Increased expression of human endogenous retrovirus K in endomyocardial biopsies from patients with cardiomyopathy - a transcriptomics meta-analysis

Most studied, investigating transcriptional changes in myocardial biopsies focus on human genes. However, the presence and potential consequence of persistent expression of viral genes within the myocardium is unclear. The aim of the study was to analyze viral gene expression in RNAseq data from end...

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Bibliographic Details
Published in:BMC genomics 2024-07, Vol.25 (1), p.707-9, Article 707
Main Authors: Heckmann, Markus B, Finke, Daniel, Sauerbrey, Leander, Frey, Norbert, Lehmann, Lorenz H
Format: Article
Language:English
Subjects:
Analysis
Biopsy
Cardiomyopathies - genetics
Cardiomyopathies - metabolism
Cardiomyopathies - pathology
Cardiomyopathies - virology
Cardiomyopathy
Cardiomyopathy, Dilated
Cardiovascular disease
Care and treatment
Data analysis
Dilated cardiomyopathy
Endogenous retrovirus K
Endogenous retroviruses
Endogenous Retroviruses - genetics
Gene expression
Gene Expression Profiling
Gene sequencing
Genes
Genetic aspects
Genomes
Heart
Humans
Ischemia
Myocardium
Myocardium - metabolism
Myocardium - pathology
Oxidative phosphorylation
Phosphorylation
Risk factors
RNA sequencing
RNAseq
Statistical analysis
Transcriptome
Transcriptomics
Variance analysis
Viral expression
Viruses
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Summary:Most studied, investigating transcriptional changes in myocardial biopsies focus on human genes. However, the presence and potential consequence of persistent expression of viral genes within the myocardium is unclear. The aim of the study was to analyze viral gene expression in RNAseq data from endomyocardial biopsies. The NCBI Bioproject library was screened for published projects that included bulk RNA sequencing data from endomyocardial biopsies from both healthy and diseased patients with a sample size greater than 20. Diseased patients with hypertrophic, dilated, and ischemic cardiomyopathies were included. A total of 507 patients with 507 samples from 6 bioprojects were included and mapped to the human genome (hg38). Unmappable sequences were extracted and mapped to an artificial 'super-virus' genome comprising 12,182 curated viral reference genomes. Subsequently, the sequences were reiteratively permutated and mapped again to account for randomness. In total, sequences from 68 distinct viruses were found, all of which were potentially human pathogenic. No increase in cardiotropic viruses was found in patients with dilated cardiomyopathy. However, the expression levels of the particle forming human endogenous retrovirus K were significantly increased (q 
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-024-10595-6