open access

Vol 24, No 5 (2017)
Original articles — Basic science and experimental cardiology
Published online: 2017-04-27
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Heart failure: Pilot transcriptomic analysis of cardiac tissue by RNA-sequencing

Concetta Schiano, Valerio Costa, Marianna Aprile, Vincenzo Grimaldi, Ciro Maiello, Roberta Esposito, Andrea Soricelli, Vittorio Colantuoni, Francesco Donatelli, Alfredo Ciccodicola, Claudio Napoli
DOI: 10.5603/CJ.a2017.0052
·
Pubmed: 28497843
·
Cardiol J 2017;24(5):539-553.

open access

Vol 24, No 5 (2017)
Original articles — Basic science and experimental cardiology
Published online: 2017-04-27

Abstract

Background: Despite left ventricular (LV) dysfunction contributing to mortality in chronic heart failure (HF), the molecular mechanisms of LV failure continues to remain poorly understood and myocardial biomarkers have yet to be identified. The aim of this pilot study was to investigate specific transcriptome changes occurring in cardiac tissues of patients with HF compared to healthy condition patients to improve diagnosis and possible treatment of affected subjects.

Methods: Unlike other studies, only dilated cardiomyopathy (DCM) (n = 2) and restrictive cardiomyopathy (RCM) (n = 2) patients who did not report family history of the disease were selected with the aim of obtaining a homogeneous population for the study. The transcriptome of all patients were studied by RNA-sequencing (RNA-Seq) and the read counts were adequately filtered and normalized using a recently developed user-friendly tool for RNA-Seq data analysis, based on a new graphical user interface (RNA-SeqGUI).

Results: By using this approach in a pairwise comparison with healthy donors, we were able to identify DCM- and RCM-specific expression signatures for protein-coding genes as well as for long noncoding RNAs (lncRNAs). Differential expression of 5 genes encoding different members of the mediator complex was disclosed in this analysis. Interestingly, a significant alteration was found for genes which had never been associated with HF until now, and 27 lncRNA/mRNA pairs that were significantly altered in HF patients.

Conclusions: The present findings revealed specific expression pattern of both protein-coding and lncRNAs in HF patients, confirming that new LV myocardial biomarkers could be reliably identified using Next-Generation Sequencing-based approaches.

Abstract

Background: Despite left ventricular (LV) dysfunction contributing to mortality in chronic heart failure (HF), the molecular mechanisms of LV failure continues to remain poorly understood and myocardial biomarkers have yet to be identified. The aim of this pilot study was to investigate specific transcriptome changes occurring in cardiac tissues of patients with HF compared to healthy condition patients to improve diagnosis and possible treatment of affected subjects.

Methods: Unlike other studies, only dilated cardiomyopathy (DCM) (n = 2) and restrictive cardiomyopathy (RCM) (n = 2) patients who did not report family history of the disease were selected with the aim of obtaining a homogeneous population for the study. The transcriptome of all patients were studied by RNA-sequencing (RNA-Seq) and the read counts were adequately filtered and normalized using a recently developed user-friendly tool for RNA-Seq data analysis, based on a new graphical user interface (RNA-SeqGUI).

Results: By using this approach in a pairwise comparison with healthy donors, we were able to identify DCM- and RCM-specific expression signatures for protein-coding genes as well as for long noncoding RNAs (lncRNAs). Differential expression of 5 genes encoding different members of the mediator complex was disclosed in this analysis. Interestingly, a significant alteration was found for genes which had never been associated with HF until now, and 27 lncRNA/mRNA pairs that were significantly altered in HF patients.

Conclusions: The present findings revealed specific expression pattern of both protein-coding and lncRNAs in HF patients, confirming that new LV myocardial biomarkers could be reliably identified using Next-Generation Sequencing-based approaches.

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Keywords

cardiovascular disease, heart failure, noncodingRNA, mediator complex, RNA-sequencing

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About this article
Title

Heart failure: Pilot transcriptomic analysis of cardiac tissue by RNA-sequencing

Journal

Cardiology Journal

Issue

Vol 24, No 5 (2017)

Pages

539-553

Published online

2017-04-27

DOI

10.5603/CJ.a2017.0052

Pubmed

28497843

Bibliographic record

Cardiol J 2017;24(5):539-553.

Keywords

cardiovascular disease
heart failure
noncodingRNA
mediator complex
RNA-sequencing

Authors

Concetta Schiano
Valerio Costa
Marianna Aprile
Vincenzo Grimaldi
Ciro Maiello
Roberta Esposito
Andrea Soricelli
Vittorio Colantuoni
Francesco Donatelli
Alfredo Ciccodicola
Claudio Napoli

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