Biology subjects

Liang, G.

Publications and source records attributed to Liang, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-probe, high-yield spatial mapping of diverse short RNA motifs

Spatial transcriptomics has revolutionized our understanding of RNA biology. Hybridization-based methods map mRNA transcripts by tiling multiple labeled probes along each molecule to generate a visible fluorescent signal, restricting applicability to long transcripts. Short RNA motifs, consequently, can only accommodate a single probe and remain a spatially invisible dimension of RNA biology. Here we present SMOOTHY-FISH, a single probe strategy that directly visualizes short RNA motifs at the single-molecule resolution. By optimizing probe brightness, binding specificity, and target accessibility, our single ~20-nucleotide probe reached the practical ceiling of hybridization-based detection. We quantitatively mapped previously inaccessible short motifs - splice-isoform junctions, individual microRNAs, and structural conformations - in single cells and mouse brain tissues, each validated against orthogonal methods. This unveiled biological phenomena that were previously unknown: ratios of alternatively spliced isoforms are tightly regulated across cell populations, subcellular miRNA fractions are precisely maintained, and a designed RNA structure was found to have a prominent alternative conformation. These findings demonstrate that short RNA motifs possess key spatial information that has yet to be discovered. With SMOOTHY-FISH's optimized single probe technique, short RNA motifs are converted into a new routinely measurable axis of spatial transcriptomics.

molecular biology↗

bioRxiv2026

Pseudomonas aeruginosa CRISPR-Cas primes a minimal proline-codon toxin to abort anti-CRISPR phages

Pseudomonas aeruginosa typically carries type I-F CRISPR-Cas systems, which are targeted by diverse (pro)phage-encoded anti-CRISPR (Acr) proteins. Here, we show that [~]26% of P. aeruginosa Cas effectors are reprogrammed by a regulatory RNA guide (CreA) to transcriptionally silence a conserved small RNA toxin (CreT) that arrests cell growth upon Cas inactivation. This toxin unprecedentedly employs two consecutive proline codons, thus termed "proline-codon toxin". Combined phylogenetic and genetic analyses unraveled that CreTA has forced P. aeruginosa to reject prophages whose Acrs disrupt Cas-DNA binding, which is essential for CreT repression. We further show that Acr-armed lytic phages designed to overcome CRISPR adaptive immunity can be instead aborted by CreTA-mediated defense in vitro and in a mouse model. Our findings unravel intra-genomic arms races between CreTAs and anti-CRISPR phages, and underscore the necessity of rational engineering of strain-specific therapeutic phages to penetrate the layered CRISPR and TA barriers of multidrug-resistant P. aeruginosa.

microbiology↗

bioRxiv2026

HDAC Inhibition Sensitizes Pancreatic Tumors to DNA Damage by Global Redistribution of the Transcriptional Machinery

The DNA damage response (DDR) is critical for pancreatic ductal adenocarcinoma (PDAC) development and therapeutic responses, including to genotoxic agents. While epigenetic modulators have been shown to contribute to the DDR, how chromatin regulation dictates responses to DNA damage in PDAC remains incompletely understood. Here, we identify Class I histone deacetylases (HDACs) as critical regulators of the DDR. HDAC1/2 directs the genomic distribution of H3K27ac, ensuring sufficient BRD4 and RNA polymerase II (Pol II) occupancy at DDR gene promoters. HDAC inhibition by entinostat shifts the balance of H3K27 acetylation preferentially towards intergenic regions, diverting BRD4 and Pol II from promoters, thereby suppressing DDR gene expression. In line with this, HDAC inhibition heightens DNA damage and sensitizes PDAC to diverse DNA-damaging and DDR-targeting agents. Since the clinical development of HDAC inhibitors has been limited by systemic toxicity, we developed bottlebrush prodrug (BPD) nanoparticles for tumor-selective entinostat delivery. Entinostat-BPD achieved tumor-specific HDAC inhibition while displaying potent efficacy and reduced systemic toxicity. These findings reveal an HDAC-dependent DDR vulnerability and offer combinational and precision targeting strategies to facilitate clinical translation and improve PDAC patient outcomes. SIGNIFICANCE STATEMENTThe ability of tumor cells to tolerate DNA damage limits the efficacy of many anticancer therapies. Our study reveals that pancreatic cancer cells enforce this resistance by sustaining expression of DNA damage response (DDR) genes through Class I histone deacetylases (HDACs). HDACs maintain genome-wide acetylation patterns required for efficient recruitment of the transcriptional machinery to DDR genes. Pharmacological HDAC inhibition disrupts this process and sensitizes pancreatic cancer cells to diverse DNA-damaging agents. To overcome systemic toxicity that limits translational potential, we further establish a bottlebrush prodrug nanoparticle platform that enables tumor-selective HDAC inhibition. Given the central role of the DDR in cancer, targeting HDAC-mediated DDR regulation through drug combinations and precision delivery may have broad therapeutic relevance across cancer types.

cancer biology↗

bioRxiv2026

Yawning reveals energy-dynamics mismatch and neural inertia across state transitions

Yawning is a highly conserved behavior, yet its neural dynamics across arousal state transitions remain poorly understood. Classical reflex models fail to account for the precise timing of yawns during large-scale changes in brain network organization. Here, we investigated the neural signatures of yawning using simultaneous electroencephalography (EEG), electromyography (EMG), and kinematic recordings in a beagle model during wakefulness and propofol anesthesia. Propofol-associated yawning exhibited marked temporal asymmetry, with 89.2% of events occurring during emergence from anesthesia. To resolve the fast neural dynamics surrounding these events, we applied empirical mode decomposition coupled with the Hilbert-Huang transform (EMD-HHT) analyses. Across induction, recovery, and wakefulness, yawning was consistently associated with a transient decoupling between local and global network dynamics: a brief increase in local {gamma}-band power coincided with a drop in network flexibility, quantified by instantaneous frequency volatility; IFV). We termed this reproducible motif as "Energy-Dynamics Mismatch" (EDM). A machine learning classifier leveraging EDM features reliably decoded the brain state immediately preceding yawning. We further validated the presence of this signature in an independent human cohort during anesthesia induction. These findings indicate that yawning is not a passive reflex, but is tightly linked to moments of network instability during state transitions. From a computational perspective, EDG may reflect a transient "control effort" that preserves information integration in the presence of "neural inertia." This dynamic signature may provide a quantitative biomarker for monitoring arousal transitions brain-computer interface (BCI) interface state-alerting. Significance StatementYawning is a ubiquitous and evolutionarily conserved behavior, yet its neural basis remains elusive. Using high-resolution neural recordings in a cross-species model, we show that yawning is not a passive reflex, but reliably coincides with a distinct, transient brain-state signature. Specifically, yawning occurs when local high-frequency cortical activity briefly increases while global network flexibility decreases - a pattern we term an "Energy-Dynamics Mismatch" (EDM). We propose that EDM reflects a compensatory neural process engaged during moments of network instability, consistent with overcoming neural inertia to preserve information integration. By identifying this conserved neural marker, this work advances the biological understanding of yawning and suggests a potential biomarker for detecting critical brain states in future BCI.

neuroscience↗

bioRxiv2026

Dual Control of LDL-cholesterol Levels by ANGPTL3 and ANGPTL8

BACKGROUNDInactivation of ANGPTL3 (angiopoietin-like protein 3, A3) is a proven therapeutic strategy for lowering plasma lipid levels independently of the LDL receptor (LDLR), yet the optimal approach to inactivate A3 remains unclear. A3 is proteolytically cleaved and circulates as full-length (A3-FL), N-terminal (A3-Nter) and C-terminal (A3-Cter) fragments. The specific contribution of each form of A3, and of its paralog, ANGPTL8 (A8), in modulating circulating levels of ApoB-Containing Lipoproteins (ABCLs) remain poorly defined. Clarifying these relationships will inform next-generation A3-directed therapies. METHODSWe performed liver perfusion studies to directly compare the number and composition of VLDL particles secreted from mice with and without A3. To amplify effects on cholesterol metabolism, we generated Ldlr-/- mice expressing wildtype A3 (A3-WT), A3-FL or A3-Nter, with or without co-expression of A8, and analyzed plasma lipids, circulating A3 and A8 complexes, and intravascular lipase activities. Complementary in vitro assays and structural modeling were used to assess relative endothelial lipase (EL) inhibition by A3 alone or in complex with A8. RESULTSLiver perfusion studies revealed that A3 inactivation does not alter the rates of hepatic secretion of VLDL in wildtype or Ldlr-/- mice. Inactivation of A8 alone lowered plasma LDL-cholesterol (C) levels by [~]20%, an effect dependent upon the expression of both EL and A3. Maximal inhibition of lipoprotein lipase (LPL) required co-expression of A8 plus both A3-FL and A3-Nter, indicating that A3 cleavage, in addition to A8 expression, is essential for maximal LPL inhibition. In contrast, A8 expression, but not A3 cleavage, was required for optimal EL inhibition. CONCLUSIONSA8 acts in concert with A3 to differentially modulate LPL- and EL-mediated lipolysis, which antagonizes hepatic clearance of newly-secreted atherogenic ABCLs. This mechanistic framework refines our understanding of A3-targeted lipid lowering and highlights the therapeutic potential of dual A3- plus A8-directed strategies to treat dyslipidemia and prevent atherosclerotic cardiovascular disease. Clinical perspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIInactivation of A3 lowers circulating ABCL levels without altering hepatic secretion rates of VLDL-ApoB or -TG. C_LIO_LIProteolytic cleavage of A3 is required for maximal inhibition of LPL. C_LIO_LIInactivation of A8 lowers LDL-C levels through an A3- and EL-dependent, but LDLR-independent, mechanism. C_LI What are the clinical implications?O_LICombining A8 inhibition with A3-inactivating therapies offers a strategy to achieve greater reduction in LDL-C levels and atherosclerotic cardiovascular risk. C_LI

molecular biology↗

bioRxiv2026

Lacticaseibacillus rhamnosus GR-1 attenuates Escherichia coli-induced endometritis in mice, accompanied by modulation of uterine microbiota and metabolite profiles

ObjectiveEndometritis in dairy cows is a highly prevalent infectious disease in cattle farming, which can cause persistent inflammatory responses in the uterus. This study aimed to evaluate the therapeutic efficacy of Lacticaseibacillus rhamnosus (L. rhamnosus) GR-1 against Escherichia coli (E. coli)-induced endometritis in mice and investigate its regulatory effects on uterine microbiota and metabolites. MethodsA total of 36 female BALB/c mice aged 7-8 weeks were randomly divided into 4 groups: CONT group, ECOL group (1.0x108 CFU/mL E. coli), AMP group (0.1 mg/kg ampicillin), and GR-1 group (1.0x109 CFU/mL L. rhamnosus GR-1). Uterine morphological characteristics were observed, and the expression of uterine inflammatory cytokines, oxidative apoptosis-related genes and proteins, as well as related reproductive indices were detected. 16S rRNA sequencing and metabolomic sequencing were performed to evaluate the profiles of uterine microbiota and metabolites. ResultsL. rhamnosus GR-1 effectively alleviated E. coli-induced uterine edema and inflammatory infiltration, and modulated the levels of inflammatory factors (MPO, IL-6, IL-1{beta}, TNF-, IL-10 and MDA) in the uterus. Meanwhile, this strain elevated the levels of antioxidant factors (GSH-Px and SOD), inhibited the expression of the oxidative apoptosis-related factors Keap1, Bax and caspase-3, and upregulated that of Nrf2, HO-1, NQO1 and Bcl-2. Furthermore, treatment with L. rhamnosus GR-1 increased the abundance of beneficial uterine microbiota, promoted the accumulation of L-isoleucyl-L-proline and N-acetylcysteine, and ameliorated the pregnancy status of mice. ConclusionL. rhamnosus GR-1 enhanced uterine anti-inflammatory and antioxidant stress capacity to alleviate E. coli-induced endometritis in mice. It modulated uterine microbiota and metabolites, and also improved the reproductive capacity of mice. Thus it may provide a potential antibiotic alternative for the treatment of dairy cow endometritis.

microbiology↗

bioRxiv2025

Single-cell RNA sequencing and large-scale bulk combination with machine learning reveal gastric cancer-related macrophage heterogeneity

BackgroundThe tumor microenvironment (TME) significantly impacts cancer progression and overall patient survival. However, the complexity of tumor cell-TME interactions in gastric cancer (GC) and their underlying molecular basis remain to be systematically elucidated. MethodsWe performed single-cell RNA sequencing (scRNA-seq) on paired tumor and adjacent tissues from 3 treatment-naive GC patients. We conducted an in-depth characterization of the cellular composition and molecular features of the GC TME, with a particular focus on tumor-associated macrophages (TAMs) subsets and their mediated intercellular communication. Investigating the effect of C1q on the polarisation of THP-1 induced macrophages through migration and invasion experiments ResultsTranscriptomic analysis of 56,151 single cells identified a key TAM subset - C1QA{square} TAMs. This subset is characterized by high expression of genes including C1QA, C1QB, C1QC and FN1, exhibiting a distinct M2-like macrophage phenotype. We developed a LASSO-based predictive model, C1Q-LASSO, to accurately stratify patients based on survival outcomes and chemotherapy responses, independently of established prognostic parameters. In vitro functional experiments further confirmed that C1q directly promotes malignant phenotypes in GC cells. Additionally, C1q significantly enhances the malignant progression of gastric cancer induced by M2 macrophages. ConclusionsUtilizing scRNA-seq technology, this study systematically delineated the heterogeneous landscape of the GC immune microenvironment and its complex cellular interaction network at single-cell resolution. We first identified and functionally validated the C1QA{square} TAM subset, demonstrating its association with poor prognosis and pro-tumorigenic functions.

cancer biology↗

bioRxiv2025

Lithium Chloride Inhibits Iron Dysregulation and Ferroptosis in Induced Pluripotent Stem Cells with ApoE4/E4 from a sporadic Alzheimer's disease patient

Alzheimers disease (AD), particularly its sporadic form (SAD, 95% AD patients), is strongly associated with the apolipoprotein E4 ApoE4 genotype and characterized by oxidative stress, iron dysregulation, and increased susceptibility to ferroptosis. Lithium, a well-established neuroprotective agent, has shown potential to mitigate several pathological mechanisms in AD, including ferroptosis. This study investigates the therapeutic potential of lithium chloride in human induced pluripotent stem cells (iPSCs) derived from a SAD patient with ApoE4/E4 genotype, and compared effects with those of isogenic gene-edited ApoE3/E3 control. Lithium treatment significantly improved cell viability in ApoE4/E4 iPSCs. It also reversed key ferroptosis phenotypes, including elevated cytosolic Fe2+, increased expression of divalent metal transporter 1, reduced level of glutathione peroxidase 4, enhanced lipid peroxidation, and excessive ROS production. Moreover, lithium normalized mitochondrial respiration and reduced proton leak, indicating preservation of mitochondrial function and protection against mitochondrial damage and cell death. Lithium also reduced the expression of type 1 InsP3 receptor (InsP3R-1) protein, a Ca2+ channel located on the endoplasmic reticulum (ER) membrane. Together, these findings highlight lithiums inhibition of ferroptosis through modulation of iron metabolism, antioxidant defenses, and inhibition of disrupted Ca2+ signaling. Given its demonstrated efficacy in reversing ApoE4-driven cellular vulnerabilities, lithium salt warrants further investigation for the treatment of AD.

cell biology↗

bioRxiv2025

Highly accurate prophage island detection with PIDE

As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify prophages through computational methods. Here, we introduce PIDE for identifying prophages from bacterial genomes or metagenome-assembled genomes. PIDE integrates a pre-trained protein language model and gene density clustering algorithm to distinguish prophages. Benchmarking on bacterial genomes with experimental prophage annotation demonstrates that PIDE pinpoints prophages with precise boundaries. Applying PIDE to 4,744 human gut representative genomes reveals 24,467 prophages with widespread functional capacity. PIDE is open source and is available at https://github.com/chyghy/PIDE.

bioinformatics↗

bioRxiv2024

Intranasal Lithium Chloride Nanoparticles Inhibit Inflammatory Pyroptosis in Brains and Ameliorate Memory Loss and Depression Behavior in 5xFAD mice

BackgroundAlzheimers disease (AD) is a devastating neurodegenerative disease (AD) and has no treatment that can cure or halt the disease progression. This study explored the therapeutic potential of lithium salt dissolved in Ryanodex formulation vehicle (RFV) and delivered to the brain by intranasal application. We first compared lithium concentrations in the brain and blood of wild-type mice following intranasal or oral administration of lithium chloride (LiCl) dissolved in either RFV or water. The beneficial and side effects of intranasal versus oral LiCl in RFV in these mice were assessed and potential mechanisms underlying the efficacy of anti-inflammation and anti-pyroptosis in the brains were also investigated in both wild-type (WT) and 5XFAD Alzheimers Disease (AD) mice brains. MethodsFor the study of brain versus blood lithium concentrations, WT B6SJLF1/J mice at 2 months of age were treated with intranasal or oral LiCl (3 mmol/kg) dissolved in RFV or in water. Brain and blood lithium concentrations were measured at various times after drugs administration. Brain/blood lithium concentration ratios were then determined. For studying therapeutic efficacy versus side effects and their underlying mechanisms, 5XFAD and WT B6SJLF1/J mice were treated with intranasal LiCl (3 mmol/kg) daily, Monday to Friday each week, in RFV beginning at 2 or 9 months of age with a 12-week treatment duration. Animal behaviors were assessed for depression (tail suspension), cognition (fear conditioning and Y maze), olfaction (buried food test), and motor functions (rotarod) at the age of 5 and 12 months. Blood and brain tissue were harvested from these mice at 13 months. Blood biomarkers for the functions of thyroid (thyroid stimulating hormone, TSH) and kidney (creatinine) were measured using ELISA. Changes in protein expression levels of the endoplasmic reticulum Ca2+ release channels type 1 InsP3 receptors (InsP3R-1), malondialdehyde (MDA)-modified proteins and 4-hydroxy-2-nonenal (4-HNE), pyroptosis regulatory proteins (NLR family pyrin domain containing 3 (NLRP3), cleaved caspase-1, N-terminal of Gasdermin D (GSDMD)), cytotoxic (IL-1{beta}, IL-18, IL-6, TNF-) and cytoprotective (IL-10) cytokines and synapse proteins (PSD-95, synapsin-1) were determined using immunoblotting. Mouse body weights were monitored regularly. ResultsCompared to oral LiCl in RFV nanoparticles, intranasal treatment of WT mice with LiCl in RFV markedly decreased blood concentrations at the time frame of 30-120 minutes. The ratio of brain/blood lithium concentration after Intranasal lithium chloride in RFV significantly increased, in comparison to those after oral administration lithium chloride in RFV or intranasal administration of lithium chloride in water. Intranasal lithium chloride in RFV inhibited both memory loss and depressive behavior in adult and aged 5XFAD mice. Additionally intranasal treatment of aged 5XFAD mice with LiCl in RFV effectively suppressed the increases in InsP3R-1, intracellular oxidative stress markers (4-HNE-bound and MDA-modified proteins), pyroptosis activation proteins (NLRP3, cleaved caspase-1, N-terminal GSDMD) and cytotoxic cytokines (IL-1{beta}, IL-6, TNF-), but reversed the down-regulation of cytoprotective cytokine IL-10. Intranasal LiCl in RFV also alleviated the loss of the postsynaptic synapse protein PSD-95, but not synapsin-1, in aged 5XFAD mice. Blood level of the kidney function marker creatinine was significantly increased in 5XFAD than in WT mice in an age-dependent manner and this elevation was abolished by intranasal delivery of LiCl in RFV. Intranasal LiCl in RFV for 12 weeks in both WT or 5XFAD mice did not affect blood biomarkers for thyroid function, nor did it affect smell or muscle function or body weight. ConclusionIntranasal administration of LiCl in RFV significantly decreased lithium blood concentrations and increased brain/blood lithium concentration ratio, in comparison to its oral administration. Intranasal administration of LiCl in RFV robustly protected against both memory loss and depressive-like behavior, while had no side effects concerning thyroid and kidney toxicity in 5XFAD mice. These lithium-induced beneficial effects were strongly associated with lithiums suppression of InsP3R-1 Ca2+ channel receptor increase, pathological neuroinflammation and activation of the pyroptosis pathway, as well as the loss of some synaptic proteins. Intranasal delivery of lithium salt in RFV could become an effective and potent inhibitor of pathological inflammation/pyroptosis in the CNS and serve as a new treatment for both AD-associated dementia and depression with minimal unwanted side effects including peripheral organ toxicity.

neuroscience↗

bioRxiv2024

Intranasal dantrolene nanoparticles inhibit lipopolysaccharide-induced depression and anxiety behavior in mice

This study investigates the therapeutic effectiveness of intranasal dantrolene nanoparticles pretreatment to inhibit lipopolysaccharide (LPS)-induced pathological inflammation and synapse destruction and depressive and anxiety behavior in mice. B6SJLF1/J adult mice were pretreated with intranasal dantrolene nanoparticles (dantrolene: 5mg/kg), daily, Monday to Friday, 5 days per week, for 4 weeks. Then, mice were treated with intraperitoneal injection of LPS (5mg/kg) for one time. Behavioral tests for depression and anxiety were performed 24 hours after a one-time LPS injection. Biomarkers for pyroptosis-related inflammation cytokines (IL-1{beta} and IL-18) in blood and brains were measured using enzyme-linked immunosorbent assay (ELISA) and immunoblotting, respectively. The changes of primary proteins activation inflammatory pyroptosis (NLRP3: NLR family pyrin domain containing 3, Caspase-1, N-GSDMD: N terminal protein gasdermin D) and synapse proteins (PSD-95 and synpatin-1) in brains were measured using immunoblotting. Intranasal dantrolene nanoparticles robustly inhibited LPS-induced depression and anxiety behavior. Intranasal dantrolene nanoparticles significantly inhibited LPS-induced pathological elevation of IL-1{beta} and IL-18 in the blood and brain and inhibited LPS induced activation of pyroptosis. Intranasal dantrolene nanoparticles significantly ameliorated decrease of PSD-95 and synpatin-1 proteins in brains. Thus, intranasal dantrolene nanoparticles has demonstrated neuroprotection against inflammation mediated depression and anxiety behaviors and should be studied furthermore as a future effective drug treatment of major depression disorder or anxiety psychiatric disorder.

animal behavior and cognition↗

bioRxiv2024

Small mammals in biodiversity hotspot harbor viruses of epidemic potential

Metagenomic sequencing has transformed our understanding of viral diversity in wildlife and its threat to human health. Despite this progress, many studies have lacked systematic and ecologically informed sampling, which has left numerous potentially emergent viruses undiscovered, and the drivers of their ecology and evolution poorly understood. We conducted an extensive analysis of viruses in the lung, spleen, and gut of 1,688 animals from 38 mammalian species across 428 sites in Yunnan, China--a hotspot for zoonotic diseases. We identified 162 mammalian viral species, including 102 novel species and 24 posing potential risks to humans due to their relationships with known pathogens associated with serious diseases and their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-species transmission, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.

microbiology↗

bioRxiv2024

FEDKEA: Enzyme function prediction with a large pretrained protein language model and distance-weighted k-nearest neighbor

Recent advancements in sequencing technologies have led to the identification of a vast number of hypothetical proteins, surpassing current experimental capabilities for annotation. Enzymes, crucial for diverse biological functions, have garnered significant attention; however, accurately predicting enzyme EC numbers for proteins with unknown functions remains challenging. Here, we introduce FEDKEA, a novel computational method that integrates ESM-2 and distance-weighted KNN (k-nearest neighbor) to enhance enzyme function annotation. FEDKEA first employs a fine-tuned ESM-2 model with four fully connected layers to distinguish from other proteins. For predicting EC numbers, it adopts a hierarchical approach, utilizing distinct models and training strategies across the four EC number levels. Specifically, the classification of the first EC number level utilizes a fine-tuned ESM-2 model with three fully connected layers, while transfer learning with embeddings from this model supports the second and third-level tasks. The fourth-level classification employs a distance-weighted KNN model. Compared to existing tools such as CLEAN and ECRECer, two state-of-the-art computational methods, FEDKEA demonstrates superior performance. We anticipate that FEDKEA will significantly advance the prediction of enzyme functions for uncharacterized proteins, thereby impacting fields such as genomics, physiology and medicine. FEDKEA is easy to install and currently available at: https://github.com/Stevenleizheng/FEDKEA

bioinformatics↗

bioRxiv2024

Ultra-resolution Deconvolution of Spatial Transcriptomics Unveils Spatiotemporal Cellular Dynamics in Complex Microenvironments

Immune cells infiltrate tissues in response to exogenous pathogens or spontaneous tumors, generating protective immunity to safeguard tissues. Despite advancements in spatial transcriptomics (ST), the precise spatial distribution and functional specialization of immune cells within tissue microenvironments remain elusive. Here, we introduce an ultra-precision ST deconvolution algorithm (UCASpatial) that enhances the mapping of cell subpopulations to spatial locations by leveraging the contribution of genes indicative of cell identity through entropy-based weighting. Using both in silico and real ST datasets, we demonstrate that UCASpatial improves the robustness and accuracy in identifying low-abundant cell subpopulations and distinguishing transcriptionally heterogeneous cell subpopulations. Applying UCASpatial to human colorectal cancer (CRC), we link genomic alterations in individual cancer clones to multi-cellular characteristics of the tumor immune microenvironment (TIME) and reveal the co-evolution of tumor cells and TIME at a clonal resolution. We show that the copy number gain on chromosome 20q (chr20q-gain) in tumor cells orchestrates a T cell-excluded TIME, indicative of resistance to immunotherapy in CRC, and is associated with tumor-intrinsic human endogenous retrovirus subfamily H (HERV-H) silencing and impaired type I interferon response. In murine wound healing models, we illuminate the spatiotemporal dynamics of individual cell subsets across various stages of the healing process. We discovered that the scarring-healing mice (C57BL/6) exhibited a replacement of Prg4+ chondrogenic progenitors to Igfbp5+ chondrocytes in the wound bed at the regeneration stage, a change not observed in the regenerative strain (MRL/MpJ). The Igfbp5+ chondrocyte, spatially coordinating with Cd36+ Gpnmb+ Il1b- macrophage and Fmod+ fibroblast, forms a pro-fibrotic community associated with regeneration failure. The cell-cell interactions within this three-cell cluster, mediated by the IL11-IL11RA axis, drive the pro-fibrotic community formation and limit regeneration in C57BL/6 mice. Our findings present UCASpatial as a versatile tool for deciphering fine-grained cellular landscapes in ST and exploring intercellular mechanisms in complex and dynamic microenvironments.

bioinformatics↗

bioRxiv2024

Single cell transcriptome profiling reveals pathogenesis of Bullous Pemphigoid

Bullous pemphigoid (BP) triggers profound functional changes in both non-immune and immune cells in the skin and circulation, yet the underlying mechanisms remain elusive. In this study, we conducted single-cell transcriptome analysis on donor-matched lesional and non-lesional skin, as well as blood samples from BP patients. Lesional skin non-immune cells coordinately upregulated metabolism, wound healing, immune activation, and cell migration associated pathways. Skin LAMP3+ DCs derived from cDC2 exhibited higher pro-inflammatory signatures than those from cDC1, and VEGFA+ mast cells driving BP progression, were predominantly from lesional skin. As BP patients transition from active to remission stages, blood B cell function shifts from differentiation and memory formation to heightened type 1 interferon signaling and reduced IL-4 response. Blood CX3CR1+ZNF683+ and LAG3+ exhausted T cells exhibited the highest TCR expansion among clones shared with skin CD8+T cells, suggesting they likely represent BP-reactive cells fueling skin CD8+T cell clonal expansion. Clinical parameters for BP severity correlated positively with blood NK cell IFN-{gamma} production, whereas correlated negatively with NK cell AREG production. In lesional skin, NK cell-keratinocyte interactions exhibited reduced AREG-EGFR and enhanced IFNG-IFNGR1/2 signaling. NK cell-derived AREG mitigates IFN-{gamma}-induced keratinocyte apoptosis, highlighting a crucial balance between AREG and IFN-{gamma} in BP progression. These results reveal significant functional shifts in BP pathology within skin and blood cells and suggest new therapeutic targets for disease management. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/601141v2_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@18517f2org.highwire.dtl.DTLVardef@e743e9org.highwire.dtl.DTLVardef@11b9228org.highwire.dtl.DTLVardef@11884c3_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

The Magic Impacts of Sounds on Consumer's Brain: How Do Natural Sounds Nudge Green Product Purchase?

Despite extensive research on nudging techniques aimed at promoting green consumption, the influence of natural sounds on encouraging environmentally friendly behavior remains relatively understudied. It is valuable to examine how sounds matter in green marketing, as more and more firms are using background sounds in video advertisements. Drawing on the Stimulus-Organism-Response model, we propose that natural sound increase early attentional congruency associated with green products, thereby promoting customers purchase of green products. To test on our theory, we conducted an experiment using an event-related potentials (ERP) method and employed a hierarchical drift-diffusion model (HDDM). The results show that compared with unnatural sounds, natural sounds not only increased the purchase rates for green products but also enhanced decision-making efficiency (drift rate) in favor of purchasing green products. Additionally, consumers also exhibited a reduced frontal early P2 wave (150-230ms) in response to green products under natural sounds, indicating that natural sounds increased the early attentional congruency associated with green products. More importantly, the early attentional congruency provides an explanation for how natural sounds nudge the efficiency of purchasing decisions for green products. This study thus contributes to the discovery of a new psychological path that helps deepen our understanding of how natural sounds can nudge green consumption. It also provides actionable implications for green consumption market managers.

neuroscience↗

bioRxiv2024

iVirP: An integrative, efficient, and user-friendly pipeline to annotate viral contigs from raw reads of metagenome or VLP sequencing

Metagenome sequencing and virus-like particles sequencing make it possible to explore the virome in the humans and other organisms. One way to analyze the sequencing data is to assemble reads into contigs according to the overlapping regions, and then the predicted viral contigs are screened out to conduct deeper dives. iVirP (integrative virome pipeline) is a user-friendly pipeline that includes the whole process of viral contigs discovery from the quality control of raw data to the filter of high quality viral contigs. This pipeline also features a branching function that can estimate the abundance of known eukaryotic viruses in a short period, while reducing host contamination. It is suitable for the rapid diagnosis of pathogens. Throughout iVirP, many details that might affect the experience of users are optimized carefully to reduce the time spent on dealing with usage and errors. iVirP was tested on a published, high-quality VLP sequencing dataset and was able to well reproduce the conclusions of the corresponding research. The benchmark indicates that iVirP could accurately assemble viral contigs from real sequencing data. iVirP is easy to install and currently available at https://github.com/li-bw18/iVirP.

bioinformatics↗

bioRxiv2023

ESM-PVP: Identification and classification of phage virion proteins with a large pretrained protein language model and an MLP neural network

Bacteriophages, also known as phages, are essential for the stability of the microbiome system due to their ability to infect prokaryotes, another significant component of the microbiome. Thus, understanding the functions of phage proteins could help us unravel the nature of phages and their roles in the microbiome. However, limited by the low throughput of experimental techniques, a vast number of phage proteins remain unannotated in terms of their functions. Computational methods are expected to solve this restriction due to their high throughput and cost-effectiveness. In this study, we focused on one aspect of functional annotation for phage proteins, the identification and classification of phage virion proteins, and the integration of a large pretrained protein language model and an MLP neural network dramatically improved the performance of these two tasks. Additionally, we compared our model with some previous deep learning models using a newly collected, independent benchmark dataset, demonstrating the strong generalization ability of our model for both tasks. The source codes of ESM-PVP and the software for the PVP identification task have been uploaded to: https://github.com/li-bw18/ESM-PVP.

bioinformatics↗