A map of human circular RNAs in clinically relevant tissues

Philipp G Maass,Aisha V Sauer,Alessandro Aiuti,Sebastian Memczak,Irene Hollfinger,Petar Glažar,Luisa Schreyer,Friedrich C Luft,Okan Toka,Gunnar Dittmar,Nikolaus Rajewsky

doi:10.1007/s00109-017-1582-9

Abstract

Cellular circular RNAs (circRNAs) are generated by head-to-tail splicing and are present in all multicellular organisms studied so far. Recently, circRNAs have emerged as a large class of RNA which can function as post-transcriptional regulators. It has also been shown that many circRNAs are tissue- and stage-specifically expressed. Moreover, the unusual stability and expression specificity make circRNAs important candidates for clinical biomarker research. Here, we present a circRNA expression resource of 20 human tissues highly relevant to disease-related research: vascular smooth muscle cells (VSMCs), human umbilical vein cells (HUVECs), artery endothelial cells (HUAECs), atrium, vena cava, neutrophils, platelets, cerebral cortex, placenta, and samples from mesenchymal stem cell differentiation. In eight different samples from a single donor, we found highly tissue-specific circRNA expression. Circular-to-linear RNA ratios revealed that many circRNAs were expressed higher than their linear host transcripts. Among the 71 validated circRNAs, we noticed potential biomarkers. In adenosine deaminase-deficient, severe combined immunodeficiency (ADA-SCID) patients and in Wiskott-Aldrich-Syndrome (WAS) patients’ samples, we found evidence for differential circRNA expression of genes that are involved in the molecular pathogenesis of both phenotypes. Our findings underscore the need to assess circRNAs in mechanisms of human disease.Key messagescircRNA resource catalog of 20 clinically relevant tissues.circRNA expression is highly tissue-specific.circRNA transcripts are often more abundant than their linear host RNAs.circRNAs can be differentially expressed in disease-associated genes.

Highlights

Introduction cultivated until passage six inM-199, supplemented with 20% FCS
By identifying and validating selected circRNAs in these human tissues relevant to clinical research, we provide multiple examples of abundant and highly tissue-specific circRNA expression in host genes that have been associated with pathogenesis of human disease
We found a circRNA in ROBO1, a gene upregulated in ADA-SCID and WAS

Summary

Introduction

Introduction cultivated until passage six inM-199, supplemented with 20% FCS. Single samples, each from one donor, were used for sequencing.Patients or patients’ parents signed informed consent on anonymous data collection for research studies conducted on biological samples of patients with primary immunodeficiencies (three Wiskott-Aldrich syndrome samples, four ADA-SCID samples) at San Raffaele Hospital (TIGET02), approved by the San Raffaele Scientific Institute’s Ethical Committee. The circRNA co-transcriptional splicing can compete with linear splicing events and can depend on the binding of the RNA-binding proteins, MBNL1 or QKI, in intronic sequences [5, 6]. CircRNAs are resistant to the exonuclease RNase R that solely digests linear transcripts. This feature can be used to validate circRNA candidates by comparing their abundance in the RNase R-treated and untreated samples [11]. CircRNAs found in clinical specimens, like blood, reveal that these abundant transcripts could serve as biomarkers [12]. By identifying and validating selected circRNAs in these human tissues relevant to clinical research, we provide multiple examples of abundant and highly tissue-specific circRNA expression in host genes that have been associated with pathogenesis of human disease

Methods

Results

Conclusion