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Table 3 Omic studies using lung tissue in IPF research

From: Tissue is an issue in the search for biomarkers in idiopathic pulmonary fibrosis

Study Patients/sample type Method Factors in IPF
[30] 3 IPF-UIP Oligonucleotide microarray Muscle and smooth muscle markers, ECM proteins, factors associated with ECM formation, cell contraction, and actin filament organization increased in UIP
2 CTD-UIP
3 controls from lung cancer surgery
5 controls from CLONTECH
SLB
[31] 15 IPF Affymetrix oligonucletide DNA microarray Genes involved in development, epithelium, ECM structure/turnover, cellular growth, and differentiation upregulated in IPF
12 HP
8 NSIP
Controls (trauma victims)
SLB
[32] 14 IPF Whole human genome oligonucleotide microarray Factors involved in ECM turnover, structural constituents and degradation, and cell adhesion molecules increased in IIP
2 NSIP
10 familial IIP (6 UIP, 4 NSIP)
9 normal controls
Autopsy
SLB
Lung transplant
[33] 23 IPF (stable) Agilent 4 × 4 whole human genome microarray 579 genes expressed differently in IPF and IPF-AEx: heat shock proteins, alpha-defensins, histones, and CCNA2
8 IPF-AEx
12 control lung
Lung transplant
Autopsy
[34] 6 stable or slowly progressive IPF Serial analysis of gene expression (SAGE) About 100 of transcripts upregulated in progressive IPF
6 progressive IPF
SLB
[35] 119 IPF-UIP Affymetrix Elevated expression of cilium genes associated with microscopic honeycombing, MUC5B, and MMP-7
50 controls Microarray
Lung tissue samplesa RT-PCR
[36] 14 IPF Proteome analysis: two-dimensional gel electrophoresis and MALDI-TOF-MS 51 upregulated and 38 downregulated proteins in IPF
10 controls (donors)
Lung transplant IHC
[37] IPF 14 2-dimensional DIGE technique and MALDI-TOF-MS Stress-induced genes upregulated in IPF and fNSIP
fNSIP 8
Controls 10 (organ donors)
Lung transplant
[38] 8 IPF Affymetrix oligonucleotide microarray 255 genes differentially expressed between IPF and controls
8 PH-IPF
7 controls
Lung transplant
SLB
[39] 40 IPF Gene expression microarray 2,940 genes differentially expressed between IPF and controls
8 controls IHC
SLB  
[40] 94 IPF Agilent gene expression microarray 2,130 DMRs of which 738 associated with changes in gene expression
67 controls CHARM array
Lung tissue samplesa  
  1. UIP usual interstitial pneumonia, IPF idiopathic pulmonary fibrosis, CTD connective tissue disease, ECM extracellular matrix, HP hypersensitivity pneumonitis, NSIP nonspecific interstitial pneumonia, IIP idiopathic interstitial pneumonia, SLB surgical lung biopsy, AEx acute exacerbation of IPF, CCNA2 cyclin A2, MUC5B mucin-5 subtype B, MMP matrix metalloproteinase, fNSIP fibrotic nonspecific interstitial pneumonia, DMR differentially methylated regions, IHC immunohistochemistry, RT-PCR reverse transcriptase polymerase chain reaction.
  2. aLung tissue specimens (type not specified) obtained from the Lung Tissue Research Consortium.