A susceptibility biomarker identification strategy based on significantly differentially expressed ceRNA triplets for
Yuqing Zou1, Yahui Wang1, Zherou Rong1
1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China.
Insights
Researchers identified novel biomarkers for ischemic cardiomyopathy (ICM), a deadly heart condition lacking diagnostic tools. This discovery aids ICM diagnosis and treatment and offers a new strategy for other diseases.
Area of Science:
- Cardiovascular Biology
- Genomics
- Biomarker Discovery
Background:
- Ischemic cardiomyopathy (ICM) is a prevalent and fatal heart disease.
- The absence of effective biomarkers hinders ICM research and clinical management.
- Identifying reliable biomarkers is crucial for advancing the understanding and treatment of ICM.
Purpose of the Study:
- To identify novel susceptibility biomarkers for ischemic cardiomyopathy (ICM).
- To develop a robust strategy for biomarker discovery in diseases lacking public data.
- To aid in the diagnosis and treatment of ICM.
Main Methods:
- Utilized RNA-Seq and miRNA-Seq data from ICM and normal samples.
- Constructed significantly differentially expressed competing endogenous RNA (ceRNA) triplets using permutation tests.
- Screened candidate ICM susceptible genes within enriched ceRNA triplets and identified correlated lncRNAs.
Main Results:
- Identified eight ICM susceptibility genes and their significantly correlated lncRNAs.
- Achieved high classification accuracy for the identified biomarkers.
- Demonstrated the potential of the proposed strategy for discovering biomarkers in other complex diseases.
Conclusions:
- The identified eight genes and correlated lncRNAs serve as promising biomarkers for ICM diagnosis and treatment.
- The developed strategy offers a valuable approach for biomarker discovery in diseases lacking public databases.
- This research contributes to improving the clinical management of ischemic cardiomyopathy.
Abstract:
Ischemic cardiomyopathy (ICM) is a common human heart disease that causes death. No effective biomarkers for ICM could be found in existing databases, which is detrimental to the in-depth study of this disease. In the present study, ICM susceptibility biomarkers were identified using a proposed strategy based on RNA-Seq and miRNA-Seq data of ICM and normal samples. Significantly differentially expressed competing endogenous RNA (ceRNA) triplets were constructed using permutation tests and differentially expressed mRNAs, miRNAs and lncRNAs. Candidate ICM susceptible genes were screened out as differentially expressed genes in significantly differentially expressed ceRNA triplets enriched in ICM-related functional classes. Finally, eight ICM susceptibility genes and their significantly correlated lncRNAs with high classification accuracy were identified as ICM susceptibility biomarkers. These biomarkers would contribute to the diagnosis and treatment of ICM. The proposed strategy could be extended to other complex diseases without disease biomarkers in public databases.
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