Long non-coding RNA profile study identifies a metabolism-related signature for colorectal cancer.

Abstract

BACKGROUND:

Heterogeneity in colorectal cancer (CRC) patients provides novel strategies in clinical decision-making. Identifying distinctive subgroups in patients can improve the screening of CRC and reduce the cost of tests. Metabolism-related long non-coding RNA (lncRNA) can help detection of tumorigenesis and development for CRC patients.

METHODS:

RNA sequencing and clinical data of CRC patients which extracted and integrated from public databases including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were set as training cohort and validation cohort. Metabolism-related genes were acquired from Kyoto Encyclopedia of Genes and Genomes (KEGG) and the metabolism-related lncRNAs were filtered using correlation analysis. The risk score was calculated based on lncRNAs with prognostic value and verified through survival curve, receiver operating characteristic (ROC) curve and risk curve. Prognostic factors of CRC patients were also analyzed. Nomogram was constructed based on the results of cox regression analyses. The different immune status was observed in the single sample Gene Set Enrichment Analysis (ssGSEA).

RESULTS:

The training cohort and the validation cohort enrolled 432 and 547 CRC patients respectively. A total of 23 metabolism-related lncRNAs with prognostic value were screened out and 10 of which were significantly differentially expressed between tumour and normal tissues. Finally, 8 lncRNAs were used to establish a risk score (DICER1-AS1, PCAT6, GAS5, PRR7-AS1, MCM3AP-AS1, GAS6-AS1, LINC01082 and ADIRF-AS1). Patients were divided into high-risk and low-risk groups according to the median of risk scores in training cohort and the survival curves indicated that the survival prognosis was significantly different. The area under curve (AUC) of the ROC curve in two cohorts were both greater than 0.6. The age, tumour stage and risk score were selected as independent factors and used to construct a nomogram to predict CRC patients' survival rate with the c-index of 0.806. The ssGSEA indicated that the risk score was associated with immune cells and functions.

CONCLUSIONS:

Our systematic study established a metabolism-related lncRNA signature to predict outcomes of CRC patients which may contribute to individual prevention and treatment.

• Authors: Yongqu Lu, Wendong Wang, Zhenzhen Liu, Junren Ma, Xin Zhou, Wei Fu
• Journal: Molecular medicine (Cambridge, Mass.) (Mol Med) Vol. 27 Issue 1 Pg. 83 (08 03 2021) ISSN: 1528-3658 [Electronic] England
• PMID: 34344319 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © 2021. The Author(s).

Chemical References

• Biomarkers, Tumor
• RNA, Long Noncoding

Topics

• Biomarkers, Tumor
• Colorectal Neoplasms (genetics, metabolism, mortality, pathology)
• Computational Biology (methods)
• Databases, Genetic
• Energy Metabolism (genetics)
• Gene Expression Profiling
• Gene Expression Regulation, Neoplastic
• Gene Ontology
• Gene Regulatory Networks
• Humans
• Prognosis
• RNA, Long Noncoding (genetics)
• ROC Curve
• Risk Factors
• Transcriptome