Biology subjects

Sun, L.

Publications and source records attributed to Sun, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Periplasmic gatekeeping of phage DNA entry by rSAM enzyme-mediated maturation of an effector with His-X-Ser repeats

In the relentless arms race between bacteria and phages, bacteria have evolved a variety of defense strategies to combat phage infection. However, no bacterial system has been identified that specifically target the phage DNA entry phase. Here, we present a novel bacterial antiphage system, termed HXS, which provides broad-spectrum and robust antiphage activity by interfering with phage DNA entry. The HXS system consists of two radical S-adenosylmethionine (rSAM) enzymes (HxsB and HxsC), a small protein (HxsD), and the effector HxsA with a peptidoglycan-binding domain and five His-Xaa-Ser (HXS) repeats. HxsB/HxsC catalyze rSAM enzyme-dependent maturation of HxsA, including N-terminal processing and a site-specific +8 Da modification, thereby producing a periplasmic effector required for HXS defense. Biochemical evidence supports a model in which the matured effector likely engages incoming DNA electrostatically to arrest entry, establishing an rSAM enzyme-modified protein effector in antiphage defense.

microbiology↗

bioRxiv2026

Assessing Hardy-Weinberg Equilibrium in T2T-aligned 1000 Genomes Project

Quality control of markers in genome-wide association studies often includes testing for Hardy-Weinberg equilibrium (HWE). However, this is usually implemented in a homogeneous population without stratifying by sex. Previous work indicates sex-based selection at numerous autosomal loci in cohorts with active recruitment. Sex chromosome sequences can also interfere with autosomal SNPs. We examined genome-wide sex-specific HWE deviations across populations in the telomere-to-telomere (T2Tv2)-aligned high-coverage whole genome sequence of the 1000 Genomes Project data of 2,490 individuals. Our analysis was restricted to bi-allelic SNPs with non-missing genotypes and MAF>=5% in both sexes of the five super-populations. We employed a robust allele-based approach for HWE testing, which enabled the quantification of directional deviations from HWE. A second-order omnibus meta-analysis combining results from the five super-populations and both sexes revealed that 0.9% autosomal SNPs exhibited a significant deviation from HWE at p<5e-8. Most of these deviations were found to be associated with genomic features relating to poor sequence quality. Filtering results to reliable genomic regions yielded 255 autosomal and 1 NPR X chromosomal SNPs, of which 140 autosomal SNPs also showed significant heterogeneity across populations but not across sexes. 8 SNPs in a 15-bp region on chr14 showed excess heterozygosity in both sexes of the AFR (African) super-population. We also generated a well-performing multivariate predictor of HWD (deviation from HWE) using multiple sequence features, which could be combined with HWD estimates in future studies to select SNPs that deviate from HWE due to technical rather than biological reasons. Author SummaryWe conducted a specific quality control test, which compares the observed and expected genotype counts, on an updated version of the 1000 Genomes Project whole genome sequence data generated on [~]2500 individuals. We first performed this analysis by grouping the data by ancestry and sex. We then combined and contrasted the group results. We found that most regions that differed between observed and expected counts overlapped regions of the genome which are difficult to sequence using current short read technology. In the remaining regions we found an interesting cluster of SNPs in a single ancestry, where there is a gross excess of heterozygous genotypes. GWASes typically use a standard strict threshold for this quality control test for genotyping arrays to remove SNPs. Here we suggest a more nuanced approach that is applicable to whole genome sequence data.

genomics↗

bioRxiv2025

3'to 5'translation of linear mRNAs?

3[->]5 translation (termed "backward translation") mediated by eukaryotic circular RNAs has been reported recently. Whether linear mRNA can produce proteins through backward translation remained elusive. Here, we demonstrate that linear mRNAs can mediate backward translation in vitro. Backward translation was detected in human cells transfected with expression vectors used to produce linear mRNAs. Importantly, synthetic linear mRNAs could produce backward translation signal in multiple in vitro translation systems, with a level comparable to that of conventional 5 to 3 forward translation. Furthermore, we demonstrated that a single translation initiating sequence (TIS) was able to drive backward and forward translation in an in vitro experimental setup, with the efficiency of backward translation found to be significant lower than that of forward translation. In summary, this study further reinforces the notion of translation flexibility, demonstrates a broader applicability of backward translation and heralds a new strategy in synthetic biology.

cell biology↗

bioRxiv2025

Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq

Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate a integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated projectomic atlas with their distinct spectrum of neurotransmitter/neuropeptide and the receptors-related gene profiles and depicted PFC neural signal transmission network. By which, we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, leveraging machine learning, we predicted neuron projections with high accuracy by combining gene profiles and spatial information. As a proof of concept, we used this model to predict projections of fear recall engram neurons. This study facilitates our understanding of brain multi-modal network and neural computation.

neuroscience↗

bioRxiv2025

Lipid nanoparticle protein coronas form via lipoprotein fusion rather than shell-like adsorption

The protein corona influences the in vivo biodistribution of ionizable lipid nanoparticles (LNPs) in nucleic acid delivery, yet its structural architecture remains poorly defined. Using cryo-transmission electron microscopy, we visualized LNP-protein interactions in their native state. We show that, unlike the discrete "fuzzy" shells observed on hard nanoparticles, LNPs displayed no peripheral protein shell. Instead, controlled incubation and competitive "dual-particle" assays, supported by molecular dynamics simulations, indicate that LNP membranes undergo localized thickening and electron-dense remodeling consistent with lipoprotein integration rather than surface adsorption. Similar features were observed in extracellular vesicles, suggesting this behavior is shared among lipid-based carriers, and proteomic analysis identified apolipoproteins as the dominant associated proteins. Together, these findings support a model in which the biological identity of LNPs arises through membrane remodeling rather than shell-like adsorption, and provide a framework for the rational design of targeted nanomedicines. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/695162v2_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@a6f2b2org.highwire.dtl.DTLVardef@879d12org.highwire.dtl.DTLVardef@159196dorg.highwire.dtl.DTLVardef@945749_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Mitochondrial control of fuel switching via carnitine biosynthesis

Environmental adaptation often involves a shift in energy utilization toward mitochondrial fatty acid oxidation, which requires carnitine. Besides dietary sources of animal origin, carnitine biosynthesis from trimethyllysine (TML) is essential, particularly for those who consume plant-based diets; however, its molecular regulation and physiological role remain elusive. Here, we identify SLC25A45 as a mitochondrial TML carrier that controls carnitine biosynthesis and fuel switching. SLC25A45 deficiency decreased the carnitine pool and impaired mitochondrial fatty acid oxidation, shifting reliance to carbohydrate metabolism. Slc25a45-deficient mice were cold-intolerant and resistant to lipid mobilization by GLP1 receptor agonist (GLP-1RA), rendering them resistant to adipose tissue loss. Our study suggests that mitochondria serve as a regulatory checkpoint in fuel switching, with implications for metabolic adaptation and the efficacy of GLP-1RA-based anti-obesity therapy.

biochemistry↗

bioRxiv2025

Development of the Early Childhood Duodenum across Ancestry, Geography and Environment

During early childhood, the proximal small intestinal mucosa plays a central role in growth, metabolism, immune priming, and neuronal development. Yet the cellular architecture and environmental responsiveness of the human small intestinal mucosa during this period remain poorly defined. Here, we generate a comprehensive cellular and spatial map of the duodenum from 87 children aged 6 months to 13 years, representing diverse ancestries and geographic contexts. This atlas integrates single-cell transcriptomic and spatial profiling with data on diet, social drivers of health, and environmental exposures. Using these data, we define mucosal cellular composition and chart its developmental trajectory in early childhood. Comparative analyses of children residing in the United States (US) and Pakistan reveal a differentiated enterocyte subset expressing the aquaglyceroporin, AQP10 (AQP10+ enterocyte), that is enriched in children from the US. We show that emergence of this enterocyte state depends on lipid exposure to intestinal stem cells and correlates with dietary fat intake. We also identify a previously-undescribed thyrotropin-releasing hormone (TRH+) enteroendocrine cell and provide evidence for a local endocrine-epithelial-lymphocyte circuit. Our work establishes a detailed framework for pediatric duodenal mucosal development and illuminates how intestinal cellular dynamics are shaped by age and environment.

developmental biology↗

bioRxiv2025

Mitochondria-derived PEP licenses glycerolipid synthesis via SLC25A35

Mitochondria provide a variety of metabolites, in addition to ATP, to meet cell-specific needs. One such metabolite is phosphoenolpyruvate (PEP), which contains a higher-energy phosphate bond than ATP and has diverse biological functions. However, how mitochondria-generated PEP is delivered to the cytosol and fulfills cell-specific requirements remains elusive. Here, we show that SLC25A35 regulates mitochondrial PEP efflux and glyceroneogenesis in lipogenic cells that utilize the pyruvate-to-PEP bypass. Reconstitution and structural studies demonstrated PEP transport by SLC25A35 in a pH gradient-dependent manner. Loss of SLC25A35 in adipocytes impaired the conversion of mitochondrial PEP into glycerol-3-phosphate, thereby reducing glycerolipid synthesis. Significantly, hepatic inhibition of SLC25A35 in obese mice alleviated steatosis and improved systemic glucose homeostasis. Together, these results suggest that mitochondria facilitate glycerolipid synthesis by providing PEP via SLC25A35, offering lipogenic mitochondria as a target to limit glycerolipid synthesis, a pivotal step in the pathogenesis of hepatic steatosis and Type 2 diabetes.

cell biology↗

bioRxiv2025

Structural and biochemical studies of human PP2A(B55) holoenzyme and ENSA protein complex

The serine/threonine protein phosphatase 2A (B55) holoenzyme (PP2A(B55)), a key cell cycle regulator, is tightly regulated by ENSA, whose phosphorylation at Ser67 inhibits PP2A(B55). The structural basis for how pENSA orchestrates this inhibition to govern mitotic progression remains unclear. In this study, we disapproved the previous hypothesis of direct ENSA-PP2A A subunit interaction, and showed that the ENSA-PP2A(B55) interaction requires the PP2A holoenzyme. We then determined cryo-EM structure of the PP2A(B55)-ENSAS67D complex at 3.03 [A] resolution, which reveals four distinct regions of ENSA, each engaging specific sites on the B55 or C subunits. The structure reveals an extended, inhibited conformation of the PP2A(B55) holoenzyme, which contrasts sharply with the contracted, active state of apo PP2A(B55). pENSA binding induces the C subunit to shift away from the B55 subunit, with the pS67-containing motif inserting into the catalytic site of C subunit and locking the PP2A(B55) holoenzyme in an inactive state. Our work also revealed novel ligand-binding surfaces on B55, and expanded definition of the short linear motif (SliM). Overall, our work provided novel insights into PP2A regulation during cell cycle, and offers new avenues for the discovery of specific PP2A(B55) inhibitors and modulators.

biophysics↗

bioRxiv2025

Selective Inactivation of Astrocytic Monoacylglycerol Lipase for Alzheimer Disease Therapy

Alzheimers disease (AD) is the leading cause of dementia in the elderly, yet effective therapies remain lacking. Here, we identify monoacylglycerol lipase (MAGL), the principal enzyme that degrades the endocannabinoid 2-arachidonoylglycerol (2-AG) in the brain, specifically in astrocytes as a promising therapeutic target for AD. APP transgenic (TG) mice with astrocyte-specific MAGL deletion (TG-aKO), but not neuron-specific deletion (TG-nKO), exhibit markedly reduced A{beta} pathology, neurodegeneration, and neuroinflammation, along with preserved synaptic structure and function and improved cognition. These benefits are recapitulated in TG mice by AAV-mediated silencing of astrocytic MAGL, whereas MAGL overexpression exacerbates neuropathology and accelerates synaptic and cognitive decline. Transcriptomic analyses reveal that dysregulated synapse-, inflammation-, and AD-related gene expression profiles are reversed in TG-aKO mice. MAGL expression is elevated in astrocytes from both AD patients and TG mice. Remarkably, a single intracerebroventricular (ICV) injection of AAV-MAGL-shRNA administered at either presymptomatic or postsymptomatic stages prevents or reverses neuropathology and synaptic and cognitive impairments in TG mice, providing preclinical evidence that astrocytic MAGL silencing represents an effective therapeutic strategy for AD.

neuroscience↗

bioRxiv2025

3' to 5' Translation of Circular RNAs?

For decades, the 5[->]3 direction of translation has been a central dogma of molecular biology(1). Here we present evidence that eukaryotic circular RNAs (circRNAs) can serve as templates for 3[->]5 backward translation (BT), yielding polypeptides with distinct sequence and structural features not found in canonical proteomes. Mining of more than 6,000 multi-omics datasets identified [~]1 million candidate BT proteins across eukaryotes, including 59,000 high-confidence human BT proteins supported by mass spectrometry. Genetic combinatorial experiments (KO and KI) and cell-free translation of synthetic circRNAs establish BT as a conserved mechanism. Loss-of-function studies of hs.circCAPN15 in human and dm.circROLS in Drosophila underscore the functional importance of BT-derived proteins. Our work challenges the long-standing unidirectional translation paradigm, expands the functional landscape of the genetic code, and reveals a hitherto hidden layer of proteomic complexity with broad implications for biology and therapeutics.

molecular biology↗

bioRxiv2025

Metabolic pathway competition sensitizes thioredoxin reductase-depleted Candida albicans to cell wall stress and antifungals

Candida albicans is the most common invasive human fungal pathogen. Each of the currently available 3 antifungal drug classes is limited by toxicities, drug interactions or inadequate penetration of critical tissues. We discovered a connection between C. albicans TOR and thioredoxin reductase, Trr1. Fungal and human thioredoxin reductases diverge fundamentally and are essential for repair of oxidatively damaged macromolecules, so they may be promising drug targets. We found that Trr1 is required for C. albicans growth at human body temperatures, hyphal growth regulation and management of oxidative and cell wall stress. Its depletion sensitizes C. albicans to AmphotericinB and to an echinocandin. TRR1-depleted cells have lower cell wall glucan content. Metabolomics experiments highlighted their perturbed pentose phosphate pathway (PPP). They have sharply elevated activity of glucose-6-phosphate dehydrogenase, the first, rate-limiting enzyme of the PPP. A key glycolytic, gluconeogenic and UDP-glucose biosynthetic enzyme each show decreased activity. UDP-glucose is the substrate of cell wall glucan-producing enzymes. We propose that Trr1-depleted cells accelerated glucose-6-phosphate flux into the PPP, driven by demand for NADPH reducing equivalents, diminishes glucose-6-phosphate availability for UDP-glucose production and hence for cell wall construction, weakening the wall. Strikingly dysregulated signaling pathways in Trr1-depleted cells contribute to their stress hypersensitivities.

microbiology↗

bioRxiv2025

Energy Landscape Analysis Reveals Thalamic Modulation of Brain State Transitions During Movie Watching

Understanding how large-scale brain networks dynamically coordinate during complex, real-world experiences remains a crucial topic in contemporary neuroscience. Leveraging naturalistic paradigm, this study employed energy landscape modeling to characterize the temporal dynamics of brain state transitions and their functional significance. Using the Sherlock fMRI dataset, we identified two dominant brain states: a perception- and attention-oriented state, and an introspective, integrative state, each associated with distinct canonical brain networks. State transitions were differentially associated with the recruitment of these networks and manifested as either the "easy" or "hard" route, depending on the energy required for the transition. Notably, we demonstrated that the probability of specific state transitions robustly predicted inter-subject correlation within three clusters: subcortical-rich, salience/attention-rich, and DMN-rich regions. This indicates that flexible reorganization of cortical networks underlies shared neural engagement during ecologically valid experiences. Critically, the thalamus emerged as a central modulator, displaying activity changes and dynamic nucleus-specific thalamocortical connectivity changes tied to distinct transition profiles. Together, our findings shed light on the energetic and network mechanisms that orchestrate brain dynamics during naturalistic cognition and underscore the pivotal role of cortico-thalamo-cortical circuits in governing flexible, collective neural responses to richly structured real-life stimuli.

neuroscience↗

bioRxiv2025

Graft protection by myeloid progenitor cells using lethal or non-lethal preconditioning.

Myeloid progenitor cell (MPC) therapy can protect against infection and can be used as an irradiation countermeasure, but can also prevent rejection of matched grafts. Here we report on the matching requirements between MPCs and skin grafts, and on the development of a non-lethal preconditioning model that supports MPC-induced protection of skin grafts. Mouse MPCs (mMPC) were obtained from HSC following 10-day ex vivo expansion. Skin grafts were tested in host mice that either received a lethal dose of irradiation and reconstitution with allogeneic mMPC and third party HSCs or were given injections with depleting antibodies and chemotherapeutics followed by transplantation of mMPC without HSC. mMPC-matched grafts were protected and no significant difference was observed between mice receiving irradiation and fully matched grafts (major and minor transplantation antigens), partially matched grafts (major only), and fully matched grafts in mice that received sublethal irradiation. Haploidentical grafts (half of the MHC alleles not matched at all) are not protected. We conclude that closely matched mMPCs are sufficient to prevent rejection. We also show that mMPCs are effective in a trachea transplant model. Graft protection does not require either lethal preconditioning or an accompanying HSC transplantation, and affects both T- and B-cell responses.

immunology↗

bioRxiv2025

Susceptibility to Task-irrelevant Auditory Distractors in Relation to Visual Working Memory in Children With and Without ADHD

ObjectiveAttention-deficit/hyperactivity disorder (ADHD) is a prevalent neurodevelopmental disorder in children and is often associated with increased distractibility. Previous research has reported that susceptibility to task-irrelevant visual distractions is associated with visual working memory (WM) capacity. However, how neural responses to task-irrelevant auditory distractors are related to visual WM capacity in children with and without ADHD remains poorly understood. MethodsIn this study, we collected electroencephalography (EEG) signals from 72 children with ADHD and 88 typically developing (TD) children across two experiments, during which they performed visual tasks of varying difficulty while task-irrelevant auditory distractors were presented. The mismatch negativity (MMN) amplitude was measured as a neural index of susceptibility to auditory distractors, and the K score was assessed as a behavioral indicator of visual WM capacity. ResultsTD children showed opposite patterns across the two experiments: under low audiovisual competition, those with higher visual working memory capacity were more susceptible to task-irrelevant sounds, whereas under high competition, children with lower capacity showed greater susceptibility to distraction. In contrast, children with ADHD showed a stable association, with lower visual WM capacity consistently predicting higher susceptibility to task-irrelevant auditory distractors regardless of competition level. ConclusionsThese findings provide novel evidence that susceptibility to task-irrelevant auditory distraction is closely related to visual WM capacity in both children with and without ADHD, but the patterns of this relationship differ between typical and atypical neurodevelopment and are modulated by audiovisual competition.

neuroscience↗

bioRxiv2025

Defective Microhomology-Mediated End-joining in SMARCB1-Deficient Tumors

Rhabdoid tumors (RTs) are highly aggressive cancers driven by biallelic mutation of SMARCB1, a core subunit of the BAF (SWI/SNF) complex. We found that SMARCB1-deficient tumors have a defect in the microhomology-mediated end-joining (MMEJ) pathway, and SMARCB1 is essential for maintaining the protein level of the core MMEJ protein Polymerase Q (POLQ). Mechanistically, SMARCB1 facilitates the nuclear export of the POLQ mRNA through its interaction with the nuclear pore complex. Interestingly, loss of MMEJ in RT cells leads to a compensatory activation of, and a hyper-dependence on, the Fanconi Anemia (FA)/BRCA pathway. Knockout or inhibition of this pathway selectively kills RT cells. Notably, RBM39 degraders, novel splicing modulators, effectively inhibit the FA/BRCA pathway and kill RT cells. SMARCB1 and other cBAF/pBAF components are important for maintenance of MMEJ activity and POLQ protein level, suggesting that BAF-deficient cancers more broadly may be treated by targeted inhibition of the FA/BRCA pathway. TeaserSMARCB1-deficient tumors lose POLQ protein and MMEJ repair, forcing a hyper-dependence on the FA/BRCA pathway.

cancer biology↗

bioRxiv2025

HPV16 E6 oncoprotein promotes microhomology-mediated viral integration by upregulating POLQ expression

Integration of the high-risk Human Papillomavirus 16 (HPV16) genome into the host chromosome, frequently driven by microhomology-mediated end joining (MMEJ), is a critical step in the carcinogenesis of HPV-associated tumors. However, the mechanisms by which viral oncoproteins manipulate the error-prone MMEJ pathway remain poorly defined. Here, we demonstrate that the HPV16 E6 oncoprotein upregulates MMEJ to facilitate viral genome integration. This heightened MMEJ activity is driven by a marked increase in the protein levels of DNA Polymerase Theta (POLQ), a central enzyme of the MMEJ pathway. Mechanistically, we show that the elevation of POLQ levels in response to HPV16 E6 expression is dependent on the host E3 ubiquitin ligase UBE3A/E6AP but is independent of p53 degradation. E6 activates UBE3A to promote the ubiquitination and degradation of RAD23A, a shuttle protein required for delivering polyubiquitinated POLQ to the proteasome. Consequently, the loss of functional RAD23A phenocopies the effect of HPV16 E6, leading to POLQ stabilization and increased MMEJ activity. By elucidating the E6-UBE3A-RAD23A-POLQ axis, our findings reveal a novel mechanism through which HPV manipulates the host DNA repair machinery to promote its integration and oncogenic potential.

molecular biology↗

bioRxiv2025

Emergence of Individualized Functional Topography in the Neonatal Brain

The early postnatal period represents a critical phase for establishing the brains fundamental architecture. However, how individualized functional topography emerges and shapes long-term cognition remains unknown. Using multimodal neuroimaging data from 419 neonates, we map personalized functional topographies in the first weeks of life and reveal their association with 18-month neurocognitive outcomes. Unique and stable functional topographies are already present at birth, with interindividual variability organized along a conserved sensorimotor-to-association hierarchy. These individualized maps encode early brain maturity and robustly predict cognitive, language, and motor outcomes at 18-month of age, with predictive features concentrated at network boundaries. This functional refinement is structurally anchored by concurrent maturation in cortical myelination and sulcal depth. Preterm birth results in distinctive topographic alterations characterized by accelerated maturation of association networks. Our work establishes a foundation for precision models of early brain development and elucidates its significance for long-term neurocognitive outcomes.

neuroscience↗