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Gene for osteosarcoma typing and osteosarcoma prognosis evaluation and application thereof

An osteosarcoma and genetic technology, applied in the field of biomedicine, can solve the problems of inability to well explain patient heterogeneity, inability to well guide patients in personalized treatment such as targeted therapy

Pending Publication Date: 2022-01-04
SHANGHAI CHANGZHENG HOSPITAL +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] The existing clinical staging (TNM) and grading (pathological) diagnostic methods cannot well explain the heterogeneity of patient prognosis, nor can they guide patients well for personalized treatment such as chemotherapy and targeted therapy

Method used

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  • Gene for osteosarcoma typing and osteosarcoma prognosis evaluation and application thereof
  • Gene for osteosarcoma typing and osteosarcoma prognosis evaluation and application thereof
  • Gene for osteosarcoma typing and osteosarcoma prognosis evaluation and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0049]Example 1 Gene Screening for Osteosarcoma Type and Estimation of Osteosarcoma Prognosis

[0050] Through the screening of single-cell high-throughput sequencing data in the GEO public database (the full name is Gene Expression Omnibus, which is a gene expression database created and maintained by the National Center for Biotechnology Information NCBI), we screened out an osteosarcoma numbered GSE152048 10x single-cell sequencing data, 6 cases of classical osteosarcoma (osteogenic osteosarcoma) data were selected for subsequent analysis. In addition, single-cell sequencing data of cancellous bone samples from 9 degenerated patients undergoing surgery in Shanghai Changzheng Hospital were selected. The above two data sets were combined for molecular classification and prognosis analysis of osteosarcoma.

[0051] Visualized UMAPs and different cell clusters were obtained by unsupervised dimensionality reduction and cluster analysis on the above datasets. UMAP (Uniform Mani...

Embodiment 2

[0069] Example 2 TARGET-OS classification and survival analysis

[0070] Validation in the overall osteosarcoma public database samples, osteosarcoma sequencing data were screened from The Cancer Genome Atlas (TCGA) database. Normalized RNA-Seq FPKM and Clinic files were downloaded from the TCGA Data Portal on January 30, 2021.

[0071] According to the expression levels of 44 genes in each case sample in the Target-OS dataset, 85 osteosarcoma cases and clinical information were classified, and we can divide the clinical cases in the Target-OS dataset into corresponding Cluster1, Cluster2 and Cluster3. For example, patients with high expression of type A genes and low expression of type B and C genes are defined as Cluster1, patients with high expression of type C genes and low expression of type B and A genes are defined as Cluster2, patients with high expression of type B genes, Patients with low expression of type A and type C genes were defined as Cluster3. We show the ...

Embodiment 3

[0073] Embodiment 3 analytical method

[0074] The single-cell sample preparation, sequencing and analysis methods described in Example 1 are as follows:

[0075] 1. Sample preparation and sequencing

[0076] All samples were cold-chain transported to the laboratory within 1 hour of separation. Following standard 10x Genomics sample preparation, tissue samples were first cut into 2-4 mm sized pieces, digested with collagenase, and incubated in a shaker at 37°C. The digested and incubated cell suspension is filtered through a mesh strainer, and the filtered contents are centrifuged to remove enzymes. Take the supernatant to count the cells, adjust the cell density according to the results of cell technology, and then perform single-cell sequencing. Single Cell Sequencing 10xGenomics Single Cell A Chip Kit, Single Cell 3'Library and Gel Bead KitV2 were used to perform 3' single cell RNA sequencing on the cell suspension of each sample, and the number of recovered target cells...

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Abstract

In the invention, aiming at tumor heterogeneity, the difference of cytodynamics and molecular characteristics between conventional osteosarcoma and normal cancellous bone is compared, and based on a single-cell RNA sequencing (scRNA-seq) technology, a gene detection kit, a gene detection chip technology or an immunohistochemical method, the obvious differentiation direction of osteosarcoma cells is detected, and the possible interaction between each cell type in the tumor microenvironment is researched. According to the differentiation direction of the osteosarcoma cells, conventional osteosarcoma can be divided into three types, the tumor microenvironment characteristics of each type are described, and prognosis of each type is verified according to the cancer genome atlas (TCGA) data.

Description

technical field [0001] The invention belongs to the technical field of biomedicine, and specifically relates to a gene, a detection kit, a detection chip and an application thereof for the classification of osteosarcoma and the assessment of the prognosis of osteosarcoma. Background technique [0002] Osteosarcoma (OS) is the most common primary bone malignancy. Before the widespread use of chemotherapy in the 1970s, surgical resection was the main treatment modality available to patients with OS. The implementation of adjuvant chemotherapy has significantly improved the prognosis of OS patients, and the five-year survival rate of non-metastatic patients has increased from 20% to more than 60%. However, the prognosis of patients with metastatic or recurrent disease did not improve significantly, with a survival rate of only 20% in both groups. Subsequently, treatment patterns and outcomes for patients with OS have not evolved much over the past four decades. Therefore, th...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886G01N33/574G01N33/543C12N15/11
CPCC12Q1/6886G01N33/57488G01N33/57407G01N33/54306C12Q2600/106C12Q2600/112C12Q2600/118C12Q2600/158
Inventor 肖建如魏海峰周旺张浩龚海熠王霆
Owner SHANGHAI CHANGZHENG HOSPITAL
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