Molecular dysfunctions in acute rejection after renal transplantation revealed by integrated analysis of transcription factor, microRNA and long noncoding RNA

• Published in: Genomics (San Diego, Calif.) Calif.), 2013-10, Vol.102 (4), p.310-322
• Main Authors: Sui, Weiguo, Lin, Hua, Peng, Wujian, Huang, Yuanshuai, Chen, Jiejing, Zhang, Yue, Dai, Yong
• Format: Article
• Language: English
• Subjects: Acute Disease; Biopsy; Computational Biology; data collection; Gene Expression; genomics; Graft Rejection - genetics; Graft Rejection - metabolism; Humans; Kidney - metabolism; kidney transplant; Kidney Transplantation; Long noncoding RNA, linc-MD1, human; Microarray Analysis; microarray technology; microRNA; MicroRNAs; MicroRNAs - genetics; non-coding RNA; patients; Protein Array Analysis; Protein microarrays; proteomics; RNA, Long Noncoding - genetics; signal transduction; Signal Transduction - genetics; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2013.05.002

Acute rejection remains a problem in renal transplantation. To further illustrate the mechanism of rejection, we integrated protein array-based proteomics and RNA microarray-based genomics to investigate the transcription factor, microRNA and long noncoding RNA of biopsies of three patients with acute rejections and a control group. 99 transcription factors were identified in acute rejection biopsies compared to normal renal tissue. We correlated transcription factor data with microRNA and long noncoding RNA data sets and reported the expression of 5 transcription factors (AP-1, AP-4, STATx, c-Myc and p53), 12 miRNAs and 32 lncRNAs in acute rejection biopsies. Pathway analysis demonstrated that over-presentation of transcription factor pathway plays a critical role in acute rejection. This is the first study to comprehensively report the acute rejection transcription factor pathway. Integrative analysis of the transcription factor, microRNA and long noncoding RNA provided an expansive view of molecular signaling pathways in acute rejection after renal transplantation. •Reveal the relationship between TFs and acute renal rejection to the public•Integrative analysis provides an expansive view of molecular signaling pathways in AR.•The first comprehensive view of TF pathway in AR after renal transplantation.•Provide novel methods to prevent and treat acute renal rejection•Provide a novel researching method for rejection of other solid organ transplantation