Division of Cardiology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, Colorado, United States of America.
ARCA biopharma, Westminster, Colorado, United States of America.
PLoS One. 2019 Aug 30;14(8):e0221519. doi: 10.1371/journal.pone.0221519. eCollection 2019.
To investigate the biologic relevance of cross-platform concordant changes in gene expression in intact human failing/hypertrophied ventricular myocardium undergoing reverse remodeling.
Information is lacking on genes and networks involved in remodeled human LVs, and in the associated investigative best practices.
We measured mRNA expression in ventricular septal endomyocardial biopsies from 47 idiopathic dilated cardiomyopathy patients, at baseline and after 3-12 months of β-blocker treatment to effect left ventricular (LV) reverse remodeling as measured by ejection fraction (LVEF). Cross-platform gene expression change concordance was investigated in reverse remodeling Responders (R) and Nonresponders (NR) using 3 platforms (RT-qPCR, microarray, and RNA-Seq) and two cohorts (All 47 subjects (A-S) and a 12 patient "Super-Responder" (S-R) subset of A-S).
For 50 prespecified candidate genes, in A-S mRNA expression 2 platform concordance (CcpT), but not single platform change, was directly related to reverse remodeling, indicating CcpT has biologic significance. Candidate genes yielded a CcpT (PCR/microarray) of 62% for Responder vs. Nonresponder (R/NR) change from baseline analysis in A-S, and ranged from 38% to 100% in S-R for PCR/microarray/RNA-Seq 2 platform comparisons. Global gene CcpT measured by microarray/RNA-Seq was less than for candidate genes, in S-R R/NR 17.5% vs. 38% (P = 0.036). For S-R global gene expression changes, both cross-cohort concordance (CccT) and CcpT yielded markedly greater values for an R/NR vs. an R-only analysis (by 22 fold for CccT and 7 fold for CcpT). Pathway analysis of concordant global changes for R/NR in S-R revealed signals for downregulation of multiple phosphoinositide canonical pathways, plus expected evidence of a β1-adrenergic receptor gene network including enhanced Ca2+ signaling.
Two-platform concordant change in candidate gene expression is associated with LV biologic effects, and global expression concordant changes are best identified in an R/NR design that can yield novel information.
研究在接受反向重构的完整人类衰竭/肥大心室心肌中，跨平台一致的基因表达变化的生物学相关性。
缺乏关于参与重构的人类左心室（LV）的基因和网络的信息，以及相关的调查最佳实践。
我们测量了 47 例特发性扩张型心肌病患者的室间隔内膜心肌活检标本中的 mRNA 表达，这些患者在接受β受体阻滞剂治疗 3-12 个月后，左心室（LV）射血分数（LVEF）发生了反向重构。使用 3 个平台（RT-qPCR、微阵列和 RNA-Seq）和两个队列（所有 47 例患者（A-S）和 A-S 的 12 例“超级应答者”（S-R）亚组）研究了反向重构应答者（R）和非应答者（NR）的跨平台基因表达变化一致性。
对于 50 个预设候选基因，在 A-S 中，2 个平台的一致性（CcpT），而不是单个平台的变化，与反向重构直接相关，表明 CcpT 具有生物学意义。候选基因在 A-S 的基线分析中产生了应答者与非应答者（R/NR）变化的 CcpT（PCR/微阵列）为 62%，而在 S-R 的 PCR/微阵列/RNA-Seq 2 个平台比较中范围为 38%至 100%。通过微阵列/RNA-Seq 测量的全局基因 CcpT 小于候选基因，在 S-R 的 R/NR 中为 17.5%比 38%（P=0.036）。对于 S-R 的全局基因表达变化，跨队列一致性（CccT）和 CcpT 均为 R/NR 分析产生了明显更高的值，而不是仅 R 分析（CccT 为 22 倍，CcpT 为 7 倍）。在 S-R 中，对 R/NR 的一致的全局变化的途径分析显示了多个磷酸肌醇经典途径下调的信号，以及预期的β1-肾上腺素能受体基因网络的证据，包括增强的 Ca2+信号。
候选基因表达的 2 个平台一致性变化与 LV 的生物学效应相关，而在 R/NR 设计中，最佳识别全局表达一致性变化可以产生新的信息。
