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本实验室以生物信息学和癌症基因组学为主导,利用大规模高通量测序技术研究肿瘤免疫的一系列属性。目前,我们用最前沿的单细胞测序技术研究免疫细胞和肿瘤细胞的相互关系,以发现免疫治疗的疗效和生物标记物,以及发现新的免疫治疗靶点。我们也积极参与国际癌症基因组项目,结合癌症基因组大数据挖掘发现和癌症的发生和疗效相关的基因或者基因变种,发现新型的的癌症诊断和个体化治疗方法。本实验室已经建立了干、湿试验技术和大型研究团队,为今后科研快速产出打下了良好的基础。

现有Technician, 博士后,工程师等数个职位虚席以待。详情请见

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Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing

Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. We performed deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8+ T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8+ T cells and Tregs and represses the CD8+ T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers.

Highlights

  • Single-cell RNA-seq reveals distinctive functional composition of T cells in HCC
  • Clonal enrichment of infiltrating Tregs and exhausted CD8 T cells in HCC
  • LAYN is linked to the suppressive function of tumor Treg and exhausted CD8 T cells
  • Combined expression and TCR-based analyses show connectivity among T cell subsets

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Want to touch cancer big data in 1 second? Go GEPIA!

Tremendous amount of RNA sequencing data have been produced by large consortium projects such as TCGA and GTEx, creating new opportunities for data mining and deeper understanding of gene functions. We introduce GEPIA (Gene Expression Profiling Interactive Analysis), a web-based tool to deliver fast and customizable functionalities based on TCGA and GTEx data. GEPIA is available at http://gepia.cancer-pku.cn/.

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Check out our APP – GE-mini

Here we present to you our new Android APP: GE-mini.

This GE-mini APP is designed to exhibit gene expression profiling of a given gene over many tissue types including tumors. The underlying data are based on RNA Sequencing results from both TCGA and GTEx after they are normalized and integrated. The current version, based on the September 2015 release of TCGA and the phs000424.v6.p1 release of GTEx, contains >19,000 total samples across 33 cancer types and 53 normal tissue types.

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