Biology subjects

Su, J.

Publications and source records attributed to Su, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

miR-128 Regulates Hypertensive Vascular Remodeling via PPAR-γ

OBJECTIVEThis study aimed to explore the role and underlying mechanism of microRNA-128 (miR-128) in regulating vascular remodeling in spontaneously hypertensive rats (SHRs), focusing on its targeting of peroxisome proliferator-activated receptor {gamma} (PPAR-{gamma}) and modulation of the Toll-like receptor 4/nuclear factor-{kappa}B (TLR4/NF-{kappa}B) inflammatory pathway. METHODSAll experimental procedures were approved by the Animal Care and Use Committee of Fujian Medical University. In vivo, ten-week-old male SHRs were randomly assigned to three groups: renal denervation (RDN, n=6), sacubitril/valsartan (Sac/Val, n=6), and Sham (n=6). Age-matched Wistar-Kyoto (WKY) rats served as normotensive controls (n=6).Eight weeks after intervention, mesenteric arteries were harvested for histological, functional, and molecular analyses. Serum miR-128 levels were measured by quantitative real-time polymerase chain reaction (qRT-PCR). The expression levels of key proteins in the vascular wall were assessed via immunofluorescence (IF), immunohistochemistry (IHC), and Western blotting (WB). Bioinformatics analysis and RNA sequencing (RNA-seq) were employed to identify core genes and signaling pathways associated with hypertension-induced pathological inflammation. RESULTSIn vivo, in the SHR sham-operated group, elevated blood pressure, severe vascular remodeling, and impaired vasodilatory function were observed, accompanied by downregulated miR-128 expression and upregulated TLR4/NF-{kappa}B signaling activity (all p < 0.0001).RDN postoperative, miR-128 expression was significantly restored, which in turn inhibited the TLR4/NF-{kappa}B pathway, reduced the production of pro-inflammatory cytokines (including IL-1{beta}, IL-6, and TNF-), and ameliorated vascular dilation dysfunction in SHRs (all p < 0.0001). Mechanistically, miR-128 negatively regulated the TLR4/NF-{kappa}B signaling pathway while upregulating the expression of PPAR-{gamma} (p < 0.05). CONCLUSIONRDN not only exerts a hypotensive effect but also improves hypertensive vascular remodeling. miR-128 inhibits excessive inflammation in vascular smooth muscle cells and alleviates vascular remodeling in SHRs via the PPAR-{gamma}/TLR4/NF-{kappa}B axis. These findings identify miR-128 as a potential therapeutic target for RDN in the treatment of hypertension, providing a novel regulatory strategy for the precision management of cardiovascular diseases.

bioinformatics↗

bioRxiv2026

DOMINO: Learning Domain Co-occurrence for Multidomain Protein Design

Multidomain proteins arise through the reuse and recombination of structural domains, yet natural architectures represent a sparse, structured sample of the possible domain-combination space. Here, we introduce DOMINO, a two-stage framework that learns domain co-occurrence from TED-annotated multidomain proteins and uses the learned patterns to generate new multidomain sequences. DOMIN, a contrastive retrieval model, embeds domains into a latent compatibility space and retrieves candidate partners for a query domain from a TED-derived domain pool, including pairings not observed in the TED-derived co-occurrence set. DOMO, a conditional autoregressive sequence model, converts each retrieved domain pair into a full-length protein sequence by jointly generating the specified domain regions and the non-domain sequence context between and around them. DOMIN recovers hierarchical patterns of natural domain co-occurrence and expands the observed CATH homologous-superfamily co-occurrence network with candidate novel pairings. DOMO realizes both held-out natural pairs and DOMIN-retrieved pairs as proteins with high domain recovery and high AlphaFold-predicted structural confidence. Applied at scale, DOMINO generated 5 million retrieval-derived multidomain proteins, with sampled designs showing recovery of the specified domains, diverse CATH annotations, and sequence novelty relative to UniRef100. Together, these results support domain co-occurrence as a predictive design prior and demonstrate a scalable strategy for exploring multidomain protein architectures through new combinations of existing structural modules.

bioinformatics↗

bioRxiv2026

Density-dependent facilitation of livestock by small mammal ecosystem engineers

Small mammals and large herbivores have co-evolved in grasslands for millions of years, yet how they interplay remains unclear. Although large herbivores can significantly affect the smaller ones, the reversal effect is largely unknown. On the Qinghai-Tibetan Plateau, plateau pikas (Ochotona curzoniae) are often considered pests that compete with livestock at high densities. Using field experiments, we show that the presence of pikas facilitates weight gains of yaks (Bos grunniens) by improving vegetation composition at a moderate density level. Compared to the pika-present treatment, pika removal dramatically increased cover of the poisonous Stellera forbs by two-fold, reducing the abundance and protein content of palatable grasses and sedges, yak foraging efficiency, and yak weight gain by up to 42%. Notably, we found a humped relationship between yak weight gains and pika burrow densities in the pika-present plots; the facilitative effect of pikas on yaks was highest at about 200 burrows/ha, but shifted to a competitive effect at pika densities exceeding 400 burrows/ha. These results provide the first empirical evidence that maintaining a moderate density of small mammalian herbivores can benefit growth performance of livestock by improving vegetation composition. Our study highlights the significance of moderate populations of ecosystem-engineering small mammals in sustaining pastoral productivity in rangelands.

ecology↗

bioRxiv2026

Evolutionary Divergence of Structure-Function Coupling between Human and Macaque: Spatial Patterns and Transcriptomic Basis

Structural-functional coupling (SFC) provides critical insights into how the brains structural architecture constrains functional organization for supporting higher-order cognition. Investigating evolutionary differences in SFC between humans and macaques may provide new insights into the neural basis of unique human cognitive abilities. In this study, we analyzed multimodal magnetic resonance imaging data from anesthetized and awake adult rhesus macaques and adult humans to examine cross-species divergences in SFC. Moreover, we integrated transcriptomic data to elucidate the molecular mechanisms underlying evolutionary differences in SFC patterns. We find that humans and macaques exhibit distinct SFC patterns: the human brain shows high SFC in the lateral and medial prefrontal cortex, whereas macaques show high SFC in the sensorimotor cortex. Notably, language-related regions in the human lateral temporal cortex exhibit relatively low SFC. Furthermore, the human whole-brain SFC pattern and the evolutionary differences in SFC between humans and macaques are negatively correlated with cortical evolutionary expansion. By integrating human and macaque transcriptomes, we reveal that the macaque SFC specifically associated genes are primarily involved in basic physiological functions, whereas the human SFC specifically associated genes exhibit evolutionary adaptations in synaptic function, neurotransmitter secretion, and other molecular processes. Moreover, the human-specific genes showing significant overlap with Human Accelerated Regions genes were mainly enriched in cell types of astrocyte and oligodendrocyte and in diseases of schizophrenia and Alzheimers diseases. Overall, these findings advance our understanding of the intricate relationships of SFC in human and macaque brains and provide novel insights in understanding evolutionary conservation and species specificity in cognitive function and gene regulation.

evolutionary biology↗

bioRxiv2026

Cholesterol Biosynthesis is a Targetable Vulnerability of CEBPA-mutant Acute Myeloid Leukemia

Bi-allelic CEBPA mutations occur in 5-15% of acute myeloid leukemia (AML) patients. The precise molecular consequences of CEBPA mutations, especially in combination with frequently co-occurring mutations in TET2, WT1, and GATA2, remain incompletely understood. Here, we present a robust human model of CEBPA-mutant AML through gene editing of healthy bone marrow-derived hematopoietic stem cells. Loss of the CEBPA-p42 isoform expressed in healthy cells with concomitant upregulation of the leukemic CEBPA-p30 isoform resulted in a myeloproliferative phenotype. Concurrent loss-of-function mutations in TET2 or WT1 drove full leukemic transformation, while GATA2 haploinsufficiency promoted erythroid precursor accumulation without overt AML. Single-cell transcriptomics and low-input proteomics revealed enhanced myeloid output, increased interferon signaling and elevated cholesterol biosynthesis in leukemic cells. Targeting cholesterol synthesis enhanced chemosensitivity, highlighting a potential therapeutic vulnerability, particularly relevant for CEBPA-mutant patients harboring co-mutations in TET2 or WT1, which have poor outcomes. Statement of significanceInduction of CEBPA-p30 by CRISPR/Cas gene editing in healthy human BM HSCs drives overt AML in vivo. TET2 and WT1 loss accelerate leukemogenesis, while GATA2 haploinsufficiency redirects differentiation toward erythroid precursors potentially driving acute erythroid leukemia. CEBPA-p30 AML exhibits cholesterol biosynthesis dependency, revealing a therapeutic vulnerability to statins.

cancer biology↗

bioRxiv2026

Functional activation reveals a repressor-gated fourth type VI secretion system in clinical Pseudomonas aeruginosa

Pseudomonas aeruginosa is a major opportunistic pathogen in which the type VI secretion system (T6SS) contributes to interbacterial competition and virulence. While most strains encode three T6SSs, we here functionally characterize a fourth system (H4-T6SS) in a clinical P. aeruginosa isolate. The H4-T6SS gene cluster is transcriptionally silent under laboratory conditions. By promoter rewiring, we demonstrate that the H4-T6SS assembles a contractile machine and mediates effector secretion and robust inter- and intraspecific antagonism. We identify a dominant pore-forming effector and its secretion pathway and a silent yet conserved nuclease effector. Genetic and biochemical analyses show that H4-T6SS expression is activated by an H4-encoded transcriptional regulator and repressed by H-NS family proteins. Analysis of over 1,200 clinical isolates reveals that the H4-T6SS is distributed across lineages and geographic regions. Finally, we observe functional crosstalk between H4- and H2-T6SSs. Together, these findings establish H4-T6SS as a functional and repressor-gated secretion system that expands the competitive arsenal of clinical P. aeruginosa.

microbiology↗

bioRxiv2026

Evolutionary genomics of local adaptation, climate vulnerability, and linarin metabolism in Opisthopappus longilobus

Global climate change and human activities are posing substantial threats to biodiversity. The genus Opisthopappus (O. taihangensis and O. longilobus), endemic to Chinas Taihang Mountains, possesses great ecological, ornamental and medicinal value. However, it is confronted with the pressures of habitat fragmentation and climate change. Here, we present the first haplotype-resolved, chromosome-scale genome assembly of O. longilobus ([~]2.95 Gb) and re-sequence 115 individuals across its range. Comparative analyses show Opisthopappus is sister to Artemisia-Chrysanthemum, with Opisthopappus and Chrysanthemum diverging at 5.15-5.18 million years ago. A profound genetic divergence is evident between O. taihangensis and O. longilobus, resulting in two distinct lineages within each species, driven by geography and climate. Our analyses indicate restricted gene flow, low diversity, and recurrent demographic bottlenecks collectively contribute to their endangerment. By integrating population genomics and environmental variables, we identified 4,437 core adaptive genes linked to water deprivation, and metabolism. Genomic offset predicts higher maladaptation risk in populations under drastic climate change. Furthermore, diverged promoters of two O-methyltransferase genes, OMT250 and OMT310, likely underlie the differential acacetin/linarin accumulation between C. morifolium and O. longilobus. These findings advance understanding of Opisthopappus evolution and climate vulnerability, offering a model for genomics-guided biodiversity conservation.

plant biology↗

bioRxiv2026

Array-CNCC: precise aggregation and arrayed plating facilitate quantitative phenotyping of human cranial neural crest cells and craniofacial disease modelling

Facial development is highly sensitive to genetic and environmental perturbation, with craniofacial malformation associated with over one-third of congenital birth defects. The face arises during an early and largely inaccessible window of embryonic development, with a large contribution from transient and multipotent cranial neural crest cells (CNCCs). Assessment of the molecular and cellular mechanisms driving normal and disordered human facial development therefore relies greatly on the use of in vitro cellular models. Here, we adapted a neurosphere-based CNCC differentiation protocol to facilitate robust quantification of early specification and migration events. Introduction of single-cell aggregation with arrayed plating enabled standardisation of neurosphere size, growth and patterning. Inclusion of fibronectin coating enhanced the efficiency of neurosphere attachment and synchronicity of CNCC migration timing. To demonstrate application of the Array-CNCC method, we developed a strategy for mosaic co-culture, which can facilitate differentiation of wildtype untreated cells directly alongside cells exposed to distinct drug treatments or genetic alterations. Finally, we present a screening approach which we use to test the impact of distinct extracellular matrix components on neurosphere morphology, CNCC migration and gene expression. Together, the Array-CNCC method is highly amenable to quantitative phenotyping and screening approaches, enabling enhanced craniofacial disease modelling with both cellular and molecular readouts.

developmental biology↗

bioRxiv2026

MOV10 inhibits SADS-CoV replication by enhancing TRIM24-mediated K63-linked TRAF3 ubiquitination and this inhibition is antagonized by viral N protein

The global outbreak of SARS-CoV-2 has resulted in a renewed focus on coronaviruses with the potential for cross-species transmission and mutation risks. In particular, swine acute diarrhea syndrome coronavirus (SADS-CoV), potentially originating from intermediate horseshoe bat (Rhinolophus affinis), is a novel coronavirus that causes acute diarrhea, vomiting, and high mortality in suckling piglets. Innate immunity plays a crucial role in defending the host against invading pathogens. Previous studies have identified several host factors that inhibit SADS-CoV replication through innate immunity; however, research on SADS-CoV remains insufficient compared to that on other coronaviruses. In this study, the host factor Moloney leukemia virus 10 protein (MOV10) inhibited SADS-CoV replication by promoting interferon (IFN) production. Mechanistically, MOV10 exerted its antiviral effect primarily through its N-terminal domain, which regulated the TNF receptor-associated factor 3 (TRAF3)-mediated innate immune pathway. Specifically, we reveal that MOV10 enhanced tripartite motif-containing 24 (TRIM24)-mediated K63-linked ubiquitination of TRAF3, thereby promoting IFN production and inhibiting SADS-CoV replication. Furthermore, we identified the strategies by which SADS-CoV evaded innate immunity. The viral N protein inhibited the antiviral effect of MOV10 by disrupting interaction between MOV10 and TRAF3, and by promoting K48-linked polyubiquitination of TRAF3, leading to TRAF3 degradation via the ubiquitin-proteasome pathway. Collectively, our findings reveal the role of MOV10 in antiviral immunity and how SADS-CoV evades host immune defense.

molecular biology↗

bioRxiv2026

A plug-and-play ROI imaging module and deep-learning denoising framework extend three-photon microscopy to 1.7 mm depth

Three-photon microscopy (3PM) has extended optical imaging beyond the reach of two-photon microscopy (2PM), but its practical depth remains far below theoretical predictions because of low photon efficiency and severe noise contamination. Here we present an integrated hardware and software solution that addresses these limitations. We developed a plug-and-play region-of-interest (ROI) imaging module that selectively excites neuron-occupied regions to improve power efficiency and reduce photothermal stress. The module incorporates frame-partitioned accumulative (FPA) imaging for high signal-to-noise ratio (SNR) structural acquisition, automated neuron segmentation, and motion-robust registration for stable recordings. Complementing this, OptiCal is a cascaded deep-learning framework that removes mixed noise including periodic, motion-induced, and random components. Together, these innovations enable high-fidelity imaging to 1.7 mm depth, extending the practical limit of 3PM by about 400 {micro}m while maintaining low excitation power. Our results reveal reliable calcium activity and behavior-correlated dynamics in deep medial prefrontal cortex of awake mice.

neuroscience↗

bioRxiv2025

Transport of endo-β-mannosidase AtEBM from cytoplasm to the vacuole through autophagy pathway in Arabidopsis

Autophagy is a conserved eukaryotic intracellular degradation pathway that exhibits specialized forms, such as the biosynthetic cytoplasm-to-vacuole targeting (Cvt) pathway in yeast. This pathway selectively delivers several hydrolase precursors to the vacuole. While the core autophagy machinery is highly conserved between yeast and plants, the existence of a similar Cvt-like pathway for vacuolar hydrolase trafficking in plants remains unclear. Here, we found that Arabidopsis thaliana endo-{beta}-mannosidase (AtEBM), a glycosidase involved in degrading vacuolar N-glycans released from glycoproteins, is selectively transported to the vacuole via autophagy. Further analyses revealed that AtEBM directly interacts with the core autophagy protein ATG8 through an ATG8-interacting motif (AIM). This interaction is essential for sequestering AtEBM into autophagosomes. Remarkably, the AIM is conserved among EBM orthologs across the green plant lineage. In addition, several phenotypic studies showed that atebm mutants generated through CRISPR-Cas9 editing did not exhibit autophagy defects, including early senescence and hypersensitivity to nutrient starvation, but rather had reduced fecundity. Thus, these findings reveal a Cvt-like pathway in plants that fulfills a biosynthetic role by selectively delivering the glycosidase AtEBM to the vacuole.

cell biology↗

bioRxiv2025

Dissecting sequence determinants of DNA methylation and in silico perturbation

DNA methylation shapes cellular identity and genome function, yet the sequence logic that governs its establishment remains largely unresolved. Here we present MethylAI, a cross-species-pretrained and human-specialized deep learning framework that predicts single-CpG methylation states directly from genomic sequence with high fidelity. Through quantitative attribution, MethylAI uncovers intrinsic cis-regulatory principles embedded in DNA, revealing conserved transcription factor (TF) motifs whose influence extends beyond CpG composition. Activated motifs demarcate gene-body CpG islands, encode lineage-defining methylation states, and align with TF occupancy and diverse histone modifications, thereby linking sequence syntax to local chromatin regulation. CTCF perturbation experiments validated MethylAI-predicted methylation shifts at activated motifs, showing strong concordance with in silico perturbations. Mapping genetic variants onto methylation-linked active motifs further uncovered widespread connections to zinc-finger TF families, providing mechanistic insight into how noncoding variation contributes to human traits and diseases. By transforming DNA sequence into interpretable methylation grammar, MethylAI establishes a generalizable framework for decoding the regulatory architecture of the human epigenome.

genomics↗

bioRxiv2025

METTL3-mediated SOCS3 m6A Modification in Preserving CD4+ T Cell Homeostasis in HIV Infected Long-term Non-progressors

The maintenance of normal CD4+ T cell levels in human immunodeficiency virus (HIV) infected long-term non-progressors (LTNPs) remains elusive. N6-methyladenosine (m6A) regulates RNA metabolism and immune function, but its role in LTNP pathogenesis is unelucidated. This study integrated in vivo analyses of peripheral blood mononuclear cells (PBMCs) from LTNPs, typical progressors (TPs), ART-treated patients, and healthy controls with in vitro experiments using the MT2-HIV-1B model to explored the m6A regulatory role in LTNPs. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified uniquely elevated m6A modification abundance and METTL3 expression in LTNPs vs. TPs. Differential m6A and mRNA analysis bighlighted enrichment of innate immunity/inflammation pathways, particularly the SOCS/IL/JAK axis. Further experiments confirmed that METTL3 mediates m6A modification of SOCS3, which suppresses JAK2/STAT4 phosphorylation to modulate IL-12/IFN-{gamma}/IL-4 expression. These findings uncover a novel m6A-METTL3-SOCS3 regulatory axis underlying HIV long-term non-progression, explaining preserved CD4+ T cell homeostasis in LTNPs. IMPOTANCE LTNPs represent a unique subset of HIV-infected individuals who naturally maintain normal CD4 T cell levels and slow disease progression, offering a valuable model to dissect host protective mechanisms against HIV. mA modification has emerged as a pivotal regulator roles in HIV replication and T cell activation, yet its contribution to LTNP biology has remained unclear. This novel mechanism provides a potential explanation for the maintenance of normal CD4+ T cell levels in LTNPs. Our findings shed light on the molecular basis of HIV-1 long-term non-progression and offered crucial insights for developing functional cure for AIDS and new host immune strategies.

immunology↗

bioRxiv2025

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↗

bioRxiv2025

In vivo reprogramming of cytotoxic effector CD8+ T cells via fractalkine-conjugated mRNA-LNP

Selective in vivo reprogramming of cytotoxic effector CD8+ T (Teff) cells holds tremendous promise as a therapeutic tool but has not yet been accomplished. Here, we demonstrate that fractalkine-conjugated mRNA lipid nanoparticles (mRNA-LNP) can specifically target and deliver mRNA to CX3CR1+ Teff cells in vitro and in vivo. In mice, fractalkine-conjugated LNP target up to 90% of blood and splenic Teff cells, and delivery of IL-2-encoding mRNA to Teff cells enables robust exogenous IL-2 secretion. In rhesus macaques, fractalkine-conjugated mRNA-LNP target up to [~]100% of peripheral blood Teff cells and delivery of CD62L-mRNA enables transient CD62L expression. Collectively, these data demonstrate the potential of natural receptor ligand-based targeting of mRNA-LNP for effective and efficient transient in vivo modification of Teff cells.

immunology↗

bioRxiv2025

Inhibition of CGRP receptor ameliorates AD pathology by reprogramming lipid metabolism through HDAC11/LXRβ/ABCA1 signaling

The Calcitonin gene-related peptide (CGRP) receptor has gained attention in Alzheimers Disease (AD) research due to its involvement in regulating neuroinflammation. However, its role and mechanism in AD pathology remain unclear. Here, we demonstrate that CALCRL, a core component of the CGRP receptor, is upregulated in the hippocampus of AD dementia patients and 5xFAD mice. Knockout of the CGRP receptor ligand Calca or pharmacological blockade using Rimegepant (Rim), reduces soluble A{beta}1-42 oligomer-induced neuronal death and glial inflammation. Rim treatment also rescues neurobehavioral impairments, neurodegeneration, and lipid metabolism dysfunction in 5xFAD mice. Mechanistically, these effects are mediated through HDAC11 inhibition, which enhances LXR{beta} acetylation and ABCA1 expression, promoting the reprogramming of neuronal lipid metabolism. Importantly, this CALCRL/HDAC11/LXR{beta}/ABCA1 axis is conserved across both humans and mice. Our findings uncover a novel mechanism underlying AD pathogenesis and highlight the therapeutic potential of targeting CGRP signaling in AD. HIGHLIGHTSInhibition of CGRP receptor ameliorates disease pathology in models of AD HDAC11 mediates CGRP receptor function in AD HDAC11 is a pivotal regulator in lipid metabolism by LXR{beta}/ABCA1 signaling The HDAC11/LXR{beta}/ABCA1 axis is conserved in AD humans and mice

neuroscience↗

bioRxiv2025

The MUC1 extracellular domain and cytoplasmic tail play distinct roles during Salmonella invasion of enterocytes

The intestinal mucus layer consists of secreted and transmembrane (TM) mucins expressed on the apical surface of enterocytes. The TM mucin MUC1 has a highly O-glycosylated extracellular domain (ED) and a cytoplasmic tail (CT) with signaling potential. MUC1 is a target for the Salmonella adhesin SiiE, which mediates apical invasion of the bacterium into enterocytes. Here, we determined the contributions of the MUC1 ED and CT to Salmonella invasion and subsequent host immune responses. Enzymatic removal of the MUC1 ED from HT29-MTX intestinal cultures blocked Salmonella invasion to levels comparable to MUC1 knockout cells. CRISPR-mediated targeted deletion of the MUC1 CT (MUC1-{Delta}CT) did not quantitatively affect Salmonella invasion. To investigate downstream host responses, RNAseq transcriptomics analysis of uninfected and Salmonella-infected MUC1-WT, MUC1-{Delta}CT, and {Delta}MUC1 cultures was performed. Deletion of full-length MUC1 greatly altered the transcriptome, while only a small group of 132 genes was differentially expressed in MUC1-{Delta}CT cultures during infection. Several of these CT-dependent genes are related to the NF{kappa}B pathway. Immunoblot analysis demonstrates that under uninfected conditions, expression of NF{kappa}B subunits RelB, NfkB1-p105, NfkB2-p100, and I{kappa}B was significantly lower in MUC1-WT compared to MUC1-{Delta}CT and {Delta}MUC1 cultures. Secretion of cytokines and immune factors was severely reduced in {Delta}MUC1 cultures, coinciding with reduced Salmonella invasion. In MUC1-{Delta}CT cultures, only galectin-3 and IL-18 secretion were significantly reduced. We conclude that the MUC1 ED is essential for Salmonella invasion, while the CT modulates the canonical and non-canonical NF{kappa}B pathway, pointing at distinct roles for MUC1 domains in microbe-host interactions and signaling. ImportanceThe intestinal mucus layer plays an important role in separating commensal and pathogenic microbes from the underlying epithelium. The transmembrane mucin MUC1 is expressed by different types of intestinal epithelial cells and is thought to have important protective and signaling functions. However, enteropathogenic Salmonella bacteria can hijack MUC1 through engagement with the SiiE adhesin which leads to bacterial invasion of enterocytes at the apical surface. In this study, we determined how the different MUC1 domains contributed to Salmonella invasion and subsequent host responses. We found that the glycosylated MUC1 extracellular domain, but not the cytoplasmic tail, is essential for bacterial invasion. In infected and uninfected intestinal cultures, the MUC1 cytoplasmic tail modulates immune responses including NF{kappa}B activation and cytokine secretion. Our study contributes to our understanding of the diverse functions of transmembrane mucins at the intestinal microbe-host interface.

microbiology↗

bioRxiv2025

SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation

Integrating transcriptome-wide single-cell gene expression data with spatial context significantly enhances our understanding of tissue biology, cellular interactions, and disease progression. Although single-cell RNA sequencing (scRNA-seq) provides high-resolution gene expression data, it lacks crucial spatial context, whereas spatial transcriptomics techniques offer spatial resolution but are limited in the transcriptomic coverage. To address these limitations, integrating scRNA-seq and spatial transcriptomics data is essential. We introduce SpaGene, a novel deep learning framework designed to integrate scRNA-seq data and spatial transcriptomics data. SpaGene consists of two encoder-decoder pairs combined with two translators and two discriminators to effectively impute missing gene expressions within spatial transcriptomics datasets. We benchmarked SpaGene against existing state-of-the-art methods across diverse datasets. Across the datasets, SpaGene achieved an average 33% higher Pearson correlation coefficient (PCC), 21% higher Structural similarity index (SSIM), and 6.6% lower Root mean squared error (RMSE) compared to the existing approaches, highlighting its capability to reliably impute missing genes and provide comprehensive transcriptomics profiles. Application of our model to lung tumor tissue revealed immune cell enrichment at tumor boundaries, restricted myeloid cell trafficking in adjacent normal regions, and microenvironmental-driven pathways linked to immune neighborhoods. These results provide novel insight into immune exclusion and tumor-immune interactions that drive tumor progression, highlighting potential avenues for therapeutic development. Thus, SpaGene extends the power of spatial transcriptomics by delivering spatially resolved, enhanced transcriptome data that enable deeper biological understanding.

bioinformatics↗