Plasma transcriptome profiling in patients with chronic kidney disease and end-stage renal disease

Cardiovascular disease is the major cause of morbidity and death in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD). Patients with CKD and ESRD are at high risk for myocardial dysfunction, ischemia and heart failure. The mechanisms linking impaired renal function and increased risk for cardiovascular diseases, however, remain elusive. In addition, conventional therapeutics proven effective in reducing cardiovascular events in general population fail to provide similar benefits in uremic patients. There is a clear need to identify novel mediators of cardiovascular complications in uremic patients to provide insights into the pathogenesis, to tailor clinical care based on cardiovascular risks, and to develop new therapeutic strategies. It has become increasingly clear that the transcription of the eukaryotic genome is far more pervasive and complex than previously appreciated. While the expression of messenger RNAs (mRNAs) and microRNAs (miRNAs) account for only ~1% of all transcribed species, up to 90% of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs), a heterogeneous group of non-coding transcripts longer than 200 nucleotides. LncRNAs have been shown to be functional and involved in specific physiological and pathological processes through epigenetic, transcriptional and post-transcriptional mechanisms. While the roles of lncRNAs in human diseases including cancer and neurodegenerative disorders are beginning to emerge, it remains unclear how lncRNA regulation contributes to cardiovascular complications in patients with renal dysfunction. In this proposal, we seek to apply next-generation sequencing technology to investigate circulating (plasma) lncRNA expression in control subjects and in patients with CKD and ESRD. We will test the hypothesis that circulating lncRNA expression signature can reflect the underlying kidney disease states in patients with CKD and ESRD. In addition, we will determine if circulating lncRNA expression signature could be a sensitive and specific biomarker to predict adverse cardiovascular events in patients with ESRD. Overall design: During the initial exploratory phase, plasma total RNA was isolated from 48 study subjects (28 ESRD, 8 CKD and 12 controls), followed by amplicon-based RNA sequencing (AmpliSeq TranscriptomeTM, Thermo Fisher), which allows simultaneous quantification of 20812 human transcripts, including 2228 lncRNAs. Differential expression analyses following RNASeq identified lncRNAs that were altered with ESRD, compared to control/CKD, as well as lncRNAs that were linked to adverse CV outcomes in uremic patients. The prognostic role of plasma lncRNAs in patients with ESRD were then validated in an independent cohort of 111 subjects.

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Lai CF, Chen YT, Gu J, Nerbonne JM, Lin CH, Yang KC