Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 1,297 records · Page 72Linked to original sources

bioRxiv2020

MFG-E8 Signaling Promotes Elastolysis and Calcification in the Aging Aortic Wall

Milk fat globule-EGF factor 8 (MFG-E8) protein increases with age and is mainly secreted by vascular smooth muscle cells in the arterial wall. Here, we investigated the role of MFG-E8 signaling during proinflammation, elastolysis, fibrosis, and calcification within the aging arterial wall. In vivo studies indicated that (1) Elastic lamina breaks collagen deposition and calcium-phosphorus products were markedly increased in the aging arterial wall of rats; (2) MFG-E8 protein abundance was markedly increased while intact tropoelastin (TPELN), an element of repair of the elastic fibers, was markedly decreased in the aging arterial wall of rats; (3) The absence of MFG-E8 markedly alleviated age-associated increases in elastic lamina breaks, collagen deposition and calcium-phosphorus products in mice; and (4) MFG-E8 deficiency significantly decreased age-associated increases in matrix metalloproteinase type II (MMP-2) activation, alkaline phosphatase, and runt-related transcription factor 1 (Runx1) expression in the aortic walls of mice. The in vitro studies demonstrated that (1) treating either young or old rat VSMCs with recombinant human MFG-E8 protein (rhMFG-E8) significantly reduced TPELN levels while MFG-E8 gene silencing significantly increased TPELN levels; (2) rhMFG-E8 treatment activated MMP-2 levels in both young and old VSMCs; and (3) MMP-2 bound to and cleaved TPELN secreted from VSMCs. Thus, these findings suggest that MFG-E8 signaling promotes age-associated adverse structural remodeling, including elastolysis, fibrosis, and calcification; however, MFG-E8 deficiency markedly mitigates these adverse effects in mice.

pathology↗

bioRxiv2020

Structural basis for repurposing a 100-years-old drug suramin for treating COVID-19

The COVID-19 pandemic by non-stop infections of SARS-CoV-2 has continued to ravage many countries worldwide. Here we report the discovery of suramin, a 100-year-old drug, as a potent inhibitor of the SARS-CoV-2 RNA dependent RNA polymerase (RdRp) through blocking the binding of RNA to the enzyme. In biochemical assays, suramin and its derivatives are at least 20-fold more potent than remdesivir, the currently approved nucleotide drug for COVID-19. The 2.6 [A] cryo-EM structure of the viral RdRp bound to suramin reveals two binding sites of suramin, with one site directly blocking the binding of the RNA template strand and the other site clash with the RNA primer strand near the RdRp catalytic active site, therefore inhibiting the viral RNA replication. Furthermore, suramin potently inhibits SARS-CoV-2 duplication in Vero E6 cells. These results provide a structural mechanism for the first non-nucleotide inhibitor of the SARS-CoV-2 RdRp and a rationale for repurposing suramin for treating COVID-19. One Sentence SummaryDiscovery and mechanism of suramin as potent SARS-CoV-2 RNA polymerase inhibitor and its repurposing for treating COVID-19.

molecular biology↗

bioRxiv2020

Integrative identification by Hi-C revealed distinct advanced structural variations in Lung Adenocarcinoma tissue

Advanced three-dimensional structure variations of chromatin in large genome fragments, such as conversion of A/B compartment, topologically associated domains (TADs) and chromatin loops are related closely to occurrence of malignant tumors. However, the structural characteristics of lung cancer still remain uncovered. In this study, we used high-throughput chromosome (HiC) confirmation capture to detect 2 non-smoking female lung adenocarcinoma (LUAD) tumor and paired normal tissues. The results indicated that significant chromatin variations were detected in tumor tissues compared with normal tissues. At compartment scale, the main conversion type of compartment is A[->]B in tumor tissues, which concentrated mainly on chromosome 3 (33.6%). Total of 216 tumor-specific TADs were identified in tumor tissues, which distributed mainly in chr1 (19), chr2 (15) and chr3(17). Finally we observed 41 distinct enhancer-promoter loops in tumor tissue, which associated closely to tumor-related pathways including MAPK, PI3K-AKT, Ras, Wnt and Ras1. The most important observation in this study was that we identified 5 important genes (SYT16, NCEH1, NXPE3, MB21D2, and DZIP1L), which were detected in both A[->]B compartment, TADs and chromatin loops. Four of these genes (NCEH1, NXPE3, MB21D2, and DZIP1L) located on q arm of chromosome 3, which also revealed the importance of chr3 in occurrence of structural variations in LUAD.

cancer biology↗

bioRxiv2020

CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators

Cellular RNA is decorated with over 170 types of chemical modifications. Many modifications in mRNA, including m6A and m5C, have been associated with critical cellular functions under physiological and/or pathological conditions. To understand the biological functions of these modifications, it is vital to identify the regulators that modulate the modification rate. However, a high-throughput method for unbiased screening of these regulators is so far lacking. Here, we report such a method combining pooled CRISPR screen and reporters with RNA modification readout, termed CRISPR integrated gRNA and reporter sequencing (CIGAR-seq). Using CIGAR-seq, we discovered NSUN6 as a novel mRNA m5C methyltransferase. Subsequent mRNA bisulfite sequencing in HAP1 cells without or with NSUN6 and/or NSUN2 knockout showed that NSUN6 and NSUN2 worked on non-overlapping subsets of mRNA m5C sites, and together contributed to almost all the m5C modification in mRNA. Finally, using m1A as an example, we demonstrated that CIGAR-seq can be easily adapted for identifying regulators of other mRNA modification.

molecular biology↗

bioRxiv2020

Circulating Clonally Expanded T Cells Reflect Functions of Tumor Infiltrating T Cells

Understanding the relationship between tumor and peripheral immune environments could allow longitudinal immune monitoring in cancer. Here, we examined whether T cells that share the same TCR{beta} and are found in both tumor and blood can be interrogated to gain insight into the ongoing tumor T cell response. Paired transcriptome and TCR{beta} repertoire of circulating and tumor-infiltrating T cells were analyzed from matched tumor and blood from patients with metastatic melanoma at the single cell level. We found that in circulating T cells matching clonally expanded tumor-infiltrating T cells (circulating TILs), gene signatures of effector functions, but not terminal exhaustion, reflect those observed in the tumor. In contrast, features of exhaustion are displayed predominantly by T cells present only in tumor. Finally, genes associated with a high degree of blood-tumor TCR sharing were overexpressed in tumor tissue after immunotherapy. These data demonstrate that circulating TILs, identified by TCRs shared with T cells in tumors, have unique transcriptional expression patterns that may have utility for the interrogation of T cell function in cancer immunotherapy. SummaryCombining transcriptomic and TCR{beta} repertoire analysis of circulating and tumor-infiltrating CD8 T cells from patients with metastatic melanoma, we identify a blood-based population with effector properties that reflect those of clonally related tumor-resident T cells.

immunology↗

bioRxiv2020

Prime-boost vaccination of mice and Rhesus macaques with two novel adenovirus vectored COVID-19 vaccine candidates

COVID-19 vaccines are being developed urgently worldwide, among which single-shot adenovirus vectored vaccines represent a major approach. Here, we constructed two novel adenovirus vectored COVID-19 vaccine candidates on simian adenovirus serotype 23 (Sad23L) and human adenovirus serotype 49 vectors (Ad49L) carrying the full-length gene of SARS-CoV-2 spike protein (S), designated Sad23L-nCoV-S and Ad49L-nCoV-S vaccines, respectively. The immunogenicity elicited by these two vaccine strains was individually evaluated in mice. Specific humoral and cellular immune responses were proportionally observed in a dose-dependent manner, and stronger response was obtained by boosting. Furthermore, five rhesus macaques were intramuscularly injected with a dose of 5x109 PFU Sad23L-nCoV-S vaccine for prime vaccination, followed by boosting with 5x109 PFU of Ad49L-nCoV-S vaccine at 4-week interval. Three macaques were injected with Sad23L-GFP and Ad49L-GFP vectorial viruses as negative controls. Both mice and macaques tolerated well the vaccine inoculations without detectable clinical or pathologic changes. In macaques, prime-boost vaccination regimen induced high titers of 103.16 S-binding antibody (S-BAb), 102.75 cell receptor binding domain (RBD)-BAb and 102.38 neutralizing antibody (NAb) to pseudovirus a week after boosting injection, followed by sustained high levels over 10 weeks of observation. Robust IFN-{gamma} secreting T-cell response (712.6 SFCs/106 cells), IL-2 secreting T-cell response (334 SFCs/106 cells) and intracellular IFN-{gamma} expressing CD4+/CD8+ T cell response (0.39%/0.55%) to S peptides were detected in the vaccinated macaques. It was concluded that prime-boost immunization with Sad23L-nCoV-S and Ad49L-nCoV-S vaccines can safely elicit strong immunity in animals in preparation of clinical phase 1/2 trials.

immunology↗

bioRxiv2020

Medium-chain acyl-CoA dehydrogenase, a gatekeeper of mitochondrial function in glioblastoma multiforme

Glioblastoma (GBM) is among the deadliest of human cancers. Despite extensive efforts, it has proven to be highly resistant to chemo- and immune-based therapeutic strategies, and little headway has been made with targeted inhibitors. Like many cancers, metabolism is dysregulated in GBM. Thus, to identify new vulnerabilities and drug targets in GBM, we conducted genetic screens using pooled RNAi libraries targeting metabolic enzymes. We screened multiple glioma stem cell-derived (GSC) xenograft models, which revealed that several enzymes involved in the mitochondrial metabolism of fatty acids were required for tumor cell proliferation. From among these, we focused on medium-chain acyl-CoA dehydrogenase (MCAD), which oxidizes medium-chain fatty acids, due to its consistently high score across all of our screens, as well as its high expression level in multiple GSC models and its upregulation in GBM compared to normal brain. In this manuscript, we describe the dependence of GBM on sustained fatty acid metabolism to actively catabolize lipid species that would otherwise damage the mitochondrial structure. The uptake of mediumchain fatty acids lacks negative feedback regulation; therefore, in the absence of MCAD, medium-chain fatty acids accumulate to toxic levels, inducing reactive oxygen species (ROS), mitochondrial damage and failure, and apoptosis. Taken together, our findings uncover a previously unappreciated protective role exerted by MCAD in GBM cells, making it a unique and therapeutically exploitable vulnerability.

cancer biology↗

bioRxiv2020

A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2

Mutations and transient conformational movements of receptor binding domain (RBD) that make neutralizing epitopes momentarily unavailable, present immune escape routes to SARS-CoV-2. To mitigate viral escape, we developed a cocktail of neutralizing antibodies (NAbs) targeting epitopes located on different domains of spike (S) protein. Screening of a library of monoclonal antibodies generated from peripheral blood mononuclear cells of COVID-19 convalescent patients yielded potent NAbs, targeting N-terminal domain (NTD) and RBD domain of S, effective at nM concentrations. Remarkably, combination of RBD-targeting NAbs and NTD-binding NAb, FC05, dramatically enhanced the neutralization potency in cell-based assays and animal model. Results of competitive SPR assays and cryo-EM structures of Fabs bound to S unveil determinants of immunogenicity. Combinations of immunogens, identified in NTD and RBD of S, when immunized in rabbits elicited potent protective immune responses against SARS-CoV-2. These results provide a proof-of-concept for neutralization-based immunogen design targeting SARS-CoV-2 NTD and RBD. One sentence summaryImmunogens identified in the NTD and RBD of the SARS-CoV-2 spike protein using a cocktail of non-competing NAbs when injected in rabbits elicited a potent protective immune response against SARS-CoV-2.

microbiology↗

bioRxiv2020

Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution

In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the "down" conformation, indicating they are more prone to adopt this receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. These results collectively indicate that strong RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.

biophysics↗

bioRxiv2020

Mining the potential of VRS1-5 gene to raise barley grain yield

VRS1-5 genes determine spike row types during the early stages of spike development in barley (Hordeum vulgare), yet their functions for the determination of grain yield during the late stages of spike development are largely unknown. To assess the role of VRS1-5 genes in determining grain yield components, we sequenced VRS1-5 genes from 894 worldwide barley accessions and measured 19 spike morphology traits in four environments. Single nucleotide polymorphism SNP markers and gene marker-based haplotypes for VRS1-5 displayed close associations with spike morphology traits. We further developed a spatiote-temporal transcriptome atlas (255 samples) at 17 stages and five positions along the spike, that linked spike morphology to spikelet development and expression patterns of VRS1-5 genes. Phenotypic measurements demonstrated that mutations in VRS1-5 suppress the initiation of spikelet primordia and, trigger spikelet abortion by increasing cytokinin content and improving sensitivity of spikelet primordia to cytokinin. Our integrated results illustrate how breeding can globally alter spike morphology through diversity at the VRS1-5 genes, which show great potential in increasing barley grain yield.

developmental biology↗

bioRxiv2020

Reporting quality of trend analyses in leading medicine and oncology journals

Reporting quality of clinical research is critical for evidence-based medicine and reproducibility of clinical research. Most of the works focused on reporting quality of clinical trials and observational longitudinal studies. However, few focused on that of trend analyses. The reporting of recommended statistic metrics in trend analyses was also largely unclear. Therefore, we examined reporting quality of the trend analyses based on reporting of recommended statistic metrics. We systemically searched the PubMed for the trend-analysis articles published in 10 leading medicine and oncology journals during the 11 years from 2008 to 2018. The studies published after 2019 were not included due to the sudden, significant increase of publication number during and immediately after the COVID-19 pandemic. Only original articles, research letters and meta-analyses/systematic reviews were included. We scored the reporting quality of these articles based on whether they reported p-values/effect-sizes, and beta/co-efficient/slope/annual-percentage-change (APC). There were 297 qualified articles, among which 193 (66.0%) and 216 (72.7%) articles reported P-value and effect-size, respectively. Only 13 (5.8%) analyses reported neither p-value/effect size nor beta/coefficient/slope/APC. In multivariable regression models, author affiliation of epidemiology department was associated with less reporting effect-size, but that of statistics department with more reporting. Interestingly, U.S. senior-authors (versus non-U.S.) more likely reported p-values. No factors were independently linked to reporting APC. The reporting quality of trend analyses in leading medicine and oncology journals appear moderate and should be further improved. We thus call for more research and awareness of reporting-quality in trend analyses in oncology research and beyond.

scientific communication and education↗

bioRxiv2020

Hyaluronic Acid Fuels Pancreatic Cancer Growth

Rewired metabolism is a hallmark of pancreatic ductal adenocarcinomas (PDA). Previously, we demonstrated that PDA cells enhance glycosylation precursor biogenesis through the hexosamine biosynthetic pathway (HBP) via activation of the rate limiting enzyme, glutamine-fructose 6-phosphate amidotransferase 1 (GFAT1). Here, we genetically ablated GFAT1 in PDA cell lines, which completely blocked proliferation in vitro and led to cell death. In contrast, GFAT1 knockout did not impair tumor growth, suggesting that cancer cells can maintain fidelity of glycosylation precursor pools by scavenging nutrients from the tumor microenvironment. Here, we show that hyaluronic acid (HA), an abundant carbohydrate polymer in pancreatic tumors composed of repeating N-acetyl-glucosamine (GlcNAc) and glucuronic acid sugars, can bypass GFAT1 to refuel the HBP via the GlcNAc salvage pathway. Furthermore, HA facilitates proliferation in nutrient-starved wild-type PDA. Together, these data show HA can serve as a nutrient fueling PDA metabolism beyond its previously appreciated structural and signaling roles.

cancer biology↗

bioRxiv2020

AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

BackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling. ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly. ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

genetics↗

bioRxiv2020

Performance and efficiency of machine learning algorithms for analyzing rectangular biomedical data

Most of the biomedical datasets, including those of omics, population studies and surveys, are rectangular in shape and have few missing data. Recently, their sample sizes have grown significantly. Rigorous analyses on these large datasets demand considerably more efficient and more accurate algorithms. Machine learning (ML) algorithms have been used to classify outcomes in biomedical datasets, including random forests (RF), decision tree (DT), artificial neural networks (ANN) and support vector machine (SVM). However, their performance and efficiency in classifying multi-category outcomes in rectangular data are poorly understood. Therefore, we aimed to compare these metrics among the 4 ML algorithms. As an example, we created a large rectangular dataset using the female breast cancers in the Surveillance, Epidemiology, and End Results-18 (SEER-18) database which were diagnosed in 2004 and followed up until December 2016. The outcome was the 6-category cause of death, namely alive, non-breast cancer, breast cancer, cardiovascular disease, infection and other cause. We included 58 dichotomized features from ~53,000 patients. All analyses were performed using MatLab (version 2018a) and the 10-fold cross validation approach. The accuracy in classifying 6-category cause of death with DT, RF, ANN and SVM was 72.68%, 72.66%, 70.01% and 71.85%, respectively. Based on the information entropy and information gain of feature values, we optimized dimension reduction (i.e. reduce the number of features in models). We found 22 or more features were required to maintain the similar accuracy, while the running time decreased from 440s for 58 features to 90s for 22 features in RF, from 70s to 40s in ANN and from 440s to 80s in SVM. In summary, we here show that RF, DT, ANN and SVM had similar accuracy for classifying multi-category outcomes in this large rectangular dataset. Dimension reduction based on information gain will significantly increase models efficiency while maintaining classification accuracy.

bioinformatics↗

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

Emotional tagging retroactively promotes memory integration through rapid neural reactivation and reorganization

Neutral events preceding emotional experiences are thought to be better remembered by tagging them as significant to simulate future event predictions. Yet, the neurobiological mechanisms how emotion transforms initially mundane events into strong memories remain unclear. By two behavioral and one fMRI studies with adapted sensory preconditioning paradigm, we show rapid neural reactivation and reorganization underlying emotion-tagged retroactive memory enhancement. Behaviorally, emotional tagging enhanced initial memory for neutral associations across the three studies. Neurally, emotional tagging potentiated reactivation of overlapping neural traces in the hippocampus and stimulus-relevant neocortex. Moreover, it induced large-scale hippocampal-neocortical reorganization supporting such retroactive benefit, as characterized by enhanced hippocampal-neocortical coupling modulated by the amygdala during online processing, and a shift from stimulus-relevant neocortex to transmodal prefrontal-parietal areas during offline post-tagging rest. Together, emotional tagging retroactively promotes associations between past neutral events through stimulating rapid reactivation of overlapping representations and reorganizing related memories into an integrated network.

neuroscience↗

bioRxiv2020

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, thus influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans, to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations, with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

microbiology↗

bioRxiv2020

The deacylase SIRT5 supports melanoma viability by regulating chromatin dynamics

Cutaneous melanoma remains the most lethal skin cancer, and ranks third among all malignancies in terms of years of life lost. Despite the advent of immune checkpoint and targeted therapies, only roughly half of patients with advanced melanoma achieves a durable remission. SIRT5 is a member of the sirtuin family of protein deacylases that regulate metabolism and other biological processes. Germline Sirt5 deficiency is associated with mild phenotypes in mice. Here we show that SIRT5 is required for proliferation and survival across all cutaneous melanoma genotypes tested, as well as uveal melanoma, a genetically distinct melanoma subtype that arises in the eye and is incurable once metastatic. Likewise, SIRT5 is required for efficient tumor formation by melanoma xenografts and in an autochthonous mouse Braf;Pten-driven melanoma model. Via metabolite and transcriptomic analyses, we find that SIRT5 is required to maintain histone acetylation and methylation levels in melanoma cells, thereby promoting proper gene expression. SIRT5-dependent genes notably include MITF, a key lineage-specific survival oncogene in melanoma, and the c-MYC proto-oncogene. SIRT5 may represent a novel, druggable genotype-independent addiction in melanoma.

cancer biology↗