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Li S, Lin L, Zhao J, Yang Z, Zhong Y, Huang L, Chen J, Zhang L, Ding Y, Xie T. The Study of the Influence of IL5RA Variants on Chronic Obstructive Pulmonary Disease. COPD 2023; 20:338-347. [PMID: 37905709 DOI: 10.1080/15412555.2023.2270729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease, and its pathogenesis is influenced by genetic factors. This study aimed to evaluate the role of IL5RA genetic variation in the risk of COPD. In this study, 498 patients with COPD and 498 normal controls were recruited. Subsequently, five SNPs (rs3804795, rs2290610, rs13097407, rs334782, and rs3856850) in the IL5RA gene were genotyped. Logistic analysis examined the association of five single nucleotide polymorphisms (SNPs) in IL5RA with the risk of COPD under various genetic models. Furthermore, the association between IL5RA and susceptibility to COPD was comprehensively analyzed with stratification based on age, sex, smoking, and alcohol consumption. Our study showed that IL5RA rs13097407 reduced susceptibility to COPD (OR = 0.43, p < 0.001, p (FDR)< 0.001). On the other hand, rs3856850 was associated with an increased risk of COPD (OR = 1.71, p = 0.002, p (FDR) = 0.002). Interestingly, the effect of IL5RA SNPs on susceptibility to COPD was found to be influenced by factors such as sex and smoking. IL5RA gene variants were significantly associated with susceptibility to COPD.
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Affiliation(s)
- Siguang Li
- Department of General Practice, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Lingsang Lin
- Department of General Practice, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Jie Zhao
- Department of Pulmonary and Critical Care Medicine, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Zehua Yang
- Department of Pulmonary and Critical Care Medicine, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Yi Zhong
- Department of General Practice, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Linhui Huang
- Department of Pulmonary and Critical Care Medicine, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Jie Chen
- Department of General Practice, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Lei Zhang
- Department of Pulmonary and Critical Care Medicine, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Yipeng Ding
- Department of General Practice, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Department of Pulmonary and Critical Care Medicine, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Tian Xie
- Department of Pulmonary and Critical Care Medicine, Hainan affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
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Li JX, Huang XZ, Fu WP, Zhang XH, Mauki DH, Zhang J, Sun C, Dai LM, Zhong L, Yu L, Zhang YP. Remote regulation of rs80245547 and rs72673891 mediated by transcription factors C-Jun and CREB1 affect GSTCD expression. iScience 2023; 26:107383. [PMID: 37609638 PMCID: PMC10440715 DOI: 10.1016/j.isci.2023.107383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/30/2022] [Accepted: 07/11/2023] [Indexed: 08/24/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD), the third leading cause of death worldwide, is influenced by genetic factors. The genetic signal rs10516526 in the glutathione S-transferase C-terminal domain containing (GSTCD) gene is a highly significant and reproducible signal associated with lung function and COPD on chromosome 4q24. In this study, comprehensive bioinformatics analyses and experimental verifications were detailly implemented to explore the regulation mechanism of rs10516526 and GSTCD in COPD. The results suggested that low expression of GSTCD was associated with COPD (p = 0.010). And C-Jun and CREB1 transcription factors were found to be essential for the regulation of GSTCD by rs80245547 and rs72673891. Moreover, rs80245547T and rs72673891G had a stronger binding ability to these transcription factors, which may promote the allele-specific long-range enhancer-promoter interactions on GSTCD, thus making COPD less susceptible. Our study provides a new insight into the relationship between rs10516526, GSTCD, and COPD.
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Affiliation(s)
- Jin-Xiu Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650000, China
| | - Xue-Zhen Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
| | - Wei-ping Fu
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Xiao-hua Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
| | - David H. Mauki
- Faculty of Pharmaceutical Sciences, Institute of Biomedicine and Biotechnology, Center for Cancer Immunology, Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518000, Guangdong China
| | - Jing Zhang
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Chang Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710000, China
| | - Lu-Ming Dai
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Li Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710000, China
- Provincial Demonstration Center for Experimental Biology Education, Shaanxi Normal University, Xi’an 710000, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
| | - Ya-ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650000, China
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Xu S, Liu W, Gong L, Li X, Chu W, Han M, Shi S, Zhou D. Association of ADRB2 gene polymorphisms and intestinal microbiota in Chinese Han adolescents. Open Life Sci 2023; 18:20220646. [PMID: 37554965 PMCID: PMC10404897 DOI: 10.1515/biol-2022-0646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/17/2023] [Accepted: 05/31/2023] [Indexed: 08/10/2023] Open
Abstract
Gut microbiota are closely related to health, and the β2-adrenergic receptor (ADRB2) gene is associated with gastrointestinal diseases. However, little is known about the relationship between ADRB2 gene polymorphisms and intestinal microbiota. In the present study, we aimed to explore the relationship between ADRB2 gene polymorphisms and gut microbiota in Chinese Han adolescents. Data analysis showed that the relative abundance, PICRUSt function prediction, and Chao1 and ACE indices of gut microbiota were significantly different between males and females (P < 0.05). The rs1042711 was positively associated with the relative abundance of Actinobacteria, Coriobacteriia, Bifidobacteriales, Erysipelotrichi, and Erysipelotrichales. The rs12654778 was negatively associated with Bacilli, Lactobacillales, Bacteroidaceae, and Bacteroides. rs1042713 was positively associated with Lactobacillales and Bifidobacteriales. The rs1042717 was positively associated with Bifidobacteriales and negatively associated with Veillonellaceae. The rs1042719 was negatively associated with Erysipelotrichi and Erysipelotrichales and positively associated with Erysipelotrichi, Erysipelotrichales, Bifidobacteriales, and Ruminococcaceae in females. The rs1801704 was positively associated with Erysipelotrichi, Erysipelotrichales, Bifidobacteriales, Actinobacteria, Coriobacteriia, and Bifidobacteriales. The rs2053044 was positively associated with Ruminococcaceae, Dialister, Firmicutes, Clostridia, Clostridiales, Bifidobacteriales, and Faecalibacterium and negatively associated with Bacilli, Lactobacillales, Lachnospiraceae, and Porphyromonadaceae (P < 0.05). These results suggested that the relative abundance, diversity, and PICRUSt function predictions of male and female gut microbiomes differ significantly and that ADRB2 gene polymorphisms were associated with gut microbiome abundance in Chinese Han adolescents.
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Affiliation(s)
- Shanrong Xu
- College of Life Science, Anqing Normal University, Anqing, 246133, P. R. China
- Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, 400014, P. R. China
| | - Wenqi Liu
- College of Life Science, Anqing Normal University, Anqing, 246133, P. R. China
| | - Li Gong
- College of Life Science, Anqing Normal University, Anqing, 246133, P. R. China
| | - Xinyang Li
- Chongqing Traditional Chinese Medicine Hospital, Chongqing, 400021, P. R. China
| | - Wenwen Chu
- College of Life Science, Anqing Normal University, Anqing, 246133, P. R. China
| | - Meng Han
- College of Life Science, Anqing Normal University, Anqing, 246133, P. R. China
| | - Shuiqin Shi
- College of Life Science, Anqing Normal University, 1318 North Jixian Road, Anqing, 246133, P. R. China
| | - Duoqi Zhou
- College of Life Science, Anqing Normal University, 1318 North Jixian Road, Anqing, 246133, P. R. China
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Nandanpawar P, Sahoo L, Sahoo B, Murmu K, Chaudhari A, Pavan kumar A, Das P. Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita. Front Genet 2023; 14:1153911. [PMID: 37359361 PMCID: PMC10285081 DOI: 10.3389/fgene.2023.1153911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.
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Affiliation(s)
- P. Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - L. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - B. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - K. Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - A. Chaudhari
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - A. Pavan kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - P. Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
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Fu Y, Liu L, Wu H. Role of Genetic Polymorphisms in IL12Rβ2 in Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2022; 17:1671-1683. [PMID: 35923356 PMCID: PMC9342432 DOI: 10.2147/copd.s366844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/25/2022] [Indexed: 11/23/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is the most common chronic inflammatory airway disease. Il-12r beta 2 (IL-12Rβ2) is important for the production of pathogenic Th1 cells. We aimed to explore the association between IL-12Rβ2 genetic variants and COPD risk among southern Chinese Han population. Methods We recruited 996 participants to perform an association analysis through SNPStats online software. We used false-positive report probability analysis to detect whether the positive findings were noteworthy. Haploview 4.2 software and SNPStats were used to conduct the haplotype analysis and linkage disequilibrium. Finally, the interaction of SNP-SNP in COPD risk was evaluated by multi-factor dimensionality reduction. Results The study found evidence that genetic loci in IL-12Rβ2 (rs2201584, rs1874791, rs6679356, and rs3790567) were potentially associated with the COPD susceptibility. In particular, IL-12Rβ2-rs2201584 and -rs1874791 showed close associations with COPD risk in both overall and several stratified analyses. Overall analysis or several stratified analyses indicated that allele A or homozygous genotype AA of IL-12Rβ2-rs2201584 were risk factors for COPD (Allele A: OR (95% CI) = 1.23 (1.02–1.48), p = 0.033; genotype AA: OR (95% CI) = 1.76 (1.15–2.69), p = 0.009). The allele A or homozygous genotype AA of IL-12Rβ2- rs1874791 were also risk factors for COPD (Allele A: OR (95% CI) = 1.36 (1.10–1.68), p = 0.004; genotype AA: OR (95% CI) = 2.17 (1.18–3.99), p = 0.013). Conclusion Intronic variants in IL-12Rβ2 (rs2201584, rs1874791, rs6679356, and rs3790567) were associated with the COPD susceptibility. In particular, there were sufficient evidences that IL-12Rβ2-rs2201584 and -rs1874791 were associated with the increasing risk of COPD.
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Affiliation(s)
- Yihui Fu
- Department of Respiratory and Critical Care Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, 570311, People’s Republic of China
| | - Lirong Liu
- Department of Respiratory and Critical Care Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, 570311, People’s Republic of China
| | - Haihong Wu
- Department of Respiratory and Critical Care Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, 570311, People’s Republic of China
- Correspondence: Haihong Wu, Department of Respiratory and Critical Care Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), #19, Xiuhua Road, Xiuying District, Haikou, 570311, People’s Republic of China, Tel/Fax +86 13976906068, Email
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Cai MX, Wei B, Liao SE, Fu JY, Liu YJ, Li LX. Association between ADRB2 regulatory region polymorphisms and susceptibility to childhood asthma. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:1132-1140. [PMID: 34753545 DOI: 10.7499/j.issn.1008-8830.2108054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To study the association of β2-drenergic receptor (ADRB2) regulatory region single nucleotides polymorphism (SNP)/haplotypes at rs11168070, rs17108803, rs2053044, rs12654778, rs11959427, and rs2895795 loci with childhood asthma. METHODS A total of 143 children with asthma who attended the hospital from October 2016 to October 2020 were enrolled as the asthma group, among whom 61 children had mild symptoms (mild group) and 82 children had moderate-to-severe symptoms (moderate-to-severe group). A total of 137 healthy children were enrolled as the control group. Peripheral venous blood samples were collected from the two groups. The SNaPshot SNP technique was used to analyze the SNP and haplotypes of the ADRB2 regulatory region at rs11168070, rs17108803, rs2053044, rs12654778, rs11959427, and rs2895795 loci in all children. The asthma group and the control group were compared in terms of the association of ADRB2 regulatory region SNP and haplotypes at the above six loci with susceptibility to asthma and severity of asthma. RESULTS Polymorphisms were observed in the ADRB2 regulation region at the above six loci in both the asthma group and the control group, with significant differences between the two groups in the distribution of genotype and allele frequencies at rs2895795 (-1429T /A), rs2053044(-1023G/A), and rs12654778 (-654G/A) loci (P<0.05). Linkage disequilibrium of SNP was observed at the six loci of the ADRB2 regulatory region.The haplotypes of TATGCT, TATGGC, and AGTGCT were associated with susceptibility to childhood asthma, among which TATGCT and TATGGC were risk factors for childhood asthma (OR=1.792 and 1.946 respectively, P<0.05), while AGTGCT was a protective factor (OR=0.523, P<0.05). CONCLUSIONS SNP/haplotype of the ADRB2 regulatory region is associated with the susceptibility to childhood asthma. The haplotypes of TATGCT and TATGGC formed by such SNP/haplotype are risk factors for childhood asthma, while AGTGCT is a protective factor.
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Affiliation(s)
- Ming-Xuan Cai
- General Hospital of the Northern Theater of the Chinese People's Liberation Army, Shenyang 110016, China
| | - Bing Wei
- General Hospital of the Northern Theater of the Chinese People's Liberation Army, Shenyang 110016, China
| | - Shi-E Liao
- General Hospital of the Northern Theater of the Chinese People's Liberation Army, Shenyang 110016, China
| | - Jin-Yue Fu
- General Hospital of the Northern Theater of the Chinese People's Liberation Army, Shenyang 110016, China
| | - Ya-Jun Liu
- General Hospital of the Northern Theater of the Chinese People's Liberation Army, Shenyang 110016, China
| | - Ling-Xue Li
- General Hospital of the Northern Theater of the Chinese People's Liberation Army, Shenyang 110016, China
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Abudureheman Z, Li L, Zhong X, Xu J, Gong H, Yilamujiang S, Ren J, Xie C, Zheng A, Tuerxun D, Abudukadeer A, Aini P, Xu A, Zou X. The rs74794265 SNP of the SREK1 Gene is Associated with COPD in Kashi, China. Int J Chron Obstruct Pulmon Dis 2021; 16:2631-2636. [PMID: 34556983 PMCID: PMC8453436 DOI: 10.2147/copd.s321150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/03/2021] [Indexed: 11/24/2022] Open
Abstract
Background Kashi city is situated near the Taklamakan desert and has a high incidence rate of chronic obstructive pulmonary disease (COPD). In this study, we aimed to explore the relationship between the SNP of the SREK1 gene locus rs74794265 and the susceptibility to COPD among the Uyghur population in Kashi, XinJiang, China. Methods A total of 541 patients with COPD and 534 control subjects were included in this study. Sanger sequencing was used to analyze the SNP of the SREK1 gene locus rs74794265 site. The distribution of genotypes in different genetic models between the case and control group were analyzed by logistic regression analysis after adjusting for age, sex, and smoking history. Results The SREK1 gene SNP locus rs74794265 included two genotypes, namely, C/C and C/T, of which C/C was the wildtype; The risk of COPD was significantly lower in patients with heterozygous C/T in rs74794265 [p=0.0236, OR=0.3677 (0.1547–0.8742)], and the allele frequency of T was also significantly lower in the patient group [p=0.0245, OR=0.3728 (0.1577–0.8811)]. The heterozygous C/T of rs74794265 among non-smoking COPD patients was significantly lower than other COPD patients [p=0.0298, OR=0.3217 (0.1156–0.8949)], and there was no significant correlation of the heterozygous C/T genotype in smokers. Conclusion We found that the rs74794265 heterozygous C/T genotype significantly reduces the risk of COPD. The C/T genotype is likely a protective factor for COPD in the Kashi region. We speculate that the occurrence of COPD in this area is probably more related to desert climate condition and genetic factors than smoking status.
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Affiliation(s)
- Zulipikaer Abudureheman
- Department of Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, People's Republic of China
| | - Li Li
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - XueMei Zhong
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - JingRan Xu
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - Hui Gong
- Department of Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, People's Republic of China
| | - Subinuer Yilamujiang
- Department of Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, People's Republic of China
| | - Jie Ren
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - ChengXin Xie
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - AiFang Zheng
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - Dilala Tuerxun
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - Ayiguzali Abudukadeer
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - Paierda Aini
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - AiMin Xu
- Department of Clinical Laboratory, First People's Hospital of Kashi, Kashi, People's Republic of China
| | - XiaoGuang Zou
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, People's Republic of China
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Integration of SNP Disease Association, eQTL, and Enrichment Analyses to Identify Risk SNPs and Susceptibility Genes in Chronic Obstructive Pulmonary Disease. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3854196. [PMID: 33457407 PMCID: PMC7785362 DOI: 10.1155/2020/3854196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease caused by the disturbance of genetic and environmental factors. Single-nucleotide polymorphisms (SNPs) play a vital role in the genetic dissection of complex diseases. In-depth analysis of SNP-related information could recognize disease-associated biomarkers and further uncover the genetic mechanism of complex diseases. Risk-related variants might act on the disease by affecting gene expression and gene function. Through integrating SNP disease association study and expression quantitative trait loci (eQTL) analysis, as well as functional enrichment of containing known causal genes, four risk SNPs and four corresponding susceptibility genes were identified utilizing next-generation sequencing (NGS) data of COPD. Of the four risk SNPs, one could be found in the SNPedia database that stored disease-related SNPs and has been linked to a disease in the literature. Four genes showed significant differences from the perspective of normal/disease or variant/nonvariant samples, as well as the high performance of sample classification. It is speculated that the four susceptibility genes could be used as biomarkers of COPD. Furthermore, three of our susceptibility genes have been confirmed in the literature to be associated with COPD. Among them, two genes had an impact on the significance of expression correlation of known causal genes they interact with, respectively. Overall, this research may present novel insights into the diagnosis and pathogenesis of COPD and susceptibility gene identification of other complex diseases.
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Cai Y, Liu R, Lu X, Zhang Q, Wang X, Lian H, Wang H. Correlation in gene expression between the aggravation of chronic obstructive pulmonary disease and the occurrence of complications. Bioengineered 2020; 11:1245-1257. [PMID: 33108241 PMCID: PMC8291885 DOI: 10.1080/21655979.2020.1839216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Aggravation of the chronic obstructive pulmonary disease (COPD) often leads to a slew of complications, but the correlation between COPD aggravation and the complications on the basis of molecular level remains unclear. In this study, gene expression profiles of COPD in patients at early and aggravation stages were collected and differentially-expressed genes were selected. Meanwhile, gene expression data implicated in COPD complications were analyzed to establish a regulatory network of COPD aggravation and COPD related complications. In addition, the gene enrichment function of DAVID6.7 was utilized to evaluate the similarities between COPD aggravation and COPD complications in term of biological process. By analyzing the genes of COPD aggravation and the COPD complications, we found 18 genes highly related to COPD aggravation, among which haptoglobin (HP) was correlated with 14 complications, followed by ADRB2, LCK and CA1, which were related to 13, 11 and 11 complications, respectively. As far as the complications concerned, obesity was regulated by 17 of the 18 genes, which indicated that there was a close correlation between COPD aggravation and obesity. Meanwhile, lung cancer, diabetes and heart failure were regulated by 15, 15 and 14 genes, respectively, among the 18 selected genes. This study suggested the driver genes of COPD aggravation were capable of extensively regulating COPD complications, which would provide a theoretical basis for development of cures for COPD and its complications.
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Affiliation(s)
- Yuchen Cai
- Department of Mathematics, School of Science, Hainan University , Haikou, Hainan Province, China
| | - Runhan Liu
- Department of Mathematics, School of Science, Hainan University , Haikou, Hainan Province, China
| | - Xinhe Lu
- School of Life and Pharmaceutical Science , Haikou, Hainan Province, China
| | - Qiming Zhang
- School of Electrical and Information Engineering, Anhui University of Science and Technology , Huainan, Anhui Province, China
| | - Xinwei Wang
- College of Information Science and Engineering, Ocean University of China , Qingdao, Shandong Province, China
| | - Huijing Lian
- School of Economics, Hainan University , Haikou, Hainan Province, China
| | - Haohua Wang
- Department of Mathematics, School of Science, Hainan University , Haikou, Hainan Province, China
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Lu H, Xu D, Yang Y, Feng Q, Sun J, Li Q, Zhao J, Zhou X, Niu H, Liu J, He P, Ding Y. Genetic Polymorphisms of CYP2C9/ CYP2C19 in Chronic Obstructive Pulmonary Disease. COPD 2020; 17:595-600. [PMID: 32757668 DOI: 10.1080/15412555.2020.1780577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a high incidence in the elderly and significantly affects the quality of life. CYP2C9 and CYP2C19 play an important role in tobacco-related diseases and inflammatory reactions. Thus, we aim to investigate the association between CYP2C9/CYP2C19 polymorphisms and the risk of COPD. In this study, a total of 821 subjects were recruited which include 313 COPD cases and 508 healthy controls. Seven SNPs of CYP2C9/CYP2C19 were selected for genotyping. The odds ratios (ORs) and 95% confidence interval (95% CI) were calculated using logistic regression analysis to evaluate the association between COPD risk and CYP2C9/CYP2C19 polymorphisms. Our study showed that A allele of rs9332220 in CYP2C9 was associated with reducing COPD risk (OR = 0.64, 95% CI = 0.43-0.94, p = 0.021). And rs111853758 G allele carrier could significantly decrease 0.35-fold COPD risk compared with T allele carrier (OR = 0.65, 95% CI = 0.45-0.96, p = 0.027). Furthermore, sex-based stratification analysis showed that rs9332220 and rs111853758 polymorphisms were associated with the risk of COPD in males. This is the first study to investigate the association between CYP2C9 and CYP2C19 genetic polymorphisms and COPD risk, which may give a new perspective on the prevention and diagnosis of COPD.
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Affiliation(s)
- Hui Lu
- Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China.,Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
| | - Dongchuan Xu
- Department of Emergency, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Yixiu Yang
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Qiong Feng
- Hainan Affiliated Hospital of Hainan Medical University, University of South China, Haikou, Hainan, China
| | - Juan Sun
- Department of Emergency, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Quanni Li
- Department of Emergency, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jie Zhao
- Hainan Affiliated Hospital of Hainan Medical University, University of South China, Haikou, Hainan, China
| | - Xiaoli Zhou
- Department of Emergency, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Huan Niu
- Department of Emergency, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jianfang Liu
- Hainan Affiliated Hospital of Hainan Medical University, University of South China, Haikou, Hainan, China
| | - Ping He
- Department of Emergency, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Yipeng Ding
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
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11
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Huang X, Mu X, Deng L, Fu A, Pu E, Tang T, Kong X. The etiologic origins for chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis 2019; 14:1139-1158. [PMID: 31213794 PMCID: PMC6549659 DOI: 10.2147/copd.s203215] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/18/2019] [Indexed: 12/27/2022] Open
Abstract
COPD, characterized by long-term poorly irreversible airway limitation and persistent respiratory symptoms, has resulted in enormous challenges to human health worldwide, with increasing rates of prevalence, death, and disability. Although its origin was thought to be in the interactions of genetic with environmental factors, the effects of environmental factors on the disease during different life stages remain little known. Without clear mechanisms and radical cure for it, early screening and prevention of COPD seem to be important. In this review, we will discuss the etiologic origins for poor lung function and COPD caused by specific adverse effects during corresponding life stages, as well as try to find new insights and potential prevention strategies for this disease.
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Affiliation(s)
- Xinwei Huang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China.,Medical School, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
| | - Xi Mu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
| | - Li Deng
- The Pathology Department, First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, People's Republic of China
| | - Aili Fu
- Department of Oncology, Yunfeng Hospital, Xuanwei City, Yunnan Province, People's Republic of China
| | - Endong Pu
- Department of Thoracic Surgery, Yunfeng Hospital, Xuanwei City, Yunnan Province, People's Republic of China
| | - Tao Tang
- Medical School, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
| | - Xiangyang Kong
- Medical School, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
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