Browse > Article
http://dx.doi.org/10.7314/APJCP.2013.14.11.6347

Partial Least Squares Based Gene Expression Analysis in EBV-Positive and EBV-Negative Posttransplant Lymphoproliferative Disorders  

Wu, Sa (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Zhang, Xin (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Li, Zhi-Ming (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Shi, Yan-Xia (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Huang, Jia-Jia (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Xia, Yi (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Yang, Hang (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Jiang, Wen-Qi (Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine)
Publication Information
Asian Pacific Journal of Cancer Prevention / v.14, no.11, 2013 , pp. 6347-6350 More about this Journal
Abstract
Post-transplant lymphoproliferative disorder (PTLD) is a common complication of therapeutic immunosuppression after organ transplantation. Gene expression profile facilitates the identification of biological difference between Epstein-Barr virus (EBV) positive and negative PTLDs. Previous studies mainly implemented variance/regression analysis without considering unaccounted array specific factors. The aim of this study is to investigate the gene expression difference between EBV positive and negative PTLDs through partial least squares (PLS) based analysis. With a microarray data set from the Gene Expression Omnibus database, we performed PLS based analysis. We acquired 1188 differentially expressed genes. Pathway and Gene Ontology enrichment analysis identified significantly over-representation of dysregulated genes in immune response and cancer related biological processes. Network analysis identified three hub genes with degrees higher than 15, including CREBBP, ATXN1, and PML. Proteins encoded by CREBBP and PML have been reported to be interact with EBV before. Our findings shed light on expression distinction of EBV positive and negative PTLDs with the hope to offer theoretical support for future therapeutic study.
Keywords
Post-transplant lymphoproliferative disorder; Epstein-Barr virus; partial least squares;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Adamson AL, Kenney S (1999). The Epstein-Barr virus BZLF1 protein interacts physically and functionally with the histone acetylase CREB-binding protein. J Virol, 73, 6551-8.
2 Ashburner M, Ball CA, Blake JA, et al (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25, 25-9.   DOI   ScienceOn
3 Auer RL, Dighiero G, Goldin LR, et al (2007). Trinucleotide repeat dynamic mutation identifying susceptibility in familial and sporadic chronic lymphocytic leukaemia. Br J Haematol, 136, 73-9.   DOI   ScienceOn
4 Chakraborty S, Datta S, Datta S (2012). Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies. Bioinformatics, 28, 799-806.   DOI   ScienceOn
5 Craig FE, Johnson LR, Harvey SA, et al (2007). Gene expression profiling of Epstein-Barr virus-positive and -negative monomorphic B-cell posttransplant lymphoproliferative disorders. Diagn Mol Pathol, 16, 158-68.   DOI   ScienceOn
6 Gosselin. R, Rodrigue. D, Duchesne C (2010). A Bootstrap-VIP approach for selecting wavelength intervals in spectral imaging applications. Chemometrics and Intelligent Laboratory Systems, 100, 12-21.   DOI   ScienceOn
7 Gottschalk S, Rooney CM, Heslop HE (2005). Post-transplant lymphoproliferative disorders. Annu Rev Med, 56, 29-44.   DOI   ScienceOn
8 Shannon P, Markiel A, Ozier O, et al (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 13, 2498-504.   DOI   ScienceOn
9 Shi M, Gan YJ, Davis TO, Scott RS (2013). Downregulation of the polyamine regulator spermidine/spermine N-acetyltransferase by Epstein-Barr virus in a Burkitt's lymphoma cell line. Virus Res.
10 Stelzl U, Worm U, Lalowski M, et al (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-68.   DOI   ScienceOn
11 Wang L, Grossman SR, Kieff E (2000). Epstein-Barr virus nuclear protein 2 interacts with p300, CBP, and PCAF histone acetyltransferases in activation of the LMP1 promoter. Proc Natl Acad Sci U S A, 97, 430-5.   DOI
12 Martins JPA, Teofilo RF, Ferreira MMC (2010). Computational performance and cross-validation error precision of five PLS algorithms using designed and real data sets. Journal of Chemometrics, 24, 320-32.
13 Irizarry RA, Hobbs B, Collin F, et al (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-64.   DOI   ScienceOn
14 Ji G, Yang Z, You W (2011). PLS-Based Gene Selection and Identification of Tumor-Specific Genes. Ieee Transactions On Systems, Man, And Cybernetics-Part C: Applications And Reviews, 41, 830-41.   DOI   ScienceOn
15 Kanehisa M, Goto S (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 28, 27-30.   DOI   ScienceOn
16 Morscio J, Dierickx D, Ferreiro JF, et al (2013). Gene expression profiling reveals clear differences between EBV-positive and EBV-negative posttransplant lymphoproliferative disorders. Am J Transplant, 13, 1305-16.   DOI   ScienceOn
17 Nelson BP, Nalesnik MA, Bahler DW, et al (2000). Epstein-Barr virus-negative post-transplant lymphoproliferative disorders: a distinct entity? Am J Surg Pathol, 24, 375-85.   DOI   ScienceOn
18 Nicewonger J, Suck G, Bloch D, Swaminathan S (2004). Epstein-Barr virus (EBV) SM protein induces and recruits cellular Sp110b to stabilize mRNAs and enhance EBV lytic gene expression. J Virol, 78, 9412-22.   DOI   ScienceOn
19 Paya CV, Fung JJ, Nalesnik MA, et al (1999). Epstein-Barr virus-induced posttransplant lymphoproliferative disorders. ASTS/ASTP EBV-PTLD Task Force and The Mayo Clinic Organized International Consensus Development Meeting. Transplantation, 68, 1517-25.   DOI   ScienceOn