Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers

Kemal Marc Akat; D’Vesharronne Moore-McGriff; Pavel Morozov; Miguel Brown; Tasos Gogakos; Joel Correa Da Rosa; Aleksandra Mihailovic; Markus Sauer; Ruiping Ji; Aarthi Ramarathnam; Hana Totary-Jain; Zev Williams; Thomas Tuschl; P. Christian Schulze

doi:10.1073/pnas.1401724111

New Research In

Edited by Christine E. Seidman, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, and approved June 10, 2014 (received for review January 28, 2014)

Significance

Heart failure (HF) has a high morbidity and mortality and its incidence is increasing worldwide. While protein biomarkers have been established for diagnostic and prognostic evaluation of patients with HF, there is currently no systematic assessment of RNA biomarkers. We determined the composition of myocardial tissue and circulating microRNAs (miRNAs) in a large cohort of patients with stable and advanced HF and compared it to the composition of normal adult and fetal samples. The advanced HF patients underwent mechanical unloading with left ventricular assist devices and samples were collected at different postoperative time points. Our findings provide the underpinning for miRNA-based therapies and emphasize the usefulness of circulating miRNAs as biomarkers for heart injury performing similar to established diagnostic protein biomarkers.

Abstract

Heart failure (HF) is associated with high morbidity and mortality and its incidence is increasing worldwide. MicroRNAs (miRNAs) are potential markers and targets for diagnostic and therapeutic applications, respectively. We determined myocardial and circulating miRNA abundance and its changes in patients with stable and end-stage HF before and at different time points after mechanical unloading by a left ventricular assist device (LVAD) by small RNA sequencing. miRNA changes in failing heart tissues partially resembled that of fetal myocardium. Consistent with prototypical miRNA–target-mRNA interactions, target mRNA levels were negatively correlated with changes in abundance for highly expressed miRNAs in HF and fetal hearts. The circulating small RNA profile was dominated by miRNAs, and fragments of tRNAs and small cytoplasmic RNAs. Heart- and muscle-specific circulating miRNAs (myomirs) increased up to 140-fold in advanced HF, which coincided with a similar increase in cardiac troponin I (cTnI) protein, the established marker for heart injury. These extracellular changes nearly completely reversed 3 mo following initiation of LVAD support. In stable HF, circulating miRNAs showed less than fivefold differences compared with normal, and myomir and cTnI levels were only captured near the detection limit. These findings provide the underpinning for miRNA-based therapies and emphasize the usefulness of circulating miRNAs as biomarkers for heart injury performing similar to established diagnostic protein biomarkers.

Footnotes

↵¹To whom correspondence may be addressed. Email: ttuschl{at}rockefeller.edu or pcs2121{at}cumc.columbia.edu.

Author contributions: K.M.A., T.T., and P.C.S. designed research; K.M.A., D.M.-M., A.M., R.J., and A.R. performed research; H.T.-J. and Z.W. contributed new reagents/analytic tools; K.M.A., P.M., M.B., T.G., J.C.D.R., M.S., and T.T. analyzed data; and K.M.A., T.T., and P.C.S. wrote the paper.
Conflict of interest statement: T.T. is a cofounder of and scientific advisor to Alnylam Pharmaceuticals and a scientific advisor to Regulus Therapeutics.
This article is a PNAS Direct Submission.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE53081).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1401724111/-/DCSupplemental.

Freely available online through the PNAS open access option.

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