Biology subjects

Hu, M.

Publications and source records attributed to Hu, M..

At least 217 records · Page 12Linked to original sources

bioRxiv2019

Cell-autonomous regulation of epithelial cell quiescence by calcium channel Trpv6

Epithelial homeostasis and regeneration require a pool of quiescent cells. How the quiescent cells are established and maintained is poorly understood. Here we report that Trpv6, a cation channel responsible for epithelial Ca2+ absorption, functions as a key regulator of cellular quiescence. Genetic deletion and pharmacological blockade of Trpv6 promoted zebrafish epithelial cells to exit from quiescence and re-enter the cell cycle. Reintroducing Trpv6, but not its channel dead mutant, restored the quiescent state. Ca2+ imaging showed that Trpv6 is constitutively open in vivo. Mechanistically, Trpv6-mediated Ca2+ influx maintained the quiescent state by suppressing insulin-like growth factor (IGF)-mediated Akt and Tor signaling. In zebrafish epithelia and human colon cancer cells, Trpv6/TRPV6 elevated intracellular Ca2+ levels and activated PP2A, which down-regulated IGF signaling and promoted the quiescent state. Our findings suggest that Trpv6 mediates constitutive Ca2+ influx into epithelial cells to continuously suppress growth factor signaling and maintain the quiescent state.

developmental biology↗

bioRxiv2019

FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller. Highlights- Frequently Interacting Regions (FIREs) can be used to identify tissue and cell-type-specific cis-regulatory regions. - An R software, FIREcaller, has been developed to identify FIREs and clustered FIREs into super-FIREs.

bioinformatics↗

bioRxiv2019

Common DNA sequence variation influences 3-dimensional conformation of the human genome

The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. To address these questions, we performed Hi-C on Lymphoblastoid Cell Lines (LCLs) from 20 individuals. We identified thousands of regions across the genome where 3D chromatin conformation varies between individuals and found that this conformational variation is often accompanied by variation in gene expression, histone modifications, and transcription factor (TF) binding. Moreover, we found that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality and density of local cis contacts. We mapped hundreds of Quantitative Trait Loci (QTLs) associated with 3D chromatin features and found evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk. Our results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized.

genomics↗

bioRxiv2019

VHL Synthetic Lethality Signatures Uncovered by Genotype-specific CRISPR-Cas9 Screens

BackgroundGenome-wide CRISPR-Cas9 essentiality screening represents a powerful approach to identify genetic vulnerabilities in cancer cells. Here, we applied this technology and designed a strategy to identify target genes that are synthetic lethal (SL) with von Hippel-Lindau (VHL) tumor suppressor gene. Inactivation of VHL has been frequently found in clear cell renal cell carcinoma (ccRCC). Its SL partners serve as potential drug targets for the development of targeted cancer therapies.\n\nResultsWe performed parallel genome-wide CRISPR screens in two pairs of isogenic ccRCC cell lines that differ only in the VHL status. Comparative analyses of screening results not only confirmed a well-known role for mTOR signaling in renal carcinoma, but also identified DNA damage response and selenocysteine biosynthesis pathways as major SL targets in VHL-inactivated cancer cells. Follow-up studies provided cellular and mechanistic insights into SL interactions of these pathway genes with the VHL gene.\n\nConclusionsUsing isogenic CRISPR screening approach, we uncovered novel biological processes that are SL with VHL, which can be exploited for drug development for ccRCC. Our CRISPR and RNA-seq datasets provide a rich resource for future investigation of the function of the VHL tumor suppressor protein. Our work demonstrates the efficiency of CRISPR-based synthetic lethality screening in human isogenic cell pairs. Similar strategies could be employed to unveil SL partners with other oncogenic drivers.

cancer biology↗

bioRxiv2019

Data Resource Profile:The Dementias Platform UK (DPUK) Data Portal

The Dementias Platform UK (DPUK) Data Portal is a data repository facilitating access to data for 3 370 929 individuals in 42 cohorts. The Data Portal is an end-to-end data management solution providing a secure, fully auditable, remote access environment for the analysis of cohort data. All projects utilising the data are by default collaborations with the cohort research teams generating the data. The Data Portal uses UK Secure eResearch Platform (UKSeRP) infrastructure to provide three core utilities: data discovery, access, and analysis. These are delivered using a 7 layered architecture comprising: data ingestion, data curation, platform interoperability, data discovery, access brokerage, data analysis and knowledge preservation. Automated, streamlined, and standardised procedures reduce the administrative burden for all stakeholders, particularly for requests involving multiple independent datasets, where a single request may be forwarded to multiple data controllers. Researchers are provided with their own secure lab using VMware which is accessed using two factor authentication. Over the last 2 years, 160 project proposals involving 579 individual cohort data access requests were received. These were received from 268 applicants spanning 72 institutions (56 academic, 13 commercial, 3 government) in 16 countries with 84 requests involving multiple cohorts. Project are varied including multi-modal, machine learning, and Mendelian randomisation analyses. Data access is usually free at point of use although a small number of cohorts require a data access fee.

neuroscience↗

bioRxiv2018

Inhibition of tetrameric Patched1 by Sonic Hedgehog through an asymmetric paradigm

The Hedgehog (Hh) pathway controls embryonic development and postnatal tissue maintenance and regeneration. Inhibition of oligomeric Hh receptor Patched (Ptch) by the secreted and post-translationally modified ligand Hh relieves suppression of the signaling cascades. Here, we report the cryo-EM structure of tetrameric Ptch1 in complex with palmitoylated N-terminal signaling domain of human Sonic hedgehog (ShhNp). The structure shows that four Ptch1 protomers are organized as a loose dimer of dimers and each dimer binds to one ShhNp through two distinct inhibitory interfaces. Ptch1-A binds to ShhNp through the well-characterized Ca2+-mediated interface on the globular domain of ShhNp, and Ptch1-B primarily interacts with the N-terminal peptide and the palmitoyl moiety. Map comparison reveals that the cholesteryl moiety of native ShhN occupies a recently identified extracellular steroid binding pocket in Ptch1-B. Our structure elucidates the tetrameric assembly of Ptch1 and suggests asymmetric mode of actions of the Hh ligands for inhibiting the potential cholesterol transport activity of Ptch1.

biophysics↗

bioRxiv2018

Antibacterial activity of total flavonoids from Ilex rotunda Thunb. and different antibacterials on different multidrug-resistant bacteria alone or in combination

The problem of bacterial resistance is becoming more and more serious, which has become an urgent problem to be solved in human and veterinary. One approach to control and delay bacterial resistance is combination therapy in which antibiotics are given together with other antimicrobial or non-antimicrobial agents. Studies have shown that flavonoids from Traditional Chinese medicine (TCM) possess a high level of antibacterial activity against antibiotic resistant strains. The aim of this study was to evaluate the antibacterial effects of a combined therapy of total flavonoids from Ilex rotunda Thunb. and antibiotics against seven kinds of veterinary bacteria which were multidrug resistance bacteria. A microdilution checkerboard method was used to determine the minimal inhibitory concentrations of both types of antimicrobials, alone and in combination. The fractional inhibitory concentration index was calculated and used to classify observed collective antibacterial activity as synergistic, additive, indifferent or antagonistic.\n\nFrom the performed tests, the total flavonoids and antimicrobial agents were combined to inhibit different multidrug-resistant bacteria, such as Escherichia coli, Streptococcus, Pseudomonas aeruginosa, Enterococcus faecalis, Proteus vulgaris, Staphylococcus aureus, Acinetobacter baumannii. For these bacteria, total flavonoids from Ilex Rotunda Thunb. presented synergistic or additive with different antibiotics and had a certain antibacterial effect on the separated multidrug-resistant bacteria. The study shows total flavonoids from Ilex rotunda Thunb. have potential as adjuvants for the treatment of animal bacterial diseases.

microbiology↗

bioRxiv2018

Fatigue and cognitive performance change in MS: multifactorial with disparate influences

BackgroundFatigue is a common and disabling symptom in Multiple Sclerosis (MS) with a variety of direct and indirect influences, but remains poorly understood. Performance-based and self-report measures of fatigue are only weakly correlated and may have independent predictors. We adopted a multifactorial approach, utilising a measure of concurrent cognitive performance change in order to examine the clinical, psychological, and cognitive factors influencing subjective and objective fatigue in MS.\n\nMethodsSixty-one people with MS were assessed. Subjective fatigue was measured using the Modified Fatigue Impact Scale, Fatigue Assessment Instrument, and a Visual Analogue Scale (VAS). The Conners Continuous Performance Test 3 (CCPT3) and VAS were administered before and after two hours of cognitive testing, representing a period of cognitive effort. The differences in scores formed measures of objective performance fatigue and subjective fatigue change, respectively. We examined differences across baseline fatigue, fatigue change and performance change classifications, using regression analysis to uncover predictors of subjective fatigue and performance change.\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@81ec81org.highwire.dtl.DTLVardef@1ce44e8org.highwire.dtl.DTLVardef@10e1bdeorg.highwire.dtl.DTLVardef@147c5ceorg.highwire.dtl.DTLVardef@10b831f_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONDemographic and clinical features of the sample\n\nC_TABLECAPTION C_TBL ResultsDepression, sleep, and emotion-focused coping each predicted baseline fatigue and together explained 53.5% of variance. Increased subjective fatigue was linked with anxiety, lower self-efficacy and gender. Cognitive performance change on the CCPT3 was however predicted by estimated general cognitive ability, self-efficacy and post-intervention fatigue.\n\nConclusionSubjective fatigue in MS is a multifactorial construct, with subjective and objective cognitive performance fatigue largely influenced by indirect psychological and cognitive factors. The varying factors driving subjective and objective fatigue suggest that future studies need to take into account these disparate aspects when developing fatigue assessment tools. Targeting influential fatigue drivers such as psychological variables, and even using gender specific interventions may have the potential to improve the burden of fatigue and quality of life of people with MS.

neuroscience↗

bioRxiv2018

MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in analysis of chromatin interactions centered on cohesin, CTCF and H3K4me3 associated regions in multiple cell types. MAPS is freely available at https://github.com/ijuric/MAPS.

bioinformatics↗

bioRxiv2018

BAMM-SC: A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies

The recently developed droplet-based single cell transcriptome sequencing (scRNA-seq) technology makes it feasible to perform a population-scale scRNA-seq study, in which the transcriptome is measured for tens of thousands of single cells from multiple individuals. Despite the advances of many clustering methods, there are few tailored methods for population-scale scRNA-seq studies. Here, we have developed a BAyesiany Mixture Model for Single Cell sequencing (BAMM-SC) method to cluster scRNA-seq data from multiple individuals simultaneously. Specifically, BAMM-SC takes raw data as input and can account for data heterogeneity and batch effect among multiple individuals in a unified Bayesian hierarchical model framework. Results from extensive simulations and application of BAMM-SC to in-house scRNA-seq datasets using blood, lung and skin cells from humans or mice demonstrated that BAMM-SC outperformed existing clustering methods with improved clustering accuracy and reduced impact from batch effects. BAMM-SC has been implemented in a user-friendly R package with a detailed tutorial available on www.pitt.edu/~Cwec47/singlecell.html.

bioinformatics↗

bioRxiv2018

Integrative analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes

Gene regulation is important for cells and tissues to function. At the genomic level, it has been studied from two aspects, the identification of expression quantitative trait loci (eQTLs) and identification of long-range chromatin interactions. It is important to understand their relationship, such as whether eQTLs regulate their target genes through physical chromatin interaction. Although previous studies have suggested enrichment of eQTLs in regions with a high chromatin interaction frequency, it is unclear whether this relationship is consistent across different tissues and cell lines and whether there would be any tissue-specific patterns. Here, we performed integrative analyses of eQTL and high-throughput chromatin conformation capture (Hi-C) data from 11 human primary tissue types and 2 human cell lines. We found that chromatin interaction frequency is positively correlated with the number of genes having eQTLs, and eQTLs and their target genes are more likely to fall in the same topologically associating domains than that expected from randomly generated control datasets. These results are consistent across all tissues and cell lines we evaluated. Moreover, in dorsolateral prefrontal cortex, spleen, hippocampus, pancreas and aorta, tissue-specific eQTLs are enriched in tissue-specific frequently interacting regions. These results reveal a more detailed picture of the complicated relationship between different mechanisms of gene regulation.\n\nAuthor summaryWhole-genome gene regulation has been studied in tissues and cell lines from multiple perspectives, including identification of expression quantitative trait loci (eQTLs) and identification of long-range chromatin interactions. These two complementary approaches focus on different aspects of gene regulation, one being statistical across individuals while the other being physical within a sample. Integrating results from these two approaches will help us understand their relationships, such as whether eQTLs regulate their target genes through physical chromatin interaction. We performed comprehensive analyses using data from multiple human tissues and cell lines, and showed that chromatin interaction frequency is positively associated with eQTL results in all evaluated tissues and cell lines. The observed relationships also displayed tissue-specific pattern in some tissues. Our results revealed a more detailed picture of the complicated relationship between the different mechanisms of gene regulation.

systems biology↗

bioRxiv2018

A particle-filter framework for robust cryoEM 3D reconstruction

Electron cryo-microscopy (cryoEM) is now a powerful tool in determining atomic structures of biological macromolecules under nearly natural conditions. The major task of single-particle cryoEM is to estimate a set of parameters for each input particle image to reconstruct the three-dimensional structure of the macromolecules. As future large-scale applications require increasingly higher resolution and automation, robust high-dimensional parameter estimation algorithms need to be developed in the presence of various image qualities. In this paper, we introduced a particle-filter algorithm for cryoEM, which was a sequential Monte Carlo method for robust and fast high-dimensional parameter estimation. The cryoEM parameter estimation problem was described by a probability density function of the estimated parameters. The particle filter uses a set of random and weighted support points to represent such a probability density function. The statistical properties of the support points not only enhance the parameter estimation with self-adaptive accuracy but also provide the belief of estimated parameters, which is essential for the reconstruction phase. The implementation of these features showed strong tolerance to bad particles and enabled robust defocus refinement, demonstrated by the remarkable resolution improvement at the atomic level.

biophysics↗

bioRxiv2017

Uterine progesterone signaling is a target for metformin therapy in polycystic ovary syndrome

Impaired progesterone (P4) signaling is linked to endometrial dysfunction and infertility in women with polycystic ovary syndrome (PCOS). Here we report for the first time that elevated expression of progesterone receptor (PGR) isoforms A and B parallels increased estrogen receptor (ER) expression in PCOS-like rat uteri. The aberrant PGR-targeted gene expression in PCOS-like rats before and after implantation overlaps with dysregulated expression of Fkbp52 and Ncoa2, two genes that contribute to the development of uterine P4 resistance. In vivo and in vitro studies of the effects of metformin on the regulation of the uterine P4 signaling pathway under PCOS conditions showed that metformin directly inhibits the expression of PGR and ER along with the regulation of several genes that are targeted dependently or independently of PGR-mediated uterine implantation. Functionally, metformin treatment corrected the abnormal expression of cell-specific PGR and ER and some PGR-target genes in PCOS-like rats with implantation. Additionally, we documented how metformin contributes to the regulation of the PGR-associated MAPK/ERK/p38 signaling pathway in the PCOS-like rat uterus. Our data provide novel insights into how metformin therapy regulates uterine P4 signaling molecules under PCOS conditions.

physiology↗

bioRxiv2017

Removing unwanted variation between samples in Hi-C experiments

Hi-C data is commonly normalized using single sample processing methods, with focus on comparisons between regions within a given contact map. Here, we aim to compare contact maps across different samples. We demonstrate that unwanted variation, of likely technical origin, is present in Hi-C data with replicates from different individuals, and that properties of this unwanted variation changes across the contact map. We present BNBC, a method for normalization and batch correction of Hi-C data and show that it substantially improves comparisons across samples, including in a QTL analysis as well as differential enrichment across cell types.

genomics↗

bioRxiv2017

Reliable sensory processing in mouse visual cortex through inhibitory interactions between Somatostatin and Parvalbumin interneurons

Cortical neurons often respond to identical sensory stimuli with large variability. However, under certain conditions, the same neurons can also respond highly reliably. The circuit mechanisms that contribute to this modulation, and their influence on behavior remains unknown. Here we used novel double transgenic mice, dual-wavelength calcium imaging and temporally selective optical perturbation to identify an inhibitory neural circuit in visual cortex that can modulate the reliability of pyramidal neurons to naturalistic visual stimuli. Our results, supported by computational models, suggest that somatostatin interneurons (SST-INs) increase pyramidal neuron reliability by suppressing parvalbumin interneurons (PV-INs) via the inhibitory SST[->]PV circuit. Using a novel movie classification task, we further show that, by reducing variability, activating SST-INs can improve the ability of mice to discriminate between ambiguous stimuli. Together, these findings reveal a novel role of the SST[->]PV circuit in modulating the fidelity of neural coding critical for visual perception.

neuroscience↗

bioRxiv2017

Curvature regulates subcellular organelle location to control intracellular signal propagation

The shape of the cell is connected to its function; however, we do not fully understand underlying mechanisms by which global shape regulates a cells functional capabilities. Using theory, experiments and simulation, we investigated how physiologically relevant cell shape changes affect subcellular organization, and consequently intracellular signaling, to control information flow needed for phenotypic function. Vascular smooth muscle cells going from a proliferative and motile circular shape to a contractile fusiform shape show changes in the location of the sarcoplasmic reticulum, inter-organelle distances and differential distribution of receptors in the plasma membrane. These factors together lead to the modulation of signals transduced by the M3 muscarinic receptor/Gq/PLC{beta} pathway at the plasma membrane, amplifying Ca2+ dynamics in the cytoplasm and the nucleus resulting in phenotypic changes, as determined by increased activity of myosin light chain kinase in the cytoplasm and enhanced nuclear localization of the transcription factor NFAT. Taken together, our observations show a systems level phenomenon whereby global cell shape affects subcellular organization to modulate signaling that enables phenotypic changes.

cell biology↗

bioRxiv2017

Direct Conversion Of Human Fibroblasts Into Osteoblasts And Osteocytes With Small Molecules And A Single Factor, Runx2

Human osteoblasts can be induced from somatic cells by introducing defined factors, however, the strategy limits cells therapeutic applications for its multi-factor and complicated genetic manipulations that may bring uncertainty into the genome. Another important cell type in bone metabolism, osteocytes, which play a central role in regulating the dynamic nature of bone in all its diverse functions, have not been obtained from transdifferetiation so far. Herein, we have established procedures to convert human fibroblast directly into osteocyte-like and osteoblast-like cells using a single transcription factor, Runx2 and chemical cocktails by activating Wnt and cAMP/PKA pathways. These induced osteoblast-like cells express osteogenic markers and generate mineralized nodule deposition. A good performance of bone formation from these cells was observed in subcutaneous site of mouse at 4 weeks post-transplantation. Moreover, further studies convert human fibroblasts into osteocyte-like cells by orchestrating timing of the aforementioned chemical cocktails exposure. These osteocyte-like cells express osteocyte-specific markers and display characteristic morphology features of osteocytes. In summary, this study provides a promising strategy for cell-based therapy in bone regenerative medicine by direct reprogramming of fibroblasts into osteocytes and osteoblasts.

cell biology↗

bioRxiv2017

HUGIn: Hi-C Unifying Genomic Interrogator

MotivationHigh throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChlA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability.\n\nResultsWe developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell liens. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTLs results and functional genomics data.\n\nAvailabilityHUGIn is available at http://yunliweb.its.unc.edu/HUGIn.\n\nContactyunli@med.unc.edu and hum@ccf.org\n\nSupplementary information:

genetics↗