Biology subjects

Dai, Y.

Publications and source records attributed to Dai, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Multimodal spatial transcriptomics determines repeat expansion, huntingtin aggregation, and selective cortical neuron loss in Huntington Disease

Huntingtons disease (HD) is caused by CAG expansion in HTT, yet how somatic repeat instability and huntingtin aggregation relate to selective cell loss in the human brain remains unclear. We have developed a multimodal spatial transcriptomics approach that enables defining transcriptional programs with subcellular resolution, somatic CAG repeat lengths, and six other pathology marks including huntingtin aggregates in every cell of intact brain sections. Imaging 428,173 cells in HD cortex revealed selective vulnerability: L5-6 NP and L6b deep-layer excitatory neurons undergo >50% loss, closely linked to very large (>380{+/-}55) somatic expansions. Intranuclear aggregation was most prevalent at intermediate somatic repeat expansion (220-300 CAGs) and was accompanied by broader transcriptional changes. In contrast, chandelier and somatostatin+ inhibitory interneurons are lost despite only modest repeat expansion or aggregation. These data provide a comprehensive resource and establish a broadly applicable framework for connecting repeat expansion and protein pathology across diverse cell types. Short Bullet pointsO_LIDevelopment of a novel, multimodal spatial transcriptomics platform enables definition of RNA transcriptomes with subcellular resolution, somatic repeat expansions, and protein accumulation in cells within tissue sections C_LIO_LIGeneration of two complementary datasets for HD and control cortex: 428,173 cells to quantify comprehensively cell-type vulnerability, and a deeper multimodal dataset in which CAG repeat expansion, huntingtin aggregation, six additional pathological readouts, and expression of 1,128 genes were measured in 185,721 cells, providing a comprehensive resource for the neurodegeneration community. C_LIO_LIDeep layer excitatory neuron loss (L5-6 NP and L6b) was associated with very large somatic CAG expansions (>380{+/-}55), while selective inhibitory neuron loss (chandelier and somatostatin interneurons) occurred with modest CAG repeat expansion or huntingtin intranuclear aggregation C_LIO_LIIntranuclear aggregation, not somatic repeat expansion, was more predictive of transcriptional changes, including chromatin remodeling and RNA export factors C_LI

neuroscience↗

bioRxiv2025

From genomic decay to functional advantage: Trait-based evidence for long-term host residency of a next-generation coral probiotic

A key bottleneck in microbiome engineering is ensuring the long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of the population MC10, identified by such signatures, has shown persistent colonization in corals in a companion study. Whether this persistence translates into a measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the coral model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both sympatric control strains. To understand the mechanistic basis of this probiotic efficacy, we characterized the functional profile of MC10 using an integrated multi-omics approach. The genome of MC10 is enriched in genes associated with host-interaction, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, which were phenotypically confirmed by detectable iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated motility-to-sessility proteomic reprogramming, downregulating flagellar motor components while upregulating flagellin and biofilm regulators. This response was distinct from its sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4s functional profile, particularly its sensitivity to oxidative stress, contrasts with the traits typically favored in conventional probiotic screens. Our results move beyond the descriptive identification of a coral probiotic by providing initial mechanistic insight into traits associated with long-term host association and improved thermal performance. These findings validate an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities, informing the rational design of durable probiotics.

microbiology↗

bioRxiv2025

A programmable mRNA platform for miRNA detection via miRNA-mRNA2 triplex-mediated ribosomal frameshifting

Programmed -1 ribosomal frameshifting (-1 PRF) is a recoding mechanism utilized by viruses to expand their coding capacity and modulate the stoichiometric ratio of -1 frame and 0 frame translation products. The stability of mRNA secondary structure at the ribosomal entry site within the frameshifting stimulating elements (FSEs) determines the frameshifting efficiency. Here, we report the development of a programmable mRNA-based platform that detects specific mature microRNA (miRNA or miR) by converting their presence into a quantifiable protein output through miRNA-triggered -1 PRF. We designed a triplex-forming mRNA (TF-mRNA) platform to selectively trap target miRNAs through the formation of major-groove mRNA-miRNA-mRNA (miR-mRNA2) triplexes. Bio-layer interferometry and fluorescence binding studies confirmed that TF-mRNA forms stable complexes with cognate miRNAs with low nanomolar affinity and prolonged dissociation rate. Critically, the formation of miR-mRNA2 triplex robustly stimulated ribosomal frameshifting in a cell-free dual-luciferase translation system, acting as a miRNA-dependent molecular switch. The generality of this TF-mRNA platform has been verified for several disease-associated purine-rich miRNAs, and it is suitable for targeting a wide range of other purine-enriched miRNAs. This programmable TF-mRNA platform establishes a foundation for developing novel diagnostic tools and synthetic biology circuits that convert the presence of miRNA into a quantifiable protein output. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/690164v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1d6d9f7org.highwire.dtl.DTLVardef@8008e6org.highwire.dtl.DTLVardef@1c8344borg.highwire.dtl.DTLVardef@e153ec_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

A Chromatin-Structure-Guided Framework for Predictive and Interpretable Regulatory Genomics

Chromatin organization shapes gene regulation by linking distal elements across megabase scales, yet most predictive genomics models still treat the genome as linear, without incorporating three-dimensional structure. Hi-C provides genome-wide chromatin conformation information, but its contact maps are population-averaged, distance-biased, and noisy, obscuring the biologically specific contacts. We present CHROME, a framework built on a self-avoiding polymer ensemble null model that identifies physically specific, non-random Hi-C contacts. By integrating these contacts into graph representations, CHROME enables efficient information transfer across spatially connected loci. It integrates sequence, chromatin accessibility, or pre-trained embeddings into a graph attention architecture to predict cell line-specific ChIP-seq profiles, consistently outperforming local encoder baselines and generalizing to an unseen cell line. The resulting graph embeddings also enhance prediction on tissue-specific eQTL and ClinVar variant pathogenicity, outperforming local sequence-based embeddings. Beyond predictive performance, CHROME provides interpretability through attention-derived neighbor-to-center contributions that reveal how spatially connected loci influence local regulatory activity over multi-megabase distances. Together, these results show that incorporating physically validated chromatin interactions enables more accurate and interpretable modeling of gene regulation and variant effects.

genomics↗

bioRxiv2025

Zwitterionic hydrogel designs for conducting polymers enable bioelectronics with suppressed foreign body response

For long-term, continuous operation of implantable biosensors and electrophysiological devices, the foreign body response (FBR) is a major obstacle that needs to be overcome. As the FBR progresses, any implanted device will become damaged and isolated from its physiological environment, due to encapsulation by fibrotic tissue and inflammatory immune cells. To achieve more compatible and low-impedance biointerfaces, conducting polymers, such as PEDOT:PSS, have been extensively explored as ideal materials. However, FBR on such conducting polymers remains an unmet challenge. We report a zwitteronic-hydrogel-based double-network design for PEDOT:PSS that can significantly suppress the FBR by 64%, in addition to improving conductivity by more than one order of magnitude. Surprisingly, the FBR level of this design is even lower than that of the parent zwitteronic hydrogel by 53%. Our further immunological investigations at the histological, cellular, and transcriptomic levels give deeper insights into the unique effects that come from the chemical heterogeneity. Furthermore, chronic electrocardiographic recording in mice demonstrate the benefit of this material design to long-term, implanted electrophysiology, which provides indications for the future development of immunocompatible electronic polymers.

bioengineering↗

bioRxiv2025

Ventral striatal astrocytes contribute to reinforcement learning

Astrocytes influence synaptic plasticity and neuronal function through astrocytic calcium dynamics (ACD). However, astrocytes contribution to cognitive operations like reinforcement learning (RL) remains unclear. To examine this, we trained mice on a RL dependent probabilistic decision-making task. We attenuated ACD across distinct striatal regions, and found ACD attenuation specifically in ventral striatum (VS) increased decision noisiness and impaired reward-guided choice performance. This effect was largely due to a reduction in "win-stay" behavior. Using in-vivo calcium imaging, we found that VS ACD correlated with reward prediction errors (RPEs). Furthermore, these trial-by-trial ACD fluctuations predicted trial-by-trial choice variability. In-silico lesions of a biologically constrained circuit model suggest that astrocytes could regulate behavioral variability by sharing RPE signals across populations of striatal neurons. Together, these results suggest that VS astrocytes contribute to cortico-striatal functions to mediate decision noisiness.

neuroscience↗

bioRxiv2025

Asymmetry in hydrophobicity induces electric potential in non-charged protein condensates

The capacity of biomolecular condensates to establish and modulate electrochemical equilibria is emerging as an important functioning mechanism in cellular biochemistry. However, the physical chemistry basis of the electric potentials arising from biomacromolecular phase transitions remains unclear. Here, we show that asymmetry in hydrophobicity, which is a generalizable feature in condensate system, can directly encode an electric potential gradient between the dilute and the dense phases. We demonstrate that using a non-charged intrinsically disordered protein, ion-dependent kosmotropic effect can encode measurable pH and interphase potential gradients into condensate. All-atom molecular dynamics simulations further reveal that the distinct intrinsic transfer free energy of ions defines the ion partitioning capability of condensates via favorable interactions with protein backbones. The simulation also shows the existence of both interfacial and interphase electric potentials. These built-in potentials modulate the partitioning and reactivity of charged solutes, enabling non-enzymatic, potential-dependent chemistry within condensates. Our findings identify hydrophobic asymmetry as a simple and generalizable mechanism for charging biological matter, linking water activity and ion energetics to the emergent electrochemistry of condensates.

biophysics↗

bioRxiv2025

Mapping the Subtype-Specific PARP1 ADP-ribosylated Proteome in Breast Cancer Cells

Breast cancers are molecularly heterogeneous, with subtype-specific differences in transcriptional programs, chromatin architecture, and therapeutic responses. While PARP1 has been extensively studied in the context of DNA repair, emerging evidence implicates its catalytic activity in a broader set of cellular processes, including the regulation of gene expression. Here, we employed an NAD analog-sensitive PARP1 (asPARP1) chemical genetics approach combined with mass spectrometry to map the ADP-ribosylated proteome across six human breast cancer cell lines representing luminal and basal/triple negative subtypes. We identified thousands of PARP1 substrates and hundreds of Glu/Asp ADPRylation sites, revealing both shared and subtype-specific modifications in cell lines maintained under basal growth conditions. Luminal-specific substrates were enriched in chromatin and transcriptional regulators, whereas basal-specific substrates were preferentially linked to translation and RNA processing, highlighting lineage-dependent PARP1 activity. Transcription factors emerged as major substrates, with TFAP2A serving as a proof-of-concept; it is selectively ADPRylated in luminal cells and inhibition of PARP1-mediated ADPRylation modulates its promoter occupancy in a subtype-specific manner. Our data provide a new resource for studying subtype-specific PARP1-mediated ADPRylation in breast cancer cells. Collectively, our findings expand the conceptual framework for PARP1 function beyond DNA repair, offering mechanistic insights into subtype-specific gene regulation and potential determinants of PARP inhibitor sensitivity in breast cancer.

cancer biology↗

bioRxiv2025

Towards the Development of Isoenergetic Peptide Nucleic Acid Based Probes Targeting Double-Stranded RNAs Through Enhancing Sequence-Specific Stacking Interactions

Peptide nucleic acid (PNA), a synthetic nucleic acid analog, exhibits substantial potential in biotechnology and therapeutic applications due to its high binding affinity and nuclease/protease resistance. Chemically modified PNAs capable of forming stable triplex structures with double-stranded RNAs (dsRNAs) under near-physiological conditions further expand their utility by enabling sequence-specific precise targeting and probing of functional RNA structural motifs. However, the presence of inverted Watson-Crick pairs (C-G and U-A) may significantly weaken the triplex formation of the dsRNA-binding PNAs (dbPNAs). Our previous work demonstrated that dbPNA P3 (composed of L, T, and Q monomers for the recognition of G-C, A-U, and C-G base pairs, respectively) can stimulate ribosomal frameshifting by binding to rHP2, a model RNA hairpin structure in an mRNA, albeit with suboptimal efficiency, due to its significantly weakened Q*C-G triple formation. We hypothesize that incorporating s2U adjacent to Q may offer unique stacking and hydrogen bonding interactions facilitating the development of isoenergetic dbPNA-based probes binding toward dsRNAs with varied sequences. In this study, we investigate how incorporating s2U adjacent to Q residues in P3 influences its binding to rHP2. Bio-layer interferometry (BLI) and non-denaturing polyacrylamide gel electrophoresis (PAGE) analyses demonstrate that substituting T with s2U at the N-terminal position adjacent to Q (P3-2QT) enhances binding affinity by [~]10-fold compared to unmodified P3, whereas C-terminal substitution (P3-TQ2) yields only a 2-fold improvement. Consistent with these findings, a cell-free dual-luciferase reporter assay reveals that P3-2QT significantly increases ribosomal frameshifting efficiency compared to P3 and P3-TQ2. Molecular dynamics simulations further indicate that P3-2QT maintains enhanced PNA-PNA stacking stability, particularly between s2U3 and Q4, suggesting a structural basis for its superior activity. Intriguingly, analogous s2U substitution in the P5 oligomer with the Q replaced by L does not confer a comparable enhancement in binding to the target RNA (rHP1) and frameshifting stimulation, highlighting the context-dependent nature of this modification. To assess the broader applicability of the s2U-Q motif, we examined its effect in dbPNAs targeting the RNA panhandle structure of influenza virus A and precursor microRNA-21, respectively. Both PAGE and BLI data confirm that s2U incorporation improves binding affinity, reinforcing the generality of this strategy. These findings underscore the potential of sequence-dependent uracil thiolation in optimizing triplex-forming dsRNA-binding PNAs, warranting further exploration of modified nucleobase designs to enhance their binding and functional properties. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/662161v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@15d86aborg.highwire.dtl.DTLVardef@1347369org.highwire.dtl.DTLVardef@852040org.highwire.dtl.DTLVardef@84b0a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThiolation of uracil upstream of Q base in PNA markedly enhances triplex binding affinity and enables isoenergetic and orthogonal targeting/activation. C_LIO_LIN-terminal s2U modification adjacent to Q residues increases PNA-dsRNA binding by [~]10-fold and significantly boosts ribosomal frameshifting efficiency. C_LIO_LIBiophysical assays and molecular dynamics simulations reveal that thiolation improves PNA stacking stability and slows dissociation, thereby enhancing functional activity toward structured RNA targets. C_LIO_LIThe general applicability of s2U modification is demonstrated with influenza A virus RNA panhandle structure and precursor micoRNA-21 targets, underscoring its broad potential for optimizing PNA-based therapeutics and biotechnological tools. C_LI

biochemistry↗

bioRxiv2025

Self-inactivating AAV-CRISPR at different ages enables sustained amelioration of Huntington's disease deficits in BAC226Q mice

Huntingtons disease (HD) is a monogenic autosomal dominant neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene, yielding a gain-of-toxic-function mutant Huntingtin protein mHTT. CRISPR/Cas9 is a potentially powerful therapeutic tool for treating HD by eliminating mutant HTT (mHTT) gene. We developed a specific SaCas9 guide RNA to target human mHTT, and a self-inactivating gene editing system that abolishes SaCas9 after a short transient expression for high gene editing efficiency and maximal safety to prevent off-target effects. Both conventional and the new self-inactivating gene editing systems achieved successful elimination of mHTT gene, 60-90% mHTT protein and 90% of mHTT aggregation in BAC226Q HD mouse brains, which resulted in significant long-term rescue of neural pathology, motor deficits, weight loss and shortened lifespan. These beneficial effects were observed when gene editing was applied before, at and well after the on-set of pathological and behavioral abnormalities. These proof-of-concept data demonstrate that gene editing can be a highly effective therapeutic approach for HD and other inherited neurodegenerative diseases. One Sentence SummarySelf-inactivating CRISPR for mutant huntingtin in HD mice achieved long-term rescue of neural pathology, motor deficits, weight loss and survival.

neuroscience↗

bioRxiv2025

Regulatory elements of pancreas development license the initiation of pancreatic ductal adenocarcinoma

Cellular plasticity and transitional cellular states are crucial for tissue regeneration across multiple organs. In the pancreas, oncogenic Kras hijacks this program, acting on tissue-specific enhancers to prevent the resolution of acinar-to-ductal metaplasia (ADM) and lock regeneration into a pro-inflammatory state that progresses to cancer. Enhancer transcription, an early event during cellular state transitions, can generate stable enhancer-associated long noncoding RNAs (lncRNAs) positioned near key transcription factors and chromatin contact boundaries, often enriched for disease-associated variants. While enhancer-associated lncRNAs have been implicated in transcriptional regulation and genome organization, their role in pancreas regeneration and cancer initiation has remained unexplored. In this study, we investigated the expression of epithelial long noncoding RNAs (lncRNAs) and their target genes in PDAC precursor lesion formation. We focus on lncRNAs transcribed from enhancer elements near cell identity transcription factors. We demonstrate that LINC00673, expressed from a Sox9-associated super-enhancer during pancreatic development, is reactivated in PDAC. Conditional deletion of LINC00673 in the murine pancreatic epithelium accelerates resolution of ADM and significantly impairs PDAC initiation. Notably, LINC00673 harbors a variant associated with risk of developing PDAC. Our study identifies a critical function of LINC00673 in regulating both cell-autonomous and non-cell-autonomous processes during pancreas regeneration and Kras-driven cancer initiation. Furthermore, we highlight a previously unrecognized role of transcribed super-enhancers in facilitating long-range gene regulation during pancreatic cancer initiation. These findings reveal a novel regulatory layer linking developmental enhancer activity, cellular plasticity and pancreatic disease progression. TeaserLong noncoding RNAs from developmental enhancers play a role in long-range gene regulation with crucial biological impacts in development and cancer. Grant supportThis project has been supported by the Danish Cancer Society (R302-A17481). LA is supported by core funding of the Biotech Research and Innovation Center, the Danish Cancer Society (R302-A17481, R322-A17.350), The Novo Nordisk Foundation (NNF21OC0070884) and The Innovation Fund (Eurostars 2807). The Novo Nordisk Foundation Center for Stem Cell Biology was supported by Novo Nordisk Foundation grants NNF17CC0027852.

cell biology↗

bioRxiv2025

Multiple-omics analyses of the Alviniconcha holobiont reveal multi-faceted adaptations to deep-sea hydrothermal vents

Deep-sea hydrothermal vents are extreme environments with constantly fluctuating physicochemical conditions - but dense animal aggregations thrive primarily through symbiosis with chemoautotrophic bacteria to exploit the unusual chemistry. Alviniconcha snails, which harbor symbionts in their enlarged gill at an intracellular-extracellular intermediate state, are a prime example. Here, we present chromosome-level genomes of two Alviniconcha species (A. adamantis and A. marisindica) to investigate the adaptations of this holobiont. Significant expansion of solute carrier families enhances nutrient transport between the two parties. Alviniconcha lacks complete methionine biosynthesis pathways, compensated by symbiont provisioning, highlighting host-symbiont metabolic complementarity. High myoglobin expression in gills, contradicting prior reports of hemoglobin, suggests myoglobin-mediated oxygen storage to mitigate fluctuating environmental oxygen. Spatial transcriptomics further delineated gills functional zones on the gill filament responsible for symbiont digestion via phagocytosis in bacteriocytes, oxygen transport in secretory zones, and ciliary water flow regulation. Our findings elucidate molecular and physiological adaptations underpinning the Alviniconcha holobionts success in dynamic and treacherous vent ecosystems.

microbiology↗

bioRxiv2025

Habenula alterations in resting state functional connectivity among autistic individuals

BackgroundThe reward-based theoretical framework of autism suggests that altered reward circuitry contributes to core symptoms. Recent prior research has revealed autism-related structural alterations in the habenula, a small epithalamic structure associated with motivation and emotion; however, potential alterations in functional connectivity (FC) remain unexplored. MethodsAnatomical and resting state functional magnetic resonance imaging (rs-fMRI) data were accessed for 1,479 participants (N=661 autism; agem: 16.68{+/-}8.23 years) in the Autism Brain Imaging Data Exchange (ABIDE). To investigate habenula alterations, we conducted a whole-brain resting state FC analysis using manually delineated subject-specific seeds, followed by regression analyses to explore age and brain-behavior interactions. ResultsAcross the entire sample, extensive habenula connectivity was observed within the midbrain dopaminergic reward system. Compared to neurotypical (NT) controls, autistic participants exhibited significantly increased habenular connectivity with the bilateral middle and superior temporal gyri. From childhood to early adulthood, autistic adolescents displayed an accelerated developmental habenula FC trajectory than NTs with the cingulate gyrus. Between groups, habenula hyperconnectivity was inversely associated with behavioral scores for social motivation and communication. ConclusionsThis study provides novel evidence of habenula connectivity alterations in autism, highlighting atypical FC with sensory processing regions. Further findings suggest that habenula circuitry develops differently among autistic adolescents, with links between habenula hyperconnectivity and social behaviors. Taken together, these results contribute to emerging evidence that the dopaminergic reward system may play a critical role in the pathophysiology of autism.

neuroscience↗

bioRxiv2025

Phenotypic and Functional Characterization of Oncohistone Mutations in Breast Cancers

Although mutations in genes encoding histones display a similar prevalence to that of some other somatic mutations in cancer, the underlying mechanisms by which histone mutations drive tumorigenesis have not been fully explored. Herein, we curated missense mutations occurring in core histone genes in breast cancers using data from MSK-IMPACT and cBioPortal to identify high frequency breast cancer-associated histone gene mutations. We characterized 17 high frequency oncohistone mutations in H2A H2B, and H3 that are enriched in breast cancer samples and occurred at glutamate (E), aspartate (D), serine (S), and arginine (R) residues. Many of these mutants co-occur with PIK3CA mutations in breast cancer samples. The oncohistone mutants were expressed in MCF-7 breast cancer cells or MCF-10A mammary epithelial cells and screened for effects on oncogenic phenotypes in a variety of cell- and tumor-based assays (i.e., proliferation, migration, invasion, competitive outgrowth, transformation). In addition, we examined the effects of selected mutants on DNA damage and gene expression. Our results indicate that the collection of oncohistone mutants that we screened have varying phenotypic and functional effects. Some can promote cancer-related phenotypes, with H2B-E76Q, H3-E97K, and H3-E105K eliciting strong oncogenic phenotypes and alterations in gene expression. All three of these mutants showed cooperativity with an activating mutation in PIK3CA (E545K), or a chemical activator of PI3K (UCL-TRO-1938), in assays of MCF-10A proliferation. H3-E105K also strongly promoted transformation of MCF-10A cells in an assay of growth on low attachment substrate independently of PIK3CA. Our results indicate that some high frequency oncohistone mutants can have oncogenic activity in breast cancers, and may act as potential cancer drivers. Collectively, these observations presented here can be used as a resource to connect biological and molecular outcomes to oncohistones in breast cancers. SignificanceIn this study, we identified and characterized 17 high frequency oncohistone mutations in H2A H2B, and H3 that are enriched in breast cancer samples and promote cancer-related phenotypes when expressed in cells. Many of these oncohistone mutations co-occur in breast cancer samples with mutations in PIK3CA, the most frequently mutated gene in breast cancer, and may act as potential cancer drivers.

cancer biology↗

bioRxiv2025

scRegulate: Single-Cell Regulatory-Embedded Variational Inference of Transcription Factor Activity from Gene Expression

MotivationAccurately inferring transcription factor (TF) activity from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in computational biology. While existing methods rely on statistical models, motif enrichment, or prior-based inference, they often depend on deterministic assumptions about regulatory relationships and rely on static regulatory databases. Few approaches effectively integrate prior biological knowledge with data-driven inference to capture novel, dynamic, and context-specific regulatory interactions. ResultsTo address these limitations, we develop scRegulate, a generative deep learning framework leveraging variational inference to estimate TF activities guided by experimental TF-target gene relationships and progressively adapted based on the input scRNA-seq data. By integrating structured biological constraints with a probabilistic latent space model, scRegulate offers a scalable and biologically grounded estimation of TF activity and gene regulatory network (GRN). Comprehensively bench-marking on public experimental and synthetic datasets demonstrates scRegulates superior ability. Further, scRegulate accurately recapitulates experimentally validated TF knockdown effects on a Perturb-seq dataset for key TFs. Applied to experimental human PBMC scRNA-seq data, scRegulate infers cell-type-specific GRNs and identifies differentially active TFs aligned with known regulatory pathways. scRegulates TF activity representations capture transcriptional heterogeneity, enabling accurate clustering of cell types. scRegulate is highly efficient, frequently an order of magnitude faster than common baselines. Collectively, our results establish scRegulate as a powerful, interpretable, and scalable framework for inferring TF activities and GRNs from single-cell transcriptomics. AvailabilityResults and scripts available at github.com/YDaiLab/scRegulate. Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2025

Single-Cell eQTL Mapping Reveals Cell Type-Specific Genetic Regulation in Lung Cancer

Genome-wide association studies (GWAS) have identified over 50 lung cancer risk loci; however, the precise cellular context of these genetic mechanisms remains unclear due to limitations in bulk tissue eQTL analyses. Here, we present the largest single-cell eQTL atlas of human lung tissue to date, profiling 222 donors using multiplexed scRNA-seq. We identified 16,785 eQTLs across 17 cell types, with over 90% of sc-eQTLs and 59% eGene being cell-type-specific, and fewer than 23% were detectable in paired bulk datasets. Integration with GWAS for non-small cell lung cancer highlighted epithelial and immune cells as key contributors to genetic susceptibility, identifying 28 candidate genes within known risk loci and 24 in novel regions. Notably, 47% of established NSCLC susceptibility loci exhibited cell-type-specific pleiotropic genetic regulation. This study provides a valuable resource of lung sc-eQTLs and illuminates how genetic variation modulates gene expression in a cell-type-specific fashion, contributing to lung cancer susceptibility.

genetics↗

bioRxiv2025

Tissue-wide profiling of human lungs reveals spatial sequestration of macrophages in tuberculosis

The immune response to human tuberculosis (TB), particularly in the context of complex lung pathology, remains incompletely understood. Here, we employed whole-slide spatial proteomics to map immune cell organization in TB-affected human lung tissues. Our analysis revealed pronounced spatial segregation of major immune cell populations in non-necrotizing TB lesions. At the tissue level, macrophages and lymphocytes formed distinct cellular communities associated with specific pathological features. At the lesion level, macrophages and B cells showed an inverse relationship in both abundance and spatial distribution. Proinflammatory T cells preferentially accumulated in macrophage-rich lesions but remained largely separated from macrophages. Interestingly, lesions exhibiting clear segregation between T cells and macrophages were more common in subclinical TB than in active disease. These findings suggest that spatial isolation of macrophages from effector lymphocytes may help temper inflammation and potentially prevent lesion progression to necrosis, while also enabling immune evasion by Mycobacterium tuberculosis. One Sentence SummaryXiao et al. reveal spatial segregation of immune cells in TB-lung tissue and link the microenvironmental dynamics to disease states of tuberculosis.

immunology↗

bioRxiv2025

Phase transition pathways encode distinct physicochemical properties of biomolecular condensates

The same intrinsically disordered proteins (IDPs) can form biomolecular condensates through distinct thermodynamic phase transition processes, such as temperature-dependent and osmosis-dependent pathways. These distinct thermodynamic driving forces should, in principle, induce phase transition by modulating different features of the solvent environments, so that different driving forces should correspond with distinct sequence grammars for phase transition. However, whether the molecular driving force is pathway-dependent and how these different pathways can define the properties and functions of condensates are largely unknown. Here, by employing a diverse set of solid-state and solution-state NMR techniques, we uncover that different phase transition pathways of the monomer unit of an IDP define the types of molecular interactions driving phase transition and stabilizing dense phases. By establishing a complete chemical shift profile of the IDP unit, we identified a unique interaction mode that specifically initiates the upper critical solution temperature transition process, an anion-dependent cation-pi interaction, in which Asp acts as a bistable molecular switch regulating a stepwise Arg-Tyr interaction in a critical temperature-dependent manner. We further show that the pathway-dependent molecular interactions encode condensates formed by the same IDP to exhibit different physical and electrochemical properties, which in turn enable distinct functions of condensates. Our study shows that besides the defined sequence grammar of a given IDP, the molecular driving forces under specific transition processes are different and can determine the structure and properties of condensates, which emphasizes an overlooked role of transition pathway on encoding the functions of condensates.

biophysics↗