Biology subjects

Qian, X.

Publications and source records attributed to Qian, X..

84 records · Page 5Linked to original sources

bioRxiv2020

Co-expression signatures of combinatorial gene regulation

Gene co-expression analyses provide a powerful tool to determine gene associations. The interaction of transcription factors (TFs) with their target genes is an essential step in gene regulation, yet to what extent TFs-target gene associations are recovered in co-expression studies remains unclear. Using the wealth of data available for Arabidopsis, we show here that protein-DNA interactions are overall poor indicators of TF-target co-expression, yet the inclusion of TF-TF interaction information significantly enhance co-expression signals. These results highlight the impact of combinatorial gene control on such gene association networks. We integrated this information to predict higher-order regulatory complexes, which are difficult to identify experimentally. We demonstrate that genes strongly co-expressed with a TF are also enriched in indirect targets. Our results have significant implications on the empirical understanding of complex gene regulatory networks and transcription factor function, and the significance of co-expression from the perspective of protein-protein and protein-DNA interactions.

systems biology↗

bioRxiv2020

SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections

Changes in cell identities and positions underlie tissue development and disease progression. Although, single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell-states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single Cell Resolution IN Situ Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRISHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity and quantitative qualities of SCRINSHOT facilitate single cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions.

molecular biology↗

bioRxiv2020

Hybridization-based In Situ Sequencing (HybISS): spatial transcriptomic detection in human and mouse brain tissue

Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional dimension to investigate spatial cell typing and cell atlases, disease architecture or even data driven discoveries. The field of spatially resolved transcriptomic technologies is emerging as a vital tool to profile gene-expression, continuously pushing current methods to accommodate larger gene panels and larger areas without compromising throughput efficiency. Here, we describe a new version of the in situ sequencing (ISS) method based on padlock probes and rolling circle amplification. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes with high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. Here we present hybridization-based in situ sequencing (HybISS) that allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a target amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.

molecular biology↗

bioRxiv2019

Spatial and temporal transcriptomics reveal microglia-astroglia crosstalk in the amyloid-β plaque cell niche of Alzheimer’s disease

The linear cause-consequence relationship linking amyloid-{beta} peptide (A{beta}) accumulation to neuronal dysfunction in Alzheimer disease (AD) is gradually replaced by the concept that A{beta} initiates complex inflammatory-like cellular alterations that progressively become A{beta} independent and lead to brain dyshomeostasis. Little is known about the pathophysiology of this cellular phase of AD. We use here two orthogonal technologies, Spatial Transcriptomics and in situ sequencing, to analyse the transcriptome changes in cells in the amyloid-{beta} plaque niche in a knock-in mouse model for AD. We identify a multicellular co-expressed gene network of 57 Plaque-Induced Genes (PIGs) that define a series of co-ordinated and spatially restricted microglia, astroglia and oligodendrocyte responses to progressing amyloid plaques encompassing complement, oxidative stress and inflammation. A separate oligodendrocyte network suggests abnormal myelination. Spatial Transcriptomics provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.

neuroscience↗

bioRxiv2019

Numerical simulation for behind armor blunt trauma of human torso under non-penetrating ballistic impact

A human torso finite element model with high bio-fidelity was developed to study the behind armor blunt trauma (BABT) of pistol cartridge on human torso with bulletproof composite structure (BCS) and the effect of buffer layer (expandable polyethylene, EPE) on BABT. The bulletproof structure was made of multilayered composite of aluminum alloy (AlSi10Mg) and thermoplastic polyurethanes (TPU), and the ANSYS/LS-DYNA software was used to simulate the blunt ballistic impact process of pistol cartridge on human torso. Results indicated that the BCS could resist the shooting speed of 515 m/s without being broken. During the process of pistol cartridge shooting the BCS, the energy of pistol cartridge was transmitted to the human organs through the BCS, thereby causing human injury. Moreover, the mechanical response parameters of various organs were determined by the distance between the human organs and the impact point. The sternal fracture and liver rupture were not produced based on the threshold stress of sternum and liver injury, no matter whether the buffer layer was added or not. According to the Axelsson injury model, a slight to moderate injury was created when there was no buffer layer, but the injury level was trace to slight caused by the buffer layer with thickness of 1.0 mm, and the buffer layer with thickness of 2.5 mm and 5.0 mm caused subtle BABT. It was concluded that the buffer layer could effectively reduce the BABT, and the reduction was related to the thickness of the buffer layer. This study reveals the mechanism of the BABT, which can provide a theoretical basis for the design of the bulletproof structure and the evaluation of structural bulletproof performance and protection performance.

bioengineering↗

bioRxiv2019

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

Granulomas are the pathological hallmark of Tuberculosis (TB), and the niche in which bacilli can either grow and disseminate or the immunological microenvironment in which host cells interact to prevent bacterial dissemination. Here, after in situ sequencing, thirty-four immune transcripts in lung sections from Mycobacterium tuberculosis-infected mice were aligned to the tissue morphology at cellular resolution, allowing the analysis of local immune interactions in the granuloma.\n\nCo-localizing transcript networks at <10 m in C57BL/6 mouse granulomas increased in complexity with time after infection. B-cell clusters developed late after infection. Transcripts from activated macrophages were enriched at subcellular distances from M. tuberculosis. Encapsulated C3HeB/FeJ granulomas showed necrotic centers with transcripts associated with immunosuppression (foxp3, il10), while those in the granuloma rims associated with activated T cells and macrophages. Highly diverse networks with common interactors were observed in similar lesions.\n\nThus, different immune landscapes of M. tuberculosis granulomas depending on the time after infection, the histopathological features of the lesion and the proximity to bacteria were here defined.

immunology↗

bioRxiv2018

Pan-cancer analysis on microRNA-mediated gene activation

While microRNAs (miRNAs) were widely considered to repress target genes at mRNA and/or protein levels, emerging evidence from in vitro experiments has shown that miRNAs can also activate gene expression in particular contexts. However, this counterintuitive observation has rarely been reported or interpreted in in vivo conditions. We systematically explored the positive correlation between miRNA and gene expressions and its potential implications in tumorigenesis, based on 8375 patient samples across 31 major human cancers from The Cancer Genome Atlas (TCGA). Results indicated that positive miRNA-gene correlations are surprisingly prevalent and consistent across cancer types, and show distinct patterns than negative correlations. The top-ranked positive correlations are significantly involved in the immune cell differentiation and cell membrane signaling related processes, and display strong power in stratifying patients in terms of survival rate, demonstrating their promising clinical relevance. Although intragenic miRNAs generally tend to co-express with their host genes, a substantial portion of miRNAs shows no obvious correlation with their host gene due to non-conservation. A miRNA can upregulate a gene by inhibiting its upstream suppressor, or shares transcription factors with that gene, both leading to positive correlation. The miRNA/gene sites associated with the top-ranked positive correlations are more likely to form super-enhancers compared to randomly chosen pairs, suggesting a potential epigenetics mechanism underlying the upregulation. Wet-lab experiments revealed that positive correlations partially remain in the in vitro condition. Our study provides the field with new perspectives on the critical role of miRNA in gene regulation and novel insights regarding the complex mechanisms underlying miRNA functions, and reveals the clinical significance of the potential positive regulation of gene expression by miRNA.

bioinformatics↗

bioRxiv2018

A spatial atlas of inhibitory cell types in mouse hippocampus

Understanding the function of a tissue requires knowing the spatial organization of its constituent cell types. In the cerebral cortex, single-cell RNA sequencing (scRNA-seq) has revealed the genome-wide expression patterns that define its many, closely related cell types, but cannot reveal their spatial arrangement. Here we introduce probabilistic cell typing by in situ sequencing (pciSeq), an approach that leverages prior scRNA-seq classification to identify cell types using multiplexed in situ RNA detection. We applied this method to map the inhibitory neurons of hippocampal area CA1, a cell system critical for memory function, for which ground truth is available from extensive prior work identifying the laminar organization of subtly differing cell types. Our method confidently identified 16 interneuron classes, in a spatial arrangement closely matching ground truth. This method will allow identifying the spatial organization of fine cell types across the brain and other tissues.

neuroscience↗

bioRxiv2018

Tenuivirus uses a molecular bridge strategy to overcome insect midgut barriers for virus persistent transmission

Many persistent transmitted plant viruses, including Rice stripe tenuivirus (RSV), cause serious damages to crop productions in China and worldwide. Although many reports have indicated that successful insect-mediated virus transmission depends on proper virus-insect vector interactions, the mechanism(s) controlling interactions between viruses and insect vectors for virus persistent transmission remained poorly understood. In this study, we used RSV and its small brown planthopper (SBPH) vector as a working model to elucidate the molecular mechanism controlling RSV virion entrance into SBPH midgut for persistent transmission. We have now demonstrated that this non-enveloped Tenuivirus uses its non-structural glycoprotein NSvc2 as a helper component to bridge the specific interaction between virion and SBPH midgut cells, leading to overcome SBPH midgut barriers for virus persistent transmission. In the absence of this glycoprotein, purified RSV virion is not capable of entering SBPH midgut cells. In RSV-infected cells, glycoprotein NSvc2 is processed into two mature proteins: an amino-terminal protein NSvc2-N and a carboxyl-terminal protein NSvc2-C. We determined that NSvc2-N interacted with RSV virion and bound directly to midgut lumen surface via its N-glycosylation sites. Upon recognition by midgut cells, the midgut cells underwent endocytosis followed by compartmentalizing RSV virion and NSvc2 into early and then late endosomes. The acidic condition inside the late endosome triggered conformation change of NSvc2-C and caused cell membrane fusion via its highly conserved fusion loop motifs, leading to the release of RSV virion from endosome into cytosol. In summary, our results showed for the first time that a rice Tenuivirus uses a molecular bridge strategy to ensure proper interactions between virus and insect midgut for successful persistent transmission.\n\nAuthor summaryOver 75% of the known plant viruses are insect transmitted. Understanding how plant viruses interacted with their insect vectors during virus transmission is one of the key steps to manage virus diseases worldwide. Both the direct and indirect virus-insect vector interaction models have been proposed for virus non-persistent and semi-persistent transmission. However, the indirect virus-vector interaction mechanism during virus persistent transmission has not been reported previously. In this study, we developed a new reverse genetics technology and demonstrated that the circulative and propagative transmitted Rice stripe tenuivirus utilizes a glycoprotein NSvc2 as a helper component to ensure a specific interaction between Tenuivirus virion and midgut cells of small brown planthopper (SBPH), leading to conquering the midgut barrier of SBPH. This is the first report of a helper component mediated-molecular bridge mechanism for virus persistent transmission. These new findings and our new model on persistent transmission expand our understanding of molecular mechanism(s) controlling virus-insect vector interactions during virus transmission in nature.

pathology↗

bioRxiv2018

Radiogenomics-based Risk Prediction of Glioblastoma Multiforme with Clinical Relevance

GBM is the most common and aggressive primary brain tumor. Although the TMZ-based radiochemotherapy improves overall GBM patients survival, it also increases the frequency of false positive post-treatment magnetic resonance imaging (MRI) assessments for tumor progression. Pseudoprogression is a treatment-related reaction with an increase in contrast-enhancing lesion size at the tumor site or resection margins which mimics tumor recurrence on MRI. Accurate and reliable prognostication of GBM progression is urgently needed in the clinical management of GBM patients. Clinical data analysis indicates that the patients with PsP had superior overall and progression-free survival rates. In this study, we aimed to develop a prognostic model to evaluate tumor progression potential of GBM patients following standard therapies. We applied a dictionary learning scheme to obtain imaging features of GBM patients with PsP or TTP from the Wake dataset. Based on these radiographic features, we then conducted radiogenomics analysis to identify the significantly associated genes. These significantly associated genes were then used as features to construct a 2YS logistic regression model. GBM patients were classified into low-and high-survival risk groups based on the individual 2YS scores derived from this model. We tested our model using an independent TCGA dataset and found that 2YS scores were significantly associated with the patients overall survival. We further used two cohorts of the TCGA data to train and test our model. Our results show that 2YS scores-based classification results from the training and testing TGCA datasets were significantly associated with the overall survival of patients. We also analyzed the survival prediction ability of other clinical factors (gender, age, KPS, normal cell ratio) and found that these factors were not related or weakly correlated with patients survival. Overall, our studies have demonstrated the effectiveness and robustness of the 2YS model in predicting clinical outcomes of GBM patients after standard therapies.

bioinformatics↗

bioRxiv2018

LFAQ: towards unbiased label-free absolute protein quantification by predicting peptide quantitative factors

Mass spectrometry (MS) has become a prominent choice for large-scale absolute protein quantification, but its quantification accuracy still has substantial room for improvement. A crucial issue is the bias between the peptide MS intensity and the actual peptide abundance, i.e., the fact that peptides with equal abundance may have different MS intensities. This bias is mainly caused by the diverse physicochemical properties of peptides. Here, we propose a novel algorithm for label-free absolute protein quantification, LFAQ, which can correct the biased MS intensities by using the predicted peptide quantitative factors for all identified peptides. When validated on datasets produced by different MS instruments and data acquisition modes, LFAQ presented accuracy and precision superior to those of existing methods. In particular, it reduced the quantification error by an average of 46% for low-abundance proteins.

bioinformatics↗

bioRxiv2017

DNA 5-Hydroxymethylcytosines from Cell-free Circulating DNA as Diagnostic Biomarkers for Human Cancers

DNA modifications such as 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) are epigenetic marks known to affect global gene expression in mammals(1, 2). Given their prevalence in the human genome, close correlation with gene expression, and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology(3), we report here genome-wide 5hmC profiling in circulating cell-free DNA (cfDNA) and in genomic DNA of paired tumor/adjacent tissues collected from a cohort of 90 healthy individuals and 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver, or thyroid cancer. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-associated 5hmC signatures in cfDNA were identified with specificity for different cancers. 5hmC-based biomarkers of circulating cfDNA demonstrated highly accurate predictive value for patients with colorectal and gastric cancers versus healthy controls, superior to conventional biomarkers, and comparable to 5hmC biomarkers from tissue biopsies. This new strategy could lead to the development of effective blood-based, minimally-invasive cancer diagnosis and prognosis approaches.

cancer biology↗