A5101587089- Single-cell and spatial transcriptomics
- Immune cells in cancer
- Cancer Genomics and Diagnostics
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- SARS-CoV-2 and COVID-19 Research
- Neuroscience and Neuropharmacology Research
- Extracellular vesicles in disease
- Memory and Neural Mechanisms
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- Respiratory viral infections research
- MicroRNA in disease regulation
- CAR-T cell therapy research
- Genomics and Phylogenetic Studies
- Neuroinflammation and Neurodegeneration Mechanisms
- vaccines and immunoinformatics approaches
- Metabolomics and Mass Spectrometry Studies
- COVID-19 Clinical Research Studies
- RNA modifications and cancer
- Alzheimer's disease research and treatments
- Wastewater Treatment and Nitrogen Removal
- Gene expression and cancer classification
- Epilepsy research and treatment
- Cell Image Analysis Techniques
Shanghai Jiao Tong University
2017-2025
Shanghai Ninth People's Hospital
2024-2025
Cancer Institute (WIA)
2025
Hubei University of Chinese Medicine
2025
Sun Yat-sen University
2025
Jinshan Hospital of Fudan University
2021-2024
Nanjing Medical University
2021-2024
Shanghai Cancer Institute
2024
Army Medical University
2024
Southwest Hospital
2024
Abstract It has been known that, the novel coronavirus, 2019-nCoV, which is considered similar to SARS-CoV, invades human cells via receptor angiotensin converting enzyme II (ACE2). Moreover, lung that have ACE2 expression may be main target during 2019-nCoV infection. However, some patients also exhibit non-respiratory symptoms, such as kidney failure, implying could invade other organs. To construct a risk map of different organs, we analyzed single-cell RNA sequencing (scRNA-seq) datasets...
Cancer immunotherapy has revolutionized cancer treatment, and it relies heavily on the comprehensive understanding of immune landscape tumor microenvironment (TME). Here, we obtain a detailed cell atlas esophageal squamous carcinoma (ESCC) at single-cell resolution. Exhausted T NK cells, regulatory cells (Tregs), alternatively activated macrophages tolerogenic dendritic are dominant in TME. Transcriptional profiling coupled with receptor (TCR) sequencing reveal lineage connections...
The intracellular delivery of biofunctional enzymes or therapeutic proteins through systemic administration is great importance in intervention various diseases. However, current strategies face substantial challenges owing to biological barriers, including susceptibility protein degradation and denaturation, poor cellular uptake, low transduction efficiency into the cytosol. Here, we developed a biomimetic nanoparticle platform for proteins. Through biocompatible strategy, guest are caged...
Tumor progression is closely related to tumor tissue metabolism and reshaping of the microenvironment. Oral squamous cell carcinoma (OSCC), a representative hypoxic tumor, has heterogeneous internal metabolic environment. To clarify relationship between different regions immune microenvironment (TME) in OSCC, Single (SC) spatial transcriptomics (ST) sequencing OSCC tissues were performed. The proportion TME ST data was obtained through SPOTlight deconvolution using SC GSE103322 data....
Abstract Previous studies have demonstrated a strong association between carbamazepine‐induced S tevens– J ohnson syndrome and toxic epidermal necrolysis ( CBZ ‐induced SJS / TEN ) HLA ‐ B *1502 in Chinese, A *3101 but not ‐B*1502 Caucasians Japanese. Cases with negative for were reported recently Southeast Asia. Negative correlations *0702 or *4001 also been reported, suggesting possible protective role. Here, we genotyped 18 cases , comparison ‐tolerant normal controls Southern Han C...
The differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, a priori knowledge limited biomarkers could restrict trajectory tracking.We employed marker-free RNA-Seq to characterize comprehensive transcriptional profiles 507 randomly selected from seven stages between embryonic day 11.5 postnatal 2.5 during mouse development, also 52 Epcam-positive cholangiocytes 3.25 livers. LSPCs in developing livers were...
The underlying pathophysiological mechanisms of cerebral ischemia reperfusion injury (CIRI) is intricate, and current studies suggest that neuron, astrocyte, microglia, endothelial cell, pericyte all have different phenotypic changes specific cell types after ischemic stroke. And microglia account for the largest proportion CIRI. Previous transcriptomic stroke typically focused on 24 hours CIRI, obscuring dynamics cellular subclusters throughout disease process. Therefore, traditional...
The long-term characteristics of anti-SARS-CoV-2 antibodies among COVID-19 patients remain largely unclear. Tracking the longevity these can provide a forward-looking reference for monitoring COVID-19.
Abstract Single-cell sequencing has advanced our understanding of cellular heterogeneity and disease pathology, offering insights into behavior immune mechanisms. However, extracting meaningful phenotype-related features is challenging due to noise, batch effects, irrelevant biological signals. To address this, we introduce Deep scSTAR (DscSTAR), a deep learning-based tool designed enhance phenotype-associated features. DscSTAR identified HSP+ FKBP4+ T cells in CD8+ cells, which linked...
Head and neck squamous cell carcinoma (HNSCC) demonstrates significant heterogeneity, necessitating improved molecular classification for precision treatment. We integrated single-cell bulk RNA sequencing data from 59,376 cells across ten datasets using Scissor scSTAR packages. Molecular subtyping was performed through ssGSEA WGCNA analysis, with immune infiltration evaluated CIBERSORT. developed a machine learning-based risk prediction model 54 algorithms. identified three subtypes distinct...
Sex differences in the pathogenesis of a variety diseases have drawn increasing attention. However, it remains unclear whether such exist chemotherapy-induced neuropathic pain. Here, we conducted retrospective analysis clinical case data and found that peripheral sensory disorders occurred earlier females than males following bortezomib (BTZ) treatment patients with multiple myeloma. BTZ led to an early elevation intercellular adhesion molecule–1, which triggered infiltration monocytes into...
Electroencephagraphy (EEG) of many dementia patients has been characterized by an increase in low frequency field potential oscillations. One the characteristics early stage Alzheimer's disease (AD) is theta band power (4–7 Hz). However, mechanism(s) underlying changes oscillations are still unclear. To address this issue, we investigate associated with β-Amyloid (Aβ) peptide (one main markers AD) using a computational model, and mediating toxicity hippocampal pyramidal neurons. We use...
Differential expression (DE) gene detection in single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) data is a key step to understand the biological question investigated. Filtering genes suggested improve performance of DE methods, but influence filtering has not been demonstrated. Furthermore, optimal methods for different scRNA-seq datasets are divergent, and should benefit from data-specific strategies. However, existing tools did take into consideration. There lack metrics...
Abstract Cell-state transition can reveal additional information from single-cell ribonucleic acid (RNA)-sequencing data in time-resolved biological phenomena. However, most of the current methods are based on time derivative gene expression state, which restricts them to short-term evolution cell states. Here, we present State Transition Across-samples RNA-seq (scSTAR), overcomes this limitation by constructing a paired-cell projection between conditions with an arbitrary span maximizing...
Background: Human adenovirus (HAdV) is common pathogens that cause various respiratory diseases. The genetic diversity of viruses caused by recombination considered to be the main source emerging outbreaks. aim this study explore evolutionary relationship and events HAdV genome in tract infections Jiangsu Province. Methods: Whole-genome sequencing (WGS) technology was used sequence 66 patients with infection (37 influenza-like illness (ILI) 29 hospitalized pneumonia) from Epidemiological...
Most patients with clear cell renal carcinoma (ccRCC) have an impaired response to immune checkpoint blockade (ICB) therapy. Few biomarkers can predict responsiveness, and there is insufficient evidence extend them ccRCC clinical use. To explore subtypes signatures of immunocytes good predictive performance for ICB outcomes in the context, we reanalyzed two single-cell RNA sequencing (scRNA-seq) datasets from receiving treatment. A subtype proliferative CD4+ T cells regulatory a...
Abstract Background Prostate cancer (PCA) is the fifth leading cause of cancer-related deaths worldwide, with limited treatment options in advanced stages. The immunosuppressive tumor microenvironment (TME) PCA results lower sensitivity to immunotherapy. Although molecular subtyping expected offer important clues for precision PCA, there currently a shortage dependable and effective typing methods available clinical practice. Therefore, we aim propose novel stemness-based classification...
T cell immunity is critical for human defensive immune response. Exploring the key molecules during process provides new targets cell-based immunotherapies. CMC1 a mitochondrial electron transport chain (ETC) complex IV chaperon protein. By establishing in-vitro culture system and Cmc1 gene knock out mice, we evaluated role of in activation differentiation. The B16-OVA tumor model was used to test possibility targeting improving anti-tumor immunity. We identified as positive regulator CD8+T...
Abstract Recent advances in tumor molecular subtyping have revolutionized precision oncology, offering novel avenues for patient-specific treatment strategies. However, a comprehensive and independent comparison of these methodologies remains unexplored. This study introduces ‘Themis’ (Tumor HEterogeneity analysis on Molecular subtypIng System), an evaluation platform that encapsulates few representative methods, including Stemness, Anoikis, Metabolism, pathway-based classifications,...
Abstract Motivation Single-cell transcriptomic data are commonly accompanied by extremely high technical noise due to the low RNA concentrations from individual cells. Precise identification of differentially expressed genes and cell populations heavily dependent on effective reduction noise, e.g. gene filtering. However, there is still no well-established standard in current approaches Investigators usually filter out based single fixed threshold, which leads both over- under-stringent...