Biology subjects

Zhang, F.

Publications and source records attributed to Zhang, F..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

The Multiple Roles of Gamma Interferon in Intraepithelial T Cell-Villous Enterocyte Interactions in Active Celiac Disease

We compared duodenal biopsies showing active celiac disease (CeD) to normal controls using single cell RNA sequencing, cyclic immunofluorescence, RNAScope and proximity ligation assays. There is increased infiltration of villous but not crypt epithelium T cells bearing either {beta} or {gamma}{delta} T cell receptors (TCRs) in CeD. Both T cell subsets are activated cytotoxic T lymphocytes (CTLs) and surprisingly are the predominant mucosal source of IFN{gamma}. In response to this IFN{gamma},villous but not crypt enterocytes show an IFN{gamma} signature, including nuclear phospho-STAT1 protein, class II HLA molecules and IFN{gamma}-inducible chemokines known to recruit CTLs (e.g., CCL3, CCL4, CXCL10, and CXCL11) and receptors for these chemokines are expressed on the infiltrating CTLs. Villous enterocytes also display increased HLA-E and HLA-B mRNAs and proteins. Bioinformatic analyses (NICHES) and proximity ligation assays show frequent binding of both {beta} and {gamma}{delta} TCRs with enterocyte HLA-E or HLA-B, but not HLA-DR. In contrast, NKG2C, proposed as an alternative trigger of CTL activation, is infrequently-expressed and shows few interactions with HLA-E. Our data suggest that activated intraepithelial CTLs produce IFN{gamma} which recruits additional CTLs and increases antigen-dependent killing of villous epithelium using either conventional or HLA-E antigen presentation. SignifanceAnalyses of diagnostic biopsies from celiac disease patients reveals critical roles for IFN{gamma} actions on enterocytes and a surprising role of HLA-E in antigen presntation. Activated cytotoxic T lymphocytes (CTLs) that are the primary source of mucosal IFN{gamma}, leading to IFN{gamma} signaling in villous enterocytes, including expression of phospho-STAT1 protein, class II HLA molecules, and chemokines that attract CTLs. Bioinformatic ligand receoptor analyses and proximity ligation assays showed frequent interactions between intraepithelial CTLs and enterocyte HLA-E or HLA-B, indicating that IFN{gamma} production by the CTLs likely promotes further CTL recruitment and antigen-dependent killing of the villous epithelium.

immunology↗

bioRxiv2024

Estrus-Tracking Cortical Neurons Integrate Social cues and Reproductive states to Adaptively Control Sexually Dimorphic Sociosexual Behaviors

Female sociosexual behaviors, essential for survival and reproduction, are adaptively modulated by ovarian hormones. However, the neural mechanisms integrating internal hormonal states with external social cues to guide these behaviors remain poorly understood. Here we identified primary estrous-sensitive Cacna1h-expressing medial prefrontal (mPFCCacna1h+) neurons that orchestrate adaptive sociosexual behaviors. Bidirectional manipulation of mPFCCacna1h+ neurons drives opposite-sex-directed behavioral shifts between estrus and diestrus females. In males, these neurons serve opposite functions compared to estrus females, mediating sexually dimorphic effects via anterior hypothalamic outputs. Miniscope imaging reveals mixed-representation of self-estrous states and social target sex in distinct mPFCCacna1h+ subpopulations, with biased-encoding of opposite-sex social cues in estrus females and males. Mechanistically, ovarian hormone-driven upregulation of Cacna1h-encoded T-type calcium channels underlies estrus-specific activity changes and sexual-dimorphic function of mPFCCacna1h+ neurons. These findings uncover a prefrontal circuit that integrates internal hormonal states and target-sex information to exert sexually bivalent top-down control over adaptive social behaviors.

neuroscience↗

bioRxiv2024

Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways

Degradation of many yeast mRNAs involves decapping by the Dcp1:Dcp2 complex. Previous studies on decapping activators Edc3 and Scd6 suggested their limited roles in mRNA decay. RNA-seq analysis of mutants lacking one or both proteins revealed that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation that are masked in the single mutants. These transcripts are frequently targeted by decapping activators Dhh1 and Pat1, and the collective evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2. Ribosome profiling shows that redundancy between Scd6 and Edc3 and their functional interactions with Dhh1 and Pat1 extend to translational repression of particular transcripts, including a cohort of poorly translated mRNAs displaying interdependent regulation by all four factors. Scd6/Edc3 also participate with Dhh1/Pat1 in post-transcriptional repression of proteins required for respiration and catabolism of alternative carbon sources, which are normally expressed only in limiting glucose. Simultaneously eliminating Scd6/Edc3 increases mitochondrial membrane potential and elevates metabolites of the tricarboxylic acid and glyoxylate cycles typically observed only during growth in low glucose. Thus, Scd6/Edc3 act redundantly, in parallel with Dhh1 and in cooperation with Pat1, to adjust gene expression to nutrient availability by controlling mRNA decapping and decay.

genetics↗

bioRxiv2024

Universal features of Alternative splicing in response to diverse environmental stimuli in rice and the vital roles of TFs in AS regulation

BackgroundPre-mRNA alternative splicing (AS) plays essential roles in response to environmental stimuli in plants. However, the universal and specific features of splicing in response to diverse environmental conditions remain not fully understood. Recent studies have shown the co-transcriptional characteristics of splicing, which lead to the reasonable speculation that the elements or factors regulating transcription can also affect splicing. Among of which, the effects of transcription factors on alternative splicing in plants under environmental stimuli are still confusing. A large amount 0f public available RNA sequencing data are valuable resources to be re-analyzed for answering questions beyond the aims of their original studies. ResultsWe explored the universal features of AS using a standard RNA-seq dataset TENOR, which stems from rice samples under controlled diverse conditions to provide comprehensive and comparable AS analysis under various conditions. We found that AS widely occurs in rice under stimuli, with significant tissue specificity, temporal dynamics, commonality among different stresses or treatments as well as significant difference between differential alternative splicing and expressed genes (DASGs and DEGs) in rice under environmental stimuli. The majority of DASGs under various stresses are splicing factors and transcription factors. The correlation analysis shows that the expression level of transcription factors is significantly correlated with the PSI of AS events. The predominant transcription factors correlating with alternative splicing events come from bHLH, bzip and hsfa families. We validated the effects of transcription factors on AS by analyzing RNA-seq data from transcription factor mutants and found substantial differential AS events between mutants and wild type. Furthermore, the significant correlation was discovered between the transcription levels of transcription factors and splicing factors. ConclusionWe found universal features of AS and the predominant AS events of SFs and TFs in plants under diverse environments. We propose that TFs might regulated AS of download genes partly by changing the patterns of their own transcription and splicing to further regulate the transcription of SFs. This work illuminate the studies on the possible mechanisms by which TFs modulate AS in plant, especially under environmental stimuli.

plant biology↗

bioRxiv2024

Identification of an intrinsically disordered region (IDR) in arginyltransferase 1 (ATE1)

Arginyltransferase 1 (ATE1) catalyzes arginylation, an important post-translational modification (PTM) in eukaryotes that plays a critical role in cellular homeostasis. The disruption of ATE1 function is implicated in mammalian neurodegenerative disorders and cardiovascular maldevelopment, while post-translational arginylation has also been linked to the activities of several important human viruses such as SARS-CoV-2 and HIV. Despite the known significance of ATE1 in mammalian cellular function, past biophysical studies of this enzyme have mainly focused on yeast ATE1, leaving the mechanism of arginylation in mammalian cells unclear. In this study, we sought to structurally and biophysically characterize mouse (Mus musculus) ATE1. Using size-exclusion chromatography (SEC), small angle X-ray scattering (SAXS), and hydrogen deuterium exchange mass spectrometry (HDX-MS), assisted by AlphaFold modeling, we found that mouse ATE1 is structurally more complex than yeast ATE1. Importantly, our data indicate the existence of an intrinsically disordered region (IDR) in all mouse ATE1 splice variants. However, comparative HDX-MS analyses show that yeast ATE1 does not have such an IDR, consistent with prior X-ray, cryo-EM, and SAXS analyses. Furthermore, bioinformatics approaches reveal that mammalian ATE1 sequences, as well as in a large majority of other eukaryotes, contain an IDR-like sequence positioned in proximity to the ATE1 GNAT active-site fold. Computational analysis suggests that the IDR likely facilitates the formation of the complex between ATE1 and tRNAArg, adding a new complexity to ATE1 structure and providing new insights for future studies of ATE1 functions. For Table of Contents Use Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/609426v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@130d030org.highwire.dtl.DTLVardef@1b40613org.highwire.dtl.DTLVardef@1fb0ae5org.highwire.dtl.DTLVardef@88426d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

The clinical antiprotozoal drug halofuginone promotes weight loss by elevating GDF15 and FGF21

Obesity is a debilitating disease with increasing worldwide prevalence. Despite its high prevalence, specific pharmacologic intervention for obesity is challenging. Here, we report that halofuginone, an FDA-approved anti-scleroderma and anti-protozoal drug, is a promising anti-obesity agent in rodent models. Halofuginone suppressed food intake, increased energy expenditure, and resulted in weight loss in preclinical diet-induced obese mouse models, while also decreasing insulin resistance and hepatic steatosis. By combining genetic and pharmacological tools with transcriptomics, we identified that halofuginone increases FGF21 and GDF15 levels via ATF4. Using knockout mice, we show these hormones are both necessary for its anti-obesity effects. Thus, our study first reports the beneficial metabolic effects of halofuginone and underscores its utility to treat obesity and its associated metabolic complications.

pharmacology and toxicology↗

bioRxiv2024

The role of TRPV4 in acute sleep deprivation-induced fear memory impairment

Acute sleep deprivation (ASD) negatively impacts fear memory, but the underlying mechanisms are not fully understood. Transient receptor potential vanilloid 4 (TRPV4), a cation channel which is closely correlated with the concentration of Ca2+, and neuronal Ca2+ overloading is a crucial inducement of learning and memory impairment. This study utilized an acute sleep-deprived mouse model combined with fear conditioning to investigate these mechanisms. mRNA sequencing revealed increased expression of TRPV4 in mice with ASD-induced fear memory impairment. Notably, knockdown of TRPV4 reversed ASD-induced fear memory impairment. ASD leads to the increased concentration of Ca2+. Additionally, we observed a reduction in spine density and a significant decrease in postsynaptic density protein 95 (PSD95), which is associated with synaptic plasticity, in sleep-deprived fear memory impairment mice. This indicates that ASD may cause overloaded Ca2+, disrupting synaptic plasticity and impairing fear memory. Moreover, TRPV4 knockdown significantly decreased Ca2+ concentration, mitigated the loss of dendritic spines and reduction of PSD95, contributing to the restoration of fear memory. These findings indicate a potential protective role of TRPV4 knockdown in counteracting ASD-induced fear memory deficits. Collectively, our results highlight that TRPV4 may be a potential therapeutic target in mediating fear memory impairment due to ASD and underscore the importance of sleep management for conditions like PTSD.

neuroscience↗

bioRxiv2024

The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing

Primary sclerosing cholangitis (PSC) is a chronic progressing cholestatic disease that often co-occurs with inflammatory bowel disease (PSC-IBD). PSC-IBD affecting the colon (PSC-UC) is likened clinically to ulcerative colitis (UC), however differences include a right colon dominance, less severe inflammatory presentation and a greater lifetime risk of colorectal cancer. To understand the basis of clinical differences, we combine single-cell mRNA and antigen receptor sequencing, 16S ribosomal DNA analysis and spatial transcriptomics on biopsies from multiple colon regions of both PSC-UC and UC patients in remission or at the time of relapse. We discover disease-specific cell and microbial profiles between these cohorts, highlighting a distinct landscape in the right colon of PSC-UC patients and an epithelial-endothelial cell state that may contribute to intestinal permeability in UC. We show the expansion of an activated mast cell state in both diseases during flare, and demonstrate the requirement of TMEM176B in sustaining this activated state. Together this work demonstrates that PSC-UC and UC are distinct diseases with common cell mechanisms during inflammation, providing cellular and microbial insights to improve treatment of both patient cohorts.

cell biology↗

bioRxiv2024

Paraptosome: A Novel Pathological Feature in Paraptotic Cell Death

Paraptosis is a novel form of programmed cell death characterized by distinct morphological features such as swelling of the endoplasmic reticulum and mitochondria, and cytoplasmic vacuolation. Unlike apoptosis, paraptosis does not involve the activation of caspases or DNA fragmentation. These unique features make paraptosis an intriguing target for cancer therapy, particularly against apoptosis-resistant cells. Here, we report a novel morphological feature of paraptosis: the formation of high-density spherical structure, which we tentatively term "paraptosome." We found that these putative paraptosomes originate from the Golgi apparatus, appearing as high-density formations under light microscopy and colocalizing with the trans-Golgi marker {beta}4GALT1-RFP. Time-lapse confocal microscopy and immunostaining demonstrated that putative paraptosomes form due to Golgi stress or disintegration, leading to severe disruption of Golgi function. Furthermore, we show that paraptosis inducers such as glabridin, morusin, and honokiol can cause significant alterations in the endoplasmic reticulum, mitochondria, autophagosomes, and lysosomes in U251MG glioblastoma cells; however, the formation of putative paraptosomes is not induced by isolated stress inducers. Collectively, these findings suggest that the putative paraptosome may be a novel characteristic structure of paraptosis. The discovery of paraptosomes provides a unique marker for defining paraptotic cell death and offers new insights into the characteristic pathological phenomena associated with multiple organelle dysfunction. This finding broadens the scope of cell biology research by introducing a new structural paradigm linked to paraptosis and may have implications for developing targeted therapies against apoptosis-resistant cancers.

cell biology↗

bioRxiv2024

Astrocyte extracellular matrix modulate neuronal dendritic development

Major developmental events occurring in the hippocampus during the third trimester of human gestation and neonatally in altricial rodents include rapid and synchronized dendritic arborization and astrocyte proliferation and maturation. We tested the hypothesis that signals sent by developing astrocytes to developing neurons modulate dendritic development in vivo. We altered neuronal development by neonatal (third trimester-equivalent) ethanol exposure in mice; this treatment increased dendritic arborization in hippocampal pyramidal neurons. We next assessed concurrent changes in the mouse astrocyte translatome by translating ribosomal affinity purification (TRAP)-seq. We followed up on ethanol-inhibition of astrocyte Chpf2 and Chsy1 gene translation because these genes encode for biosynthetic enzymes of chondroitin sulfate glycosaminoglycan (CS-GAG) chains (extracellular matrix components that inhibit neuronal development and plasticity) and have not been explored before for their roles in dendritic arborization. We report that Chpf2 and Chsy1 are enriched in astrocytes and their translation is inhibited by ethanol, which also reduces the levels of CS-GAGs measured by Liquid Chromatography/Mass Spectrometry. Finally, astrocyte-conditioned medium derived from Chfp2-silenced astrocytes increased neurite branching of hippocampal neurons in vitro. These results demonstrate that CS-GAG biosynthetic enzymes in astrocytes regulates dendritic arborization in developing neurons.

neuroscience↗

bioRxiv2024

Long-Range Enhancer Networks Gradually Emerge as Key Regulators During Human Cortical Neurogenesis

The chromatin in the human brain cortex shows more enhancer-enhancer contacts than in macaques and mice, yet the organization of these contacts across cellular states and their mechanisms remain unclear. Here, we developed SCOPE-C, a cost-effective technique designed for mapping DNase I Hypersensitive Sites and their spatial interactions, with the potential for scalability to single-cell resolution. Employing SCOPE-C, we generated a comprehensive chromatin map detailing cis-regulatory elements in four cell types during neurogenesis in human, macaque, and mouse fetal cortex. This map introduces a model of long-range enhancer networks that regulate gene transcription during human cortical neurogenesis. In this model, CTCF-mediated loop extrusion forms stripes of enhancer interaction hubs extending up to 10 Mb in human Excitatory Neurons. Enriched with human-specific enhancers and neuropsychiatric disorder-linked SNPs, these remarkably long-range networks predominantly control EN marker genes, suggesting their critical role in robust gene expression during human cortical neurogenesis.

genomics↗

bioRxiv2024

Origin and stepwise improvement of vertebrate lungs

Lungs, essential for terrestrial vertebrates and present in bony fishes but absent in cartilaginous fishes, provide an ideal model for studying organ origination. Our study analyzed single-cell RNA sequencing data from mature and developing vertebrate lungs, revealing substantial similarities in cell composition, developmental trajectories and gene expression pattern across species. Notably, most lung-related genes are also present in cartilaginous fishes, indicating that gene presence alone does not guarantee lung development. We identified thousands of lung regulatory elements specific to bony fishes, with higher concentrations around genes such as tbx4 and the hoxb gene cluster. These regulatory changes might contribute to lung emergence as well as the unique co-expression patterns in lung epithelial cells, such as those related to pulmonary surfactants and cell morphology. Our research also revealed that AT1 cells are specific to mammals, and we identified a mammal-specific gene, sfta2. Knockout experiments demonstrated that sfta2 deletion causes severe respiratory defects in mice, underscoring its critical role in specialized mammalian lungs. In conclusion, our results demonstrate that the origin and evolution of lungs are driven by a complex interplay of regulatory network modifications and the emergence of new genes, underscoring the multifaceted nature of organ evolution.

evolutionary biology↗

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

Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs

Emerging immunotherapies such as immune checkpoint blockade (ICB) and chimeric antigen receptor T-cell (CAR-T) therapy have revolutionized cancer treatment and have improved the survival of patients with multiple cancer types. Despite this success many patients are unresponsive to these treatments or relapse following treatment. CRISPR activation and knockout (KO) screens have been used to identify novel single gene targets that can enhance effector T cell function and promote immune cell targeting and eradication of tumors. However, cancer cells often employ multiple genes to promote an immunosuppressive pathway and thus modulating individual genes often has a limited effect. Paralogs are genes that originate from common ancestors and retain similar functions. They often have complex effects on a particular phenotype depending on factors like gene family similarity, each individual genes expression and the physiological or pathological context. Some paralogs exhibit synthetic lethal interactions in cancer cell survival; however, a thorough investigation of paralog pairs that could enhance the efficacy of cancer immunotherapy is lacking. Here we introduce a sensitive computational approach that uses sgRNA sets enrichment analysis to identify cancer-intrinsic paralog pairs which have the potential to synergistically enhance T cell-mediated tumor destruction. We have further developed an ensemble learning model that uses an XGBoost classifier and incorporates features such as gene characteristics, sequence and structural similarities, protein-protein interaction (PPI) networks, and gene coevolution data to predict paralog pairs that are likely to enhance immunotherapy efficacy. We experimentally validated the functional significance of these predicted paralog pairs using double knockout (DKO) of identified paralog gene pairs as compared to single gene knockouts (SKOs). These data and analyses collectively provide a sensitive approach to identify previously undetected paralog pairs that can enhance cancer immunotherapy even when individual genes within the pair has a limited effect.

bioinformatics↗

bioRxiv2024

A smartphone-based genetically recombinant whole-cell biosensor for highly sensitive monitoring of polychlorinated biphenyls (PCBs)

Polychlorinated biphenyls (PCBs) are highly carcinogenic and persistent pollutants commonly found in ecosystems. Their complex congeners pose a huge challenge to instrumental analysis and ELISA methods, which prefer single and known targets. To overcome this limitation, here we developed an Escherichia coli whole-cell biosensor (WCB) for simultaneously detecting multiple PCB congeners. In this sensor, PCBs were firstly converted into hydroxylated PCBs (OH-PCBs) by bphAB degradation circuits, which then serve as high-affinity targets of transcriptional factor HbpRCBP6-based sensing pathways for sensitive response through extensive chassis screening. The resulting biosensor BL21(DE3)/HbpRCBP6-bphAB shows the lowest detection limits for 2-CBP (2-chlorobiphenyl) to date and can recognize various PCB homologues, including 3-CBP, 4-CBP, 2,3-diCBP and 2,2-diCBP, with detection limits of 0.06-1 M. Further investigation of the docking structure and binding energy reveal that HbpRCBP6 has a stronger affinity for OH-PCBs than for PCBs, indicating that the conversion of PCB by BphAB enzymes is a key step to improve the sensitivity of WCB. Subsequently, we developed an immobilized hydrogel WCB and a smartphone-based detection procedure to facilitate real-time and user-friendly PCB detection. This study will not only advance the biomonitoring of PCB contaminants but also provide an innovative strategy for developing metabolic pathway-sensing proteins combined biosensor. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/601110v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@10772cdorg.highwire.dtl.DTLVardef@22699org.highwire.dtl.DTLVardef@1343c27org.highwire.dtl.DTLVardef@595859_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

MitoStructSeg: A Comprehensive Platform for Mitochondrial Structure Segmentation and Analysis

Mitochondrial morphology and structural changes are closely associated with metabolic dysfunction and disease progression. However, the structural complexity of mitochondria presents a major challenge for accurate segmentation and analysis. Most existing methods focus on delineating entire mitochondria but lack the capability to resolve fine internal features, particularly cristae. In this study, we introduce MitoStructSeg, a deep learning-based framework for mitochondrial structure segmentation and quantitative analysis. The core of MitoStructSeg is AMM-Seg, a novel model that integrates domain adaptation to improve cross-sample generalization, dual-channel feature fusion to enhance structural detail extraction, and continuity learning to preserve spatial coherence. This architecture enables accurate segmentation of both mitochondrial membranes and intricately folded cristae. MitoStructSeg further incorporates a quantitative analysis module that extracts key morphological metrics, including surface area, volume, and cristae density, allowing comprehensive and scalable assessment of mitochondrial morphology. The effectiveness of our approach has been validated on both human myocardial tissue and mouse kidney tissue, demonstrating its robustness in accurately segmenting mitochondria with diverse morphologies. In addition, we provide an open source, user-friendly tool to ensure practical usability.

bioinformatics↗

bioRxiv2024

Single-cell based integrative analysis of transcriptomics and genetics reveals robust associations and complexities for inflammatory diseases

BackgroundUnderstanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible. MethodsWe present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of two recent algorithms, based on networks (scGWAS) or single-cell disease scores (scDRS), according to accuracy/sensitivity and interpretability (M. J. Zhang et al. 2022; Jia et al. 2022). While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,1,73 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC) (F. Zhang et al. 2023; Ishigaki et al. 2022; Smillie et al. 2019; de Lange et al. 2017). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls. ResultsWe first found that single-cell based tool scDRS called superior numbers of supported cell states, like MERTK+ myeloid cells in RA, which were overlooked by network-based scGWAS. While scGWAS was advantageous for gene exploration, scDRS captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5 scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohns disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.

bioinformatics↗

bioRxiv2024

Viral Insulin/IGF-like Peptides Selectively Activate Host Insulin/IGF Signaling pathways during Grouper Iridovirus Infection

Until our recent discovery of viral insulin/IGF-1-like peptides (VILPs), examples of viral mimicry were mostly limited to immunomodulatory proteins and growth factors. We previously showed that six viruses in the Iridoviridae family encode genes mimicking insulin and IGF-1. While VILP-carrying viruses are isolated from fish, the role of VILPs in host-pathogen interactions remain elusive. In this study, we used the Grouper Iridovirus (GIV), one of the VILP-carrying viruses, to examine the impact of the GIV-VILPs on the host IGF-1R/IR system during infection. Our structural analysis revealed that GIV-VILP is 35% identical to both zebrafish insulin and 35 IGF-1. We also showed that GIV-VILPs are early viral transcripts and resulting peptides are secreted during viral infection. Both single-chain (sc, resembling IGF-1) and double chain (dc, resembling insulin) forms of chemically synthesized GIV-VILPs can stimulate insulin receptor (IR) and IGF-1 receptor (IGF1R) phosphorylation. They could also stimulatepost-receptor signaling in both grouper kidney (GK) and zebrafish AB.9 cells as potently as insulin. Notably, supernatants obtained from GIV-infected cells could stimulate insulin/IGF system in a dose dependent manner. Interestingly, GIV-VILP was able to selectively activate the Akt/PI3K pathway while had no or minimal effect on Erk/MAPK pathway. Using either IR, IGF1R or dual inhibitors, we illustrated that inhibition of IR signaling suppressed GIV viral replication while inhibition of IGF1R enhanced viral replication. Consistent with selective signaling action of PI3K/Akt pathway, inhibition of the Akt reduced GIV viral replication however Erk pathway inhibition did not affect it. In summary, GIV-VILP is produced during GIV infection and manipulates host insulin/IGF signaling in a selective manner. Our findings reveal a previously unknown viral strategy in which viruses mimic a host hormone to exploit the hosts endocrine system. This discovery unveils a novel viral pathogenesis mechanism, broadens our understanding of viral mimicry, and opens a new avenue to better understand viral strategies to manipulate the host.

microbiology↗