Array CGH reveals genomic aberrations in human emphysema

Jin Soo Choi, Woon Jeong Lee, Seung Ho Baik, Hyoung Kyu Yoon, Kweon Haeng Lee, Yeul Hong Kim, Young Lim, Young Pil Wang

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Emphysema is the major component of chronic obstructive pulmonary disease (COPD), which is the fourth leading cause of death in the world. Several epidemiologic studies suggest that genetic factors may have an important role in the pathogenesis of emphysema. We analyzed the gene expression profiles of chromosomal aberrations using array comparative genomic hybridization (array CGH) in 32 patients with emphysema to identify the candidate genes that might be causally involved in the pathogenesis of emphysema. Copy number gains and losses were detected in chromosomal regions, and the corresponding genes were confirmed by real-time polymerase chain reaction. Several frequently altered loci were found, including a gain at 5p15.33 (60% of the study subjects), and a loss at 7q22.1 (31% of the study subjects). DNA gains were identified at a high frequency at 1p, 5p, 11p, 12p, 15q, 17p, 18q, 21q, and 22q, whereas DNA losses were frequently found at 7q and 22q. We found that the fold change levels were highest at the CYP4B1 (1p33), JUN (1p32.1), NOTCH2 (1p12-p11.2), SDHA (5p15.33), KCNQ1 (11p15.5-p15.4), NINJ2 (12p13.33), PCSK6 (15q26.3), ABR (17p13.3), CTDP1 (18q23), RUNX1 (21q22.12) and HDAC10 (22q13.33) gene loci. We also observed losses in the MUC17 (7q22.1), COMT (22q11.21) and GSTT1 (22q11.2) genes. These studies show that array CGH is a useful tool for the identification of gene alterations in cases of emphysema and that the aforementioned genes might represent potential candidate genes involved in the pathogenesis of emphysema.

Original languageEnglish
Pages (from-to)165-172
Number of pages8
JournalLung
Volume187
Issue number3
DOIs
Publication statusPublished - 2009 Jun 1

Fingerprint

Emphysema
Genes
Comparative Genomic Hybridization
DNA
Transcriptome
Chromosome Aberrations
Chronic Obstructive Pulmonary Disease
Real-Time Polymerase Chain Reaction
Epidemiologic Studies
Cause of Death

Keywords

  • Array CGH
  • Chromosomal aberration
  • Emphysema
  • Lung cancer
  • Real-time polymerase chain reaction

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine

Cite this

Choi, J. S., Lee, W. J., Baik, S. H., Yoon, H. K., Lee, K. H., Kim, Y. H., ... Wang, Y. P. (2009). Array CGH reveals genomic aberrations in human emphysema. Lung, 187(3), 165-172. https://doi.org/10.1007/s00408-009-9142-x

Array CGH reveals genomic aberrations in human emphysema. / Choi, Jin Soo; Lee, Woon Jeong; Baik, Seung Ho; Yoon, Hyoung Kyu; Lee, Kweon Haeng; Kim, Yeul Hong; Lim, Young; Wang, Young Pil.

In: Lung, Vol. 187, No. 3, 01.06.2009, p. 165-172.

Research output: Contribution to journalArticle

Choi, JS, Lee, WJ, Baik, SH, Yoon, HK, Lee, KH, Kim, YH, Lim, Y & Wang, YP 2009, 'Array CGH reveals genomic aberrations in human emphysema', Lung, vol. 187, no. 3, pp. 165-172. https://doi.org/10.1007/s00408-009-9142-x
Choi JS, Lee WJ, Baik SH, Yoon HK, Lee KH, Kim YH et al. Array CGH reveals genomic aberrations in human emphysema. Lung. 2009 Jun 1;187(3):165-172. https://doi.org/10.1007/s00408-009-9142-x
Choi, Jin Soo ; Lee, Woon Jeong ; Baik, Seung Ho ; Yoon, Hyoung Kyu ; Lee, Kweon Haeng ; Kim, Yeul Hong ; Lim, Young ; Wang, Young Pil. / Array CGH reveals genomic aberrations in human emphysema. In: Lung. 2009 ; Vol. 187, No. 3. pp. 165-172.
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abstract = "Emphysema is the major component of chronic obstructive pulmonary disease (COPD), which is the fourth leading cause of death in the world. Several epidemiologic studies suggest that genetic factors may have an important role in the pathogenesis of emphysema. We analyzed the gene expression profiles of chromosomal aberrations using array comparative genomic hybridization (array CGH) in 32 patients with emphysema to identify the candidate genes that might be causally involved in the pathogenesis of emphysema. Copy number gains and losses were detected in chromosomal regions, and the corresponding genes were confirmed by real-time polymerase chain reaction. Several frequently altered loci were found, including a gain at 5p15.33 (60{\%} of the study subjects), and a loss at 7q22.1 (31{\%} of the study subjects). DNA gains were identified at a high frequency at 1p, 5p, 11p, 12p, 15q, 17p, 18q, 21q, and 22q, whereas DNA losses were frequently found at 7q and 22q. We found that the fold change levels were highest at the CYP4B1 (1p33), JUN (1p32.1), NOTCH2 (1p12-p11.2), SDHA (5p15.33), KCNQ1 (11p15.5-p15.4), NINJ2 (12p13.33), PCSK6 (15q26.3), ABR (17p13.3), CTDP1 (18q23), RUNX1 (21q22.12) and HDAC10 (22q13.33) gene loci. We also observed losses in the MUC17 (7q22.1), COMT (22q11.21) and GSTT1 (22q11.2) genes. These studies show that array CGH is a useful tool for the identification of gene alterations in cases of emphysema and that the aforementioned genes might represent potential candidate genes involved in the pathogenesis of emphysema.",
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