A5037021543- Single-cell and spatial transcriptomics
- Zebrafish Biomedical Research Applications
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Acute Lymphoblastic Leukemia research
- RNA modifications and cancer
- Metabolism and Genetic Disorders
- Gene expression and cancer classification
- Cancer Cells and Metastasis
- Pregnancy and preeclampsia studies
- Gout, Hyperuricemia, Uric Acid
- MicroRNA in disease regulation
- Advanced biosensing and bioanalysis techniques
- Cancer Genomics and Diagnostics
- Renal and related cancers
- Immune cells in cancer
- Alcohol Consumption and Health Effects
- Acute Myeloid Leukemia Research
- Mathematical Biology Tumor Growth
- Immune Cell Function and Interaction
- Cancer, Lipids, and Metabolism
- Body Composition Measurement Techniques
- Ginseng Biological Effects and Applications
- Colorectal Cancer Treatments and Studies
- Peptidase Inhibition and Analysis
Shanghai Jiao Tong University
2011-2025
Shanghai Cancer Institute
2025
Renji Hospital
2025
University of California, San Francisco
2023-2025
Hangzhou Hospital of Traditional Chinese Medicine
2011-2024
Shanghai Ninth People's Hospital
2022-2024
Nanjing Medical University
2016-2023
California University of Pennsylvania
2023
Affiliated Hospital of Nantong University
2023
Nantong University
2023
Identifying terminal nematode cells Single-cell RNA sequencing provides the power to identify developmental trajectory of an organism. However, identifying temporal lineage cell development can be difficult without large-scale analyses. Packer et al. sequenced more than 80,000 from embryos roundworm Caenorhabditis elegans determine expression genes directing types. Because all somatic in a C. individual have been mapped, authors are able connect gene with lineages over time during...
The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences autologously derived are major contributor to therapy failure. To interrogate the molecular determinants CAR T-cell persistence, we extensively characterized premanufacture 71 patients with B-cell malignancies on trial receive anti-CD19 therapy. We performed RNA-sequencing analysis sorted subsets from all patients, followed by...
Single-cell RNA-seq data contain a large proportion of zeros for expressed genes. Such dropout events present fundamental challenge various types analyses. Here, we describe the SCRABBLE algorithm to address this problem. leverages bulk as constraint and reduces unwanted bias towards genes during imputation. Using both simulation several experimental data, demonstrate that outperforms existing methods in recovering events, capturing true distribution gene expression across cells, preserving...
KMT2A-rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is a devastating malignancy with dismal outcome, and younger age at diagnosis associated increased risk of relapse. To discover age-specific differences critical drivers that mediate poor outcome in KMT2A-r ALL, we subjected leukemias normal hematopoietic cells from patients different ages to single-cell multiomics analyses. We uncovered the following new insights: <6 months have significantly lineage plasticity. Steroid...
Abstract The initiation and progression of cancer are intricately linked to the tumor microenvironment (TME). Understanding function specific cancer-TME interactions poses a major challenge due in part complexity vivo microenvironment. Here we predict from single cell transcriptomic maps both human colorectal cancers (CRCs) mouse CRC models, ask how these altered organoid (tumoroid) cultures, functionally recapitulate myeloid-carcinoma vitro. Tumoroid cultures suppress gene expression...
Sample multiplexing enables pooled analysis during single-cell RNA sequencing workflows, thereby increasing throughput and reducing batch effects. A challenge for all techniques is to link sample-specific barcodes with cell-specific barcodes, then demultiplex sample identity post-sequencing. However, existing demultiplexing tools fail under many real-world conditions where barcode cross-contamination an issue. We therefore developed deMULTIplex2, algorithm inspired by a mechanistic model of...
Abstract NOP 2/Sun domain family, member 2 ( NSUN 2) is a nuclear RNA methyl‐transferase catalyzing 5‐methylcytosine formation. Evidence shows that correlated with cell unlimited proliferation. However, its functional role in gallbladder carcinoma GBC ), which the most common biliary tract malignancy and has poor prognosis, remains to be determined. Here we found was highly expressed tissues as well lines. silencing repressed proliferation tumorigenesis both vitro vivo. Conversely,...
Cerebral cavernous malformation (CCM) is a genetic, cerebrovascular disease. Familial CCM caused by genetic mutations in KRIT1, CCM2, or PDCD10 Disease onset earlier and more severe individuals with mutations. Recent studies have shown that lesions arise from excess mitogen-activated protein kinase 3 (MEKK3) signaling downstream of Toll-like receptor 4 (TLR4) stimulation lipopolysaccharide derived the gut microbiome. These findings suggest gut-brain disease axis but fail to define it explain...
Abstract RUNX1 is frequently mutated in myeloid and lymphoid malignancies. It has been shown to negatively regulate Toll-like receptor 4 (TLR4) signaling through nuclear factor κB (NF-κB) lung epithelial cells. Here we show that regulates TLR1/2 TLR4 inflammatory cytokine production by neutrophils. Hematopoietic-specific loss increased the of proinflammatory mediators, including tumor necrosis factor-α (TNF-α), bone marrow neutrophils response agonists. Hematopoietic also resulted profound...
Abstract Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is lack open-source software comprehensive processing, analysis, and visualization such data generated using all existing experimental protocols. Here, we present scATAC-pro quality assessment, single-cell data. computes range control metrics several key steps protocols, with flexible choice methods. It generates summary...
Hematopoietic stem cell (HSC) ontogeny is accompanied by dynamic changes in gene regulatory networks. We performed RNA-seq and histone mark ChIP-seq to define the transcriptomes epigenomes of cells representing key developmental stages HSC mice. The five populations analyzed were embryonic day 10.5 (E10.5) endothelium hemogenic from major arteries, an enriched population prehematopoietic (pre-HSCs), fetal liver HSCs, adult bone marrow HSCs. Using epigenetic signatures, we identified...
Abstract Aberrant RNA alternative splicing in cancer generates varied novel isoforms and protein variants that facilitate progression. Here, we employed the advanced long-read full-length transcriptome sequencing on gallbladder normal tissues, tumors, cell lines to establish a comprehensive transcriptomic atlas. It is of note receptor tyrosine kinases were one most dynamic components with highly variable transcript, Erb-B2 kinase 2 (ERBB2) as prime representative. A designated ERBB2 i14e,...
Abstract Large-scale scATAC-seq experiments are challenging because of their costs, lengthy protocols, and confounding batch effects. Several sample multiplexing technologies aim to address these challenges, but do not remove effects introduced when performing transposition reactions in parallel. We demonstrate that sample-to-sample variability nuclei-to-Tn5 ratios is a major cause develop MULTI-ATAC, method pools samples prior transposition, as solution. MULTI-ATAC provides high accuracy...
SUMMARY Colorectal cancer (CRC) is a leading cause of deaths, predominantly initiated by genetic inactivation the APC tumor suppressor. Current dogma holds that promotes tumorigenesis via hyperactivation WNT pathway transcriptional effector, β-CATENIN. Although β-CATENIN activation required for initiation, activating mutations in are infrequent. Here, we ask what underlies selective pressure comparing oncogenic effects loss to hyperactivation. We find activates β-CATENIN-independent fetal...
Many R packages have been developed for transcriptome analysis but their use often requires familiarity with and integrating results of different scripts to wrangle the datatypes. Furthermore, exploratory data analyses generate multiple derived datasets such as subsets or transformations, which can be difficult track. Here we present PIVOT, an R-based platform that wraps open source a uniform user interface graphical management allows non-programmers interactively explore transcriptomics...
The highly conserved protease TASP1 not only takes part in critical site-specific proteolysis, but also plays an important role numerous liquid and solid malignancies. However, the expression its biological regulation function malignant gallbladder carcinoma (GBC) remain fully unknown. Here we observed that levels were substantially overexpressed GBC samples compared with non-tumor tissues. High level was closely associated T stage metastasis, correlated poor prognosis patients. depletion of...
Aims: The aim of the present study was to investigate effects rutin on potassium oxonate-induced hyperuricemia and renal dysfunction in mice. Methods: Rutin administered orally 1 h after oxonate at doses 25, 50 100 mg·kg-1. Serum uric acid levels kidney function parameters were assayed. Mouse uromodulin serum, urine determined by ELISA method. Simultaneously, expression organic ion transporters detected. Results: significantly decreased serum urate, creatinine blood urea nitrogen, levels,...
Abstract Betaine as a dietary alkaloid has attracted the attention of patients with kidney diseases. This study aimed to investigate effects betaine on serum uric acid levels and function, explore their underlying mechanisms in potassium oxonate-induced hyperuricemic mice. at 5, 10, 20, 40 mg/kg was orally administered mice for 7 days found significantly reduce increase fractional excretion dose-dependent manner. It effectively restored renal protein level alterations urate transport-related...
Abstract Neuroendocrine carcinoma (NEC) of the gallbladder (GB-NEC) is a rare but extremely malignant subtype cancer (GBC). The genetic and molecular signatures GB-NEC are poorly understood; thus, targeting currently unavailable. In present study, we applied whole-exome sequencing (WES) technology to detect gene mutations predicted somatic single-nucleotide variants (SNVs) in 15 cases 22 general GBC. GB-NECs, C > T mutation was predominant among 6 types SNVs. TP53 showed highest frequency...
Abstract Background Our previous studies showed that Salvianolic acid B (Sal B) inhibited 7,12-dimethylbenz[a]anthracene (DMBA)-induced oral carcinogenesis in hamsters and such anti-cancer effects might be related to the inhibition of angiogenesis. This study was aimed further investigate anti-proliferative effect Sal on most common type cancer, squamous cell carcinoma (OSCC) possible mechanisms action with respect angiogenesis inhibition. Methods Two well-characterized lines, CAL27 SCC4,...