Transcriptional dissection of differentially expressed long non-coding RNAs and messenger RNAs reveals the potential molecular mechanism after kidney transplantation

Hengcheng Zhang, Guodong Shi, Qingqiao Hu, Henglu Zhang, Ming Zheng, Kuirong Jiang, Min Gu


Background: Kidney transplantation has given benefits to patients, although the associated genetic mechanisms are unclear. The present study aimed to understand the changes in gene expression and genetic pathways after kidney transplantation with the administration of immunosuppressive drugs.
Methods: The transcriptome data of blood samples from kidney transplantation recipients, obtained by RNA-seq, were reannotated to a more complete human genome (GRCh38/hg38). We compared the differentially expressed genes (DEGs) at pretransplant and 1 week, 3 months and 6 months posttransplant; researched the temporal variation of the DEGs; and constructed a long non-coding RNA (lncRNA)-messenger RNA (mRNA) network.
Results: We found that compared to that at pretransplantation, 1,766 genes and 3,530 genes were upregulated and downregulated, respectively, at 1 week after kidney transplantation, and the number of DEGs declined over time. These DEGs were separated into 16 clusters, and the temporal variation expression was established by the average expression of the DEGs. A pathway analysis suggested that the immune reaction was attenuated and that the expression of ribosome-related proteins was reduced.
Conclusions: The lncRNA-mRNA network had 235 connections between 138 lncRNAs and 170 mRNAs. This work generated a gene profile based on temporal variation and revealed a significantly altered lncRNA-mRNA axis contributing to molecular regulation, suggesting the potential gene mechanism of kidney transplantation and the effects of immunosuppressive drugs.