T cell subsets in lung cancer and feature genes thereof

A gene and cell technology, applied in the field of identification, characterization and enrichment of T cell subsets, can solve problems such as categories, differentiation and inhibited pathways are not fully understood

Active Publication Date: 2019-05-21
PEKING UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the types, differentiation and inhibition pathways of T cells (tumor infiltrat...

Method used

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  • T cell subsets in lung cancer and feature genes thereof
  • T cell subsets in lung cancer and feature genes thereof
  • T cell subsets in lung cancer and feature genes thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0201] Example 1 Acquisition of single-cell transcriptome data of T cells

[0202] 1. Clinical sample collection

[0203] Surgical tissue and peripheral blood, including cancer tissue and adjacent normal tissue, were collected from Peking University Cancer Hospital and Peking University Third Hospital, and peripheral blood (3ml) was collected. Patients with non-small cell lung cancer, including squamous cell carcinoma and adenocarcinoma, did not receive preoperative adjuvant radiotherapy or chemotherapy, a total of 9 cases. This study complied with the medical ethics standards of the Declaration of Helsinki and was approved by the Medical Ethics Committee of Peking University.

[0204] Blood samples were collected in EDTA anticoagulant tubes and temporarily stored on ice before surgery; cancer tissue and adjacent normal tissue samples were collected during the operation, and necrotic tissue was removed from the cancer tissue; adjacent normal tissue was normal tissue at least ...

Embodiment 2

[0259] Embodiment 2 biological information analysis

[0260] 1. Data comparison and quality control

[0261] For the reads (reads) obtained from the sequencer, the low-quality parts are first removed, and the retention criteria are as follows: ① unknown bases cannot exceed 10% of the total sequence of a given read, ② bases with a quality value lower than 5 cannot More than 50%, ③ cannot contain linker sequences. Use GSNAP software to complete the alignment, the human genome reference sequence version is hg19, and the parameter selection --novelsplicing 1-n 10-i 1-M 2. When calculating gene expression, the reference gene set used is from UCSC's "knownGene.txt", and the R language package "findOverlaps" is used to count the attribution of reads on the gene, and the TPM value is used to calibrate the expression of each gene in each cell amount, the formula used is:

[0262] where C ij Expressed as the number of reads for gene i in cell j.

[0263] T cells with low data vol...

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Abstract

The invention discloses T cell subsets in lung cancer and feature genes thereof. A single-cell transcriptome analysis technology is adopted, and by analyzing a single-cell gene expression profile of infiltrating T cells in the lung cancer tissue, the T cell subsets capable of reflecting body tumor immune states of patients with the lung cancer are separated and characterized, namely the exhaustedCD 8+ T cells or regulatory T cells capable of expressing genes including TNFRSF9, TNFRSF18 and LAYN are separated and characterized. Through research, relations between lung cancer prognosis and thenew feature genes which include TNFRSF9, TNFRSF18 and LAYN and are expressed by the cell subsets are further determined. Therefore, the T cell subsets in lung cancer and the feature genes thereof canbe used for diagnosis and monitoring of lung cancer prognosis and serve as new targets for lung cancer immunotherapy.

Description

technical field [0001] The present invention relates to the field of biotechnology, in particular to the identification, characterization and enrichment of cells or cell subgroups in general, especially T cell subgroups derived from lung cancer tissue. The present invention also relates to a series of markers for the isolation of T cell subsets in lung cancer, isolation methods and the resulting preparations, and the use of isolated T cell subsets in lung cancer for drug research and development and for diagnosis, treatment and other clinical and clinical applications. non-clinical applications. Background technique [0002] It is generally believed that the adaptive immune response involving T lymphocytes is one of the main ways for the human body to fight against tumor cells. [0003] At present, immunotherapy has become an indispensable link in the clinical treatment of tumors. Immunotherapy drugs and regimens involve the stages of the body's immune system recognizing a...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886C12N15/11G01N33/68
Inventor 张泽民张园园郭心怡郑良涛郑春红胡学达
Owner PEKING UNIV
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