Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 739 records · Page 41Linked to original sources

bioRxiv2020

Power analysis of transcriptome-wide association study

The transcriptome-wide association study (TWAS) has emerged as one of several promising techniques for integrating multi-scale omics data into traditional genome-wide association studies (GWAS). Unlike GWAS, which associates phenotypic variance directly with genetic variants, TWAS uses a reference dataset to train a predictive model for gene expressions, which allows it to associate phenotype with variants through the mediating effect of expressions. Although effective, this core innovation of TWAS is poorly understood, since the predictive accuracy of the genotype-expression model is generally low and further bounded by expression heritability. This raises the question: to what degree does the accuracy of the expression model affect the power of TWAS? Furthermore, would replacing predictions with actual, experimentally determined expressions improve power? To answer these questions, we compared the power of GWAS, TWAS, and a hypothetical protocol utilizing real expression data. We derived non-centrality parameters (NCPs) for linear mixed models (LMMs) to enable closed-form calculations of statistical power that do not rely on specific protocol implementations. We examined two representative scenarios: causality (genotype contributes to phenotype through expression) and pleiotropy (genotype contributes directly to both phenotype and expression), and also tested the effects of various properties including expression heritability. Our analysis reveals two main outcomes: (1) Under pleiotropy, the use of predicted expressions in TWAS is superior to actual expressions. This explains why TWAS can function with weak expression models, and shows that TWAS remains relevant even when real expressions are available. (2) GWAS outperforms TWAS when expression heritability is below a threshold of 0.04 under causality, or 0.06 under pleiotropy. Analysis of existing publications suggests that TWAS has been misapplied in place of GWAS, in situations where expression heritability is low. Author SummaryWe compared the effectiveness of three methods for finding genetic effects on disease in order to quantify their strengths and help researchers choose the best protocol for their data. The genome-wide association study (GWAS) is the standard method for identifying how the genetic differences between individuals relate to disease. Recently, the transcriptome-wide association study (TWAS) has improved GWAS by also estimating the effect of each genetic variant on the activity level (or expression) of genes related to disease. The effectiveness of TWAS is surprising because its estimates of gene expressions are very inaccurate, so we ask if a method using real expression data instead of estimates would perform better. Unlike past studies, which only use simulation to compare these methods, we incorporate novel statistical calculations to make our comparisons more accurate and universally applicable. We discover that depending on the type of relationship between genetics, gene expression, and disease, the estimates used by TWAS could be actually more relevant than real gene expressions. We also find that TWAS is not always better than GWAS when the relationship between genetics and expression is weak and identify specific turning points where past studies have incorrectly used TWAS instead of GWAS.

bioinformatics↗

bioRxiv2020

Open Source ImmGen: network perspective on metabolic diversity among mononuclear phagocytes

We dissect metabolic variability of mononuclear phagocyte (MNP) subpopulations across different tissues through integrative analysis of three large scale datasets. Specifically, we introduce ImmGen MNP Open Source dataset that profiled 337 samples and extended previous ImmGen effort which included 202 samples of mononuclear phagocytes and their progenitors. Next, we analysed Tabula Muris Senis dataset to extract data for 51,364 myeloid cells from 18 tissues. Taken together, a compendium of data assembled in this work covers phagocytic populations found across 38 different tissues. To analyse common metabolic features, we developed novel network-based computational approach for unbiased identification of key metabolic subnetworks based on cellular transcriptional profiles in large-scale datasets. Using ImmGen MNP Open Source dataset as baseline, we define 9 metabolic subnetworks that encapsulate the metabolic differences within mononuclear phagocytes, and demonstrate that these features are robustly found across all three datasets, including lipid metabolism, cholesterol biosynthesis, glycolysis, and a set of fatty acid related metabolic pathways, as well as nucleotide and folate metabolism. We systematically define major features specific to macrophage and dendritic cell subpopulations. Among other things, we find that cholesterol synthesis appears particularly active within the migratory dendritic cells. We demonstrate that interference with this pathway through statins administration diminishes migratory capacity of the dendritic cells in vivo. This result demonstrates the power of our approach and highlights importance of metabolic diversity among mononuclear phagocytes.

immunology↗

bioRxiv2020

An ancient deletion in the ABO gene affects the composition of the porcine microbiome by altering intestinal N-acetyl-galactosamine concentrations

We have generated a large heterogenous stock population by intercrossing eight divergent pig breeds for multiple generations. We have analyzed the composition of the intestinal microbiota at different ages and anatomical locations in > 1,000 6th- and 7th- generation animals. We show that, under conditions of exacerbated genetic yet controlled environmental variability, microbiota composition and abundance of specific taxa (including Christensenellaceae) are heritable in this monogastric omnivore. We fine-map a QTL with major effect on the abundance of Erysipelotrichaceae to chromosome 1q and show that it is caused by a common 2.3-Kb deletion inactivating the ABO acetyl-galactosaminyl-transferase gene. We show that this deletion is a trans-species polymorphism that is [≥]3.5 million years old and under balancing selection. We demonstrate that it acts by decreasing the concentrations of N-acetyl-galactosamine in the cecum thereby reducing the abundance of Erysipelotrichaceae strains that have the capacity to import and catabolize N-acetyl-galactosamine.

genetics↗

bioRxiv2020

An Antioxidant Enzyme Therapeutic for COVID-19

The COVID-19 pandemic has taken a significant toll on people worldwide, and there are currently no specific antivirus drugs or vaccines. We report herein a therapeutic based on catalase, an antioxidant enzyme that can effectively breakdown hydrogen peroxide and minimize the downstream reactive oxygen species, which are excessively produced resulting from the infection and inflammatory process. Catalase assists to regulate production of cytokines, protect oxidative injury, and repress replication of SARS-CoV-2, as demonstrated in human leukocytes and alveolar epithelial cells, and rhesus macaques, without noticeable toxicity. Such a therapeutic can be readily manufactured at low cost as a potential treatment for COVID-19.

biochemistry↗

bioRxiv2020

Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation

As a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica. Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.

plant biology↗

bioRxiv2020

Field-based body temperatures reveal behavioralthermoregulation strategies of the Atlantic marsh fiddler crab Minuca pugnax

Behavioral thermoregulation is an important defense against the negative impacts of climate change for ectotherms. In this study we examined the use of burrows by a common intertidal crab, Minuca pugnax, to control body temperature. To understand how body temperatures respond to changes in the surface temperature and explore how efficiently crabs exploit the cooling potential of burrows to thermoregulate, we measured body, surface, and burrow temperature data during low tide on Sapelo Island, GA in March, May, August, and September of 2019. We found that an increase in 1{degrees}C in the surface temperature led to a 0.70-0.71{degrees}C increase in body temperature for females and an increase in 0.75-0.77{degrees}C in body temperature for males. Body temperatures of small females were 0.3{degrees}C warmer than large females for the same surface temperature. Female crabs used burrows more efficiently for thermoregulation compared to the males. Specifically, an increase of 1{degrees}C in the cooling capacity (the difference between the burrow temperature and the surface temperature) led to an increase of 0.42-0.50{degrees}C for females and 0.34-0.35{degrees}C for males in the thermoregulation capacity (the difference between body temperature and surface temperature). The body temperature that crabs began to use burrows to thermoregulate was estimated to be around 24{degrees}C, which is far below the critical body temperatures that could lead to death. Many crabs experience body temperatures of 24{degrees}C early in the reproductive season, several months before the hottest days of the year. Because the use of burrows involves fitness trade-offs, these results suggest that warming temperatures could begin to impact crabs far earlier in the year than expected.

animal behavior and cognition↗

bioRxiv2020

kTWAS: integrating kernel-machine with transcriptome-wide association studies improves statistical power and reveals novel genes

The power of genotype-phenotype association mapping studies increases greatly when contributions from multiple variants in a focal region are meaningfully aggregated. Currently, there are two popular categories of variant aggregation methods. Transcriptome-wide association studies (TWAS) represent a category of emerging methods that select variants based on their effect on gene expressions, providing pretrained linear combinations of variants for downstream association mapping. In contrast, kernel methods such as SKAT model genotypic and phenotypic variance using various kernel functions that capture genetic similarity between subjects, allowing non-linear effects to be included. From the perspective of machine learning, these two methods cover two complementary aspects of feature engineering: feature selection/pruning, and feature modeling. Thus far, no thorough comparison has been made between these categories, and no methods exist which incorporate the advantages of TWAS and kernel-based methods. In this work we developed a novel method called kTWAS that applies TWAS-like feature selection to a SKAT-like kernel association test, combining the strengths of both approaches. Through extensive simulations, we demonstrate that kTWAS has higher power than TWAS and multiple SKAT-based protocols, and we identify novel disease-associated genes in WTCCC genotyping array data and MSSNG (Autism) sequence data. The source code for kTWAS and our simulations are available in our GitHub repository (https://github.com/theLongLab/kTWAS).

bioinformatics↗

bioRxiv2020

Mass-spectrometry-based near complete draft of the Saccharomyces cerevisiae proteome

Proteomics approaches designed to catalogue all open reading frames (ORFs) under a defined set of growth conditions of an organism have flourished in recent years. However, no proteome has been sequenced completely so far. Here we generate the largest yeast proteome dataset, including 5610 identified proteins using a strategy based on optimized sample preparation and high-resolution mass spectrometry. Among the 5610 identified proteins, 94.1% are core proteins, which achieves near complete coverage of the yeast ORFs. Comprehensive analysis of missing proteins in our dataset indicate that the MS-based proteome coverage has reached the ceiling. A review of protein abundance shows that our proteome encompasses a uniquely broad dynamic range. Additionally, these values highly correlate with mRNA abundance, implying a high level of accuracy, sensitivity and precision. We present examples of how the data could be used, including re-annotating gene localization, providing expression evidence of pseudogenes. Our near complete yeast proteome dataset will be a useful and important resource for further systematic studies.

biochemistry↗

bioRxiv2020

Mouse thy1-positive spermatogonia suppress the proliferation of spermatogonial stem cells by Extracellular vesicles in vitro

The self-renewal of mammalian spermatogonial stem cells (SSCs) supports spermatogenesis to produce spermatozoa, and this is precisely controlled in a stem niche microenvironment in the seminiferous tubules. Although studies have revealed the role of the surrounding factors in SSCs, little is known about whether the division of SSCs is controlled by extracellular vesicles. Here, extracellular vesicles were found in the basal compartment of seminiferous tubules in mouse, rat, rabbit and human testes. In the mice, the testicular extracellular vesicles are secreted by spermatogonia and are taken up by SSCs. Further, the extracellular vesicles from thy1-positive spermatogonia were purified by anti-Thy1-coupled magnetic beads, and which suppress their proliferation of SSCs but not lead to the apoptosis in vitro.

cell biology↗

bioRxiv2020

Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife

A few animals have been suspected to be intermediate hosts of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, a large-scale single-cell screening of SARS-CoV-2 target cells on a wide variety of animals is missing. Here, we constructed the single-cell atlas for 11 representative species in pets, livestock, poultry, and wildlife. Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Furthermore, we screened the expression patterns of receptors for 144 viruses, resulting in a comprehensive atlas of virus target cells. Taken together, our work provides a novel and fundamental strategy to screen virus target cells and susceptible species, based on single-cell transcriptomes we generated for domesticated animals and wildlife, which could function as a valuable resource for controlling current pandemics and serve as an early warning system for coping with future infectious disease threats.

cell biology↗

bioRxiv2020

Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships

Cyclin-dependent kinase 9 (CDK9) plays a key role in transcription elongation, and more recently it was also identified as the molecular target of a series of diaminothiazole compounds that reverse epigenetic silencing in a phenotypic assay. To better understand the structural basis underlying these compounds activity and selectivity, we developed a comparative modeling approach that we describe herein. Briefly, this approach draws upon the strong structural conservation across the active conformation of all protein kinases, and their shared pattern of interactions with Type I inhibitors. Because of this, we hypothesized that the large collection of inhibitor/kinase structures available in the Protein Data Bank (PDB) would enable accurate modeling of this diaminothiazole series in complex with each CDK family member. We apply this new comparative modeling pipeline to build each of these structural models, and then demonstrate that these models provide retrospective rationale for the structure-activity relationships that ultimately guided optimization to the lead diaminothiazole compound MC180295 (14e). We then solved the crystal structure of the 14e/CDK9 complex, and found the resulting structure to be in excellent agreement with our corresponding comparative model. Finally, inspired by these models, we demonstrate how structural changes to 14e can be used to rationally tune this compounds selectivity profile. With the emergence of CDK9 as a promising target for therapeutic intervention in cancer, we anticipate that comparative modeling can provide a valuable tool to guide optimization of potency and selectivity of new inhibitors targeting this kinase.

cancer biology↗

bioRxiv2020

Transduction catalysis: doxorubicin accelerates and enhances rAAV-mediated gene expression in the cortex of mouse, cat and monkey

Rapid and efficient gene transduction via recombinant adeno-associated viruses (rAAVs) is highly desirable across many basic and clinical research domains. Here we report vector co-infusion with doxorubicin, a clinical anti-cancer drug, markedly enhanced rAAV-mediated gene expression in the cerebral cortex across mammalian species (cat, mouse, and macaque), acting throughout the time-period examined and detectable at just three days post-transfection. This enhancement showed serotype generality, being common to rAAV serotypes 2, 8, 9 and PHP.eB tested, and was observed both locally, and at remote locations consistent with doxorubicin undergoing retrograde axonal transport. All these effects were observed at doses matching human blood plasma levels in clinical therapy, and lacked detectable cytotoxicity as assessed by cell morphology, activity, apoptosis and behavioral testing. Altogether, this study identifies an effective means to improve the capability and scope of in vivo rAAV applications, accelerating and augmenting gene transduction at doxorubicin concentrations paralleling medical practice. HighlightsO_LIAnti-cancer drug doxorubicin doubles the rate of rAAV-mediated transgene expression C_LIO_LIDoxorubicin enhancement generalizes across rAAV serotypes and animal species C_LIO_LIThe effect is observed in both locally and retrogradely infected cortical neurons C_LIO_LIThe effective dosage is free from appreciable cytotoxicity and matches clinical settings C_LI

neuroscience↗

bioRxiv2020

Adverse neurological effects of short-term sleep deprivation in aging mice are prevented bySS31 peptide

Sleep deprivation is a potent stress factor that disrupts regulatory pathways in the brain resulting in cognitive dysfunction and increased risk of neurodegenerative disease with increasing age. Prevention of the adverse effects of sleep deprivation could be beneficial in older individuals by restoring healthy brain function. We report here on the ability of SS31, a mitochondrial specific peptide, to attenuate the negative neurological effects of short-term sleep deprivation in aging mice. C57BL/6 female mice, 20 months old, were subcutaneously injected with SS31 (3mg/kg) or saline daily for 4 days. Sleep deprivation was 4 hours daily for the last 2 days of SS31 treatment. Mice were immediately tested for learning ability followed by collection of brain and other tissues. In sleep deprived mice treated with SS31, learning impairment was prevented, brain mitochondrial ATP levels and synaptic plasticity regulatory proteins were restored, and ROS and inflammatory cytokines levels were decreased in the hippocampus. The observations suggest possible therapeutic benefits of SS31 for alleviating adverse neurological effects of acute sleep loss.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pathology↗

bioRxiv2020

Deep learning approach for automated cancer detection and tumor proportion score estimation of PD-L1 expression in lung adenocarcinoma

Background This study proposed a computational method to detect the cancer areas and calculate the tumor proportion score (TPS) of PD-L1 immunohistochemistry (IHC) expression for lung adenocarcinoma based on deep learning and transfer learning.Patients and methods PD-L1 22C3 and SP142 IHC slides of lung adenocarcinoma samples on digitized whole-slide images (WSI) database were employed. We build a deep convolutional neural network (DCNN) to automatically segment cancer regions. TPS was calculated based on segmented areas and then compared with the interpretations of pathologists.Results We trained a DCNN model based on 22C3 dataset and fine-tuned it with SP142 dataset. We obtain a robust performance on cancer region detection on both datasets, with a sensitivity of 93.36% (22C3) and 92.80% (SP142) and a specificity of 93.97% (22C3) and 89.25% (SP142). With all the coefficient of determinations larger than 0.9 and Fleiss’ and Cohen’s Kappa larger than 0.8 (between mean or median of pathologists and TPS calculated by our method), we also found out the strong correlation between the TPS estimated by our computational method and estimation from multiple pathologists’ interpretations of 22C3 and SP142 respectively.Conclusion We provide an AI method to efficiently predict cancer region and calculate TPS in PD-L1 IHC slide of lung adenocarcinoma on two different antibodies. It demonstrates the potential of using deep learning methods to conveniently access PD-L1 IHC status. In the future, we will further validate the AI tool for automated scoring PD-L1 in large volume samples.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pathology↗

bioRxiv2020

Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets

Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrated that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells followed a more complex differentiation, where Hfn4a was associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms. We provide a global single cell resolution view of chromatin accessibility of kidney development. The dataset is available via interactive public websites.

developmental biology↗

bioRxiv2020

COVIEdb: A database for potential immune epitopes of coronaviruses

2019 novel coronavirus (2019-nCoV) has caused large-scale pandemic COVID-19 all over the world. Its essential to find out which parts of the 2019-nCoV sequence are recognized by human immune system for vaccine development. And for the prevention of the potential outbreak of similar coronaviruses in the future, vaccines against immunogenic epitopes shared by different human coronaviruses are essential. Here we predict all the potential B/T-cell epitopes for SARS-CoV, MERS-CoV, 2019-nCoV and RaTG13-CoV based on the protein sequences. We found YFKYWDQTY in ORF1ab protein, VYDPLQPEL and TVYDPLQPEL in spike (S) protein might be pan-coronavirus targets for vaccine development. All the predicted results are stored in a database COVIEdb (http://biopharm.zju.edu.cn/coviedb/).

bioinformatics↗

bioRxiv2020

UHRF1 drives the poor prognosis associated with RB loss in osteosarcoma

Loss of function mutations at the retinoblastoma (RB1) gene are associated with increased mortality, metastasis and poor therapeutic outcome in several cancers, including osteosarcoma (OS). However, the mechanism(s) through which RB1 loss worsens clinical outcome remain to be elucidated. Ubiquitin-like with PHD and Ring Finger domains 1 (UHRF1) has been identified as a critical downstream effector of the RB/E2F signaling pathway that is overexpressed in various cancers. Here, we show that UHRF1 upregulation is critical in rendering OS cells more aggressive. Using novel OS genetically engineered mouse models, we determined that knocking-out Uhrf1 considerably reverses the poorer survival associated with Rb1 loss. We also found that high UHRF1 expression correlates with increased clinical presentation of metastatic disease. Based on gain- and loss-of-function assays, we found that UHRF1 promotes cell proliferation, migration, invasion, and metastasis. UHRF1-mediated cell mobility results as a consequence of altered extracellular vesicles and their cargo, including urokinase-type plasminogen activator (uPA). Our work presents a new mechanistic insight into RB1 loss-associated poor prognosis and a novel oncogenic role of UHRF1 through regulation of exosome secretion that is critical for OS metastasis. This study provides substantial support for targeting UHRF1 or its downstream effectors as novel therapeutic options to improve current treatment for OS.

cancer biology↗

bioRxiv2020

Neural Stimulation in vitro and in vivo by Photoacoustic Nanotransducers

Neuromodulation is an invaluable approach for study of neural circuits and clinical treatment of neurological diseases. Here, we report semiconducting polymer nanoparticles based photoacoustic nanotransducers (PANs) for neural stimulation. Our PANs strongly absorb light in the near-infrared second window and generate localized acoustic waves. PANs can also be surface-modified to selectively bind onto neurons. PAN-mediated activation of primary neurons in vitro is achieved with ten 3-nanosecond laser pulses at 1030 nm over a 3 millisecond duration. In vivo neural modulation of mouse brain activities and motor activities is demonstrated by PANs directly injected into brain cortex. With millisecond-scale temporal resolution, sub-millimeter spatial resolution and negligible heat deposition, PAN stimulation is a new non-genetic method for precise control of neuronal activities, opening potentials in non-invasive brain modulation.

neuroscience↗