Biology subjects

Chen, H.

Publications and source records attributed to Chen, H..

At least 19 recordsLinked to original sources

bioRxiv2018

MicroRNA-200c suppresses epithelial-mesenchymal transition of ovarian cancer by targeting cofilin-2

This study investigated the effects of microRNA-200c (miR-200c) and cofilin-2 (CFL2) in regulating epithelial-mesenchymal transition (EMT) in ovarian cancer. The level of miR-200c was lower in invasive SKOV3 cells than that in non-invasive OVCAR3 cells, whereas CFL2 showed the opposite trend. Bioinformatics analysis and dual-luciferase reporter gene assays indicated that CFL2 was a direct target of miR-200c. Furthermore, SKOV3 and OVCAR3 cells were transfected with miR-200c mimic or inhibitor, pCDH-CFL2 (CFL2 overexpression), or CFL2 shRNA (CFL2 silencing). MiR-200c inhibition and CFL2 overexpression resulted in elevated levels of both CFL2 and vimentin while reducing E-cadherin expression. They also increased ovarian cancer cell invasion and migration in vitro and in vivo and increased the tumor volumes. Conversely, miR-200c mimic and CFL2 shRNA exerted the opposite effects as those aforementioned. In addition, the effects of pCDH-CFL2 and CFL2 shRNA were reversed by the miR-200c mimic and inhibitor, respectively. This finding suggested that miR-200c could be a potential tumor suppressor by targeting CFL2 in the EMT process.

cancer biology↗

bioRxiv2018

CRISPR/Cas9 screens Reveal Dasatinib Targets of Inhibiting T cell Activation and Proliferation

Immune response by T cells is essential for a healthy body against cancer, infection, and pathophysiological alteration. The activation and expansion of T cells can be inhibited by dasatinib, a tyrosine inhibitor, thus improving the outcome of diseases, such as autoimmune disease, graft-versus-host disease, and transplant rejection. The underlying mechanism of inhibition by dasatinib is elusive. Here, we designed and synthesized a CRISPR/Cas9 screening library that includes 6,149 genes. Using the library, we performed dasatinib CRISPR/cas9 screening in Jurkat cell, a T lymphocyte cell. We firstly identified survival essential genes for Jurkat cells. Comparing with other CRISPR/Cas9 screenings, we obtained Jurkat cell specific essential genes. By comparing dasatinib treatment to control, we identified a set of dasatinib targets, which includes known targets: CSK, LCK, ZAP70, and previously unknown targets: ZFP36L2, LRPPRC, CFLAR, PD-1, CD45 et al. Visualizing these target genes on T cell receptor signaling pathway, we found several genes could be inhibited by dasatinib. Furthermore, we introduced a framework, 9-square, to classify genes and found a group of genes that are associated with dasatinib resistance, possibly linking the side effects of dasatinib. These data reveal a set of dasatinib targets and demonstrate the molecular potential functions of dasatinib. Identification of dasatinib targets will broaden our understanding to its molecular mechanism, and thus benefits to clinical outcome.

cancer biology↗

bioRxiv2018

Epigenome-wide association analysis of daytime sleepiness in the Multi-Ethnic Study of Atherosclerosis reveals African-American specific associations

Study ObjectivesExcessive daytime sleepiness (EDS) is a consequence of inadequate sleep, or of a primary disorder of sleep-wake control. Population variability in prevalence of EDS and susceptibility to EDS are likely due to genetic and biological factors as well as social and environmental influences. Epigenetic modifications (such as DNA methylation-DNAm) are potential influences on a range of health outcomes. Here, we explored the association between DNAm and daytime sleepiness quantified by the Epworth Sleepiness Scale (ESS).\n\nMethodsWe performed multi-ethnic and ethnic-specific epigenome-wide association studies for DNAm and ESS in 619 individuals from the Multi-Ethnic Study of Atherosclerosis. Replication was assessed in the Cardiovascular Health Study (CHS). Genetic variants in genes proximal to ESS-associated DNAm were analyzed to identify methylation quantitative trait loci and followed with replication of genotype-sleepiness associations in the UK Biobank.\n\nResults61 methylation sites were associated with ESS (FDR [≤] 0.1) in African Americans only, including an association in KCTD5, a gene strongly implicated in sleep. One association (cg26130090) replicated in CHS African Americans (p-value 0.0004). We identified a sleepiness-associated methylation site in the gene RAI1, a gene associated with sleep and circadian phenotypes. In a follow-up analysis, a genetic variant within RAI1 associated with both DNAm and sleepiness score. The variants association with sleepiness was replicated in the UK Biobank.\n\nConclusionsOur analysis identified methylation sites in multiple genes that may be implicated in EDS. These sleepiness-methylation associations were specific to African Americans. Future work is needed to identify mechanisms driving ancestry-specific methylation effects.\n\nStatement of SignificanceExcessive daytime sleepiness is associated with negative health outcomes such as reduction in quality of life, increased workplace accidents, and cardiovascular mortality. There are race/ethnic disparities in excessive daytime sleepiness, however, the environmental and biological mechanisms for these differences are not yet understood. We performed an association analysis of DNA methylation, measured in monocytes, and daytime sleepiness within a racially diverse study population. We detected numerous DNA methylation markers associated with daytime sleepiness in African Americans, but not in European and Hispanic Americans. Future work is required to elucidate the pathways between DNA methylation, sleepiness, and related behavioral/environmental exposures.

genomics↗

bioRxiv2018

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

Nucleosomes restrict the occupancy of most transcription factors (TF) by reducing binding and accelerating dissociation, while a small group of TFs have high affinities to nucleosome-embedded sites and facilitate nucleosome displacement. To mechanistically understand this process, we investigated two S. cerevisiae TFs, Reb1 and Cbf1. We show these factors bind their sites within nucleosomes with similar affinities to naked DNA, trapping a partially unwrapped nucleosome without histone eviction. Both the binding and dissociation rates of Reb1 and Cbf1 are significantly slower at the nucleosomal sites relative to DNA, demonstrating that the high affinities are achieved by increasing the dwell time on nucleosomes to compensate for reduced binding. Reb1 also shows slow migration rate in the yeast nuclei. These properties are similar to human pioneer factors (PFs), suggesting the mechanism of nucleosome targeting is conserved from yeast to human.

molecular biology↗

bioRxiv2018

Decreased kinesin-1 mitigates NMDA-induced exicitotoxicity and ischemia-evoked neurodegeneration

N-methyl-D-aspartate receptor (NMDAR) is highly compartmentalized in neurons and the dysfunction has been implicated in various neuropsychiatric and neurodegenerative disorders. Recent failure to exploit NMDAR antagonization as a potential therapeutic target has driven the need to identify molecular mechanisms that regulate NMDAR compartmentalization. Here, we report that neural activity-dependent reduction of Kif5b, the heavy chain of kinesin-1, protected neurons against NMDA-induced excitotoxicity and ischemia-provoked neurodegeneration. Direct binding of Kinesin-1 to the GluN2B cytoplasmic tails regulated levels of NMDAR at extrasynaptic sites and the subsequent influx of calcium mediated by extrasynaptic NMDAR via regulating the insertion of NMDARs into neuronal surface. Transient increase of Kif5b restored the surface levels of NMDAR and the decreased neuronal susceptibility to NMDA-induced excitotoxicity. Our findings reveal that kinesin-1 regulates extrasynaptic NMDAR targeting and signaling, and the reduction of kinesin-1 could be regulated by neural activity and could be exploited to postpone or halt neurodegeneration.

neuroscience↗

bioRxiv2018

FT/FD-GRF5 repression loop directs growth to increase soybean yield

Major advances in crop yield are eternally needed to cope with population growth. To balance vegetative and reproductive growth plays an important role in agricultural yield. To extend vegetative phase can increase crop yield, however, this strategy risks loss of yield in the field as crops may not mature in time before winter come. Here, we identified a repression feedback loop between GmFTL/GmFDL and GmGRF5-1 (Glycine-max-Flowering-Locus-T/Glycine-max-FDL and Glycine-max-GROWTH-REGULATING-FACTOR5-1), which functions as a pivotal regulator in balancing vegetative and reproductive phases in soybean. GmFTL/GmFDL and GmGRF5-1 directly repress gene expression each other. Additionally, GmGRF5-1 enhances vegetative growth by directly enhancing expression of photosynthesis- and auxin synthesis-related genes. To modulate the loop, such as fine-tuning GmFTL expression to trade-off vegetative and reproductive growth, increases substantially soybean yield in the field. Our findings not only uncover the mechanism balancing vegetative and reproductive growth, but open a new window to improve crop yield.

plant biology↗

bioRxiv2018

AhRLK1, a CLAVATA1-like leucine-rich repeat receptor-like kinase of peanut, confers increased resistance to bacterial wilt in tobacco

Bacterial wilt caused by Ralstonia solanacearum is a devastating disease that infects hundreds of plant species. Host factors involved in disease resistance and pathogenesis remain poorly characterized. An up regulated and leucine-rich repeat receptor-like kinase characterized as CLAVATA1 and named AhRLK1 was obtained by microarray analysis in response to R. solanacearum in peanut. AhRLK1 contained presumably, a signal peptide, ten leucine-rich repeat (LRR) domains and conserved motifs of intracellular kinases. For subcellular localization, the AhRLK1 protein was visualized only in the plasma membrane. After inoculation with R. solanacearum, AhRLK1 was constantly up regulated in the susceptible variety Xinhuixiaoli but showed little changed in the resistant cultivar Yueyou92. Different hormones, including salicylic acid, abscisic acid, methyl jasmonate, and ethephon, induced expression, but expression was completely down regulated under cold and drought treatments. Transient overexpression provoked a hypersensitive response (HR) in Nicotiana benthamiana following agro-infiltration. Furthermore, in transgenic tobacco with overexpression of the gene, the resistance to R. solanacearum increased significantly. By contrast, most representative defense-responsive genes in HR, SA, JA and ET signal pathways such as NtHIN1, NtPR2, NtLOX1, and NtACS6, among others, were considerably up regulated in the AhRLK1 transgenic lines. Additionally, the EDS1 and PAD4 in the R gene signal were also up regulated in transgenic plants, but the NDR1 and NPR1 genes were down regulated. Accordingly, we suggest that AhRLK1 increases the defense response to R. solanacearum via HR and hormone defense signalling, associated with the EDS1 pathway of R gene signalling. The results provide new understanding of CLV1 function and will contribute to genetic enhancement of peanut.

plant biology↗

bioRxiv2018

AIM-SNPtag: a computationally efficient approach for developing ancestry-informative SNP panels

Inferring an individuals ancestry or group membership using a small set of highly informative genetic markers is very useful in forensic and medical genetics. However, given the huge amount of SNP data available from a diverse of populations, it is challenging to develop informative panels by exhaustively searching for all possible SNP combination. In this study, we formulate it as an algorithm problem of selecting an optimal set of SNPs that maximizes the inference accuracy while minimizes the set size. Built on this conception, we develop a computational approach that is capable of constructing ancestry informative panels from multi-population genome-wide SNP data efficiently. We evaluate the performance of the method by comparing the panel size and membership inference accuracy of the constructed SNP panels to panels selected through empirical procedures in former studies. For the membership inference of population groups including Asian, European, African, East Asian and Southeast Asian, a 36-SNP panel developed by our approach has an overall accuracy of 99.07%, and a 21-SNP subset of the panel has an overall accuracy of 95.36%. In comparison, the existing panel requires 74 SNPs to achieve an accuracy of 94.14% on the same set of population groups. We further apply the method to four subpopulations within Europe (Finnish, British, Spain and Italia); a 175-SNP panel can discriminate individuals of those European subpopulations with an accuracy of 99.36%, of which a 68-SNP subset can achieve an accuracy of 95.07%. We expect our method to be a useful tool for constructing ancestry informative markers in forensic genetics.

bioinformatics↗

bioRxiv2018

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation

The nucleus houses, organizes, and protects chromatin to ensure genome integrity and proper gene expression, but how the nucleus adapts mechanically to changes in the extracellular environment is poorly understood. Recent studies have revealed that extracellular chemical or physical stresses induce chromatin compaction via mechanotransductive processes. We report that increased extracellular multivalent cations lead to increased heterochromatin levels through mechanosensitive ion channels. This increase in heterochromatin results in increased chromatin-based nuclear rigidity, which suppresses nuclear blebbing in cells with perturbed chromatin or lamins. Furthermore, transduction of elevated extracellular cations rescues nuclear morphology in model and patient cells of human diseases, including progeria and the breast cancer model cell line MDA-MB-231. We conclude that nuclear mechanics and morphology, including abnormal phenotypes found in human diseases, can be modulated by cell sensing of the extracellular environment and consequent changes to histone modification state and chromatin-based nuclear rigidity, without requiring direct mechanical perturbations to the cell interior.

cell biology↗

bioRxiv2018

Genome wide association study of body weight, body mass index, adiposity, and fasting glucose in 3,173 outbred rats

Objective Obesity is influenced by genetic and environmental factors. Despite success of human genome wide association studies (GWAS), the specific genes that confer obesity remain largely unknown. The objective of this study was to use outbred rats to identify genetic loci underlying obesity and related morphometric and metabolic traits.Methods We measured obesity-relevant traits including body weight, body length, body mass index, fasting glucose, and retroperitoneal, epididymal, and parametrial fat pad weight in 3,173 male and female adult N/NIH heterogeneous stock (HS) rats across three institutions, providing data for the largest rat GWAS to date. Genetic loci were identified using a linear mixed model that accounted for the complex family relationships of the HS and covariate to account for differences among the three phenotyping centers.Results We identified 32 independent loci, several of which contained only a single gene (e.g. Epha5, Nrg1 and Klhl14) or obvious candidate genes (Adcy3, Prlhr). There were strong phenotypic and genetic correlations among obesity-related traits, and extensive pleiotropy at individual loci.Conclusions These studies demonstrate utility of HS rats for investigating the genetics of obesity related traits across institutions and identify several candidate genes for future functional testing.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2018

Multiple modulation synthesis with high spatial resolution for noninvasive deep neurostimulation

Noninvasive neurostimulation plays a pivotal role in direct control of neural circuit and modulating neuronal function. However, it is difficult to balance both spatial focality and depth of penetration in stimulating deep neurons. Here, we designed time-division, frequency & polarity modulation synthesis (TMFPMS) for stimulating deep neurons noninvasively with low-frequency envelope. We demonstrated its spatial resolution: mm-level via computational simulation including finite element analysis and Hodgkin-Huxley action potential model. Taken together, the results of this study indicate that TMFPMS neurostimulation with high spatial resolution is steerable and may replace traditional implanted electrode.

neuroscience↗

bioRxiv2018

A lysosomal dimmer switch regulates cellular quiescence depth

Numerous physiological and pathological phenomena are associated with the quiescent state of a cell. Cellular quiescence is a heterogeneous resting state; cells in deep than shallow quiescence require stronger growth stimulation to exit quiescence and reenter the cell cycle. Despite the importance of quiescent cells such as stem and progenitor cells to tissue homeostasis and repair, cellular mechanisms controlling the depth of cellular quiescence are poorly understood. Here we began by analyzing transcriptome changes as rat embryonic fibroblasts moved progressively deeper into quiescence under increasingly longer periods of serum starvation. We found that lysosomal gene expression was significantly upregulated in deep than shallow quiescence, which compensated for gradually reduced autophagy flux observed during quiescence deepening. Consistently, we show that inhibiting lysosomal function drove cells deeper into quiescence and eventually into a senescence-like irreversibly arrested state. By contrast, increasing lysosomal function progressively pushed cells into shallower quiescence. That is, lysosomal function modulates quiescence depth continuously like a dimmer switch. Mechanistically, we show that lysosomal function prevents quiescence deepening by reducing oxidative stress in the cell. Lastly, we show that a gene expression signature developed by comparing deep and shallow quiescent cells can correctly classify senescent and aging cells in a wide array of cell lines in vitro and tissues in vivo, suggesting that quiescence deepening, senescence, and aging may share common regulatory mechanisms.

cell biology↗

bioRxiv2018

Genome-wide association studies in Samoans give insight into the genetic etiology of fasting serum lipid levels.

The current understanding of the genetic architecture of lipids has largely come from genome-wide association studies. To date, few studies have examined the genetic architecture of lipids in Polynesians, and none have in Samoans, whose unique population history, including many population bottlenecks, may provide insight into the biological foundations of variation in lipid levels. Here we performed a genome-wide association study of four fasting serum lipid levels: total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and triglycerides (TG) in a sample of 2,849 Samoans, with validation genotyping for associations in a replication cohort comprising 1,798 Samoans and American Samoans. We identified multiple genome-wide significant associations (P < 5 x 10-8) previously seen in other populations - APOA1 with TG, CETP with HDL, and APOE with TC and LDL - and several suggestive associations (P < 1 x 10-5), including an association of variants downstream of MGAT1 and RAB21 with HDL. However, we observed different association signals for variants near APOE than what has been previously reported in non-Polynesian populations. The association with several known lipid loci combined with the newly-identified associations with variants near MGAT1 and RAB21 suggest that while some of the genetic architecture of lipids is shared between Samoans and other populations, part of the genetic architecture may be Polynesian-specific.

genetics↗

bioRxiv2018

Wnt/Fgf crosstalk is required for the specification of tracheal basal progenitor cells

Basal progenitor cells are critical for the establishment and maintenance of the tracheal epithelium. However, it remains unclear how these progenitor cells are specified during foregut development. Here, we found that ablation of the Wnt chaperon protein Gpr177 (also known as Wntless) in the epithelium causes significant reduction in the numbers of basal progenitor cells accompanied by cartilage loss in Shh-Cre;Gpr177loxp/loxp mutants. Consistent with the association between cartilage and basal cell development, Nkx2.1+p63+ basal cells are co-present with cartilage nodules in Shh-Cre;Ctnnb1DM/loxp mutants which keep partial cell-cell adhesion but not the transcription regulation function of {beta}-catenin. More importantly, deletion of Ctnnb1 in the mesenchyme leads to the loss of basal cells and cartilage concomitant with the reduced transcript levels of Fgf10 in Dermo1-Cre;Ctnnb1loxp/loxp mutants. Furthermore, deletion of Fgf receptor 2 (Fgfr2) in the epithelium also leads to significantly reduced numbers of basal cells, supporting the importance of the Wnt/Fgf crosstalk in early tracheal development.

developmental biology↗

bioRxiv2018

Understanding visual attention with RAGNAROC: A Reflexive Attention Gradient through Neural AttRactOr Competition

A quintessential challenge for any perceptual system is the need to focus on task-relevant information without being blindsided by unexpected, yet important information. The human visual system incorporates several solutions to this challenge, one of which is a reflexive covert attention system that is rapidly responsive to both the physical salience and the task-relevance of new information. This paper presents a model that simulates behavioral and neural correlates of reflexive attention as the product of brief neural attractor states that are formed across the visual hierarchy when attention is engaged. Such attractors emerge from an attentional gradient distributed over a population of topographically organized neurons and serve to focus processing at one or more locations in the visual field, while inhibiting the processing of lower priority information. The model moves towards a resolution of key debates about the nature of reflexive attention, such as whether it is parallel or serial, and whether suppression effects are distributed in a spatial surround, or selectively at the location of distractors. Most importantly, the model develops a framework for understanding the neural mechanisms of visual attention as a spatiotopic decision process within a hierarchy and links them to observable correlates such as accuracy, reaction time, and the N2pc and PD components of the EEG. This last contribution is the most crucial for repairing the disconnect that exists between our understanding of behavioral and neural correlates of attention.

neuroscience↗

bioRxiv2018

Efficient variant set mixed model association tests for continuous and binary traits in large-scale whole genome sequencing studies

With advances in Whole Genome Sequencing (WGS) technology, more advanced statistical methods for testing genetic association with rare variants are being developed. Methods in which variants are grouped for analysis are also known as variant-set, gene-based, and aggregate unit tests. The burden test and Sequence Kernel Association Test (SKAT) are two widely used variant-set tests, which were originally developed for samples of unrelated individuals and later have been extended to family data with known pedigree structures. However, computationally-efficient and powerful variant-set tests are needed to make analyses tractable in large-scale WGS studies with complex study samples. In this paper, we propose the variant-Set Mixed Model Association Tests (SMMAT) for continuous and binary traits using the generalized linear mixed model framework. These tests can be applied to large-scale WGS studies involving samples with population structure and relatedness, such as in the National Heart, Lung, and Blood Institutes Trans-Omics for Precision Medicine (TOPMed) program. SMMAT tests share the same null model for different variant sets, and a virtue of this null model, which includes covariates only, is that it needs to be only fit once for all tests in each genome-wide analysis. Simulation studies show that all the proposed SMMAT tests correctly control type I error rates for both continuous and binary traits in the presence of population structure and relatedness. We also illustrate our tests in a real data example of analysis of plasma fibrinogen levels in the TOPMed program (n = 23,763), using the Analysis Commons, a cloud-based computing platform.

genetics↗

bioRxiv2018

Whole-neuron synaptic mapping reveals local balance between excitatory and inhibitory synapse organization

The balance between excitatory and inhibitory (E and I) synaptic inputs is thought to be critical for information processing in neural circuits. However, little is known about the principles of spatial organization of E and I synapses across the entire dendritic tree of mammalian neurons. We developed a new, open-source, reconstruction platform for mapping the size and spatial distribution of E and I synapses received by individual, genetically-labeled, layer 2/3 cortical pyramidal neurons (PNs) in vivo. We mapped over 90,000 E and I synapses across twelve L2/3 PNs and uncovered structured organization of E and I synapses across dendritic domains as well as within individual dendritic segments in these cells. Despite significant, domain-specific, variations in the absolute density of E and I synapses, their ratio is strikingly balanced locally across dendritic segments. Computational modeling indicates that this spatially-precise E/I balance dampens dendritic voltage fluctuations and strongly impacts neuronal firing output.

neuroscience↗

bioRxiv2018

Modeling circRNAs expression pattern with integrated sequence and epigenetic features identifies H3K79me2 as regulators for circRNAs expression

Circular RNAs (circRNAs) are an abundant class of noncoding RNAs with widespread, cell/tissue specific pattern. Because of their involvement in the pathogenesis of multiple disease, they are receiving increasing attention. Previous work suggested that epigenetic features might be related to circRNA expression. However, current algorithms for circRNAs prediction neglect these features, leading to constant results across different cells.\n\nHere we built a machine learning framework named CIRCScan, to predict expression status and expression levels of circRNAs in various cell lines based on sequence and epigenetic features. Both expression status and expression levels can be accurately predicted by different groups of features. For expression status, the top features were similar in different cells. However, the top features for predicting expression levels were different in different cells. Noteworthy, the importance of H3K79me2 ranked high in predicting both circRNAs expression status and levels across different cells, indicating its important role in regulating circRNAs expression. Further validation experiment in K562 confirmed that knock down of H3K79me2 did result in reduction of circRNA production.\n\nOur study offers new insights into the regulation of circRNAs by incorporating epigenetic features in prediction models in different cellular contexts.

bioinformatics↗