Biology subjects

Huang, J.

Publications and source records attributed to Huang, J..

At least 541 records · Page 30Linked to original sources

bioRxiv2020

Wireless Ensembles of Sub-mm Microimplants Communicating as a Network near 1 GHz in a Neural Application

Multichannel electrophysiological sensors and stimulators, especially those used for studying the nervous system, are most commonly based on monolithic microelectrode arrays. Such architecture limits the spatial flexibility of individual electrode placement, posing constraints for scaling to a large number of nodes, particularly across non-contiguous locations. We describe the design and fabrication of sub-millimeter size electronic microchips ("Neurograins") which autonomously perform neural sensing or electrical microstimulation, with emphasis on their wireless networking and powering. An [~]1 GHz electromagnetic transcutaneous link to an external telecom hub enables bidirectional communication and control at the individual neurograin level. The link operates on a customized time division multiple access (TDMA) protocol designed to scale up to 1000 neurograins. The system is demonstrated as a cortical implant in a small animal (rat) model with anatomical limitations restricting the implant to 48 neurograins. We suggest that the neurograin approach can be generalized to overcome many scalability issues for wireless sensors and actuators as implantable microsystems.

neuroscience↗

bioRxiv2020

Evolutionary Dynamics of Non-Coding Regions in Pancreatic Ductal Adenocarcinoma

While the non-coding genome appears to play a role, the dynamic nature of noncoding alterations with respect to clonal progression of solid tumors remains unexplored. To address this gap in knowledge we performed multiregional whole genome sequencing and clonal analysis to elucidate the evolutionary dynamics of non-coding regions in pancreatic cancer relative to those of the coding genome. We find that the mutational burden of noncoding DNA is higher than coding DNA. However, when noncoding DNA was segregated into enhancer and non-enhancer regions, enhancers were more similar to coding DNA. Mutational signatures of noncoding and coding DNA further revealed the similar mutational spectra of enhancers to coding DNA whereas the mutational spectra of non-enhancer, noncoding DNA had an entirely different pattern. These findings shed light on the role of noncoding DNA in pancreatic cancer.

cancer biology↗

bioRxiv2020

A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD

The spread of SARS-CoV-2 confers a serious threat to the public health without effective intervention strategies1-3. Its variant carrying mutated Spike (S) protein D614G (SD614G) has become the most prevalent form in the current global pandemic4,5. We have identified a large panel of potential neutralizing antibodies (NAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 S6. Here, we focused on the top 20 potential NAbs for the mechanism study. Of them, the top 4 NAbs could individually neutralize both authentic SARS-CoV-2 and SD614G pseudovirus efficiently. Our epitope mapping revealed that 16/20 potent NAbs overlapped the same steric epitope. Excitingly, we found that one of these potent NAbs (58G6) exclusively bound to a linear epitope on S-RBD (termed as 58G6e), and the interaction of 58G6e and the recombinant ACE2 could be blocked by 58G6. We confirmed that 58G6e represented a key site of vulnerability on S-RBD and it could positively react with COVID-19 convalescent patients plasma. We are the first, as far as we know, to provide direct evidences of a linear epitope that can be recognized by a potent NAb against SARS-CoV-2 S-RBD. This study paves the way for the applications of these NAbs and the potential safe and effective vaccine design.

immunology↗

bioRxiv2020

Long-term survival of salmon-attached SARS-CoV-2 at 4 degree as a potential source of transmission in seafood markets

Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. Here we showed that salmon-attached SARS-CoV-2 at 4{degrees}C could remain infectious for more than one week, suggesting that fish-attached SARS-CoV-2 may be a source of transmission.

microbiology↗

bioRxiv2020

Orthosteric-allosteric dual inhibitors of PfHT1 as selective anti-malarial agents

Artemisinin-resistant malaria parasites have emerged and been spreading, posing a significant public health challenge. Anti-malarial drugs with novel mechanisms of action are therefore urgently needed. In this report, we exploit a "selective starvation" strategy by selectively inhibiting Plasmodium falciparum hexose transporter 1 (PfHT1), the sole hexose transporter in Plasmodium falciparum, over human glucose transporter 1 (hGLUT1), providing an alternative approach to fight against multidrug-resistant malaria parasites. Comparison of the crystal structures of human GLUT3 and PfHT1 bound to C3361, a PfHT1-specific moderate inhibitor, revealed an inhibitor binding-induced pocket that presented a promising druggable site. We thereby designed small-molecules to simultaneously block the orthosteric and allosteric pockets of PfHT1. Through extensive structure-activity relationship (SAR) studies, the TH-PF series was identified to selectively inhibit PfHT1 over GLUT1 and potent against multiple strains of the blood-stage P. falciparum. Our findings shed light on the next-generation chemotherapeutics with a paradigm-shifting structure-based design strategy to simultaneously targeting the orthosteric and allosteric sites of a transporter. Significance statementBlocking sugar uptake in P. falciparum by selectively inhibiting the hexose transporter PfHT1 kills the blood-stage parasites without affecting the host cells, indicating PfHT1 as a promising therapeutic target. Here, we report the development of novel small-molecule inhibitors that are selectively potent to the malaria parasites over human cell lines by simultaneously targeting the orthosteric and the allosteric binding sites of PfHT1. Our findings established the basis for the rational design of next-generation anti-malarial drugs.

pharmacology and toxicology↗

bioRxiv2020

A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica

Accumulation of anthocyanin is a desirable trait to be selected in rice domestication, but the molecular mechanism of anthocyanin biosynthesis in rice remains largely unknown. In this study, a novel allele of chromogen gene C, OrC1, from Oryza rufipongon was cloned and identified as a determinant regulator of anthocyanin biosynthesis. Although OrC1 functions in purple apiculus, leaf sheath and stigma in indica background, it only promotes purple apiculus in japonica. Transcriptome analysis revealed that OrC1 regulates flavonoid biosynthesis pathway and activates a few bHLH and WD40 genes of ternary MYB-bHLH-WD40 complex in indica. Differentially expressed genes and metabolites were found in the indica and japonica backgrounds, indicating that OrC1 activated the anthocyanin biosynthetic genes OsCHI, OsF3H, OsANS, OsINS and OsANR and produced six metabolites independently. Artificial selection and domestication of C1 gene in rice occurred on the coding region in the two subspecies independently. Our results reveal the regulatory system and domestication of C1, provide new insights into MYB transcript factor involved in anthocyanin biosynthesis, and show the potential of engineering anthocyanin biosynthesis in rice. Author summaryAccumulation of anthocyanin is a selection trait in rice domestication, whereas the mechanisms regulating the anthocyanin biosynthetic pathway in rice remain unresolved. Here, a novel allele of chromogen gene C from wild rice (Oryza rufipongon) was identified as a determinant regulator of anthocyanin biosynthesis. A key question is to what extent the involvement of the C1 gene can explain coloration variability of cultivated rice, where anthocyanin accumulation has been eliminated by artificial selection. Our results reveal the functional chromogen gene C from wild rice causes different coloration phenotypes, regulates various anthocyanin biosynthetic genes and produces different metabolites in indica and japonica. Artificial selection and domestication of the C1 gene in rice only occurs within the coding region of the two subspecies independently.

plant biology↗

bioRxiv2020

A rapid and efficient screening system for neutralizing antibodies and its application for the discovery of potent neutralizing antibodies to SARS-CoV-2 S-RBD

Neutralizing antibodies (Abs) have been considered as promising therapeutics for the prevention and treatment of pathogens. After the outbreak of COVID-19, potent neutralizing Abs to SARS-CoV-2 were promptly developed, and a few of those neutralizing Abs are being tested in clinical studies. However, there were few methodologies detailly reported on how to rapidly and efficiently generate neutralizing Abs of interest. Here, we present a strategically optimized method for precisive screening of neutralizing monoclonal antibodies (mAbs), which enabled us to identify SARS-CoV-2 receptor-binding domain (RBD) specific Abs within 4 days, followed by another 2 days for neutralization activity evaluation. By applying the screening system, we obtained 198 Abs against the RBD of SARS-CoV-2. Excitingly, we found that approximately 50% (96/198) of them were candidate neutralizing Abs in a preliminary screening of SARS-CoV-2 pseudovirus and 20 of these 96 neutralizing Abs were confirmed with high potency. Furthermore, 2 mAbs with the highest neutralizing potency were identified to block authentic SARS-CoV-2 with the half-maximal inhibitory concentration (IC50) at concentrations of 9.88 ng/ml and 11.13 ng/ml. In this report, we demonstrated that the optimized neutralizing Abs screening system is useful for the rapid and efficient discovery of potent neutralizing Abs against SARS-CoV-2. Our study provides a methodology for the generation of preventive and therapeutic antibody drugs for emerging infectious diseases.

immunology↗

bioRxiv2020

In-depth analysis reveals complex molecular etiology of idiopathic cerebral palsy

Cerebral palsy (CP), the most prevalent physical disability in children, has long been ignored with regard to its inherent molecular mechanism. In this work, we performed in-depth clinical and molecular analysis on 120 idiopathic CP families, and identified in half of the patients the underlying risk factors. By a compilation of 117 CP-related genes, we recognized the characteristic features in terms of inheritance and function, and proposed a dichotomous classification system according to the expression patterns. In two patients with both CP and intellectual disability, we revealed that the defective TYW1, a tRNA hypermodification enzyme, caused microcephaly and problems in motion and cognition by hindering neuronal proliferation and migration. We developed an algorithm and proved in mice brain that this malfunctioning hypermodification specifically perturbed the translation of a subset of proteins involved in cell cycling. In a CP patient with normal intelligence, we identified a mitochondrial enzyme GPAM, the hypomorphic form of which led to hypomyelination of corticospinal tract. We confirmed that the aberrant Gpam in mice perturbed the lipid metabolism in astrocyte, resulting in suppressed astrocyte proliferation and a shortage of lipid contents supplied for oligodendrocyte myelination. This work broadened the scope of understanding of CP etiology and paved a way for innovative therapeutic strategies.

genetics↗

bioRxiv2020

Electronic cigarettes induce mitochondrial DNA damage and trigger toll-like receptor 9-mediated atherosclerosis

ObjectiveBoth electronic cigarette (e-cig) use and toll-like receptor 9 (TLR9) activation have been implicated in promoting atherosclerosis. In this study we aimed to investigate the causative relationship of e-cig exposure on TLR9 activation and atherosclerosis development. Approach and ResultsEight-week-old ApoE-/- mice fed normal chow diet were exposed to e-cig vapor (ECV) for 2 h/day, 5 days/week for 16 weeks. We found that ECV exposure significantly induced atherosclerotic lesions as examined by Oil Red O staining of aortic root and greatly upregulated TLR9 expression in classical monocytes and in the atherosclerotic plaques, which the latter was corroborated by upregulated TLR9 expression in human femoral artery atherosclerotic plaques in e-cig smokers. Intriguingly, we found a significant increase of damaged mitochondria DNA level in the circulating blood of ECV exposed mice. Furthermore, administration of TLR9 antagonist prior to ECV exposure not only alleviated atherosclerotic lesion and the upregulation of TLR9 in plaques, but also attenuated the increase of plasma levels of inflammatory cytokines, reduced the accumulation of lipid and macrophages, and decreased the frequency of blood CCR2+ classical monocytes. Surprisingly, we found that the cytoplasmic mtDNA isolated from ECV extract-treated cells can greatly enhance the expression of TLR9 in reporter cells. ConclusionE-cig induces mtDNA damage and the mtDNA in circulating blood stimulates the expression of TLR9, which elevate the expression of proinflammatory cytokines in monocyte/macrophage and consequently lead to atherosclerosis. Our results raise the possibility that intervention of TLR9 activation is a potential pharmacologic target of ECV-related inflammation and cardiovascular diseases.

pharmacology and toxicology↗

bioRxiv2020

Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

The importance of structural variants (SVs) on phenotypes and human diseases is now recognized. Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed, few benchmarking procedures are available to confidently assess their performances in biological and clinical research. To facilitate the validation and application of those approaches, our work established an Asian reference material comprising identified benchmark regions and high-confidence SV calls. We established a high-confidence SV callset with 8,938 SVs in an EBV immortalized B lymphocyte line, by integrating four alignment-based SV callers [from 109x PacBio continuous long read (CLR), 22x PacBio circular consensus sequencing (CCS) reads, 104x Oxford Nanopore long reads, and 114x optical mapping platform (Bionano)] and one de novo assembly-based SV caller using CCS reads. A total of 544 randomly selected SVs were validated by PCR and Sanger sequencing, proofing the robustness of our SV calls. Combining trio-binning based haplotype assemblies, we established an SV benchmark for identification of false negatives and false positives by constructing the continuous high confident regions (CHCRs), which cover 1.46Gb and 6,882 SVs supported by at least one diploid haplotype assembly. Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology, disease, and clinical diagnosis.

genomics↗

bioRxiv2020

Dietary Protein on Growth Performance, Serum Biochemical Index and offspring of Hu ewes in late pregnancy

The purpose of this study was to explore the effects of ewe growth performance, serum biochemical indicators and lamb growth and development at different protein levels in late pregnancy. A total of 15 pregnant ewes (46.4 {+/-} 1.38kg initial BW) were assigned to 3 groups with 5 ewes in each group in a randomized block design. P1, P2 and P3 of three groups were fed diets with different levels of crude protein at 11.25%, 12.5% and 13.75% (low, medium and high) respectively, while the dietary energy levels remained unchanged. Choose ewes with the same body condition from 90 days of pregnancy to different protein diets during delivery, and feed the same diets during lactation. New-born lambs were left to suckle their dams freely for the first three days and were kept with their dams till weaning at 60 days of age. Dietary protein levels during late gestation showed no significant effect on the weight gain of ewes and their offspring in the late pregnancy (P > 0.05) but had significant effects on blood urea nitrogen (BUN), glucose (GLU), C-reactive protein (CRPL3) and ammonia nitrogen (NH3L) before parturition, and on triglyceride (TG) in lactating ewes. Dietary protein levels during late gestation had significant effects on birth height, body length, chest depth, chest circumference, straight crown hip length and curved crown hip length of lambs (P < 0.05) as well as on weaning body length, chest circumference, head width and head length (P < 0.05). The results showed that although different dietary protein levels during late gestation have no significant effects on growth performance of ewes, singleton, twins and triplets, it affects lambs body shape and ewes metabolism. Therefore, the optimum protein concentration for the growth of ewes and subsequent lambs in this experiment is 11.25%.

physiology↗

bioRxiv2020

Genome-wide association study of TP53 R249S mutation in hepatocellular carcinoma with aflatoxin B1 exposure and hepatitis B virus infection in Guangxi

Background/AimsDietary aflatoxin B1 (AFB1) exposure, which induces DNA damage and codon 249 mutation of the TP53 gene, is one of the major risk factors for hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) infection and AFB1 exert synergistic effects to promote carcinogenesis and TP53 R249S mutation in HCC. MethodsA genome-wide association study (GWAS) was conducted on 485 cases of HCC with chronic HBV infection, followed by a two-stage replication study on 270 cases with chronic HBV infection. Susceptibility variants for the TP53 R249S mutation in HCC were identified based on both GWAS and replication analysis. The associations of identified variants with expression levels of their located genes were validated in 20 paired independent samples. ResultsOur results showed that TP53 R249S was significantly associated with ADAMTS18 rs9930984 (adjusted P = 4.84x10-6), WDR49 rs75218075 (adjusted P = 7.36 x 10-5) and SLC8A3 rs8022091 (adjusted P = 0.042). Additionally, ADAMTS18 mRNA expression was significantly higher in HCC tissue, compared with paired non-tumor tissue (P = 0.041) and patients carrying the TT genotype at rs9930984 showed lower ADAMTS18 expression in non-tumor tissue, compared with those carrying the GT genotype (P = 0.0028). ConclusionsTP53 expression is significantly associated with R249S mutation in HCC. Our collective results suggest that rs9930984, rs75218075 and rs8022091 are associated with susceptibility to the R249S mutation in cases of HCC exposed to AFB1 and HBV infection.

genetics↗

bioRxiv2020

SARS-CoV-2 suppresses mRNA expression of selenoproteins associated with ferroptosis, ER stress and DNA synthesis

A significant, positive association between selenium status and prognosis of SARS-CoV-2 infection has been identified among COVID-19 patients in China. Moreover, a German study revealed a pronounced deficit of serum selenium and SELENOP concentrations in COVID-19 patients, and selenium deficiency was associated with mortality risk from COVID-19. The present study investigated the influence of SARS-CoV-2 on gene expression of host selenoproteins which mediate many beneficial actions of selenium. We found that SARS-CoV-2 suppressed mRNA expression of selenoproteins associated with ferroptosis (GPX4), endoplasmic reticulum stress (SELENOF, SELENOK, SELENOM and SELENOS) and DNA synthesis (TXNRD3), while SARS-CoV-2 increased gene expression of IL-6 (an inflammatory cytokine positively correlated with severity of COVID-19), in Vero cells. These results provide a deeper insight into the connection between selenium and SARS-CoV-2 pathogenesis.

microbiology↗

bioRxiv2020

Elucidation of tumor-stromal heterogeneity and the ligand-receptor interactome by single cell transcriptomics in real-world pancreatic cancer biopsies

Precision medicine approaches in pancreatic ductal adenocarcinoma (PDAC) are imperative for improving disease outcomes. However, the long-term fidelity of recently deployed ex vivo preclinical platforms, such as patient-derived organoids (PDOs) remains unknown. Through single-cell RNA sequencing (scRNA-seq), we identify substantial transcriptomic evolution of PDOs propagated from the parental tumor, which may alter predicted drug sensitivity. In contrast, scRNA-seq is readily applicable to limited biopsies from human primary and metastatic PDAC and identifies most cancers as being an admixture of previously described epithelial transcriptomic subtypes. Integrative analyses of our data provide an in-depth characterization of the heterogeneity within the tumor microenvironment, including cancer-associated fibroblast (CAF) subclasses, and predicts for a multitude of ligand-receptor interactions, revealing potential targets for immunotherapy approaches. While PDOs continue to enable prospective therapeutic prediction, our analysis also demonstrates the complementarity of using orthogonal de novo biopsies from PDAC patients paired with scRNA-seq to inform clinical decision-making. Statement of SignificanceThe application of single-cell RNA sequencing to diagnostic pancreatic cancer biopsies provides in-depth transcriptomic characterization of the tumor epithelium and microenvironment, while minimizing potential artifacts introduced by an intervening ex vivo passaging step. Thus, this approach can complement the use of patient-derived organoids in implementing precision oncology.

cancer biology↗

bioRxiv2020

Requirement of the antimicrobial peptide CRAMP for macrophages to eliminate phagocytosed E. coli through an autophagy pathway

Host-derived antimicrobial peptides play an important role in the defense against extracellular bacterial infections. However, the capacity of antimicrobial peptides derived from macrophages as potential antibacterial effectors against intracellular pathogens remains unknown. In this study, we report that normal (wild type, WT) mouse macrophages increased their expression of the cathelicidin-related antimicrobial peptide (CRAMP) after infection by viable E. coli or stimulation with inactivated E. coli and its product LPS, a process involving activation of NF-{kappa}B followed by protease-dependent conversion of CRAMP from an inactive precursor to an active form. The active CRAMP was required by WT macrophages to eliminate phagocytosed E. coli, with participation of autophagy-related proteins ATG5, LC3-II, and LAMP-1 as well as conjugation of the bacteria with p62. The autophagy-mediated elimination of E. coli was impaired in CRAMP-/- macrophages resulting in retention of intracellular bacteria and fragmentation of macrophages. These results indicate CRAMP as a critical component in autophagy-mediated clearance of intracellular E. coli by macrophages.

immunology↗

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

Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate

Antiviral strategies to inhibit Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and the pathogenic consequences of COVID-19 are urgently required. Here we demonstrate that the NRF2 anti-oxidant gene expression pathway is suppressed in biopsies obtained from COVID-19 patients. Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular anti-viral program, which potently inhibits replication of SARS-CoV2 across cell lines. The anti-viral program extended to inhibit the replication of several other pathogenic viruses including Herpes Simplex Virus-1 and-2, Vaccinia virus, and Zika virus through a type I interferon (IFN)-independent mechanism. In addition, induction of NRF2 by 4-OI and DMF limited host inflammatory responses to SARS-CoV2 infection associated with airway COVID-19 pathology. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2. One Sentence SummaryNRF2 agonists 4-octyl-itaconate (4-OI) and dimethyl fumarate inhibited SARS-CoV2 replication and virus-induced inflammatory responses, as well as replication of other human pathogenic viruses.

microbiology↗

bioRxiv2020

SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response

The most severe and fatal infections with SARS-CoV-2 result in the acute respiratory distress syndrome, a clinical phenotype of coronavirus disease 2019 (COVID-19) that is associated with virions targeting the epithelium of the distal lung, particularly the facultative progenitors of this tissue, alveolar epithelial type 2 cells (AT2s). Little is known about the initial responses of human lung alveoli to SARS-CoV-2 infection due in part to inability to access these cells from patients, particularly at early stages of disease. Here we present an in vitro human model that simulates the initial apical infection of the distal lung epithelium with SARS-CoV-2, using AT2s that have been adapted to air-liquid interface culture after their derivation from induced pluripotent stem cells (iAT2s). We find that SARS-CoV-2 induces a rapid global transcriptomic change in infected iAT2s characterized by a shift to an inflammatory phenotype predominated by the secretion of cytokines encoded by NF-kB target genes, delayed epithelial interferon responses, and rapid loss of the mature lung alveolar epithelial program. Over time, infected iAT2s exhibit cellular toxicity that can result in the death of these key alveolar facultative progenitors, as is observed in vivo in COVID-19 lung autopsies. Importantly, drug testing using iAT2s confirmed an antiviral dose-response to remdesivir and demonstrated the efficacy of TMPRSS2 protease inhibition, validating a putative mechanism used for viral entry in human alveolar cells. Our model system reveals the cell-intrinsic responses of a key lung target cell to infection, providing a physiologically relevant platform for further drug development and facilitating a deeper understanding of COVID-19 pathogenesis.

molecular biology↗