Table 3 Omic studies using lung tissue in IPF research

[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 samples^a

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 samples^a