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Bladder cancer exhausted T cell subset as well as characteristic genes and application thereof

A cell and gene technology, applied in the field of identification of T cell subsets, can solve the problem that TIL types and inhibition pathways are not fully understood.

Inactive Publication Date: 2020-10-09
BEIJING UNIV OF CHEM TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Although the mechanism of interaction between the immune system and cancer tissue plays an important role in the development and improvement of immunotherapy, as well as in the detection of tumor development and progression, the types of TILs and their inhibitory pathways have not been fully understood

Method used

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  • Bladder cancer exhausted T cell subset as well as characteristic genes and application thereof
  • Bladder cancer exhausted T cell subset as well as characteristic genes and application thereof
  • Bladder cancer exhausted T cell subset as well as characteristic genes and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0045] Example 1 Single-cell transcriptome sequencing

[0046] 1. Clinical sample collection

[0047] In this study, peripheral blood, bladder cancer tissue and normal tissue adjacent to cancer were selected from 3 patients with bladder urothelial cancer, which were collected and provided by Xuanwu Hospital of Capital Medical University. All patients have provided written informed consent. Collect the bladder cancer tissue, normal tissue adjacent to the cancer and peripheral blood from the patient. All patients are required to have no history of autoimmune diseases or other cancers, bladder cancer that has not received neoadjuvant chemotherapy or other anti-tumor therapy before surgery, and the tumor diameter is greater than 1 cm. For sample collection, immediately after the operation, fresh samples should be transported back to the laboratory smoothly at 4°C, and cell separation experiments should be carried out within 2 hours to ensure maximum cell viability.

[0048] 2. Isolati...

Embodiment 2

[0071] Example 2 Analysis of gene expression in different cell subgroups

[0072] Through single-cell transcriptome sequencing, according to Cellranger data statistics, Seurat standardization, dimensionality reduction, clustering, etc., the sequencing results are analyzed, and clustering is performed according to the gene expression between cells. Cluster analysis is used to identify cell subtypes. According to the clustering results, the t-SNE dimensionality reduction algorithm is used to display the distribution of cells in a two-dimensional space. The specific analysis method is as follows:

[0073] ⑴Data standardization and noise reduction

[0074] Seurat uses the global normalization method “LogNormalize” to standardize the gene expression matrix by default. For each cell, the expression of each gene is divided by the overall expression of the cell, which is converted to relative abundance, and then multiplied by Normalization factor (default 10000), and then log conversion. ...

Embodiment 3

[0099] Example 3CD8 + Pathway enrichment analysis of differentially expressed genes in exhausted T cells

[0100] Gene pathway enrichment analysis is a process of analyzing the metabolic pathways of genes in cells and their functions. In the present invention, Matescape is used to perform pathway enrichment analysis on differentially expressed genes. Metascape is a portal site that provides genetic annotation and analysis resources. The website is http: / / metascape.org. It integrates more than forty biological information databases, such as GO / KEGG terms, canonical pathways, hall mark gene sets, UniProt and DrugBank, etc. Common databases are included. We can easily use this website to perform enrichment analysis of biological pathways and analysis of protein interaction network structure. We submit the differential gene list of the cluster to be analyzed on the homepage of the website, select the species information as H.sapiens, and then click the analysis option to get the res...

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Abstract

According to the invention, single-cell transcriptome sequencing is carried out on peripheral blood, normal bladder tissues and bladder cancer tissue-derived T cells of an infiltrated bladder cancer patient by utilizing a single-cell transcriptome sequencing analysis technology, a bladder cancer specific T cell subset, namely CD8<+> exhausted T cells, is identified, and characteristic genes, namely genes LUC7L3, IKZF3 and TRGC2, expressed by the CD8<+> exhausted T cells are determined. The characteristic genes can be used for identifying or authenticating CD8<+> exhausted T cells from bladdercancer, can be further used for auxiliary diagnosis, prognosis and immunotherapy of bladder cancer, and provide related detection reagents or kits.

Description

Technical field [0001] The present invention relates to the field of tumor molecular biology and biotechnology, in particular to the identification of cell subgroups, especially the identification of T cell subgroups derived from bladder cancer tissue. Background technique [0002] Bladder cancer is one of the most common malignant tumors of the urinary system. In 2018, CA magazine reported that there were approximately 549,000 new cases and 200,000 deaths of bladder cancer worldwide, and men accounted for approximately 75% of the overall disease burden. In the United States, the incidence of bladder cancer ranks fourth, and the number of male patients is four times that of females. In my country, the incidence of bladder cancer is 6.69 per 100,000, and the incidence is increasing over time, which greatly threatens the health of our people, especially male patients. Bladder cancer varies greatly due to gender, race, and region. It can occur in all age groups, and its high incid...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886C12Q1/6869G01N33/574G01N33/53C12N5/0783
CPCC12Q1/6886C12Q1/6869G01N33/57407G01N33/53C12N5/0636C12Q2600/158C12Q2600/118
Inventor 杨昭王璐瑶喻长远白素杭沈宗毅
Owner BEIJING UNIV OF CHEM TECH
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