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Chen, W.

Publications and source records attributed to Chen, W..

At least 415 records · Page 23Linked to original sources

A missense KCNQ1 Mutation Impairs Insulin Secretion in Neonatal Diabetes

KCNQ1/Kv7 is a voltage-gated K+ channel that regulates heart rhythm, glucose and salt homeostasis. Mutations of KCNQ1 are primarily associated with long-QT syndrome and type 2 diabetes; however, thus far KCNQ1 mutations have not been associated with monogenetic diabetes. Here, we identified a homozygous KCNQ1 missense mutation (R397W) in an individual with permanent neonatal diabetes (PND). To identify the mechanisms that link the mutation to the disease, we introduced the mutation into human embryonic stem cells (hESCs), and used them to derived pancreatic {beta}-like cells (hESC-{beta} cell). In early {beta}-like cells, we observed atypical membrane electrical activity, increased levels of cytoplasmic Ca2+, and a hypersecretion of insulin. Upon extended culture, their insulin secretion decreased and the number of apoptotic cells increased, resulting in a reduction in the numbers of {beta}-like cells. Late-stage {beta}-like cells exhibited a decrease in the expression of metabolic genes, e.g. HNF4, PDX1 and GLUT1, providing a possible mechanism for {beta}-cell dysfunction. Our study identifies KCNQ1 as a novel candidate gene of monogenetic diabetes and shows that KCNQ1 regulates {beta}-cell function and survival.

cell biology↗

ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress

Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for relative and absolute quantification (iTRAQ) labeling based quantitative proteomics approach was used to detected changes in protein level. Two-week-old seedlings of the cold tolerance rice variety Kongyu131 were treated at 8{degrees}C for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to control group. Functional analysis revealed most of regulation proteins involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulation proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is providing new insights into cold stress responses in rice on proteomic aspect.

plant biology↗

SeqDistK: a Novel Tool for Alignment-free Phylogenetic Analysis

Algorithms for constructing phylogenetic trees are fundamental to study the evolution of viruses, bacteria, and other microbes. Established multiple alignment-based algorithms are inefficient for large scale metagenomic sequence data because of their high requirement of inter-sequence correlation and high computational complexity. In this paper, we present SeqDistK, a novel tool for alignment-free phylogenetic analysis. SeqDistK computes the dissimilarity matrix for phylogenetic analysis, incorporating seven k-mer based dissimilarity measures, namely d2, d2S, d2star, Euclidean, Manhattan, CVTree, and Chebyshev. Based on these dissimilarities, SeqDistK constructs phylogenetic tree using the Unweighted Pair Group Method with Arithmetic Mean algorithm. Using a golden standard dataset of 16S rRNA and its associated phylogenetic tree, we compared SeqDistK to Muscle - a multi sequence aligner. We found SeqDistK was not only 38 times faster than Muscle in computational efficiency but also more accurate. SeqDistK achieved the smallest symmetric difference between the inferred and ground truth trees with a range between 13 to 18, while that of Muscle was 62. When measures d2, d2star, d2S, Euclidean, and k-mer size k=5 were used, SeqDistK consistently inferred phylogenetic tree almost identical to the ground truth tree. We also performed clustering of 16S rRNA sequences using SeqDistK and found the clustering was highly consistent with known biological taxonomy. Among all the measures, d2S (k=5, M=2) showed the best accuracy as it correctly clustered and classified all sample sequences. In summary, SeqDistK is a novel, fast and accurate alignment-free tool for large-scale phylogenetic analysis. SeqDistK software is freely available at https://github.com/htczero/SeqDistK.

bioinformatics↗

Lineage-specific regulatory changes in the pathological cardiac remodeling of hypertrophy cardiomyopathy unraveled by single-nucleus RNA-seq and spatial transcriptomics

BACKGROUNDHypertrophy cardiomyopathy (HCM) is the most common cardiac genetic disorder with the histopathological features of cardiomyocyte hypertrophy and cardiac fibrosis. The pathological remodeling that occurs in the myocardium of HCM patients may ultimately progress to heart failure and death. A thorough understanding of the cell type-specific changes in the pathological cardiac remodeling of HCM is crucial for developing successful medical therapies to prevent or mitigate the progression of this disease. METHODSWe performed single-nucleus RNA-seq of the cardiac tissues from 10 HCM patients and 2 healthy donors, and conducted spatial transcriptomic assays of 4 cardiac tissue sections from 3 HCM patients. Comparative analyses were performed to explore the lineage-specific changes in expression profile, subpopulation composition and intercellular communication in the cardiac tissues of HCM patients. Based on the results of independent analyses including pseudotime ordering, differential expression analysis, and differential regulatory network analysis, we prioritized candidate therapeutic targets for mitigating the progression to heart failure or attenuating the cardiac fibrosis in HCM. Using the spatial transcriptomic data, we examined the spatial activity patterns of the key candidate genes, pathways and subpopulations. RESULTSUnbiased clustering of 55,122 nuclei from HCM and healthy conditions revealed 9 cell lineages and 28 clusters. Significant expansion of vascular-related lineages and contraction of cardiomyocytes, fibroblasts and myeloid cells in HCM were observed. The transcriptomic dynamics during the transition towards the failing state of cardiomyocytes in HCM were uncovered. Candidate target genes for mitigating the progression to heart failure in HCM were obtained such as FGF12, IL31RA, BDNF, S100A1, CRYAB and PROS1. The transcriptomic dynamics underlying the fibroblast activation were also uncovered, and candidate targets for attenuating the cardiac fibrosis in HCM were obtained such as RUNX1, MEOX1, AEBP1, LEF1 and NRXN3. CONCLUSIONSWe provided a comprehensive analysis of the lineage-specific regulatory changes in HCM. Our analysis identified a vast array of candidate therapeutic target genes and pathways to prevent or attenuate the pathological remodeling of HCM. Our datasets constitute a valuable resource to examine the lineage-specific expression changes of HCM at single-nucleus and spatial resolution. We developed a web-based interface (http://snsthcm.fwgenetics.org/) for further exploration.

pathology↗

Decoding molecular and cellular heterogeneity of nucleus accumbens with high-throughput scRNA-seq and MERFISH

The nucleus accumbens (NAc) plays an important role in regulating multiple behaviors and its dysfunction has been linked to many neural disorders. However, the molecular, cellular and anatomic heterogeneity underlying its functional diversity remains incompletely understood. Here, we generate a cell census of the mouse NAc using high-throughput single cell RNA sequencing and multiplexed error-robust FISH, revealing a high level of cell heterogeneity in this brain region. We show that the transcriptional and spatial diversity of neuron subtypes underlie NAcs anatomic and functional heterogeneity, and possibly contribute to the pathogenesis of different neurological disorders. These findings explain how the seemingly simple neuronal composition of the NAc achieves its highly heterogenous structure and diverse functions. Collectively, our study generates a spatially resolved cell taxonomy for understanding the NAc structure and function, which demonstrates the importance of combining molecular and spatial information in revealing the fundamental features of the nervous system.

neuroscience↗

Botrytis cinerea BcPTP1 is a late infection phase, cysteine rich protein cytotoxic effector

Botrytis cinerea is a broad-host-range necrotrophic phytopathogen responsible for serious crops diseases. To facilitate infection, B. cinerea secretes a large number of effectors that induce plant cell death. In screening secretome data of B. cinerea during infection stage, we identified a phytotoxic protein (BcPTP1) that can also induce immune resistance in plants. BcPTP1 is a small (90 aa), cysteine rich protein without any known domains. Transiently expression of BcPTP1 in leaves caused chlorosis that intensifies with time and eventually lead to cell death. Point mutations in eight of the 10 cysteine residues of BcPTP1 abolished the toxic effect, however residual toxic activity remained after heating the peptide, suggesting contribution of unknown epitopes to protein phytotoxic effect. The transcript level of the bcptp1 gene was low during the first 36 h after inoculation and increased sharply upon transition to the late infection stage, suggesting a role of BcPTP1 in lesion spreading. While statistically insignificant, deletion of the bcptp1 gene led to slightly smaller lesions on bean leaves. Further analyses indicated that BcPTP1 is internalized into plant cells after secreting into the apoplast and its phytotoxic effect is negatively regulated by the receptor-like kinases BAK1 and SOBIR1. Collectively, our findings show that BcPTP1 is a virulence factor that toxifies the host cells and facilitates lesion spreading during the late infection stage.

pathology↗

DeeReCT-TSS: A novel meta-learning-based method annotates TSS in multiple cell types based on DNA sequences and RNA-seq data

The accurate annotation of transcription start sites (TSSs) and their usage is critical for the mechanistic understanding of gene regulation under different biological contexts. To fulfill this, on one hand, specific high-throughput experimental technologies have been developed to capture TSSs in a genome-wide manner. On the other hand, various computational tools have also been developed for in silico prediction of TSSs solely based on genomic sequences. Most of these computational tools cast the problem as a binary classification task on a balanced dataset and thus result in drastic false positive predictions when applied on the genome-scale. To address these issues, we present DeeReCT-TSS, a deep-learning-based method that is capable of TSSs identification across the whole genome based on both DNA sequences and conventional RNA-seq data. We show that by effectively incorporating these two sources of information, DeeReCT-TSS significantly outperforms other solely sequence-based methods on the precise annotation of TSSs used in different cell types. Furthermore, we develop a meta-learning-based extension for simultaneous transcription start site (TSS) annotation on 10 cell types, which enables the identification of cell-type-specific TSS. Finally, we demonstrate the high precision of DeeReCT-TSS on two independent datasets from the ENCODE project by correlating our predicted TSSs with experimentally defined TSS chromatin states. Our application, pre-trained models and data are available at https://github.com/JoshuaChou2018/DeeReCT-TSS_release.

bioinformatics↗

Glutamatergic and GABAergic neurons mediate distinct neurodevelopmental phenotypes of STXBP1 encephalopathy

Heterozygous pathogenic variants in syntaxin-binding protein 1 (STXBP1, also known as MUNC18-1) cause STXBP1 encephalopathy and are among the most frequent causes of developmental and epileptic encephalopathies and intellectual disabilities. STXBP1 is an essential protein for presynaptic neurotransmitter release, and its haploinsufficiency impairs glutamatergic and GABAergic neurotransmission. However, the mechanism underlying the broad spectrum of neurological phenotypes is poorly understood. Here we show that glutamatergic and GABAergic neurons mediate distinct disease features with few overlaps. Glutamatergic and GABAergic neurons-specific Stxbp1 haploinsufficient mice exhibit different subsets of the cognitive and seizure phenotypes observed in the constitutive Stxbp1 haploinsufficient mice. Developmental delay and most of the motor and psychiatric phenotypes are only recapitulated by GABAergic Stxbp1 haploinsufficiency. Thus, the contrasting roles of excitatory and inhibitory signaling in STXBP1 encephalopathy identify GABAergic dysfunction as a main disease mechanism and reveal the possibility to selectively modulate disease phenotypes by targeting specific neurotransmitter systems.

neuroscience↗

Long-range single-molecule mapping of chromatin modification in eukaryotes

The epigenetic modifications of histones are essential markers related to the development and pathogenesis of diseases, including human cancers. Mapping histone modification has emerged as the widely used tool for studying epigenetic regulation. However, existing approaches are limited by fragmentation and short-read sequencing represent the average chromatin status in samples and cannot provide information about the long-range chromatin states. We leveraged the advantage of long read sequencing to develop a method "BIND&MODIFY" for profiling the histone modification of individual DNA fibers. Our approach is based on the recombinant fused protein A-M.EcoGII, which tethers the methyltransferase M.EcoGII to the protein binding sites and locally labels the neighboring DNA regions through artificial methylations. We demonstrated that the aggregated BIND&MODIFY signal matches the bulk-level ChIP-seq and CUT&TAG, verify the single-molecule heterogenous histone modification status, and quantify the correlation between distal elements. This method could be an essential tool in future third-generation sequencing ages.

genomics↗

Lung adenocarcinoma cell-derived exosomal miR-328 promote osteoclastogenesis by targeting Nrp2

Bone metastasis of lung cancer and detailed mechanisms are still elusive, and the roles of exosomes derived from lung adenocarcinoma cells in this process have attracted much attention. In this study, we found that A549 cell-derived exosomes (A549-Exos) promoted osteogenesis and bone resorption in vitro. Furthermore, A549-Exos target bone in vivo and promoted bone resorption in vivo. Mechanistically, A549-Exosomal miR-328 promoted bone resorption by targeting Nrp2 and A549-ExosmiR-328 Inhibitors inhibited bone resorption in vivo. Thus, A549-Exosomal miR-328 promote osteoclastogenesis by targeting Nrp2 and A549-ExosmiR-328 Inhibitors may serve as a potential nanomedicine for the treatment of bone metastasis.

cancer biology↗

Stem cell-free therapy for glaucoma to preserve vision

Glaucoma is the leading cause of irreversible blindness with trabecular meshwork (TM) dysfunction resulting in elevated intraocular pressure and retinal ganglion cell (RGC) damage leading to vision loss. In this study, we discovered that secretome, derived from human TM stem cells, via minimal invasive periocular injection, can reduce intraocular pressure, restore TM homeostasis, protect RGC, and restore RGC function in both steroid-induced and genetic myocilin mutant mouse models of glaucoma. The secretome upregulated the COX2-PGE2 axis via mitochondrial TMEM177 and led to activation of endogenous stem cells and TM regeneration. Inhibition of COX2 abolished the protective effect of secretome on TM cells. Secretome treatment also enhanced RGC survival and function. Proteomic analysis revealed that the secretome is enriched with proteins involved in extracellular matrix modulation leading to the remodeling of TM to restore homeostasis. This study highlights the feasibility of stem cell-free therapy for glaucoma with minimal invasive administration and the involvement of multiple novel pathways for a cumulative regenerative effect on the TM to protect RGC. Brief summaryThis study describes a cell-free treatment using stem cell secretome in two animal models of glaucoma and explores the potential mechanisms

cell biology↗

Machine Learning Identification of Capsid Mutations to Improve AAV Production Fitness

The adeno-associated virus (AAV) holds great potential for gene therapy efforts by providing a viable vector. However, current efforts are constrained by a lack of AAV variants that exhibit specific tropisms or immunogenicity and a lack of sustainable industrial projection. Departing from experimental approaches to addressing these issues, we built a model to predict residue mutations to improve AAV production fitness. Our model leverages the evolutionary paradigm and microenvironment characteristics by analyzing structural AAV data without needing domain knowledge or experimental fitness data for AAV as inputs. When testing our model's predictions for AAV2 residue mutations, we found a threefold increase in the percent of mutations yielding variants with better production fitness than wild type compared to random mutations, achieving a p-value of 7.46x10-12. Given these results, our machine learning approach of using structural data to approximate fitness data has the potential to accelerate AAV development.

bioinformatics↗

Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells

The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.

genomics↗

Single-cell RNA sequencing uncovers the excitatory/inhibitory synaptic unbalance in the retrosplenial cortex after peripheral nerve injury

Nerve injury in the somatosensory pathway may induce maladaptive changes at the transcriptional or protein level, contributing to the development and maintenance of neuropathic pain. In contrast to the retrosplenial cortex (RSC), which processes nociceptive information and exhibits structural and molecular changes after nerve injury, detailed transcriptional changes in the RSC are not yet known. Here we confirm the involvement of the RSC in regulating pain sensation and observe that the same peripheral stimulation activates more retrosplenial neurons after nerve injury; reducing the activities of CaMKII+ splenial cells relieves peripheral pain hypersensitivity after nerve injury. Using a single-cell RNA sequencing (scRNA-seq) approach, we identified cell-type-specific gene expression changes after nerve injury, and the gene set enrichment analysis results revealed suppressed ion homeostasis in CaMKII+ neurons. Furthermore, examination of the expression of genes encoding ligand-gated ion channels showed a decrease in Gabar1a but an increase in Gria1 in CaMKII+ neurons; consistently, we confirmed the unbalanced excitatory/inhibitory synaptic transmission by using the electrophysiological recording approach. Moreover, micro-infusion of 1-Naphthyl acetyl spermine in the RSC to reduce excitatory synaptic transmission alleviated peripheral pain hypersensitivity. Our data confirm the involvement of the RSC in pain regulation and provide information on cell type-dependent transcriptomic changes after nerve injury, which will contribute to the understanding of the mechanisms mediating neuropathic pain.

neuroscience↗

Postnatal lymph node expansion of stromal progenitors towards reticular and CD34+ stromal cell subsets is determined by distinct transcriptional programs

Gut-draining mesenteric lymph nodes (mLN) provide the framework and microenvironment to shape intestinal adaptive immune responses. We previously delineated transcriptional signatures in LN stromal cells (SC), pointing to tissue-specific variability in composition and immuno-modulatory function of SCs. Here, we dissect the tissue-specific epigenomic DNA accessibility and CpG methylation landscape of LN non-endothelial SCs and identify a microbiota-independent core epigenomic signature of LN SCs. By combined analysis of transcription factor (TF) binding sites together with the gene expression profiles of non-endothelial SCs, we delineated TFs poising skin-draining peripheral LN (pLN) SCs for pro-inflammatory responses. Furthermore, using scRNA-seq, we dissected the developmental trajectory of mLN SCs derived from postnatal to aged mice, identifying two distinct putative progenitors, namely CD34+ SC and fibroblastic reticular stromal cell (FRC) progenitors, which both feed the rapid postnatal LN expansion. Finally, we identified Irf3 as a key differentiation TF inferred from the epigenomic signature of mLN SCs that is dynamically expressed along the differentiation trajectories of FRCs, and validated Irf3 as a regulator of Cxcl9+ FRC differentiation. Together, our data constitute a comprehensive transcriptional and epigenomic map of mLN development and dissect location-specific, microbiota-independent properties of mLN non-endothelial SCs. As such, our findings represent a valuable resource to identify core transcriptional regulators that impinge on the developing mLN early in life, thereby shaping long-lasting intestinal adaptive immune responses.

immunology↗

BSCL2/Seipin Deficiency in Heart Causes Energy Deficit and Heart Failure via Inducing Excessive Lipid Catabolism

Heart failure (HF) is one of the leading causes of death world-wide and is associated with cardiac metabolic perturbations. Human Type 2 Berardinelli-Seip Congenital Lipodystrophy (BSCL2) disease is caused by mutations in the BSCL2 gene. Global lipodystrophic Bscl2-/- mice exhibit hypertrophic cardiomyopathy. Whether BSCL2 plays a direct role in regulating cardiac substrate metabolism and/or contractile function remains unknown. Here we show that mice with cardiac-specific deletion of Bscl2 (Bscl2cKO) developed dilated HF. Myocardial BSCL2 deletion led to elevated ATGL expression and FA oxidation (FAO) along with reduced cardiac lipid contents. Cardiac dysfunction in Bscl2cKO mice was independent of mitochondrial dysfunction and oxidative stress, but associated with decreased metabolic reserve and ATP levels. Importantly, heart failure in Bscl2cKO mice could be partially reversed by pharmacological inhibition of FAO, or prevented by high fat diet (HFD) feeding. Lipidomic analysis further identified markedly reduced glycerolipids, glycerophospholipids, NEFA and acylcarnitines in Bscl2cKO hearts, which were partially normalized by FAO inhibition or HFD. Our study reveals a new form of HF with excessive lipid catabolism, and identifies a crucial cardiomyocyte-specific role of BSCL2 in controlling cardiac lipid catabolism, energy state and contractile function. It also provides novel insights into metabolically treating energy-starved HF using FAO inhibitor or HFD.

physiology↗

Molecular classification reveals the diverse genetic features and prognosis of gastric cancer: a multi-omics consensus ensemble clustering

BackgroundGastric cancer (GC) is the fifth most common tumor around the world, it is necessary to reveal novel molecular subtypes to guide the selection of patients who may benefit from specific target therapy. MethodsMulti-omics data, including RNA-sequence of transcriptomics (mRNA, LncRNA, miRNA), DNA methylation and gene mutation of TCGA-STAD cohort was used for the clustering. Ten classical clustering algorithms were applied to recognize patients with different molecular features via the R package "MOVICS". The activated signaling pathways were evaluated using the single-sample gene set enrichment analysis. The difference distribution of gene mutations, copy number alterations and tumor mutation burden was compared, and potential response to immunotherapy and chemotherapy was assessed as well. ResultsTwo molecular subtypes (CS1 and CS2) were recognized by ten clustering algorithms with further consensus ensembles. Patients in the CS1 group were found to contain a shorter average overall survival time (28.5 vs. 68.9 months, P = 0.016), and progression-free survival (19.0 vs. 63.9 months, P = 0.008) compared to the CS2 group. CS1 group contained more activation of extracellular associated biological process, while CS2 group displayed the activation of cell cycle associated pathways. The significantly higher total mutation numbers and neo antigens were observed in CS2 group, along with the specific mutation of TTN, MUC16 and ARID1A. Higher infiltration of immunocytes were also observed in CS2 group, reflected to the potential benefit from immunotherapy. Moreover, CS2 group also can response to 5-fluorouracil, cisplatin, and paclitaxel. The similar diverse of clinical outcome of CS1 and CS2 groups were successfully validation in external cohorts of GSE62254, GSE26253, GSE15459, and GSE84437. ConclusionNovel insight into the GC subtypes was obtained via integrative analysis of five omics data by ten clustering algorithms, which can provide the idea to the clinical target therapy based on the specific molecular features.

cancer biology↗

Extraction, purification and anti-TMV effects of α (β)-2,7,11-cembratriene-4,6-diol from tobacco leaves

BackgroundAcetone ethanol extracts from tobacco leaves have antiviral activity against TMV, but the antiviral effects of their specialized metabolites have not been systematically studied yet, especially the underlying mechanism is still unexplored. ResultsThe tobacco cembranoids ({beta})-2,7,11-cembratriene-4,6-diol (({beta})-CBD) were extracted and purified with an effective and green protocol including innovatively added 5% phosphoric acid for elution, one time silica gel chromatographic column separation and impurity removal and further HPLC purification. The results of antiviral activities against tobacco mosaic virus (TMV) with the local lesion counting method showed that ({beta})-CBD have in vivo higher protective effects of 73.2% and 71.6%, at 75.0 M, respectively, than control agent Ningnanmycin (53.1%). Notably, The results of ELISA and and TMV-GFP fluorescent optical imaging assay indicated a obviously reduced viral protein and weaker GFP fluorescence signal and smaller infection area, which confirmed their anti-TMV activities at protein level. Furthermore, the enhanced production of SA and JA and the significantly increased transcription of of JA signaling pathway (COI1 and PDF1.2) and SA signaling pathway genes (PR1, NPR1 and EDS1) in treated plants further conformed that exogenously applied ({beta})-CBD can effectively elicit the tobacco plant immunity against TMV. ConclusionsThe ({beta})-CBD mainly stimulates disease resistance of tobacco plants to resist TMV and it can be used as bioagents to control TMV in the future.

plant biology↗