Biology subjects

Shen, N.

Publications and source records attributed to Shen, N..

36 records · Page 2Linked to original sources

bioRxiv2022

Temporally integrated transcriptome analysis reveals ASFV pathology and host response dynamics

African swine fever virus (ASFV) causes a lethal swine hemorrhagic disease and is currently responsible for widespread damage to the pig industry. The molecular mechanisms of ASFV pathogenicity and its interaction with host responses remain poorly understood. In this study, we profiled the temporal viral and host transcriptomes in porcine alveolar macrophages (PAMs) infected at 6, 12, 24 and 48 hours with highly virulent (SY18) and low virulent (HuB20) ASFV strains. We first identified profound differences in the virus expression programs between SY18 and HuB20, while the transcriptome dynamics in host cells were dominated by infection time. Through integrated computational analysis and experimental validation, we identified differentially expressed genes and related biological processes, and elaborated differential usage of the NF-kappaB related pathways by the two virus strains. In addition, we observed that compared to the highly virulent SY18 strain, HuB20 infection quickly activates expression of receptors, sensors, regulators, as well as downstream effectors, including cGAS, STAT1/2, IRF9, MX1/2, suggesting rapid induction of a strong immune response. Lastly, we constructed a host-virus coexpression network, which shed light on pathogenic functions of several ASFV genes. Taken together, these results will provide a basis for further mechanistic studies on the functions of both viral and cellular genes that are involved in different responses. Author SummarySince it was first described in Kenya in 1921, ASF has spread across sub-Saharan Africa, the Caribbean, the Western Europe, the Trans-Caucasus region, and the Russian Federation. Recent outbreaks have also been reported in Asia, which has devastated the pig industry, resulting in an approximately 40% reduction in pork worldwide. In the absence of effective vaccine or treatment, the mortality for infections with highly virulent strains approaches 100%, while low virulent strains causing less mortality spreads fast recently. Nevertheless, the mechanisms of ASFV pathogenicity, especially the differences between highly and low virulent strains remain poorly understood. Here, we used RNA-seq to analyze the viral and host transcriptome changes in PAMs infected with a virulent strain (SY18) or an attenuated strain (HuB20) at different stages. We found that the presence of ASFV significantly affected the cellular transcriptome profile. In addition, we did temporal and described the dynamic expression programs induced in the host cells by ASFV infection of different virulence strains. In particular, we identified differential gene expression patterns in host innate immune responses and expressed cytokines and chemokines between ASFV strains of different virulence. Our study provides new insights into ASFV pathogenicity research and novel drug or vaccine targets.

microbiology↗

bioRxiv2021

Detecting expressed cancer somatic mutations from single-cell RNA sequencing data

Identifying expressed somatic mutations directly from single-cell RNA sequencing (scRNA-seq) data is challenging but highly valuable. Computational methods have been attempted but no reliable methods have been reported to identify somatic mutations with high fidelity. We present RESA -- Recurrently Expressed SNV Analysis, a computational framework that identifies expressed somatic mutations from scRNA-seq data with high precision. We test RESA in multiple cancer cell line datasets, where RESA demonstrates average area under the curve (AUC) of 0.9 on independently held out test sets, and achieves average precision of 0.71 when evaluated by bulk whole exome, which is substantially higher than previous approaches. In addition, RESA detects a median of 201 mutations per cell, 50 times more than what was reported in experimental technologies with simultaneous expression and mutation profiling. Furthermore, applying RESA to scRNA-seq from a melanoma patient, we demonstrate that RESA recovers the known BRAF driver mutation of the sample and melanoma dominating mutational signatures, identifies mutation associated expression signatures, reveals nondriver perturbed and stage specific cancer hallmarks, and unveils the complex relationship between genomic and transcriptomic intratumor heterogeneity. Therefore, RESA could provide novel views in the study of intratumor heterogeneity and relate genetic alterations to transcriptional changes at single cell level.

bioinformatics↗

bioRxiv2021

The transcription factor Zeb2 drives differentiation of age-associated B cells

Age-associated B-cells (ABCs) accumulate during infection, aging and autoimmunity, contributing to lupus pathogenesis. Here, we screen for transcription factors driving ABC formation and find Zeb2 is required for human and mouse ABC differentiation in-vitro. ABCs are reduced in ZEB2 haploinsufficient individuals and in mice lacking Zeb2 in B-cells. In mice with TLR7-driven lupus, Zeb2 is essential for ABC formation and autoimmune pathology. Zeb2 binds to the +20kb intronic enhancer of Mef2b, repressing Mef2b-mediated germinal center B-cell differentiation and promoting ABC formation. Zeb2 also targets genes important for ABC specification and function including Itgax. Zeb2-driven ABC differentiation requires Jak-Stat signaling, and treatment with the Jak1/3 inhibitor tofacitinib reduces ABC accumulation in autoimmune mice and patients. Zeb2 thus emerges as a driver of B-cell autoimmunity. One-Sentence SummaryZeb2 is essential for Age-associated B cells differentiation and function.

immunology↗

bioRxiv2021

CRISPRa screen on a genetic risk locus shared by multiple autoimmune diseases identifies a dysfunctional enhancer that affects IRF8 expression through cooperative lncRNA and DNA methylation machinery

Dysregulated transcription factors represent a major class of drug targets that mediate the abnormal expression of many critical genes involved in SLE and other autoimmune diseases. Although strong evidence suggests that natural human genetic variation affects basal and inducible gene expression, it is still a considerable challenge to establish a biological link between GWAS-identified non-coding genetic risk variants and their regulated gene targets. Here, we combine genetic data, epigenomic data, and CRISPR activation (CRISPRa) assays to screen for functional variants regulating IRF8 expression. Using CRISPR-mediated deletion and 3D chromatin structure analysis, we demonstrate that the locus containing rs2280381 is a cell-type-specific distal enhancer for IRF8 that spatially interacts with the IRF8 promoter. Further, rs2280381 mediates IRF8 expression through enhancer RNA AC092723.1, which recruits TET1 to the IRF8 promoter to modulate IRF8 expression by affecting methylation levels. The alleles of rs2280381 modulate PU.1 binding and chromatin state to differentially regulate AC092723.1 and IRF8 expression. Our work illustrates a strategy to define the functional genetic variants modulating transcription factor gene expression levels and identifies the biologic mechanism by which autoimmune diseases risk genetic variants contribute to the pathogenesis of disease.

genetics↗

bioRxiv2021

Evidence-based precision nutrition improves clinical outcomes by analyzing human and microbial molecular data with artificial intelligence

Many studies have shown that foods and nutritional ingredients play an important role in healthy human homeostasis, either directly or via the microbiome. We have developed an objective, integrated, and automated approach to personalized food and supplement recommendations that is powered by artificial intelligence and individualized molecular data from the gut microbiome, the human host, and their interactions. The process starts with a clinically validated transcriptomic analysis of a persons stool (and some cases also blood) sample, from which the following molecular data are computed using clinically validated bioinformatics: 1. Quantitative strain-level taxonomic classification of all microorganisms, 2. Gene expression level for microbial genes, 3. Gene expression level for all human genes. These molecular data are converted into personalized nutritional recommendations (foods and supplements) using algorithms derived from clinical research studies and domain knowledge. We describe an application of our precision nutrition technology platform to human populations with irritable bowel syndrome (IBS), depression, anxiety, and type 2 diabetes (T2D). In these pilot interventional studies, our precision nutrition program achieved significant improvements in clinical outcomes of IBS (39% for severe IBS), depression (31% for severe depression), anxiety (31% for severe anxiety), and the risk score for T2D (>30% reduction relative to the control arm). These data support the integration of data-driven precision nutrition into the standard of care.

systems biology↗

bioRxiv2020

Single cell gene fusion detection by scFusion

Gene fusions are widespread in tumor cells and can play important roles in tumor initiation and progression. Using full length single cell RNA sequencing (scRNA-seq), gene fusions can now be detected at single cell level. However, scRNA-seq data has a high noise level and contains various technical artefacts that can lead to spurous fusion discoveries. Here we present a computational tool, scFusion, for gene fusion detection based on scRNA-seq. scFusion can efficiently and sensitively detect fusions with a low false discovery rate. In a T cell data, scFusion detected the invariant TCR gene recombinations in Mucosal-associated invariant T cells that many methods developed for bulk-data failed to detect. In a multiple myeloma data, scFusion detected the known recurrent fusion IgH-WHSC1, which was associated with overexpression of the WHSC1 oncogene.

bioinformatics↗

bioRxiv2020

Structural insights into the recognition of histone H3Q5 serotonylation by WDR5

Serotonylation of histone H3Q5 (H3Q5ser) is a recently identified posttranslational modification of histones that apparently acts as a permissive marker for gene activation in synergy with H3K4me3 during neuronal cell differentiation. However, any proteins which specifically recognize H3Q5ser remain unknown. Here, we discovered that WDR5 interacts with the N-terminal tail of histone H3 and functions as a reader for H3Q5ser. Crystal structures of WDR5 in complex with H3Q5ser and H3K4me3Q5ser peptides revealed that the serotonyl group is accommodated in a shallow surface pocket of WDR5. Experiments in neuroblastoma cells demonstrate that WDR5 colocalizes with H3Q5ser in the promoter regions of cancer-promoting genes, where it promotes gene transcription to induce cell proliferation. Thus, beyond revealing a previously unknown mechanism through which WDR5 reads H3Q5ser to activate transcription, our study suggests that this WDR5-H3Q5ser mediated epigenetic regulation apparently promotes tumorigenesis.

biochemistry↗

bioRxiv2020

SLE non-coding Genetic Risk Variant Determines the Epigenetic Dysfunction of an Immune Cell Specific Enhancer that Controls Disease-critical microRNA Expression

The human genome contains millions of putative regulatory elements, which regulate gene expression. We are just beginning to understand the functional consequences of genetic variation within these regulatory elements. Since the bulk of common genetic variation impacting polygenic disease phenotypes localizes to these non-coding regions of the genome, understanding the consequences will improve our understanding of the mechanisms mediating genetic risk in human disease. Here, we define the systemic lupus erythematosus (SLE) risk variant rs2431369 as likely causal for SLE and show that it is located in a functional regulatory element that modulates miR-146a expression. We use epigenomic analysis and genome-editing to show that the rs2431697-containing region is a distal enhancer that specifically regulates miR-146a expression in a cell-type dependent manner. 3D chromatin structure analysis demonstrates physical interaction between the rs2431697-containing region and the miR-146a promoter. Further, our data show that NF-kB binds the disease protective allele in a sequence-specific manner, leading to increased expression of this immunoregulatory microRNA. Our work provides a strategy for using disease-associated variants to define the functional regulatory elements of non-coding RNA molecules such as miR-146a and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.

genetics↗

bioRxiv2020

Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity that may underly population disparities in this disease

Systemic lupus erythematosus (SLE), a worldwide autoimmune disease with high heritability, shows differences in prevalence, severity and age of onset among different ancestral groups. Previous genetic studies have focused more on European populations, which appear to be the least affected. Consequently, the genetic variations that underly the commonalities, differences and treatment options in SLE among ancestral groups have not been well elucidated. To address this, we undertook a genome-wide association study, increasing the sample size of Chinese populations to the level of existing European studies. Thirty-eight novel SLE-associated loci and incomplete sharing of genetic architecture were identified. Nine disease loci showed clear ancestral group heterogeneity and implicated antibody production as a potential mechanism for differences in disease manifestation. Polygenic risk scores performed significantly better when trained on matched ancestral data sets. These analyses help to reveal the genetic bases for disparities in SLE among ancestral groups.

genetics↗

bioRxiv2019

A screening platform based on epitope editing for drug discovery

The interaction between an antibody and its epitope has been daily utilized in various biological studies; however it has been rarely explored whether small molecules can alter the interaction. We discovered that small molecules could alter/edit surface properties of amyloid beta (A{beta}) epitopes, and consequently inhibit or enhance corresponding antibody recognition. Remarkably, this editing effect could generate functional changes including protein aggregation behaviors, cell cytokine secreting and in vivo microglia activation. According to this discovery, we proposed a screen platform based on epitope editing for drug discovery (SPEED). With a small library of compounds, we validated that SPEED could be used to seek new leads for A{beta} species. We also demonstrated that this platform could potentially be extended to other targets including tau protein and PD-L1 protein. The SPEED is a simple, fast and label-free screening method. We believe that the SPEED strategy could be universally applicable for seeking and validating drug candidates and imaging ligands.

biochemistry↗

bioRxiv2019

Human bone marrow mesenchymal stem/stromal cell behaviour is coordinated via mechanically activated osteocyte-derived extracellular vesicles

Osteocytes are mechanosensitive cells that are believed to play a fundamental role in coordinating bone mechanoadaptation via the secretion of paracrine factors. However, the exact mechanisms by which osteocytes relay mechanical signals to effector cells is poorly understood. In this study, we demonstrated that osteocytes subjected to a physiologic fluid shear secrete a distinct collection of factors that significantly enhance human MSC recruitment and osteogenesis. Utilising proteomics we generated an extensive map of proteins within the mechanically activated osteocyte secretome, identifying numerous paracrine factors that are modified by mechanical stimulation. Moreover, we identified the presence of extracellular vesicles (EVs) and further demonstrated that these mechanically activated osteocyte derived EVs (MAEVs) coordinate human MSCs recruitment and osteogenesis. This indicates that mechanical conditioning of parent cells can modify EVs and demonstrates the pro-osteogenic potential of MAEVs as a cell-free therapy to enhance bone regeneration and repair in diseases such as osteoporosis.

physiology↗

bioRxiv2019

P38α Regulates Expression of DUX4 in Facioscapulohumeral Muscular Dystrophy

FSHD is caused by the loss of repression at the D4Z4 locus leading to DUX4 expression in skeletal muscle, activation of its early embryonic transcriptional program and muscle fiber death. While progress toward understanding the signals driving DUX4 expression has been made, the factors and pathways involved in the transcriptional activation of this gene remain largely unknown. Here, we describe the identification and characterization of p38 as a novel regulator of DUX4 expression in FSHD myotubes. By using multiple highly characterized, potent and specific inhibitors of p38/{beta}, we show a robust reduction of DUX4 expression, activity and cell death across FSHD1 and FSHD2 patient-derived lines. RNA-seq profiling reveals that a small number of genes are differentially expressed upon p38/{beta} inhibition, the vast majority of which are DUX4 target genes. Our results reveal a novel and apparently critical role for p38 in the aberrant activation of DUX4 in FSHD and support the potential of p38/{beta} inhibitors as effective therapeutics to treat FSHD at its root cause. VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/700195v2_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@d2d55corg.highwire.dtl.DTLVardef@1b5c8fcorg.highwire.dtl.DTLVardef@19e4667org.highwire.dtl.DTLVardef@202b96_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2019

Human Retina-on-a-Chip: Merging Organoid and Organ-on-a-Chip Technology to Generate Complex Multi-Layer Tissue Models

The devastating effects and incurable nature of hereditary and sporadic retinal diseases such as Stargardt disease, age-related macular degeneration or retinitis pigmentosa urgently require the development of new therapeutic strategies. Additionally, the prevalence of retinal toxicities is becoming more and more an issue of novel targeted therapeutic agents. To date, (ophthalmologic) drug development largely relies on animal models. Inadequate translatability of results from animal models to humans, however, limits advances in drug development and discovery. Hence, the establishment of more relevant human tissue-based in vitro models is of upmost importance. The discovery of self-forming retinal organoids (ROs) derived from human embryonic stem cells (hESCs) or human induced pluripotent stem cells (hiPSCs) is a promising approach to model the complex stratified retinal tissue. Yet, ROs lack vascularization and cannot recapitulate the important physiological interactions of matured photoreceptors and the retinal pigment epithelium (RPE). In this study, we present the retina-on-a-chip (RoC), a novel microphysiological model of the human retina integrating more than seven different essential retinal cell types derived from hiPSCs in a vasculature-like perfusion and enabling, for the first time, the recapitulation of the interaction of mature photoreceptor segments with RPE in vitro. We show that this interaction enhances the formation of outer segment like-structures and the establishment of in vivo-like physiological processes such as outer segment phagocytosis and calcium dynamics. In addition, we demonstrate the applicability of the RoC for drug testing, by reproducing the retinopathic side effects of the anti-malaria drug chloroquine and the antibiotic gentamicin. The developed hiPSC-based RoC has the potential to promote drug development and provide new insights into the underlying pathology of retinal diseases.

bioengineering↗

bioRxiv2018

Genome-wide association study reveals sex-specific genetic architecture of facial attractiveness

Facial attractiveness is a complex human trait of great interest in both academia and industry. Literature on sociological and phenotypic factors associated with facial attractiveness is rich, but its genetic basis is poorly understood. In this paper, we conducted a genome-wide association study to discover genetic variants associated with facial attractiveness using 3,928 samples in the Wisconsin Longitudinal Study. We identified two genome-wide significant loci and highlighted a handful of candidate genes, many of which are specifically expressed in human tissues involved in reproduction and hormone synthesis. Additionally, facial attractiveness showed strong and negative genetic correlations with BMI in females and with blood lipids in males. Our analysis also suggested sex-specific selection pressure on variants associated with lower male attractiveness. These results revealed sex-specific genetic architecture of facial attractiveness and provided fundamental new insights into its genetic basis.

genetics↗

bioRxiv2018

HDL-AuNPs-BMS nanoparticle conjugates as molecularly targeted therapy for leukemia

In previous work, gold nanoparticles (AuNPs) with adsorbed high-density lipoprotein (HDL) nanoparticles have been utilized to deliver oligonucleotides, yet HDL-AuNPs functionalized with small molecule inhibitors have not been systematically explored. Here, we report an AuNP-based therapeutic system (HDL-AuNPs-BMS) for acute myeloid leukemia (AML) by delivering BMS309403 (BMS), a small molecule that selectively inhibits AML-promoting factor fatty acid binding protein 4 (FABP4). HDL-AuNPs-BMS are synthesized using a gold nanoparticle as template to control conjugate size and ensure a spherical shape to engineer HDL-like nanoparticle containing BMS. The zeta potential and size of the HDL-AuNPs obtained from transmission electron microscopy (TEM) show that the nanoparticles are electrostatically stable and 25 nm in diameter. Functionally, compared to free drug, HDL-AuNPs-BMS conjugates are more readily internalized by AML cells and have more pronounced effect on downregulation of DNA methyltransferase 1 (DNMT1), reduction of global DNA methylation, and restoration of epigenetically-silenced tumor suppressor p15INK4b coupled with AML growth arrest. Importantly, systemic administration of HDL-AuNPs-BMS conjugates into AML-bearing mice inhibits DNMT1-dependent DNA methylation, induces AML cell differentiation and diminishes AML disease progression without obvious side effects. In summary, these data, for the first time, demonstrate HDL-AuNPs as an effective delivery platform with great potential to attach distinct inhibitors, and HDL-AuNPs-BMS conjugates as a promising therapeutic platform to treat leukemia.

cancer biology↗

bioRxiv2017

MicroRNA-21 Regulates Metabolic Adaptation of Pathogenic TH17 cells and Controls Autoimmune Inflammation

TH17 cells exhibit great heterogeneity and variable functional states in vivo. However, metabolic reprogramming of TH17 cells in vivo and its regulation during autoimmunity and host defence is unknown. Here we report that TH17 cells derived in vivo show discrete metabolic states. Metabolic states of TH17 cells in vivo were controlled at the epigenetic level, with conserved regulatory region of key metabolic regulators show distinct chromatin accessibility as demonstrated by chromatin landscape profiling. TGF-{beta}1 signaling was further shown to be crucial for remodeling of TH17 cell chromatin states, Ahr and miR-21 were identified as essential metabolic regulators for TH17 cells. Understanding metabolic reprogramming of TH17 cells in vivo may therefore provide more defined therapeutic intervention to TH17 cell mediated autoimmune diseases and insights into TH17 cell mediated host defence.

immunology↗

bioRxiv2017

Intrinsic specificity differences between transcription factor paralogs partly explain their differential in vivo binding

Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. Our finding was possible due to a unique combination of carefully designed high-throughput assays and rigorous computation modeling, integrated into a unified framework called iMADS. We used iMADS to quantify, model, and analyze specificity differences between 11 paralogous TFs from 4 distinct human TF families. Our finding of differential specificity between closely related TFs has important implications for the interpretation of the regulatory effects of non-coding genetic variants.

genomics↗

bioRxiv2017

T-bet+ CD11c+ B Cells Are Critical For Anti-Chromatin IgG Production In The Development Of Lupus

A hallmark of systemic lupus erythematosus is high titers of circulating autoantibody. A novel CD11c+ B cell subset has been identified that is critical for the development of autoimmunity. However, the role of CD11c+ B cells in the development of lupus is unclear. Chronic graft-versus-host disease (cGVHD) is a lupus-like syndrome with great autoantibody production. In the present study we investigated the role of CD11c+ B cells in the pathogenesis of lupus in the cGVHD model. Here, we found the percentage and absolute number of CD11c+ B cells and titer of sera anti-chromatin IgG and IgG2a antibody were increased in cGVHD mice. CD11c+ plasma cells from cGVHD mice produced large amounts of anti-chromatin IgG2a upon stimulation. Depletion of CD11c+ B cells reduced anti-chromatin IgG and IgG2a production. T-bet expression was further shown to be upregulated in CD11c+ B cells. Knockout of T-bet in B cells alleviated cGVHD. The percentage of T-bet+ CD11c+ B cells was elevated in lupus patients and positively correlated with serum anti-chromatin levels. Our findings suggest T-bet+ CD11c+ B cells contribute to the pathogenesis of lupus and provides potential target for therapeutic intervention.

immunology↗