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T-cell subset for cancers and characteristic genes

A cell subgroup and gene technology, applied in animal cells, genetic engineering, plant genetic improvement, etc., can solve problems such as categories, differentiation, and inhibited pathways that are not fully understood.

Active Publication Date: 2018-12-25
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 infiltrating lymphocytes, TILs) infiltrating into cancer tissues have not been fully understood so far.

Method used

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  • T-cell subset for cancers and characteristic genes
  • T-cell subset for cancers and characteristic genes
  • T-cell subset for cancers and characteristic genes

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0164] Example 1 Acquisition of single-cell transcriptome data of T cells

[0165] 1. Clinical sample collection

[0166] From August 2014 to June 2015, surgical tissues and peripheral blood were collected from patients at Peking University People's Hospital and Beijing Shijitan Hospital, including cancer tissues (3-5 mm in diameter) and adjacent normal tissues, and peripheral blood ( 3ml). There were 5 patients with hepatocellular carcinoma who did not receive preoperative adjuvant radiotherapy or chemotherapy. This study complied with the medical ethics standards of the Declaration of Helsinki and was approved by the Medical Ethics Committee of Peking University.

[0167] 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 5cm away fr...

Embodiment 2

[0222] Embodiment 2 biological information analysis

[0223] 1. Data comparison and quality control

[0224] 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. Alignment was done using GSNAP software. 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:

[0225] where C ij Expressed as the number of reads for gene i in cell j.

[0226] T cells with low data volume and data quality need to be filtered out. Keep cells that meet the following criteria: ① CD3D TPM is greater than...

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Abstract

The invention isolates and characterizes a T-cell subset capable of reflecting body tumor immunity state, namely exhaustible CD8+T-cells to express genes WARS and ACP5 as well as regulatory T-cells toexpress genes STAM and BATF, by analyzing single cell gene expression profiles of T-cells infiltrated in cancer tissues through single cell transcriptome analysis. Further determined by researches are new characteristic genes WARS and ACP5 expressed by the cell subset, and a relationship between the STAM and BATF and prognosis of tumor, as well as application of the genes in tumor prognosis diagnosis and monitoring, and application as new tumor immunotherapy targets.

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 tumor tissues. The present invention also relates to a series of markers for the isolation of T cell subpopulations in tumors, isolation methods and resulting preparations, and the use of isolated T cell subpopulations for drug research and development and for diagnosis, therapy and other clinical and non-clinical application. Background technique [0002] It is generally believed that the adaptive immune response involving T lymphocytes is considered to be 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 and attacking cancer cell...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C07K14/47C12N15/12C12N5/0783C12Q1/02G01N33/574
CPCC07K14/47C12N5/0636C12Q1/6886C12Q2600/118C12Q2600/158G01N33/5011G01N33/505G01N33/574G01N33/57438
Inventor 张泽民郑春红郑良涛张园园郭心怡胡学达
Owner PEKING UNIV
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