Transcriptome-wide map of m6A circRNAs identified in hypoxic pulmonary hypertension rat model

Abstract

Hypoxic pulmonary hypertension (HPH) is a lethal disease. CircRNAs and m ⁶A circRNAs have been reported to be associated with cancer progression, but the expression profiling of m ⁶A circRNAs has not been identified in HPH. This study was to investigate the transcriptome-wide map of m ⁶A circRNAs in HPH. In this study, hypoxia-induced PH rat model was established. Total RNA was extracted and purified from lungs of rats, then circRNAs were detected and annotated by RNA-seq analysis. m ⁶A RNA Immunoprecipitation (MeRIP) was performed following rRNA depletion, and RNA-seq library was constructed. CircRNA–miRNA–mRNA co-expression network was also constructed. In vitro, total m ⁶A was measured. m ⁶A circXpo6 and m ⁶A circTmtc3 were detected in pulmonary artery smooth muscle cells (PASMCs) and pulmonary artery endothelial cells (PAECs) exposed to 21% O ₂ and 1% O ₂ for 48 h, respectively. m ⁶A abundance in 166 circRNAs was significantly upregulated and m ⁶A abundance in 191 circRNAs was significantly downregulated in lungs of HPH rats. m ⁶A abundance in circRNAs was significantly reduced in hypoxia in vitro. m ⁶A circRNAs were mainly derived from single exons of protein-coding genes. m ⁶A influenced the circRNA–miRNA–mRNA co-expression network in hypoxia. m ⁶A circXpo6 and m ⁶A circTmtc3 were downregulated in hypoxia. In general, our study firstly identified the transcriptome-wide map of m ⁶A circRNAs in HPH. m ⁶A level in circRNAs was decreased in lungs of HPH rats and in PASMCs and PAECs exposed to hypoxia. Downregulated or upregulated m ⁶A level influenced circRNA–miRNA–mRNA co-expression network in HPH. Moreover, we firstly identified two downregulated m ⁶A circRNAs in HPH: circXpo6 and circTmtc3. We suggested that m ⁶A circRNAs may be used as a potential diagnostic marker or therapy target in the future.

Author summary

HPH is a disease with great morbidity and mortality. It is often caused by chronic hypoxic lung diseases, such as chronic obstructive pulmonary disease and interstitial lung diseases. It lacks effective therapy methods so far. CircRNAs are a type of non-coding RNAs and can be used as biomarkers because they are differentially enriched in specific cell types or tissues and not easily degraded. m ⁶A is identified as the most universal modification on non-coding RNAs in eukaryotes. CircRNAs can be modified by m ⁶A. m ⁶A circRNAs in HPH is not well understood yet. Here we identify the transcriptome-wide map of m ⁶A circRNAs in HPH. We elucidate that m ⁶A level in circRNAs is decreased in lungs of HPH rats and in PASMCs and PAECs exposed to hypoxia. We find that downregulated or upregulated m ⁶A level influences circRNA– miRNA–mRNA co-expression network in HPH. Moreover, we are the first to identify two downregulated m ⁶A circRNAs in HPH: circXpo6 and circTmtc3. We suggest that m ⁶A circRNAs may be used as a potential diagnostic marker or therapy target in the future.