Biology subjects

Hao, S.

Publications and source records attributed to Hao, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Oxidative Stress and Tissue Remodeling in a Rat Abdominal Seroma Model

Seroma is a common complication following abdominoplasty and other procedures involving extensive soft tissue dissection. Although animal seroma models have been reported, the stromal pathology underlying post-abdominoplasty seroma, particularly the role of oxidative stress, remains poorly characterized. Here, we developed a rat abdominal seroma model by surgically separating the subcutaneous tissue from the underlying muscle fascia and investigated the temporal evolution of the associated stromal response. Seroma developed in 9 of 20 operated rats, corresponding to a formation rate of 45.0%. Longitudinal ultrasound demonstrated that fluid accumulation peaked around postoperative day (POD) 7 and largely resolved by POD30. Despite macroscopic fluid resolution, substantial stromal remodeling persisted. Compared with normal abdominal tissue, seroma-associated tissues at POD14 and POD35 exhibited increased collagen deposition, macrophage accumulation, oxidative injury, and vascular remodeling. Additionally, at POD35, macrophage accumulation and 4-hydroxynonenal staining were greater than at POD14, whereas collagen deposition and vascular density remained elevated with no significant differences between postoperative time points. To our knowledge, this study presents the first rat model specifically designed to reproduce post-abdominoplasty seroma and the first temporal characterization of oxidative stress within seroma-associated tissue. These findings reveal that seroma fluid resolution does not coincide with stromal recovery and identify persistent oxidative stress, inflammation, fibrosis, and vascular remodeling as important features of seroma pathology.

bioengineering↗

bioRxiv2026

A fibroblast-rich transcriptomic axis reflects stromal remodeling within the CMS4 phenotype in colorectal cancer

Bulk-tumor expression signatures can reflect cellular composition as well as tumor-cell programs. We evaluated a frozen, equal-weight 87-gene score in colorectal cancer using 11 Gene Expression Omnibus (GEO) cohorts, TCGA COAD/READ, and E-MTAB-12862. In GEO (1,783 tumors; 441 progression-related events), the hazard ratio per score standard deviation was 1.33 (95% confidence interval, 1.19-1.49). The estimate was similar in seven disease-free-survival cohorts. In 376 TCGA tumors, the hazard ratio was 1.25 (1.03-1.52) for progression-free interval. The association did not reproduce in E-MTAB-12862: among 948 stage I-III tumors with 436 recurrence-free-survival events, the hazard ratio was 1.05 (0.95-1.16). The frozen score correlated with CMS4, cancer-associated fibroblast, and stromal measures. The stromal-remodeling module produced a GEO estimate similar to the full score, whereas removing that module attenuated the association. Composition residualization did not detect additional prognostic information after accounting for the measured CMS4 and stromal components. Single-cell and spatial analyses localized the gene program to fibroblast-rich compartments. The 87-gene score mainly reflects a fibroblast-rich, matrix-remodeling component of CMS4 rather than an independent prognostic subtype. Its prognostic association varied across cohorts, and current evidence does not support clinical use.

cancer biology↗

bioRxiv2026

AAV VP1 unique region (VP1u) determines GPR108 dependence for AAV transduction of human airway epithelium and its rescue by Doxorubicin

rAAV2.5T was identified through directed evolution of an AAV capsid library in polarized human airway epithelium (HAE) cultured at an air-liquid interface (ALI). The capsid gene of rAAV2.5T is a chimera of the N-terminal unique region of AAV2 VP1 (VP1u) and the VP2 and VP3 regions of AAV5 with a single A581T substitution at the variable region (VR) VIII of the capsids. GPR108, a G protein-coupled receptor, is known as an essential host factor for the transduction of rAAV2 but not of rAAV5. Both AAV2 and AAV5 VP1u colocalized well with GPR108 and, to a lesser extent, with the trans-Golgi network (TGN). GPR108 knockout (KO) abolished rAAV2.5T transduction in both HeLa cells and HAE-ALI cultures. Remarkably, short-term treatment with doxorubicin (DOX) at 2 {micro}M completely restored transduction, indicating that DOX can compensate for the loss of GPR108 function. DOX enhanced rAAV2.5T transduction by 50-100-fold in wild-type HAE-ALI cultures and by over 300-fold in the GPR108-deficient cultures. Mechanistic studies demonstrated that this enhancement resulted from altered intracellular trafficking that promoted efficient vector nuclear import, rather than increased vector internalization, proteasome inhibition, or activation of the DNA damage response. Importantly, we identified that the N-terminal 15 amino acids of AAV2 VP1u as the primary determinant of rAAV2.5T dependence on GPR108 for transduction. Collectively, these findings demonstrate that productive transduction of rAAV2.5T in polarized HAE cultures depends on GPR108-mediated intracellular trafficking that limits efficient nuclear entry, and that DOX can relieve this constraint by promoting efficient vector import. SignificanceAAV2.5T is an airway-tropic vector with considerable promise for pulmonary gene therapy. We found that host factor GPR108 is required for rAAV2.5T trafficking from the TGN to the nucleus and that this step constitutes a major bottleneck to productive transduction in polarized HAE. In contrast, KIAA0319L (AAVR) plays a key role in AAV intracellular trafficking from the endosome to the TGN but not in internalization into polarized HAE during apical transduction. Transient treatment with low-dose doxorubicin (DOX, 2 {micro}M) enhanced rAAV2.5T transduction in HAE by 50-100-fold through a significant increase in vector nuclear import. Notably, DOX can overcome the transduction deficit caused by GPR108 deficiency, but not that caused by AAVR deficiency. Mechanistically, the N-terminal 15 amino acids of the VP1u confer GPR108 dependence during rAAV2.5T apical transduction of polarized HAE. DOX bypasses this requirement by promoting efficient nuclear import without affecting vector internalization, inhibiting proteasomes, or inducing DNA damage response.

microbiology↗

bioRxiv2026

Evolutionary Origins of Molecular Programs Underlying Brain Circuitry

The vertebrate pallium harbors independently evolved structures that, nevertheless, support strikingly similar sensory and cognitive circuit architectures. The mechanisms and evolutionary timing driving the emergence of these parallel pallial circuits remain unelucidated. Here, we integrated spatial transcriptomic and single-nucleus RNA-seq datasets from eight representative vertebrate species spanning approximately 500 million years of evolution to reconstruct the evolutionary assembly of the primary sensory-allocortical (Pr-Al) molecular axis, a conserved cortical hierarchical axis defined in our prior work. We uncovered that Pr- and Al-like neuronal identities are deeply conserved across sarcopterygians, encompassing all tetrapods and lobe-finned fishes. Intriguingly, this ancestral neuronal homology is uncoupled from spatially partitioned patterning: only tetrapods further compartmentalized these Pr- and Al- neurons into distinct pallium regions. Functional enrichment of Pr- and Al- gene programs uncovered a conserved tetrapod genetic core suite including MAPK signaling and axon guidance pathways. This core toolkit underwent sequential functional refinement from amphibians through mammals. Notably, mammals and birds convergently evolved association-cortical molecular profiles enriched for synaptic regulatory genes to support advanced cognitive functions. Collectively, this work delineates a stepwise vertebrate pallium evolutionary paradigm that explains how conserved molecular modules shape spatially organized brain circuitry across deep evolutionary time.

evolutionary biology↗

bioRxiv2026

Single-cell transcriptomic atlas of mouse oocyte development from growth to ovulation

Oocyte growth and maturation depend on tightly coordinated programs within oocytes and their surrounding granulosa cells, yet defining the transcriptional continuum of growing oocytes has been challenging due to their large size and the limitations of current droplet-based and spatial transcriptomic platforms. Here, we optimized a high-density array-based platform called Stereo-cell for high-throughput dual-modality profiling of large mouse oocytes, allowing for both the preservation of morphology and transcript capture. By integrating unsupervised transcriptomic clustering with cell morphological features, we delineated successive temporal windows from growing oocytes to metaphase II and uncovered stage-linked shifts from early programs toward later programs. We also profiled the ovarian somatic fraction, reconstructed granulosa-cell subtype relationships, and placed ovarian cell states in tissue context using single-cell-resolution spatial data.

developmental biology↗

bioRxiv2026

Correction of multiple splicing mutations associated with CFTR exon 18 using a single exon-specific U1 snRNA

Splice site mutations represent a major class of pathogenic mutations in many diseases, as these changes disrupt normal splicing leading to gene expression changes. Cystic fibrosis (CF) results from mutations to the cystic fibrosis transmembrane conductance regulator (CFTR) gene that encodes an essential ion channel. Approximately 13% of the over 2,100 known CFTR mutations disrupt 3 or 5 splice sites and are predicted to cause splicing defects. Because each splicing mutation is rare, developing individualized therapies to treat each one is financially challenging. Exon specific U1 snRNA (ExSpeU1) targets the non-conserved intronic region downstream the 5 splice site (ss) to rescue exon skipping. Because this approach is exon-rather than mutation-specific, a single agent can potentially rescue multiple mutations. In this study, we have developed a platform to systematically classify all patient variants associated with an exon that are predicted to affect splicing and then determine their rescue potential using ExSpeU1. Here we report the results of these studies. Our minigene reporter study shows that 7 of 10 exon 18 variants resulted in exon skipping. Four mutations at the 3 and 5 ss were rescued at least partially using a single ExSpeU1. Using a luciferase reporter, we observe that the splicing rescue is reflected at the protein level. Lastly, we demonstrate exon-targeting ExSpeU1s can also rescue 3 and 5 ss mutations. Overall, this study exemplifies the power of our platform to screen and rescue multiple patient-derived splicing mutations using a single agent.

genetics↗

bioRxiv2026

Critical role of cell competition in gliomagenesis

ABSTRACTMalignant glioma is incurable. Using a mouse genetic mosaic system to generate sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null OPCs outcompete wildtype counterparts during their expansion. Blocking competition by mutating/strengthening wildtype OPCs impeded both pre-malignant progression and malignant expansion of glioma. "In-tissue" phosphoproteomic profiling revealed an enrichment of phosphopeptides related to RNA splicing and protein translation at the peak of cell competition, suggesting that competitiveness may stem from unique protein species. Among candidates was mTORC1, whose pharmacological inhibition or genetic disruption resulted in a loss of competitiveness in our mouse model. Finally, analysis of patient biopsies and interrogating the role of individual gliomagenic mutations in OPC competition supported its relevance in human gliomas. Together, these findings identified the driving role of competitive interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic strategies to target this process.

cancer biology↗

bioRxiv2026

Distinct p21 dynamics drive alternative routes to whole-genome duplication through a common CDK4/6-dependent polyploid G0 state

Whole-genome duplication (WGD) fuels tumor evolution and therapy resistance, yet the molecular mechanisms governing the switch from the canonical mitotic cell cycle to the endoreplication cycle remain unclear. Here, we combine single-cell proteomics, manifold learning, and live-cell imaging to map the intersection of the mitotic and endoreplication cycles in breast cancer cells exposed to genotoxic agents. We identify two distinct routes to WGD driven by distinct p21 dynamics. High p21 induction induces G2 exit and endocycling, whereas insufficient p21 permits mitotic entry followed by slippage and endomitosis. This therapy-induced switch acts as a facultative stress response, generating drug-resistant polyploid populations that propagate genomic instability through replication stress and the generation of replication-competent micronuclei. Both paths to WGD converge on a common polyploid G0 state dependent on cyclin D1:CDK4/6 activity to complete the transition to the endoreplication cycle, revealing a shared vulnerability. Sequential treatment with genotoxic agents followed by CDK4/6 inhibitors preserves the cytotoxic efficacy of DNA-damaging drugs while simultaneously blocking entry into the endoreplication cycle and WGD-driven evolutionary rescue. These findings reveal the molecular rules governing the switch from the mitotic to endoreplication cycle and highlight the potential of WGD-blocking drugs as adjuvant therapies to inhibit drug resistance and suppress tumor evolution.

cell biology↗

bioRxiv2025

Brain endothelial PRMT5-ANGPTL4 axis regulates cerebellar inhibitory synaptogenesis and motor coordination

Brain vasculature is essential for central nervous system function, but its specific roles in synaptic development and motor function regulation are poorly understood. In this study, we identify a cerebrovascular signaling axis wherein endothelial PRMT5 critically regulates inhibitory synaptogenesis and motor coordination. Cerebrovascular-specific deletion of Prmt5 gene leads to excessive inhibitory synaptic input onto Purkinje cells and progressive motor deficits in mice. Mechanistically, PRMT5 deficiency epigenetically upregulates the expression of the secreted factor ANGPTL4 through reduced symmetric dimethylation of H3R8 and H4R3, along with increased H3K9 acetylation at the Angptl4 promoter, thereby driving excessive inhibitory synaptogenesis onto Purkinje cells. Importantly, Angptl4 deletion in brain endothelium normalizes inhibitory synaptic input onto Purkinje cells and restores motor coordination in PRMT5-deficient mice. Together, these findings define the endothelial PRMT5-ANGPTL4 axis as a key regulator of cerebellar inhibitory circuitry and motor function, highlighting cerebrovascular mechanisms as potential therapeutic targets for motor coordination disorders. Teaser Cerebrovascular PRMT5 prevents excessive inhibitory synaptogenesis via epigenetic repression of Angptl4.

neuroscience↗

bioRxiv2025

Midbrain microglia-integrated organoids as a next-generation tool for chronic morphine withdrawal research: A pilot study

In the midst of an opioid epidemic, opioid use disorder (OUD) can lead to significant clinical impairment or distress (such as opioid dependence and/or addiction) and overdose deaths. Therefore, it is significant to elucidate the exact molecular mechanisms of OUD and identify more effective therapies. Human induced pluripotent stem cell (hiPSC)-derived organoids are self-organized 3D tissues and mimic in vivo human organs. Increasingly, human-specific features of opioid abuse are being investigated using emerging brain organoids, which faithfully model the key functional, structural and biological complexities of neural tissues. However, a significant limitation of brain organoids is the absence of microglia which plays a fundamental role in OUD-related remodeling of neural circuits. In this pilot study, using hiPSC KOLF2.1J cell line, we developed our approach for generating both midbrain organoid and microglia and verified that our midbrain organoid was successfully integrated with microglia. We found that chronic exposure to morphine triggers key elements of immune responses including increased TNF signaling and downregulation of sirtuin3 (Sirt3, a mitochondrial protein, preventing oxidative stress) and manganese superoxide dismutase (MnSOD, located in the mitochondrial matrix) in microglia-organoid co-cultures. Our findings suggest that immunocompetent midbrain organoids provide excellent models with which to study human-specific mechanisms of neuroinflammation and neurodegeneration. By combining disease relevance with scalability, the model system can be utilized as an effective tool for drug screening and toxicity testing.

neuroscience↗

bioRxiv2025

Integrative genomic and transcriptomic analyses uncover regulatory landscape of symbiotic nitrogen fixation in soybean natural population

Symbiotic nitrogen fixation (SNF) is a key trait in legume productivity, yet the genetic and regulatory basis underlying its natural variation remains poorly understood. Here, we integrated genome, transcriptome, and chromatin accessibility data from a soybean diversity panel comprising 380 accessions, including 108 wild and 272 cultivated lines. Genome-wide association studies (GWAS) detected multiple loci for SNF traits but with limited resolution due to polygenic architecture and environmental influences. Independent component analysis (ICA) identified 136 co-expression modules; ten ICs were strongly correlated with SNF phenotypes and enriched in circadian clock components (e.g., GmLHY1a/b), lipid metabolism, or defense signaling pathways. Transcriptome-wide association studies (TWAS) linked 1,453, 806, and 178 genes to NFP, NW, and NFE traits, respectively. Among TWAS hits, 185 transcription factors were identified, with 39.0% overlapping selective sweeps, suggesting regulatory evolution under domestication. To further dissect expression regulation, we performed eQTL mapping and detected 4,654 significant eQTLs, including 1,241 local (cis), 2,505 distal (trans), and 908 mixed. By integrating ATAC-seq data from sorted nodule nuclei, we found that eQTLs, particularly local eQTLs, are significantly enriched within open chromatin regions, indicating their regulatory potential. Notably, we validated the circadian clock gene GmLHY1b as a negative regulator of nodulation using CRISPR mutagenesis and CUT&Tag. Our integrative study provides comprehensive genomic and transcriptomic resources from a diverse soybean population, offering novel insights into SNF regulatory networks and a valuable foundation for future SNF research and soybean improvement.

plant biology↗

bioRxiv2025

Renin Cells Drive Kidney Neurovascular Development and Arterial Remodeling when Renin Activity is Deficient

Renin cells synthesize and release the hormone-enzyme renin to regulate blood pressure and fluid-electrolyte homeostasis. Their function and identity depend on communication with surrounding cells and nerve fibers within complex kidney structure. Because renin cells are rare -0.01 % of kidney cells-conventional histological approaches cannot capture their interaction with nerve fibers and surrounding cells within the nephron and its vasculature. Using a novel ultrabright renin cell-specific tdTomato reporter mouse, high-resolution 3D imaging, and single-cell RNA-Seq, we mapped the interactions of renin cells with growing axons during normal kidney vascular development, in response to threats to homeostasis, and a severe arterial disease caused by a defective renin enzyme. During embryonic kidney development, stromal and renin cell progenitors assemble the arterioles, express axon attractants and neurotrophins that establish the precise innervation of renin cells and arterioles in a centrifugal pattern. Hypotension and sodium depletion led to an increase in the volume and number of renin cells along the arterioles. Renin enzymatic deficiency led to hypertrophy and endocrine transformation of renal arterioles, aberrant axon sprouting and sympathetic hyperinnervation suggesting a feed-forward mechanism whereby renin cells and axons co-induce each other, orchestrate neurovascular development and arteriolar remodeling when renin cells are over stimulated.

developmental biology↗

bioRxiv2025

Synergistic Control of Mitochondrial Dynamics and Function by ERAD and Autophagy in Brown Adipocytes

Mitochondrial quality control is essential for maintaining cellular energy homeostasis, particularly in brown adipocytes where dynamic mitochondrial remodeling supports thermogenesis. Although the SEL1L-HRD1 endoplasmic reticulum (ER)-associated degradation (ERAD) pathway and autophagy are two major proteostatic systems, how these pathways intersect to regulate mitochondrial integrity in metabolically active tissues remains poorly understood. Here, using adipocyte-specific genetic mouse models combined with high-resolution 2D and 3D ultrastructural imaging technologies, we reveal an unexpected synergy between SEL1L-HRD1 ERAD and autophagy in maintaining mitochondrial structure and function in brown adipocytes. Loss of ERAD alone triggers compensatory autophagy, whereas combined deletion of both pathways (double knockout, DKO) results in severe mitochondrial abnormalities, including the accumulation of hyperfused megamitochondria penetrated by ER tubules, even under basal room temperature conditions. These phenotypes are absent in mice lacking either pathway individually or in SEL1L-IRE1 DKO, highlighting the pathway-specific coordination between ERAD and autophagy. Mechanistically, dual loss of ERAD and autophagy induces ER expansion, excessive ER-mitochondria contact, upregulation of mitochondria-associated membrane (MAM) tethering proteins, impaired calcium transfer, and defective mitochondrial turnover. As a result, DKO adipocytes accumulate dysfunctional mitochondria, exhibit respiratory deficits, and fail to sustain thermogenesis. Collectively, our study uncovers a cooperative and previously unrecognized mechanism of mitochondrial surveillance, emphasizing the critical role of ERAD-autophagy crosstalk in preserving mitochondrial integrity and thermogenic capacity in brown fat. One-sentence summaryOur study uncovers a previously unrecognized synergy between SEL1L-HRD1 ERAD and autophagy that is essential for preserving mitochondrial integrity and thermogenic capacity in brown adipocytes, revealing new opportunities for targeting mitochondrial dysfunction in metabolic disease.

cell biology↗

bioRxiv2025

Application of Spectral Domain Optical Coherence Tomography To Guide Cochlear Implant Electrode Array

HypothesisA custom spectral domain optical coherence tomography (SD-OCT) platform can be used for real-time guidance of a cochlear implant electrode array (EA). BackgroundWith current cochlear implant surgical techniques, placement of the EA is a blind maneuver in which the surgeon relies on tactile feedback as the EA advances through the cochlear lumen. Cochlear implant trauma is a leading factor for poor speech performance outcomes and loss of residual hearing following surgery. Optical coherence tomography (OCT) is a non-invasive imaging modality that provides real-time visualization of tissue microstructure at higher spatial resolutions compared to clinical CT and MRI. Already adopted as standard of care in ophthalmology, OCT has the potential to assist the surgeon in real-time visualization of the EA trajectory. Unlike commercial systems, our custom OCT system allows tailored wavelength, scanning geometry, and real-time processing, which are critical factors for navigating the compact anatomy of the facial recess to image the cochlea. MethodsA custom-built SD-OCT system was used to image cochlear microanatomy in mice and human cadaveric temporal bones. The OCT system was then used to guide a mock EA in human cadaveric temporal bones in real-time using individual B scans that were reviewed sequentially as the EA was being advanced through the round window. ResultsUsing our OCT system, high-resolution (< 5.0 m) images of cochlear microanatomy were obtained in both mice and cadaveric human temporal bones with an image sensitivity of [~]104 dB. Following cochleostomy in cadaveric temporal bones, real-time sequential OCT B-scans were used to reliably guide placement of the EA through the scala tympani. ConclusionOur custom-built SD-OCT platform can generate high-resolution real-time visualization and orientation of mammalian cochlear microanatomy that can be used to assist with real time guidance of a CI EA. This technology has the potential to serve as a real-time surgical image guidance tool to minimize EA trauma and further our understanding of human cochlear pathophysiology.

bioengineering↗

bioRxiv2025

Deciphering the Sequence Basis and Application of Transcriptional Initiation Regulation in Plant Genomes Through Deep Learning

Transcription initiation is a critical regulatory step in plant gene expression, yet its sequence determinants remain largely elusive. Here we introduce GenoRetriever, an interpretable deep learning model that deciphers the sequence basis of transcriptional initiation regulation across plant genomes. Trained on STRIPE-seq data from 16 soybean tissues and six other crop species, GenoRetriever identifies 27 core sequence motifs that govern transcription start site (TSS) selection and usage. The model predicts TSS locations and usage levels with high accuracy, as validated by in silico motif insertions, saturation mutagenesis, and CRISPR-Cas9 promoter editing. It further reveals that 31.85% of natural variation between wild and domesticated soybean drives shifts in promoter motif usage during domestication, and uncovers lineage-specific motif effects between monocots and dicots. This interpretable model and its user-friendly web server for promoter analysis and design make GenoRetriever both a methodological innovation and practical tool for plant functional genomics and crop improvement.

plant biology↗

bioRxiv2025

A tumor necrosis factor-α responsive cryptic promoter drives overexpression of the human endogenous retrovirus ERVK-7

Endogenous retroviruses (ERVs) shape human genome functionality and influence disease pathogenesis, including cancer. ERVK-7, a significant ERV, acts as an immune modulator and prognostic marker in lung adenocarcinoma (LUAD). Although ERVK-7 overexpression has been linked to the amplification of the 1q22 locus in approximately 10% of LUAD cases, it predominantly arises from alternative regulatory mechanisms. Our findings indicate that the canonical 5 long terminal repeat (LTR) of ERVK-7 is methylated and inactive, necessitating the use of alternative upstream promoters. We identified two novel transcripts, ERVK-7.long and ERVK-7.short, arising from distinct promoters located 2.8 kb and 13.8 kb upstream of the 5LTR of ERVK-7, respectively. ERVK-7.long is predominantly overexpressed in LUAD. Through comprehensive epigenetic mapping and single-cell transcriptomics, we demonstrate that ERVK-7.long activation is predetermined by cell lineage, specifically in small airway epithelial cells (SAECs), where its promoter displays tumor-specific H3K4me3 modifications. Single-cell RNA sequencing further reveals a distinct enrichment of ERVK-7.long in LUAD tumor cells and alveolar type 2 epithelial cells, underscoring a cell-type-specific origin. Additionally, inflammatory signaling significantly influences ERVK-7 expression; TNF- enhances ERVK-7.long, while interferon signaling preferentially augments ERVK-7.short by differential recruitment of NF-{kappa}B/RELA and IRF to their respective promoters. This differential regulation clarifies the elevated ERVK-7 expression in LUAD compared to lung squamous cell carcinoma (LUSC). Our study elucidates the complex regulatory mechanisms governing ERVK-7 in LUAD and proposes these transcripts as potential biomarkers and therapeutic targets, offering new avenues to improve patient outcomes.

cancer biology↗

bioRxiv2025

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 lead cis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.

immunology↗

bioRxiv2025

Integrative Mapping of Pre-existing Immune Landscapes for Vaccine Response Prediction

Predicting individual vaccine responses remains a significant challenge due to the complexity and variability of immune processes. To address this gap, we developed immunaut, an open-source, data-driven framework implemented as an R package specifically designed for all systems vaccinologists seeking to analyze and predict immunological outcomes across diverse vaccination settings. Leveraging one of the most comprehensive live attenuated influenza vaccine (LAIV) datasets to date - 244 Gambian children enrolled in a phase 4 immunogenicity study - immunaut integrates humoral, mucosal, cellular, transcriptomic, and microbiological parameters collected before and after vaccination, providing an unprecedentedly holistic view of LAIV-induced immunity. Through advanced dimensionality reduction, clustering, and predictive modeling, immunaut identifies distinct immunophenotypic responder profiles and their underlying baseline determinants. In this study, immunaut delineated three immunophenotypes: (1) CD8 T-cell responders, marked by strong baseline mucosal immunity and extensive prior influenza virus exposure that boosts memory CD8 T-cell responses, without generating influenza virus-specific antibody responses; (2) Mucosal responders, characterized by pre-existing systemic influenza A virus immunity (specifically to H3N2) and stable epithelial integrity, leading to potent mucosal IgA expansions and subsequent seroconversion to influenza B virus; and (3) Systemic, broad influenza A virus responders, who start with relatively naive immunity and leverage greater initial viral replication to drive broad systemic antibody responses against multiple influenza A virus variants beyond those included in the LAIV vaccine. By integrating pathway-level analysis, model-derived contribution scores, and hierarchical decision rules, immunaut elucidates how distinct immunological landscapes shape each response trajectory and how key baseline features, including pre-existing immunity, mucosal preparedness, and cellular support, dictate vaccine outcomes. Collectively, these findings emphasize the power of integrative, predictive frameworks to advance precision vaccinology, and highlight immunaut as a versatile, community-available resource for optimizing immunization strategies across diverse populations and vaccine platforms. One-Sentence SummaryUsing one of the most comprehensive LAIV datasets compiled to date, immunaut, an integrative machine learning framework, identifies distinct immunophenotypic responder groups shaped by baseline immune landscapes, advancing precision vaccinology and guiding more effective, personalized immunization strategies. Graphical abstractImmunaut, an automated framework for mapping and predicting vaccine response immunotypes. Step 1 outlines the identification of vaccine response outcomes using pre- and post-vaccination data integration across immune features, including antibodies, flu-specific T-cells, and immunophenotyping at mucosal and systemic sites. Clustering methods define the vaccine response landscape, stability, and validation through t-SNE-based visualization. Step 2 leverages an automated machine learning modeling approach, to enhance the accuracy and interpretability of vaccine response predictions, enabling stratification and targeted intervention strategies for personalized vaccine immunogenicity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/634302v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@62276corg.highwire.dtl.DTLVardef@a5f25org.highwire.dtl.DTLVardef@eca34borg.highwire.dtl.DTLVardef@1d4999b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗