the tumor than in corresponding normal samples. Enrichment analysis using a set of 435 genes that have copy number reduction and increased expression identified mitosis as the most enriched gene set and FOXM1 and E2F family transcription factors as potential regulators. For mitotic genes, the average expression increase in tumor compared to normal is independent of copy number. In contrast, while DepMap common essential genes are generally more highly expressed in cancer than normal tissue, the relative increase in expression tracks well with copy number. Similarly, expression differences for gene sets such as S-phase, rRNA processing and DNA repair show increased expression in cancer versus normal, but changes also track with copy number. Thus, genes with increased expression despite copy number reduction may represent the output of key pro-tumorigenic transcriptional programs and could be potential therapeutic targets.

cancer biology↗

bioRxiv2026

Pharmacologic DPP-4 inhibition promotes CD8⁺ T cell metabolic fitness to enhance anti-tumor activity

Metabolic dysfunction is a hallmark of CD8+ T cell exhaustion in the tumor microenvironment. Thus, there is growing interest in developing strategies that enhance anti-tumor functions of CD8+ T cells via metabolic reprogramming. Here, we identify dipeptidyl peptidase 4 (DPP-4) as a previously unknown regulator of CD8+ T cell function and metabolism. We discovered that DPP-4 is upregulated in exhausted CD8+ T cells. Pharmacological inhibition of DPP-4 with the FDA-approved anti-diabetic drug sitagliptin transcriptionally and metabolically reprogrammed CD8+ T cells, increasing spare mitochondrial respiratory capacity, proliferation, cytotoxic mediator production, and antigen-specific cancer cell killing capability. The functional effects of sitagliptin were dependent on upregulation of glutamate decarboxylase 1 (GAD1), an enzyme that feeds glutamate into the tricarboxylic acid (TCA) cycle, highlighting a new role for GAD1 in CD8+ T cell respiration and proliferation. We found that systemic inhibition of DPP-4 in preclinical mouse glioblastoma (GBM) models prolongs survival in a CD8+ T cell-dependent manner, and retrospective clinical cohort analysis revealed better outcomes in GBM patients using DPP-4 inhibitors. Importantly, preconditioning of Chimeric Antigen Receptor (CAR) T-cells with DPP-4 inhibition enhanced their cytotoxicity, persistence, and therapeutic efficacy in pediatric GBM. Together, our findings provide mechanistic and biological rationale for repurposing readily accessible DPP-4 inhibitors to enhance anti-tumor CD8+ T cell responses.

immunology↗

bioRxiv2026

Integration of QTL Mapping, Transcriptomics, and Genome Resequencing Identifies Yield-Associated Genes for Salt Stress in Rice

Salinity and sodicity stresses adversely affect rice growth and yield. To overcome yield losses, suitable tolerant rice cultivars can be developed through a marker-assisted breeding (MAB) program. In the present study, genomic regions associated with sodicity stress tolerance at the reproductive stage were identified using a high-density 50kSNP array in a recombinant inbred line (RIL) population derived from the contrasting rice genotypes CSR11 and MI48. A total of 50 QTLs were detected for various yield-related traits; further, 19 QTLs with [≥]15% of phenotypic variance were selected for integrated (omics) analysis. RNA sequencing of leaves and panicles at the reproductive stage under sodic stress conditions was employed to find differentially expressed genes. A total of 1368 and 1410 SNPs; 104 and 144 indels were found for MI48 and CSR11, respectively, within the QTL regions from resequencing. At chromosomes 1 and 6, colocalized QTLs (qPH1-1/qGP1-1 and qGP6-2/qSSI6-2) were discovered. Differentially expressed genes (DEGs) were mapped over the QTL regions selected, and SNP variations and indels were screened for colocalized QTLs. Potential candidate genes, namely Os-pGlcT1 (Os01g0133400), OsHKT2;1 (Os06g0701600) and OsHKT2;4 (Os06g0701700), OsANTH12 (Os06g0699800), and OsPTR2 (Os06g0706400), were identified as being responsible for glucose transport, ion homeostasis, pollen germination, and nitrogen use efficiency, respectively, under salt stress. Finally, our study provides important insights into the genes and potential mechanisms affecting grain yield under sodic stress in rice, which will contribute to the development of molecular markers for rice breeding programs.

plant biology↗

bioRxiv2026

BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning

Protein function annotation is fundamental to understanding biological mechanisms, designing therapeutics, and advancing biomedical research. Current computational methods either rely on shallow sequence similarity or treat function prediction as isolated classification tasks, failing to capture the integrative reasoning across sequence, structure, domains, and interactions that expert biologists perform to infer function. We introduce BioReason-Pro, the first multimodal reasoning large language model (LLM) for protein function prediction that integrates protein embeddings with biological context to generate structured reasoning traces. A key input into BioReason-Pro is the set of GO term predictions made by GO-GPT, our autoregressive transformer that captures hierarchical and cross-aspect dependencies of GO terms. BioReason-Pro is trained via supervised fine-tuning on synthetic reasoning traces generated by GPT-5 for over 130K proteins and further optimized through reinforcement learning. It achieves 73.6% Fmax on GO term prediction and an LLM judge score of 8/10 on functional summaries, substantially outperforming previous methods. Evaluations with human protein experts show that BioReason-Pro annotations are preferred over ground truth UniProt annotations in 79% of cases. Remarkably, BioReason-Pro predicted a novel interaction partner for the renal cancer biomarker RCDG1, which we confirmed in the lab by co-immunoprecipitation. In other binding-partner predictions, its per-residue attention localized to the exact contact residues resolved in cryo-EM structures. Together, GO-GPT and BioReason-Pro establish a framework for protein function prediction that combines precise ontology modeling with interpretable biological reasoning.

molecular biology↗

bioRxiv2026

Unpaired TCRα + TCRβ sequencing is sufficient for training machine learning TCR-epitope recognition predictors

T-cell recognition of infected and malignant cells is elicited by the binding of heterodimeric T-Cell Receptors (TCRs) to epitopes and both the TCR and the TCR{beta} chains play a key role in these interactions. Machine learning tools trained on databases of TCRs recognizing diverse epitopes are useful for identifying epitope-specific TCRs in large TCR repertoire datasets. However, collecting paired TCR{beta} sequences to train such tools is associated with significant sequencing costs. Here we demonstrate that unpaired TCR + TCR{beta} sequencing of epitope-specific T cells can be used for training TCR-epitope recognition predictors at a much reduced cost compared to standard single-cell TCR sequencing protocols and with no impact on prediction accuracy. Applying this approach to some unseen epitopes used in the IMMREP community benchmark demonstrates improved accuracy compared to both existing machine learning models and AlphaFold3-based predictions.

immunology↗

bioRxiv2026

Brain Transcriptomics Across Diverse Sleep-Wake Manipulations Reveals Multiple Homeostatic Pathways in Drosophila

Sleep is governed by two processes: a circadian process that times sleep and wake and a homeostatic process that drives sleep as a function of prior wake history. Discovered in the fruit fly Drosophila, the period (per) gene is a "universal" cornerstone of the circadian clock, robustly oscillating at the transcript level, in all organs and tissues and in essentially all animals. We hypothesized that there may be a comparable factor (we term "sleeper") for sleep homeostasis. To identify sleeper genes, we performed a wide-ranging transcriptomic analysis to identify genes whose expression tracks sleep-wake history in the Drosophila brain. We analyzed a variety of methods to manipulate sleep-wake and subsequent rebound including mechanical, thermogenetic, optogenetic, pharmacological and baseline sleep across 7 datasets. Using a log2 fold change threshold of 1, we did not identify any gene that was sleep-wake dependent across all datasets, raising the possibility that genes identified with a single method of sleep manipulation are related to the nature of the manipulation and not necessarily to sleep. Nonetheless, we did identify genes whose expression changed with sleep-wake in a consistent direction across at least 2 datasets. These analyses highlight previous processes implicated in sleep homeostasis such as mitochondrial oxidative phosphorylation as well as provide potentially novel pathways such as ribosome biogenesis. In addition, we also examined genes whose expression correlates with prior sleep-wake history and/or predicted subsequent sleep rebound across these datasets. Among significantly correlated genes we observed some that were correlated with recent (<3h) sleep history while others were correlated with much longer (>6h) time frames suggesting temporally distinct pathways for integrating waking experience. This analysis also highlights specific GO pathways for sleep/wake/rebound. Applying a novel GPT based paper search algorithm, we call fl.ai, we identified several sleep-wake regulated genes with demonstrated function in sleep regulation consistent with an in vivo homeostatic function. These include those involved in immunity, neuropeptide signaling, glucose transport, and neuronal excitability. Collectively, these studies suggest that sleep homeostasis is a much more molecularly distributed process than the core circadian clock.

neuroscience↗

bioRxiv2026

SuperCell2.0 enables semi-supervised construction of multimodal metacell atlases

Multimodal single-cell atlases comprising hundreds of thousands of cells provide unique resources for exploring complex biological tissues and generating testable hypotheses. To streamline the analysis of such large datasets, we introduce SuperCell2.0, a robust workflow to build (semi-)supervised multimodal metacells. We demonstrate that multimodal metacells outperform metacells built with a single modality, improve inter-modality consistency, and facilitate integration of multiomic single-cell datasets. SuperCell2.0 can further leverage full or partial cell type annotations to improve metacell quality. This workflow enables us to construct multimodal metacell atlases from blood and tumor samples and identifies interferon-primed monocytes and macrophages in the circulation and in the tumor microenvironment. Markers derived from the metacell analysis enable us to sort and phenotypically characterize this population in healthy donors. Overall, our work demonstrates how SuperCell2.0 facilitates the analysis of large multimodal single-cell atlases.

bioinformatics↗

bioRxiv2026

Redox-activated induction of Warburg-type metabolism in the adult heart

Proliferating cells rewire glucose metabolism away from oxidative ATP production towards glycolysis and anabolic branch pathways (the Warburg effect). In contrast, the contractile function of terminally differentiated cardiomyocytes in the heart critically depends upon mitochondrial ATP generation. Adult cardiomyocytes are largely non-proliferative but undergo hypertrophy in response to increased heart workload. A fundamental question in the field is how cardiac metabolism is modified to balance competing energetic and anabolic demands. We previously reported that the redox-signalling H2O2-generating enzyme, NADPH oxidase 4 (NOX4), facilitates compensated cardiac function in hearts undergoing hypertrophic remodelling. Here, we show that NOX4 induces Warburg-type reprogramming of glucose metabolism in the healthy heart, with increased flux into the pentose phosphate, serine and nucleotide biosynthetic pathways. Using an integrated multiomics approach, we uncover a NOX4-regulated network involving interplay between direct transcriptional activation of metabolic genes via NRF2 [aka NFE2L2] and ATF4 and a broader epigenetic regulation. This reprogramming of glucose intermediary metabolism along with previously reported NOX4-mediated enhancement of fatty acid oxidation may serve to optimally support the dual requirements of increased energy demand and remodelling in the heart. Our findings identify a novel paradigm for redox-regulated Warburg-type metabolic reprogramming in the terminally differentiated heart.

physiology↗

bioRxiv2026

A prelimbic molecular clock of protein synthesis for memory persistence

Emotionally salient associative memories can endure for long periods, yet the mechanisms that determine their long-term stability remain unclear. Here we show that the prelimbic (PL) cortex integrates temporally structured translational programs to control both the consolidation and reconsolidation of cued threat memories. Using Pavlovian threat conditioning with in vivo fiber photometry, we found that PL calcium dynamics tightly track memory strength: discrete threat-predictive cues evoked robust activity during recent and single-timepoint remote retrieval, whereas prior retrieval selectively weakened remote expression, independent of contextual influences. Translational profiling of PL Camk2a cells uncovered a biphasic consolidation program, with an early phase characterized by ER stress-linked translational repression and robust oligodendrocyte plasticity, followed by a delayed phase engaging synaptic growth pathways. Loss- and gain-of-function approaches demonstrated that eIF2-regulated, cap-independent translation is essential for recent consolidation and for the enduring stabilization of remote memory, whereas retrieval-induced destabilization engages a mechanistically distinct, eIF4E-dependent translational pathway required for reconsolidation. These findings identify the PL cortex as a dynamic node in which discrete modes of translational control govern the long-term persistence of emotional memories.

neuroscience↗