Biology subjects

Wang, D.

Publications and source records attributed to Wang, D..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

The impact of dietary fibers on gut microbiome of young children: insights from ex vivo experiments and an observational cohort

During weaning period, the intake of dietary fibres changes and increases dramatically. Given the considerable structural differences, we hypothesized that different fibres may vary in their function. The objective of the study was to explore the impact of specific dietary fibres (arabinoxylan, cellulose, pectin and xyloglucan) on the gut microbiome of children below 3 years. By using ex vivo fecal fermentation experiments, cellular models and cohort data analysis, we assessed how these fibres and their combinations influence infants gut microbiota composition, diversity, metabolite production and possible actions on the gut epithelial barrier function. We found that the fermentation with arabinoxylan, xyloglucan and pectin resulted in an increased production of short-chain fatty acids. These fibres also promoted the generation of metabolites with potential health benefits, such as indole-3-lactic acid. By combining the ex vivo fermentation and cellular co-culture experiments, arabinoxylan and xyloglucan were found to be able to maintain gut epithelial barrier integrity upon lipopolysaccharide challenge, and a blend of cellulose, pectin, and xyloglucan dampened different LPS induced cytokines. Moreover, pectin was found supporting the growth of a wide range of microbial species ex vitro and correlated positively with -diversity in young children in an observational cohort. Our findings provided insights into the potential benefits of diverse fibre intakes during early life. Further studies are needed to understand the mechanisms and the effectiveness of specific fibres on the gut microbiome development in young children.

microbiology↗

bioRxiv2026

A T-cell engager platform induces deep plasma cell depletion in autoimmune dry eye

Bispecific T cell engagers (TCEs) have transformed targeted immunotherapy but remain constrained by ex vivo manufacturing and systemic delivery, limiting their application in autoimmune disorders. Here, we introduce the first in vivo TCE platform, utilizing a T cell-targeted integration-deficient lentiviral vector (T-IDLE) to reprogram endogenous T cells into engineered T cells secreting BCMAxCD3 TCEs (STCEs) directly in vivo. In murine Sjogrens syndrome-associated dry eye model, a single intravenous administration of T-IDLESTCE achieved deep and sustained depletion of plasmablasts and plasma cells, reversing lacrimal gland inflammation and restoring tear production without detectable off-target transduction. Longitudinal studies in cynomolgus monkeys confirmed translational promise, demonstrating potent plasma cell clearance and favorable safety profiles over 12 weeks post-vector dosing. Mechanistic analyses demonstrated attenuation of Th1/Th17-mediated inflammation and controlled cytokine responses, accompanied by negligible vector integration in non-T cell lineages, thereby substantiating the safety profile of the integration-deficient design. This first-in-class in vivo TCE approach represents a manufacturing-free, scalable immunotherapy strategy for autoantibody-mediated diseases.

bioengineering↗

bioRxiv2026

Comorbid HIV and Cocaine Use Exacerbate Accelerated Brain Aging

BackgroundHIV and cocaine use (CU) each relate to cognitive deficits and brain abnormalities, yet their combined impact on brain aging remains unclear. This study examined how comorbid HIV and CU relate to brain aging and cognitive impairment. MethodsWe trained a morphometry-based brain-age model using harmonized Human Connectome Project-Aging data (HCP-A; n=725) with Gaussian Process Regression. The model was applied to an independent cohort with varying HIV/CU burden (HIV-/CU-, n=34; one disorder [HIV+/CU- or HIV-/CU+], n=72; HIV+/CU+, n=80). Brain age gap (BAG; predicted minus chronological age) was examined in relation to comorbidity burden and neurocognitive impairment (NCI; NIH Toolbox), adjusting for age, sex, education, depression, and image-quality indices. Analyses on SHapley Additive exPlanation (SHAP) values characterized network-wise feature-level contributions to brain age estimates. ResultsA dose-dependent effect of comorbidity burden on BAG was observed, with the HIV+/CU+ group showing the highest BAG. Greater BAG was associated with increased likelihood of NCI, and BAG partially mediated the relationship between comorbidity burden and NCI, with a stronger mediation effect in the two-disorder group than in the one-disorder group. Structural contributors to elevated BAG in the HIV/CU cohort included cortical thickness in the visual, ventral attention, and frontoparietal networks, and sulcal depth in the sensorimotor network. ConclusionComorbid HIV/CU is linked to accelerated structural brain aging. BAG may reflect brain-level alterations underlying the association between comorbid HIV/CU and cognitive impairment, and may help identify network-specific targets for intervention.

neuroscience↗

bioRxiv2026

Noncanonical loops regulated by EMF1 and cohesin-associated factors shape the distinct 3D genome architecture in plants

In mammals, cohesin-mediated chromatin loop extrusion is blocked at boundaries, where CTCF, WAPL, and PDS5s co-bind and regulate cohesin, establishing an impermeable barrier with no exceptions. In contrast, our study revealed that in Arabidopsis, some noncanonical contacts have emerged between the boundary flanking regions, which suggest that cohesin is not absolutely blocked but enables sliding beyond boundaries. We identified these interactions as noncanonical loops and clarified their regulatory proteins. Firstly, the plant-specific boundary binding protein EMF1 is essential for noncanonical loops formation. Surprisingly, although both Arabidopsis WAPLs and PDS5s inhibit loop extension as mammals, PDS5s do not co-bind and cooperate with WAPLs at boundaries. Instead, PDS5s bind to boundary-flanking regions enriched with H3K4me1 through their Tudor domains, restricting further extension of noncanonical loops. Consequently, pds5a/b/c mutants lose noncanonical loops, resulting in emergence of larger canonical loops but anchored on boundaries and co-upregulation of anchored gene pairs. Collectively, our findings reveal that the plant-specific noncanonical loop, regulated by plant-specific EMF1 and PDS5 proteins, is the fundamental structure of the distinctive chromatin organization of plants, which provides novel mechanistic insights into eukaryotic chromatin architecture regulation.

plant biology↗

bioRxiv2026

The effects of breeding timing, clutch size, and nesting strategy on reproductive success in the crested ibis (Nipponia nippon)

O_LIStudying the reproduction process, which is a key determinant of individual and population fitness in endangered species, is challenging but urgently needed. The crested ibis (Nipponia nippon), a flagship endangered species recovering from an extreme population bottleneck, provides a valuable opportunity to examine how life-history strategies shape reproductive success and inform future conservation practices. C_LIO_LIWe monitored 176 breeding pairs of crested ibis over three consecutive breeding seasons and investigated the effects of three key life-history traits, namely breeding timing, clutch size, and nesting strategy (solitary versus colonial), on reproductive success (hatching and fledging success). C_LIO_LIOur analysis found that both hatching and fledging success declined significantly as breeding initiated later, and a positive association between clutch size and reproductive success in this species. These patterns were robust and repeatable across three years. Unlike other closely related species in this family, sibling competition is generally non-lethal, leading to large clutch sizes fledged in this endangered species. We consider this pattern to be a main reason underlying the rapid population recovery observed in the crested ibis. On the other hand, nesting strategy (colonial vs. solitary breeding) had no detectable effect on reproductive success. This pattern indicates the crested ibis can adopt different breeding strategies across habitats, highlighting its capacity to flexibly adjust breeding behavior in response to local environmental conditions. C_LIO_LIOur results provide an integrative assessment of how key life-history traits shape reproductive outcomes in a wild population of the crested ibis, serving as a foundation for evaluating its current status of population recovery and refining future conservation strategies for endangered avian species sharing similar life-history characteristics. C_LI

zoology↗

bioRxiv2026

Polyploid cardiomyocytes define disease-specific transcriptional states in the mammalian heart

The adult mammalian heart has a limited regenerative capacity. Following injury, cardiomyocytes undergo a hypertrophic response accompanied by polyploidization, which has been described as a barrier to proliferation and regeneration of the heart1,2. However, the unique molecular programs of polyploidy, or genome multiplied cardiomyocytes, and their influence on the disease-related myocardial remodelling process remains unclear. Here, we integrate single-nuclei and high-resolution spatial multi-omics across human, rat, and mouse hearts to define novel cardiac cell states and their tissue niches in ischemic and non-ischemic heart disease. Computational analysis across scales allowed us to generate detailed networks of the cardiac tissue remodelling process as well as tissue and sub-cellular environments uniquely enriched in polyploid cardiomyocytes or their diploid origins. We identify a conserved, dichotomous transcriptional program distinguishing diploid from polyploid cardiomyocytes. Polyploid cardiomyocytes demonstrated rewired metabolic and chromatin-remodeling transcriptional programs and recapitulate the gene signature of immature human fetal cardiomyocytes. Notably, we observe that polyploid cardiomyocytes--rather than the general myocyte population--are the primary sites of enrichment for major heart-failure drug targets, including the mineralocorticoid, {beta}1-adrenergic, and glucagon-like peptide-1 receptors. Based on our cross-species dataset we further identified TNIK, a Wnt-pathway regulator expressed in polyploid cardiomyocytes across species, as a potential therapeutic target and demonstrate that pharmacological TNIK inhibition improves cardiac function after myocardial infarction in rats. Together, this species-spanning, disease-resolved study redefines cardiomyocyte heterogeneity in heart disease and suggests a therapeutic path to heart failure treatment by targeting polyploid cardiomyocytes.

genomics↗

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

Impaired Associative Memory, Inference, and Theta Dynamics in Postictal Psychosis of Epilepsy

Postictal psychosis (PIP) is a severe complication occurring in 2% of people with epilepsy (PWE) whose underlying pathophysiology remains poorly understood. Although historically considered separate from other forms of psychosis, newer evidence demonstrates a shared genetic susceptibility. People with schizophrenia are typically impaired at both associative learning and inferring connections between overlapping associations. Successful associative encoding, retrieval, and inference can each be predicted by changes in frontotemporal theta band activity, which is impaired in rodent models and people with schizophrenia. Here, we recorded high-density scalp EEG from PWE with history of PIP and well-matched control participants while they undertook a memory inference task. We found that associative memory and inference were both impaired in the PIP group, despite no difference in item recognition. Moreover, we found disrupted theta activity during memory encoding and the retrieval of inferred associations in PWE with PIP that likely originated from the medial temporal and frontal lobes. These results suggest a pattern of behavioural deficits and altered neural dynamics common to both PIP and schizophrenia. Interpreted in conjunction with previous genetic studies, they may reflect shared neural mechanisms contributing to psychopathology in both conditions and argue that PIP is a model of more general psychoses.

neuroscience↗

bioRxiv2026

Structure-based design of soluble prefusion-stabilized herpes simplex virus type 2 glycoprotein B antigens

Herpes simplex virus type 2 (HSV-2) causes genital herpes through latent infection and periodic reactivation. Although antivirals alleviate symptoms, no prophylactic or therapeutic vaccines have been licensed. Glycoprotein B (gB) is a class III fusion protein that mediates entry by irreversibly transitioning from a metastable prefusion conformation to a stable postfusion conformation. Leveraging prior structure-based designs for human cytomegalovirus (HCMV) gB, we engineered amino acid substitutions in HSV-2 gB to stabilize its prefusion conformation. Cryo-EM of the engineered construct revealed a prefusion conformation and non-native dimers of gB trimers. Introduction of N-linked glycosylation sites resulted in the gB-G3 variant, which exhibited improved expression and reduced dimerization. Cryo-EM of gB-G3 bound to neutralizing antibodies yielded a 2.8 [A] resolution structure of the stabilized prefusion conformation in a closed state, which differs from the open states observed in recently published HSV gB structures. Both prefusion and postfusion gB variants were evaluated for immunogenicity in mice, delivered either as a protein subunit or mRNA vaccine. Each gB conformation elicited robust humoral and cellular responses. However, prefusion stabilization of gB did not improve neutralizing antibody titers relative to the postfusion construct, consistent with prior observations for HCMV gB. Collectively, these findings reveal insights into prefusion gB conformational dynamics, provide stabilized reagents for studying gB-directed immune responses and inform HSV-2 vaccine design.

microbiology↗

bioRxiv2026

High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation

The de novo design of high-affinity protein binders remains a central challenge in protein engineering and therapeutic discovery. While deep generative models have advanced backbone generation and interface design, achieving picomolar or nanomolar binding affinities typically demands extensive experimental screening or iterative in vitro maturation. A general computational approach for the direct production of high-affinity binders has remained elusive. Here, we introduce an integrated framework that synergizes PPIFlow, a flow-matching-based generative model, with a novel in silico maturation strategy. PPIFlow employs a pairformer architecture to explicitly reason over pair-wise geometric and chemical interactions, modeling protein backbone rigid-body transformations as continuous flows. To bridge the affinity gap, we implement a dedicated in silico affinity maturation stage that combines interface rotamer enrichment with partial flow refinement to optimize energetic packing. This pipeline is further accelerated by AF3Score, a score-only adaptation of AlphaFold3 that enables high-fidelity and computationally efficient candidate prioritization. Across a diverse set of therapeutic targets, this synergistic approach consistently produces picomolar and nanomolar affinity binders without experimental affinity maturation. Notably, the framework proves highly effective for the de novo design of single-domain antibodies (VHHs), producing sub-nanomolar binders across multiple targets. These results establish that coupling robust backbone generation with focused in silico maturation renders the purely computational design of high-affinity binders feasible.

biochemistry↗

bioRxiv2026

Hydrogen-bonding changes cause differences in imipenem breakdown activity in OXA-48 variants

The {beta}-lactamase OXA-48 efficiently hydrolyses carbapenem antibiotics, especially imipenem. Carbapenem resistance is a rising clinical concern, and is frequently associated with OXA-48 and its variants. OXA-48 variants carrying different mutations in the {beta}5-{beta}6 loop differ in hydrolytic activity towards imipenem. OXA-517 has a higher KM, but similar kcat for imipenem hydrolysis, compared to OXA-48, whereas OXA-163 and -405, which have similar mutations in the {beta}5-{beta}6 loop, are less active. Multiscale simulations (using quantum mechanics/molecular mechanics, QM/MM) of deacylation of the respective imipenem acylenzymes show this to be most efficient when the deacylating water (DW) acts as a hydrogen bond (H-bond) donor to imipenem, and the carboxylated Lys73 base is less hydrated. Calculated barriers for deacylation correlate very well with experimental data, but for OXA-163 and -405 only when DW acts as a H-bond acceptor. Dynamics simulations of imipenem acylenzyme complexes show that mutations in the {beta}5-{beta}6 loop change the active site H-bond network. In OXA-48, the DW H-bonding pattern linked to high activity is more frequently sampled, and in OXA-517 it is stabilised through H-bonding to Thr213; explaining the higher kcat values compared to OXA-163 and -405, where this is not the case. Furthermore, simulations of non-covalent imipenem complexes indicate that increased KM for OXA-517 is linked to lower binding affinity, caused by repositioning of bound imipenem. Our work identifies the molecular basis for differences in imipenem hydrolytic activity between OXA-48 variants, offering detailed insights into how active site interactions alter the dynamics and reaction efficiencies related to antibiotic resistance.

biochemistry↗

bioRxiv2026

A comprehensive proteome and the first phosphoproteome reveal extensive phosphorylation of carbohydrate metabolism in Cryptosporidium parvum sporozoites

Cryptosporidium parvum is an obligate intracellular apicomplexan parasite and a major cause of diarrheal disease in humans and animals worldwide. Despite its public health importance, the molecular regulation of parasite metabolism, particularly at the post-translational level, remains poorly understood. Here, we present a comprehensive proteomic analysis and the first phosphoproteomic profile of excysted C. parvum sporozoites, the invasive stage responsible for host cell entry. Using data-independent acquisition-based mass spectrometry, we identified 2,272 proteins, representing approximately 58% of the predicted parasite proteome, and 8,994 phosphorylation sites across 833 phosphoproteins. Comparative analyses revealed weak correlations between transcript and protein abundance, underscoring extensive post- transcriptional regulation in sporozoites. Functional enrichment analyses showed that proteins involved in carbohydrate metabolism, particularly glycolysis, are highly abundant in the sporozoite proteome. In contrast, phosphoproteomic data revealed that many core glycolytic enzymes exhibit relatively low phosphorylation propensity, suggesting limited reliance on phosphorylation-based regulation for basal energy metabolism at this stage. To integrate proteomic and phosphoproteomic measurements acquired independently, we developed a relative phosphorylation index (RPI) that enables comparative assessment of phosphorylation propensity across proteins. Application of this metric highlighted selective phosphorylation of proteins associated with signaling, cytoskeletal organization, and host-parasite interaction, while key metabolic entry-point enzymes, such as hexokinase, showed high abundance but minimal detectable phosphorylation, in contrast to their mammalian counterparts. Together, these findings provide the most comprehensive molecular resource to date for C. parvum sporozoites and reveal a phosphorylation landscape that emphasizes regulatory and structural processes over core metabolic flux. This work establishes a foundation for understanding parasite-specific regulatory strategies and may inform the identification of novel therapeutic targets against cryptosporidiosis. Author SummaryCryptosporidium parvum is a microscopic parasite that causes diarrheal disease in humans and animals worldwide, yet we still know surprisingly little about how it regulates its biology at the molecular level. In this study, we set out to better understand how the parasite prepares for infection by examining the proteins present in sporozoites, the life stage that actively invades host cells. We generated the most comprehensive protein catalog to date for C. parvum sporozoites and, for the first time, mapped thousands of chemical modifications known as protein phosphorylation. These modifications often act as molecular switches that control how proteins behave. We found that proteins involved in basic energy production are extremely abundant but show relatively little phosphorylation, while proteins linked to cell structure, movement, and interaction with the host are more frequently modified. This suggests that the parasite prioritizes regulation of invasion-related processes over fine-tuning its core metabolism at this stage. By providing a detailed molecular resource and a new way to compare protein phosphorylation patterns, our work lays the groundwork for future studies of parasite biology and may help guide the search for new strategies to combat cryptosporidiosis.

microbiology↗

bioRxiv2026

Iron Deficiency Drives Sarcopenia in the Elderly: HIF-1α-Mediated Fibro-Adipogenic Progenitor Differentiation Induces Fat Infiltration and Impairs Muscle Function

Abnormal iron metabolism is closely linked to sarcopenia; however, the specific iron metabolism features of fat-infiltrating sarcopenia remain poorly understood. Proteomic sequencing revealed that in skeletal muscle with severe fat infiltration, the expression of iron utilization-related proteins was significantly downregulated, whereas that of iron uptake and storage proteins was markedly upregulated, thereby presenting an abnormal iron deficiency (ID) phenotype. Nevertheless, the mechanism by which ID drives intramuscular fat infiltration has not been fully elucidated. Using clinical samples, aged murine ID models, and in vitro cell assays, this study is the first to demonstrate that ID stabilizes hypoxia-inducible factor-1 (HIF-1), promoting aberrant adipogenic differentiation of fibro-adipogenic progenitors (FAPs), disrupting the homeostatic balance between satellite cells (SCs) and FAPs, exacerbating skeletal muscle fat infiltration, and impairing muscle repair capacity. Notably, treatment with the HIF-1 inhibitor PX478 reversed these pathological alterations and improved muscle function. Collectively, our findings identify the ID-HIF-1-FAPs axis as a key driver of intramuscular fat infiltration, offering a novel therapeutic target for the clinical management of fat-infiltrating sarcopenia.

cell biology↗

bioRxiv2026

Hidden stop codons orchestrate mRNA fate by ambushing ribosomal frameshifting associated with codon usage

In eukaryotes, the mRNA stability is generally shaped by codon usage bias, the uneven preferences for synonymous codons, in a translation-dependent manner. However, the conserved mechanism linking codon to mRNA decay remains elusive. Hidden stop codons (HSCs), defined as stop codons located in the +1 or -1 frame relative to canonical ORF, are widespread across all genomes but largely uncharacterized. Here, we demonstrate that in both fungi and human cells, HSCs play an conserved and mechanistic role in promoting mRNA decay by rapidly terminating out-of-frame translation promoted by nonoptimal codons, primarily through +1 ribosomal frameshifting. In the filamentous fungus Neurospora crassa, partially deleting HSCs via synonymous substitutions in the clock gene frequency increases mRNA stability and disrupts circadian rhythmicity. In human cells, acute depletion of translation termination factor eRF1 impairs recognition of HSCs, leading to global stabilization of mRNAs enriched in nonoptimal codons and HSCs. In both Neurospora and humans, these mRNAs are in part degraded through the NMD pathway via UPF1. Collectively, these findings suggest that in eukaryotes, HSCs serve as surveillance elements to monitor ribosomal frameshifting and out-of-translation promoted by nonoptimal codons, thereby initiating mRNA decay through NMD.

molecular biology↗

bioRxiv2026

Non-invasive tracking of hippocampal theta oscillations

Hippocampal theta oscillations play a crucial role in the formation of episodic memories by binding multisensory information into coherent episodes. Brain stimulation studies suggest that memory performance can be modulated by targeting these oscillations, offering a potential way of treating memory disorders. However, to effectively engage these rhythms, precise knowledge about their presence, frequency, phase and location is required, which has been a challenge, particularly for non-invasive methods such as magnetoencephalography (MEG). Here, we first asked if hippocampal signals are detectable in MEG recordings. Using simultaneous MEG-intracranial EEG (iEEG) data, we show that invasively recorded hippocampal activity is reflected in MEG sensor signals, demonstrating the feasibility of detecting deep-brain activity non-invasively. Building on this, we introduce a MEG-based analysis pipeline to track hippocampal theta frequency over time. Applied across three independent datasets, the pipeline captured characteristic hippocampal theta frequency patterns in both rodents and humans, and MEG-derived hippocampal frequencies were consistent with those observed simultaneously in intracranial EEG. These findings provide evidence that MEG can reliably track individual hippocampal oscillatory dynamics, paving the way for future non-invasive closed-loop interventions that adapt stimulation frequency and timing to ongoing oscillations.

neuroscience↗

bioRxiv2026

EOLA1, a novel mitochondria-localized protein critical for heart functions via regulating mitochondrial translation

Mitochondria possess their own mRNA translation system, mediated by specialized mitoribosomes. Dysregulation of mitochondrial translation disrupts metabolic homeostasis and is linked to various pathologies, including metabolic syndromes, neurological disorders, and cardiac diseases. Using CRISPR/Cas9 screening, we identified EOLA1 (endothelial-overexpressed lipopolysaccharide-associated factor 1) as a novel mitochondrial matrix protein essential for metabolic homeostasis. Knockout of Eola1 severely affects mitochondrial translation and consequently the oxidative phosphorylation in mammalian cells. Mechanistically, EOLA1 physically interacts with mitochondrial 12S ribosomal RNA (12S mt-rRNA) and the mitochondrial Tu translation elongation factor (TUFM), facilitating efficient translation elongation of mitochondrial-encoded mRNAs. Furthermore, genetic ablation of Eola1 in mice induced severe cardiac dysfunction, demonstrating its indispensable role in maintaining heart function through mitochondrial translation control. Together, our findings establish EOLA1 as a key regulator of mitochondrial translation via its interactions with 12S mt-rRNA and TUFM, highlighting its importance in cellular metabolism and a potential role in cardiac disease pathogenesis.

molecular biology↗

bioRxiv2026

Coordinated inhibition of SOX9 and cell cycle progression by microRNA-200 restricts sebaceous gland fate specification

The microRNA-200 family (miR-200s) is widely recognized for their potent role in inhibiting epithelial-to-mesenchymal transition and cell cycle progression in cancer. However, their functional specificity in normal epithelial development remains poorly understood. Here we show that miR-200s are highly enriched in hair matrix progenitors but conspicuously absent from the upper hair follicle (HF), the anatomical location where sebaceous gland (SG) and HF stem cells are specified. We demonstrate that elevated miR-200 expression in this region abolishes SG fate specification while permitting hair morphogenesis. Genome-wide identification of miR-200 targets reveals that miR-200s regulate multiple negative regulators of WNT signaling, in addition to cell cycle regulators. Single-cell and spatial transcriptomic analyses uncover a mutually exclusive expression patterns between WNT activity and SOX9 in the upper HF, which is disrupted by miR-200 induction, resulting in compromised SOX9 function. Mechanistically, genome-wide identification of SOX9 targets uncovers a broad network of lipid and fatty acid metabolism genes critical for the transition of upper HF progenitors to the SG fate. The coordinated inhibition of the SOX9-dependent lipogenic program and the potent restriction of cell cycle progression, both mediated by miR-200s, collectively blocks SG specification. Taken together, this work reveals an unexpected specificity of miR-200 in restricting epithelial plasticity and elucidates a spatially defined SOX9 regulatory network essential for SG development.

developmental biology↗

bioRxiv2026

SegJointGene: joint cell segmentation and spatial gene prioritization by information entropy guided convolutional neural networks

MotivationSpatial sequencing technologies enable the single-cell-level study of molecular organization in tissues. Revealing such spatial patterns relies on accurate cell segmentation. In complex tissues with dense cell packing, segmentation based solely on nuclear staining is insufficient for accurate cell boundary detection. This limitation arises because accurate segmentation necessitates the delineation of cell morphology, which is driven by molecular activities such as cytoskeletal dynamics, cell-cell adhesion, and intercellular signaling. Thus, integrating molecular information, including gene or protein expression, has the potential to improve segmentation, but remains computationally challenging. ResultsTo address this, we developed SegJointGene, a deep learning framework that jointly performs cell segmentation and spatial gene prioritization by integrating nuclei-based images with spatial gene or protein expression data. SegJointGene designs an information-entropy-guided convolutional neural network together with a computational information discarding score to identify genes that are important for cell-type-specific segmentation. The model iteratively refines gene prioritization and cell boundaries, producing convergent segmentation results along with prioritized spatial genes or proteins across cell types. We applied and benchmarked SegJointGene on various real spatial datasets, including spatial transcriptomics from the mouse hippocampus and distinct regions of the whole mouse brain, as well as spatial proteomics data from human tonsil. Across datasets, SegJointGene outperformed existing methods by 5-20% in accurately assigning molecular signals to cell boundaries. Robustness analyses further demonstrated stable performance across varying gene numbers and imaging resolutions. In addition, the genes prioritized by SegJointGene were enriched for structural, developmental, and synaptic signaling pathways, supporting their relevance to spatial tissue organization. Availabilityhttps://github.com/daifengwanglab/segjointgene

bioinformatics↗