Search bioRxiv⌕ Search

Biology subjects

Hu, M.

Publications and source records attributed to Hu, M..

At least 55 records · Page 3Linked to original sources

Accurate and robust 3D genome feature discovery from multiplexed DNA FISH

Multiplexed DNA FISH (also known as FISH Omics) is a powerful imaging technology to map three-dimensional (3D) genome organization in thousands of single cells at kilobase resolution. However, existing computational approaches to identify 3D genome features, such as A/B compartments, topologically associating domains (TADs) and chromatin loops, have been mainly adapted from Hi-C and do not account for the distinct measurement errors across the three XYZ physical axes. Here we present ArcFISH (accurate and robust chromatin analysis from FISH data), which explicitly models axis-specific measurement errors in a unified statistical framework to detect multi-level 3D genome features. Comprehensive evaluations using multiple simulated as well as experimental datasets show that ArcFISH reliably identifies chromatin loops under heterogeneous measurement errors, detects TAD boundaries highly enriched for active histone marks H3K4me3 and H3K36me3, and requires as few as 30 chromatin traces to faithfully assign A/B compartments. Applying ArcFISH to multiplexed DNA FISH data from mouse embryonic stem cells and mouse excitatory neurons reveals cell-type-specific chromatin loops and TADs, overlapping with differentially expressed genes. ArcFISH is freely available at https://hyuyu104.github.io/ArcFISH.

genomics↗

Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation

Female mammals are born with a finite pool of non-growing oocytes (NGOs) housed in primordial follicles, which form the ovarian reserve that determines reproductive lifespan. Mechanisms underlying the reserves long-term maintenance and subsequent follicular activation remain elusive. Using total RNA sequencing and de novo transcriptome assembly, we first captured the comprehensive oocyte transcriptome across perinatal oogenesis in mice. We show that NGOs establish accessible chromatin at gene regulatory elements--including promoters and enhancers--partly driven by newly evolved endogenous retroviruses (ERVs). In NGOs, epigenetic priming for follicular activation involves prior loading of transcription factors TCF3 and TCF12 and non-phosphorylated form of RNA polymerase II at these sites. This primed state is counteracted by repression via Polycomb Repressive Complex 1-mediated H2AK119 ubiquitylation. We propose that ERV-mediated epigenetic priming underlies the ovarian reserves long-term maintenance and establishes a transcriptionally competent yet repressive configuration that enables rapid gene activation upon oocyte growth.

developmental biology↗

Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

Programmable control of gene expression in specific cell types is essential for both basic discovery and therapeutic intervention, yet current strategies lack scalability across diverse cellular contexts. Here, we introduce SPICE (Splicing Proportions In Cell types), an integrated experimental and computational framework that harnesses alternative RNA splicing as a programmable modality for cell type-specific gene regulation. To power SPICE, we constructed a massively parallel reporter assay (MPRA) comprising 46,372 human-derived sequences and profiled exon skipping across 43 cell lines spanning 10 lineages, uncovering widespread cell type-specific exon skipping. Using this data, we trained deep learning models that both predict splicing in unseen contexts and generate synthetic sequences with programmed, cell type-specific splicing patterns. Leveraging these models, we further engineered sequences that selectively splice in cells harboring oncogenic splicing factor mutations, demonstrating translational potential. SPICE provides a generalizable strategy for dissecting splicing regulation and engineering alternative splicing as a gene expression regulatory layer for research and therapeutic applications. One Sentence SummaryWe introduce SPICE, an integrated framework that couples large-scale splicing assays with generative design to uncover regulatory principles and design programmable, cell-specific gene expression for research and therapeutic applications.

molecular biology↗

The O-glycosyltransferase SECRET AGENT Participates in Abscisic Acid-Induced Microtubule Remodeling and Stomatal Closure in Arabidopsis thaliana

Secret Agent (SEC) encodes the major O-GlcNAc transferase in Arabidopsis thaliana and has been implicated in stress and signaling pathways, but its role in stomatal regulation remains unknown. In this study, we investigated the function of SEC in abscisic acid (ABA)-induced stomatal closure and drought responses. Loss of SEC function in the sec-5 mutant delayed stomatal closure and increased water loss under drought, whereas SEC overexpression enhanced stomatal responsiveness and drought tolerance. Pharmacological assays revealed that sec-5 was less sensitive to microtubule-stabilizing and -disrupting drugs during ABA-induced stomatal closing, consistent with a defect in cytoskeletal dynamics. Confocal imaging and quantitative analysis of microtubule rearrangements showed that SEC loss-of-function mutation retarded microtubule reorganization in response to ABA, with abnormal microtubule bundling and density. Mechanistically, SEC physically interacted with -tubulin 4 (TUA4) in both yeast two-hybrid and bimolecular fluorescence complementation assays, suggesting tubulin as a potential substrate of SEC-modified O-GlcNAcylation. Together, these findings establish SEC as a key regulator of ABA-induced microtubule remodeling in guard cells, thereby linking O-GlcNAcylation to stomatal regulation and drought tolerance.

plant biology↗

Decoding the Oral Microbiome: Metagenomic Insights into Host Metabolic Health

The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole-metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual-energy X-ray absorptiometry (DXA). Using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide -oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20,293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.

microbiology↗

Ethylene receptors are functionally conserved in calcium permeability across the green lineage

The gaseous hormone ethylene plays a key role in regulating plant growth and stress responses. Although Ca{superscript 2} has long been implicated in ethylene signaling, the identity of molecules controlling Ca{superscript 2} permeability involved has remained elusive. Here we show that Arabidopsis ethylene receptors ETR1 and ERS1 are Ca2+ permeable, and that ETR1 mediates ethylene-induced cytosolic Ca2+ increase and regulates hypocotyl elongation. Homologs of ETR1 from eight land plant and algal species also exhibit Ca{superscript 2} permeability, suggesting an evolutionarily conserved function. We further demonstrate ethylene enhances the Ca2+ permeability of ETR1 and its homologue from the charophyte Klebsormidium flaccidum. These findings uncover a previously unrecognized but conserved role of ethylene receptors in Ca{superscript 2} permeability regulation in the green lineage, with broad implications for Ca{superscript 2} signaling in plant development and environmental adaptation.

plant biology↗

HLA-DQ2/8 genotype imprints strain-level gut microbiome and constrains pantothenate availability in healthy adults

HLA-DQ2/8 haplotypes are established genetic risk factors for autoimmune diseases and are known to influence gut microbiota assembly in early life. However, their impact on the adult microbiome and functional consequences for host physiology remain unclear. Here, we performed a genotype-stratified multi-omics analysis of 60 healthy adults, including 28 HLA-DQ2/8 carriers and 32 non-carriers. We found that host HLA-DQ2/8 genotype was significantly associated with gut microbiome composition, with an effect size exceeding that of sex and BMI. HLA-DQ2/8 carriers exhibited higher gut microbial alpha-diversity, lower virulence factor abundance, and a distinct species profile enriched in butyrate-producing taxa. We identified pervasive intra-species phylogenetic and functional divergence linked to the DQ2/8 genotype. This diversification reflects predicted HLA-restricted microbial peptide-binding specificities, suggesting a possible role for antigen presentation-mediated immune selection, a mechanism further supported by AlphaFold3 structural modeling. We found an enrichment of microbial pathways for pantothenate and coenzyme A (CoA) biosynthesis in carriers, primarily driven by functionally divergent Blautia obeum strains. This functional shift paralleled lower levels of serum pantothenate and HDL-cholesterol in the host. Our findings suggest a potential genotype-microbiome-host axis where antigen presentation-mediated immune selection may modulate microbial adaptation, with possible implications for the host availability of essential cofactor precursors and lipid metabolism.

microbiology↗

Engineering magnetically guided bacteriophages for precision antimicrobial therapy and targeted biofilm eradication

Viruses, including bacteriophages, rely on passive diffusion to reach their hosts, limiting the efficacy of virus-based therapies and leading to off-target accumulation with systemic effects. Here, we present a strategy to confer controllable motility to bacteriophages by incorporating iron nanoparticles (FeNPs) into their head structures while preserving infectivity. Cryo-electron microscopy (Cryo-EM) and transmission electron microscopy-energy dispersive spectroscopy (TEM-EDS) confirmed the FeNP presence in the phages head. FeNP-tagged phages can be magnetically enriched and isolated from bacterial prey cultures, eliminating the need for ultracentrifugation. Under magnetic guidance, these engineered phages exhibit rapid and directed movement through complex microenvironments, including mazes and polymer barriers, enabling precise bacterial targeting and biofilm eradication in a microfluidic system. In an in vivo wound infection model, magnetically guided phages successfully navigated from the peritoneum to the biofilms on the wound, thus selectively eliminating biofilms while minimizing systemic exposure to other organs. Hence, our approach confers viral mobility, thus enhancing the precision and efficacy of bacteriophage-based biotechnological and therapeutic applications.

microbiology↗

Absolute hand determination of glycofibrils from natural sources in cryo-EM

Glycans are one of the four fundamental macromolecules that constitute life. However, compared with proteins and nucleic acids, our understanding of the structures and functional mechanisms of glycans remains limited. Moreover, it is generally challenging to obtain high-resolution three-dimensional structures of glycans. Recent studies have demonstrated the potential of the CryoSeek strategy in enabling high-throughput structural determination of glycans, thereby presenting novel avenues for their structural investigation. Meanwhhile, unlike proteins, near atomic resolution density maps of glycofibrils do not inherently facilitate the determination of absolute hand, which is a prerequisite for building atomic models of glycofibrils. Existing absolute hand determination methods have severe limitations in the cases of glycofibrils from natural sources. In this study, we introduce Ahaha, a straightforward and efficient method for determining such absolute hand in cryo-EM. With their absolute hand measured by Ahaha, we built atomic models of four glycofibrils derived from a natural water sample, facilitating the study of glycans. The online service of Ahaha is available at https://cryoseek.org/ahaha.

biophysics↗

A Tonic Signaling Code Predicts CAR-T Cell Efficacy in Diffuse Midline Glioma

Diffuse midline glioma (DIPG/DMG) is a uniformly fatal pediatric brain tumor with no effective cure. Although CAR T-cell therapy shows promise, clinical outcomes remain inconsistent due to limited persistence and premature exhaustion. Reliable predictive biomarkers are lacking, and proposed exhaustion or stemness markers provide limited utility. Here, we systematically compare multiple CAR-T constructs targeting clinically-relevant antigen B7-H3 and identify antigen-independent CAR activation, or tonic signaling, as a key determinant of therapeutic performance. We find that B7-H3 CAR-T cells with restrained tonic signaling display superior tumor killing, persistence, and resistance to exhaustion, along with reduced CAR membrane clustering, in patient-derived DIPG models. Integrated multi-omics and single-cell profiling further reveal a CAR-T tonic signaling-associated gene signature that outperforms conventional exhaustion or stemness markers in predicting therapeutic efficacy across multiple clinical trials, including DIPG and other tumor types. Together, these findings define a mechanistic and predictive framework to guide CAR design and improve clinical outcomes.

cancer biology↗

Disrupted Regional Dynamics of Structure-Function Connectivity Coupling in Euthymic Bipolar Disorder

BackgroundBipolar disorder (BD) is characterized by persistent disturbances in emotional regulation and cognitive function, even during euthymia, yet its neural mechanisms remain unclear. Given evidence of structural and dynamic functional connectivity (dFC) abnormalities in BD, investigating dynamic structure-function connectivity coupling (SC-FC coupling) may provide insights into the pathophysiology of the disorder. MethodsDiffusion tensor imaging and resting-state fMRI data were collected from 61 euthymic BD-I patients and 54 healthy controls (HC). Structural connectivity was derived using probabilistic tractography, and dFC was estimated with a sliding-window approach. SC-FC coupling was quantified as the extent to which structural features predicted dFC using multivariate linear regression. Abnormal SC-FC coupling in BD was assessed at both the network and regional levels, relative to HC. Over time, SC-FC coupling was categorized into high- and low-coupling states, and dynamic state analyses of dwell time, occurrence rate, and transition probabilities were performed in the affected brain regions. ResultsNetwork-level analyses indicated that BD exhibits lower SC-FC coupling in subcortical regions compared with HC. Regional analyses revealed significantly reduced dynamic SC-FC coupling in two thalamic subregions (medial posterior and rostral temporal) and in the right primary somatosensory cortex in BD compared to HC. Dynamic analyses further demonstrated thalamic instability: BD showed shorter dwell times in high-coupling states, increased occurrence of low-coupling states, and more frequent high-to-low coupling transitions than HC. These abnormalities suggest that BD is characterized by disrupted structure-function integration and unstable thalamocortical dynamics. ConclusionOur findings reveal regional abnormalities in SC-FC coupling dynamics in BD, indicating persistent dysfunction of structure-function integration during euthymia. Dynamic coupling measures may provide preliminary insights into potential biomarkers for disease monitoring.

neuroscience↗

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families-- including the complete circadian toolkit--were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4{degrees}C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

evolutionary biology↗

The Rational Irrational: Better Learners Show Stronger Frequency Heuristics

Does favoring less valuable options that deliver more frequent rewards reflect flawed decision-making or an adaptive strategy under complex environments? Frequency effects, defined as a bias toward more frequently rewarded but less valuable options, have traditionally been viewed as maladaptive decision-making deficits. In the present study, we used a within-subject design in which participants completed a four-option reinforcement learning task twice, once under a baseline condition and once with a reward frequency manipulation, to test whether better baseline learning predicts greater or lesser susceptibility to frequency-based biases. Participants were first trained on two fixed option pairs and then transferred their knowledge to novel pairings in a testing phase. Across conditions, higher training accuracy generally predicted higher test accuracy, with one critical exception: on trials where a more valuable option was pitted against a more frequently rewarded but less valuable alternative, participants with higher training accuracy exhibited a stronger bias toward the more frequent option. Moreover, baseline optimal choice rates in these specific trials were unrelated to--and even slightly negatively correlated with--optimal choice rates under the frequency condition. Computational modeling further showed that participants with better baseline learning performance were better fit by frequency-sensitive models in the frequency condition and they weighed frequency-based processing more heavily than value-based processing. Overall, these findings suggest that frequency effects, rather than signaling flawed learning, manifest more strongly in individuals with better baseline learning performance. This seemingly irrational bias may, under conditions of uncertainty, reflect a flexible, adaptive strategy that emerges among the best learners when value-based approaches are costly or unreliable. Author SummaryIn daily life, people often face choices between familiar, frequently encountered options and unfamiliar alternatives that may be more valuable. For example, we may keep visiting a local restaurant we know well instead of trying a new one with better reviews. This tendency, known as the frequency effect, reflects a bias toward options that yield more frequent rewards, even when those rewards are smaller and suboptimal overall. Traditionally, such behavior has been interpreted as a sign of neuropsychological impairments or flawed learning, while our study found the opposite. We asked 495 participants to complete a reinforcement learning task under two conditions: one with balanced reward frequencies and another in which one option was rewarded more frequently despite being less valuable than its alternative. Surprisingly, we found that better learners in the balanced condition were more likely to show frequency effects when reward frequencies were manipulated and uneven. Computational modeling confirmed that these individuals shifted from value-based strategies to frequency-based ones when the environment made value-based decisions more difficult. These findings suggest that frequency effects are not simply errors. Instead, they may represent an adaptive shortcut that emerges more strongly in better decision-makers as a flexible strategy for navigating uncertain environments when value-based calculations are costly or unreliable

neuroscience↗

SPACE: spatially resolved multiomic analysis for high-throughput CRISPR screening in 3D models

Current spatial CRISPR screening technologies are limited by targeted readouts and high costs, restricting the scope of biological discovery. Here we present SPAtial Cell Exploration (SPACE), a spatial CRISPR screening platform that integrates whole-transcriptome profiling ([~]18,000 genes), multiplexed protein detection ([~]68 markers), and CRISPR perturbation mapping at subcellular resolution. SPACE significantly reduces whole-transcriptome profiling costs compared to sequencing methods while preserving spatial context. We demonstrate SPACE by screening 43 CRISPR knockouts (KOs) across [~]100,000 cells in hundreds of cancer-associated fibroblast (CAF)-tumor spheroids, obtaining whole-transcriptome and multiplexed protein readout from the same exact cells. SPACE revealed previously unknown regulatory mechanisms on tumor extracellular matrix (ECM) remodeling, and identified spatially-resolved ligand-receptor interactions and perturbation-specific spatial gene signatures that are not detectable with dissociation-based methods. This scalable, cost-effective platform provides a transformative framework for high-throughput spatial perturbation studies in complex tissue models.

cell biology↗

Site- and Structure-Specific Characterization of Glycoproteins of H11: Potent Vaccine Candidates against Parasitic Worm Haemonchus

Parasitic worms (helminths) infections pose significant threats to global health and livestock economies. While mass spectrometry (MS)-based glycomics have revealed that helminths express complex, immunomodulatory N-glycans, site- and structure-specific characterization of intact glycopeptides remain challenging. Here we employed advanced MS-based intact glycoproteomics to explore the N-glycosylation profile of H11 antigen - an important vaccine antigen from pathogenic parasite Haemonchus contortus. We successfully identified seven glycosylated aminopeptidases carrying 19 N-glycosylation sites with 31 distinct N-glycan structures. Notably, 13 N-glycopeptides were significantly enriched by H11-induced protective IgG antibodies. Our findings revealed a high degree of structural heterogeneity and abundant core fucosylation among the identified N-glycopeptides. Additionally, molecular docking studies demonstrated those IgG-recognized N-glycopeptides are situated on the protein surface or adjacent to the substrate-access channels, strongly indicating their potential as antigenic epitopes. Overall, our work represents the first comprehensive glycoproteome of an economically important parasitic worm. These results hold important implications for the rational design of vaccines against H. contortus and other related metazoan parasites.

pathology↗

The Establishment of Cell-Type Specific Gene Regulation in the Sea Urchin Embryo

Cell-fate commitment in metazoan development relies on precise gene regulatory programs. This study presents a comprehensive single-cell atlas of gene expression (scRNA-seq), nascent transcription (scSLAM-seq), and chromatin accessibility (scATAC-seq) in the purple sea urchin, Strongylocentrotus purpuratus, from early cleavage to pluteus larva stages. Our findings reveal a dynamic regulatory landscape with extensive usage of distal and intronic regulatory elements, which often exhibit cell-type-specific motifs and accessibility profiles that closely track gene expression. We identify a major wave of zygotic genome activation (ZGA) at the 128-cell stage, coinciding with the loss of developmental plasticity, alongside evidence of restricted, lineage-specific gene activation preceding widespread ZGA. Motif analysis highlights distinct regulatory grammars for these early accessible regions. Regulatory element usage largely clusters by germ layer, indicating shared accessibility among related cell types. We delve into the regulatory intricacies of neurons and skeletogenic cells. Sea urchin neurodevelopment proceeds through three distinct lineages, utilizing transcription factors with conserved roles in mammalian neurogenesis. Surprisingly, skeletogenic cells show significant transcriptional and regulatory diversity across their subpopulations, and we identify novel genes associated with calcification. This research offers unprecedented insights into the dynamic regulatory genome of a non-chordate deuterostome, highlighting both conserved principles of gene regulation and unique features that underscore the sea urchins importance as a model for understanding developmental and evolutionary genomics in ecologically critical marine species.

developmental biology↗

DALE-Eval: A comprehensive cell type-specific expression deconvolution benchmark for transcriptomics data

Deconvolution of bulk transcriptomic data unlocks rich, cell type-specific insights from complex tissue samples. While cell type fraction deconvolution has been extensively developed and bench-marked, the next frontier--cell type-specific expression (CTSE) deconvolution--remains largely underexplored. Here, we introduce DALE-Eval, a comprehensive benchmark of CTSE methods, featuring novel evaluation metrics, identification of key drivers of performance, and practical recommendations for maximizing the value of CTSE in downstream applications.

bioinformatics↗

The SMARCA5-DMRT1 Pioneer Complex Establishes Epigenetic Priming to Direct Male Germline Development

The establishment of cell type-specific chromatin landscapes is essential for cellular identity, but how these landscapes are generated remains poorly understood. Here, we demonstrate that the chromatin remodeler SMARCA5 establishes epigenetic priming that is required for retinoic acid (RA)-induced differentiation in the male germline. Germ cell-specific deletion of Smarca5 results in a complete loss of differentiating spermatogonia, phenocopying vitamin A-deficient mice that lack RA signaling. During the perinatal transition from prospermatogonia to undifferentiated spermatogonia, SMARCA5 is recruited to binding sites of the pioneer transcription factor DMRT1, which are located at distal putative enhancers and promoters of germline genes. The SMARCA5-DMRT1 pioneer complex establishes chromatin accessibility at these loci, generating poised enhancers and promoters that serve as RA receptor (RAR)-binding sites. Thus, SMARCA5 licenses transcriptional responses to RA that enable spermatogenic differentiation. Our findings uncover a mechanism linking pioneer factor activity to external signal responsiveness. HighlightsSMARCA5 is required for spermatogonial differentiation The SMARCA5-DMRT1 pioneer complex establishes epigenetic priming for differentiation SMARCA5 remodels inaccessible DMRT1-binding sites to an accessible state SMARCA5 shapes chromatin states that enable retinoic acid responsiveness

developmental biology↗