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Integrating Single-Cell Transcriptome and Network Analysis to Characterize the Therapeutic Response of Chronic Myeloid Leukemia. Int J Mol Sci 2022; 23:ijms232214335. [PMID: 36430822 PMCID: PMC9695508 DOI: 10.3390/ijms232214335] [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: 09/12/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disease characterized by a unique BCR-ABL fusion gene. Tyrosine kinase inhibitors (TKIs) were developed to target the BCR-ABL oncoprotein, inhibiting its abnormal kinase activity. TKI treatments have significantly improved CML patient outcomes. However, the patients can develop drug resistance and relapse after therapy discontinues largely due to intratumor heterogeneity. It is critical to understand the differences in therapeutic responses among subpopulations of cells. Single-cell RNA sequencing measures the transcriptome of individual cells, allowing us to differentiate and analyze individual cell populations. Here, we integrated a single-cell RNA sequencing profile of CML stem cells and network analysis to decipher the mechanisms of distinct TKI responses. Compared to normal hematopoietic stem cells, a set of genes that were concordantly differentially expressed in various types of stem cells of CML patients was revealed. Further transcription regulatory network analysis found that most of these genes were directly controlled by one or more transcript factors and the genes have more regulators in the cells of the patients who responded to the treatment. The molecular markers including a known drug-resistance gene and novel gene signatures for treatment response were also identified. Moreover, we combined protein-protein interaction network construction with a cancer drug database and uncovered the drugs that target the marker genes directly or indirectly via the protein interactions. The gene signatures and their interacted proteins identified by this work can be used for treatment response prediction and lead to new strategies for drug resistance monitoring and prevention. Our single-cell-based findings offered novel insights into the mechanisms underlying the therapeutic response of CML.
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Li L, Liu R, Peng C, Chen X, Li J. Pharmacogenomics for the efficacy and side effects of antihistamines. Exp Dermatol 2022; 31:993-1004. [PMID: 35538735 DOI: 10.1111/exd.14602] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/01/2022] [Accepted: 05/09/2022] [Indexed: 11/27/2022]
Abstract
Antihistamines, especially H1 antihistamines, are widely used in the treatment of allergic diseases such as urticaria and allergic rhinitis, mainly for reversing elevated histamine and anti-allergic effects. Antihistamines are generally safe, but some patients experience adverse reactions, such as cardiotoxicity, central inhibition, and anticholinergic effects. There are also individual differences in antihistamine efficacy in clinical practice. The concept of individualized medicine has been deeply rooted in people's minds since it was put forward. Pharmacogenomics is the study of the role of inheritance in individual variations in drug response. In recent decades, pharmacogenomics has been developing rapidly, which provides new ideas for individualized medicine. Polymorphisms in the genes encoding metabolic enzymes, transporters, and target receptors have been shown to affect the efficacy of antihistamines. In addition, recent evidence suggests that gene polymorphisms influence urticaria susceptibility and antihistamine therapy. Here, we summarize current reports in this area, aiming to contribute to future research in antihistamines and clinical guidance for antihistamines use in individualized medicine.
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Affiliation(s)
- Liqiao Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Runqiu Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Cong Peng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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3
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Sun N, Ma D, Gao P, Li Y, Yan Z, Peng Z, Han F, Zhang Y, Qi X. Construction of a Prognostic Risk Prediction Model for Obesity Combined With Breast Cancer. Front Endocrinol (Lausanne) 2021; 12:712513. [PMID: 34566889 PMCID: PMC8458964 DOI: 10.3389/fendo.2021.712513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 11/30/2022] Open
Abstract
The improvement in the quality of life is accompanied by an accelerated pace of living and increased work-related pressures. Recent decades has seen an increase in the proportion of obese patients, as well as an increase in the prevalence of breast cancer. More and more evidences prove that obesity may be one of a prognostic impact factor in patients with breast cancer. Obesity presents unique diagnostic and therapeutic challenges in the population of breast cancer patients. Therefore, it is essential to have a better understanding of the relationship between obesity and breast cancer. This study aims to construct a prognostic risk prediction model combining obesity and breast cancer. In this study, we obtained a breast cancer sample dataset from the GEO database containing obesity data [determined by the body mass index (BMI)]. A total of 1174 genes that were differentially expressed between breast cancer samples of patients with and without obesity were screened by the rank-sum test. After weighted gene co-expression network analysis (WGCNA), 791 related genes were further screened. Relying on single-factor COX regression analysis to screen the candidate genes to 30, these 30 genes and another set of TCGA data were intersected to obtain 24 common genes. Finally, lasso regression analysis was performed on 24 genes, and a breast cancer prognostic risk prediction model containing 6 related genes was obtained. The model was also found to be related to the infiltration of immune cells. This study provides a new and accurate prognostic model for predicting the survival of breast cancer patients with obesity.
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Affiliation(s)
- Na Sun
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Dandan Ma
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Pingping Gao
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yanling Li
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zexuan Yan
- Institute of Pathology and Southwest Cancer Center, Key Laboratory of the Ministry of Education, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zaihui Peng
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
- *Correspondence: Yi Zhang, ; Xiaowei Qi,
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
- *Correspondence: Yi Zhang, ; Xiaowei Qi,
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Comments on 'Association of FcϵRIβ polymorphisms with risk of asthma and allergic rhinitis: evidence based on 29 case-control studies'. Biosci Rep 2020; 40:225723. [PMID: 32638994 PMCID: PMC7374272 DOI: 10.1042/bsr20193424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022] Open
Abstract
Guo et al. (Bioscience Reports (2018) 38, BSR20180177) published a meta-analysis concerning the association between five single nucleotide polymorphisms (SNPs) in the high-affinity IgE receptor β chain (FcεRIβ) gene, namely E237G, -109 C/T, RsaI_in2, RsaI_ex7, and I181L, and risk of asthma and allergic rhinitis based on available 29 case–control studies. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of association of SNPs in FcεRIβ gene with allergic diseases risk. They found that FcεRIβ E237G (237G vs. 237E: OR = 1.28, 95% CI = 1.06–1.53) and −109 C/T (TT vs. CT+CC: OR = 1.58, 95% CI = 1.26–1.98) were risk factors for allergic diseases. Guo et al.’s findings are interesting, but we found that several issues should be clarified after carefully reading the paper. Here, we intended to comment on these data clarifications.
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Hines EA, Szakaly RJ, Leng N, Webster AT, Verheyden JM, Lashua AJ, Kendziorski C, Rosenthal LA, Gern JE, Sorkness RL, Sun X, Lemanske RF. Comparison of temporal transcriptomic profiles from immature lungs of two rat strains reveals a viral response signature associated with chronic lung dysfunction. PLoS One 2014; 9:e112997. [PMID: 25437859 PMCID: PMC4249857 DOI: 10.1371/journal.pone.0112997] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 10/17/2014] [Indexed: 11/25/2022] Open
Abstract
Early life respiratory viral infections and atopic characteristics are significant risk factors for the development of childhood asthma. It is hypothesized that repeated respiratory viral infections might induce structural remodeling by interfering with the normal process of lung maturation; however, the specific molecular processes that underlie these pathological changes are not understood. To investigate the molecular basis for these changes, we used an established Sendai virus infection model in weanling rats to compare the post-infection transcriptomes of an atopic asthma susceptible strain, Brown Norway, and a non-atopic asthma resistant strain, Fischer 344. Specific to this weanling infection model and not described in adult infection models, Sendai virus in the susceptible, but not the resistant strain, results in morphological abnormalities in distal airways that persist into adulthood. Gene expression data from infected and control lungs across five time points indicated that specific features of the immune response following viral infection were heightened and prolonged in lungs from Brown Norway rats compared with Fischer 344 rats. These features included an increase in macrophage cell number and related gene expression, which then transitioned to an increase in mast cell number and related gene expression. In contrast, infected Fischer F344 lungs exhibited more efficient restoration of the airway epithelial morphology, with transient appearance of basal cell pods near distal airways. Together, these findings indicate that the pronounced macrophage and mast cell responses and abnormal re-epithelialization precede the structural defects that developed and persisted in Brown Norway, but not Fischer 344 lungs.
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Affiliation(s)
- Elizabeth A. Hines
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Renee J. Szakaly
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ning Leng
- Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anais T. Webster
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jamie M. Verheyden
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Amber J. Lashua
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Christina Kendziorski
- Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Louis A. Rosenthal
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ronald L. Sorkness
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Xin Sun
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail: (XS); (RFL)
| | - Robert F. Lemanske
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail: (XS); (RFL)
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Guo A, Zhu W, Zhang C, Wen S, Chen X, Chen M, Zhang J, Su J, Chen W, Zhao Y, Yan S, He Y, Liu Z, Zhou H, Chen X, Li J. Association of FCER1A genetic polymorphisms with risk for chronic spontaneous urticaria and efficacy of nonsedating H1-antihistamines in Chinese patients. Arch Dermatol Res 2014; 307:183-90. [DOI: 10.1007/s00403-014-1525-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/15/2014] [Accepted: 11/03/2014] [Indexed: 01/01/2023]
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Yang HJ, Zheng L, Zhang XF, Yang M, Huang X. Association of the MS4A2 gene promoter C-109T or the 7th exon E237G polymorphisms with asthma risk: a meta-analysis. Clin Biochem 2014; 47:605-11. [PMID: 24495860 DOI: 10.1016/j.clinbiochem.2014.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 01/01/2014] [Accepted: 01/22/2014] [Indexed: 01/25/2023]
Abstract
BACKGROUND AND OBJECTIVE A large number of studies have examined the association between the Membrane-spanning 4 domains, superfamily A, number 2 (MS4A2) gene C-109T (rs1441586) or E237G (rs569108) variants and asthma risk. However, the results are inconsistent and inconclusive. To derive a more precise estimation, a meta-analysis was performed. METHODS Meta-analyses were conducted with the data from case-control association studies (24 studies with 4496 asthmatics and 4571 controls for E237G variant and 9 studies including 2005 cases and 1868 control for C-109T polymorphisms, respectively). Random-effects model was used to calculate summary odds ratios (ORs). RESULTS For the MS4A2 gene E237G variant, no significant associations with asthma were found in overall population; we observed an elevated risk of atopic asthma among subjects with the 237G allele (OR=1.341, 95% CI: 1.039-1.732 for G versus E and OR=1.374, 95% CI: 1.032-1.828 for EG+GG versus EE) in the stratified meta-analysis. As for the MS4A2 gene C-109T polymorphism, no significant associations with asthma risk were observed in the total population; in subgroup analysis by ethnicity of subjects we found increased asthma risk among Asians carrying T allele (OR=1.140, 95% CI: 1.019-1.276 for T versus C and OR=1.359, 95% CI: 1.029-1.794 for TT versus CC). CONCLUSIONS Data indicated that the MS4A2 gene E237G variant may be a risk factor for developing atopic asthma and the promoter -109T allele is a potential risk factor of asthma in Asians.
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Affiliation(s)
- Hai-Jun Yang
- Department of Preventive Medicine, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, PR China.
| | - Lan Zheng
- Department of Respiratory Medicine, Hubei Hospital of Traditional Chinese Medicine Affiliated to Hubei University of Chinese Medicine, Wuhan 430061, Hubei, PR China
| | - Xue-Fei Zhang
- Department of Preventive Medicine, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, PR China
| | - Min Yang
- Department of Preventive Medicine, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, PR China
| | - Xing Huang
- Department of Preventive Medicine, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, PR China
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Potaczek DP. Links between allergy and cardiovascular or hemostatic system. Int J Cardiol 2013; 170:278-85. [PMID: 24315352 DOI: 10.1016/j.ijcard.2013.11.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 11/03/2013] [Accepted: 11/17/2013] [Indexed: 12/28/2022]
Abstract
In addition to a well-known immunologic background of atherosclerosis and influences of inflammation on arterial and venous thrombosis, there is growing evidence for the presence of links between allergy and vascular or thrombotic disorders. In this interpretative review, five pretty well-documented areas of such overlap are described and discussed, including: (1) links between atherosclerosis and immunoglobulin E or atopy, (2) mutual effects of blood lipids and allergy, (3) influence of atopy and related disorders on venous thromboembolism, (4) the role of platelets in allergic diseases, and (5) the functions of protein C system in atopic disorders.
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Affiliation(s)
- Daniel P Potaczek
- Institute of Laboratory Medicine, Philipps-Universität Marburg, Marburg, Germany; John Paul II Hospital, Krakow, Poland.
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AKHABIR LOUBNA, SANDFORD ANDREWJ. Genome-wide association studies for discovery of genes involved in asthma. Respirology 2011; 16:396-406. [DOI: 10.1111/j.1440-1843.2011.01939.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Joubert BR, Reif DM, Edwards SW, Leiner KA, Hudgens EE, Egeghy P, Gallagher JE, Hubal EC. Evaluation of genetic susceptibility to childhood allergy and asthma in an African American urban population. BMC MEDICAL GENETICS 2011; 12:25. [PMID: 21320344 PMCID: PMC3048491 DOI: 10.1186/1471-2350-12-25] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 02/14/2011] [Indexed: 01/23/2023]
Abstract
BACKGROUND Asthma and allergy represent complex phenotypes, which disproportionately burden ethnic minorities in the United States. Strong evidence for genomic factors predisposing subjects to asthma/allergy is available. However, methods to utilize this information to identify high risk groups are variable and replication of genetic associations in African Americans is warranted. METHODS We evaluated 41 single nucleotide polymorphisms (SNP) and a deletion corresponding to 11 genes demonstrating association with asthma in the literature, for association with asthma, atopy, testing positive for food allergens, eosinophilia, and total serum IgE among 141 African American children living in Detroit, Michigan. Independent SNP and haplotype associations were investigated for association with each trait, and subsequently assessed in concert using a genetic risk score (GRS). RESULTS Statistically significant associations with asthma were observed for SNPs in GSTM1, MS4A2, and GSTP1 genes, after correction for multiple testing. Chromosome 11 haplotype CTACGAGGCC (corresponding to MS4A2 rs574700, rs1441586, rs556917, rs502581, rs502419 and GSTP1 rs6591256, rs17593068, rs1695, rs1871042, rs947895) was associated with a nearly five-fold increase in the odds of asthma (Odds Ratio (OR) = 4.8, p = 0.007). The GRS was significantly associated with a higher odds of asthma (OR = 1.61, 95% Confidence Interval = 1.21, 2.13; p = 0.001). CONCLUSIONS Variation in genes associated with asthma in predominantly non-African ethnic groups contributed to increased odds of asthma in this African American study population. Evaluating all significant variants in concert helped to identify the highest risk subset of this group.
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Affiliation(s)
- Bonnie R Joubert
- US Environmental Protection Agency (EPA), National Exposure Research Laboratory, Durham, NC, USA.
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Potaczek DP, Nishiyama C, Sanak M, Szczeklik A, Okumura K. Genetic variability of the high-affinity IgE receptor alpha-subunit (FcepsilonRIalpha). Immunol Res 2010; 45:75-84. [PMID: 18726713 DOI: 10.1007/s12026-008-8042-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Our knowledge on the variability of FCER1A gene encoding for alpha-subunit of the high-affinity immunoglobulin E receptor (FcepsilonRI) that plays a central role in the pathogenesis of allergy and related disorders, has been recently much extended. Last findings from FCER1A mutational screening and genetic association studies, followed by functional analyses of the polymorphisms, are briefly summarized in this mini-review. The association between FCER1A gene variants and total serum IgE levels seems especially interesting and, supported by functional analyses of polymorphisms, may provide a rationale for pharmacogenetic studies on anti-IgE therapy that indirectly suppresses FcepsilonRI expression.
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Affiliation(s)
- Daniel P Potaczek
- Atopy (Allergy) Research Center, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
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FcepsilonRIalpha gene -18483A>C polymorphism affects transcriptional activity through YY1 binding. Immunogenetics 2009; 61:649-55. [PMID: 19685047 DOI: 10.1007/s00251-009-0391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 07/27/2009] [Indexed: 10/20/2022]
Abstract
Three frequent genetic polymorphisms in the human high-affinity IgE receptor alpha-subunit (FcepsilonRIalpha) were shown to be associated with allergic disorders and/or total serum IgE levels in allergic patients. Two of these were previously demonstrated to affect FcepsilonRIalpha expression while the third -18483A>C (rs2494262) has not yet been subjected to functional studies. We hypothesized that the -18483A>C variant affects transcriptional activity of the FcepsilonRIalpha distal promoter in monocytes in which FcepsilonRIalpha transcription is driven through that regulatory region. Indeed, we confirmed preferential binding of the YY1 transcription factor to the -18483C allele, resulting in lower transcriptional activity when compared with the -18483A allele.
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Lee JY, Park AK, Lee KM, Park SK, Han S, Han W, Noh DY, Yoo KY, Kim H, Chanock SJ, Rothman N, Kang D. Candidate gene approach evaluates association between innate immunity genes and breast cancer risk in Korean women. Carcinogenesis 2009; 30:1528-31. [PMID: 19372141 DOI: 10.1093/carcin/bgp084] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This study was conducted to investigate the role of common variation in innate immunity-related genes as susceptibility factors to breast cancer risk in Korean women. METHODS Total 1536 single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed by Illumina GoldenGate assay in 209 cases and the same numbers of controls. Both SNP and gene-based tests were used to evaluate the association with breast cancer risk. The robustness of results was further evaluated with permutation method, false discovery rate and haplotype analyses. RESULTS Both SNP and gene-based analyses showed promising associations with breast cancer risk for 17 genes: OR10J3, FCER1A, NCF4, CNTNAP1, CTNNB1, KLKB1, ITGB2, ALOX12B, KLK2, IRAK3, KLK4, STAT6, NCF2, CCL1, C1QR1, MBP and NOS1. The most significant association with breast cancer risk was observed for the OR10J3 SNP (rs2494251, P-value = 1.2 x 10(-4)) and FCER1A SNP (rs7548864, P-value = 7.7 x 10(-4)). Gene-based permutation and false discovery rate P-values for OR10J3 SNP (rs2494251) with breast cancer risk were also significant (P = 4 x 10(-5) and 0.008, respectively). Haplotype analyses supported these findings that OR10J3 and FCER1A were most significantly associated with risk for breast cancer (P = 2 x 10(-4) and 0.004, respectively). CONCLUSION This study suggests that common genetic variants in the OR10J3 and FCER1A be strongly associated with breast cancer risk among Korean women.
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Affiliation(s)
- Ji-Young Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, 103 Daehak-Ro, Jongno-Gu, Seoul 110-799, Korea
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Potaczek DP, Nishiyama C, Sanak M, Szczeklik A, Okumura K, Ogawa H. FCER1A gene exon 1A polymorphisms in Japanese and Polish subjects--a comparative analysis of haplotypes. Allergy 2008; 63:626-7. [PMID: 18394141 DOI: 10.1111/j.1398-9995.2008.01675.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- D P Potaczek
- Atopy (Allergy) Research Center, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
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