Biology subjects

Liang, Y.

Publications and source records attributed to Liang, Y..

At least 217 records · Page 12Linked to original sources

bioRxiv2023

Opposing implications of co-evolutionary lineages and traits of gut microbiome on human health status

Little is known about the co-evolutionary history of the human gut microbe and its relevance to host physiology. Here, we constructed a gut prokaryotic genomic database of wild primates (pSGBs) and compared it with the human gut prokaryotic database (hSGBs) to define shared co-evolutionary clusters (SCEC-hSGBs) and co-evolutionary traits of hSGBs. We analyzed the evolutionary trends of specific functions like carbohydrate-active enzymes and antibiotic resistance in hSGBs and uncovered host-jumping events and genome reduction tendencies in SCEC-hSGBs. Intriguingly, the SCEC-hSGBs and the super enrichers of the traits (SUEN-hSGBs), which are putatively partially derived from carnivores, showed opposite implications for host health status. Specifically, SUEN-hSGBs are enriched in various diseases, showing a negative correlation with gut biodiversity and disproportionate contributions to the known health-negative marker taxa and metabolite. Our study provides insight into the origin and adaptability of human gut microbes and references for developing probiotics and microbiome-based host health prediction.

microbiology↗

bioRxiv2023

Decoding fMRI Data: A Comparison Between Support Vector Machines and Deep Neural Networks

Multivoxel pattern analysis (MVPA) examines the differences in fMRI activation patterns associated with different cognitive conditions and provides information not possible with the conventional univariate analysis. Support vector machines (SVMs) are the predominant machine learning method in MVPA. SVMs are intuitive and easy to apply. The limitation is that it is a linear method and mainly suitable for analyzing data that are linearly separable. Convolutional neural networks (CNNs), a class of AI models originally developed for object recognition, are known to have the ability to approximate nonlinear relationships. CNNs are rapidly becoming an alternative to SVMs. The purpose of this study is to compare the two methods when they are applied to the same datasets. Two datasets were considered: (1) fMRI data collected from participants during a cued visual spatial attention task (the attention dataset) and (2) fMRI data collected from participants viewing natural images containing varying degrees of affective content (the emotion dataset). We found that (1) both SVM and CNN are able to achieve above chance level decoding accuracies for attention control and emotion processing in both the primary visual cortex and the whole brain with, (2) the CNN decoding accuracies are consistently higher than that of the SVM, (3) the SVM and CNN decoding accuracies are generally not correlated with each other, and (4) the heatmaps derived from SVM and CNN are not significantly overlapping. These results suggest that (1) there are both linearly separable features and nonlinearly separable features in fMRI data that distinguish cognitive conditions and (2) applying both SVM and CNN to the same data may yield a more comprehensive understanding of neuroimaging data. Key pointsO_LIWe compared the performance and characteristics of SVM and CNN, two major methods in MVPA analysis of neuroimaging data, by applying them to the same two fMRI datasets. C_LIO_LIBoth SVM and CNN achieved decoding accuracies above chance level for both datasets in the chosen ROIs and the CNN decoding accuracies were consistently higher than those of SVM. C_LIO_LIThe heatmaps derived from SVM and CNN, which assess the contribution of voxels or brain regions to MVPA decoding performance, showed no significant overlap, providing evidence that the two methods depend on distinct brain activity patterns for decoding cognitive conditions. C_LI

bioinformatics↗

bioRxiv2023

Exploration of an enzyme-product mapping approach for plant-derived diterpene synthases

Plant-derived diterpene synthases (PdiTPSs) play a critical role in the formation of structurally and functionally diverse diterpenoids. However, the relationship between PdiTPSs and the specificity or promiscuity of their products remains unclear. To explore this correlation, the sequences of 199 functionally characterized PdiTPSs and their corresponding 3D structures were collected and manually corrected. Using this compiled annotated database, the correlations among PdiTPSs sequences, domains, structures and their corresponding products were comprehensively analyzed. However, utilizing sequence similarity network (SSN), phylogenetic trees, and structural topology features alone was insufficient for effective functional classification of PdiTPSs as these methods could not establish a clear mapping between the enzymes and products. Surprisingly, residues verified to play a function through mutagenesis experiments were located within 8[A] of the substrate. Aromatic residues surrounding the substrate exhibited selectivity towards its chemical structure. Specifically, tryptophan (W) was preferentially located around the linear substrate geranylgeranyl pyrophosphate (GGPP), while phenylalanine (F) and tyrosine (Y) were preferentially located around the initial cyclized diterpene intermediate. This analysis revealed the functional space of residues surrounding the substrate of PdiTPSs, most of which have not been experimentally explored. These findings provide guidance for screening specific residues for mutation studies to change the catalytic products of PdiTPSs, allowing us to better understand the correlation between PdiTPSs and their products.

plant biology↗

bioRxiv2023

Projectome-defined subtypes and modular intra-hypothalamic subnetworks of peptidergic neurons

The hypothalamus plays a vital role in coordinating essential neuroendocrine, autonomic, and somatomotor responses for survival and reproduction. While previous studies have explored population-level projections of hypothalamic neurons, the specific innervation patterns of individual hypothalamic axons remain unclear. To understand the organization of hypothalamic axon projections, we conducted a comprehensive reconstruction of single-cell projectomes from 7,180 mouse hypothalamic neurons expressing specific neuropeptides. Our analysis identified 31 distinct subtypes based on projectome-defined characteristics, with many exhibiting long-range axon collateral projections to multiple brain regions. Notably, these subtypes selectively targeted specific subdomains within downstream areas, either unilaterally or bilaterally. Furthermore, we observed that individual peptidergic neuronal types encompassed multiple projectome-defined subtypes, explaining their diverse functional roles. Additionally, by examining intra-hypothalamic axon projections, we uncovered six modular subnetworks characterized by enriched intramodular connections and distinct preferences for downstream targets. This modular organization of the intra-hypothalamic network likely contributes to the coordinated organization of hypothalamic outputs. In summary, our comprehensive projectome analysis reveals the organizational principles governing hypothalamic axon projections, providing a framework for understanding the neural circuit mechanisms underlying the diverse and coordinated functions of the hypothalamus.

neuroscience↗

bioRxiv2023

Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adjust, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. The Shannon index was significantly higher in sandy samples than in muddy samples. The co-occurrence network was tighter and more species were involved in community building in sandy samples. The principal coordinates analysis identified a significant separation between different sediment types and between stations (LiCun estuary, LC and ZhanQiao Pier, ZQ). Proteobacteria, which had a relative abundance of approximately 50% at all phylum levels, was significantly more abundant at ZQ, while Campilobacterota and Firmicutes were significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. The RDA results, where each months samples were concentrated individually, showed reduced variation between months when the amplicon sequence variant was replaced by KEGG orthologs, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria. HighlightsO_LISandy sediments have more bacterial species involved in community building. C_LIO_LIDifferent substrates from different stations have their own phylum biomarkers. C_LIO_LISubstrates have a greater influence on shaping bacterial function. C_LIO_LITemporal changes have a greater shaping power on bacteria than on gene families. C_LI Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/542048v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1834e64org.highwire.dtl.DTLVardef@18fc695org.highwire.dtl.DTLVardef@369657org.highwire.dtl.DTLVardef@1c85a13_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

The renal capsule: a vibrant and adaptive cell environment of the kidney in homeostasis, disease and aging

The kidney is a complex organ that governs many physiological parameters. It is roughly divided into three parts, the renal pelvis, medulla, and cortex. Covering the cortex is the renal capsule, a serosal tissue that provides protection and forms a barrier for the kidney. Serosal tissues of many organs have been recently shown to play a vital role in homeostasis and disease. Analyses of the cells that reside in these tissues have identified distinct cell types with unique phenotypes. Here, we characterized this niche and found that it is mainly comprised of fibroblasts and macrophages, but also includes other diverse cell types. Characterizing renal capsule-associated macrophages, we found that they consist of a distinct subset (i.e., TLF+ macrophages) that is nearly absent in the kidney parenchyma. Injury, disease, and other changes that involve the kidney, affected the cell composition of the renal capsule, indicating its dynamic response to changes within the organ parenchyma. Lastly, we studied age-related changes in the renal capsule and found that aging affected the cell composition and inflammatory phenotype of macrophages, increased CD8 T cells and other lymphocyte counts, and promoted a senescence-associated phenotype in fibroblasts. Taken together, our data illustrate the complexity and heterogeneity of the renal capsule and its underlying changes during aging and disease, improving our understanding of the kidney serosa that may be valuable for novel renal therapies.

immunology↗

bioRxiv2023

High-resolution molecular atlas of a lung tumor in 3D

Cells live and interact in three-dimensional (3D) cellular neighborhoods. However, histology and spatial omics methods mostly focus on 2D tissue sections. Here we present a 3D spatial atlas of a routine clinical sample, an aggressive human lung carcinoma, by combining in situ quantification of 960 cancer-related genes across [~]340,000 cells with measurements of tissue-mechanical components. 3D cellular neighborhoods subdivided the tumor microenvironment into tumor, stromal, and immune multicellular niches. Interestingly, pseudotime analysis suggested that pro-invasive epithelial-to-mesenchymal transition (EMT), detected in stroma-infiltrating tumor cells, already occurred in one region at the tumor surface. There, myofibroblasts and macrophages specifically co-localized with pre-invasive tumor cells and their multicellular molecular signature identified patients with shorter survival. Moreover, cytotoxic T-cells did not infiltrate this niche but colocalized with inhibitory dendritic and regulatory T cells. Importantly, systematic scoring of cell-cell interactions in 3D neighborhoods highlighted niche-specific signaling networks accompanying tumor invasion and immune escape. Compared to 2D, 3D neighborhoods improved the characterization of immune niches by identifying dendritic niches, capturing the 3D extension of T-cell niches and boosting the quantification of niche-specific cell-cell interactions, including druggable immune checkpoints. We believe that 3D communication analyses can improve the design of clinical studies investigating personalized, combination immuno-oncology therapies.

systems biology↗

bioRxiv2023

A novel bacterial signal transduction system specifically senses and responds to peptidoglycan damage

The peptidoglycan (PG) layer is a mesh-like structure within the cell envelope essential for maintenance of cell shape and resistance to osmotic stress, and therefore is a primary target of many important and widely used antibiotics, such as {beta}-lactams. In Gram-negative bacteria, while signal transduction systems that monitor the state of the inner- and outer-membranes have been extensively studied and well understood, much less is known about how cells sense and respond to PG-targeting stresses. Here we show that a novel bacterial two-component system (PghKR) from Shewanella oneidensis is capable of sensing and responding to PG damage. This system is specifically activated in cells exposed to various PG-targeting antibiotics or carrying a defect in PG synthesis, resulting in induced expression of blaA and relV, which encode a {beta}-lactamase conferring resistance to {beta}-lactams and a small ppGpp synthetase responsible for antibiotic tolerance, respectively. Intriguingly, the PghKR homologs are widespread among several classes of Proteobacteria and the periplasmic domain of sensor kinase PghK contains a family 9 carbohydrate-binding module that is required for signal perception, implying that the signals could be the glycan fragments of PG. Overall, our results provide critical insights into the regulation of PG homeostasis in Gram-negative bacteria.

microbiology↗

bioRxiv2023

BATF relieves hepatic steatosis by inhibiting PD1 and promoting energy metabolism

The rising prevalence of nonalcoholic fatty liver disease (NAFLD) has become a global health threat that needs to be addressed urgently. Basic leucine zipper ATF-like transcription factor (BATF) is commonly thought to be involved in immunity, but its effect on lipid metabolism is not clear. Here, we investigated the function of BATF in hepatic lipid metabolism. BATF alleviated high-fat diet (HFD)-induced hepatic steatosis and inhibited elevated programmed cell death protein (PD)1 expression induced by HFD. A mechanistic study confirmed that BATF regulated fat accumulation by inhibiting PD1 expression and promoting energy metabolism. PD1 antibodies alleviated hepatic lipid deposition. In conclusion, we identified the regulatory role of BATF in hepatic lipid metabolism and that PD1 is a target for alleviation of NAFLD. This study provides new insights into the relationship between BATF, PD1 and NAFLD.

molecular biology↗

bioRxiv2023

Repurposing the Memory-promoting Meclofenoxate Hydrochloride as a Treatment for Parkinson's Disease through Integrative Multi-omics analysis

Parkinson s disease (PD) is a devastating neurodegenerative disorder with growing prevalence worldwide and, as yet, no effective treatment. Drug repurposing promises to be invaluable for the identification of novel therapeutics for the treatment of PD due to the associated shortened drug development time, fewer safety concerns, and reduced costs. Here, we compiled gene expression data from 1,231 healthy human brains and 357 PD patients across ethnicities, brain regions, Braak stages, and disease status. By integrating them with multiple-source PD-associated genomic data, we found a conserved PD-associated gene co-expression module, and its alignment with the CMAP database successfully identified 15 drug candidates. Among these, we selected meclofenoxate hydrochloride (MH) and sodium phenylbutyrate (SP) for experimental validation because they are capable of passing through the blood brain barrier. In primary neurons, MH was found to prevent the neuronal death and synaptic damage associated with PD and to reverse the abnormal mitochondrial metabolism caused by PD. In hippocampal tissues, MH and SP were found to prevent the destruction of mitochondria, to reduce lipid peroxidation and to protect dopamine synthesis by PET-CT examination, malondialdehyde (MAD) testing and glutathione (GSH) testing, and immunohistochemical tests. Finally, MH was found to have the ability to improve gait behavior, and reduce anhedonic and depressive-like behaviors that are characteristics of PD mice. Taken together, our findings support the contention that MH may have the potential to ameliorate PD by improving mitochondrial metabolism and brain function.

biochemistry↗

bioRxiv2023

Spatial architecture of high-grade glioma reveals tumor heterogeneity within distinct domains

High-grade gliomas are aggressive primary brain cancers with poor response to standard regimens, driven by immense heterogeneity. In isocitrate dehydrogenase (IDH) wild-type high-grade glioma (glioblastoma, GBM), increased intra-tumoral heterogeneity is associated with more aggressive disease. Recently, spatial technologies have emerged to dissect this complex heterogeneity within the tumor ecosystem by preserving cellular organization in situ. Here, we construct a high-resolution molecular landscape of GBM and IDH-mutant high-grade glioma patient samples to investigate the cellular subtypes and spatial communities that compose high-grade glioma using digital spatial profiling and spatial molecular imaging. This uncovered striking diversity of the tumor and immune microenvironment, that is embodied by the heterogeneity of the inferred copy-number alterations in the tumor. Reconstructing the tumor architecture revealed two distinct niches, one composed of tumor cell states that most closely resemble normal glial cells, associated with microglia; and the other niche populated by monocytes and mesenchymal tumor cells. We further reveal that communication between tumor and immune cells is underpinned by tumor-specific ligands, such as TGF{beta} signaling in astrocyte-like tumor cells. This primary study reveals high levels of intra-tumoral heterogeneity in high-grade gliomas, associated with a diverse immune landscape within spatially localized regions.

cancer biology↗

bioRxiv2023

Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity

Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.

immunology↗

bioRxiv2023

High-throughput screening of functional neo-antigens and their specific TCRs via the Jurkat reporter system combine with droplet microfluidics

T-cell receptor (TCR)-engineered T cells can precisely recognize a broad repertoire of targets derived from both intracellular and surface proteins of tumor cells. TCR-T adoptive cell therapy has shown safety and promising efficacy in solid tumor immunotherapy. However, antigen-specific functional TCR screening is time-consuming and expensive, which limits its application clinically. Here, we developed a novel integrated antigen-TCR screening platform based on droplet microfluidics technology, enabling high-throughput peptide-major histocompatibility complex (pMHC) library-to-TCR library screening with high sensitivity and low background signal. We introduced DNA barcoding technology to label peptide antigen candidate-loaded antigen-presenting cells (APCs) and Jurkat reporter cells to check the specificity of pMHC-TCR candidates. Coupled with the next-generation sequencing pipeline, interpretation of the DNA barcodes and the gene expression level of the Jurkat T-cell activation pathway provided a clear peptide-MHC-TCR recognition relationship. Our proof-of-principle study demonstrates that the platform could achieve unbiased pMHC-TCR library-on-library screening, which is expected to be used in the cross-reactivity and off-target testing of candidate pMHC-TCR libraries in clinical applications.

bioengineering↗

bioRxiv2023

ADAM10 mediates macroglial cell fate decisions in the developing brain

ADAMs (a disintegrin and metalloproteinase) are transmembrane proteins with cell adhesion and protease activities that contain disintegrin and metalloproteinase domains. ADAM10, a member of the ADAM family, is widely expressed in the brain. There are >40 substrates reported for ADAM10, including Notch, Delta-like ligand-1 (Dll1), and N-cadherin. To date, however, its function in the brain has been largely unknown. We used genetic manipulation to delete Adam10 specifically from glial progenitors in developing brains and observed that conditional knockout mice showed locomotor abnormalities. They all died within 4 months with apparent defects in the cerebellum. By comprehensively analyzing data from bulk RNA sequencing, single-cell RNA sequencing, and staining of the cerebellum, we found that ADAM10 promoted astrocyte generation under physiological conditions. Upon the removal of Adam10 in glial progenitors, the production of oligodendrocytes vastly increased, whereas the generation of astrocytes was substantially inhibited. Our results showed that ADAM10 plays a critical role in macroglial cell fate decisions during brain development.

neuroscience↗

bioRxiv2023

A Potent and Selective CDKL5/GSK3 Chemical Probe is Neuroprotective

Despite mediating several essential processes in the brain, including during development, cyclin-dependent kinase-like 5 (CDKL5) remains a poorly characterized human protein kinase. Accordingly, its substrates, functions, and regulatory mechanisms have not been fully described. We realized that availability of a potent and selective small molecule probe targeting CDKL5 could enable illumination of its roles in normal development as well as in diseases where it has become aberrant due to mutation. We prepared analogs of AT-7519, a known inhibitor of several cyclin dependent and cyclin-dependent kinase-like kinases that has been advanced into Phase II clinical trials. We identified analog 2 as a highly potent and cell-active chemical probe for CDKL5/GSK3 (glycogen synthase kinase 3). Evaluation of its kinome-wide selectivity confirmed that analog 2 demonstrates excellent selectivity and only retains GSK3/{beta} affinity. As confirmation that our chemical probe is a high-quality tool to use in directed biological studies, we demonstrated inhibition of downstream CDKL5 and GSK3/{beta} signaling and solved a co-crystal structure of analog 2 bound to CDKL5. A structurally similar analog (4) proved to lack CDKL5 affinity and maintain potent and selective inhibition of GSK3/{beta}. Finally, we used our chemical probe pair (2 and 4) to demonstrate that inhibition of CDKL5 and/or GSK3/{beta} promotes the survival of human motor neurons exposed to endoplasmic reticulum (ER) stress. We have demonstrated a neuroprotective phenotype elicited by our chemical probe pair and exemplified the utility of our compounds to characterize the role of CDKL5/GSK3 in neurons and beyond.

cell biology↗

bioRxiv2023

Excess PrPC inhibits muscle cell differentiation via miRNA-enhanced liquid-liquid phase separation implicated in myopathy

The cellular prion protein (PrPC), a glycoprotein existing in membrane-bound and cytoplasmic forms, has functional importance in skeletal muscle, but the mechanism behind the phenomenon remains poorly understood. Here we report that PrPC is overexpressed and located in the cytoplasm of the skeletal muscle of six myopathy patients; cytoplasmic PrPC strongly inhibits skeletal muscle cell autophagy and blocks myoblast differentiation. PrPC selectively binds to a subset of miRNAs during myoblast differentiation, and the co-localization of PrPC with miR-214-3p was clearly observed in the skeletal muscle of six myopathy patients but not in that of four age-matched controls. We demonstrate that PrPC is overexpressed in skeletal muscle cells under pathological conditions and inhibits muscle cell differentiation via physically interacting with a subset of miRNAs to significantly inhibit autophagy-related protein 5-dependent autophagy, and selectively recruits these miRNAs into phase-separated condensates in living myoblasts, which in turn greatly enhances liquid-liquid phase separation (LLPS) of PrPC and results in the subsequent PrP aggregation and muscle bundle formation in myopathy patients characterized by incomplete muscle regeneration. Our findings show how excess PrPC can inhibit muscle cell differentiation via miRNA-enhanced LLPS implicated in myopathy.

biochemistry↗

bioRxiv2023

N-of-one differential gene expression without control samples using a deep generative model

Differential gene expression analysis of bulk RNA sequencing data plays a major role in the diagnosis, prognosis, and understanding of disease. Such analyses are often challenging due to a lack of good controls and the heterogeneous nature of the samples. Here, we present a deep generative model that can replace control samples. The model is trained on RNA-seq data from healthy tissues and learns a low-dimensional representation that clusters tissues very well without supervision. When applied to cancer samples, the model accurately identifies representations close to the tissue of origin. We interpret these inferred representations as the closest normal to the disease samples and use the resulting count distributions to perform differential expression analysis of single cancer samples without control samples. In a detailed analysis of breast cancer, we demonstrate how our approach finds subtype-specific cancer driver and marker genes with high specificity and greatly outperforms the state-of-the-art method in detecting differentially expressed genes, DESeq2. We further show that the significant genes found using the model are highly enriched within cancer-specific driver genes across different cancer types. Our results show that the in silico closest normal provides a more favorable comparison than control samples.

bioinformatics↗

bioRxiv2023

Alterations in Germinal Center Formation and B Cell Activation during Severe Orientia tsutsugamushi Infection in Mice

Scrub typhus is a poorly studied but life-threatening disease caused by the intracellular bacterium Orientia tsutsugamushi (Ot). Cellular and humoral immunity in Ot-infected patients is not long-lasting, waning as early as one-year post-infection; however, its underlying mechanisms remain unclear. To date, no studies have examined germinal center (GC) or B cell responses in Ot-infected humans or experimental animals. This study was aimed at evaluating humoral immune responses at acute stages of severe Ot infection and possible mechanisms underlying B cell dysfunction. Following inoculation with Ot Karp, a clinically dominant strain known to cause lethal infection in C57BL/6 mice, we measured antigen-specific antibody titers, revealing IgG2c as the dominant isotype induced by infection. Splenic GC responses were evaluated by immunohistology, co-staining for B cells (B220), T cells (CD3), and GCs (GL-7). Organized GCs were evident at day 4 post-infection (D4), but they were nearly absent at D8, accompanied by scattered T cells throughout splenic tissues. Flow cytometry revealed comparable numbers of GC B cells and T follicular helper (Tfh) cells at D4 and D8, indicating that GC collapse was not due to excessive death of these cell subtypes at D8. B cell RNAseq analysis revealed significant differences in expression of genes associated with B cell adhesion and co-stimulation at D8 versus D4. The significant downregulation of S1PR2 (a GC-specific adhesion gene) was most evident at D8, correlating with disrupted GC formation. Signaling pathway analysis uncovered downregulation of 71% of B cell activation genes at D8, suggesting attenuation of B cell activation during severe infection. This is the first study showing the disruption of B/T cell microenvironment and dysregulation of B cell responses during Ot infection, which may help understand the transient immunity associated with scrub typhus. Author SummaryScrub typhus is an understudied disease caused by the intracellular bacterium O. tsutsugamushi. A hallmark of scrub typhus is the unexplained, non-durable immunity after infection. While cellular immune responses are known to be important for controlling this infection, our understanding of B cell and GC responses remains limited. In this study, we examined B cell activation and GC responses using our recently established murine model of severe scrub typhus. We measured bacterial antigen-specific antibody titers and identified IgG2c, an IFN-{gamma}-driven isotype, as the major IgG subtype. We also found that O. tsutsugamushi infection disrupted spleen morphology, exemplified by randomly dispersed T cells and lost GC structures. Transcriptomic analysis of purified splenic B cells demonstrated reduced expression of genes encoding critical adhesion and co-stimulation molecules, including GC-adhesion gene S1PR2, at severe stages of infection. Several humoral immune response pathways relevant to B cell receptor signaling, B cell activation and differentiation were significantly downregulated during infection. This study is the first report describing humoral immunity in a scrub typhus mouse model and provides detailed evidence that B cell and GC responses are impaired during acute infection.

immunology↗