COL18A1 as the Candidate Gene for the Prognostic Marker of Breast Cancer According to the Analysis of the DNA Copy Number Variation by Array CGH

Ki-Tae Hwang; Jung Kee Chung; In Mok Jung; Seung Chul Heo; Young Joon Ahn; Hye Seong Ahn; Mee Soo Chang; Jeong-Ah Kim; Wonshik Han; Dong-Young Noh

doi:10.4048/jbc.2010.13.1.37

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Hwang, Chung, Jung, Heo, Ahn, Ahn, Chang, Kim, Han, and Noh: COL18A1 as the Candidate Gene for the Prognostic Marker of Breast Cancer According to the Analysis of the DNA Copy Number Variation by Array CGH

Original Article

Journal of Breast Cancer

Journal of Breast Cancer 2010; 13(1): 37-45.

Published online: 31 March 2010

DOI: https://doi.org/10.4048/jbc.2010.13.1.37

COL18A1 as the Candidate Gene for the Prognostic Marker of Breast Cancer According to the Analysis of the DNA Copy Number Variation by Array CGH

Ki-Tae Hwang, Jung Kee Chung, In Mok Jung, Seung Chul Heo, Young Joon Ahn, Hye Seong Ahn, Mee Soo Chang¹, Jeong-Ah Kim², Wonshik Han^2,³, Dong-Young Noh^2,³

Department of Surgery, Seoul National University Boramae Hospital, Seoul, Korea.

¹Department of Pathology, Seoul National University Boramae Hospital, Seoul, Korea.

²Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea.

³Department of Surgery, College of Medicine, Seoul National University, Seoul, Korea.

Corresponding author (dynoh@plaza.snu.ac.kr)

Received 29 July 2009 Accepted 4 November 2009

Abstract

Purpose

We tried to select and validate the candidate gene for the prognostic marker of breast cancer by comparing the analysis of copy number variation (CNV) between normal breast tissues and breast cancer tissues by performing array comparative genomic hybridization (CGH).

Methods

Array CGH was performed with using the fresh frozen tissues of 77 breast cancer patients. We selected the clones with more than a 20% frequency of gain or loss, and the clones with gain or loss in more than 2 consecutive clones. We finally selected the clones that were statistically significant on the survival analysis. We searched for the candidate gene that belonged to the candidate clones and we selected the final candidate gene that is assumed to be most related to the carcinogenesis of breast cancer by searching for information of the individual gene. We performed RT-PCR to validate the RNA expression of the final candidate gene with using the breast tissues of another 20 breast cancer patients.

Results

Eleven (10 in the gain group and 1 in the loss group) clones were finally selected as candidate clones. The significant CNVs with gain were found in the regions of 1q23.1, 1q41, 1q44, 5p15.33, 8q21.3, 15q26.3, 17q12 and 21q22.3 and the significant CNV with loss was found in 14q32.33. COL18A1 (21q22.3) was selected as the final candidate gene and the RT-PCR results revealed that the expression of COL18A1 was up-regulated in the cancer tissues of 18 of the other 20 (90%) breast cancer patients.

Conclusion

We selected COL18A1 (21q22.3) as the candidate gene for the prognostic marker of breast cancer by comparing the analysis of CNVs from the array CGH. The RNA of COL18A1 was over-expressed in breast cancer tissue, as determined by RT-PCR.

Keywords: Breast neoplasms, Collagen type XVIII, Gene amplification, Microarray analysis

Figures and Tables

Figure 1

Survival curve of systemic recurrence-free survival analysis for the clone which contains COL18A1 gene (c2806) by Kaplan-Meier test. The survival of the group with gain of c2806 clone was better than that without gain of c2806 clone and the difference of survival between two groups was statistically significant (p=0.008) by log rank test.

Figure 2

Results of validation test by RT-PCR for the RNA expression of COL18A1. The RNA expression of COL18A1 was up-regulated in breast cancer tissues compared to normal breast tissues in 18 of 20 (90%) breast cancer patients. Difference of the RNA expression was statistically significant (p<0.0001). RPLP0 was used as reference gene. OD ratio=(OD[COL18A1_Caner]/OD [RPLP0_Cancer])/(OD[COL18A1_Normal]/OD[RPLP0_Normal].

OD=optical density.

Table 1

Clinicopathological characteristics of the patients

TM=total mastectomy; BCS=breast conserving surgery.

Table 2

Statistically significant candidate clone list in gain and loss group

SRFS=systemic recurrence-free survival; OS=overall survival; kb=kilobase; NS=not significant.

Table 3

Common regions showing gain or loss in more than 50% of all 77 samples

kb=kilobase.

Table 4

Candidate gene list from candidate clones in gain and loss group

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