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Huang, H.

Publications and source records attributed to Huang, H..

At least 37 records · Page 2Linked to original sources

Mechanisms of KCNQ1 Channel Dysfunction in Long QT Syndrome Involving Voltage Sensor Domain Mutations

Loss-of-function (LOF) mutations in human KCNQ1 are responsible for susceptibility to a life-threatening heart rhythm disorder, the congenital long-QT syndrome (LQTS). Hundreds of KCNQ1 mutations have been identified, but the molecular mechanisms responsible for impaired function are poorly understood. Here, we investigated the impact of 51 KCNQ1 variants located within the voltage sensor domain (VSD), with an emphasis on elucidating effects on cell surface expression, protein folding and structure. For each variant, the efficiency of trafficking to the plasma membrane, the impact of proteasome inhibition, and protein stability were assayed. The results of these experiments, combined with channel functional data, provided the basis for classifying each mutation into one of 6 mechanistic categories. More than half of the KCNQ1 LOF mutations destabilize the structure of the VSD, resulting in mistrafficking and degradation by the proteasome, an observation that underscores the growing appreciation that mutation-induced destabilization of membrane proteins may be a common human disease mechanism. Finally, we observed that 5 of the folding-defective LQTS mutants are located in the VSD S0 helix, where they interact with a number of other LOF mutation sites in other segments of the VSD. These observations reveal a critical role for the S0 helix as a central scaffold to help organize and stabilize the KCNQ1 VSD and, most likely, the corresponding domain of many other ion channels.\n\nOne Sentence SummaryLong QT syndrome-associated mutations in KCNQ1 most often destabilize the protein, leading to mistrafficking and degradation.

biochemistry

Evaluating a sepsis prediction machine learning algorithm using minimal electronic health record data in the emergency department and intensive care unit

IntroductionSepsis is a major health crisis in US hospitals, and several clinical identification systems have been designed to help care providers with early diagnosis of sepsis. However, many of these systems demonstrate low specificity or sensitivity, which limits their clinical utility. We evaluate the effects of a machine learning algodiagnostic (MLA) sepsis prediction and detection system using a before-and-after clinical study performed at Cabell Huntington Hospital (CHH) in Huntington, West Virginia. Prior to this study, CHH utilized the St. Johns Sepsis Agent (SJSA) as a rules-based sepsis detection system.\n\nMethodsThe Predictive algoRithm for EValuation and Intervention in SEpsis (PREVISE) study was carried out between July 1, 2017 and August 30, 2017. All patients over the age of 18 who were admitted to the emergency department or intensive care units at CHH were monitored during the study. We assessed pre-implementation baseline metrics during the month of July, 2017, when the SJSA was active. During implementation in the month of August, 2017, SJSA and the MLA concurrently monitored patients for sepsis risk. At the conclusion of the study period, the primary outcome of sepsis-related in-hospital mortality and secondary outcome of sepsis-related hospital length of stay were compared between the two groups.\n\nResultsSepsis-related in-hospital mortality decreased from 3.97% to 2.64%, a 33.5% relative decrease (P = 0.038), and sepsis-related length of stay decreased from 2.99 days in the pre-implementation phase to 2.48 days in the post-implementation phase, a 17.1% relative reduction (P < 0.001).\n\nConclusionReductions in patient mortality and length-of-stay were observed with use of a machine learning algorithm for early sepsis detection in the emergency department and intensive care units at Cabell Huntington Hospital, and may present a method for improving patient outcomes.\n\nTrial RegistrationClinicalTrials.gov, NCT03235193, retrospectively registered on July 27th 2017.

clinical trials

Common risk variants identified in autism spectrum disorder

Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 ASD cases and 27,969 controls that identifies five genome-wide significant loci. Leveraging GWAS results from three phenotypes with significantly overlapping genetic architectures (schizophrenia, major depression, and educational attainment), seven additional loci shared with other traits are identified at equally strict significance levels. Dissecting the polygenic architecture we find both quantitative and qualitative polygenic heterogeneity across ASD subtypes, in contrast to what is typically seen in other complex disorders. These results highlight biological insights, particularly relating to neuronal function and corticogenesis and establish that GWAS performed at scale will be much more productive in the near term in ASD, just as it has been in a broad range of important psychiatric and diverse medical phenotypes.

genetics

Structural network maturation of the preterm human brain

During the 3rd trimester, large-scale of neural circuits are formed in the human brain, resulting in the adult-like brain networks at birth. However, how the brain circuits develop into a highly efficient and segregated connectome during this period is unknown. We hypothesized that faster increases of connectivity efficiency and strength at the brain hubs and rich-club are critical for emergence of an efficient and segregated brain connectome. Here, using high resolution diffusion MRI of 77 preterm-born and term-born neonates scanned at 31-42 postmenstrual weeks (PMW), we constructed the structural connectivity matrices and performed graph-theory-based analyses. We found faster increases of nodal efficiency mainly at the brain hubs, distributed in primary sensorimotor regions, superior-middle frontal and posterior cingulate gyrus during 31-42PMW. The rich-club and within-module connections were characterized by higher rates of edge strength increases. Edge strength of short-range connections increased faster than that of long-range connections. The nodal efficiencies of the hubs predicted individual postmenstrual ages more accurately than those of non-hubs. Collectively, these findings revealed regionally differentiated maturation in the baby brain structural connectome and more rapid increases of the hub and rich-club connections, which underlie network segregation and differentiated brain function emergence.

neuroscience

UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants

Understanding the association of genetic variation with its functional consequences in proteins is essential for the interpretation of genomic data and identifying causal variants in diseases. Integration of protein function knowledge with genome annotation can assist in rapidly comprehending genetic variation within complex biological processes. Here, we describe mapping UniProtKB human sequences and positional annotations such as active sites, binding sites, and variants to the human genome (GRCh38) and the release of a public genome track hub for genome browsers. To demonstrate the power of combining protein annotations with genome annotations for functional interpretation of variants, we present specific biological examples in disease-related genes and proteins. Computational comparisons of UniProtKB annotations and protein variants with ClinVar clinically annotated SNP data show that 32% of UniProtKB variants co-locate with 8% of ClinVar SNPs. The majority of co-located UniProtKB disease-associated variants (86%) map to pathogenic ClinVar SNPs. UniProt and ClinVar are collaborating to provide a unified clinical variant annotation for genomic, protein and clinical researchers. The genome track hubs, and related UniProtKB files, are downloadable from the UniProt FTP site and discoverable as public track hubs at the UCSC and Ensembl genome browsers.

genomics

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model

Red-shanked doucs (Pygathrix nemaeus) are endangered, foregut-fermenting colobine primates which are difficult to maintain in captivity. There are critical gaps in our understanding of their natural dietary habits including consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric adaptations, including their unique microflora. To address these knowledge gaps, we used the douc as a model to study relationships between gastrointestinal microbial community structure, diet, and health. We analyzed published fecal samples as well as detailed dietary history from doucs with four distinct lifestyles (wild, semi-wild, semi-captive, and captive) and determined gastrointestinal bacterial microbiome composition using 16S rRNA sequencing. A clear gradient of microbiome composition was revealed along an axis of natural lifestyle disruption, including significant associations with diet, health, biodiversity, and microbial function. We identified potential microbial biomarkers of douc dysbiosis, including Bacteroides and Prevotella. Our results suggest a gradient-like shift in captivity causes an attendant shift to severe gut dysbiosis, thereby resulting in gastrointestinal issues.

microbiology

System-level studies of a cell-free transcription-translation platform for metabolic engineering

Current methods for assembling biosynthetic pathways in microorganisms require a process of repeated trial and error and have long design-build-test cycles. We describe the use of a cell-free transcription-translation (TX-TL) system as a biomolecular breadboard for the rapid engineering of the 1,4-butanediol (BDO) pathway. We demonstrate the reliability of TX-TL as a platform for engineering biological systems by undertaking a careful characterization of its transcription and translation capabilities and provide a detailed analysis of its metabolic output. Using TX-TL to survey the design space of the BDO pathway enables rapid tuning of pathway enzyme expression levels for improved product yield. Leveraging TX-TL to screen enzyme variants for improved catalytic activity accelerates design iterations that can be directly applied to in vivo strain development.

bioengineering

Targeting posttranslational modifications of RioK1 inhibits the progression of colorectal and gastric cancers

RioK1 has recently been shown to play important roles in cancers, but its posttranslational regulation is largely unknown. Here we report that RioK1 is methylated at K411 by SETD7 methyltransferase, and that lysine-specific demethylase 1 (LSD1) reverses its methylation. The mutated RioK1 (K411R) that cannot be methylated exhibits a longer half-life than does the methylated RioK1. FBXO6 specifically interacts with K411-methylated RioK1 through its FBA domain to induce RioK1 ubiquitination. Casein kinase 2 (CK2) phosphorylates RioK1 at T410, which stabilizes RioK1 by antagonizing K411 methylation and impeding the recruitment of FBXO6 to RioK1. Functional experiments demonstrate the RioK1 methylation reduces the tumor growth and metastasis in CRC and GC. Importantly, the protein levels of CK2 and LSD1 show an inverse correlation with FBXO6 and SETD7 expression in human CRC tissues. Therefore, this study highlights the importance of a RioK1 methylation-phosphorylation switch in determining CRC and GC development.

cancer biology

Impaired social contacts with familiar anesthetized conspecific in CA3-restricted BDNF knockout mice

Familiarity is the vital characteristic conveyed by social cues to determine behaviors towards conspecific. Here we characterize social contacts to familiar vs unfamiliar male conspecific, anesthetized to eliminate inter-male aggression. During initial 10 min (phase-1), subjects contacted demonstrators vigorously regardless of familiarity. During subsequent 80 min (phase-2), however, they contacted more with familiar than unfamiliar conspecifics. Then, this test was applied on highly aggressive mice with hippocampal CA3-restricted BDNF knockout (KO), in which aggression may mask other behaviors. KO showed less preference to contacting familiar conspecific than wild type (WT) during phase-2 but no differences during phase-1. Among non-social behaviors, eating duration was shorter in the presence of familiar than unfamiliar conspecific in WT, but same in KO. Additionally, KO exhibited reduced pain sensitization. Altogether, these findings suggest that KO has deficits in circuits that process social cues from familiar conspecifics and pain and, possibly, underlie empathy-like behaviors.

animal behavior and cognition

Dependence of Intravoxel Incoherent Motion MR threshold b-value selection for separating perfusion and diffusion compartment and liver fibrosis diagnostic performance.

PurposeTo explore how the selection of threshold b-value impacts Intravoxel Incoherent Motion (IVIM) diffusion parameters of PF (f), Dslow (D),and Dfast (D*) values and their performance for liver fibrosis detection.\n\nMaterials and MethodsFifteen healthy volunteers and 33 hepatitis-b patients were included. With a 1.5 T MR scanner and respiration gating, IVIM data was acquired with 10 b-values of 10,20,40,60,80,100,150, 200, 400, and 800 s/mm2. Signal measurement was performed on right liver. Segmented-unconstrained analysis was used to compute IVIM parameters, and six threshold b-values between 40 and 200 s/mm2 were compared. PF, Dslow, and Dfast values were placed along the x-axis, y-axis, and z-axis, and a plane was defined to separate volunteers from patients.\n\nResultsHigher threshold b-values were associated with higher PF measurement; while lower threshold b-values led to higher Dslow and Dfast measurements. The dependence of PF, Dslow, and Dfast on threshold b-value differed between healthy livers and fibrotic livers; with the healthy livers showing a higher dependence. Threshold b-value=60 s/mm2 showed the largest mean distance between healthy liver datapoints vs. fibrotic liver datapoints in 3-dimensional space.\n\nConclusionFor segmented-unconstrained analysis, the selection of threshold b-value=60 s/mm2 improves IVIM diffusion differentiation between healthy livers and fibrotic livers.

biophysics

Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium

As technology advances, whole genome sequencing (WGS) is likely to supersede other genotyping technologies. The rate of this change depends on its relative cost and utility. Variants identified uniquely through WGS may reveal novel biological pathways underlying complex disorders and provide high-resolution insight into when, where, and in which cell type these pathways are affected. Alternatively, cheaper and less computationally intensive approaches may yield equivalent insights. Understanding the role of rare variants in the noncoding gene-regulating genome, through pilot WGS projects, will be critical to determine which of these two extremes best represents reality. With large cohorts, well-defined risk loci, and a compelling need to understand the underlying biology, psychiatric disorders have a role to play in this preliminary WGS assessment. The WGSPD consortium will integrate data for 18,000 individuals with psychiatric disorders, beginning with autism spectrum disorder, schizophrenia, bipolar disorder, and major depressive disorder, along with over 150,000 controls.

genomics

Single nucleus analysis of the chromatin landscape in mouse forebrain development

Genome-wide analysis of chromatin accessibility in primary tissues has uncovered millions of candidate regulatory sequences in the human and mouse genomes1-4. However, the heterogeneity of biological samples used in previous studies has prevented a precise understanding of the dynamic chromatin landscape in specific cell types. Here, we show that analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples can resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types. Our strategy is based on a combinatorial barcoding assisted single cell assay for transposase-accessible chromatin5 and is optimized for nuclei from flash-frozen primary tissue samples (snATAC-seq). We used this method to examine the mouse forebrain at seven development stages and in adults. From snATAC-seq profiles of more than 15,000 high quality nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell-types in foetal and adult forebrains. We further define cell-type specific cis regulatory sequences and infer potential master transcriptional regulators of each cell population. Our results demonstrate the feasibility of a general approach for identifying cell-type-specific cis regulatory sequences in heterogeneous tissue samples, and provide a rich resource for understanding forebrain development in mammals.

genomics

Discovery Of The First Genome-Wide Significant Risk Loci For ADHD

Attention-Deficit/Hyperactivity Disorder (ADHD) is a highly heritable childhood behavioral disorder affecting 5% of school-age children and 2.5% of adults. Common genetic variants contribute substantially to ADHD susceptibility, but no individual variants have been robustly associated with ADHD. We report a genome-wide association meta-analysis of 20,183 ADHD cases and 35,191 controls that identifies variants surpassing genome-wide significance in 12 independent loci, revealing new and important information on the underlying biology of ADHD. Associations are enriched in evolutionarily constrained genomic regions and loss-of-function intolerant genes, as well as around brain-expressed regulatory marks. These findings, based on clinical interviews and/or medical records are supported by additional analyses of a self-reported ADHD sample and a study of quantitative measures of ADHD symptoms in the population. Meta-analyzing these data with our primary scan yielded a total of 16 genome-wide significant loci. The results support the hypothesis that clinical diagnosis of ADHD is an extreme expression of one or more continuous heritable traits.

genetics

A Combined Use Of Intravoxel Incoherent Motion MRI Parameters Can Differentiate Early Stage Hepatitis-B Fibrotic Livers From Healthy Livers

This study investigated a combined use of IVIM parameters Dslow (D), PF (f) and Dfast (D*) for liver fibrosis evaluation. 16 healthy volunteers (F0) and 33 hepatitis-b patients (stage F1= 15, stage F2-4 = 18) were included. With a 1.5-T MR scanner and respiration-gating, IVIM diffusion weighted imaging was acquired using a single-shot echo-planar imaging sequence with ten b-values of 10, 20, 40, 60, 80, 100, 150, 200, 400, and 800 s/mm2. Signal measurement was performed on right liver parenchyma. With a 3-dimensional tool, Dslow, PF, and Dfast values were placed along the x-axis, y-axis, and z-axis, and a plane was defined to separate healthy volunteers from patients. 3-dimensional tool demonstrated healthy volunteers and all patients with liver fibrosis could be separated. Classification and Regression Tree showed a combination of PF (PF < 12.55%), Dslow (Dslow < 1.152 x10-3 mm2/s) and Dfast (Dfast <13.36 x10-3 mm2/s) could differentiate healthy subjects and all fibrotic livers (F1-F4) with an area under the curve of logistic regression (AUC) of 0.986. The AUC for differentiation of healthy livers vs. F2-4 livers was 1. PF offered the best diagnostic value, followed by Dslow; however, all three parameters of PF, Dslow, and Dfast contributed to liver fibrosis detection.

biophysics

Cross-Species Complementation Reveals Conserved Functions For EARLY FLOWERING 3 Between Monocots And Dicots

Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana and crop species, circadian clock factors have been identified as critical for growth, flowering and circadian rhythms. Outside of A. thaliana, however, little is known about the molecular function of clock genes. Therefore, we sought to compare the function of Brachypodium distachyon and Seteria viridis orthologs of EARLY FLOWERING3, a key clock gene in A. thaliana. To identify both cycling genes and putative ELF3 functional orthologs in S. viridis, a circadian RNA-seq dataset and online query tool (Diel Explorer) was generated as a community resource to explore expression profiles of Setaria genes under constant conditions after photo- or thermo-entrainment. The function of ELF3 orthologs from A. thaliana, B. distachyon, and S. viridis were tested for complementation of an elf3 mutation in A. thaliana. Despite comparably low sequence identity versus AtELF3 (less than 37%), both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time and arrhythmic clock phenotypes. Molecular analysis using affinity purification and mass spectrometry to compare physical interactions also found that BdELF3 and SvELF3 could be integrated into similar complexes and networks as AtELF3, including forming a composite evening complex. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss of ELF3 at the molecular and physiological level.\n\nOne Sentence SummaryOrthologs of a key circadian clock component ELF3 from grasses functionally complement the Arabidopsis counterpart at the molecular and physiological level, in spite of high sequence divergence.

plant biology

Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection

Approximately three quarters of acute HCV infections evolve to a chronic state, while one quarter are spontaneously cleared. Genetic predispositions strongly contribute to the development of chronicity. We have conducted a genome-wide association study to identify genomic variants underlying HCV spontaneous clearance using Immunochip in European and African ancestries. We confirmed two previously reported significant associations, in the IL28B/IFNL41,2 and MHC regions, with spontaneous clearance in the European population. We further fine-mapped the MHC association to a region of about 50 kilo base pairs, down from 1 mega base pairs in the previous study. Additional analyses suggested that the association in the MHC locus might be significantly stronger for virus subtype 1a than 1b, suggesting that viral subtype may have influenced the genetic mechanism underlying the clearance of HCV.

immunology

Profiling Of Lysine-Acetylated Proteins In Human Urine

Biomarker is the measurable change associated with a physiological or pathophysiological process, its nature is change. Contrast to the blood which is under homeostatic controls, urine reflects changes in the body earlier and more sensitive therefore is a better biomarker source. Lysine acetylation is an abundant and highly regulated post-translational modification. It plays a pivotal role in modulating diverse biological processes and is associated with various important diseases. Enrichment or visualization of proteins with specific post-translational modifications provides a method for sampling the urinary proteome and reducing sample complexity. In this study, we used anti-acetyllysine antibody-based immunoaffinity enrichment combined with high-resolution mass spectrometry to profile lysine-acetylated proteins in normal human urine. A total of 629 acetylation sites on 315 proteins were identified, including some very low-abundance proteins. This is the first proteome-wide characterization of lysine acetylation proteins in normal human urine. Our dataset provides a useful resource for the further discovery of the lysine acetylated proteins as biomarker in urine.

molecular biology

Mapping Human Hematopoietic Hierarchy At Single Cell Resolution By Microwell-seq

The classical hematopoietic hierarchy, which is mainly built with fluorescence-activated cell sorting (FACS) technology, proves to be inaccurate in recent studies. Single cell RNA-seq (scRNA-seq) analysis provides a solution to overcome the limit of FACS-based cell type definition system for the dissection of complex cellular hierarchy. However, large-scale scRNA-seq is constrained by the throughput and cost of traditional methods. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using extremely simple devices. Using Microwell-seq, we constructed a single-cell resolution transcriptome atlas of human hematopoietic differentiation hierarchy by profiling more than 50,000 single cells throughout adult human hematopoietic system. We found that adult human hematopoietic stem and progenitor cell (HSPC) compartment is dominated by progenitors primed with lineage specific regulators. Our analysis revealed differentiation pathways for each cell types, through which HSPCs directly progress to lineage biased progenitors before differentiation. We propose a revised adult human hematopoietic hierarchy independent of oligopotent progenitors. Our study also demonstrates the broad applicability of Microwell-seq technology.

cell biology