title: Molecular pathways involved in loss of kidney graft function with tubular atrophy and interstitial fibrosis.
abstract: Loss of kidney graft function with tubular atrophy (TA) and interstitial fibrosis (IF) causes most kidney allograft losses. We aimed to identify the molecular pathways involved in IF/TA progression. Kidney biopsies from normal kidneys (n = 24), normal allografts (n = 6), and allografts with IF/TA (n = 17) were analyzed using high-density oligonucleotide microarray. Probe set level tests of hypotheses tests were conducted to identify genes with a significant trend in gene expression across the three groups using Jonckheere-Terpstra test for trend. Interaction networks and functional analysis were used. An unsupervised hierarchical clustering analysis showed that all the IF/TA samples were associated with high correlation. Gene ontology classified the differentially expressed genes as related to immune response, inflammation, and matrix deposition. Chemokines (CX), CX receptor (for example, CCL5 and CXCR4), interleukin, and interleukin receptor (for example, IL-8 and IL10RA) genes were overexpressed in IF/TA samples compared with normal allografts and normal kidneys. Genes involved in apoptosis (for example, CASP4 and CASP5) were importantly overexpressed in IF/TA. Genes related to angiogenesis (for example, ANGPTL3, ANGPT2, and VEGF) were downregulated in IF/TA. Genes related to matrix production-deposition were upregulated in IF/TA. A distinctive gene expression pattern was observed in IF/TA samples compared with normal allografts and normal kidneys. We were able to establish a trend in gene expression for genes involved in different pathways among the studied groups. The top-scored networks were related to immune response, inflammation, and cell-to-cell interaction, showing the importance of chronic inflammation in progressive graft deterioration.
authors.affiliation: Department of Surgery, Division of Transplant, Virginia Commonwealth University, Richmond, Virginia 23298-0057, United States of America. dgmaluf@vcu.edu
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Maluf
authors.forename: Valeria R
authors.initials: VR
authors.lastname: Mas
authors.forename: Kellie J
authors.initials: KJ
authors.lastname: Archer
authors.forename: Kenneth
authors.initials: K
authors.lastname: Yanek
authors.forename: Eric M
authors.initials: EM
authors.lastname: Gibney
authors.forename: Anne L
authors.initials: AL
authors.lastname: King
authors.forename: Adrian
authors.initials: A
authors.lastname: Cotterell
authors.forename: Robert A
authors.initials: RA
authors.lastname: Fisher
authors.forename: Marc P
authors.initials: MP
authors.lastname: Posner
mesh_terms: D000328:Adult; D000818:Animals; D018946:Chemokine CCL5 / Q000097:blood / Q000235:genetics / Q000378:metabolism; D018925:Chemokines / Q000097:blood / Q000235:genetics / Q000378:metabolism; D005260:Female; D005355:Fibrosis; D020869:Gene Expression Profiling; D006084:Graft Rejection / Q000097:blood* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007668:Kidney / Q000378:metabolism* / Q000473:pathology / Q000503:physiopathology; D007674:Kidney Diseases / Q000097:blood* / Q000209:etiology / Q000235:genetics; D016030:Kidney Transplantation / Q000009:adverse effects / Q000379:methods*; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D054387:Receptors, CXCR / Q000097:blood / Q000235:genetics / Q000378:metabolism; D019718:Receptors, CXCR4 / Q000097:blood / Q000235:genetics / Q000378:metabolism; D019707:Receptors, Chemokine / Q000097:blood / Q000235:genetics / Q000378:metabolism; D018123:Receptors, Interleukin / Q000097:blood / Q000235:genetics / Q000378:metabolism
chemical_list: C527276:CXCR4 protein, human; D018946:Chemokine CCL5; D018925:Chemokines; D054387:Receptors, CXCR; D019718:Receptors, CXCR4; D019707:Receptors, Chemokine; D018123:Receptors, Interleukin