Biology subjects

Sun, L.

Publications and source records attributed to Sun, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Glial cells gate small RNA transport from germline to brain during transgenerational epigenetic inheritance of behavior

How circulating RNAs reach their target tissue is not well understood. In C. elegans, small RNA signals that convey exposure to pathogenic Pseudomonas travel from the intestine to germline to neurons, allowing both learned pathogen avoidance and the transgenerational inheritance of this information for four generations, but how this Cer1 retrotransposon-bound RNA signal reaches the nervous system was previously unknown. We found that the RNA transporter SID-1, long thought to act in the intestine or germline, instead functions in a single cell type, the amphid sheath glia, where it is necessary and sufficient for learned avoidance. SID-1 mediates uptake of germline-derived RNA, followed by transcytosis to a neighboring sensory neuron, where the P11 target gene maco-1 is silenced. This glial "filter", which uses highly conserved molecular components to transcytose RNAs to neurons, reveals a general mechanism for gating small RNA access to the nervous system, paralleling the mammalian blood-brain barrier.

genetics↗

bioRxiv2026

Pediatric brain charts reveal ADHD biotypes with distinct developmental, molecular, and therapeutic profiles

Attention-deficit/hyperactivity disorder (ADHD) exhibits profound clinical heterogeneity; however, its underlying neurobiological substrates remain unclear. Here, leveraging large - scale structural magnetic resonance imaging data from 12,663 typically developing children and 1,699 children with ADHD across Chinese and United States cohorts, we construct population specific pediatric brain charts via hierarchical Bayesian normative modeling to quantify individual deviations in cortical morphology. Data-driven clustering identifies two robust, cross - ethnically replicable ADHD biotypes: an infra - normal biotype characterized by widespread cortical thinning and a supra - normal biotype marked by cortical thickening. Multivariate analyses reveal distinct brain-behavior architectures: cortical deviations correlate preferentially with symptom severity in the infra-normal biotype but with both symptom severity and cognitive performance in the supranormal biotype. Clinically, the infra-normal biotype demonstrates a superior response to methylphenidate over atomoxetine, whereas the supra-normal biotype responds comparably to both. Transcriptomic analyses identify biotype-specific molecular signatures converging with ADHD genome-wide association study (GWAS) risk loci but exhibiting distinct expression patterns in the brain. These findings classify ADHD heterogeneity into neurobiologically distinct, clinically informed biotypes, providing a mechanistic framework for precision psychiatry in pediatric ADHD.

neuroscience↗

bioRxiv2026

Bee phylosymbiosis: the relative importance of host phylogeny, behavioral traits, and environment

Phylosymbiotic studies investigate how microbiomes recapitulate their host phylogeny and can thus reveal the evolution of host-microbe relationships. In bees, the extent of phylosymbiosis and its relationship with host ecological traits remain unclear. We integrated public bee 16S rRNA metabarcoding data to investigate how host phylogeny and ecological traits affected the bacterial community associated with 178 bee species. Our results highlight only moderate phylosymbiosis patterns in bees, with the corbiculates associated with diverse lineage-specific microbial communities, while the non-corbiculates were predominantly associated with Wolbachia. Across all bee taxa, Wolbachia was also consistently negatively associated with Lactobacillus. Finally, our analysis revealed that the host ecological traits had only marginal effects on microbial composition. Although eusocial bees harbored distinct microbiomes, the effect of social behavior was confounded by host phylogeny. Climate showed no general effect across bee taxa, but within some genera, microbiomes were more homogeneous among bees from arid and semi-arid regions than among those from other climatic regions. Together, our findings reveal that broad-scale patterns in bee microbiomes emerge primarily as lineage-specific host-microbe associations, with ecological traits acting only weakly and often at a taxon-specific level.

microbiology↗

bioRxiv2026

Combining an autoactivated cGAS mutant with membrane-tethered IL-12 via mRNA lipid nanoparticles promotes systemic tumor control

Local tumor therapies rarely induce systemic immunity capable of controlling metastatic disease. Here, we engineer an mRNA lipid nanoparticle (LNP) platform to coordinate innate immune sensing and T cell activation in situ through co-delivery of an autoactivated cyclic GMP-AMP synthase mutant (cGASR241E) and membrane-tethered IL-12 (IL-12TM). cGASR241E mRNA LNPs autonomously generated cyclic GMP-AMP in vivo, activating host STING signaling and initiating antitumor responses. Co-administration with IL-12TM mRNA LNPs promoted localized cytokine production, reduced regulatory T cells, and restored effector function in tumor-infiltrating T cells. This combination elicited systemic antitumor immunity and suppressed distal tumors across multiple mouse models. The therapeutic efficacy required CD8+ T cells and IFNg; signaling in host, supporting a model in which innate DNA sensing is coupled to IL-12-mediated T cell functional reinforcement. In addition, the combination enhanced responsiveness to PD-L1 blockade. Together, these findings establish a clinically translatable strategy to integrate cGAS-STING activation with cytokine-driven T cell programming to drive systemic tumor control.

cancer biology↗

bioRxiv2026

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

bioRxiv2026

The L-type voltage-gated Ca2+ channel CaV1.2 regulates fibroblast-like synoviocytes invasiveness during rheumatoid arthritis

Fibroblast-like synoviocytes (FLS) are major drivers of synovial tissue inflammation and damage during rheumatoid arthritis (RA). A hallmark of the aggressiveness of RA-FLS is their invasiveness but the molecular mechanisms that regulate this invasiveness remain poorly understood. The KCa1.1 (BK, Slo1, MaxiK, KCNMA1) potassium channel is a major regulator of RA-FLS pathogenicity and inhibiting KCa1.1 expression or its activity with selective blockers reduces RA-FLS invasiveness and reduces disease severity and joint damage in rat models of RA. KCa1.1 blockade induces a Ca2+ influx in RA-FLS whose intracellular signaling results in increased cell adhesion to the extracellular matrix and thus a reduction in cell migration. However, the identity of the Ca2+-permeable channel responsible for the Ca2+ influx has remained elusive. Here, we demonstrate the co-expression of KCa1.1 with the L-type voltage-gated CaV1.2 channels at the plasma membrane of primary human and rat FLS. Selective blocking of the CaV1.2 channel blunts the Ca2+ influx induced by KCa1.1 blockade and abrogates the effects of KCa1.1 blockade on RA-FLS invasiveness, migration, cell shape, and podoplanin expression. Whereas KCa1.1 blockers reduce disease severity in rat models of RA, treating rats with the collagen-induced arthritis model of RA with both blockers of KCa1.1 and CaV1.2 eliminates the therapeutic benefits of treatment with KCa1.1 blockers alone. Together, these data demonstrate a physical and functional coupling of KCa1.1 and CaV1.2 channels in FLS during RA and its rat model that regulate the invasive phenotype of the FLS through modulation of intracellular Ca2+ homeostasis.

cell biology↗

bioRxiv2026

Ligand-specific endothelial Notch signaling coordinates brain pericyte specification and expansion

Pericyte specification and expansion must be coordinated with vascular growth to establish a functional cerebrovascular network, yet how endothelial signals control these distinct developmental transitions remains incompletely understood. Here, using genetic manipulation, single-cell transcriptomic analysis, and longitudinal in vivo imaging in zebrafish, we identify ligand-specific endothelial Notch signaling as a mechanism coordinating brain pericyte development. Endothelial Jag2b is required for efficient pericyte specification from pericerebral progenitor pools and subsequently promotes Notch-dependent pericyte proliferation and population expansion. By contrast, endothelial Dll4 restrains pericyte proliferation and functionally opposes Jag2b-dependent expansion, demonstrating that distinct endothelial Notch ligands generate different developmental outputs. Endothelial Notch activation increases jag2b expression, and genetic interaction analyses establish Jag2b as an important mediator of Notch-dependent pericyte expansion. Moreover, genetic disruption of piezo1 reduces brain pericyte abundance, whereas endothelial jag2b expression rescues this phenotype, placing Jag2b downstream of Piezo1-dependent hemodynamic signaling. Together, these findings reveal a ligand-specific endothelial Notch program that integrates hemodynamic cues with endothelial-pericyte communication to coordinate the specification and expansion of brain pericytes during cerebrovascular development.

developmental biology↗

bioRxiv2026

Meta2Data: Automated data processing for large scale microbiome data re-analysis

Meta2Data is a modular, largely automated pipeline implemented in Python and Bash for the retrieval, standardization, and processing of public microbiome sequencing data. It retrieves metadata from major public repositories, including INSDC and CNCB, using user-provided keywords or BioProject/BioSample identifiers. Retrieved metadata are standardized using a synonym dictionary and then subjected to manual curation. Based on the curated metadata, Meta2Data downloads the corresponding raw sequencing data and processes them using standardized workflows based on DADA2 or VSEARCH. The pipeline supports both single- and multiple-target-region datasets and produces integrated feature tables, taxonomic assignments, and phylogenetic trees for downstream microbial community analyses. Availability and ImplementationMeta2Data is freely available at https://github.com/LinyangSun/Meta2Data and archived on Zenodo at https://doi.org/10.5281/zenodo.20670433

bioinformatics↗

bioRxiv2026

Pervasive Somatic Mutations in NF1 Drive Cell Type and Spatially Specific Clonal Selection in Neurofibromatosis

Tumorigenesis is a multi-step process shaped by the accumulation of somatic driver mutations, but identifying the earliest steps and cell of origin of tumorigenesis remains challenging. Single cell genomics in >1.7 million single cells across donors with the cancer predisposition syndrome neurofibromatosis type 1 (NF-1), shows that somatic 'second-hit' mutations in NF1 are pervasive and show positive clonal selection in oligodendrocytes (OLs) and OL precursor cells (OPCs), but are exceedingly rare in neurons and other lineages. Combined spatial genotyping and transcriptomic analysis enabled dissection of cell autonomous and non-autonomous effects of second-hit mutations including clonal expansion of mutant OPCs with strong bias for cerebral gray matter versus white matter, suggesting that gray matter influences OPC proliferation and differentiation via non-cell autonomous interactions between OPCs and neurons. NF1-null OL lineage cells upregulate CDKN2A--a tumor suppressor frequently lost in NF1-mutant tumors--whereas brain cancers from these same individuals show CDKN2A loss across multiple cancer cell states, suggesting CDKN2A loss in OPCs is a critical step in tumor progression. Our findings reveal developmentally early, exquisitely lineage-specific NF1 somatic mutations in premalignant NF-1 brain, suggest cell autonomous and non-autonomous roles in clonal selection in brain, and suggest that clones harboring cancer driver mutations can persist over a lifetime in phenotypically normal tissues.

genetics↗

bioRxiv2026

Tissue resident CD4+ memory T-cells mark response to immune checkpoint inhibition in high-grade glioma

Background: Immune checkpoint inhibitors (ICI) are efficacious in many solid tumors, but response in glioma is restricted to a small subgroup. The determinants of response and resistance to ICI remain poorly understood. Methods: Here we exploit a syngeneic hypermutated high-grade glioma model with dichotomous response to combined PD-1 and CTLA-4 inhibition to unravel determinants of tumor-infiltrating T-cells driving response. Tumor-infiltrating T-cells from ICI-responsive and non-responsive tumors were analyzed by single-cell RNA and T-cell receptor sequencing and tumor-reactive T-cell receptor clonotypes were functionally validated to characterize their transcriptional phenotypes. We verify our findings in IDH1 wildtype glioblastoma patients treated with neoadjuvant pembrolizumab. Results: ICI response was associated with intratumoral clonal expansion of tumor-reactive cytotoxic T-cells and increased infiltration of CXCR6+ CD4+ tissue resident memory T-cells (Trm). CD4 stem-like memory T-cells in responding tumors demonstrated elevated interferon responses, following trajectories toward clonally expanded Trm, versus trajectories toward exhaustion in non-responsive tumors. In responsive tumors, CD4+ Trm interacted with infiltrating CXCR3+ tumor-reactive and clonally expanded, yet transcriptionally versatile cytotoxic T-cells. Probing the post neoadjuvant ICI high-grade glioma patient tissue dataset, we confirmed increased CXCR6 expression in CD4+ T cells and the association of CD4+ Trm with prolonged overall survival. Conclusion: These findings identify CD4 tissue-resident memory T-cells as determinants of ICI response in IDH1 wildtype high-grade glioma and warrant their further investigation to improve immunotherapy outcomes.

cancer biology↗

bioRxiv2026

A tRNA-derived small RNA orchestrates cardioprotection through distinct cell-type-specific mechanisms

Pathological cardiac fibrosis and hypertrophy, key contributors to adverse remodeling that drives heart failure (HF), are not adequately targeted by current therapies. We identified tRNA-Asp-GTC-3'tDR, an ischemia-induced tRNA-derived small RNA (tDR), as an endogenous regulator of both remodeling processes across cardiac fibroblasts and cardiomyocytes. In murine models of myocardial ischemia- and pressure overload-induced HF, cardiac delivery of tRNA-Asp-GTC-3'tDR reduced fibrosis and hypertrophy, preserved cardiac function, and improved survival, with limited three doses conferring durable protection after ischemia, whereas silencing it worsened both. Strikingly, tRNA-Asp-GTC-3'tDR acts through distinct mechanisms in different cell types: in fibroblasts, it assembles stress granules that sequester ribosome-loaded profibrotic transcripts, whereas in cardiomyocytes it engages pseudouridine synthase PUS7 to activate RNA autophagy. Its regulation and functions were confirmed in human cardiac cells and tissues. These findings demonstrate that a single tDR coordinates cell-type-specific protective programs in the heart, suggesting a new therapeutic axis to mitigate HF progression.

cell biology↗

bioRxiv2026

Agentic transcranial functional ultrasound imaging: @fUS

Functional ultrasound (fUS) imaging provides deep, wide-field access to brain function, but instrument cost and complex acquisition and analysis workflows restrict its wider adoption. Here we introduce @fUS, an agentic transcranial imaging platform with an open architecture that integrates purpose-built hardware with executable experimental skills and persistent structured memory. The system combines 128-channel, 16-bit acquisition at 125 MHz with GPU-based processing and enables functional imaging through the intact scalp and skull of mice, with approximately 100-m spatial resolution and 10-Hz temporal sampling, providing a basis for longitudinal studies without cranial-window surgery. Its agent connects scientific objectives to experimental design, direct instrument control and data analysis, retaining context across interactions and supporting inspectable workflows through text and hands-free voice control. Neuroscience trainees with limited engineering experience independently configured the system within 30 min. Agent-assisted exploration of whisker-stimulation datasets revealed low-frequency vascular changes beyond conventional response mapping, supported by complementary two-photon measurements of single-vessel diameter. By combining transcranial imaging with accessible instrument control and analysis, @fUS provides a foundation for wider adoption and larger, more diverse neuroscience datasets. More broadly, it offers a framework for scientific instruments in which measurement, computation and experimental reasoning are developed as parts of the same system.

bioengineering↗

bioRxiv2026

A meta-analysis on the effects of pollutants on the earthworm microbiota

Like for many other organisms, earthworms host a microbiota consisting of bacteria, fungi and other micro-organisms originating from their surrounding environment. In earthworms, these microbes, either associated with the gut, skin, kidney-like nephridia, gizzard or cocoons, aid their hosts with the digestion of organic matter, immune responses against pathogens, and/or detoxification. Unfortunately, pollution is an increasing threat to soil health and soil biodiversity, and numerous articles have characterized both the microbial communities associated with earthworms, as well as the effects of soil pollution on these microbial communities. Here, we aim to synthesize data from across 159 articles to identify consistent global patterns and gaps in the study of earthworms' microbial communities. Additionally, we combined 16S rRNA metabarcoding data from almost 30 articles in a meta-analysis to evaluate the changes in the diversity of earthworm's and surrounding soil's bacterial microbiota after pollutant exposure. Through an evidence map, we clearly showed that most of the earthworm microbiota data came from the Eisenia fetida species reared in laboratory conditions, and only a handful of studies sequenced fungi (ITS) and protists (18S rRNA) in addition to bacteria and archaea (16S rRNA). The scarcity of studies from wild populations, environmental conditions, and the low microbial diversity targets and sources, cannot support a comprehensive view on earthworm's microbial ecology. Nonetheless, results of the meta-analysis indicate that the data did not support the occurrence of significant changes in the microbiota richness and diversity as result of pollution exposure. However, the microbial communities altered their composition, becoming more dissimilar. We suspect the microbiota response to pollution to be host-species specific, but the lack of data severely limited our ability to further elucidate the effect of pollution on earthworm microbiota.

ecology↗

bioRxiv2026

Diurnal and seasonal regulation of brain mu-opioid and dopamine D2 receptor signalling in humans

Purpose: Rhythmic regulation of human neurotransmission systems, particularly the mu-opioid receptor (MOR) and dopamine D2 receptor (D2R) signaling, remains poorly understood. Although prior studies indicate possible diurnal fluctuations in D2R signaling, potential existence of diurnal rhythms in MOR signaling has yet to be investigated. Furthermore, whether and how seasonal factors may override or interact with diurnal rhythms in either system remains unexplored. Decoding these temporal dynamics and their possible links to behavioral traits, such as anxiety, may improve mood regulation models and inspire rhythm-tailored interventions. Methods: Based on a historical PET database of healthy humans scanned with [11C]carfentanil (n = 188) and [11C]raclopride (n = 184), we investigated the diurnal patterns of MOR and D2R availability in the brain, using time-of-day (TOD) of scanning as predictor. Furthermore, we examined whether the TOD differences in receptor availability were modulated by seasonal differences in the daylength (D2R and MOR) and trait-anxiety (MOR). Results: The data revealed increased MOR and decreased D2R availability in the afternoon compared to the morning scans. Interaction with the seasonal effect was, however, observed only for MOR availability, spanning brain areas including anterior cingulate, dorsomedial and dorsolateral prefrontal cortex, insula and striatum. Besides, the diurnal variation of MOR availability in these regions was also sensitive to trait-anxiety levels. Conclusions: The current results reveal the diurnal patterns in opioidergic and dopaminergic neurotransmission with an opposing trajectory. Furthermore, the data highlight a unique role of the MOR system, mediating both types of rhythmic regulations, as well as behavioral traits.

neuroscience↗

bioRxiv2026

A patient-centric therapeutic paradigm uncouples prostate cancer suppression from systemic metabolic collapse

The clinical benefits of cancer therapies are often compromised by the tolerable adverse effects that impair systemic organismal health and may evolve into latent life threats. Here, we identified profound abiraterone-induced but androgen-independent metabolic perturbations in prostate cancer patients and developed Lifehug-9892 to balance tumor therapy with systemic metabolic homeostasis. By integrating population cohorts with high-resolution metabolomics, we demonstrate that abiraterone induces profound systemic lipidomic dysregulation, characterized by the massive, pathological accumulation of desmosterol. Abiraterone inhibits but stabilizes DHCR24, leading to a metabolic trap in patients showing elevated levels of both desmosterol and cholesterol. Desmosterol accumulation is highly lipotoxic, potently triggering endothelial cell senescence and necrosis, macrophage foam cell formation, murine atherosclerosis, and hepatic senescence. To mechanistically uncouple and therapeutically rescue this systemic metabolic collapse, Lifehug-9892 was rationally designed to selectively retain on-target CYP17A1 inhibition while completely sparing DHCR24 function. Lifehug-9892 maintains potent tumor-suppressive activity while fully preserving the desmosterol-cholesterol metabolic axis and preventing systemic cardiovascular and hepatic damage. Our study uncovers a critical mechanistic link between drug-induced metabolic dysregulation and organismal health in cancer patients, providing a biochemical framework for developing patient-centric targeted therapies that preserve host homeostasis.

cancer biology↗

bioRxiv2026

Normative modelling of cortical networks identifies subtypes of type 2 diabetes associated with distinct clinical and transcriptomic profiles

Type 2 diabetes (T2D) is characterized by substantial clinical heterogeneity, yet its neurobiological substrates remain unclear. Here, we leverage normative modelling of cortical morphometric networks to quantify individual-level brain deviations using structural MRI data from 3,723 participants (1,941 T2D patients and 1,782 healthy controls) across three independent cohorts. Data-driven clustering reveals two robust T2D biotypes characterized by widespread positive (biotype 1) and negative (biotype 2) brain deviations. Despite comparable overall metabolic burdens, these biotypes feature distinct brain-metabolic coupling patterns: biotype 1 is primarily associated with lipid metabolism, whereas biotype 2 reflects a multifactorial metabolic burden spanning glycaemic control, adiposity, lipid, vascular risks, and disease duration. These divergent brain vulnerability profiles have distinct cognitive consequences; notably, biotype 2 shows poorer performance in complex cognitive tasks, aligning with negatively deviated connectivity gradients along the sensorimotor-to-association axis. Spatial transcriptomic analyses further link biotype 2 deviations to gene expression patterns enriched in insulin signalling, mitochondrial functions, tight junctions, and neurodegenerative disease pathways, alongside specific involvement of inhibitory neurons and oligodendrocyte lineage cells. Our findings provide a neurobiological understanding of T2D heterogeneity and establish a data-driven framework for characterizing personalized brain vulnerability, with implications for advancing precision diabetes medicine.

neuroscience↗

bioRxiv2026

Proteoform Barcode: An Intuitive Visualization Framework for Top-Down Proteomics

Top-down proteomics (TDP) advances biomedical research by providing a birds-eye view of proteoforms in cells, tissues, and biofluids. Thousands of proteoforms can be characterized using well-established TDP technologies, and potential proteoform biomarkers of diseases have been discovered. However, there is a lack of an easy and biologically informative approach to present the quantitative global TDP data. Here, we present proteoform barcode as a straightforward visualization approach that simultaneously displays proteoform abundance and their associated Gene Ontology (GO) biological processes, converting a list of proteoforms to a biologically informative image. The proteoform barcode allows 1) a global view of proteoforms (i.e., relative abundance and functional information) in complex biological systems (i.e., bacteria, yeast, human cells, and human plasma) and 2) the accurate distinction of samples in diverse biological conditions (i.e., control and disease) assisted by machine learning approaches. The proteoform barcode, assisted by the random forest model, accurately separated the human plasma samples of healthy controls and early-stage breast cancer. The data demonstrates the high potential of the proteoform barcode-based approach for early diagnosis of diseases in an easy and biologically informative manner.

systems biology↗

bioRxiv2026

Seasonal photoperiod cycling reduces inter-individual variability in mu-opioid receptor density in rats

RationaleThe -opioid receptor (MOR) is widely expressed across tissues and plays crucial roles in pain and stress responses, social behaviour, and immune regulation. Recent evidence indicates seasonal variation in in vivo MOR signalling; for example, short photoperiods are associated with reduced central MOR availability, increased MOR expression in brown adipose tissue (BAT), and strengthened brain-BAT interactions. However, despite this coupling with photoperiod, it remains unclear whether static daylength and dynamically changing photoperiods exert distinct effects, as adaptation to photoperiod transitions may itself induce stress-related modulation of the MOR system. Elucidating how seasonal, stress-related adaptations influence MOR signalling is essential for advancing our understanding of seasonal fluctuations in mood and stress regulation. MethodsWe compared rats housed under seasonal photoperiod cycling with those maintained under constant photoperiod conditions, using ex vivo radioligand binding to directly assess MOR density in central and peripheral tissues. ResultsRats exposed to seasonal photoperiod cycling showed markedly reduced inter-individual variability in MOR density in both the brain (including the cerebellum and striatum) and peripheral tissues (adrenal glands), whereas no tissues exhibited substantially increased variability. ConclusionsThese findings demonstrate that seasonal photoperiod cycling stabilizes MOR dynamics at the population level, suggesting stress-related synchronization of MOR signalling. The findings deepen our understanding of seasonal effects on endogenous MOR signalling, and further underscore the role of seasonal light variation in modulating mood-related processes.

neuroscience↗