Biology subjects

He, Y.

Publications and source records attributed to He, Y..

At least 595 records · Page 33Linked to original sources

bioRxiv2019

Mechanisms of tissue-specific genetic regulation revealed by latent factors across eQTLs

BackgroundGenetic regulation of gene expression, revealed by expression quantitative trait loci (eQTLs), varies across tissues in complex patterns ranging from highly tissue-specific effects to effects shared across many or all tissues. Improved characterization of these patterns may allow us to better understand the biological mechanisms that underlie tissue-specific gene regulation and disease etiology.\n\nResultsWe develop a constrained matrix factorization model to learn patterns of tissue sharing and tissue specificity of eQTLs across 49 human tissues from the Genotype-Tissue Expression (GTEx) project. The learned factors include patterns reflecting tissues with known biological similarity or shared cell types, in addition to a dense factor representing a universal genetic effect across all tissues. To explore the regulatory mechanisms that generate tissue-specific patterns of expression, we evaluate chromatin state enrichment and identify specific transcription factors with binding sites enriched for eQTLs from each factor.\n\nConclusionsOur results demonstrate that matrix factorization can be applied to learn the tissue specificity pattern of eQTLs and that it exhibits better biological interpretability than heuristic methods. We present a framework to characterize the tissue specificity of eQTLs, and we identify examples of tissue-specific eQTLs that may be driven by tissue-specific transcription factor (TF) binding, with relevance to interpretation of disease association.

genomics↗

bioRxiv2019

The GTEx Consortium atlas of genetic regulatory effects across human tissues

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the v8 data, based on 17,382 RNA-sequencing samples from 54 tissues of 948 post-mortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the underlying molecular mechanisms and their contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large diversity of tissues, we provide insights into the tissue-specificity of genetic effects, and show that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues.

genetics↗

bioRxiv2019

A Non-genetic Mechanism for Chemoresistance in Lung Cancer: The Role of Integrin β4/Paxillin Axis

Tumor heterogeneity and cisplatin resistance are a major cause of tumor relapse and poor survival. Here we show that in lung adenocarcinoma (LUAD), paxillin (PXN) and integrin beta 4 (ITGB4) are associated with tumor progression, and cisplatin resistance. Silencing PXN and ITGB4 render cisplatin tolerant cells sensitive, and immunologically neutralizing ITGB4 improves sensitivity. The N-terminal half of PXN is intrinsically disordered and interacts with ITGB4 to regulate expression of USP1 and VDAC1 which are required for maintaining genomic stability and mitochondrial function in LUAD. By virtual screening an FDA-approved compound library, we identified compounds that interact with PXN in silico and attenuate cisplatin resistance in LUAD cells. RNAseq analysis identified a double negative feedback loop between ITGB4 and microRNA miR-1-3p, suggesting that bistability could lead to stochastic switching between cisplatin-sensitive and resistant states in these cells. The data highlight an alternate, non-genetic, mechanism underlying chemoresistance in lung cancer.

cancer biology↗

bioRxiv2019

An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms

We previously reported a CRISPR-mediated knock-in strategy into introns of Drosophila genes, generating an attP-FRT-SA-T2A-GAL4-polyA-3XP3-EGFP-FRT-attP transgenic library for multiple uses (Lee et al., 2018b). The method relied on double stranded DNA (dsDNA) homology donors with [~]1 kb homology arms. Here, we describe three new simpler ways to edit genes in flies. We create single stranded DNA (ssDNA) donors using PCR and add 100 nt of homology on each side of an integration cassette, followed by enzymatic removal of one strand. Using this method, we generated GFP-tagged proteins that mark organelles in S2 cells. We then describe two dsDNA methods using cheap synthesized donors flanked by 100 nt homology arms and gRNA target sites cloned into a plasmid. Upon injection, donor DNA (1 to 5 kb) is released from the plasmid by Cas9. The cassette integrates efficiently and precisely in vivo. The approach is fast, cheap, and scalable.

genomics↗

bioRxiv2019

De novo assembly of a Tibetan genome and identification of novel structural variants associated with high altitude adaptation

Structural variants (SVs) may play important roles in human adaption to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17,900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%-1.53%) compared to other East Asian genomes (0.70%-0.98%), reflecting a unique genomic composition of Tibetans. One such archaic-hominid shared sequence, a 662-bp intronic insertion in the SCUBE2 gene, is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.

genomics↗

bioRxiv2019

Generating Templates and Growth Charts for School-Aged Brain Development

Standard brain templates and growth charts provide an invaluable resource for basic science research, with the eventual goal of contributing to the clinical care of neuropsychiatric conditions. Here, we report on a protocol to generate MRI brain templates in children and adolescents at one-year intervals from 6-to-18 years of age, with their corresponding growth charts, using a large-scale neuroimaging data resource (948 brain images from China and United States). To assure that the brain templates and growth charts are reliable and accurate, we developed a refined pipeline consisting of template construction, image registration, brain area labeling and growth chart modeling. The pipeline comprises multiple modular workflows that can be used for multiple applications. In our approach, population- and age-specific templates were first constructed to avoid systemic bias in registration. Brain areas were then labeled based on the appropriate templates, and their morphological metrics were extracted for modeling associated growth curves. We implemented warp cost as a function of age differences between individual brains and template brains. A strong U-shaped cost function was revealed, indicating larger age differences are associated with greater registration errors. This validates the necessity of age-specific reference templates in pediatric brain imaging studies. Growth chart analyses revealed preferential shape differences between Chinese and US samples in lateral frontal and parietal areas, aspects of cortex which are most variable across individuals with regard to structure and function as well as associated behavioral performance. This growth distinction is largely driven by neurodevelopmental differences between Chinese and US age-specific brain templates. The pipeline together with the brain templates and charts are publicly available and integrated into the Connectome Computation System.

neuroscience↗

bioRxiv2019

Low rate of follow-up colonoscopy after positive results of colorectal cancer screening in a Chinese urban core district

Colorectal cancer (CRC) is one of the most common cancers in China. In 2003, a systematic CRC registry that enables the determination of CRC incidence and mortality and a CRC screening project were introduced in the Jingan district of Shanghai by the municipal government. This study assessed the registry data to determine the status of CRC and CRC screening rates in the core district of an urban area of China. Data were retrieved from the Official registry information systems of Jingan district Shanghai Cance. The incidence and mortality of CRC, as well as population-based CRC screening rates, were analysed. Individuals who screened positive for CRC based upon results of a high-risk factor questionnaire (HRFQ) and a faecal immunochemical test (FIT) were selected for follow-up colonoscopy (CSPY). From the registry data collected between 2003 and 2013, the standardized incidence rate was 26.44/105, with a significant gender difference. The CRC standardized mortality rate was 10.08/105. In 2013, 17,866 individuals (21.6%) enrolled for CRC screening among the 82,602 candidate residents. The positive screening rate was 16.28% (2909/17866). Among the 2909 positives, 508 (17.5%) underwent follow-up CSPY. In 41.3% of these individuals (210/508), abnormal lesions were detected. Of these, 8 (1.57%) lesions were diagnosed as CRC, and 142 (28.0%) were identified as precancerous lesions. During the assessment period, both the incidence and mortality of CRC in the Jingan district were determined in the area of high CRC prevalence in Chin. Nevertheless, the rate of participation in CRC screening was low (21.6%), and the rate of participation in follow-up CSPY for individuals who screened positive was only 17.5%. Improved participation in CRC screening and follow-up CSPY is expected to lower the incidence and mortality of CRC significantly in the rural areas of China. (288)

cancer biology↗

bioRxiv2019

Overexpressing CsGH3.1 and CsGH3.1L reduces susceptibility to Xanthomonas citri subsp. citri by repressing auxin signaling in citrus (Citrus sinensis Osbeck)

The auxin early response gene Gretchen Hagen3 (GH3) plays dual roles in plant development and responses to biotic or abiotic stress. It functions in regulating hormone homeostasis through the conjugation of free auxin to amino acids. In citrus, GH3.1 and GH3.1L play important roles in responding to Xanthomonas citri subsp. citri (Xcc). Here, in Wanjingcheng orange (C. sinensis Osbeck), the overexpression of CsGH3.1 and CsGH3.1L caused increased branching and drooping dwarfism, as well as smaller, thinner and upward curling leaves compared with wild-type. Hormone determinations showed that overexpressing CsGH3.1 and CsGH3.1L decreased the free auxin contents and accelerated the Xcc-induced decline of free auxin levels in transgenic plants. A resistance analysis showed that transgenic plants had reduced susceptibility to citrus canker, and a transcriptomic analysis revealed that hormone signal transduction-related pathways were significantly affected by the overexpression of CsGH3.1 and CsGH3.1L. A MapMan analysis further showed that overexpressing either of these two genes significantly downregulated the expression levels of the annotated auxin/indole-3-acetic acid family genes and significantly upregulated biotic stress-related functions and pathways. Salicylic acid, jasmonic acid, abscisic acid, ethylene and zeatin levels in transgenic plants displayed obvious changes compared with wild-type. In particular, the salicylic acid and ethylene levels involved in plant resistance responses markedly increased in transgenic plants. Thus, the overexpression of CsGH3.1 and CsGH3.1L reduces plant susceptibility to citrus canker by repressing auxin signaling and enhancing defense responses. Our study demonstrates auxin homeostasis potential in engineering disease resistance in citrus.

plant biology↗

bioRxiv2019

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

Rhesus macaque (Macaca mulatta) is a widely-studied nonhuman primate. Here we present a high-quality de novo genome assembly of the Chinese rhesus macaque (rheMacS) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), the rheMacS genome assembly improves sequence contiguity by 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). To improve gene annotation, we generated more than two million full-length transcripts from ten different tissues by long-read RNA sequencing. We sequence resolve 53,916 structural variants (96% novel) and identify 17,000 ape-specific structural variants (ASSVs) based on comparison to the long-read assembly of ape genomes. We show that many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a set of candidate ASSVs that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. This improved rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies.

genomics↗

bioRxiv2019

The NALCN regulator UNC-80 functions in a subset of interneurons to affect C. elegans avoidance response to the plant hormone methyl salicylate.

NALCN (Na+ leak channel, non-selective), UNC80 and UNC79 form a non-selective, voltage-independent cation channel complex that affects a broad array of neuronal activities. The molecular and neuronal mechanisms underlying the functions of the NALCN complex remain unclear. In a screen for Caenorhabditis elegans mutants with defective avoidance response to the plant hormone methyl salicylate (MeSa), we isolated novel loss-of-function (lf) mutations in unc-80 and unc-79. unc-80 and unc-79 lf mutants exhibited defective MeSa avoidance but wild type-like responses to other odorants. Lf mutants of C. elegans nca/NALCN exhibited similar MeSa-specific avoidance defect, while lf mutants of the NALCN regulatory gene nlf-1 avoided MeSa like wild type. Using fluorescent transgenic animals, we identified a subset of unc-80-expressing neurons. Neuron-specific transgene rescue and knockdown experiments suggest that a subset of interneurons, primarily including AVA, AVE and AVG, might play a necessary and sufficient role in mediating unc-80 regulation of the MeSa avoidance. We found that unc-79 was expressed in neurons largely overlapping those expressing unc-80, which is supported by the rescue of unc-80(lf) defects using an unc-80 transgene driven by an unc-79 promoter. We also suggest that C. elegans locomotion responds more sensitively to the changes of expression levels of NALCN-related genes than the MeSa avoidance does. Together, our results identified NALCN-related genes as key regulators of the MeSa avoidance behavior and provided novel genetic and neuronal insights into the function of the NALCN channel complex.\n\nAuthor summaryNALCN (Na+ leak channel, non-selective) is a non-selective, voltage-independent cation channel that affects multiple neuronal activities and behaviors. Mutations in NALCN and its regulator UNC80 can cause serious neurological diseases. The regulation and function of the NALCN channel complex remain to be understood. From a genetic screen, we surprisingly found that the nematode Caenorhabditis elegans requires NALCN and its two regulators UNC-80 and UNC-79 to escape from the plant stress hormone methyl salicylate (MeSa). Using methods including transgenic neuronal labeling, rescues and knockdowns, we found that unc-80-expression in a subset of head interneurons, including AVA, AVE and AVG, might be necessary and sufficient to elicit the MeSa avoidance response. We also found that unc-79 functions in overlapping neurons as unc-80 to regulate C. elegans behaviors. Our findings provide novel molecular and neuronal mechanisms for understanding the regulation and function of the NALCN channel complex.

genetics↗

bioRxiv2019

Novel syngeneic animal model of tobacco-associated oral cancer reveals the activity of in situ anti-CTLA-4

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Tobacco use is the main risk factor for HNSCC, and tobacco-associated HNSCCs have poor prognosis and response to available treatments. Recently approved anti-PD-1 immune checkpoint inhibitors showed limited activity ([≤]20%) in HNSCC, highlighting the need to identify new therapeutic options. For this, mouse models that accurately reflect the complexity of the HNSCC mutational landscape and tumor immune environment are urgently needed. Here, we report the first mouse HNSCC model system that recapitulates the human tobacco-related HNSCC mutanome, in which tumors grow when implanted in the tongue of immunocompetent mice. These HNSCC lesions have similar immune infiltration and response rates to anti-PD-1 ([≤]20%) immunotherapy as human HNSCCs. Remarkably, we found that >70% of HNSCC lesions respond to intratumoral anti-CTLA-4. This syngeneic HNSCC mouse model provides a platform for the development of novel immunotherapeutic options for HNSCC.

cancer biology↗

bioRxiv2019

Efficient Long-Distance Transport in Upper Fluid of Bacterial Swarms

Flagellated bacteria move collectively in a swirling pattern on agar surfaces immersed in a thin layer of viscous \"swarm fluid\", but the role of this fluid in mediating the cooperation of the bacterial population is not well understood. Herein, we use gold nanorods (AuNRs) as single particle tracers to explore the spatiotemporal structure of the swarm fluid. We observed that individual AuNRs are transported in a plane of ~2 m above the motile cells. They can travel for long distances (>700 m) in a 2D plane at high speed (often >50 m2/s) without interferences from bacterial movements. The particles are apparently lifted up and transported by collective mixing of the small vortices around bacteria during localized clustering and de-clustering of the motile cells, exhibiting superdiffusive and non-Gaussian characteristics with alternating large-step jumps and confined lingering. Their motions are consistent with the Levy walk (LW) model, revealing efficient transport flows above swarms. These flows provide obstacle-free highways for long-range material transportations, shed light on how swarming bacteria perform population-level communications, and reveal the essential role of the fluid phase on the emergence of large-scale synergy. This approach is promising for probing complex fluid dynamics and transports in other collective systems.

microbiology↗

bioRxiv2019

Conservation and Divergence of Related Neuronal Lineages in the Drosophila Central Brain

Wiring a complex brain requires enormous cell specificity. This specificity is laid out via a developmental process where neural stem cells produce countless diverse neurons. To help elucidate this process and resolve the considerable dynamic specificity, we need to observe the development of multiple neuronal lineages. Drosophila central brain lineages are predetermined, comprised of a fixed set of neurons born in pairs in a specific order. To reveal specific roles of lineage identity, Notch-dependent sister fate specification, and temporal patterning in morphological diversification, we mapped approximately one quarter of the Drosophila central brain lineages. While we found large aggregate differences, we also discovered similar patterns of morphological specification and diversification. Lineage identity plus Notch state govern primary neuronal trajectories, whereas temporal fates diversify terminal elaborations in target-specific manners. In addition, we identified related lineages of analogous neuron types produced in similar temporal patterns. Two stem cells even yield identical series of dopaminergic neuron types, but with completely disparate sister neurons. These phenomena suggest that large changes in morphological diversity can be the consequence of relatively small differences in lineage fating. Taken together, this large-scale lineage mapping study reveals that relatively simple rules drive incredible neuronal complexity.

developmental biology↗

bioRxiv2019

Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe

Mitochondria play a critical role in generating energy to support the entire lifecycle of biological cells, yet it is still unclear how their morphological structures evolve to regulate their functionality. Conventional fluorescence microscopy can only provide [~]300 nm resolution, which is insufficient to visualize mitochondrial cristae. Here, we developed an enhanced squaraine variant dye (MitoESq-635) to study the dynamic structures of mitochondrial cristae in live cells at superresolution. The low saturation intensity and high photostability make it ideal for long-term, high-resolution STED nanoscopy. We demonstrate the time-lapsed imaging of the mitochondrial inner membrane over 50 minutes in living HeLa cells at 35.2 nm resolution for the first time. The forms of the cristae during mitochondrial fusion and fission can be clearly resolved. Our study demonstrates the emerging capability of optical STED nanoscopy to investigate intracellular physiological processes at nanoscale resolution for long periods of time with minimal phototoxicity.

biophysics↗

bioRxiv2019

Non-replication of functional connectivity differences in ASD: a multi-site study

A rapidly growing number of studies on autism spectrum disorder (ASD) have used resting-state fMRI to identify alterations of functional connectivity, with the hope of identifying clinical biomarkers or underlying neural mechanisms. However, results have been largely inconsistent across studies, and there is therefore a pressing need to determine the primary factors influencing replicability. Here, we used resting-state fMRI data from the Autism Brain Imaging Data Exchange to investigate two potential factors: denoising strategy and data site (which differ in terms of sample, data acquisition, etc.). We examined the similarity of both group-average functional connectomes and group-level differences (ASD vs. control) across 33 denoising pipelines and four independently-acquired datasets. The group-average connectomes were highly consistent across pipelines (r = 0.92{+/-}0.06) and sites (r = 0.88{+/-}0.02). However, the group differences, while still consistent within site across pipelines (r = 0.76{+/-}0.12), were highly inconsistent across sites regardless of choice of denoising strategies (r = 0.07{+/-}0.04), suggesting lack of replication may be strongly influenced by site and/or cohort differences. Across-site similarity remained low even when considering the data at a large-scale network level or when considering only the most significant edges. We further show through an extensive literature survey that the parameters chosen in the current study (i.e., sample size, age range, preprocessing methods) are quite representative of the published literature. These results highlight the importance of examining replicability in future studies of ASD, and, more generally, call for extra caution when interpreting alterations in functional connectivity across groups of individuals.

neuroscience↗

bioRxiv2019

Transcriptional Signatures of the Hierarchical Chronnectome Organization in the Human Brain

The chronnectome of the human brain represents the dynamics of functional organization in interacting regions, but its organizational principle and the underlying molecular mechanisms remain unclear. Using task-free fMRI and postmortem gene expression data, we conduct a transcriptome-chronnectome association study to investigate the spatial configurations of dynamic brain networks and their associations with transcriptional signatures. We reveal a spatial layout of network dynamics in the human brain chronnectome that reflects the cortical hierarchy and myelin content spanning from primary to transmodal areas. We further identify the transcriptional signature of this layout, with the top-related genes enriched for the ion channel and mitochondria terms. Moreover, the expression of these genes significantly predicts brain dynamics-behavior coupling. These findings highlight the hierarchical organizing principle and underlying molecular basis of the spatial configurations of dynamic brain networks, thereby contributing to our understanding of the associations among gene expression, network dynamics, and behaviors.

neuroscience↗

bioRxiv2019

A Phenome-wide Mendelian Randomisation study on genetically determined serum urate levels in UK Biobank cohort

IntroductionThe role of serum urate level has been extensively investigated in observational studies. However, the extent of any causal effect remains unclear, making it difficult to evaluate its clinical relevance.\n\nObjectivesTo explore any causal or pleiotropic association between serum urate level and a broad spectrum of disease outcomes.\n\nMethodsPhenome-wide association study (PheWAS) together with a Bayesian analysis of tree-structured phenotypic models (TreeWAS) was performed to examine disease outcomes related to genetically determined serum urate levels in 339,256 UK Biobank participants. Mendelian Randomisation (MR) analyses were performed to replicate significant findings using various GWAS consortia data. Sensitivity analyses were conducted to examine possible pleiotropic effects on metabolic traits of the genetic variants used as instruments for serum urate.\n\nResultsPheWAS analysis, examining the association with 1,431 disease outcomes, identified a multitude of disease outcomes including gout, hypertension, hypercholesterolemia, and heart diseases (e.g., coronary atherosclerosis, myocardial infarction, and ischaemic heart disease) that were associated (p<3.35e-04) with genetically determined serum urate levels. TreeWAS analysis, examining 10,750 ICD-10 diagnostic terms, identified more sub-phenotypes of cardiovascular and cerebrovascular diseases (e.g., angina pectoris, heart failure, cerebral infarction). MR analysis successfully replicated the association with gout, hypertension, heart diseases and blood lipid levels, but indicated the existence of genetic pleiotropy. Sensitivity analyses support an inference that pleiotropic effects of genetic variants on urate and metabolic traits contribute to the observational associations with cardiovascular diseases.\n\nConclusionsHigh serum urate levels are associated with different types of cardiac events. The finding of genetic pleiotropy indicates the existence of common upstream pathological elements influencing both urate and metabolic traits, and this may suggest new opportunities and challenges for developing drugs targeting a more distal mediator that would be beneficial for both the treatment of gout and the prevention of cardiovascular comorbidities.

epidemiology↗

bioRxiv2019

Angiocrine FSTL1 insufficiency leads to atrial and vein wall fibrosis via SMAD3 activation

Angiocrine factors, mediating the endothelial-mural cell interaction in vascular wall construction as well as maintenance, are incompletely characterized. Here we show that loss of follistatin-like protein 1 (FSTL1) in endothelial cells (Fstl1ECKO) led to an increase of pulmonary vascular resistance, resulting in the heart regurgitation especially with tricuspid valves. However, this abnormality was not detected in mutant mice with Fstl1 deletion in smooth muscle cells or hematopoietic cells. We further showed that there was excessive alpha-smooth muscle actin (SMA) associated with atrial endocardia, heart valves, veins and microvessels after the endothelial FSTL1 deletion. Consistently, there was an increase of collagen deposition as demonstrated in livers of Fstl1ECKO mutants. The SMAD3 phosphorylation was significantly enhanced and pSMAD3 staining was colocalized with SMA in vein walls, suggesting the activation of TGF{beta} signaling in vascular mural cells of Fstl1ECKO mice. The findings imply that endothelial FSTL1 is critical for the homeostasis of atria and veins and its insufficiency may favor cardiovascular fibrosis leading to heart failure.

developmental biology↗