A5072894189- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Cell Image Analysis Techniques
- RNA Research and Splicing
- Immunotherapy and Immune Responses
- Cancer Cells and Metastasis
- Immune cells in cancer
- Nanoplatforms for cancer theranostics
- Cancer Immunotherapy and Biomarkers
- Advanced Thermodynamics and Statistical Mechanics
- Gene expression and cancer classification
- MicroRNA in disease regulation
- Wnt/β-catenin signaling in development and cancer
- Cancer Genomics and Diagnostics
- Hippo pathway signaling and YAP/TAZ
- melanin and skin pigmentation
- RNA and protein synthesis mechanisms
- Advanced Fluorescence Microscopy Techniques
- stochastic dynamics and bifurcation
- Circular RNAs in diseases
- Microfluidic and Bio-sensing Technologies
- Spectroscopy and Quantum Chemical Studies
- Kruppel-like factors research
- Cancer-related molecular mechanisms research
- Melanoma and MAPK Pathways
University of Science and Technology of China
2021-2025
Peking University
2016-2024
University of California, Irvine
2020-2024
Anhui Provincial Hospital
2021
University of Science and Technology Beijing
2020
State Key Laboratory of Oncogene and Related Genes
2013-2019
Shanghai Jiao Tong University
2015-2019
Renji Hospital
2013
Stanford University
2008
// Yun-Li Chang 1 , Pei-Jie Zhou Lianzi Wei Wang Li Zhongzhong Ji Yu-Xiang Fang Wei-Qiang Gao 1, 2, 3 State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Hospital, School Medicine, Shanghai Jiao Tong University, 200127, China 2 Biomedical Engineering & Med-X Institute, 200030, Collaborative Innovation Center Systems Biomedicine, Correspondence to: Gao, e-mail: gao.weiqiang@sjtu.edu.cn Fang, fyx2003108@sina.com Keywords: miR-7, prostate...
Abstract Advances in single-cell technologies allow scrutinizing of heterogeneous cell states, however, detecting cell-state transitions from snap-shot transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique to identify the underlying stochastic dynamics that prescribes cell-fate transitions. By iteratively unifying transition across multiple scales, MuTrans constructs...
Abstract Time-series single-cell RNA sequencing (scRNA-seq) datasets provide unprecedented opportunities to learn dynamic processes of cellular systems. Due the destructive nature sequencing, it remains challenging link scRNA-seq snapshots sampled at different time points. Here we present TIGON, a dynamic, unbalanced optimal transport algorithm that reconstructs trajectories and population growth simultaneously as well underlying gene regulatory network from multiple snapshots. To tackle...
Motivated by the famous Waddington's epigenetic landscape metaphor in developmental biology, biophysicists and applied mathematicians made different proposals to construct for multi-stable complex systems. We aim summarize elucidate relationships among these theories from a mathematical point of view. systematically investigate compare three but closely related realizations recent literature: Wang's potential theory steady state distribution stochastic differential equations (SDEs),...
Abstract Rapid growth of single-cell transcriptomic data provides unprecedented opportunities for close scrutinizing dynamical cellular processes. Through investigating epithelial-to-mesenchymal transition (EMT), we develop an integrative tool that combines unsupervised learning and multiscale mathematical modeling to analyze transitions during cell fate decision. Our approach allows identification individual cells making between all states, inference genes drive transitions. Multiscale...
Article2 November 2022Open Access Transparent process spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data Federico Bocci orcid.org/0000-0003-4302-9906 Department of Mathematics, University California, Irvine, CA, USA NSF-Simons Center for Multiscale Cell Fate Research, Contribution: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing - original draft, review & editing Search more papers by this author Peijie...
Despite their immense therapeutic potential, cancer immunotherapies such as immune checkpoint blockers (ICBs) benefit only a small subset of patients. Toll-like receptor agonists reverse the immunosuppressive tumor microenvironment (TME) to enhance antitumor immunity, but systemic administration induces side effects. This work describes TME-responsive nanotherapeutic platform for site-specific release drug candidates in tumors with significant efficacy. Imidazoquinoline (IMQ)-derived...
Abstract Spatial transcriptomics and messenger RNA splicing encode extensive spatiotemporal information for cell states transitions. The current lineage-inference methods either lack spatial dynamics state transition or cannot capture different associated with multiple paths. Here we present tensor (STT), a method that uses transcriptomes through multiscale dynamical model to characterize multistability in space. By learning four-dimensional spatial-constrained random walk, STT reconstructs...
Immunosuppressive phenotype compromised immunotherapy efficacy of hepatocellular carcinoma. Tumor cells intrinsic mitochondria dynamics could pass effects on the extracellular microenvironment through mtDNA stress. PGAM5 anchors at and regulates functions. We aim to explore whether regulation tumor-intrinsic affects tumor-infiltrating immune in can be a therapeutic target enhance carcinoma (HCC). analyzed correlation expression infiltration using Gene Expression Omnibus (GEO) The Cancer...
Noninvasive preimplantation genetic testing for aneuploidy based on embryonic cell-free DNA (cfDNA) released in spent embryo culture media (SECM) has brought hope selecting embryos that are most likely to implant and grow into healthy babies during assisted reproduction. However, maternal contamination SECM significantly hampers the reliability of chromosome ploidy profiles, leading false negative results, particularly at high levels. Here, we present DECENT (deep copy number variation (CNV)...
Prostate cancer (PCa) is one of the most frequent tumors and leading cause deaths among males worldwide. The majority are due to recurrence subsequent development metastatic cancer. Although loss or dislocalization polarity proteins has been implicated in embryogenesis deficiency tumorigenesis, association protein expression levels with tumor metastasis remains unclear. Bioinformatics, qRT-PCR, western blot immunohistochemical (IHC) analyses were used examine Par3, a key component...
Although androgen deprivation therapy (ADT) is a standard treatment for metastatic prostate cancer, this disease inevitably recurs and progresses to ADT‐resistant stage after therapy. Accordingly, understanding the mechanism of resistance ADT finding new approach enhance efficacy may provide major benefit PCa patients. In our study, we found upregulated expression Notch receptors positive associated with ADT‐resistance progression. Using fluorescent signaling reporter system, observed that...
The RNA velocity provides a new avenue to study the stemness and lineage of cells in development scRNA-seq data analysis.Some promising extensions it are proposed community is experiencing fast developing period.However, this stage, prime importance revisit whole process analysis from mathematical point view, which will help understand rationale drawbacks different proposals.The current paper devoted purpose.We present thorough on model dynamics downstream analysis.We derived analytical...
Rosacea is a chronic inflammatory skin disorder, whose underlying cellular and molecular mechanisms remain obscure. Here, we generate single-cell atlas of facial from female rosacea patients healthy individuals. Among keratinocytes, subpopulation characterized by IFNγ-mediated barrier function damage found to be unique lesions. Blocking IFNγ signaling alleviates rosacea-like phenotypes in mice. The papulopustular featured expansion pro-inflammatory fibroblasts, Schwann, endothelial...
Epithelial-to-mesenchymal transition (EMT) plays an important role in many biological processes during development and cancer. The advent of single-cell transcriptome sequencing techniques allows the dissection dynamical details underlying EMT with unprecedented resolution. Despite several data analysis on EMT, how cell communicates regulates dynamics along trajectory remains elusive. Using transcriptomic datasets, here we infer cell–cell communications multilayer gene–gene regulation...
Breast cancer (BCa) remains as the second leading cause of cancer-related death in women worldwide. The majority deaths are due to its progression metastatic BCa. Although Grb2-associated binding protein 1 (Gab1) has been implicated tumor proliferation and metastasis multiple tumors including colorectal cancer, hepatocellular carcinoma ovarian whether how it regulates BCa still poorly understood.Western blot assay immunohistochemical (IHC) staining were performed assess expression Gab1...
Abstract Time-series spatial transcriptome data with single-cell resolution provide an opportunity to study cell differentiation, growth and migration in physical space over time. Due the destructive nature of sequencing, simultaneous reconstruction trajectories remains challenging, especially space, as coordinates obtained at different temporal snapshots are not same coordinate system. To realize this potential, we developed stVCR, which is optimal transport algorithm dynamical form,...
Cells make decisions through their communication with other cells and receiving signals from environment. Using single-cell transcriptomics, computational tools have been developed to infer cell-cell ligands receptors. However, the existing methods only deal sent by measured in data, received external system are missing inference. Here, we present exFINDER, a method that identifies such transcriptomics datasets utilizing prior knowledge of signaling pathways. In particular, exFINDER can...
Intermediate cell states (ICSs) during the epithelial–mesenchymal transition (EMT) are emerging as a driving force of cancer invasion and metastasis. ICSs typically exhibit hybrid epithelial/mesenchymal characteristics well stem (CSC) traits including proliferation drug resistance. Here, we analyze several single-cell RNA-seq (scRNA-seq) datasets to investigate relation between axes progression EMT, CSC traits, cell–cell signaling. To accomplish this task, integrate computational methods for...