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Significance of platelet adhesion-related genes in colon cancer based on non-negative matrix factorization-based clustering algorithm.

作者信息

Chi Xiao-Jv, Song Yi-Bei, Liu Deng-He, Wei Li-Qiang, An Xin, Feng Zi-Zhen, Lan Xiao-Hua, Lan Dong, Huang Chao

机构信息

Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning, China.

The First Affiliated Hospital of Guangxi Medical University, Nanning, China.

出版信息

Digit Health. 2023 Sep 26;9:20552076231203902. doi: 10.1177/20552076231203902. eCollection 2023 Jan-Dec.

DOI:10.1177/20552076231203902
PMID:37766908
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10521306/
Abstract

BACKGROUND: Although surgical methods are the most effective treatments for colon adenocarcinoma (COAD), the cure rates remain low, and recurrence rates remain high. Furthermore, platelet adhesion-related genes are gaining attention as potential regulators of tumorigenesis. Therefore, identifying the mechanisms responsible for the regulation of these genes in patients with COAD has become important. The present study aims to investigate the underlying mechanisms of platelet adhesion-related genes in COAD patients. METHODS: The present study was an experimental study. Initially, the effects of platelet number and related genomic alteration on survival were explored using real-world data and the cBioPortal database, respectively. Then, the differentially expressed platelet adhesion-related genes of COAD were analyzed using the TCGA database, and patients were further classified by employing the non-negative matrix factorization (NMF) analysis method. Afterward, some of the clinical and expression characteristics were analyzed between clusters. Finally, least absolute shrinkage and selection operator regression analysis was used to establish the prognostic nomogram. All data analyses were performed using the R package. RESULTS: High platelet counts are associated with worse survival in real-world patients, and alternations to platelet adhesion-related genes have resulted in poorer prognoses, based on online data. Based on platelet adhesion-related genes, patients with COAD were classified into two clusters by NMF-based clustering analysis. Cluster2 had a better overall survival, when compared to Cluster1. The gene copy number and enrichment analysis results revealed that two pathways were differentially enriched. In addition, the differentially expressed genes between these two clusters were enriched for POU6F1 in the transcription factor signaling pathway, and for MATN3 in the ceRNA network. Finally, a prognostic nomogram, which included the ALOX12 and ACTG1 genes, was established based on the platelet adhesion-related genes, with a concordance (C) index of 0.879 (0.848-0.910). CONCLUSION: The mRNA expression-based NMF was used to reveal the potential role of platelet adhesion-related genes in COAD. The series of experiments revealed the feasibility of targeting platelet adhesion-associated gene therapy.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/8e0e01b6dda5/10.1177_20552076231203902-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/fd3392187a03/10.1177_20552076231203902-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/2a5887c49a41/10.1177_20552076231203902-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/aaf6fbdcdf4e/10.1177_20552076231203902-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/aef5979dc5fc/10.1177_20552076231203902-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/a10ba75affac/10.1177_20552076231203902-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/e8389c5f8da1/10.1177_20552076231203902-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/0c30578de8be/10.1177_20552076231203902-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/fe110bc26274/10.1177_20552076231203902-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/8e0e01b6dda5/10.1177_20552076231203902-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/fd3392187a03/10.1177_20552076231203902-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/2a5887c49a41/10.1177_20552076231203902-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/aaf6fbdcdf4e/10.1177_20552076231203902-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/aef5979dc5fc/10.1177_20552076231203902-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/a10ba75affac/10.1177_20552076231203902-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/e8389c5f8da1/10.1177_20552076231203902-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/0c30578de8be/10.1177_20552076231203902-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/fe110bc26274/10.1177_20552076231203902-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9211/10521306/8e0e01b6dda5/10.1177_20552076231203902-fig9.jpg

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Significance of platelet adhesion-related genes in colon cancer based on non-negative matrix factorization-based clustering algorithm.

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[2]
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Transl Lung Cancer Res. 2022-6

[3]
Upregulation of lncRNA PINK1-AS Predicts the Distant Metastasis of Patients with Small Cell Lung Cancer.

Mol Biotechnol. 2023-1

[4]
New dawn for cancer cell death: Emerging role of lipid metabolism.

Mol Metab. 2022-9

[5]
Discovery and Validation of a Novel Metastasis-Related lncRNA Prognostic Signature for Colorectal Cancer.

Front Genet. 2022-5-19

[6]
Characterization of Tumor Mutation Burden-Based Gene Signature and Molecular Subtypes to Assist Precision Treatment in Gastric Cancer.

Biomed Res Int. 2022

[7]
The Expression Profile, Clinical Application and Potential Tumor Suppressing Mechanism of hsa_circ_0001675 in Head and Neck Carcinoma.

Front Oncol. 2022-5-6

[8]
The effects of Epigallocatechin-3-gallate and Dabrafenib combination on apoptosis and the genes involved in epigenetic events in anaplastic thyroid cancer cells.

Med Oncol. 2022-5-23

[9]
Analysis of the lncRNA-miRNA-mRNA Network Reveals a Potential Regulatory Mechanism of EGFR-TKI Resistance in NSCLC.

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[10]
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