Biology subjects

Zhou, Q.

Publications and source records attributed to Zhou, Q..

At least 271 records · Page 15Linked to original sources

bioRxiv2020

Structural basis for the recognition of the 2019-nCoV by human ACE2

Angiotensin-converting enzyme 2 (ACE2) has been suggested to be the cellular receptor for the new coronavirus (2019-nCoV) that is causing the coronavirus disease 2019 (COVID-19). Like other coronaviruses such as the SARS-CoV, the 2019-nCoV uses the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) to engage ACE2. We most recently determined the structure of the full-length human ACE2 in complex with a neutral amino acid transporter B0AT1. Here we report the cryo-EM structure of the full-length human ACE2 bound to the RBD of the 2019-nCoV at an overall resolution of 2.9 [A] in the presence of B0AT1. The local resolution at the ACE2-RBD interface is 3.5 [A], allowing analysis of the detailed interactions between the RBD and the receptor. Similar to that for the SARS-CoV, the RBD of the 2019-nCoV is recognized by the extracellular peptidase domain (PD) of ACE2 mainly through polar residues. Pairwise comparison reveals a number of variations that may determine the different affinities between ACE2 and the RBDs from these two related viruses.

biochemistry↗

bioRxiv2020

Single-cell Analysis of ACE2 Expression in Human Kidneys and Bladders Reveals a Potential Route of 2019-nCoV Infection

Since December 2019, a novel coronavirus named 2019 coronavirus (2019-nCoV) has emerged in Wuhan of China and spread to several countries worldwide within just one month. Apart from fever and respiratory complications, acute kidney injury has been observed in some patients with 2019-nCoV. In a short period of time, angiotensin converting enzyme II (ACE2), have been proposed to serve as the receptor for the entry of 2019-nCoV, which is the same for severe acute respiratory syndrome coronavirus (SARS). To investigate the possible cause of kidney damage in 2019-nCoV patients, we used both published kidney and bladder cell atlas data and an independent unpublished kidney single cell RNA-Seq data generated in-house to evaluate ACE2 gene expressions in all cell types in healthy kidneys and bladders. Our results showed the enriched expression of all subtypes of proximal tubule cells of kidney and low but detectable levels of expression in bladder epithelial cells. These results indicated the urinary system is a potential route for 2019-nCoV infection, along with the respiratory system and digestion system. Our findings suggested the kidney abnormalities of SARS and 2019-nCoV patients may be due to proximal tubule cells damage and subsequent systematic inflammatory response induced kidney injury. Beyond that, laboratory tests of viruses and related indicators in urine may be needed in some special patients of 2019-nCoV.

genomics↗

bioRxiv2020

Structure of dimeric full-length human ACE2 in complex with B0AT1

Angiotensin-converting enzyme 2 (ACE2) is the surface receptor for SARS coronavirus (SARS-CoV), directly interacting with the spike glycoprotein (S protein). ACE2 is also suggested to be the receptor for the new coronavirus (2019-nCoV), which is causing a serious epidemic in China manifested with severe respiratory syndrome. B0AT1 (SLC6A19) is a neutral amino acid transporter whose surface expression in intestinal cells requires ACE2. Here we present the 2.9 [A] resolution cryo-EM structure of full-length human ACE2 in complex with B0AT1. The complex, assembled as a dimer of ACE2-B0AT1 heterodimers, exhibits open and closed conformations due to the shifts of the peptidase domains (PDs) of ACE2. A newly resolved Collectrin-like domain (CLD) on ACE2 mediates homo-dimerization. Structural modelling suggests that the ACE2-B0AT1 complex can bind two S proteins simultaneously, providing important clues to the molecular basis for coronavirus recognition and infection.

biochemistry↗

bioRxiv2020

Transcranial in vivo detection of Aβ at single plaque resolution with large-field multifocal illumination fluorescence microscopy

The abnormal deposition of beta-amyloid proteins in the brain is one of the major histopathological hallmarks of Alzheimers disease. Currently available intravital microscopy techniques for high-resolution plaque visualization commonly involve highly invasive procedures and are limited to a small field-of-view within the rodent brain. Here, we report the transcranial detection of amyloid-beta deposits at the whole brain scale with 20 m resolution in APP/PS1 and arcA{beta} mouse models of Alzheimers disease amyloidosis using a large-field multifocal (LMI) fluorescence microscopy technique. Highly sensitive and specific detection of amyloid-beta deposits at a single plaque level in APP/PS1 and arcA{beta} mice was facilitated using luminescent conjugated oligothiophene HS-169. Immunohistochemical staining with HS-169, anti-A{beta} antibody 6E10, and conformation antibodies OC (fibrillar) of brain tissue sections further showed that HS-169 resolved compact parenchymal and vessel-associated amyloid deposits. The novel imaging platform offers new prospects for in vivo studies into Alzheimers disease mechanisms in animal models as well as longitudinal monitoring of therapeutic responses at a single plaque level.

neuroscience↗

bioRxiv2020

Tumor Neoantigenicity Assessment with CSiN Score Incorporates Clonality and Immunogenicity to Predict Immunotherapy Outcomes

Lack of responsiveness to checkpoint inhibitors is a central problem in the modern era of cancer immunotherapy. Tumor neoantigens are critical mediators of host immune response and immunotherapy treatment efficacy. Current studies of neoantigens almost entirely focus on total neoantigen load, which simplistically treats all neoantigens equally. Besides, neoantigen loads have been linked with treatment response and prognosis only in some studies, but not others. We developed a Cauchy-Schwarz index of Neoantigens (CSiN) score to characterize the degree of concentration of immunogenic neoantigens in truncal mutations. Unlike simple neoantigen loads, CSiN incorporates the effect of both clonality and MHC-binding affinity of neoantigens when characterizing patient neoantigen profiles. By exploiting the clinical responses in 501 treated patients (mostly by checkpoint inhibitors) and the overall survival of 1,978 baseline patients, we showed that CSiN scores predict treatment response to checkpoint inhibitors and prognosis in melanoma, lung cancer, and kidney cancer patients. CSiN substantially outperforms prior genetics-based prediction methods of responsiveness. Overall, our work fulfilled an important gap in current research involving neoantigens. One Sentence SummaryThe quality of tumor neoantigens predicts response to immunotherapy

bioinformatics↗

bioRxiv2019

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic "dark matter"). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

genomics↗

bioRxiv2019

Phase separation-mediated formation of condensed GIT/PIX enzyme complex module for compartmentalized signaling

Cells compartmentalize enzymes for broad physiological functions such as efficient metabolic reactions and spatiotemporally controlled signaling. A given enzyme or enzyme complex can participate in multiple cellular processes in response to different signal inputs by forming different cellular compartments. Here, we demonstrate that association of GIT1 and {beta}-Pix, a pair of GTPase regulatory enzymes involved in diverse cellular processes, leads to autonomous condensation of the complex via phase separation without additional scaffolding molecules. The atomic structure of the GIT/PIX complex reveals the molecular basis governing the phase separation-mediated condensation of the GIT1/{beta}-Pix complex. Importantly, the GIT1/{beta}-Pix condensates can function as a versatile modular membrane-less organelle- like structure for distinct cellular compartmentalization by binding to upstream proteins such as Paxillin in focal adhesions, Shank3 in neuronal synapses, and Scribble in cellular junctions. Thus, phase separation-mediated formation of condensed enzyme complexes provides a powerful way of dynamically concentrating limited amounts of cooperating enzymes to specific cellular compartments for optimal signaling.

cell biology↗

bioRxiv2019

Widespread interaction between ADAR1 and transcriptional byproducts

BackgroundADAR1, an adenosine-to-inosine (A-to-I) RNA editing enzyme, has an emerging role in cancer immunotherapy. ADAR1 presumably works by suppressing cellular innate immunity response to endogenously generated double-stranded RNAs through RNA editing. However, RNA species that are directly regulated by ADAR1 mediated RNA editing processes remain poorly defined. ResultsIn this study, we used a novel bioinformatics approach to track ADAR1-RNA interactions. By integrating DNA-seq, RNA-seq, and ADAR1 RNA immunoprecipitation sequencing (fRIP-seq) data of K562 cell line, we provided the first in-situ landscape profiling of ADAR1 RNA binding and editing activities. With long RNA fragments captured by ADAR1 immunoprecipitation, we were able to identify exon junctions and genomic boundaries used by ADAR1-associated RNAs and thus we could possibly trace pre-RNA processing steps that had been acting on them. Our methodology allowed us to acquire the knowledge of transcriptome-wide scenario of ADAR1 activities. Intriguingly, we found that ADAR1 had a tendency to interact with transcriptional byproducts originated from obscure regions such as introns and intergenic regions. ConclusionsOur observation might shed light on the dual role of ADAR1 proteins not only in diversifying the transcriptome, but also in reigning RNA debris from obscure regions. Moreover, as the functional potential of seemly transcriptional byproducts is just beginning to emerge, this study would bridge ADAR1 with other fields of RNA biology.

genomics↗

bioRxiv2019

The socioeconomic burden of severe mental disorder in China, 2014-2017: a prevalence study

Mental illness is a chronic disease with high morbidity and mortality rate, resulting in heavy economic burden for family and society, especially the severe ones. Chinese government has taken a series of action on the treatment and management of severe mental disorder (SMD), but the scale of economic burden caused by SMD was still unclear. In this paper, we applied prevalence-based bottom-up approach to estimate the direct and indirect economic burden of SMD in Southwest China from 2014 to 2017. We used the sampled inpatient medical record data of patient with SMD to calculate the total direct cost and estimated the indirect economic burden using human capital approach.The total ecomonic burden of SMD was USD9,733 million and direct burden was contiributed for 7.5% as USD734.5 million in four years total. The growth rate of direct medical cost was declined due to the health policy reform and total cost control policy. The indirect cost was rapidly increased in four years when estimated with DALYs reported in GBD2010 and resulting USD8,998.6 million. We next estimated the indirect burden using sample DALYs and occupation wage cost approach as sensitive analysis. We found that the indirect burden was sensitive to the key variable and the estimation approach, but the estimates share same increasing trend but with different velocity. Our study suggests that SMD in China have posed substantial economic burden at individual and social levels, with the appropriate estimation of total economic burden, our reaserch would attract more attention and be helpful for health resources distribution.

scientific communication and education↗

bioRxiv2019

Plasmodiophora brassicae in its environment-effects of temperature and light on resting spore survival in soil

Clubroot caused by Plasmodiophora brassicae is an important disease on cruciferous crops worldwide. Management of clubroot has been challenging, due largely to the millions of resting spores produced within an infected root that can survive dormant in the soil for many years. This study was conducted to investigate some of the environmental conditions that may affect the survival of resting spores in the soil. Soil samples containing clubroot resting spores (1 x 107 spores g-1 soil) were stored at various temperatures for two years. Additionally, other samples were buried in soil, or kept on the soil surface in the field. The content of P. brassicae DNA and the numbers of viable spores in the samples were assessed by quantitative polymerase chain reaction (qPCR) and pathogenicity bioassays, respectively. The results indicated that 4{degrees}C, 20{degrees}C and being buried in the soil were better conditions for spore survival than were -20{degrees}C, 30{degrees}C and at the soil surface. Most of the spores kept on the soil surface were killed, suggesting the negative effect of light on spore viability. Additional experiments confirmed that ultraviolet (UV) light contributed a large negative effect on spore viability as lower pathogenicity and less DNA content were observed from the 2-and 3-hour UV light treated spores compared to the untreated control. Finally, this work demonstrated that DNA-based quantification methods such as qPCR can be poor predictors of P. brassicae disease potential due to the presence and persistence of DNA from dead spores.

microbiology↗

bioRxiv2019

Molecular profiling of lymphovascular invasive cancer cells in TNBC using G&T-seq

Lymphovascular invasion (LVI) is a critical step in the metastatic process but have received relatively little attention due to the technical challenges associated with their isolation. In this study, we used laser capture microdissection (LCM) to isolate 97 cancer cell clusters from pathological frozen sections within lymphatic vessels, primary tumor tissue, and axillary lymph nodes of a triple negative breast cancer (TNBC) patient. Simultaneous genome and transcriptome amplification and sequencing (G&T-seq) performed on these clusters permitted a comprehensive depiction of the genomic and transcriptional profiles of cancer cells associated with LVI. Combination phylogeny analysis pointed to three evolutionarily distinct pathways of tumor clone development and metastasis in this patient, each of which was associated with a unique mRNA signature, and correlated to disparate overall survival outcomes. Moreover, hub gene evaluation found extensive down regulation of ribosomal protein mRNA to be a potential marker of poor prognosis in breast cancer patients.

cancer biology↗

bioRxiv2019

Phylogeny, transposable element and sex chromosome evolution of the basal lineage of birds

Sex chromosomes of mammals and most birds are heteromorphic, while those of many paleognaths (ratites and tinamous) are inexplicably homomorphic. To dissect the mechanisms underlying the different tempo of sex chromosome evolution, we produced high-quality genomes of 12 paleognathous species, and reconstructed their phylogeny based on alignments of the non-coding sequences extending to nearly 40% of the genome. Our phylogenomic tree grouped the South American rheas and tinamous together, and supported the independent evolution of gigantism and loss of flight among ratites. The small-bodied tinamous have much higher rates of genome-wide substitutions and transposon turnovers. Yet majorities of both have retained exceptionally long recombining regions occupying over half of the entire sex chromosome, with the rest sex-linked regions diverging from each other at a much lower rate relative to neognathous birds. Each species exhibits a punctuated sequence divergence pattern between sex chromosomes termed evolutionary strata, because of stepwise suppression of recombination. We concluded that all paleognaths share one evolutionary stratum with all other birds, and convergently formed between one to three strata after their rapid speciation. Contrary to the classic notion, we provided clear evidence that the youngest stratum of some tinamous formed without chromosomal inversion. Intriguingly, some of the encompassing W-linked genes have upregulated their expression levels in ovary, probably due to the female-specific selection. We proposed here that the unique male-only parental care system of paleognaths has reduced the intensity of sexual selection, and contributed to these species low rates of sex chromosome evolution. We also provided novel insights into the evolution of W-linked genes at their early stages.

evolutionary biology↗

bioRxiv2019

Widespread arginine phosphorylation in human cells - a novel protein PTM revealed by mass spectrometry

Arginine phosphorylation (pArg) is recently discovered as a ubiquitous protein N- phosphorylation in bacteria. However, its prevalence and roles in mammalian cells remain largely unknown due to the lack of established workflow and the inherent lability of the phosphoramidate (P-N) bond. Emerging evidence suggests that N-phosphorylation may extensively exist in eukaryotes and play crucial roles. We report an experimental phosphoproteomic workflow, which for the first time allowed to reveal the widespread occurrence of pArg in human cells by mass spectrometry. By virtue of this approach, we identified 152 high-confidence pArg sit]es derived from 118 proteins. Remarkably, the discovered phosphorylation motif and gene ontology of pArg hint a possible cellular function of arginine phosphorylation by regulating the favorability of propeptide convertase substrate. The generated extensive data set should enable a better understanding of the biological functions of eukaryotic pArg in the future.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=37 SRC=\"FIGDIR/small/725291v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (13K):\norg.highwire.dtl.DTLVardef@77b2d0org.highwire.dtl.DTLVardef@7c76f4org.highwire.dtl.DTLVardef@1658d6borg.highwire.dtl.DTLVardef@27a2e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2019

JMJD6 Cleaves MePCE to Release P-TEFb

More than 30% of genes in higher eukaryotes are regulated by promoter-proximal pausing of RNA polymerase II (Pol II). Phosphorylation of Pol II-CTD by positive transcription elongation factor (P-TEFb) is a necessary precursor event that enables productive transcription elongation. The exact mechanism on how the sequestered P-TEFb is released from the 7SK snRNP complex and recruited to Pol II-CTD remains unknown. In this report, we reveal methylphosphate capping enzyme (MePCE), a core component of the 7SK snRNP complex, as the cognate substrate for Jumonji domain-containing 6 (JMJD6)s novel proteolytic function. Our evidences consist of a crystal structure of JMJD6 bound to methyl-arginine, enzymatic assays of JMJD6 cleaving MePCE in vivo and in vitro, binding assays, and downstream effects of Jmjd6 knockout and overexpression on Pol II-CTD phosphorylation. We propose that JMJD6 assists bromodomain containing 4 (BRD4) to recruit P-TEFb to Pol II-CTD by disrupting the 7SK snRNP complex.

biochemistry↗

bioRxiv2019

Universal activation mechanism of class A GPCRs

Class A G protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. GPCR activation is an allosteric process that links agonist binding to G protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue-level changes of this trigger remain less well understood. Here, by analyzing over 230 high-resolution structures of class A GPCRs, we discovered a modular, universal GPCR activation pathway that unites previous findings into a common activation mechanism, directly linking the bottom of ligand-binding pocket with G protein-coupling region. We suggest that the modular nature of the universal GPCR activation pathway allowed for the decoupling of the evolution of the ligand binding site, G protein binding region and the residues important for receptor activation. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.

bioinformatics↗

bioRxiv2019

Molecular basis for allosteric regulation of the type 2 ryanodine receptor channel gating by key modulators

The type-2 ryanodine receptor (RyR2) is responsible for releasing Ca2+ from the sarcoplasmic reticulum of cardiomyocytes, subsequently leading to muscle contraction. Here, we report four cryo-EM structures of porcine RyR2 bound to distinct modulators that collectively provide mechanistic insight into RyR2 regulation. Ca2+ alone induces a contraction of the Central domain that facilitates the dilation of S6 bundle, but is insufficient to open the pore. The small molecule agonist PCB95 helps Ca2+ to overcome the barrier for opening. FKBP12.6 induces a relaxation of the Central domain that decouples it from the S6 bundle, stabilizing RyR2 in a closed state. Caffeine locks the Central domain in a constitutively contracted state, while further addition of ATP opens the channel by strengthening the coupling between the U-motif and S6. Our study marks an important step towards mechanistic understanding of the complicated regulation of this key channel whose aberrant activity engenders life-threatening cardiac disorders.

biochemistry↗

bioRxiv2019

Characters of neoantigens in cancer immunotherapy

Genetic mutations lead to the production of mutated proteins from which peptides are presented to T cells as cancer neoantigens. Evidence suggests that T cells that target neoantigens are the main mediators of effective cancer immunotherapies. Although algorithms have been used to predict neoantigens, only a minority are immunogenic. The factors that influence neoantigen immunogenicity are not completely understood. Here, we classified human neoantigen/neopeptide data into three categories based on their TCR-pMHC binding events. We observed a conservative mutant orientation of the anchor residue from immunogenic neoantigens which we termed the "NP" rule. By integrating this rule with an existing prediction algorithm, we found improved performance in neoantigen prioritization. To better understand this rule, we solved several neoantigen/MHC structures. These structures showed that neoantigens that follow this rule not only increase peptide-MHC binding affinity but also create new TCR-binding features. These molecular insights highlight the value of immune-based classification in neoantigen studies and may enable the design of more effective cancer immunotherapies.

cancer biology↗

bioRxiv2019

PALM-Seq: simultaneous sequencing of cell-free long RNA and small RNA

Cell-free RNA, including both long RNA and small RNA, has been considered important for its biological functions and potential clinical usage, but the major challenge is to effectively sequence them at the same time. Here we present PolyAdenylation Ligation Mediated-Seq (PALM-Seq), an integrated sequencing method for cell-free long and small RNA. Through terminal modification and addition of 3 polyadenylation and 5 adaptor, we could get mRNA, long non-coding RNA, microRNA, tRNA, piRNA and other RNAs in a single library. With target RNA depletion, all these RNAs could be sequenced with relatively low depth. Using PALM-Seq, we identified pregnant-related mRNAs, long non-coding RNAs and microRNAs in female plasma. We also applied PALM-Seq to sequence RNA from amniotic fluids, leukocytes and placentas, and could find RNA signatures associated with specific sample type. PALM-Seq provides an integrated, cost-effective and simple method to characterize the landscape of cell-free RNA, and can stimulate further progress in cell-free RNA study and usage.

molecular biology↗