title: Peripheral blood transcriptome sequencing reveals rejection-relevant genes in long-term heart transplantation.
abstract: BACKGROUND
  Peripheral blood-based gene expression patterns have been investigated as biomarkers to monitor the immune system and rule out rejection after heart transplantation. Recent advances in the high-throughput deep sequencing (HTS) technologies provide new leads in transcriptome analysis.
  
  
  METHODS
  By performing Solexa/Illumina's digital gene expression (DGE) profiling, we analyzed gene expression profiles of PBMCs from 6 quiescent (grade 0) and 6 rejection (grade 2R&3R) heart transplant recipients at more than 6 months after transplantation. Subsequently, quantitative real-time polymerase chain reaction (qRT-PCR) was carried out in an independent validation cohort of 47 individuals from three rejection groups (ISHLT, grade 0,1R, 2R&3R).
  
  
  RESULTS
  Through DGE sequencing and qPCR validation, 10 genes were identified as informative genes for detection of cardiac transplant rejection. A further clustering analysis showed that the 10 genes were not only effective for distinguishing patients with acute cardiac allograft rejection, but also informative for discriminating patients with renal allograft rejection based on both blood and biopsy samples. Moreover, PPI network analysis revealed that the 10 genes were connected to each other within a short interaction distance.
  
  
  CONCLUSIONS
  We proposed a 10-gene signature for heart transplant patients at high-risk of developing severe rejection, which was found to be effective as well in other organ transplant. Moreover, we supposed that these genes function systematically as biomarkers in long-time allograft rejection. Further validation in broad transplant population would be required before the non-invasive biomarkers can be generally utilized to predict the risk of transplant rejection.
authors.affiliation: CAS Key laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; The Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Chen
authors.forename: Haibo
authors.initials: H
authors.lastname: Zhang
authors.forename: Xue
authors.initials: X
authors.lastname: Xiao
authors.forename: Yixin
authors.initials: Y
authors.lastname: Jia
authors.forename: Weili
authors.initials: W
authors.lastname: Wu
authors.forename: Licheng
authors.initials: L
authors.lastname: Liu
authors.forename: Jun
authors.initials: J
authors.lastname: Jiang
authors.forename: Baoli
authors.initials: B
authors.lastname: Zhu
authors.forename: Xu
authors.initials: X
authors.lastname: Meng
authors.forename: Weijun
authors.initials: W
authors.lastname: Chen
mesh_terms: D000293:Adolescent; D000328:Adult; D015870:Gene Expression; D006084:Graft Rejection / Q000097:blood* / Q000235:genetics*; D016027:Heart Transplantation; D006801:Humans; D007963:Leukocytes, Mononuclear; D008297:Male; D008875:Middle Aged; D060888:Real-Time Polymerase Chain Reaction; D013997:Time Factors; D059467:Transcriptome; D055815:Young Adult
keywords: AR; CXCR4; Cardiac allograft rejection; CsA; DEGs; DGE; Digital gene expression; EMB; FDR; GO; GTD; Gene Ontology; HLA; HTS; High throughput sequencing; IL1R2; ISHLT; Interleukin-1 receptor type II; International Society for Heart and Lung Transplantation; KEGG Orthology; KO; MHC; MMF; NGS; PBLs; PBMCs; PPI; Pred; TPM; acute rejection; chemokine receptor 4; cyclosporine A; differentially expressed genes; digital gene expression; endomyocardial biopsy; false discovery rate; genome transplant dynamics; high-throughput deep sequencing; human leukocyte antigen; major histocompatibility complex; mycophenolate mophetil; next generation sequencing; number of transcripts per million clean tags; peripheral blood lymphocytes; peripheral blood mononuclear cells; prednisone; protein–protein interaction; qRT-PCR (qPCR); quantitative real-time polymerase chain reaction