Genome-wide transcriptome study using deep RNA sequencing for myocardial infarction and coronary artery calcification

XL Zhang, Jeroen van Rooij, Y Wakabayashi, SJ Hwang, YQ Yang, Mohsen Ghanbari, Daniel Bos, D Levy, AD Johnson, Joyce van Meurs, Maryam Kavousi, J Zhu, CJ O'Donnell

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Abstract

Background: Coronary artery calcification (CAC) is a noninvasive measure of coronary atherosclerosis, the proximal pathophysiology underlying most cases of myocardial infarction (MI). We sought to identify expression signatures of early MI and subclinical atherosclerosis in the Framingham Heart Study (FHS). In this study, we conducted paired-end RNA sequencing on whole blood collected from 198 FHS participants (55 with a history of early MI, 72 with high CAC without prior MI, and 71 controls free of elevated CAC levels or history of MI). We applied DESeq2 to identify coding-genes and long intergenic noncoding RNAs (lincRNAs) differentially expressed in MI and high CAC, respectively, compared with the control. Results: On average, 150 million paired-end reads were obtained for each sample. At the false discovery rate (FDR) < 0.1, we found 68 coding genes and 2 lincRNAs that were differentially expressed in early MI versus controls. Among them, 60 coding genes were detectable and thus tested in an independent RNA-Seq data of 807 individuals from the Rotterdam Study, and 8 genes were supported by p value and direction of the effect. Immune response, lipid metabolic process, and interferon regulatory factor were enriched in these 68 genes. By contrast, only 3 coding genes and 1 lincRNA were differentially expressed in high CAC versus controls. APOD, encoding a component of high-density lipoprotein, was significantly downregulated in both early MI (FDR = 0.007) and high CAC (FDR = 0.01) compared with controls. Conclusions: We identified transcriptomic signatures of early MI that include differentially expressed protein-coding genes and lincRNAs, suggesting important roles for protein-coding genes and lincRNAs in the pathogenesis of MI.

Original languageEnglish
Article number45
JournalBMC Medical Genomics
Volume14
Issue number1
DOIs
Publication statusPublished - 10 Feb 2021

Bibliographical note

Funding Information:
The Framingham Heart Study is funded by the National Institutes of Health contract N01-HC-25195; this work was also supported by the National Heart, Lung and Blood Institute, Division of Intramural Research. Funding agencies played no role in study design, data collection, analysis, interpretation of results, or writing the manuscript.

Funding Information:
This work was performed within the framework of the Biobank-Based Integrative Omics Studies (BIOS) Consortium funded by BBMRI-NL, a research infrastructure financed by the Dutch government (NWO 184.021.007). The Rotterdam study is funded by the Erasmus Medical Center and Erasmus University, Rotterdam, Netherlands Organization for the Health Research and development (ZonMw), the Research Institute for Diseases in the Elderly (RIDE), the Ministry of Education, Culture and Science, the ministry for Health, Welfare and Sports, the European Commission (DG XII), and the Municipality of Rotterdam.

Publisher Copyright:
© 2021, The Author(s).

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