Table 2.
Key array-based published studies in transplantation (AR acute rejection, CAN chronic allograft nephropathy, TOL operational tolerance, MIS minimum immunosuppression, HTN hypertension, RVA reno-vascular abnormalities, EPO erythropoietin, LDN laparoscopic donor nephrectomy, DT drug toxicity, HTN hypertension, STA patient with stable graft function)
| Author | Journal | Array type | Tissue | Phenotype | Key findings |
|---|---|---|---|---|---|
| Human studies | |||||
| Brouard et al. [49] | Proc Natl Acad Sci U S A 2007 | cDNA | Lymphocyte | TOL, AR, CAN, stable, MIS | AKR1C1, AREG, BRRN1, C1S, CCL20, CDC2, CDH2, CHEK1, DHRS2, DEPDC1, ELF3, HBB, IGFBP3, LTB4DH, MS4A1, MTHFD2, PARVG, PLXNB1, PODXL, PPAP2C, RAB30, RASGRP1, RBM9, RHOH, SLC29A, SMILE, SOX3, SPON1, TK1 and TLE4 |
| Li et al. [44] | Physiol Genomics 2007 | U133plus GeneChip | Blood | STA, AR | Globin genes onfounders in biomarker discovery from PAX gene samples for AR |
| Nagarajan et al. [89] | Clin Transplant 2007 | cDNA | Peripheral blood | HTN, RVA, EPO | Hemoglobin zeta, G2, E1, CTGF, PLA2 G2A, PDGF-A, VEGF, CDH5, GDF1, TIE, TBRG1, EPS8, FIBP, EPOR, TFRC, STAT5, Jak2 and CLK1 |
| Park et al. [90] | Transplantation 2007 | U133A 2.0 GeneChip | Kidney biopsy | Fibrotic | STAT1, STAT2, proteasome subunit [beta]-type-8, Col1A1, FN1, phosphoinositide-3-kinase regulatory subunit-3, VCAM1, GRZMA, GBP1, IER3, HLA-DRbeta, IL-10, TGFB, IFNG, IL-6 and FoxP3 |
| Mas et al. [91] | Transplantation 2007 | U133A 2.0 GeneChip | Kidney biopsy, peripheral blood, urine | CAN | TGF-beta, laminin, gamma 2, metalloproteinases-9, collagen type IX alpha 3, immunoglobulins, cytokine, chemokines receptors, EGFR, FGFR2, AGT, EGFR and TGFB |
| Morgun et al. [47] | Circ Res 2006 | Oligonucleotide | Heart biopsy, kidney and lung | AR, infection | CCL18, TRB, LTB, ITGB2, HA-1, CORO1A, IGKC, RARRES3, CCL5, HLADRB3, STAT1, C1QA, GMFG, CD74, CD14, PSCD4, BTN3A3, HLA-F and UBE2L6 |
| Hotchkiss et al. [55] | Transplantation 2006 | U133A GeneChip | Kidney biopsy | CAN | TGF-B, thrombospondin 1, PDGF, integrins, MMP7, C4B, properdin, VCAM1, Annexins, VEGF, EGF and FGF |
| Kurian et al. [54] | Transplantation 2005 | U133A GeneChip | Kidney biopsy | LDN | HIF1a, HIF1B, TNF, TNFR, TGF-B, FGF, integrins, MMP, elastin, GHRH and VEGF |
| Eikmans et al. [53] | J Am Soc Nephrol 2005 | HG U95Av2 GeneChip | Kidney cortex | CAN | Surfactant protein-C (SP-C), S100 calcium-binding protein A8 (S100A8), S100A9 and immuno-globulin genes |
| Melk et al. [62] | Kidney Int 2005 | cDNA | Kidney cortex | Renal aging | NADH dehydrogenase, APO, kynureninase PAH, dynein, CLDN8, MMP7, fibulin, tenascin, CSPG2, SERPINA3, immunoglobulins, somatostatin receptor, THY1, natriuretic peptide receptor and SLC solute transporter family |
| Zhang et al. [92] | Clin Transplant 2004 | HG U95Av2 GeneChip | Lymphocyte | Stable transplant | Membrane-type matrix metalloproteinase 1, SH3 binding protein, MEA6, TOB family 4, RBP2, IL-1A, Argininosuccinate synthetase, Brain and nasopharyngeal carcinoma, NSG-x, hVH-5 and Eosinophil Charcot-Leyden crystal protein |
| Mansfield et al. [14] | Am J Transplant 2004 | cDNA | Kidney biopsy | AR sub-types | MIP-1, CCR5, CX3CR1, DARC, SCYB10, SCYA5,SCYA3, SCYA13, SCYA2, IL2RB, IL6R, IL16, 1L15R, DEFA1, DEFB1, SCYA2, SCYA5, MST1, STAT1, STAT6, CD69, MAL, NFATC3, Annexins, CASP10, PECAM1 and VCAM1 |
| Hauser et al. [37] | Lab Invest 2004 | cDNA | Kidney biopsy | Donor source | Complements, LTF, NK4, VCAM1, interleukins, HLA, BCL6, GPX2,FBP1, PCK2, SORD, APOA4, CYP3A7, FABP1, APOM, CYP3A4, HIF1A, STAT1,TIMP1, ADAMTS1, TNFSF10 and CDC25B |
| Kainz et al. [93] | Am J Transplant 2004 | cDNA | Kidney biopsy | Donor source | Osteopontin, SOD2, RARRES1, chemokine ligand 1, antileukoproteinase, STAT1, CDH6, SPP1, SERPINA3 and GPX2 |
| Flechner et al. [56] | Am J Transplant 2004 (a) | Oligonucleotide | Kidney biopsy | CAN, drug effect | TGFB, TNFA, PDGF, ICAM, VCAM1, integrin B, MCP-1, CCR2, MPI-3B, MHC, MMP, TIMP1, RANTES, VEGF, collagen III, Angiotensin II receptor, TSP and FN1 |
| Flechner et al. [94] | Am J Transplant 2004 (b) | HG U95Av2 GeneChip | Kidney biopsy, peripheral blood | AR | AIF, CD14, CD163, CD2, CD3D, CD48, CD53, chemokines, interleukins, C1q, immunoglobulins, INFG, TCR TNF, and HLA |
| Donauer et al. [57] | Transplantation 2003 | cDNA array | CAN | AQP2, AQP3, lipoprotein lipase, PML-2, Napsin 1, precursor, Flotillin-1, Type IV collagenase, Hepatocyte growth factor activator inhibitor, RIG-like 7–1, MECI-1, PGER, TEM8, MHC class I, C1s and immunoglobulins | |
| Higgins et al. [76] | Mol Biol Cell 2004 | cDNA | Cortex, medulla, papillary tips, | Normal | Identify patterns of gene expression in discrete portions of the normal kidney |
| Sarwal et al. [1] | N Engl J Med 2003 | cDNA | Kidney biopsy, pediatrics | AR, CAN, DT and infection | TCR, HLA class II, HLA class I, immunoglobulins, lactotransferrin, chemokines, CD20, CD34, IGF1R, TNFR, MST1, NK4, duffy antigen/chemokine, receptor, STAT1, TGFR1, granzyme A, perforin, IL2R, CD53, lymphotoxin, lymphotoxin R, NFKB1, CD59, IFNGR1 and annexins |
| Scherer et al. [58] | Transplantation 2003 | HG U95Av2 GeneChip | Kidney biopsy | CAN | Keratin tumor suppressor candidate 7, OS9(APRIL), G-protein gamma7, protein/cell adhesion molecule-like, GRB2-associated binding protein 1, and PRLR |
| Chua et al. [95] | Am J Transplant 2003 | cDNA | Kidney biopsy | AR/anemia | Hb-zeta, Hb-beta, Hb-alpha2, FOLR2, FOLR3, CAH1, immunoglobulins, GPX1, and lactotransferrin |
| Zhang et al. [96] | Transplant Proc 2002 | Oligonucleotide | Lymphocyte | Stable transplant | CD80, interleukins, CD44, CD40L, CD40, VLA-5, LFA-1, TCR alpha, Lck, calcineurin, PKC, IFNG, LFA-1, TCR alpha, Lck, calcineurin, PKC, IFNG, TGFB, TNF-alpha, TNFR1, G-CSFR and PDGF receptor, |
| Akalin et al. [97] | Transplantation 2001 | Hu6800 GeneChip | Kidney biopsy | AR | HuMig, TCR RING4, ISGF-3, CD18 |
| Animal studies | |||||
| Kusaka et al. [98] | Transplantation 2007 | Agilent rat oligonucleotide array G4130A | Kidney allografts, T lymphocytes | Brain death donor | Gro1, IP-10, p53, NF kappa B, Myc, Jun, c-fos, LCN2 and SPP1 |
| Berthier et al. [99] | Kidney Int 2006 | 230 A GeneChip | Kidney allografts | CAN | MMP-11,-12,-14, ADAM-17, TIMP-1,-2 TGF-B, MMP-9, meprin and MMP-24 |
| Djamali et al. [100] | Transplantation 2005 | mouse stress toxicity GEArray | Kidney allografts | CAN | ANXA5, CASP1, CASP8, TNFRII, TRAIL, FASL, BAX, inducible nitric oxide synthase, cytochrome p450 4A, [alpha]-crystalline B, heme-oxygenase II, SOD, HSP60, HSP27, BCL-X and metallothionein |
| Schuurs et al. [101] | Am J Transplant 2004 | Oligonucleotide | Kidney allografts | HTN brain death | Water channel AQP-2, selectins, IL-6, oc-B-fibrinogen, KIM-1, HO-1, Hsp70, MnSOD2, ATF-3, EGR-1 and PIK3R1 |
| Einecke et al. [43] | Am J Transplant 2007 | Oligonucleotide | Mouse kidney | Rejection | SLC2a2, SLC1a1 |
| Leonard et al. [102] | FASEB J 2006 | HG U95Av2 GeneChip, murine U77A | Mouse kidney, human proximal tubular epithelial cells | Ischemia reperfusion injury | In mouse model: ALDH1A1, ALDH1A7, GSTM5, GSTA2, GSTP1, NQO1 and Nrf2. In human: Nrf2 is up-regulated on reoxygenation |
| Famulski et al. [60] | Am J Transplant 2006 | Oligonucleotide | Mouse kidney | AR | Define IFNG-dependent, rejection-induced transcripts (GRITs) in mouse kidney allografts. IFNG inducible: CXCl9, UBD and MHC |
| Einecke et al. [43] | Am J Transplant 2007 | Oligonucleotide | Kidney allografts, T lymphocytes | Rejection | Cytotoxic T lymphocyte-associated transcripts (CATs): CD2, CD3g, GZMB, TCRB, MES |