J. David Port

Differential Expression and Localization of the mRNA Binding Proteins, AU‐Rich Element mRNA Binding Protein (AUF1) and Hu Antigen R (HuR), in Neoplastic Lung Tissue

Modulation of gene expression at the level of mRNA stability has emerged as an important regulatory paradigm. In this context, differential expression of numerous mRNAs in normal versus neoplastic tissues has been described. Altered expression of these genes, at least in part, has been demonstrated to be at the level of mRNA stability. Two ubiquitously expressed mRNA binding proteins have recently been implicated in the stabilization (Hu antigen R/HuR) or destabilization (AU‐rich element mRNA binding protein [AUF1]/heterogeneous nuclear ribonucleoprotein D) of target mRNAs. Further, their functional activity appears to require cytoplasmic localization. In the present study, we demonstrate a strong correlation between increased cytoplasmic expression of both AUF1 and HuR with urethane‐induced neoplasia and with butylated hydroxytoluene–induced compensatory hyperplasia in mouse lung tissue. In addition, when compared with slower growing cells, rapidly growing neoplastic lung epithelial cell lines expressed a consistently higher abundance of both AUF1 and HuR proteins. Moreover, in nontumorigenic cell lines, both AUF1 and HuR protein abundance decreased with confluence and growth arrest. In contrast, in spontaneous transformants, AUF1 and HuR abundance was unaffected by changes in cell density. We suggest that growth‐regulated alterations in AUF1 and HuR abundance may have pleiotropic effects on the expression of a number of highly regulated mRNAs and that this significantly impacts the onset, maintenance, and progression of the neoplastic phenotype. Mol. Carcinog. 28:76–83, 2000.

An α2C-Adrenergic Receptor Polymorphism Alters the Norepinephrine-Lowering Effects and Therapeutic Response of the β-Blocker Bucindolol in Chronic Heart FailureCLINICAL PERSPECTIVE

Background—Adrenergic activation is an important determinant of outcomes in chronic heart failure. Adrenergic activity is regulated in part by prejunctional &agr;2C-adrenergic receptors (ARs), which exhibit genetic variation in humans. Bucindolol is a novel &bgr;-AR blocking agent that also lowers systemic norepinephrine and thus is also a sympatholytic agent. This study investigated whether &agr;2C-AR polymorphisms affect sympatholytic effects of bucindolol in patients with heart failure. Methods and Results—In the &bgr;-Blocker Evaluation of Survival Trial, adrenergic activation was estimated by systemic venous norepinephrine measured at baseline, 3 months, and 12 months posttreatment in patients treated with placebo or bucindolol. In the &bgr;-Blocker Evaluation of Survival Trial AR polymorphism substudy, DNA was collected from 1040 of the 2708 randomized patients, and &agr;2C-AR gene polymorphisms (&agr;2C Del322-325 or the wild-type counterpart) were measured by polymerase chain reaction and gel electrophoresis. Patients who were &agr;2C Del carriers (heterozygotes or homozygotes) exhibited a much greater sympatholytic response to bucindolol (decrease in norepinephrine at 3 months of 153±57 pg/mL, P=0.012 compared with placebo versus decrease of 50±13 pg/mL in &agr;2C wild type, P=0.0005 versus placebo; P=0.010 by interaction test). &agr;2C Del carriers had no evidence of a favorable survival benefit from bucindolol (mortality compared with placebo hazard ratio, 1.09; 95% CI, 0.57 to 2.08; P=0.80), whereas bucindolol-treated subjects who were wild type for the &agr;2C-AR had a 30% reduction in mortality (hazard ratio, 0.70; 95% CI, 0.51 to 0.96; P=0.025). Conclusions—In the &bgr;-Blocker Evaluation of Survival Trial AR polymorphism substudy, the norepinephrine lowering and clinical therapeutic responses to bucindolol were strongly influenced by &agr;2C receptor genotype.

Role of microRNAs in cardiovascular disease: therapeutic challenges and potentials.

MicroRNAs (miRNAs, miRs) are short approximately 22-nucleotide noncoding RNAs that bind to messenger RNA transcripts and in doing so modulate cognate gene expression. In eukaryotes, miRNAs act primarily by causing translational repression although they may also act to destabilize RNA transcripts. During the past few years, a number of studies have demonstrated that miR expression changes as a result of cardiac hypertrophy or heart failure. Additionally, cell-based and transgenic mouse studies have demonstrated that individual miRs can affect a number of aspects of cardiac biology including developmental processes, stem cell differentiation, progression of hypertrophy and failure, ion channel function, as well as angiogenesis, rates of apoptosis, and fibroblast proliferation. In this review, we will summarize several of the miRs known to change in expression in association with heart failure and outline details of what is known about their putative targets. In addition, we will review several aspects of regulation of miR expression that have not been addressed in a cardiovascular context. Finally, as is common to all new and rapidly moving fields, we will highlight some of the gaps and inconsistencies related to miR expression and cardiac phenotypes, particularly those associated with heart failure.

Temporal expression of miRNAs and mRNAs in a mouse model of myocardial infarction

Analysis of changes in gene expression is an important means to define molecular differences associated with the phenotypic changes observed in response to myocardial infarction (MI). Several studies in humans or animal models have reported differential miRNA expression in response to MI acutely (animal) or chronically (human). To determine the relative contribution of microRNA (miRNA) and mRNAs to acute and chronic temporal changes in response to MI, mRNA and miRNA expression profiles were performed in three time points post-MI. Changes in mRNA and miRNA expression was analyzed by arrays and confirmed by RT-PCR. Bioinformatic analysis demonstrated that several genes and miRNAs in various pathways are regulated in a temporal or phenotype-specific manner. Furthermore miRNA analyses indicated that miRNAs can target expression of several genes involved in multiple cardiomyopathy-related pathways. Our results suggest that: 1) Differentially regulated miRNAs are predicted to target expression of several genes in multiple biological processes involved in the response to MI; 2) antithetical and compensatory changes in miRNA expression are observed at later disease stages, including antithetical regulation of miR-29, which correlates with the expression of collagen genes, and upregulation of apoptosis-related miRNAs at early stages and antiapoptotic/growth promoting miRNAs at later stages; 3) temporally dependent changes in miRNA and mRNA expression post-MI are generally characterized by dramatic changes acutely postinjury and are normalized as disease progresses; 4) A combinatorial analysis of mRNA and miRNA expression may aid in determining factors involved in compensatory and decompensated responses to cardiac injury.

Temporal analysis of mRNA and miRNA expression in transgenic mice overexpressing Arg- and Gly389 polymorphic variants of the β1-adrenergic receptor.

Several studies in humans or transgenic animals have reported that the 389 Arg or Gly polymorphic variation of the β1-adrenergic receptor (AR) is associated with differential responses to beta-blocker therapy and/or myocardial disease progression. Analysis of changes in gene expression is an important means of defining molecular differences associated with structural or functional phenotypic variations. To determine if structural and functional myocardial phenotypic differences between β1389 Arg vs. Gly transgenic overexpressors are associated with qualitative and/or quantitative differences in gene expression, a comprehensive analysis of mRNAs and miRNAs expressed in the hearts of 3 and 6-8 mo old β1-Arg389 and β1-Gly389 overexpressor transgenic mice was performed. Changes in mRNA and miRNA expression were analyzed by arrays and partially confirmed by RT-qPCR. Bioinformatic analysis demonstrated that several genes, including those involved in PKA and CaMK signaling pathways, are regulated in a temporal- or phenotype-specific manner. Furthermore, expression signature analyses indicated that miRNAs have the potential to target expression of a number of genes involved in multiple cardiomyopathy-related pathways, and changes in miRNA expression can precede the onset of disease. Differences in gene expression between β1-Arg389 and β1-Gly389 transgenic mice are largely quantitative rather than qualitative and are associated with the development of cardiomyopathy in a time-dependent manner. Chronic β1-AR overdrive results in increased expression of components of the CaMK pathway, with correspondingly decreased levels of components of the PKA pathway. Based on the temporal and genotype-specific pattern of miRNA expression, miRNAs are likely to be important predictors of disease states, especially when miRNA expression is paired with mRNA expression, and that miRNA/mRNA expression signatures have the potential to be useful in determining the underlying risk associated with cardiac disease progression.

An α2C-Adrenergic Receptor Polymorphism Alters the Norepinephrine-Lowering Effects and Therapeutic Response of the β-Blocker Bucindolol in Chronic Heart Failure

Background—Adrenergic activation is an important determinant of outcomes in chronic heart failure. Adrenergic activity is regulated in part by prejunctional &agr;2C-adrenergic receptors (ARs), which exhibit genetic variation in humans. Bucindolol is a novel &bgr;-AR blocking agent that also lowers systemic norepinephrine and thus is also a sympatholytic agent. This study investigated whether &agr;2C-AR polymorphisms affect sympatholytic effects of bucindolol in patients with heart failure. Methods and Results—In the &bgr;-Blocker Evaluation of Survival Trial, adrenergic activation was estimated by systemic venous norepinephrine measured at baseline, 3 months, and 12 months posttreatment in patients treated with placebo or bucindolol. In the &bgr;-Blocker Evaluation of Survival Trial AR polymorphism substudy, DNA was collected from 1040 of the 2708 randomized patients, and &agr;2C-AR gene polymorphisms (&agr;2C Del322-325 or the wild-type counterpart) were measured by polymerase chain reaction and gel electrophoresis. Patients who were &agr;2C Del carriers (heterozygotes or homozygotes) exhibited a much greater sympatholytic response to bucindolol (decrease in norepinephrine at 3 months of 153±57 pg/mL, P=0.012 compared with placebo versus decrease of 50±13 pg/mL in &agr;2C wild type, P=0.0005 versus placebo; P=0.010 by interaction test). &agr;2C Del carriers had no evidence of a favorable survival benefit from bucindolol (mortality compared with placebo hazard ratio, 1.09; 95% CI, 0.57 to 2.08; P=0.80), whereas bucindolol-treated subjects who were wild type for the &agr;2C-AR had a 30% reduction in mortality (hazard ratio, 0.70; 95% CI, 0.51 to 0.96; P=0.025). Conclusions—In the &bgr;-Blocker Evaluation of Survival Trial AR polymorphism substudy, the norepinephrine lowering and clinical therapeutic responses to bucindolol were strongly influenced by &agr;2C receptor genotype.

Myocardial microRNAs associated with reverse remodeling in human heart failure

BACKGROUND In dilated cardiomyopathies (DCMs) changes in expression of protein-coding genes are associated with reverse remodeling, and these changes can be regulated by microRNAs (miRs). We tested the general hypothesis that dynamic changes in myocardial miR expression are predictive of β-blocker-associated reverse remodeling. METHODS Forty-three idiopathic DCM patients (mean left ventricular ejection fraction 0.24 ± 0.09) were treated with β-blockers. Serial ventriculography and endomyocardial biopsies were performed at baseline, and after 3 and 12 months of treatment. Changes in RT-PCR (candidate miRs) or array-measured miRs were compared based on the presence (R) or absence (NR) of a reverse-remodeling response, and a miR-mRNA-function pathway analysis (PA) was performed. RESULTS At 3 months, 2 candidate miRs were selectively changed in Rs, decreases in miR-208a-3p and miR-591. PA revealed changes in miR-mRNA interactions predictive of decreased apoptosis and myocardial cell death. At 12 months, 5 miRs exhibited selective changes in Rs (decreases in miR-208a-3p, -208b-3p, 21-5p, and 199a-5p; increase in miR-1-3p). PA predicted decreases in apoptosis, cardiac myocyte cell death, hypertrophy, and heart failure, with increases in contractile and overall cardiac functions. CONCLUSIONS In DCMs, myocardial miRs predict the time-dependent reverse-remodeling response to β-blocker treatment, and likely regulate the expression of remodeling-associated miRs. TRIAL REGISTRATION ClinicalTrials.gov NCT01798992. FUNDING NIH 2R01 HL48013, 1R01 HL71118 (Bristow, PI); sponsored research agreements from Glaxo-SmithKline and AstraZeneca (Bristow, PI); NIH P20 HL101435 (Lowes, Port multi-PD/PI); sponsored research agreement from Miragen Therapeutics (Port, PI).

Peax: interactive visual analysis and exploration of complex clinical phenotype and gene expression association.

Increasing availability of high-dimensional clinical data, which improves the ability to define more specific phenotypes, as well as molecular data, which can elucidate disease mechanisms, is a driving force and at the same time a major challenge for translational and personalized medicine. Successful research in this field requires an approach that ties together specific disease and health expertise with understanding of molecular data through statistical methods. We present PEAX (Phenotype-Expression Association eXplorer), built upon open-source software, which integrates visual phenotype model definition with statistical testing of expression data presented concurrently in a web-browser. The integration of data and analysis tasks in a single tool allows clinical domain experts to obtain new insights directly through exploration of relationships between multivariate phenotype models and gene expression data, showing the effects of model definition and modification while also exploiting potential meaningful associations between phenotype and miRNA-mRNA regulatory relationships. We combine the web visualization capabilities of Shiny and D3 with the power and speed of R for backend statistical analysis, in order to abstract the scripting required for repetitive analysis of sub-phenotype association. We describe the motivation for PEAX, demonstrate its utility through a use case involving heart failure research, and discuss computational challenges and observations. We show that our visual web-based representations are well-suited for rapid exploration of phenotype and gene expression association, facilitating insight and discovery by domain experts.