Targeted myocardial gene expression in failing hearts by RNA sequencing.
Targeted myocardial gene expression in failing hearts by RNA sequencing.
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DOI：
10.1186/s12967-016-1083-6
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发表时间：
2016-11-25
影响因子：
7.4
通讯作者：
Lowes BD
中科院分区：
文献类型：
--
作者：
Dhar K;Moulton AM;Rome E;Qiu F;Kittrell J;Raichlin E;Zolty R;Um JY;Moulton MJ;Basma H;Anderson DR;Eudy JD;Lowes BD
左心室辅助装置（LVAD）治疗的心肌恢复具有高度可变性且难以预测。下一代核糖核酸（RNA）测序是一种创新的、快速的、定量的方法，可以在少量组织中进行基因表达谱分析。我们的主要目标是确定非缺血性心肌病的基线转录谱，预测LVAD治疗后心肌的恢复。我们还试图验证失败和非失败人类心脏之间的转录差异。从衰竭（n = 16）和非衰竭（n = 8）人心脏分离RNA。将来自每个患者的RNA逆转录并在个人基因组机器（PGM）测序仪（Ion torrent）上定量测序95个心力衰竭候选基因。使用Ion Torrent Browser Suite ™进行覆盖分析以及绘制读数和比对。通过R（edgeR）中的数字基因表达数据的经验分析进行差异表达分析，以分别鉴定失败组和非失败组之间以及应答者组和非应答者组之间的差异表达基因。靶向心脏基因信使RNA（mRNA）表达与读数总数成比例进行分析。通过用Illumina Hiseq 2500测序系统进行RNA测序（RNAseq）来验证来自PGM测序仪的基因表达谱。不合格的样本人群为75%的男性，平均年龄为50岁，左心室射血分数（LVEF）为16%。肌球蛋白轻链激酶（MYLK）和白细胞介素（IL）-6基因表达在LVAD应答者中显著高于无应答者。36个心脏基因在衰竭和非衰竭心脏之间表达差异（23个降低，13个升高）。与非衰竭心脏相比，衰竭心脏中MYLK、β-1肾上腺素能受体（ADRB 1）和肌球蛋白重链（MYH）-6表达显著降低。利钠肽B（NPP B）和IL-6显著升高。从Ion torrent PGM测序仪获得的靶基因表达谱与从Illumina HiSeq2500测序系统获得的那些一致。心力衰竭与涉及收缩蛋白、代谢、肾上腺素能受体、蛋白磷酸化和信号传导因子的转录变化网络相关。心肌MYLK和IL-6表达与左心室辅助装置置入后的射血分数（EF）反应呈正相关。心肌基因表达的靶向RNA测序可用于预测LVAD治疗的应答者，并更好地表征人类心力衰竭中的转录变化。
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.
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影响因子：
8.9
作者：
Lowes, BD;Zolty, R;Bristow, MR
通讯作者：
Bristow, MR
影响因子：
8.9
作者：
Lowes, Brian D.;Zolty, Ronald;Cleveland, Joseph, Jr.
通讯作者：
Cleveland, Joseph, Jr.
影响因子：
1.9
作者：
Hou T;Tieu BC;Ray S;Recinos Iii A;Cui R;Tilton RG;Brasier AR
通讯作者：
Brasier AR
DOI：
10.1073/pnas.92.11.4862
发表时间：
1995-05-23
影响因子：
11.1
作者：
HIROTA, H;YOSHIDA, K;TAGA, T
通讯作者：
TAGA, T
影响因子：
14.9
作者：
McCarthy DJ;Chen Y;Smyth GK
通讯作者：
Smyth GK