Targeted myocardial gene expression in failing hearts by RNA sequencing
© The Author(s) 2016
Received: 6 July 2016
Accepted: 14 November 2016
Published: 25 November 2016
Myocardial recovery with left ventricular assist device (LVAD) therapy is highly variable and difficult to predict. Next generation ribonucleic acid (RNA) sequencing is an innovative, rapid, and quantitative approach to gene expression profiling in small amounts of tissue. Our primary goal was to identify baseline transcriptional profiles in non-ischemic cardiomyopathies that predict myocardial recovery in response to LVAD therapy. We also sought to verify transcriptional differences between failing and non-failing human hearts.
RNA was isolated from failing (n = 16) and non-failing (n = 8) human hearts. RNA from each patient was reverse transcribed and quantitatively sequenced on the personal genome machine (PGM) sequencer (Ion torrent) for 95 heart failure candidate genes. Coverage analysis as well as mapping the reads and alignment was done using the Ion Torrent Browser Suite™. Differential expression analyses were conducted by empirical analysis of digital gene expression data in R (edgeR) to identify differential expressed genes between failing and non-failing groups, and between responder and non-responder groups respectively. Targeted cardiac gene messenger RNA (mRNA) expression was analyzed in proportion to the total number of reads. Gene expression profiles from the PGM sequencer were validated by performing RNA sequencing (RNAseq) with the Illumina Hiseq2500 sequencing system.
The failing sample population was 75% male with an average age of 50 and a left ventricular ejection fraction (LVEF) of 16%. Myosin light chain kinase (MYLK) and interleukin (IL)-6 genes expression were significantly higher in LVAD responders compared to non-responders. Thirty-six cardiac genes were expressed differentially between failing and non-failing hearts (23 decreased, 13 elevated). MYLK, Beta-1 adrenergic receptor (ADRB1) and myosin heavy chain (MYH)-6 expression were among those significantly decreased in failing hearts compared to non-failing hearts. Natriuretic peptide B (NPPB) and IL-6 were significantly elevated. Targeted gene expression profiles obtained from the Ion torrent PGM sequencer were consistent with those obtained from Illumina HiSeq2500 sequencing system.
Heart failure is associated with a network of transcriptional changes involving contractile proteins, metabolism, adrenergic receptors, protein phosphorylation, and signaling factors. Myocardial MYLK and IL-6 expression are positively correlated with ejection fraction (EF) response to LVAD placement. Targeted RNA sequencing of myocardial gene expression can be utilized to predict responders to LVAD therapy and to better characterize transcriptional changes in human heart failure.
Left ventricular assist devices are commonly being utilized to treat patients with advanced heart failure . Mortality due to infection, bleeding, stroke, right heart failure and device malfunction continues as a significant problem in this population but increasingly patients are receiving these devices as destination therapy . Cardiac transplantation is not an option for the majority of these patients due to limitations in donor supply . Myocardial recovery with LVAD therapy to the degree that allows device explant remains relatively rare for these patients [1, 3]. LVAD therapy may be associated with myocardial atrophy, changes in transcriptional profiles, and persistent abnormalities in protein phosphorylation [4, 5].
There is however increasing evidence that a subset of patients with LVAD therapy may remodel and recover sufficient myocyte function to allow device explant. Utilizing ventricular unloading, myocardial conditioning and guideline directed heart failure medical therapy it may feasible to explant a significant number of patients with LVADs . Myocardial recovery, while unusual in ischemic cardiomyopathies, may occur in 20–25% of non-ischemic cardiomyopathy patients .
Heart failure is characterized on a molecular level by transcriptional changes involving adrenergic signaling mechanisms, calcium handling, contractile proteins, inflammation, and metabolism . Next-generation sequencing allows for gene expression quantification, the study of epigenetic effects, identification of signal nucleotide polymorphisms and measurement of transcriptional variations. Understanding the transcriptome is essential to understanding disease development, progression, and response to therapeutics. Transcriptional profiling is currently being used to guide treatment in many forms of cancer and to diagnose cardiac rejection. It is unknown if gene expression profiles can predict response to LVAD therapy. Our primary goal was to identify transcriptional profiles in non-ischemic cardiomyopathy patients that predict myocardial recovery. We also sought to verify transcriptional differences between failing and non-failing human hearts utilizing targeted non-optical sequencing.
This study was approved by the IRB at the University of Nebraska Medical Center. Failing tissue was obtained from non-ischemic cardiomyopathy patients (n = 16) who met standard criteria for LVAD placement either as destination therapy or as bridge to transplant. Tissue was obtained at the time of LVAD placement and stored in RNA later prior to freezing at −80 °C. Non-failing tissue was obtained by endomyocardial biopsy in transplant patients with normal cardiac function during routine surveillance (n = 8). Cardiac function was evaluated by echocardiography.
Isolation of RNA
RNA was isolated from approximately 10–20 mg of cardiac tissue using the RNeasy® Mini Kit (Qiagen®). Quantitative measurement of the RNA was taken using Qubit® RNA assay kit by Qubit 2.0 fluorometer (Invitrogen, Life Technologies).
Constructing RNA Library
Ion AmpliSeq™ RNA Library Kit and Custom Panels were utilized in the construction of RNA library for this investigation, and all experiments were carried out in accordance with the instructions from the manufacturer (Ion Torrent, Life Technologies). 10 ng of RNA, isolated from the cardiac tissue, is reverse transcribed to synthesize complementary deoxyribonucleic acid (cDNA) using the Ion AmpliSeq™ RNA RT Module and Applied Biosystems thermal cycler. Next target sequences were amplified using Ion AmpliSeq™ RNA Custom Panels and Library Kit (life technologies). Our custom panel was designed to target 95 cardiac genes we previously have associated with reverse remodeling in heart failure utilizing the Ion AmpliSeq™ Designer . After amplification of target sequences, primer sequences were partially digested using FuPa reagent from Ion AmpliSeq™ RNA Library Kit. Ion AmpliSeq™ adaptors were then ligated to the targeted deoxyribonucleic acid (DNA) and purification of those DNA fragments followed. Target DNA sequences were purified in a two-round purification process with Dynabeads® Magnetic Beads where surplus primer sequences and high-molecular weight DNA are isolated and discarded from the solution. Following purification of the library, the library is amplified using Ion AmpliSeq™ RNA Library Kit and further purified using single-round purification with Dynabeads® Magnetic Beads. After amplification and purification of the library, Qubit® 2.0 fluorometer was used with Qubit® dsDNA HS Assay Kit to quantitatively measure the DNA library.
Preparation of targeted DNA template
Amplified stock library was diluted for appropriate Ion library preparation. Ion One Touch™ 2 System was utilized to amplify individual diluted libraries via emulsion polymerase chain reaction (PCR) on ion sphere particles (ISPs). The template-positive ISPs were then enriched using Ion One Touch™ Enrichment System.
Sequencing was performed for all patients on the Ion Torrent PGM utilizing the Ion 316 chip. Coverage analysis as well as mapping the reads and alignment was done using the Ion Torrent Browser Suite™. Gene expression profiles from the PGM sequencer were validated with a subsequent population by performing RNAseq with the Illumina Hiseq2500 sequencing system. RNAs from 7 non failing and 3 failing samples were sequenced using the Illumina HiSeq2500 sequencing system (University of Nebraska Medical Center, DNA core facility). All paired end sequencing adaptors were trimmed using fqtrim and any reads shorter than 36 bases were discarded. A quality filter using fqtrim −q 5 was then applied to the reads. Paired end reads that passing those filters were mapped to Homo sapiens (release 37) reference sequence (GRCh37/hg19); using BowTie2 and TopHat2. The raw read counts per gene were generated using the Rsubread package.
For the LVAD responder analysis the failing heart patients were divided into two groups: responders (∆LVEF ≥ 20%) and non-responders (∆LVEF < 20%). The expression of each gene on the cardiac panel was assessed in proportion to the total reads on the chip. The differential expression analysis was conducted using edgeR package in bioconductor developed by Robinson et al. [9, 10]. Differential gene expression between the non-failing heart patients (n = 8) and failing heart patients (n = 16) was analyzed in a similar fashion. The gene Calreticulin 3 (CALR3) was removed from the data due to 21 samples had zero counts for this gene. Spearman’s correlation coefficients were calculated to evaluate inter-platform consistency for raw counts and normalized counts per million (cpm) across two platforms (Ion Torrent and Illumina). The normalization factors for the data were estimated by the trimmed mean of the M-values normalization method in the edgeR package and used to adjust for varying sequencing depths and potentially other technical effects across samples.
To further evaluate the biological pathways, log fold change utilizing Ingenuity Pathway Analysis (IPA) was carried out on the targeted panel genes between failing and non-failing samples.
Non-failing hearts, n = 8
Failing hearts, n = 16
50 ± 13.30
50 ± 16.43
Comorbid illness (%)
LVEF at presentation (%)
60 ± 4.63
15.75 + 10.75
3.68 + 0.60
LVAD in place 50%/heart transplant 44%/deceased 6%
Responder vs non-responder RNA-Seq
Failing vs non-failing RNA-Seq results
Functional and pathway analysis in IPA
Top canonical pathways
Nitric oxide signaling in the cardiovascular system
Protein kinase A signaling
Tight junction signaling
Hepatic fibrosis/hepatic stellate cell activation
Top upstream regulators
Molecular and cellular functions
1.49E−03 to 1.70E−08
1.40E−03 to 3.96E−08
1.09E−03 to 3.96E−08
Cell death and survival
1.57E−03 to 1.29E−07
Cell-to-cell signaling and interaction
1.49E−03 to 2.21E−07
Top tox lists
Cardiac necrosis/cell death
Increases heart failure
To validate the results obtained from Ion torrent PGM sequencer by RNAseq analysis, Illumina HiSeq sequencing was utilized. Ten patients were sequenced for selected 95 genes using RNAseq method on both sequencing platforms (Illumina HiSeq and Ion Torrent). Illumina data were processed to obtain raw read counts for genes by BowTie, TopHat, and Rsubread packages respectively [19–21]. To evaluate inter-platform consistency for gene expression measures, we computed Spearman’s correlation between raw counts and normalized cpm from two platforms for each individual, and the average spearman’s correlation across 10 individuals. The results demonstrated high inter-platform consistency for gene expression measures across two platforms. (Spearman R ≥ 0.83 for each patient sample, and average Spearman R = 0.84 using raw counts. Spearman R ≥ 0.84 for each patient sample and average Spearman R = 0.86 using normalized cpm).
The main findings of this study are that MYLK2 is diminished in heart failure, predicts response to LVAD therapy, and does not improve in advanced heart failure patients post LVAD who require transplantation. Our results further characterize transcriptional changes between failing and non-failing human hearts and identify gene expression profiles associated with myocardial recovery on LVAD therapy. Heart failure is a heterogeneous disease process. Etiology, disease duration, cardiac remodeling, medical therapy, and molecular signatures have all been associated with myocardial recovery in non-ischemic cardiomyopathies. Recent studies suggest that up to 20 percent of patients may recover their cardiac function within their first year post LVAD . Molecular phenotyping is increasingly being utilized as a clinical tool to risk stratify patients and guide clinical decision making. Transcriptional profiles are being utilized to screen heart transplant patient for rejection, identify patients with coronary disease, and guide treatment decisions for cancer patients. It may be feasible utilizing clinical characteristics and molecular markers to risk stratify patients for early transplant versus more prolonged aggressive attempts to recover myocardial function with medical and device therapies. Previous studies have identified myocardial microRNA (miRNA) signatures as potential biomarkers of recovery. Our results suggest that mRNA patterns may also be helpful in risk stratifying patients undergoing LVAD therapy.
Baseline MYLK and IL-6 levels were both abnormal in failing myocardium and associated with response to LVAD therapy. Myosin is comprised of two heavy chain and two pairs of light chains. Myosin light chain 2 (MLC-2) is a key regulatory component of myosin. Phosphorylation of MLC-2 is known to regulate both calcium sensitivity as well as sarcomere assembly [11, 23, 24]. MLC-2 can be phosphorylated by MYLK or protein kinase C and is dephosphorylated by light chain phosphatase. MLC-2 phosphorylation is known to be decreased in the end-stage failing human heart . Our results would suggest that down-regulation of MYLK expression maybe contributing to this process. The association of higher levels of MYLK with improved myocardial recovery on LVAD therapy is consistent with prior evidence supporting this gene as an adaptive mechanism which facilities sarcomere organization in response to hypertrophic stimuli. Persistent abnormalities in MYLK post LVAD therapy in patients who did not recover are consistent with ongoing stress and injury in this population.
IL-6 is known to be elevated systemically in heart failure and levels have been associated with severity of disease . Elevated expression of myocardial IL-6 in advanced heart failure could be contributing to this process. IL-6 can be produced by leukocytes, endothelial cells or vascular smooth muscle cells. Levels have been correlated with hemodynamic and neurohormonal variables. IL-6 is capable of producing myocardial dysfunction, vascular dilation, and muscle wasting. It is paradoxical that higher IL-6 levels at baseline are associated with enhanced recovery with LVAD therapy. IL-6 appears to be an important mediator in ventricular hypertrophy and does increase nitric oxide production . These mechanisms may play an important role in adapting to heart failure. IL-6 is extremely inducible in response to IL-1, TNFα, viral infection and angiotensin II peptide. It acts through two distinct mechanisms. The first one is a classic membrane receptor initiated pathway and the second one is trans-signaling pathway. It has been shown that IL-6 induces and activates signal transducer and activator of transcription 3 (STAT3) gene by engaging the suppressor of cytokine signaling 3 (SOCS3) gene. Multiple studies showed that the activation of STAT3 promotes cardiomyocyte survival and hypertrophy, as well as cardiac angiogenesis . Our results suggest LVAD therapy decreases myocardial IL-6 expression substantially even in patients who do not recover. Hence, it is unlikely to be contributing to the failure of myocardial recovery in patients post LVAD.
Heart failure is a complex molecular disease process involving more than IL-6 and MYLK. Numerous transcriptional changes have been described involving a complex gene network including contractile proteins, calcium handling, metabolism, signal transduction, apoptosis and inflammation [8, 29–31]. High throughput RNA sequencing now allows for the rapid quantification of gene expression in small amounts of tissue either globally or in a targeted fashion.
Most next generation sequencing technologies currently on the market use image capture, fluorescent detection or optical registration of some kind to capture sequencing data, which is then, converted to digital information. Our study utilized direct sequencing on a disposable semiconductor chip in a targeted fashion. This technology is relatively rapid, inexpensive and allows for quantification of mRNA over a broad range of gene expression levels. Between failing and non-failing human hearts we identify 36 genes that are differentially expressed. Other studies have previously identified these genes in association with heart failure and sequencing by optical and non-optical methodologies produced similar results. This suggests that RNA sequencing might provide a valuable tool to further characterize the molecular mechanisms of heart failure.
This study has several limitations. In regards to recovery, it is a single center retrospective analysis. There are several potential confounders that were not evaluated including genetic etiologies which could have impacted recovery independent of baseline gene expression. The study evaluated the transcriptome of only a limited number of genes. There are almost certainly other genes whose expression may be predictive of recovery or important mechanistically in heart failure. Finally, the transplant patients utilized as controls within this study may have different gene expression secondary to other factors such as immunosuppressive therapy independent of contractile dysfunction. For this reason we targeted candidate genes that previously have been identified in association with heart failure or myocardial remodeling.
While cardiac transplantation remains the gold standard for treating advanced heart failure, it is not an effective option for the majority of patients due to limitations in donor supply. The number of patients receiving left ventricular assist devices is growing exponentially. Less than 1% of patients are currently having their devices explanted for recovery. The rapid evolution in sequencing technologies may allow us to better classify LVAD patients who may recover. Prospective clinical trials to identify biomarkers of recovery are needed to help decision making in this population of patients. RNA signatures and clinical characteristics may ultimately help identify a subset of patients who can recover cardiac function.
MYLK2 is diminished in heart failure, predicts response to LVAD therapy, and does not improve in advanced heart failure patients post LVAD who require transplantation. Targeted next generation RNA sequencing allows rapid quantitative characterization of the transcriptional changes that occur in heart failure. Changes in this gene network involves contractile proteins, calcium handling, metabolism, signal transduction, apoptosis and inflammation. Pathway analysis suggests that these changes ultimately contribute to cardiac hypertrophy, cardiac necrosis, cell death, increased heart failure risk and cardiac fibrosis.
left ventricular assist device
personal genome machine
(empirical analysis of digital gene expression data in R)
left ventricular ejection fraction
myosin light chain kinase
Beta-1 adrenergic receptor
myosin heavy chain 6
natriuretic peptide B
polymerase chain reaction
ion sphere particles
change in left ventricular ejection fraction
counts per million
Ingenuity Pathway Analysis
New York Heart Association
change in ejection fraction
myosin light chain 2
signal transducer and activator of transcription 3
suppressor of cytokine signaling 3
BL, ER, JU, MM, DA and RZ were responsible for patient care and recruitment. KD, ER, JE and AM were responsible for laboratory analysis. JK was responsible for data analysis and FQ was responsible for statistical analysis. All authors read and approved the final manuscript.
This work was supported by the William Dodge Angle Endowment, NIH P20 HL101435, PI: Lowes, Brian, and the Free Radicals in Medicine Program at the University of Nebraska Medical Center. We also want to acknowledge Kathy Duncan for the clerical support she provided.
The authors declare that they have no competing interests.
Compliance with ethical guidelines
This study was approved by the IRB at the University of Nebraska Medical Center.
William Dodge Angle Endowment, P20 HL101435 (Brian Lowes PI).
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