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
- Advanced Measurement and Metrology Techniques
- Glioma Diagnosis and Treatment
- S100 Proteins and Annexins
- Health, Environment, Cognitive Aging
- RNA modifications and cancer
- Neuroinflammation and Neurodegeneration Mechanisms
- Immune Cell Function and Interaction
- Cancer-related molecular mechanisms research
- Immune cells in cancer
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Gene Regulatory Network Analysis
- Vascular Malformations Diagnosis and Treatment
- RNA Research and Splicing
- Ferroptosis and cancer prognosis
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- Dementia and Cognitive Impairment Research
- MicroRNA in disease regulation
- Intracranial Aneurysms: Treatment and Complications
The Ohio State University
2020-2025
Beijing Institute of Neurosurgery
2020-2025
Capital Medical University
2018-2025
Beijing Tian Tan Hospital
2019-2025
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
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 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 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 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...
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...
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...
Abstract Ganoderma lucidum immunomodulatory protein (FIP‐glu) is an active ingredient with potential immunoregulatory functions. The study was conducted to explore the activities of recombinant FIP‐glu (rFIP‐glu) and its possible mechanism in macrophage RAW264.7 cells. In vitro assays biological activity indicated that rFIP‐glu significantly activated cells possessed proinflammatory anti‐inflammatory abilities. RNA sequencing analysis Western blot showed activation involved PI3K/Akt MAPK...
Arterial remodeling is an important adaptive mechanism that maintains normal fluid shear stress in a variety of physiologic and pathologic conditions. Inward remodeling, process leads to reduction arterial diameter, plays critical role progression such common diseases as hypertension atherosclerosis. Yet, despite its pathogenic importance, molecular mechanisms controlling inward remain undefined. Mitogen-activated protein kinases (MAPKs) perform number functions ranging from control...
Myeloid cells comprise up to 50% of the total tumor mass in glioblastoma (GBM) and have been implicated promoting progression immunosuppression. Modulating response myeloid has emerged as a promising new approach for cancer treatment. In this regard, we focus on Triggering Receptor Expressed Cells 2 (TREM2), which recently novel immune modulator peripheral tumors.