School of Medicine and Health Sciences Poster Presentations

Title

Application of Novel Genomic Markers to Identify New Pathways in Left Ventricular Remodeling

Document Type

Poster

Abstract Category

Cardiology/Cardiovascular Research

Keywords

Ventricular remodeling, Congestive heart failure, RNA deep sequencing, Stress granules

Publication Date

Spring 5-1-2019

Abstract

BACKGROUND: Left ventricular assist devices (LVAD) are increasingly utilized as destination therapy for patients with advanced congestive heart failure (CHF). LVAD has been shown to reverse left ventricular (LV) remodeling by unloading the left ventricle. Transcriptional profiling of the LV tissue before and after LVAD therapy has been utilized to examine the impact of LV unloading on pathways involved in LV remodeling. In this study, we used deep sequencing of the LV tissue to study the interplay of different species of transcripts in LV remodeling. METHODS: LV samples were acquired under informed consent from patients with ischemic cardiomyopathy (ICMP) undergoing surgical placement of LVADs (PRE-LVAD). After a variable period of time, a second LV sample was acquired (POST-LVD) from the same patients, during heart transplantation. Both the PRE- and POST-LVAD samples were preserved in an RNA preservative solution and RNA was isolated by homogenization and Trizol extraction. Total nucleic acids were DNAse treated, and depleted of ribosomal RNA prior to true single molecule sequencing (tSMS) on the SeqLL RNAseq platform. Raw reads were aligned to the human genome, and then counted per transcript to render reads (R) per thousand bases of exon (K) per million (M) total informative reads (RPKM), and then compared within subjects to identify transcripts affected by the LVAD support. RESULTS: Analysis of differentially expressed genes (DEGs) identified 175 coding and 28 non-coding transcripts that were significantly affected by the mechanical unloading during LVAD support. A dominant group of transcripts (>20) were either close, or identical matches to transcripts previously identified as sequestered in stress granules (SGs). The integrated stress response (ISR) involves sequestration of low priority, translationally paused transcripts into SGs, which are self-assembling structures nucleated by a family of amyloid/prion-like proteins, such as TIA1 and G3BP1/2. LVAD support was associated with movement in well-known SG transcripts such as CEP63, CIRBP, EIF3K, TANK, TCEA3, and TPM1, in what appears to be an overall shift in the translational machinery towards transcripts essential to cardiomyocyte survival. CONCLUSIONS: The myocardial transcriptome is dynamically regulated in advanced CHF and following LVAD support. The expression profiles of coding and noncoding RNAs altered in response to LVAD support can be used to understand the pathways involved in LV remodeling. In this study, normalization of transcripts involved in stress granule formation in LV tissue suggests an important role for these pathways in reversal of LV remodeling, and provides a blueprint for druggable targets.

Open Access

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Comments

Presented at Research Days 2019.

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Application of Novel Genomic Markers to Identify New Pathways in Left Ventricular Remodeling

BACKGROUND: Left ventricular assist devices (LVAD) are increasingly utilized as destination therapy for patients with advanced congestive heart failure (CHF). LVAD has been shown to reverse left ventricular (LV) remodeling by unloading the left ventricle. Transcriptional profiling of the LV tissue before and after LVAD therapy has been utilized to examine the impact of LV unloading on pathways involved in LV remodeling. In this study, we used deep sequencing of the LV tissue to study the interplay of different species of transcripts in LV remodeling. METHODS: LV samples were acquired under informed consent from patients with ischemic cardiomyopathy (ICMP) undergoing surgical placement of LVADs (PRE-LVAD). After a variable period of time, a second LV sample was acquired (POST-LVD) from the same patients, during heart transplantation. Both the PRE- and POST-LVAD samples were preserved in an RNA preservative solution and RNA was isolated by homogenization and Trizol extraction. Total nucleic acids were DNAse treated, and depleted of ribosomal RNA prior to true single molecule sequencing (tSMS) on the SeqLL RNAseq platform. Raw reads were aligned to the human genome, and then counted per transcript to render reads (R) per thousand bases of exon (K) per million (M) total informative reads (RPKM), and then compared within subjects to identify transcripts affected by the LVAD support. RESULTS: Analysis of differentially expressed genes (DEGs) identified 175 coding and 28 non-coding transcripts that were significantly affected by the mechanical unloading during LVAD support. A dominant group of transcripts (>20) were either close, or identical matches to transcripts previously identified as sequestered in stress granules (SGs). The integrated stress response (ISR) involves sequestration of low priority, translationally paused transcripts into SGs, which are self-assembling structures nucleated by a family of amyloid/prion-like proteins, such as TIA1 and G3BP1/2. LVAD support was associated with movement in well-known SG transcripts such as CEP63, CIRBP, EIF3K, TANK, TCEA3, and TPM1, in what appears to be an overall shift in the translational machinery towards transcripts essential to cardiomyocyte survival. CONCLUSIONS: The myocardial transcriptome is dynamically regulated in advanced CHF and following LVAD support. The expression profiles of coding and noncoding RNAs altered in response to LVAD support can be used to understand the pathways involved in LV remodeling. In this study, normalization of transcripts involved in stress granule formation in LV tissue suggests an important role for these pathways in reversal of LV remodeling, and provides a blueprint for druggable targets.