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Volume 13
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Article

A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach

by
Tianfu Wei
1,2,†,
Jifeng Liu
1,2,†,
Shurong Ma
1,2,
Mimi Wang
3,
Qihang Yuan
1,2,
Anliang Huang
3,
Zeming Wu
4,
Dong Shang
1,2,3,* and
Peiyuan Yin
1,2,3,*
1
Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
2
Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
3
Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
4
iPhenome Biotechnology (Yun Pu Kang) Inc., Dalian 116000, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Metabolites 2023, 13(11), 1116; https://doi.org/10.3390/metabo13111116
Submission received: 14 August 2023 / Revised: 25 September 2023 / Accepted: 29 September 2023 / Published: 30 October 2023
(This article belongs to the Special Issue State-of-the-Art Metabolomics and Lipidomics in Life Sciences: Methods and Applications)
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Abstract

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. The in-depth study of genes and metabolites related to nucleotide metabolism will provide new ideas for predicting the prognosis of HCC patients. This study integrated the transcriptome data of different cancer types to explore the characteristics and significance of nucleotide metabolism-related genes (NMGRs) in different cancer types. Then, we constructed a new HCC classifier and prognosis model based on HCC samples from TCGA and GEO, and detected the gene expression level in the model through molecular biology experiments. Finally, nucleotide metabolism-related products in serum of HCC patients were examined using untargeted metabolomics. A total of 97 NMRGs were obtained based on bioinformatics techniques. In addition, a clinical model that could accurately predict the prognostic outcome of HCC was constructed, which contained 11 NMRGs. The results of PCR experiments showed that the expression levels of these genes were basically consistent with the predicted trends. Meanwhile, the results of untargeted metabolomics also proved that there was a significant nucleotide metabolism disorder in the development of HCC. Our results provide a promising insight into nucleotide metabolism in HCC, as well as a tailored prognostic and chemotherapy sensitivity prediction tool for patients.
Keywords: nucleotide metabolism; hepatocellular carcinoma; prognosis signature; molecular classification; chemotherapy sensitivity; tumor immune microenvironment nucleotide metabolism; hepatocellular carcinoma; prognosis signature; molecular classification; chemotherapy sensitivity; tumor immune microenvironment
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MDPI and ACS Style

Wei, T.; Liu, J.; Ma, S.; Wang, M.; Yuan, Q.; Huang, A.; Wu, Z.; Shang, D.; Yin, P. A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach. Metabolites 2023, 13, 1116. https://doi.org/10.3390/metabo13111116

AMA Style

Wei T, Liu J, Ma S, Wang M, Yuan Q, Huang A, Wu Z, Shang D, Yin P. A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach. Metabolites. 2023; 13(11):1116. https://doi.org/10.3390/metabo13111116

Chicago/Turabian Style

Wei, Tianfu, Jifeng Liu, Shurong Ma, Mimi Wang, Qihang Yuan, Anliang Huang, Zeming Wu, Dong Shang, and Peiyuan Yin. 2023. "A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach" Metabolites 13, no. 11: 1116. https://doi.org/10.3390/metabo13111116

APA Style

Wei, T., Liu, J., Ma, S., Wang, M., Yuan, Q., Huang, A., Wu, Z., Shang, D., & Yin, P. (2023). A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach. Metabolites, 13(11), 1116. https://doi.org/10.3390/metabo13111116

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