A5080893365- Single-cell and spatial transcriptomics
- Alzheimer's disease research and treatments
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Cancer Immunotherapy and Biomarkers
- Health, Environment, Cognitive Aging
- Advanced Measurement and Metrology Techniques
- S100 Proteins and Annexins
- Glioma Diagnosis and Treatment
- RNA modifications and cancer
- Neuroinflammation and Neurodegeneration Mechanisms
- Cancer-related molecular mechanisms research
- Immune cells in cancer
- Immune Cell Function and Interaction
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Gene Regulatory Network Analysis
- Cancer Genomics and Diagnostics
- Ferroptosis and cancer prognosis
- Cell Image Analysis Techniques
- Dementia and Cognitive Impairment Research
- Molecular Biology Techniques and Applications
- Vascular Malformations Diagnosis and Treatment
- Kruppel-like factors research
- MicroRNA in disease regulation
The Ohio State University
2020-2024
Beijing Institute of Neurosurgery
2020-2024
Capital Medical University
2018-2024
Shanghai Institute of Measurement and Testing Technology
2022-2024
Beth Israel Deaconess Medical Center
2024
Mayo Clinic in Arizona
2024
The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute
2022-2023
Beijing Tian Tan Hospital
2019-2023
Mayo Clinic
2023
Shanghai Jiao Tong University
2018-2021
Abstract Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, complex diseases, but its analyses still suffer from multiple grand challenges, including sequencing sparsity differential patterns in gene expression. We introduce scGNN (single-cell graph neural network) provide a hypothesis-free deep learning framework for scRNA-Seq analyses. This formulates aggregates cell–cell relationships with networks models heterogeneous...
Sex bias exists in the development and progression of nonreproductive organ cancers, but underlying mechanisms are enigmatic. Studies so far have focused largely on sexual dimorphisms cancer biology socioeconomic factors. Here, we establish a role for CD8+ T cell-dependent antitumor immunity mediating sex differences tumor aggressiveness, which is driven by gonadal androgen not chromosomes. A male frequency intratumoral antigen-experienced Tcf7/TCF1+ progenitor exhausted cells that devoid...
Abstract Background The prognosis for diffuse gliomas is very poor and the mechanism underlying their malignant progression remains unclear. Here, we aimed to elucidate role of RNA N 6,2′- O -dimethyladenosine (m 6 A) reader, YTH 6-methyladenosine binding protein 2 (YTHDF2), in regulating gliomas. Methods YTHDF2 mRNA levels functions were assessed using several independent datasets. Western blotting, quantitative polymerase chain reaction, immunohistochemistry used evaluate expression other...
Abstract Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities simultaneously to capture intricacy complex molecular mechanisms and cellular heterogeneity. Existing tools cannot effectively infer active biological networks in diverse cell types response these external stimuli. Here we present DeepMAPS for network inference from scMulti-omics. It models scMulti-omics a heterogeneous graph learns relations among cells genes within both local global contexts...
Abstract Regulatory T (Treg) cells are essential for maintaining immune homeostasis and tolerance, but the mechanisms regulating stability function of Treg have not been fully elucidated. Here we show SUMO-specific protease 3 (SENP3) is a pivotal regulator that functions by controlling SUMOylation nuclear localization BACH2. cell-specific deletion Senp3 results in cell activation, autoimmune symptoms enhanced antitumor responses. SENP3-mediated BACH2 deSUMOylation prevents export BACH2,...
Abstract Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimer’s disease (AD), but little known about the molecular mechanisms underlying this regional vulnerability. Here we utilize 10 × Visium platform to define spatial transcriptomic profile both AD and control (CT) MTG. We identify unique marker genes for cortical layers white matter, layer-specific differentially expressed (DEGs) human compared CT. Deconvolution of spots showcases significant difference...
Abstract Due to the rare incidence of spinal cord astrocytomas, their molecular features remain unclear. Here, we characterized landscapes mutations in H3 K27M, isocitrate dehydrogenase 1 ( IDH1 ) R132H, BRAF V600E, and TERT promoter 83 diffuse astrocytic tumors. Among these samples, thirty-five patients had K27M mutation; this mutant could be observed histological grade II (40%), III IV (20%) astrocytomas. were absent 58 cases tested. The V600E mutation (7/57) was only H3-wildtype...
O6methylguanine-DNA methyltransferase (MGMT) promoter methylation is a biomarker widely used to predict the sensitivity of IDH-wildtype glioblastoma temozolomide therapy. Given that IDH status has critical effects on survival and epigenetic features glioblastoma, we aimed assess role MGMT in IDH-mutant glioblastoma.This study included 187 glioblastomas 173 for comparison. Kaplan-Meier curves multivariate Cox regression were predictive effects.Compared with glioblastomas, showed significantly...
Spatially resolved transcriptomics provides a new way to define spatial contexts and understand the pathogenesis of complex human diseases. Although some computational frameworks can characterize context via various clustering methods, detailed architectures functional zonation often cannot be revealed localized due limited capacities associating information. We present RESEPT, deep-learning framework for characterizing visualizing tissue architecture from spatially transcriptomics. Given...
Abstract Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) through direct lysis of infected lung epithelial cells, which releases damage-associated molecular patterns and induces a pro-inflammatory cytokine milieu causing systemic inflammation. Anti-viral anti-inflammatory agents have shown limited therapeutic efficacy. Soluble CD24 (CD24Fc) blunts the broad inflammatory response induced by via binding to extracellular high...
Abstract Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression corresponding spatial coordinates two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results often cannot handle three-dimensional transcriptomic data. Here we introduce BSP (big-small patch), a non-parametric model...
Intratumoral regulatory T cells (Tregs) are key mediators of cancer immunotherapy resistance, including anti-PD-(L)1 immune checkpoint blockade (ICB). The mechanisms driving Treg infiltration into the tumor microenvironment (TME) and consequence on CD8+ cell exhaustion remains elusive. Herein, we report that heat shock protein gp96 (GRP94) is indispensable for infiltration, primarily through gp96's roles in chaperoning integrins. Among various gp96-dependent integrins, found only LFA-1 (αL...
Spatial omics technologies decipher functional components of complex organs at cellular and subcellular resolutions. We introduce Graph Fourier Transform (SpaGFT) apply graph signal processing to a wide range spatial profiling platforms generate their interpretable representations. This representation supports spatially variable gene identification improves expression imputation, outperforming existing tools in analyzing human mouse transcriptomics data. SpaGFT can identify immunological...
Metabolic programs are crucial for regulatory T (T reg) cell stability and function, but the underlying mechanisms that regulate reg metabolism elusive. Here, we report lysosomal TRAF3IP3 acts as a pivotal regulator in maintenance of metabolic fitness. reg–specific deletion Traf3ip3 impairs causing development inflammatory disorders stronger antitumor responses mice. Excessive mechanistic target rapamycin complex 1 (mTORC1)–mediated hyper-glycolytic is responsible instability...
Abstract 1p/19q codeletion, which leads to the abnormal expression of 1p19q genes in oligodendroglioma, is associated with chemosensitivity and favorable prognosis. Here, we aimed explore clinical implications gene non-codel gliomas. We analyzed 668 gliomas obtained from The Cancer Genome Atlas (n = 447) Chinese Glioma 221) for training validation, respectively. was significantly correlated clinicopathological features overall survival Then, derived a risk signature 25 selected that not only...
A group of genes controlled as a unit, usually by the same repressor or activator gene, is known regulon. The ability to identify active regulons within specific cell type, i.e., cell-type-specific (CTSR), provides an extraordinary opportunity pinpoint crucial regulators and target responsible for complex diseases. However, identification CTSRs from single-cell RNA-Seq (scRNA-Seq) data computationally challenging. We introduce IRIS3, first-of-its-kind web server CTSR inference scRNA-Seq...
Based on the calibration method of scanning electron microscope length measurement error based equidistant grid standard template, establish an evaluation model for uncertainty and analyze sources various uncertainties. examples, this paper elaborates process evaluating indication in microscopy templates, calculates its extended uncertainty, provides a reference templates.
Propose a length measurement error calibration method for X-ray 3D dimension measuring machine based on forest sphere. Based the of balls, establish an evaluation model uncertainty and analyze sources various uncertainties. examples, this paper elaborates process evaluating calculates its extended uncertainty, provides reference machine.
The Monte Carlo Method (MCM) is a method of evaluating measurement uncertainty by using random sampling probability distributions for distribution propagation. discrete the density function (PDF) input quantity key and difficult step in method. This article proposes based on EXCEL software analyzing functions their corresponding cumulative relationships typical types such as normal distribution, rectangular triangular trapezoidal arcsine develops an application program. experimental...