Biology subjects

Jiang, X.

Publications and source records attributed to Jiang, X..

At least 361 records · Page 20Linked to original sources

bioRxiv2020

4 β-hydroxycholesterol is a pro-lipogenic factor that promotes SREBP1c expression and activity through Liver X-receptor.

Oxysterols are oxidized derivatives of cholesterol that play signaling roles in lipid biosynthesis and homeostasis. Here we show that 4{beta}-hydroxycholesterol (4{beta}-HC), a liver and serum abundant oxysterol of poorly defined function, is a potent and selective inducer of the master lipogenic transcription factor, Sterol Regulatory Element Binding Protein 1c (SREBP1c), but not the related steroidogenic transcription factor SREBP2. Mechanistically, 4{beta}-HC acts as a putative agonist for Liver X receptor (LXR), a sterol sensor and transcriptional regulator previously linked to SREBP1c activation. Unique among the oxysterol agonists of LXR, 4{beta}-HC induced expression of the lipogenic program downstream of SREBP1c, and triggered de novo lipogenesis both in primary hepatocytes and in mouse liver. 4{beta}-HC-acted in parallel to insulin-PI3K-dependent signaling to stimulate triglyceride synthesis and lipid droplet accumulation. Thus, 4{beta}-HC is an endogenous regulator of de novo lipogenesis through the LXR-SREBP1c axis.

biochemistry↗

bioRxiv2020

Targeting KRAS-mutant stomach/colorectal tumours by disrupting the ERK2-p53 complex

KRAS is widely mutated in human cancers, resulting in nearly unchecked tumour proliferation and metastasis. No therapies have been developed for targeting KRAS-mutant tumours. Herein, we observed that mutant KRAS specifically promoted the formation of ERK2-p53 complex in stomach/colorectal tumour cells. Disruption of this complex by applying MEK1/2 and ERK2 inhibitors elicits strong apoptotic responses in a p53-dependent manner, validated by genome-wide knockout screening. Mechanistically, p53 physically associates with phosphorylated ERK2 through the hydrophobic interaction in the presence of mutant KRAS, which suppresses p53 activation by preventing the recruitment of p300/CBP; trametinib disrupts the ERK2-p53 complex by reducing ERK2 phosphorylation, allowing the acetylation of p53 protein by recruiting p300/CBP; acetylated p53 activates PUMA transcription and thereby kills KRAS-mutant tumours. Our study unveils an important role of the ERK2-p53 complex and provides a potential therapeutic strategy for treating KRAS-mutant cancer via ERK2 inhibition.

cancer biology↗

bioRxiv2020

FertilityOnline, a straight pipeline for functional gene annotation and disease mutation discovery, identifies novel infertility causative mutations in SYCE1 and STAG3

Exploring the genetic basis of human infertility is currently under intensive investigation. However, only a handful of genes are validated in animal models as disease-causing genes in infertile men. Thus, to better understand the genetic basis of spermatogenesis in human and to bridge the knowledge gap between human and other animal species, we have constructed FertilityOnline database, which is a resource that integrates the functional genes reported in literature related to spermatogenesis into an existing spermatogenic database, SpermatogenesisOnline 1.0. Additional features like functional annotation and statistical analysis of genetic variants of human genes, are also incorporated into FertilityOnline. By searching this database, users can focus on the top candidate genes associated with infertility and can perform enrichment analysis to instantly refine the number of candidates in a user-friendly web interface. Clinical validation of this database is established by the identification of novel causative mutations in SYCE1 and STAG3 in azoospermia men. In conclusion, FertilityOnline is not only an integrated resource for analysis of spermatogenic genes, but also a useful tool that facilitates to study underlying genetic basis of male infertility. AvailabilityFertilityOnline can be freely accessed at http://mcg.ustc.edu.cn/bsc/spermgenes2.0/index.html.

genetics↗

bioRxiv2020

Human Cytomegalovirus Drives WDR5 to the Virion Assembly Compartment to Facilitate Virion Assembly

We previously reported that human cytomegalovirus (HCMV) utilizes the cellular protein WDR5 to facilitate capsid nuclear egress. Here, we further show that HCMV infection drives WDR5 to the perinuclear region by a mechanism that requires viral replication and intact microtubules. WDR5 accumulated in the virion assembly compartment (vAC) and co-localized with vAC markers of gamma-tubulin ({gamma}-tubulin), early endosomes, and viral vAC marker proteins pp65, pp28, and glycoprotein B (gB). WDR5 interacted with multiple virion proteins, including MCP, pp150, pp65, pIRS1, and pTRS1, which may explain the increasing WDR5 accumulation in the vAC during infection. WDR5 was then incorporated into HCMV virions and localized to the tegument layer, as demonstrated by fractionation and immune-gold electron microscopy. Thus, WDR5 is driven to the vAC and incorporated into virions, suggesting that WDR5 facilitates HCMV replication at later stage of virion assembly besides the capsid nuclear egress stage. These data highlight that WDR5 is a potential target for antiviral therapy. ImportanceHuman cytomegalovirus (HCMV) has a large (~235-kb) genome that contains over 170 ORFs and exploits numerous cellular factors to facilitate its replication. In the late phase of HCMV infection cytoplasmic membranes are profoundly reconfigured to establish the virion assembly compartment (vAC), which is important for efficient assembly of progeny virions. We previously reported that WDR5 promotes HCMV nuclear egress. Here, we show that WDR5 is further driven to the vAC and incorporated into virions, perhaps to facilitate efficient virion maturation. This work identified potential roles for WDR5 in HCMV replication in the cytoplasmic stages of virion assembly. Taken together, WDR5 plays a critical role in HCMV capsid nuclear egress and is important for virion assembly, and thus is a potential target for antiviral treatment of HCMV-associated diseases.

pathology↗

bioRxiv2020

Hybrid capture-based sequencing enables unbiased recovery of SAR-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants

BackgroundIn response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples. MethodsEighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization. ResultsBy examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period. ConclusionsThe hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.

genomics↗

bioRxiv2020

Distribution of Epsilon-Polylysine Synthetases in Coryneform Bacteria Isolated from Cheese and Human Skin

Epsilon-polylysine ({varepsilon}-PL) is an antimicrobial commercially produced by Streptomyces fermentation and widely used in Asian countries for food preservation. Here we discovered a gene from cheese bacterium Corynebacterium variabile that showed high similarity to the {varepsilon}-PL synthetase from Streptomyces in terms of enzymatic domain architecture and gene context. By cloning it into Streptomyces coelicolor with a Streptomyces albulus {varepsilon}-PL synthetase promoter, we confirmed that its product is indeed {varepsilon}-PL. A comprehensive sequence analysis suggests that {varepsilon}-PL synthetases are widely spread among coryneform bacteria isolated from cheese and human skin; 14 out of 15 Brevibacterium isolates and 10 out of 12 Corynebacterium isolates contain Pls gene. This discovery raises the possibility that {varepsilon}-PL as a bioactive secondary metabolite might be produced and play a role in the cheese and skin ecosystems. IMPORTANCEEvery year, microbial contamination causes billions of tons of food wasted and millions of cases of foodborne illness. {varepsilon}-PL is an excellent food preservative as it is potent, wide spectrum and is heat stable and biodegradable. It has not been accepted by all countries (e.g those in the EU) partially because it was not a natural composition of food but rather originated from the soil bacteria Streptomyces, a famous producer of various antibiotic drugs and toxins. The unexpected finding of {varepsilon}-PL synthetases in cheese and skin bacteria suggests that {varepsilon}-PL may naturally exist in cheese and on our skin.

microbiology↗

bioRxiv2020

AD-linked R47H-TREM2 mutation induces disease-enhancing proinflammatory microglial states in mice and humans

The hemizygous R47H variant of TREM2, a microglia-specific gene in the brain, increases risk for late-onset Alzheimers disease (AD). In this study, we identified a subpopulation of microglia with disease-enhancing proinflammatory signatures associated with the R47H mutation in human AD brains and tauopathy mouse brains. Using transcriptomic analysis at the single-nuclei level from AD patients with the R47H or the common variant (CV)-TREM2 with matched sex, pathology and APOE status, we found that the R47H mutation was associated with cell type- and sex-specific transcriptional changes in human AD brains, with microglia exhibiting the most robust alterations. Further characterization revealed that R47H-associated microglial subpopulations had enhanced inflammatory signatures including hyperactivation of Akt, one of the signaling pathways downstream of TREM2. In a newly-generated tauopathy knock-in mouse model expressing one allele of human TREM2 (hTREM2) with either the R47H mutation or CV, R47H induced and exacerbated tau-mediated spatial memory deficits in female mice. Single-cell transcriptomic analysis of microglia from these mice also revealed transcriptomic changes induced by R47H that had significant overlaps with R47H microglia in human AD brains, including robust increases in proinflammatory cytokines, activation of Syk-Akt-signaling, and elevation of a subset of disease-associated microglial signatures. Strikingly, pharmacological Akt inhibition largely reversed the enhanced inflammatory signatures induced by R47H in primary microglia treated with tau fibrils. By unraveling the disease-enhancing properties of the R47H mutation in mouse and human, our findings shed light on an immune-linked AD subtype and provide new directions for modulating microglial immune responses to treat AD.

neuroscience↗

bioRxiv2020

BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data

Birth defect, not only poses a major challenge for infant health but also attracts the attention of countless people in the world. Chromosome abnormality directly results in diverse birth defects which are generally deleterious and even lethal. Therefore, gaining molecular regulatory insights into these diseases is important and necessary for effective prenatal screening. Recently, with the advance of next-generation sequencing (NGS) techniques, a myriad of treatises and data associated with these diseases are now constantly produced from different laboratories across the world. To meet the increasing requirements for birth-related data resources, we developed a birth defect multi-omics database (BDdb), freely accessible at http://t21omics.cngb.org and consisting of multi-omics data, circulating free DNA (cfDNA) data, as well as diseases biomarkers. Omics data sets from 138 GSE samples, 5271 GSM samples and 328 entries, and more than 2000 biomarkers of 22 birth-defect diseases in 5 different species were integrated into BDdb, which provides a user-friendly interface for searching, browsing and downloading selected data. Additionally, we re-analyzed and normalized the raw data so that users can also customize the analysis using the data generated from different sources or different High-Throughput Sequencing (HTS) methods. To our knowledge, BDdb is the first comprehensive database associated with birth-defect-related diseases. which would benefit the diagnosis and prevention of birth defects.

bioinformatics↗

bioRxiv2020

Age modulates genetic risk for multiple common diseases

Inherited genetic variation contributes to individual risk for many complex diseases and is increasingly being used for predictive patient stratification. Recent work has shown that genetic factors are not equally relevant to human traits across age and other contexts, though the reasons for such variation are not clear. Here, we introduce methods to infer the form of the relationship between genetic risk for disease and age and to test whether all genetic risk factors behave similarly. We use a proportional hazards model within an interval-based censoring methodology to estimate age-varying individual variant contributions to genetic risk for 24 common diseases within the British ancestry subset of UK Biobank, applying a Bayesian clustering approach to group variants by their risk profile over age and permutation tests for age dependency and multiplicity of profiles. We find evidence for age-varying risk profiles in nine diseases, including hypertension, skin cancer, atherosclerotic heart disease, hypothyroidism and calculus of gallbladder, several of which show evidence, albeit weak, for multiple distinct profiles of genetic risk. The predominant pattern shows genetic risk factors having the greatest impact on risk of early disease, with a monotonic decrease over time, at least for the majority of variants although the magnitude and form of the decrease varies among diseases. We show that these patterns cannot be explained by a simple model involving the presence of unobserved covariates such as environmental factors. We discuss possible models that can explain our observations and the implications for genetic risk prediction. Author summaryThe genes we inherit from our parents influence our risk for almost all diseases, from cancer to severe infections. With the explosion of genomic technologies, we are now able to use an individuals genome to make useful predictions about future disease risk. However, recent work has shown that the predictive value of genetic information varies by context, including age, sex and ethnicity. In this paper we introduce, validate and apply new statistical methods for investigating the relationship between age and genetic risk. These methods allow us to ask questions such as whether risk is constant over time, precisely how risk changes over time and whether all genetic risk factors have similar age profiles. By applying the methods to data from the UK Biobank, a prospective study of 500,000 people, we show that there is a tendency for genetic risk to decline with increasing age. We consider a series of possible explanations for the observation and conclude that there must be processes acting that we are currently unaware of, such as distinct phases of life in which genetic risk manifests itself, or interactions between genes and the environment.

genetics↗

bioRxiv2020

Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation

ABSTRACTGenotype imputation is a fundamental step in genomic data analysis such as GWAS, where missing variant genotypes are predicted using the existing genotypes of nearby ‘tag’ variants. Imputation greatly decreases the genotyping cost and provides high-quality estimates of common variant genotypes. As population panels increase, e.g., the TOPMED Project, genotype imputation is becoming more accurate, but it requires high computational power. Although researchers can outsource genotype imputation, privacy concerns may prohibit genetic data sharing with an untrusted imputation service. To address this problem, we developed the first fully secure genotype imputation by utilizing ultra-fast homomorphic encryption (HE) techniques that can evaluate millions of imputation models in seconds. In HE-based methods, the genotype data is end-to-end encrypted, i.e., encrypted in transit, at rest, and, most importantly, in analysis, and can be decrypted only by the data owner. We compared secure imputation with three other state-of-the-art non-secure methods under different settings. We found that HE-based methods provide full genetic data security with comparable or slightly lower accuracy. In addition, HE-based methods have time and memory requirements that are comparable and even lower than the non-secure methods. We provide five different implementations and workflows that make use of three cutting-edge HE schemes (BFV, CKKS, TFHE) developed by the top contestants of the iDASH19 Genome Privacy Challenge. Our results provide strong evidence that HE-based methods can practically perform resource-intensive computations for high throughput genetic data analysis. In addition, the publicly available codebases provide a reference for the development of secure genomic data analysis methods.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2020

SARS-CoV-2 envelope protein causes acute respiratory distress syndrome (ARDS)-like pathological damage and constitutes an antiviral target

Cytokine storm and multi-organ failure are the main causes of SARS-CoV-2-related death. However, the origin of the virus excessively damaging abilities remains unknown. Here we show that the SARS-CoV-2 envelope (2-E) protein alone is sufficient to cause acute respiratory distress syndrome (ARDS)-like damage in vitro and in vivo. Overexpression of 2-E protein induced rapid pyroptosis-like cell death in various susceptible cells and robust secretion of cytokines and chemokines in macrophages. Intravenous administration of purified 2-E protein into mice caused ARDS-like pathological damage in lung and spleen. Overexpressed 2-E protein formed cation channels in host cell membranes, eventually leading to membrane rupture. Newly identified channel inhibitors exhibited potent anti-SARS-CoV-2 activity and excellent protective effects against the 2-E-induced damage both in vitro and in vivo. Importantly, their channel inhibition, cell protection and antiviral activities were positively correlated with each other, supporting 2-E is a promising drug target against SARS-CoV-2.

microbiology↗

bioRxiv2020

Characterizing transcriptional regulatory sequences in coronaviruses and their role in recombination

Novel coronaviruses, including SARS-CoV-2, SARS, and MERS, often originate from recombination events. The mechanism of recombination in RNA viruses is template switching. Coronavirus transcription also involves template switching at specific regions, called transcriptional regulatory sequences (TRS). It is hypothesized but not yet verified that TRS sites are prone to recombination events. Here, we developed a tool called SuPER to systematically identify TRS in coronavirus genomes and then investigated whether recombination is more common at TRS. We ran SuPER on 506 coronavirus genomes and identified 465 TRS-L and 3509 TRS-B. We found that the TRS-L core sequence (CS) and the secondary structure of the leader sequence are generally conserved within coronavirus genera but different between genera. By examining the location of recombination breakpoints with respect to TRS-B CS, we observed that recombination hotspots are more frequently co-located with TRS-B sites than expected.

genomics↗

bioRxiv2020

CCM signaling complex (CSC) is a master regulator governing homeostasis of progestins and their mediated signaling cascades

We demonstrate that a novel signaling network among the CSC and mPRS is dynamically modulated and fine-tuned with intricate feedback regulations in PR negative cells, especially endothelial cells (ECs). Depletion of any of three CCMs (1, 2, 3) genes results in the disruption of non-classic mPRs-mediated signaling in-vitro as well as defective homeostasis of PRG in-vivo. Therefore, we propose the CSC is a master regulator of homeostasis of PRG and its associated classic and non-classic signaling cascades. Assisted with omic approaches, we identified signaling pathways involved and specific biomarkers associated with hemorrhagic events during CCM pathogenesis in-vitro and in-vivo. To our knowledge, this is the first report detailing etiology to predict the occurrence of early hemorrhagic events with a set of serum biomarkers.

neuroscience↗

bioRxiv2020

CCM signaling complex (CSC) coupling both classic and non-classic progesterone receptor signaling

Excessive progesterone (PRG) may increase breast cancer risk under hormone therapy during postmenopause or hormonal contraception. As a sex steroid hormone, PRG exerts its cellular responses through signaling cascades involving classic (genomic), non-classic (non-genomic), or both combined responses by binding to either classic nuclear PRG receptors or non-classic membrane PRG receptors. Currently, the intricate balance and switch mechanisms between these two signaling cascades remain elusive. Three genes, KRIT1 (CCM1), MGC4607 (CCM2), and PDCD10 (CCM3), have been demonstrated to form a CCM signaling complex (CSC). In this report, we discover that the CSC plays an essential role in coupling both classic and non-classic PRG signaling pathways by mediating crosstalk between them. The coupled signaling pathways were detailed through high throughput omics. One Sentence SummaryWe discover a novel signaling network among the CCM signaling complex (CSC), classic and non-classic progesterone receptors, and their ligands-progesterone/mifepristone, is dynamically modulated and fine-tuned with a series of feedback regulations; perturbation of this intricate balance, such as hormone therapy in the postmenopause or hormonal contraception regimen, or perturbed CSC signaling could result in increased risks in breast cancer or compromising tumor therapy.

neuroscience↗

bioRxiv2020

High-speed adaptive optics line-scan OCT for cellular-resolution optoretinography

Optoretinography - the non-invasive, optical imaging of light-induced functional activity in the retina - stands to provide a critical biomarker for testing the safety and efficacy of new therapies as well as their rapid translation to the clinic. Optical phase change in response to light, as readily accessible in phase-resolved OCT, offers a path towards all-optical imaging of retinal function. However, typical human eye motion adversely affects phase stability and precludes the recording of fast light-induced retinal events. Here we introduce a high-speed line-scan spectral domain OCT with adaptive optics (AO), aimed at volumetric imaging and phase-resolved acquisition of retinal responses to light. By virtue of parallel acquisition of an entire retinal cross-section (B-scan) in a single high-speed camera frame, depth-resolved tomograms at speeds up to 16 kHz were achieved with high sensitivity and phase stability. To optimize spectral and spatial resolution, an anamorphic detection paradigm was introduced enabling improved light collection efficiency and signal roll-off compared to traditional methods. The benefits in speed, resolution and sensitivity were exemplified in imaging nanometer-millisecond scale light-induced optical path length changes in cone photoreceptor outer segments. With 660 nm stimuli, individual cone responses readily segregated into three clusters, corresponding to long, middle and short-wavelength cones. Recording such optoretinograms on spatial scales ranging from individual cones, to 100 m-wide retinal patches offers a robust and sensitive biomarker for cone function in health and disease. Furthermore, incorporating this capability into an easy-to-use and ubiquitous diagnostic platform of OCT enables its widespread application to patient care and drug development.

bioengineering↗

bioRxiv2020

Electronic blood vessel

Advances in bioelectronics have great potential to address unsolvable biomedical problems in the cardiovascular system. By using poly(L-lactide-co-{varepsilon}-caprolactone) (PLC) that encapsulates the liquid metal to make flexible and bio-degradable electrical circuitry, we develop an electronic blood vessel that can integrate flexible electronics with three layers of blood vessel cells, to mimic and go beyond the natural blood vessel. It can improve the endothelization process through electrical stimulation and can enable controlled gene delivery into specific part of the blood vessel via electroporation. The electronic blood vessel has excellent biocompatibility in the vascular system and shows great patency three months post-implantation in a rabbit model. The electronic blood vessel would be an ideal platform to enable diagnostics and treatments in the cardiovascular system and can greatly empower personalized medicine by creating a direct link of vascular tissue-machine interface.

bioengineering↗

bioRxiv2020

Spatial inhibition of return is impaired in mild cognitive impairment and mild Alzheimer's disease

Spatial inhibition of return (IOR) refers to the phenomenon by which individuals are slower to respond to stimuli appearing at a previously cued location compared to un-cued locations. Here we provide evidence supporting that spatial IOR is mildly impaired in individuals with mild cognitive impairment (MCI) or mild Alzheimers disease (AD), and the impairment is readily detectable using a novel double cue paradigm. Furthermore, reduced spatial IOR in high-risk healthy older individuals is associated with reduced memory and other neurocognitive task performance, suggesting that the novel double cue spatial IOR paradigm may be useful in detecting MCI and early AD. SIGNIFICANCE STATEMENTO_LINovel double cue spatial inhibition of return (IOR) paradigm revealed a robust effect IOR deficits in individuals with mild cognitive impairment (MCI) or mild Alzheimers disease (AD) C_LIO_LISpatial IOR effect correlates with memory performance in healthy older adults at a elevated risk of Alzheimers disease (with a family history or APOE e4 allele) C_LIO_LIThe data suggests that double cue spatial IOR may be sensitive to detect early AD pathological changes, which may be linked to disease progress at the posterior brain regions (rather than the medial temporal lobe) C_LI

neuroscience↗

bioRxiv2020

Condensation of pericentrin proteins in human cells illuminates phase separation in centrosome assembly

AbstractAt the onset of mitosis, centrosomes expand the pericentriolar material (PCM) to maximize their microtubule-organizing activity. This step, termed centrosome maturation, ensures proper spindle organization and faithful chromosome segregation. However, as the centrosome expands, how PCM proteins are recruited and held together without membrane enclosure remains elusive. We found that endogenously expressed pericentrin (PCNT), a conserved PCM scaffold protein, condenses into dynamic granules during late G2/early mitosis before incorporating into mitotic centrosomes. Furthermore, the N-terminal portion of PCNT--enriched with conserved coiled-coils (CCs) and low-complexity regions (LCRs)--phase separates into dynamic condensates that selectively recruit PCM proteins and nucleate microtubules in cells. We propose that CCs and LCRs, two prevalent sequence features in the centrosomal proteome, are preserved under evolutionary pressure in part to mediate liquid-liquid phase separation, a process that bestows upon the centrosome distinct properties critical for its assembly and functions.

cell biology↗