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Table 4 Literature review of the investigated inflammation- and fibrosis-associated genes in bronchiolitis obliterans (BO), idiopathic pulmonary fibrosis (IPF) and organizing pneumonia (OP) humans and mice

From: Organizing pneumonia in mice and men

References Pulmonary disease: no. of cases/controls Materials Investigated parameters Methods
Human
Magnan et al. [16] BO: 6/7 BAL (TBB) from lung transplant recipients TGFB1, IL-6, TGFB2 Immunoassay for cytokine determination
Immunohistochemistry
Taghavi et al. [19] BO: 38/34 BAL (TBB) from lung transplant patients MMP2, MMP8, MMP9, TIMP1, TIMP2, BAL cell count ELISA
Ramirez et al. [22] BO: 13/21 BALF from lung transplant recipients IL-1b, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IFN-γ, GM-CSF, TNF-α, TGFB1, fibronectin gene expression, gelatinolytic activity Multiplex Bead Immunoassay
ELISA
Gelatin zymography
Jonigk et al. [10] BO: 12/12 Explanted lung allografts BMP4, BMPR2, LOX, MMP14, PLAU, CCL5, THBS1, TIMP1, TGFB1, COL3A1, TIMP2, TGFBR2, BMP2, PLA1, EDN1, COL1A2, COL4A1 RNA microarray (45 target genes)
Mouse
Majeski et al. [23] OP: Reovirus 1/L induction of intraluminal fibrosis Il-6, Ccl2 RiboQuant multiprobe ribonuclease protection assay
ELISA
Phillips et al. [18] IPF: 3–6 mice for each treatment group (bleomycin/saline) Bleomycin mouse model Cxcr4, Cxcl12, Col1, CD45, CD34, α-SMA, Col3 FACS, ELISA, qRT-PCR,
Immunohistochemistry
Chen et al. [17] BO: 4/4 Heterotopic tracheal transplantation from TIMP-1 null (-/-) mutation and wild-type (TIMP-1 +/+) mice Βeta-actin, Mmp3, Mmp7, Mmp9, Mmp12, Timp1, Timp2, Timp3, Timp4 Immunohistochemistry
qRT-PCR
Xu [24] BO: 6/6 Heterotopic tracheal transplantation Cxcr4 Immunohistochemistry
Immunofluorescence
Western blot
Vittal et al. [20] IPF: Bleomycin mouse model Tgfb1, FAK (PTK2), PKB/Akt qRT-PCR
Western blot
Immunohistochemistry
Shi et al. [21] IPF: Bleomycin mouse model Tgfb1, Smad3 Immunohistochemistry
  1. Significantly regulated genes are highlighted in italics
  2. ACTB beta-actin, BAL bronchoalveolar lavage, BMP bone morphogenetic protein, BMPR bone morphogenetic protein receptor, CCL CC chemokine ligand, CD40LG CD40 ligand, Cxcr4 chemokine (C-X-C motif) receptor 4, Cxcl12 chemokine (C-X-C motif) ligand 12, ECP eosinophilic cationic protein, FAK (PTK) focal adhesion kinase (protein tyrosine kinase), FasL Fas ligand, FGF1 fibroblast growth factor 1, FOXP3 forkhead box P3, GM-CSF granulocyte macrophage colony-stimulating factor, HLA human leukocyte antigen, IFN interferon, IL interleukin, IP10 interferon gamma-induced protein 10, LTA lymphotoxin-α, LOX lysyl oxidase, MCP1 monocyte chemotactic protein, MIP macrophage inflammatory protein, MIG (CXCL9) monokine induced by gamma interferon, MMP matrix metalloproteinase, MPO myeloperoxidase, NG neutrophilic granulocytes, PDGFB platelet-derived growth factor subunit B, PLAU plasminogen activator (urokinase), RPL13A 60S ribosomal protein L13a, sCD30 soluble CD30, SLPI secretory leukocyte protease inhibitor, Smad Sma and Mad-related protein family members, sRAGE soluble receptor for advanced glycation end products, TGF transforming growth factor, THBS1 thrombospondin-1, TIMP1 tissue inhibitor of matrix metalloproteinases 1, TNFα tumor necrosis factor, alpha, TNFSF7 TNF ligand superfamily member 7, VEGF vascular endothelial growth factor, YKL-40 chitinase-like glycoprotein