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Non-differential gene associated with malignant phenotype of tumor cell as well as screening method and application of non-differential gene

A technology of differential genes and tumor cells, applied in the field of bioinformatics, can solve the problems of unsatisfactory treatment effect of middle and advanced lung adenocarcinoma, high cancer heterogeneity, and numerous pathways

Active Publication Date: 2022-04-22
CHI BIOTECH CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Various treatment methods have application limitations, resulting in unsatisfactory treatment effects for advanced lung adenocarcinoma
[0003] Today, when various omics technologies (including genomics, transcriptomics, proteomics, etc.) High heterogeneity, many pathways, and frequent mutations make it difficult to find common and specific differential genes that have long-term therapeutic effects

Method used

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  • Non-differential gene associated with malignant phenotype of tumor cell as well as screening method and application of non-differential gene
  • Non-differential gene associated with malignant phenotype of tumor cell as well as screening method and application of non-differential gene
  • Non-differential gene associated with malignant phenotype of tumor cell as well as screening method and application of non-differential gene

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0111] The mRNA sequence data of 75 pairs of lung adenocarcinoma / paracancer specimens were downloaded from the NCBI-SRA database (SRA: ERP0001058). Taking the 150 cases (75 pairs) of lung adenocarcinoma and adjacent clinical tissue samples as an example, the non-differential genes in the samples were screened, and the non-differential genes ACTR1A, GSK3B, PPP1CC and RAC1 were obtained. The specific process is as follows:

[0112] ①The mRNA sequences of 75 pairs of lung adenocarcinoma / paracancer specimens were converted into FASTQ format by using the parameter split files of the software SRAToolkit v2.8.2, and the sequence alignment algorithm FANSe was used to map the first end to the transcriptome reference sequence hg19, with an error of 6 %. Genes (with >10 mapped reads) were quantified by the rpkM method.

[0113] The number of mRNA sequences is denoted by n, while the number of genes with a value greater than or equal to 0.1 rpkM in the nth mRNA sequence is denoted by m. ...

Embodiment 2

[0129] The non-differential high expression of embodiment 2 non-differential gene

[0130] In order to confirm that in random samples, the four target genes obtained in Example 1 have the same trend, the cancer and paracancerous tissues of 12 Chinese lung adenocarcinoma patients were collected for sequencing, and the four non-differential genes screened in Example 1 were explored. Whether genes are not differentially expressed in a random sample.

[0131] According to the kit manufacturer's protocol, the standard MGIEasyTM mRNA library preparation kit V2 was used to prepare the mRNA seq library from the cancer and paracancerous tissues collected from 12 Chinese patients with lung adenocarcinoma. Sequencing was performed on a BGISEQ-500 sequencer in single-end 50nt mode. After the obtained sequencing data is qualitatively and quantitatively analyzed by the FANSE series algorithm, check whether the expression level is different.

[0132] In Example 1, the expression levels of ...

Embodiment 3

[0133] Example 3 The role of non-differential genes in proliferation, migration and invasion of lung adenocarcinoma

[0134] The human lung adenocarcinoma cell lines A549, NCI-H1299 and normal lung epithelial cells HBE used in this example were all purchased from ATCC, and all cell lines had STR reports and mycoplasma negative certificates, and the cells did not appear third-class at each locus Epigenetic phenomenon, no human cell cross-contamination was found in the cells.

[0135]Cell culture: A549, NCI-H1299 and normal lung epithelial cells HBE were inoculated in the medium respectively, in 5% CO in DMEM (Gibco) 2 Cultivate in an incubator, and the medium is a medium supplemented with 10% fetal bovine serum (FBS), 110 mg / L sodium pyruvate and 1% penicillin / streptomycin at 37°C. Before transfection, 5×10 5 Cells were seeded in 6-well plates for 24 hours. Then use Lipofectamine TM 3000 Transfection Reagent (Invitrogen) Cells were transfected with 100 pmol of siRNA and in...

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Abstract

The invention belongs to the technical field of bioinformatics, and discloses a non-differential gene associated with tumor cell malignant phenotypes and a screening method and application thereof, the non-differential gene interacts with a plurality of differential genes of cancerous tissues, is ubiquitous in the cancerous tissues and para-carcinoma tissues, has relatively high abundance expression and no differential expression, and can be used for screening tumor cell malignant phenotypes. And the characteristic of playing a heavy role in a network path is realized. And sorting the genes to be distinguished through an SVM model for distinguishing cancerous tissues and para-carcinoma tissues, and removing differential genes from the genes at the first 5% of the sorted genes to obtain the non-differential genes. With the non-differential gene as a target, the non-differential gene can be used for preparing drugs for preventing or treating tumors related to the non-differential gene. Whether the non-differential genes are knocked down for preventing tumors or knocked down after tumors are formed for controlling tumor development, the screened non-differential genes can inhibit the sizes of mice tumors.

Description

technical field [0001] The application belongs to the technical field of bioinformatics, and relates to tumor targeting genes, especially non-differential genes associated with malignant phenotypes of tumor cells, screening methods and applications thereof. Background technique [0002] From the perspective of precision medicine and translational medicine, finding the common and critical cancer-causing biomacromolecules (including nucleic acids and proteins) is the core of improving the treatment effect. However, the existing key genes are difficult to meet the common and key requirements. . Taking lung adenocarcinoma with a very high mutation rate as an example, the recognized "culprits" of lung adenocarcinoma are driver genes, such as star driver genes EGFR, ALK, etc. Targeted drugs targeting these driver genes have certain effects on lung adenocarcinoma. therapeutic effect, but the effect is still unsatisfactory. Taking EGFR mutation targeted therapy for advanced lung a...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B35/20G16B20/50G16B20/30G16B20/20G06K9/62
CPCG16B20/30G16B20/20G16B20/50G16B35/20G06F18/2411G06F18/214
Inventor 刘婉婷张弓余卓
Owner CHI BIOTECH CO LTD
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