Single Nucleotide Polymorphisms in the 5′-Upstream Sequence of Chemokine Like Factor and their Associationwith Asthma_Chinese Journal of Respiratory and Critical Care Medicine

Authors：

ZHANGWei ¹ , HE Quanying ¹ , WANG Guangfa ² , ZHAO Hongshan ³ , CHI Chunhua ² , ZHAOYanni ² , DENG Xuan ³ , SU Li ² , SUN Yaoyao ³ , WANGXiaodi. ³

Department of Respiratory Medicine,Peking University People’s Hospital. Beijing, 100044, China;

Corresponding author：

ZHANGWei, Email:

Keywords：

Asthma; Chemokine like factor; Single nucleotide polymorphism; Promoter region; Genotype; Haplotype

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Objective To detect the single nucleotide polymorphisms ( SNPs) in the upstream promoter region of chemokine like factor ( CKLF) gene and analyze their possible associations with asthma and asthma-related phenotypes. Methods Direct Sequence of the 1553bp upstream promoter region of CKLF gene was performed in 245 Chinese Han human genomic DNAs ( 119 asthmatics and 126 controls) .The frequencies of alleles, genotypes, and haplotypes were determined and the association of these SNPs with asthma were further analyzed. Results Four novel SNPs, SNP88 ( T gt; C) , SNP196 ( T gt; C) , SNP568 ( C gt;G) , and SNP1047 ( C gt; G) were found in the promoter region of CKLF. The frequency of rare allele was 0. 168 ( SNP88C) , 0. 168 ( SNP196C) , 0. 352 ( SNP568G) and 0. 167 ( SNP1047G) , respectively.Haplotypes, their frequencies and the linkage disequilibrium coefficients between SNPs were constructed.Complete linkage disequilibrium( LDs) were observed between SNP88 and SNP196, SNP88 and SNP1047,as well as SNP196 and SNP1047, respectively ( D′=1. 000, r2 = 1. 000) . SNP568 was in partial LD with the other three SNPs ( r2 = 0. 366) . No association between asthma and the SNPs was observed. Conclusions Four SNPs in the regulatory region of CKLF in Chinese Han population were firstly identified. Although no significant correlation with asthma was revealed, the SNP and haplotype information is useful for other disease association studies in the future.

Citation： ZHANGWei,HE Quanying,WANG Guangfa,ZHAO Hongshan,CHI Chunhua,ZHAOYanni,DENG Xuan,SU Li,SUN Yaoyao,WANGXiaodi.. Single Nucleotide Polymorphisms in the 5′-Upstream Sequence of Chemokine Like Factor and their Associationwith Asthma. Chinese Journal of Respiratory and Critical Care Medicine, 2009, 09(4): 345-350. doi: Copy

1.	NHLBI/WHO. Workshop Report: Global Strategy for Asthma Management and Prevention [ DB /OL] . http: / / www. ginasthma.org /Guidelineitem. asp?? l1 =2&l2 = 1&intId = 60.
2.	Vercelli D. Advances in asthma and allergy genetics in 2007. J Allergy Clin Immunol, 2008, 122: 267-271.
3.	Warrier MR, Hershey GK. Asthma genetics: personalizing medicine. J Asthma, 2008, 45: 257-264.
4.	Denham S, Koppelman GH, Blakey J, et al. Meta-analysis of genome-wide linkage studies of asthma and related traits. Respir Res, 2008 , 9: 38 .
5.	韩文玲, 马大龙. 一个新的多功能细胞因子-趋化素样因子. 上海免疫学杂志, 2002, 22: 217-219.
6.	McLeish S, Turner SW. Gene-environment interactions in asthma.Arch Dis Child, 2007, 92: 1032-1035.
7.	Colobran R, Pujol-Borrell R, Armengol MP, et al. The chemokine network. II. On how polymorphisms and alternative splicing increase the number of molecular species and configure intricate patterns of disease susceptibility. Clin Exp Immunol, 2007, 150: 1-12.
8.	Ober C. Perspectives on the past decade of asthma genetics. J Allergy Clin Immunol, 2005, 116: 274-278.
9.	Han W, Lou Y, Tang J, et al. Molecular cloning and characterization of chemokine-like factor 1 ( CKLF1 ) , a novel human cytokine with unique structure and potential chemotactic activity. Biochem J,2001, 357: 127-135.
10.	谭亚夏, 钟南山. 趋化素样因子1 在支气管肺损伤与重建中的作用. 中华结核和呼吸杂志, 2002, 25: 433.
11.	谭亚夏, 叶枫, 莫红缨, 等. 趋化素样因子1 对鼠肺巨噬细胞吞噬活性的作用. 广州医学院学报, 2007, 35: 24-26.
12.	杨小琼, 邓述恺, 黄忠碧, 等. 大鼠趋化素样因子1mRNA 在哮喘大鼠肺组织中的表达. 陕西医学杂志, 2007, 36: 14-17.
13.	Tan YX, Han WL, Chen YY, et al. Chemokine-like factor 1, a novel cytokine, contributes to airway damage, remodeling and pulmonary fibrosis. Chin Med J( Engl) , 2004, 117: 1123-1129.
14.	National center for biotechnology information. Single nucleotide polymorphism database [ DB /OL] . http: / / www. ncbi. nlm. nih.gov/ sites/ entrez? db = snp&cmd = search&term = cklf, 2008-06-29.
15.	Programs for genomic applications. SeattleSNPs [ DB/OL ] .http: / / pga. gs. washington. edu/data/cklf / , 2008-08-07.
16.	International HapMap Project. HapMap data phase III [ DB/ OL] .http: / / www. hapmap. org / cgi-perl / gbrowse /hapmap3 B36/,2008-08-29.
17.	中华医学会呼吸病学分会哮喘学组. 支气管哮喘防治指南( 支气管哮喘的定义、诊断、治疗及教育和管理方案) . 中华内科杂志, 2003, 42: 817-822.
18.	Gustincich S, Manfioletti G, Del Sal G, et al. A fast method for high-quality genomic DNA extraction from whole human blood.Biotechniques, 1991, 11: 298-300, 302.
19.	Shi YY, He L. SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. Cell Res, 2005, 15: 97 -98 .
20.	Braman SS. The global burden of asthma. Chest, 2006, 130 ( 1Suppl) : 4S-12S.
21.	Ma X, Ruan G, Wang Y, et al. Two single-nucleotide polymorphisms with linkage disequilibrium in the human programmed cell death 5 gene 5′regulatory region affect promoter activity and the susceptibility of chronic myelogenous leukemia in Chinese population. Clin Cancer Res, 2005, 11: 8592-8599.
22.	Lech-Maranda E, Baseggio L, Bienvenu J, et al. Interleukin-10 gene promoter polymorphisms influence the clinical outcome of diffuse large B-cell lymphoma. Blood, 2004, 103: 3529-3534.
23.	Gonzalez P, Diez-Juan A, Coto E, et al. A single-nucleotide polymorphism in the human p27kip1 gene ( -838C > A ) affects basal promoter activity and the risk of myocardial infarction. BMC Biol, 2004, 2: 5.
24.	Skoog T, van’t Hooft FM, Kallin B, et al. A common functional polymorphism ( C→A substitution at position -863) in the promoter region of the tumour necrosis factor-α( TNF-α) gene sociated with reduced circulating levels of TNF-α. Hum Mol Genet, 1999, 8:1443-1449.
25.	Zhang J, Jin X, Fang S, et al. The functional SNP in the matrix metalloproteinase-3 promoter modifies susceptibility and lymphatic metastases in esophageal squamous cell carcinoma but not in gastric cardiac adenocarcinoma. Carcinogenesis, 2004 , 25 : 2519-2524.
26.	徐明旭, 赖茂毅, 夏东岚, 等. CKLF 基因与CKLFSF1 基因间的顺式调控元件. 细胞与分子免疫学杂志, 2003, 19: 276-278.
27.	徐明旭, 程宁, 杨松桦, 等. CKLFSF1 基因与CKLFSF2 基因间存在的顺式作用元件. 中国生物化学与分子生物学报, 2003, 19:349-353.
28.	Chowdhury MH, Nagai A, Terashima M, et al. Chemokine-like factor expression in the idiopathic inflammatory myopathies. Acta Neurol Scand, 2008, 118: 106-114.
29.	季迎, 张浩, 袁洪, 等. 趋化素样因子-1 在狼疮性肾炎患者肾组织中的表达. 中南大学学报( 医学版) , 2007, 32: 490-493.
30.	龚艳君, 洪涛, 蒋捷, 等. 大鼠趋化素样因子2 mRNA 在心肌梗死大鼠心脏中的表达. 北京大学学报( 医学版) , 2003, 35: 438-440.

1. NHLBI/WHO. Workshop Report: Global Strategy for Asthma Management and Prevention [ DB /OL] . http: / / www. ginasthma.org /Guidelineitem. asp?? l1 =2&l2 = 1&intId = 60.
2. Vercelli D. Advances in asthma and allergy genetics in 2007. J Allergy Clin Immunol, 2008, 122: 267-271.
3. Warrier MR, Hershey GK. Asthma genetics: personalizing medicine. J Asthma, 2008, 45: 257-264.
4. Denham S, Koppelman GH, Blakey J, et al. Meta-analysis of genome-wide linkage studies of asthma and related traits. Respir Res, 2008 , 9: 38 .
5. 韩文玲, 马大龙. 一个新的多功能细胞因子-趋化素样因子. 上海免疫学杂志, 2002, 22: 217-219.
6. McLeish S, Turner SW. Gene-environment interactions in asthma.Arch Dis Child, 2007, 92: 1032-1035.
7. Colobran R, Pujol-Borrell R, Armengol MP, et al. The chemokine network. II. On how polymorphisms and alternative splicing increase the number of molecular species and configure intricate patterns of disease susceptibility. Clin Exp Immunol, 2007, 150: 1-12.
8. Ober C. Perspectives on the past decade of asthma genetics. J Allergy Clin Immunol, 2005, 116: 274-278.
9. Han W, Lou Y, Tang J, et al. Molecular cloning and characterization of chemokine-like factor 1 ( CKLF1 ) , a novel human cytokine with unique structure and potential chemotactic activity. Biochem J,2001, 357: 127-135.
10. 谭亚夏, 钟南山. 趋化素样因子1 在支气管肺损伤与重建中的作用. 中华结核和呼吸杂志, 2002, 25: 433.
11. 谭亚夏, 叶枫, 莫红缨, 等. 趋化素样因子1 对鼠肺巨噬细胞吞噬活性的作用. 广州医学院学报, 2007, 35: 24-26.
12. 杨小琼, 邓述恺, 黄忠碧, 等. 大鼠趋化素样因子1mRNA 在哮喘大鼠肺组织中的表达. 陕西医学杂志, 2007, 36: 14-17.
13. Tan YX, Han WL, Chen YY, et al. Chemokine-like factor 1, a novel cytokine, contributes to airway damage, remodeling and pulmonary fibrosis. Chin Med J( Engl) , 2004, 117: 1123-1129.
14. National center for biotechnology information. Single nucleotide polymorphism database [ DB /OL] . http: / / www. ncbi. nlm. nih.gov/ sites/ entrez? db = snp&cmd = search&term = cklf, 2008-06-29.
15. Programs for genomic applications. SeattleSNPs [ DB/OL ] .http: / / pga. gs. washington. edu/data/cklf / , 2008-08-07.
16. International HapMap Project. HapMap data phase III [ DB/ OL] .http: / / www. hapmap. org / cgi-perl / gbrowse /hapmap3 B36/,2008-08-29.
17. 中华医学会呼吸病学分会哮喘学组. 支气管哮喘防治指南( 支气管哮喘的定义、诊断、治疗及教育和管理方案) . 中华内科杂志, 2003, 42: 817-822.
18. Gustincich S, Manfioletti G, Del Sal G, et al. A fast method for high-quality genomic DNA extraction from whole human blood.Biotechniques, 1991, 11: 298-300, 302.
19. Shi YY, He L. SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. Cell Res, 2005, 15: 97 -98 .
20. Braman SS. The global burden of asthma. Chest, 2006, 130 ( 1Suppl) : 4S-12S.
21. Ma X, Ruan G, Wang Y, et al. Two single-nucleotide polymorphisms with linkage disequilibrium in the human programmed cell death 5 gene 5′regulatory region affect promoter activity and the susceptibility of chronic myelogenous leukemia in Chinese population. Clin Cancer Res, 2005, 11: 8592-8599.
22. Lech-Maranda E, Baseggio L, Bienvenu J, et al. Interleukin-10 gene promoter polymorphisms influence the clinical outcome of diffuse large B-cell lymphoma. Blood, 2004, 103: 3529-3534.
23. Gonzalez P, Diez-Juan A, Coto E, et al. A single-nucleotide polymorphism in the human p27kip1 gene ( -838C > A ) affects basal promoter activity and the risk of myocardial infarction. BMC Biol, 2004, 2: 5.
24. Skoog T, van’t Hooft FM, Kallin B, et al. A common functional polymorphism ( C→A substitution at position -863) in the promoter region of the tumour necrosis factor-α( TNF-α) gene sociated with reduced circulating levels of TNF-α. Hum Mol Genet, 1999, 8:1443-1449.
25. Zhang J, Jin X, Fang S, et al. The functional SNP in the matrix metalloproteinase-3 promoter modifies susceptibility and lymphatic metastases in esophageal squamous cell carcinoma but not in gastric cardiac adenocarcinoma. Carcinogenesis, 2004 , 25 : 2519-2524.
26. 徐明旭, 赖茂毅, 夏东岚, 等. CKLF 基因与CKLFSF1 基因间的顺式调控元件. 细胞与分子免疫学杂志, 2003, 19: 276-278.
27. 徐明旭, 程宁, 杨松桦, 等. CKLFSF1 基因与CKLFSF2 基因间存在的顺式作用元件. 中国生物化学与分子生物学报, 2003, 19:349-353.
28. Chowdhury MH, Nagai A, Terashima M, et al. Chemokine-like factor expression in the idiopathic inflammatory myopathies. Acta Neurol Scand, 2008, 118: 106-114.
29. 季迎, 张浩, 袁洪, 等. 趋化素样因子-1 在狼疮性肾炎患者肾组织中的表达. 中南大学学报( 医学版) , 2007, 32: 490-493.
30. 龚艳君, 洪涛, 蒋捷, 等. 大鼠趋化素样因子2 mRNA 在心肌梗死大鼠心脏中的表达. 北京大学学报( 医学版) , 2003, 35: 438-440.

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