Biology subjects

Gao, X.

Publications and source records attributed to Gao, X..

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bioRxiv2018

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

bioinformatics↗

bioRxiv2018

Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-affected Corneas

PURPOSEKeratoconus (KC) is the most common corneal ectasia. We aimed to determine the differential expression of coding and long noncoding RNAs (lncRNAs) in human corneas affected with KC.\n\nMETHODS200ng total RNA from the corneas of 10 KC patients and 8 non-KC normal controls was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion. Paired-end 50bp sequences were generated using Illumina HiSeq 2500 Sequencer. Differential analysis was done using TopHat and Cufflinks with a gene file from Ensembl and a lncRNA file from NONCODE. Pathway analysis was performed using WebGestalt. Using the expression level of differentially expressed coding and noncoding RNAs in each sample, we correlated their expression levels in KC and controls separately and identified significantly different correlations in KC against controls followed by visualization using Cytoscape.\n\nRESULTSUsing |fold change| [≥] 2 and a false discovery rate [≤] 0.05, we identified 436 coding RNAs and 584 lncRNAs with differential expression in the KC-affected corneas. Pathway analysis indicated the enrichment of genes involved in extracellular matrix, protein binding, glycosaminoglycan binding, and cell migration. Our correlation analysis identified 296 pairs of significant KC-specific correlations containing 117 coding genes enriched in functions related with cell migration/motility, extracellular space, cytokine response, and cell adhesion, suggesting the potential functions of these correlated lncRNAs, especially those with multiple pairs of correlations.\n\nCONCLUSIONSOur RNA-Seq based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.

genomics↗

bioRxiv2018

Xist Intron 1 Repression by TALE Transcriptional Factor Improves Somatic Cell Reprogamming in Mice

Xist is the master regulator of X chromosome inactivation (XCI). In order to further understand the Xist locus in reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) and in somatic cell nuclear transfer (SCNT), we tested transcription-factor-like effectors (TALE)-based designer transcriptional factors (dTFs), which were specific to numerous regions at the Xist locus. We report that the selected dTF repressor 6 (R6) binding the intron 1 of Xist, which did not affect Xist expression in mouse embryonic fibroblasts (MEFs), substantially improved the iPSC generation and the SCNT preimplantation embryo development. Conversely, the dTF activator targeting the same genomic region of R6 decreased iPSC formation, and blocked SCNT-embryo development. These results thus uncover the critical requirement for the Xist locus in epigenetic resetting, which is not directly related to Xist transcription. This may provide a unique route to improving the reprogramming.

developmental biology↗

bioRxiv2018

Methionine metabolism influences the genomic architecture of H3K4me3 with the link to gene expression encoded in peak width

Nutrition and metabolism are known to influence chromatin biology and epigenetics by modifying the levels of post-translational modifications on histones, yet how changes in nutrient availability influence specific aspects of genomic architecture and connect to gene expression is unknown. To investigate this question we considered, as a model, the metabolically-driven dynamics of H3K4me3, a histone methylation mark that is known to encode information about active transcription, cell identity, and tumor suppression. We analyzed the genome-wide changes in H3K4me3 and gene expression in response to alterations in methionine availability under conditions that are known to affect the global levels of histone methylation in both normal rodent physiology and in human cancer cells. Surprisingly, we found that the location of H3K4me3 peaks at specific genomic loci was largely preserved under conditions of methionine restriction. However, upon examining different geometrical features of peak shape, it was found that the response of H3K4me3 peak width encoded almost all aspects of H3K4me3 biology including changes in expression levels, and the presence of cell identity and cancer associated genes. These findings reveal simple yet new and profound principles for how nutrient availability modulates specific aspects of chromatin dynamics to mediate key biological features.

genetics↗

bioRxiv2018

Spatial gradient in activity within the insula reflects dissociable neural mechanisms underlying context-dependent advantageous and disadvantageous inequity aversion

Humans are capable of integrating social contextual information into decision-making processes to adjust their attitudes towards inequity. This context-dependency emerges both when individual is better off (i.e. advantageous inequity) and worse off (i.e. disadvantageous inequity) than others. It is not clear however, whether the context-dependent processing of advantageous and disadvantageous inequity rely on dissociable or shared neural mechanisms. Here, by combining an interpersonal interactive game that gave rise to interpersonal guilt and different versions of the dictator games that enabled us to characterize individual weights on aversion to advantageous and disadvantageous inequity, we investigated the neural mechanisms underlying the two forms of inequity aversion in the interpersonal guilt context. In each round, participants played a dot-estimation task with an anonymous co-player. The co-players received pain stimulation with 50% probability when anyone responded incorrectly. At the end of each round, participants completed a dictator game, which determined payoffs of him/herself and the co-player. Both computational model-based and model-free analyses demonstrated that when inflicting pain upon co-players (i.e., the guilt context), participants cared more about advantageous inequity and became less sensitive to disadvantageous inequity, compared with other social contexts. The contextual effects on two forms of inequity aversion are uncorrelated with each other at the behavioral level. Neuroimaging results revealed that the context-dependent representation of inequity aversion exhibited a spatial gradient in activity within the insula, with anterior parts predominantly involved in the aversion to advantageous inequity and posterior parts predominantly involved in the aversion to disadvantageous inequity. The dissociable mechanisms underlying the two forms of inequity aversion are further supported by the involvement of right dorsolateral prefrontal cortex and dorsomedial prefrontal cortex in advantageous inequity processing, and the involvement of right amygdala and dorsal anterior cingulate cortex in disadvantageous inequity processing. These results extended our understanding of decision-making processes involving inequity and the social functions of inequity aversion.

neuroscience↗

bioRxiv2017

An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing

Long-reads, point-of-care, and PCR-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the global mapping between the raw electrical current signal sequence and the expected signal sequence from the pore model serves as the key building block to base calling, reads mapping, variant identification, and methylation detection. However, the ultra-long reads of nanopore sequencing and an order of magnitude difference in the sampling speeds of the two sequences make the classical dynamic time warping (DTW) and its variants infeasible to solve the problem. Here, we propose a novel multi-level DTW algorithm, cwDTW, based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa, as well as two benchmark datasets from previous studies, demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can almost always generate warping paths that are very close to the original DTW, which are remarkably more accurate than the state-of-the-art methods including Fast-DTW and PrunedDTW. Meanwhile, on the real nanopore datasets, cwDTW is about 440 times faster than FastDTW and 3000 times faster than the original DTW. Our program is available at https://github.com/realbigws/cwDTW.

bioinformatics↗

bioRxiv2017

DeepSimulator: a deep simulator for Nanopore sequencing

MotivationOxford Nanopore sequencing is a rapidly developed sequencing technology in recent years. To keep pace with the explosion of the downstream data analytical tools, a versatile Nanopore sequencing simulator is needed to complement the experimental data as well as to benchmark those newly developed tools. However, all the currently available simulators are based on simple statistics of the produced reads, which have difficulty in capturing the complex nature of the Nanopore sequencing procedure, the main task of which is the generation of raw electrical current signals.\n\nResultsHere we propose a deep learning based simulator, DeepSimulator, to mimic the entire pipeline of Nanopore sequencing. Starting from a given reference genome or assembled contigs, we simulate the electrical current signals by a context-dependent deep learning model, followed by a base-calling procedure to yield simulated reads. This workflow mimics the sequencing procedure more naturally. The thorough experiments performed across four species show that the signals generated by our context-dependent model are more similar to the experimentally obtained signals than the ones generated by the official context-independent pore model. In terms of the simulated reads, we provide a parameter interface to users so that they can obtain the reads with different accuracies ranging from 83% to 97%. The reads generated by the default parameter have almost the same properties as the real data. Two case studies demonstrate the application of DeepSimulator to benefit the development of tools in de novo assembly and in low coverage SNP detection.\n\nAvailabilityThe software can be accessed freely at: https://github.com/lykaust15/deep_simulator.

bioinformatics↗

bioRxiv2017

Computational Model for Simulating Drug-Induced Arrhythmia Sensitivity of Human iPSC-derived Cardiomyocytes

A mathematical model describing the electrophysiology and ion handling of cardiomyocytes is a complement to experimental analysis predicting drug-induced proarrhythmic potential in humans as proposed by Comprehensive in vitro Proarrhythmia Assay (CiPA). While CiPA endorses the use of the OHara Rudy (ORd) model, which was developed to simulate electrophysiology of human adult ventricular cardiomyocytes (hAVCMs), to predict drug-induced proarrhythmias; the human induced pluripotent stem cell derived-cardiomyocytes (hiPSC-CMs) was proposed for experimental verifications. The hiPSC-CMs, especially cultured in 2D culture dishes, are inherently different from hAVCMs exhibiting different ion channel density and an immature sarcoplasmic reticulum function. To reconcile this mismatch, we have developed a mathematical electrophysiology model of an hiPSC-CM by incorporating differences in gene expressions of ion channels, pumps and receptors in hiPSC-CMs against those found in hAVCMs. This model can be used to model any hiPSC-CM cell line where expression data has been obtained and replaces the background currents for K+ and Na+ in the ORd model with the known ultra-rapid K+ channel and hyperpolarization activated K+/Na+ channel currents. With this new model, three batches each from two different hiPSC-CM cell lines are compared to experimental data of action potential duration. This mathematical model recapitulates a ventricular-like action potential morphology with a Phase 2 plateau lasting a few hundred milliseconds. However, the resting membrane potential is not as depolarized (-65 to -70 mV) as that of hAVCM (-80 mV). The elevated resting membrane potential matches experimental data previously and is thought to keep rapid sodium channels from triggering membrane depolarization instead being replaced by an overexpression of L-Type Ca2+ channel current. This model is a key step in identifying the variability between different hiPSC-CM lines and even batches of the same line, opening the door to realizing analysis of patient specific preparations in the future.

physiology↗

bioRxiv2017

An essential post-developmental role for Lis1 in mice

LIS1 mutations cause lissencephaly (LIS), a severe developmental brain malformation. Much less is known about its role in the mature nervous system. LIS1 regulates the microtubule motor cytoplasmic dynein 1 (dynein), and as LIS1 and dynein are both expressed in the adult nervous system, Lis1 could potentially regulate dynein-dependent processes such as axonal transport. We therefore knocked out Lis1 in adult mice using tamoxifen-induced, Cre-ER-mediated recombination. When an actin promoter was used to drive Cre-ER expression (Act-Cre-ER), heterozygous Lis1 KO caused no obvious change in viability or behavior, despite evidence of widespread recombination by a Cre reporter three weeks after tamoxifen exposure. In contrast, homozygous Lis1 KO caused the rapid onset of neurological symptoms in both male and female mice. One tamoxifen-dosing regimen caused prominent recombination in the midbrain/hindbrain, PNS, and cardiac/skeletal muscle within a week; these mice developed severe symptoms in that time frame and were euthanized. A different tamoxifen regimen resulted in delayed recombination in midbrain/hindbrain, but not in other tissues, and also delayed the onset of symptoms. This indicates that Lis1 loss in the midbrain/hindbrain causes the severe phenotype. In support of this, brainstem regions known to house cardiorespiratory centers showed signs of axonal dysfunction in KO animals. Transport defects, neurofilament alterations, and varicosities were observed in axons in cultured DRG neurons from KO animals. Because no symptoms were observed when a cardiac specific Cre-ER promoter was used, we propose a vital role for Lis1 in autonomic neurons and implicate defective axonal transport in the KO phenotype.\n\nSIGNIFICANCE STATEMENTMammalian Lis1 is best known for its role in brain development. Lis1 binds to and regulates the microtubule motor, cytoplasmic dynein. We show that Lis1 function is needed post-developmentally and provide evidence that loss of Lis1 in the hindbrain leads to death. The effect is dose dependent in mice, as loss of only one allele does not produce an overt phenotype. However, since LIS1 haploinsufficiency causes lissencephaly (LIS) in humans, our study raises the possibility that post-developmental axonal transport defects could contribute to worsening symptoms in children with LIS1 mutations. Our data are consistent with the hypothesis is that Lis1 regulates dynein-dependent axon transport in the mature nervous system.

neuroscience↗

bioRxiv2017

Fast Periodic Stimulation (FPS): A Highly Effective Approach In fMRI Brain Mapping

Functional magnetic resonance imaging (fMRI) is a major technique for human brain mapping. We present a Fast Periodic Stimulation (FPS) fMRI approach, demonstrating its high effectiveness in defining category-selective brain regions. Observers see a dynamic stream of widely variable natural object images alternating at a fast rate (6 images/sec). Every 9 seconds, a short burst of variable face images contrasting with objects in pairs induces an objective 0.111 Hz face-selective neural response in the ventral occipito-temporal cortex and beyond. A model-free Fourier analysis achieves a two-fold increase in signal-to-noise ratio compared to a conventional block-design approach with identical stimuli. Periodicity of category contrast and random variability among images minimize low-level visual confounds while preserving naturalness of the stimuli, leading to the highest values (80-90%) of test-retest reliability yet reported in this area of research. FPS-fMRI opens a new avenue for understanding brain function with low temporal resolution methods.\n\nHighlightsFPS-fMRI achieves a two-fold increase in peak SNR over conventional approach\n\nFPS-fMRI reveals comprehensive extended face-selective areas including ATL\n\nFPS-fMRI achieves high specificity by minimizing influence of low-level visual cues\n\nFPS-fMRI achieves very high test-retest reliability (80%-90%) in spatial activation map\n\neTOC BlurbIn Brief\n\nGao et al. present a novel FPS-fMRI approach, which achieves a two-fold increase in peak signal-to-noise ratio in defining the neural basis of visual categorization while preserving ecological validity, minimizing low-level visual confounds and reaching very high (80%-90%) test-retest reliability.

neuroscience↗

bioRxiv2017

Establishment In Culture Of Expanded Potential Stem Cells

Mouse embryonic stem cells are derived from in vitro explantation of blastocyst epiblasts1,2 and contribute to both the somatic lineage and germline when returned to the blastocyst3 but are normally excluded from the trophoblast lineage and primitive endoderm4-6. Here, we report that cultures of expanded potential stem cells (EPSCs) can be established from individual blastomeres, by direct conversion of mouse embryonic stem cells (ESCs) and by genetically reprogramming somatic cells. Remarkably, a single EPSC contributes to the embryo proper and placenta trophoblasts in chimeras. Critically, culturing EPSCs in a trophoblast stem cell (TSC) culture condition permits direct establishment of TSC lines without genetic modification. Molecular analyses including single cell RNA-seq reveal that EPSCs share cardinal pluripotency features with ESCs but have an enriched blastomere transcriptomic signature and a dynamic DNA methylome. These proof-of-concept results open up the possibility of establishing cultures of similar stem cells in other mammalian species.

developmental biology↗