Biology subjects

Yu, C.

Publications and source records attributed to Yu, C..

At least 199 records · Page 11Linked to original sources

bioRxiv2020

Structural dynamics of non-synonymous SNPs of histone methyltransferase EZH2 involved in Weaver Syndrome

Enhancer of zeste homolog 2 (EZH2) is a histone H3 lysine 27 methyltransferases. Non-synonymous SNPs (nsSNPs) in the ezh2 gene may cause Weaver Syndrome that is a prominent and rare congenital disorder. Several EZH2 genetic variants have been characterized and reported, but there is no information available on their structural dynamics. Our study employs an in silico approach for structural and functional characterization of EZH2 nsSNPs. We identified 19 EZH2 nsSNPs majorly associated with Weaver Syndrome, among which four SET-domain nsSNPs including V621M, A677T, R679C, and H689Y significantly affected EZH2 structure. We conducted the triplicate of 100 ns of molecular dynamics simulations (MDS) to compare the dynamic interaction behaviors between wild-type and mutants of EZH2 with their substrate, H3K27me0 peptide. The simulation results revealed that the mutants had higher levels of structural variations as evidenced by secondary structure, density, distance plots, and principal component analysis. Compared to EZH2-WT, the mutants A677T and H689Y have shown lower binding energy with H3K27me0 peptide due to the denaturing of 310 helixes as exemplified by MM/PBSA calculations and secondary structure analysis. Our analysis shed light on mechanisms of structural variations of EZH2 nsSNPs and lay a stone to develop mutant-based therapeutic strategies for the design of target-specific scaffolds against Weaver Syndrome.

molecular biology↗

bioRxiv2020

Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy

CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody-based agents targeting CD22 or CD20 (Rituxan) on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high-affinity and specific CD22 ligands onto NK-92MI and cytokine-induced killer (CIK) cells to achieve tumor-specific CD22 targeting. These CD22-ligand modified cells exhibited significantly enhanced tumor cell binding and killing in vitro without harming healthy B cells. For effective lymphoma cell killing in vivo we further functionalized CD22 ligand-modified NK-92MI cells with the E-selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The cells containing the ligands of both CD22 and selectins resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that NK cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively.

bioengineering↗

bioRxiv2020

Meta-analysis of the effects of sleep deprivation on depression in patients and animals

ObjectiveResearch on the antidepressant effects of sleep deprivation (SD) is lagging and has not produced completely uniform results in humans and animals. The present study aimed to reassess the effect of SD on patients and animals by meta-analysis based on updated research. MethodsWe searched PubMed, Embase and Cochrane Library for articles since the first relevant literature published up to June 10th, 2019. Data on sample characteristics, features of SD, and tests for depression were extracted. ResultsFourteen articles were included, eight on humans and six on animals. We found that when the duration of SD in patients was 7-14 days, it reflected antidepression [-1.52 (-2.07, -0.97); I2=19.6%]. In animals, the results of sucrose consumption experiments showed that SD has depressogenic effects [-1.06 (-1.63, -0.49); I2=81.1%], while the results of forced swimming experiments showed that SD treated depression [-1.17 (-2.19, -0.16); I2=80.1%], regardless of the duration of sleep deprivation. ConclusionSD can be an effective antidepressant measure when the duration is 7-14 days in patients. In animal studies, SD has shown more antidepressant effects when measured by forced swimming experiments, whereas using sucrose consumption tests had the effect of worsening depression.

neuroscience↗

bioRxiv2020

Interferon-γ signaling synergizes with LRRK2 in human neurons and microglia

Increasing evidence suggests a role for interferons (IFNs) in neurodegeneration. Parkinsons disease (PD) associated kinase LRRK2 has been implicated in IFN type II (IFN) response in infections and nigral neuronal loss. However, whether and how LRRK2 synergizes with IFN-{gamma} still remains unclear. Here, we employed dopaminergic (DA) neurons and microglia differentiated from patient induced pluripotent stem cells to unravel the role of IFN-{gamma} in LRRK2-PD. We show that IFN-{gamma} induces LRRK2 expression in both DA neurons and microglial cells. LRRK2-G2019S, the most common PD-associated mutation, sensitizes DA neurons to IFN-{gamma} by decreasing AKT phosphorylation. IFN-{gamma} suppresses NFAT activity in both neurons and microglia and synergistically enhances LRRK2-induced defects of NFAT activation. Furthermore, LRRK2-G2019S negatively regulates NFAT via calcium and microtubule dynamics. Importantly, we uncover functional consequences of the reduction of NFAT activity in both cell types, namely defects of neurite elongation and alteration of microglial activation profile and motility. We propose that synergistic IFN-{gamma}/LRRK2 activation serves as a direct link between inflammation and neurodegeneration in PD.

neuroscience↗

bioRxiv2020

Clinically applicable histopathological diagnosis system for gastric cancer detection using deep learning

Gastric cancer is among the most malignant tumours with the highest incidence and mortality rates. The early detection and accurate histopathological diagnosis of gastric cancer are essential factors that can help increase the chances of successful treatment. While the worldwide shortage of pathologists has imposed burdens on current histopathology services, it also offers a unique opportunity for the use of artificial intelligence assistance systems to alleviate the workload and increase diagnostic accuracy. To the best of our knowledge, there has not been a clinically applicable histopathological assistance system with high accuracy that can generalize to whole slide images created with diverse digital scanner models from different hospitals. Here, we report a clinically applicable artificial intelligence assistance system developed at the Chinese PLA General Hospital, China, using a deep convolutional neural network trained with 2,123 pixel-level annotated H&E-stained whole slide images. The model achieved a sensitivity near 100% and an average specificity of 80.6% on a real-world test dataset, which included 3,212 whole slide images digitalized with three scanner models. We showed that the system could aid pathologists in improving diagnostic accuracy and preventing misdiagnoses. Moreover, we demonstrated that our system could perform robustly with 1,582 whole slide images from two other medical centres. Our study suggests the feasibility and benefits of using histopathological artificial intelligence assistance systems in routine practice scenarios.Competing Interest StatementXiaoqing Zhang is the founder of Thorough Images. Shuhao Wang is the co-founder and chief technology officer (CTO) of Thorough Images. Calvin Ku, Cancheng Liu, Zhuo Sun, Gang Xu, Yuefeng Wang are algorithm researchers of Thorough Images. All remaining authors have declared no conflicts of interest.View Full Text

pathology↗

bioRxiv2020

Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex

DHTKD1 is the E1 component of the 2-oxoadipic acid dehydrogenase complex (OADHc), which functions in the L-lysine degradation pathway. Mutations in DHTKD1 have been associated with 2-aminoadipic and 2-oxoadipic aciduria, Charcot-Marie-Tooth disease type 2Q (CMT2Q) and eosinophilic esophagitis (EoE). A crystal structure and inhibitors of DHTKD1 could improve the understanding of these clinically distinct disorders, but are currently not available. Here we report the identification of adipoylphosphonic acid and tenatoprazole as DHTKD1 inhibitors using targeted and high throughput screening, respectively. We furthermore elucidate the DHTKD1 crystal structure with thiamin diphosphate bound at 2.1 [A]. The protein assembles as a dimer with residues from both monomers contributing to cofactor binding. We also report the impact of ten DHTKD1 missense mutations on the encoded proteins by enzyme kinetics, thermal stability and structural modeling. Some DHTKD1 variants displayed impaired folding (S777P and S862I), whereas other substitutions rendered the enzyme inactive (L234G, R715C and R455Q) or affected the thermal stability and catalytic efficiency (V360A and P773L). Three variants (R163Q, Q305H and G729R) surprisingly showed wild type like properties. Our work provides a structural basis for further understanding of the function of DHTKD1 and a starting point for selective small molecule inhibitors of the enzyme, which could help tease apart the role of this enzyme in several human pathologies.

biochemistry↗

bioRxiv2019

hFUT1-based live cell assay to profile α1-2-fucosides enhanced influenza A virus infection

Host cell-surface glycans play critical roles in influenza A virus (IAV) infection ranging from modulation of IAV attachment to membrane fusion and host tropism. Approaches for quick and sensitive profiling of the viral avidity towards a specific type of host-cell glycan can contribute to the understanding of tropism switching among different strains of IAV. In this study, we developed a method based on chemoenzymatic glycan engineering to investigate the possible involvement of 1-2-fucosides in IAV infections. Using a truncated human fucosyltransferase 1 (hFuT1), we were able to create 1-2-linked fucosides in situ on the host cell surface to assess their influence on the host cell binding to IAV hemagglutinin and the susceptibility of host cells toward IAV induced killing. We discovered that the newly added 1-2-fucosides on host cells enhanced the infection of several human pandemic IVA subtypes. These findings suggest that glycan epitopes other than sialic aicds should be taken into consideration for assessing the human pandemic risk of this viral pathogen.

biochemistry↗

bioRxiv2019

Lipid-mediated insertion of Toll-like receptor (TLR) ligands for facile immune cell engineering

Cell-based immunotherapies have tremendous potential to treat many diseases, such as activating immunity in cancer or suppressing it in autoimmune diseases. Most cell-based cancer immunotherapies in the clinic provide adjuvant signals through genetic engineering to enhance T cell functions. However, genetically encoded signals have minimal control over dosing and persist for the life of a cell lineage. These properties make it difficult to balance increasing therapeutic efficacy with reducing toxicities. Here, we demonstrated the potential of phospholipid-coupled ligands as a non-genetic system for immune cell engineering. This system provides simple, controlled, non-genetic adjuvant delivery to immune cells via lipid-mediated insertion into plasma membranes. Lipid-mediated insertion (depoting) successfully delivered Toll-like receptor (TLR) ligands intracellularly and onto cell surfaces of diverse immune cells. These ligands depoted into immune cells in a dose-controlled fashion and did not compete during multiplex pairwise loading. Immune cell activation could be enhanced by autocrine and paracrine mechanisms depending on the biology of the TLR ligand tested. We determined that depoted ligands can functionally persist on plasma membranes for up to four days in naive and activated T cells, enhancing their activation, proliferation, and skewing cytokine secretion. Depoted ligands provide a persistent yet non-permanent adjuvant signal to immune cells that may minimize the intensity and duration of toxicities compared to permanent genetic delivery. Altogether, these findings demonstrate potential for lipid-mediated insertion (depoting) as a universal cell engineering approach with unique, complementary advantages to other cell engineering methods.

immunology↗

bioRxiv2019

Comprehensive molecular characterization of PRKCG for glioma diagnosis, prognosis and treatment prediction

Glioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies have led to massive multi-omics datasets, there lacks of comprehensive integration of glioma datasets for uncovering candidate biomarker genes. In this study, we collected a large-scale assemble of multi-omics multi-cohort datasets from worldwide public resources, involving a total of 16,939 samples across 19 independent studies. Through comprehensive multi-omics molecular profiling across different datasets, we revealed that PRKCG (Protein Kinase C Gamma), a brain-specific gene detectable in cerebrospinal fluid, is closely associated with glioma. Specifically, it presents lower expression and higher methylation in glioma samples compared with normal samples. PRKCG expression/methylation change from high to low is indicative of glioma progression from low-grade to high-grade and high RNA expression is suggestive of good survival. Importantly, PRKCG in combination with MGMT is effective to predict survival outcomes after TMZ chemotherapy in a more precise manner. Collectively, PRKCG bears the great potential for glioma diagnosis, prognosis and therapy, and PRKCG-like genes may represent a set of important genes associated with different molecular mechanisms in glioma tumorigenesis. Accordingly, our study indicates the importance of computational integrative multi-omics data analysis and represents a data-driven scheme toward precision tumor subtyping and accurate personalized healthcare. Author SummaryGlioma is a type of brain tumors that represents one of the most lethal human malignancies with little chance for recovery. Nowadays, more and more studies have adopted high-throughput sequencing technologies to decode the molecular profiles of glioma from different omics levels, accordingly resulting in massive glioma datasets generated from different projects and laboratories throughout the world. Therefore, it has become crucially important on how to make full use of these valuable datasets for computational identification of glioma candidate biomarker genes in aid of precision tumor subtyping and accurate personalized treatment. In this study, we comprehensively integrated glioma datasets from all over the world and performed multi-omics molecular data mining. We revealed that PRKCG, a brain-specific gene abundantly expressed in cerebrospinal fluid, bears the great potential for glioma diagnosis, prognosis and treatment prediction, which has been consistently observed on multiple independent datasets. In the era of big data, our study highlights the significance of computational integrative data mining toward precision medicine in cancer research.

bioinformatics↗

bioRxiv2019

Perceptual learning evidence for an interval- and modality invariant representation of subsecond time

A central theme in time perception research is whether subsecond timing relies on a dedicated centralized clock, or on distributed neural temporal dynamics. A fundamental constraint is the interval- and modality-specificity in perceptual learning of temporal interval discrimination (TID), which argues against a dedicated centralized clock, but is more consistent with multiple distributed mechanisms. Here we demonstrated an abstract, interval- and modality-invariant, representation of subsecond time in the brain. Participants practiced TID at a specific interval (100 ms), and received exposure to a transfer interval (200 ms), or to a different auditory/visual modality, through training of an orthogonal task. This double training enabled complete transfer of TID learning to the untrained interval, and mutual complete transfer between visual and auditory modalities. These results demonstrate an interval- and modality-invariant representation of subsecond time, which resembles a centralized clock, on top of the known distributed timing mechanisms and their readout and integration.

neuroscience↗

bioRxiv2019

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

O_LIPlants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24-hour period, enabling the anticipation of these events. C_LIO_LIWe used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. C_LIO_LIApproximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore we identified sequence motifs enriched in the promoters of similarly-phased genes, some potentially associated with transcription factors. C_LIO_LIWhen considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species. C_LI

plant biology↗

bioRxiv2019

Labeling proteins within Drosophila embryos by combining FRET reporters, position-specific genomic integration, and GAL4-reponsive expression

Protein interaction network (PIN) or interactome has been mapped vigorously for the entire genome. We recognize, nonetheless, that such a map could illuminate profound insights had its context been revealed. We describe a scalable protein lableling method that could re-supply natural context back to the map of protein interactome. Genetically encoded fluorescent proteins, position-specific genomic integration and GAL4-responsive expression control enable labeling proteins A, B and C each with a either an eGFP, mCherry or NirFP in specified cells of optically transparent animals such as Drosophila embryos. While following multiple proteins through development and behavior, these labels offer separable pairs of Forster resonance energy transfer between proteins A and B and proteins B and C. We test and observe FRET interactions between specific protein pairs controlling cytoskeleton, nuclear signaling and cell polarity. By using our protein labeling method, it will be possible to map protein interaction network in situ -- isPIN.

developmental biology↗

bioRxiv2019

Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living Cells

Visualizing the real-time dynamics of genome rearrangement in single living cells is core to studying genomics and diagnostics. Here, we report a robust, versatile approach named CRISPR Live-cell fluorescent in situ hybridization (LiveFISH) for multi-locus genome tracking and cytogenetic detection in a broad variety of cell types including primary cells. LiveFISH utilizes an intrinsic stability switch of CRISPR guide RNAs, which enables efficient and accurate detection of chromosomal disorders such as Patau Syndrome in prenatal amniotic fluid cells and allows multi-locus tracking in human T lymphocytes. Using LiveFISH, we are able to detect and track real-time spatiotemporal dynamics of non-homologous endogenous chromosome translocations induced by gene editing. This new approach enables FISH imaging in living primary cells, which can provide useful insights into the spatiotemporal changes of genome organization and rearrangements in normal and diseased primary cells and will enable fast cytogenetic visualization of various gene-editing associated chromosomal translocations.

bioengineering↗

bioRxiv2019

Detecting genotype-population interaction effects by ancestry principal components

Heterogeneity in the phenotypic mean and variance across populations is often observed for complex traits. One way to understand heterogeneous phenotypes lies in uncovering heterogeneity in genetic effects. Previous studies on genetic heterogeneity across populations were typically based on discrete groups of population stratified by different countries or cohorts, which ignored the difference of population characteristics for the individuals within each group and resulted in loss of information. Here we introduce a novel concept of genotype-by-population (GxP) interaction where population is defined by the first and second ancestry principal components (PCs), which are less likely to be confounded with country/cohort-specific factors. We applied a reaction norm model fitting each of 70 complex traits with significant SNP-heritability and the PCs as covariates to examine GxP interactions across diverse populations including white British and other white Europeans from the UK Biobank (N = 22,229). Our results demonstrated a significant population genetic heterogeneity for behavioural traits such as age first had sexual intercourse and qualifications. Our approach may shed light on the latent genetic architecture of complex traits that underlies the modulation of genetic effects across different populations.

genetics↗

bioRxiv2019

Discovery and Multi-center Verification of Prostate Cancer Protein Biomarkers using Single-shot Short Gradient Microflow SWATH and MRMHR Mass Spectrometry

We report and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in clinical specimens. The method uses 15-min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration and OpenSWATH software for data analysis.\n\nWe applied the method to a cohort 204 of FFPE prostate tissue samples from 58 prostate cancer patients and 10 prostatic hyperplasia patients. Altogether we identified 27,976 proteotypic peptides and 4,043 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with 2-hour gradient the accelerated method consumed only 27% instrument time, quantified 80% proteins and showed reduced batch effects. 3,800 proteins were quantified by both methods in two different instruments with relatively high consistency (r = 0.77). 75 proteins detected by the accelerated method with differential abundance between clinical groups were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, exhibiting high quantitative consistency with the 15-min SWATH method (r = 0.89) in the same sample set. We further verified the capacity of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n=154).\n\nOverall our data show that the single-shot short gradient microflow-LC SWATH MS method achieved about 4-fold acceleration of data acquisition with reduced batch effect and a moderate level of protein attrition compared to a standard SWATH acquisition method. Finally, the results showed comparable ability to separate clinical groups.

cancer biology↗

bioRxiv2019

DHTKD1 and OGDH display in vivo substrate overlap and form a hybrid ketoacid dehydrogenase complex

Glutaric aciduria type 1 (GA1) is an inborn error of lysine degradation characterized by a specific encephalopathy that is caused by toxic accumulation of lysine degradation intermediates. Substrate reduction through inhibition of DHTKD1, an enzyme upstream of the defective glutaryl-CoA dehydrogenase, has been investigated as a potential therapy, but revealed the existence of an alternative enzymatic source of glutaryl-CoA. Here we show that loss of DHTKD1 in GCDH-deficient HEK-293 cells leads to a 2-fold decrease in the established GA1 clinical biomarker glutarylcarnitine, and demonstrate that OGDH is responsible for this remaining glutarylcarnitine production. We furthermore show that DHTKD1 interacts with OGDH, DLST and DLD to form a hybrid -ketoglutaric and -ketoadipic acid dehydrogenase complex. In summary, -ketoadipic acid is an in vivo substrate for DHTKD1, but also OGDH. The classic -ketoglutaric dehydrogenase complex can exist as a previously undiscovered hybrid containing DHTKD1 displaying improved kinetics towards -ketoadipic acid.

biochemistry↗

bioRxiv2019

Deep-learning enables proteome-scale identification of phase-separated protein candidates from immunofluorescence images

Intrinsically disordered region (IDR) analysis has been widely used in the screening of phase-separated proteins. However, the precise sequences determining phase separation remain unclear. Furthermore, a large number of phase-separated proteins that exhibit relatively low IDR content remain uncharacterized. Phase-separated proteins appear as spherical droplet structures in immunofluorescence (IF) images, which renders them distinguishable from non-phase-separated proteins. Here, we transformed the problem of phase-separated protein recognition into a binary classification problem of image recognition. In addition, we established a method named IDeepPhase to identify IF images with spherical droplet structures based on convolutional neural networks. Using IDeepPhase on proteome-scale IF images from the Human Protein Atlas database, we generated a comprehensive list of phase-separated candidates which displayed spherical droplet structures in IF images, allowing nomination of proteins, antibodies and cell lines for subsequent phase separation study.

bioinformatics↗

bioRxiv2019

Cellular precision of orientation and spatial frequency maps in macaque V1

Functional organization of neuronal response properties along the surface of the neocortex is a fundamental guiding principle of neural computation in the brain. Despite this importance, the cellular precision of functional maps is still largely unknown. We address the challenge by using two-photon calcium imaging to measure cell-specific orientation and spatial frequency (SF) responses across fields of macaque V1 superficial layers. The cellular orientation maps confirm iso-orientation domains, but rarely show pinwheels. Pinwheels obtained through conventional Gaussian smoothing and vector summation of orientation responses mostly overlap with blood vessel regions, suggesting false singularities. Cellular SF maps clarify existing controversies by showing weak iso-frequency clusters, which also suggests a weak geometric relationship between orientation and SF maps. Most neurons are tuned to medium frequencies, but the tuning functions are often asymmetric with a wider low- or high-frequency branch, which may help encode low or high SF information for later decoding.

neuroscience↗