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Pandey JP. Immunoglobulin γ marker genes as effect modifiers of Epstein-Barr virus-multiple sclerosis association. Immunology 2023; 169:242-244. [PMID: 36659869 DOI: 10.1111/imm.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Affiliation(s)
- Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
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The Future of Biomarkers in Veterinary Medicine: Emerging Approaches and Associated Challenges. Animals (Basel) 2022; 12:ani12172194. [PMID: 36077913 PMCID: PMC9454634 DOI: 10.3390/ani12172194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary In this review we seek to outline the role of new technologies in biomarker discovery, particularly within the veterinary field and with an emphasis on ‘omics’, as well as to examine why many biomarkers-despite much excitement-have not yet made it to clinical practice. Further we emphasise the critical need for close collaboration between clinicians, researchers and funding bodies and the need to set clear goals for biomarker requirements and realistic application in the clinical setting, ensuring that biomarker type, method of detection and clinical utility are compatible, and adequate funding, time and sample size are available for all phases of development. Abstract New biomarkers promise to transform veterinary practice through rapid diagnosis of diseases, effective monitoring of animal health and improved welfare and production efficiency. However, the road from biomarker discovery to translation is not always straightforward. This review focuses on molecular biomarkers under development in the veterinary field, introduces the emerging technological approaches transforming this space and the role of ‘omics platforms in novel biomarker discovery. The vast majority of veterinary biomarkers are at preliminary stages of development and not yet ready to be deployed into clinical translation. Hence, we examine the major challenges encountered in the process of biomarker development from discovery, through validation and translation to clinical practice, including the hurdles specific to veterinary practice and to each of the ‘omics platforms–transcriptomics, proteomics, lipidomics and metabolomics. Finally, recommendations are made for the planning and execution of biomarker studies with a view to assisting the success of novel biomarkers in reaching their full potential.
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Pandey JP, Agostini S, Namboodiri AM, Mancuso R, Guerini FR, Meloni M, Costa AS. Immunoglobulin γ chain allotypes and humoral immunity to HSV1 in Parkinson's disease. J Neuroimmunol 2022; 371:577948. [DOI: 10.1016/j.jneuroim.2022.577948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/06/2022] [Accepted: 08/03/2022] [Indexed: 11/26/2022]
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Lin TY, Chang YC, Hsiao YJ, Chien Y, Jheng YC, Wu JR, Ching LJ, Hwang DK, Hsu CC, Lin TC, Chou YB, Huang YM, Chen SJ, Yang YP, Tsai PH. Identification of Novel Genomic-Variant Patterns of OR56A5, OR52L1, and CTSD in Retinitis Pigmentosa Patients by Whole-Exome Sequencing. Int J Mol Sci 2021; 22:ijms22115594. [PMID: 34070492 PMCID: PMC8198027 DOI: 10.3390/ijms22115594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are rare but highly heterogeneous genetic disorders that affect individuals and families worldwide. However, given its wide variability, its analysis of the driver genes for over 50% of the cases remains unexplored. The present study aims to identify novel driver genes, disease-causing variants, and retinitis pigmentosa (RP)-associated pathways. Using family-based whole-exome sequencing (WES) to identify putative RP-causing rare variants, we identified a total of five potentially pathogenic variants located in genes OR56A5, OR52L1, CTSD, PRF1, KBTBD13, and ATP2B4. Of the variants present in all affected individuals, genes OR56A5, OR52L1, CTSD, KBTBD13, and ATP2B4 present as missense mutations, while PRF1 and CTSD present as frameshift variants. Sanger sequencing confirmed the presence of the novel pathogenic variant PRF1 (c.124_128del) that has not been reported previously. More causal-effect or evidence-based studies will be required to elucidate the precise roles of these SNPs in the RP pathogenesis. Taken together, our findings may allow us to explore the risk variants based on the sequencing data and upgrade the existing variant annotation database in Taiwan. It may help detect specific eye diseases such as retinitis pigmentosa in East Asia.
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Affiliation(s)
- Ting-Yi Lin
- College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan;
| | - Yun-Chia Chang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Yu-Jer Hsiao
- College of Medicine, National Yang-Ming Chiao-Tung University, Taipei 11217, Taiwan;
| | - Yueh Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- Institute of Pharmacology, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Ying-Chun Jheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Big Data Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Jing-Rong Wu
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
| | - Lo-Jei Ching
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
| | - De-Kuang Hwang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chih-Chien Hsu
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Tai-Chi Lin
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Yu-Bai Chou
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Yi-Ming Huang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Internal Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Critical Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Correspondence: (Y.-P.Y.); (P.H.T.); Tel.: +886-2-2875-7394 (Y.-P.Y.); +886-2-2875-7394 (P.H.T.)
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- Institute of Pharmacology, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Correspondence: (Y.-P.Y.); (P.H.T.); Tel.: +886-2-2875-7394 (Y.-P.Y.); +886-2-2875-7394 (P.H.T.)
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Pandey JP, Kothera RT, Liu S, Costa AS, Mancuso R, Agostini S. Immunoglobulin Genes and Immunity to HSV1 in Alzheimer's Disease. J Alzheimers Dis 2020; 70:917-924. [PMID: 31306125 DOI: 10.3233/jad-190265] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Although genome-wide association studies (GWAS) of late-onset Alzheimer's disease (AD) have identified numerous genes that influence the risk for disease, the majority of the genetic variance of AD remains uncharacterized. Furthermore, current GWAS, despite their name, do not evaluate all genes in the human genome. One such gene complex is immunoglobulin GM (γ marker) genes on chromosome 14. GM genes are excellent candidate genes for AD because they influence immunity to herpes simplex virus type 1 (HSV1), which has been implicated in AD pathology by an increasing number of reports. The aim of this investigation was to determine if particular GM genotypes were associated with AD and mild cognitive impairment (MCI), and whether they contributed to the interindividual differences in the level of anti-HSV1 IgG antibodies. A total of 141 HSV1 seropositive individuals-56 AD patients, 48 MCI individuals, and 37 sex- and age-matched healthy controls-were characterized for GM alleles 3, 17, and 23. The homozygosity for the GM 3 allele was significantly associated with MCI (p = 0.025). GM 3/17 heterozygous AD patients had significantly higher levels of anti-HSV1 antibodies than the healthy controls expressing the same genotype (p = 0.0004). Among MCI subjects, the GM 3/17 genotype was associated with significantly higher level of anti-HSV1 antibodies as compared to the GM 17/17 homozygous genotype (pc = 0.040). Among AD patients, the GM 23+/-genotype was significantly associated with anti-HSV1 antibody responses (pc = 0.025). These results suggest that GM genes could act as potential unifiers of the genetic and viral etiology of AD.
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Affiliation(s)
- Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Ronald T Kothera
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Shufeng Liu
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA
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Pandey JP, Olsson J, Weidung B, Kothera RT, Johansson A, Eriksson S, Hallmans G, Elgh F, Lövheim H. An Ig γ Marker Genotype Is a Strong Risk Factor for Alzheimer Disease, Independent of Apolipoprotein E ε4 Genotype. THE JOURNAL OF IMMUNOLOGY 2020; 205:1318-1322. [PMID: 32709662 DOI: 10.4049/jimmunol.2000351] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/26/2020] [Indexed: 01/17/2023]
Abstract
Increasing evidence implicates HSV type 1 (HSV1) in the pathogenesis of late-onset Alzheimer disease (AD). HSV1 has evolved highly sophisticated strategies to evade host immunosurveillance. One strategy involves encoding a decoy Fcγ receptor (FcγR), which blocks Fc-mediated effector functions, such as Ab-dependent cellular cytotoxicity. Ig γ marker (GM) allotypes, encoded by highly polymorphic IGHG genes on chromosome 14q32, modulate this immunoevasion strategy, and thus may act as effect modifiers of the HSV1-AD association. In this nested case-control human study, 365 closely matched case-control pairs-whose blood was drawn on average 9.6 y before AD diagnosis-were typed for GM alleles by a TaqMan genotyping assay. APOE genotype and a genetic risk score based on nine additional previously known AD risk genes (ABCA7, BIN1, CD33, CLU, CR1, EPHA1, MS4A4E, NECTIN2, and PICALM) were extracted from a genome-wide association study analysis. Antiviral Abs were measured by ELISA. Conditional logistic regression models were applied. The distribution of GM 3/17 genotypes differed significantly between AD cases and controls, with higher frequency of GM 17/17 homozygotes in AD cases as compared with controls (19.8 versus 10.7%, p = 0.001). The GM 17/17 genotype was associated with a 4-fold increased risk of AD (odds ratio 4.142, p < 0.001). In conclusion, the results of this study demonstrate that Ig GM 17/17 genotype contributes to the risk of later AD development, independent of apolipoprotein ε4 genotype and other AD risk genes, and explain, at least in part, why every HSV1-infected person is not equally likely to develop HSV1-associated AD.
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Affiliation(s)
- Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425;
| | - Jan Olsson
- Division of Virology, Department of Clinical Microbiology, Umeå University, 901 85 Umeå, Sweden
| | - Bodil Weidung
- Division of Geriatric Medicine, Department of Public Health and Caring Sciences, Uppsala University, 751 05 Uppsala, Sweden
| | - Ronald T Kothera
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425
| | - Anders Johansson
- Department of Odontology, Umeå University, Umeå, 901 85, Sweden.,Division of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, 901 85 Umeå, Sweden
| | - Sture Eriksson
- Division of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, 901 85 Umeå, Sweden.,Division of Geriatric Medicine, Department of Community Medicine and Rehabilitation, Umeå University, 901 85 Umeå, Sweden; and
| | - Göran Hallmans
- Division of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, 901 85 Umeå, Sweden
| | - Fredrik Elgh
- Division of Virology, Department of Clinical Microbiology, Umeå University, 901 85 Umeå, Sweden
| | - Hugo Lövheim
- Division of Geriatric Medicine, Department of Community Medicine and Rehabilitation, Umeå University, 901 85 Umeå, Sweden; and.,Wallenberg Centre for Molecular Medicine, Umeå University, 901 85 Umeå, Sweden
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Shi J, Yu Y, Jin Y, Lu J, Zhang J, Wang H, Han W, Chu P, Tai J, Chen F, Ren H, Guo Y, Ni X. Functional Polymorphisms in BARD1 Association with Neuroblastoma in a regional Han Chinese Population. J Cancer 2019; 10:2153-2160. [PMID: 31258718 PMCID: PMC6584405 DOI: 10.7150/jca.26719] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 04/07/2019] [Indexed: 12/11/2022] Open
Abstract
Neuroblastoma (NB) is a sympathetic nervous system cancer for children, occupying approximately 15% of pediatric oncology deaths. BARD1, a tumor suppressor, is essential for genome stability by interaction with BRCA1. Here, we performed a systematic investigation for the association between SNPs in BARD1 and the risk of NB in Chinese population. After SNP screening in BARD1 gene, we performed case-control study of eleven selected SNPs in BARD1 with 339 NB patients and 778 cancer-free controls. The OR and 95% CI of these candidate SNPs were computed by logistic regression. After adjusted gender and age, seven out of eleven SNPs in BARD1 were significant associated with the risk of NB, including one SNP in 5'-UTR (rs17489363 G > A), two SNPs in exon (rs2229571 G > C and rs3738888 C > T), and four SNPs in intron (rs3768716 A > G, rs6435862 T > G, rs3768707 C > T and rs17487792 C > T). When stratified by the INPC, primary tumor site and the INSS, these seven SNPs were significant associated with GNB/NB, stage III/IV and adrenal origin of NB. Dual-luciferase reporter assay showed rs17489363 A allele-containing haplotypes (TAC, CAC, TAG and CAG), composed with rs34732883 T > C, and rs1129804 C > G, dramatically reduced the transcriptional activity of reporter gene. The major of our study showed that seven SNPs of BARD1 associated with increased NB risk in Chinese population, and four haplotypes could reduce transcription activity of BARD1.
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Affiliation(s)
- Jin Shi
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yongbo Yu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Jie Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Huanmin Wang
- Department of Oncological Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wei Han
- Department of Oncological Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Ping Chu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Jun Tai
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Feng Chen
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Huimin Ren
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Xin Ni
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
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Wang J, Wang Q, Wei B, Zhou Y, Qian Z, Gao Y, Chen X. Intronic polymorphisms in genes LRFN2 (rs2494938) and DNAH11 (rs2285947) are prognostic indicators of esophageal squamous cell carcinoma. BMC MEDICAL GENETICS 2019; 20:72. [PMID: 31053115 PMCID: PMC6499982 DOI: 10.1186/s12881-019-0796-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/31/2019] [Indexed: 12/14/2022]
Abstract
Background Genome wide association study (GWAS) has become the major means to screen for the genetic variants associated with risk and prognosis of different diseases. A recent GWAS has discovered three novel intronic single nucleotide polymorphisms in genes LRFN2 (rs2494938), DNAH11 (rs2285947) and PLCXD2 (rs2399395) that are associated with altered risk of esophageal squamous cell carcinoma (ESCC) among Han Chinese populations. However, the prognostic significance of these variations in ESCC remains unclear. Methods To investigate the association of three novel single nucleotide polymorphisms (rs2494938, rs2285947, rs2399395) with the prognosis of ESCC patients, we recruited 287 ESCC patients treated with surgical resection and evaluated the potential significance of the three polymorphisms through Kaplan-Meier survival analysis, log-rank test, and Cox proportional hazards regression models. Results The ESCC patients carrying genotype AA at rs2494938 had worse survival and genotype GG at 2285947 had better prognosis (Log-rank P = 0.003 and Log-rank P = 0.037, respectively). In addition, rs2494938 at 6p21.1 was independently associated with overall survival of ESCC patients in recessive model [AA vs. GG/GA, HR = 3.12, 95% CI = 1.43–6.83, P = 0.004], rs2285947 at 7p15.3 was independently associated with overall survival of ESCC patients in both dominant model [AA/GA vs. GG, HR = 1.59, 95% CI = 1.02–2.49, P = 0.042] and additive model [AA vs. GA vs. GG, HR = 1.45, 95% CI = 1.05–2.01, P = 0.025]. Conclusions This study demonstrated that the polymorphisms rs2494938 at 6p21.1 and rs2285947 at 7p15.3 may serve as independent prognostic biomarkers for ESCC, implying the potential biological role of their related genes (LRFN2 and DNAH11) in the process of ESCC development. Electronic supplementary material The online version of this article (10.1186/s12881-019-0796-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiru Wang
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, People's Republic of China
| | - Qiuzi Wang
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, People's Republic of China
| | - Bin Wei
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, People's Republic of China
| | - Yu Zhou
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, People's Republic of China
| | - Zhaoye Qian
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, People's Republic of China
| | - Yong Gao
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, People's Republic of China.
| | - Xiaofei Chen
- Department of Medical Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, People's Republic of China.
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Shi YQ, Fu GQ, Zhao J, Cheng SZ, Li Y, Yi LN, Li Z, Zhang L, Zhang ZB, Dai J, Zhang DY. Di(2-ethylhexyl)phthalate induces reproductive toxicity via JAZF1/TR4 pathway and oxidative stress in pubertal male rats. Toxicol Ind Health 2019; 35:228-238. [DOI: 10.1177/0748233718824911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Di(2-ethylhexyl)phthalate (DEHP) is a typical endocrine-disrupting chemical and reproductive toxicant. Although previous studies have attempted to describe the mechanism by which DEHP exposure results in reproductive dysfunction, few studies focused on puberty, a critical period of reproductive development, and the increased susceptibility to injury in adolescents. To elucidate the mechanism underpinning the testicular effects of DEHP in puberty, we sought to investigate the JAZF1/TR4 pathway in the testes of pubertal rats. Specifically, we focused on the role of the JAZF1/TR4 pathway in male reproduction, including the genes JAZF1, TR4, Sperm 1, and Cyclin A1. In the present study, rats were exposed to increasing concentrations of DEHP (0, 250, 500, and 1000 mg/kg/day) by oral gavages for 30 days. Then we assayed testicular zinc and oxidative stress levels. Our results indicated that DEHP exposure could lead to oxidative stress and decrease the contents of testicular zinc. Additionally, significant morphological changes and cell apoptosis were observed in testes exposed to DEHP, as identified by hematoxylin and eosin staining and the terminal deoxynucleotidyl transferase-mediated nick and labeling assay. By measuring the expression levels of the above relevant genes by qPCR, we found the DEHP-induced increased expression of JAZF1 and decreased expression of TR4, Sperm 1, and Cyclin A1. Therefore, we have demonstrated that in vivo exposure to DEHP might induce reproductive toxicity in pubertal male rats through the JAZF1/TR4 pathway and oxidative stress.
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Affiliation(s)
- Yu-Qin Shi
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
- School of Environment, Tsinghua University, Beijing, People’s Republic of China
| | - Guo-Qing Fu
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - Jing Zhao
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - Shen-Zhou Cheng
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - You Li
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - Ling-Na Yi
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - Zhen Li
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - Ling Zhang
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - Zhi-Bing Zhang
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, People’s Republic of China
| | - Juan Dai
- Wuhan Centers for Disease Prevention and Control, Wuhan, People’s Republic of China
| | - Da-Yi Zhang
- School of Environment, Tsinghua University, Beijing, People’s Republic of China
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10
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Aiello A, Accardi G, Candore G, Caruso C, Colomba C, Di Bona D, Duro G, Gambino CM, Ligotti ME, Pandey JP. Role of Immunogenetics in the Outcome of HCMV Infection: Implications for Ageing. Int J Mol Sci 2019; 20:ijms20030685. [PMID: 30764515 PMCID: PMC6386818 DOI: 10.3390/ijms20030685] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
The outcome of host-virus interactions is determined by a number of factors, some related to the virus, others to the host, such as environmental factors and genetic factors. Therefore, different individuals vary in their relative susceptibility to infections. Human cytomegalovirus (HCMV) is an important pathogen from a clinical point of view, as it causes significant morbidity and mortality in immunosuppressed or immunosenescent individuals, such as the transplanted patients and the elderly, respectively. It is, therefore, important to understand the mechanisms of virus infection control. In this review, we discuss recent advances in the immunobiology of HCMV-host interactions, with particular emphasis on the immunogenetic aspects (human leukocyte antigens, HLA; killer cell immunoglobulin-like receptors, KIRs; immunoglobulin genetic markers, GM allotypes) to elucidate the mechanisms underlying the complex host-virus interaction that determine various outcomes of HCMV infection. The results, which show the role of humoral and cellular immunity in the control of infection by HCMV, would be valuable in directing efforts to reduce HCMV spurred health complications in the transplanted patients and in the elderly, including immunosenescence. In addition, concerning GM allotypes, it is intriguing that, in a Southern Italian population, alleles associated with the risk of developing HCMV symptomatic infection are negatively associated with longevity.
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Affiliation(s)
- Anna Aiello
- Sezione di Patologia Generale, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Corso Tukory 211, 90134 Palermo, Italy.
| | - Giulia Accardi
- Sezione di Patologia Generale, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Corso Tukory 211, 90134 Palermo, Italy.
| | - Giuseppina Candore
- Sezione di Patologia Generale, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Corso Tukory 211, 90134 Palermo, Italy.
| | - Calogero Caruso
- Sezione di Patologia Generale, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Corso Tukory 211, 90134 Palermo, Italy.
| | - Claudia Colomba
- Dipartimento di Scienze per la Promozione della Salute e Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 129, 90127 Palermo, Italy.
| | - Danilo Di Bona
- Dipartimento dell'Emergenza e dei Trapianti d'Organo, Università di Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy.
| | - Giovanni Duro
- Istituto di Biomedicina e Immunologia Molecolare, Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy.
| | - Caterina Maria Gambino
- Sezione di Patologia Generale, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Corso Tukory 211, 90134 Palermo, Italy.
| | - Mattia Emanuela Ligotti
- Sezione di Patologia Generale, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Corso Tukory 211, 90134 Palermo, Italy.
| | - Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, 171 Ashley Ave, Charleston, SC 29425, USA.
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11
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Paul P, Deka H, Malakar AK, Halder B, Chakraborty S. Nasopharyngeal carcinoma: understanding its molecular biology at a fine scale. Eur J Cancer Prev 2018; 27:33-41. [PMID: 27748661 DOI: 10.1097/cej.0000000000000314] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among all cancers, the incidence of nasopharyngeal carcinoma (NPC) is quite high in the endemic regions. NPC is a head and neck cancer with poor survival rate, and is rare throughout most of the world but common in certain geographic areas, like southern Asia and some regions of North East India (Nagaland, Manipur, and Mizoram). A clear understanding of its etiology is still lacking, but NPC is widely suspected to be the result of both genetic susceptibility and exposure to environmental factors or Epstein-Barr virus infection. Diagnosis in the early stages needs a high index of clinical acumen, and, although most cross-sectional imaging investigations show the tumor with precision, confirmation is dependent on histology. This article reviews all related research reports on NPC histopathological classifications worldwide that have been published within the past 20 years. Genome-wide association studies suggested that there might be common disease mechanisms between that disease and NPC. Personalized management rules, quality assessment of life in patients, and an understanding of the essential mechanisms of recurrence could be directed toward research into recurrent NPC. Hence, this literature would offer otolaryngologists a deeper insight into the etiological and management aspects of NPC.
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Affiliation(s)
- Prosenjit Paul
- Department of Biotechnology, Assam University, Silchar, Assam, India
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12
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Du M, Tillmans L, Gao J, Gao P, Yuan T, Dittmar RL, Song W, Yang Y, Sahr N, Wang T, Wei GH, Thibodeau SN, Wang L. Chromatin interactions and candidate genes at ten prostate cancer risk loci. Sci Rep 2016; 6:23202. [PMID: 26979803 PMCID: PMC4793270 DOI: 10.1038/srep23202] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/02/2016] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies have identified more than 100 common single nucleotide polymorphisms (SNPs) that are associated with prostate cancer risk. However, the vast majority of these SNPs lie in noncoding regions of the genome. To test whether these risk SNPs regulate their target genes through long-range chromatin interactions, we applied capture-based 3C sequencing technology to investigate possible cis-interactions at ten prostate cancer risk loci in six cell lines. We identified significant physical interactions between risk regions and their potential target genes including CAPG at 2p11.2, C2orf43 at 2p24.1, RFX6 at 6q22.1, NFASC at 1q32.1, MYC at 8q24.1 and AGAP7P at 10q11.23. Most of the interaction peaks were co-localized to regions of active histone modification and transcription factor binding sites. Expression quantitative trait locus (eQTL) analysis showed suggestive eQTL signals at rs1446669, rs699664 and rs1078004 for CAPG (p < 0.004), rs13394027 for C2orf43 (p = 2.25E-27), rs10993994 and rs4631830 for AGAP7P (p < 8.02E-5). Further analysis revealed an enhancer activity at genomic region surrounding rs4631830 which was expected to disrupt HOXB-like DNA binding affinity. This study identifies a set of candidate genes and their potential regulatory variants, and provides additional evidence showing the role of long-range chromatin interactions in prostate cancer etiology.
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Affiliation(s)
- Meijun Du
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, 53226, WI, USA
| | - Lori Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Jianzhong Gao
- Beijing 3H Medical Technology Co. Ltd., Beijing, 100176, China
| | - Ping Gao
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tiezheng Yuan
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, 53226, WI, USA
| | - Rachel L Dittmar
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, 53226, WI, USA
| | - Wei Song
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Yuehong Yang
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Natasha Sahr
- Division of Biostatistics, Institute for Health &Society, Medical College of Wisconsin, Milwaukee, 53226, WI, USA
| | - Tao Wang
- Division of Biostatistics, Institute for Health &Society, Medical College of Wisconsin, Milwaukee, 53226, WI, USA
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, 53226, WI, USA
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13
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Shen H. Progress of cancer genomics. Thorac Cancer 2015; 6:557-60. [PMID: 26445603 PMCID: PMC4566999 DOI: 10.1111/1759-7714.12281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Hongbing Shen
- Department of Epidemiology and Biostatistics School of Public Health Nanjing Medical University Nanjing China
- Jiangsu Key Lab of Cancer Biomarkers Prevention and Treatment Collaborative Innovation Center for Cancer Personalized Medicine Nanjing Medical University Nanjing China
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Abstract
The last 2 decades represent a period of unparalleled advancement in the understanding of the pathogenesis of Parkinson disease (PD). The discovery of several forms of familial parkinsonism with mendelian inheritance has elucidated insights into the mechanisms underlying the degeneration of dopaminergic neurons of the substantia nigra that histologically characterize PD. α-Synuclein, the principal component of Lewy bodies, remains the presumed pathogen at the heart of the current model; however, concurrently, a diverse range of other mechanisms have been implicated. The creation of a coherent disease model will be crucial to the development of effective disease modifying therapies for sporadic PD.
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Affiliation(s)
- Stephen Mullin
- Department of Clinical Neurosciences, UCL Institute of Neurology, Rowland Hill Street, Hampstead, London NW3 2PF, UK
| | - Anthony H V Schapira
- Department of Clinical Neurosciences, UCL Institute of Neurology, Rowland Hill Street, Hampstead, London NW3 2PF, UK.
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Montes A, Perez-Pampin E, Navarro-Sarabia F, Moreira V, de la Serna AR, Magallares B, Vasilopoulos Y, Sarafidou T, Fernández-Nebro A, Ordóñez MDC, Narváez J, Cañete JD, Marquez A, Pascual-Salcedo D, Joven B, Carreira P, Moreno-Ramos MJ, Caliz R, Ferrer MA, Garcia-Portales R, Blanco FJ, Magro C, Raya E, Valor L, Alegre-Sancho JJ, Balsa A, Martin J, Plant D, Isaacs J, Morgan AW, Barton A, Wilson AG, Gómez-Reino JJ, Gonzalez A. Rheumatoid arthritis response to treatment across IgG1 allotype - anti-TNF incompatibility: a case-only study. Arthritis Res Ther 2015; 17:63. [PMID: 25885039 PMCID: PMC4411723 DOI: 10.1186/s13075-015-0571-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/20/2015] [Indexed: 12/31/2022] Open
Abstract
Introduction We have hypothesized that incompatibility between the G1m genotype of the patient and the G1m1 and G1m17 allotypes carried by infliximab (INX) and adalimumab (ADM) could decrease the efficacy of these anti-tumor necrosis factor (anti-TNF) antibodies in the treatment of rheumatoid arthritis (RA). Methods The G1m genotypes were analyzed in three collections of patients with RA totaling 1037 subjects. The first, used for discovery, comprised 215 Spanish patients. The second and third were successively used for replication. They included 429 British and Greek patients and 393 Spanish and British patients, respectively. Two outcomes were considered: change in the Disease Activity Score in 28 joint (ΔDAS28) and the European League Against Rheumatism (EULAR) response criteria. Results An association between less response to INX and incompatibility of the G1m1,17 allotype was found in the discovery collection at 6 months of treatment (P = 0.03). This association was confirmed in the replications (P = 0.02 and 0.08, respectively) leading to a global association (P = 0.001) that involved a mean difference in ΔDAS28 of 0.4 units between compatible and incompatible patients (2.3 ± 1.5 in compatible patients vs. 1.9 ± 1.5 in incompatible patients) and an increase in responders and decrease in non-responders according to the EULAR criteria (P = 0.03). A similar association was suggested for patients treated with ADM in the discovery collection, but it was not supported by replication. Conclusions Our results suggest that G1m1,17 allotypes are associated with response to INX and could aid improved therapeutic targeting in RA. Electronic supplementary material The online version of this article (doi:10.1186/s13075-015-0571-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ariana Montes
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain.
| | - Eva Perez-Pampin
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain.
| | | | - Virginia Moreira
- Rheumatology Unit, Hospital Universitario Virgen Macarena, Sevilla, Spain.
| | | | - Berta Magallares
- Rheumatology Unit, Hospital Santa Creu e San Pau, Barcelona, Spain.
| | - Yiannis Vasilopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
| | - Theologia Sarafidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
| | - Antonio Fernández-Nebro
- Servicio de Reumatología, HRU Carlos Haya, Universidad de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain.
| | - María Del Carmen Ordóñez
- Servicio de Reumatología, HRU Carlos Haya, Universidad de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain.
| | - Javier Narváez
- Department of Rheumatology, Hospital Universitario de Bellvitge, Barcelona, Spain.
| | - Juan D Cañete
- Rheumatology Unit, Hospital Clinic, Barcelona, Spain.
| | - Ana Marquez
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain.
| | - Dora Pascual-Salcedo
- Department of Immunology, Instituto de Investigación Hospital Universitario La Paz, Hospital La Paz, Madrid, Spain.
| | - Beatriz Joven
- Department of Rheumatology, Hospital 12 de Octubre, Madrid, Spain.
| | | | | | - Rafael Caliz
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain.
| | - Miguel Angel Ferrer
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain.
| | | | - Francisco J Blanco
- Rheumatology Department, Instituto de Investigacion Biomedica-Complejo Hospitalario Universitario A Coruna, A Coruna, Spain. .,Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Cesar Magro
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain.
| | - Enrique Raya
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain.
| | - Lara Valor
- Rheumatology Unit, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | | | - Alejandro Balsa
- Department of Rheumatology, Instituto de Investigación Hospital Universitario La Paz, Hospital Universitario La Paz, Madrid, Spain.
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain.
| | - Darren Plant
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - John Isaacs
- Musculoskeletal Research Group, Institute of Cellular Medicine, The Medical School, Newcastle University, Newcastle, UK. .,National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, Newcastle, UK.
| | - Ann W Morgan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, St. James's University Hospital, University of Leeds, Leeds, UK. .,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
| | - Anne Barton
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK. .,Arthritis Research UK-Centre for Genetics and Genomics, The University of Manchester, Manchester, UK.
| | | | | | - Juan J Gómez-Reino
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain. .,Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Antonio Gonzalez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain. .,Laboratorio Investigacion 10, Hospital Clinico Universitario de Santiago, Edificio de consultas, planta -2 Travesia de Choupana, sn, Santiago de Compostela, 15706, Spain.
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16
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Oxelius VA, Krueger R, Ahlstedt S, Keil T, Lau S, Wahn U. Innate IgG molecules and innate B cells expressed by immunoglobulin constant heavy G chain (Fcγ) genetic marker genes are involved in the 'allergic march' of IgE sensitization in children. Int Arch Allergy Immunol 2015; 166:25-9. [PMID: 25765251 DOI: 10.1159/000371351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/03/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Interindividual variations of immunoglobulin constant heavy G chain (IGHG) genes on chromosome 14q32.3 are identified by alternative genetic markers (GM) of IgG3, IgG1 and IgG2, respectively. They express structurally and functionally innate IgG molecules and B cells, associated with allergic disease, replicated in several studies. MATERIALS AND METHODS 1-year-old and 10-year-old, IgE-sensitized and non-sensitized children from the German Multicenter Allergy Study birth cohort were assessed by new serological methods for the mendelian IGHG (Fcγ) (GM) genes, as innate IgG molecules and innate B cells. RESULTS Food allergy sensitization in thirty-five 1-year-old children (124 not sensitized) was associated with the IGHG*bfn haplotype and B*(bfn) cells (OR 1.9, 95% CI 1.2-3.1; p = 0.010). Aeroallergen sensitization in ninety-nine 10-year-old children (95 not sensitized) was associated with the same genes (OR 1.4, 95% CI 1.02-1.9; p = 0.034). The IgE sensitization was most prominent in the restrictive homozygous IGHG*bfn/*bfn diplotype, 34% at age 1, increasing to 60% at age 10, rating the highest numbers of positive IgE tests, expressing increased levels of IgE and innate IgG2*n. CONCLUSIONS The IGHG*bfn haplotype (B*(bfn) cells) and increased innate IgG2*n levels are predictive factors for IgE sensitization in childhood. IGHG genes can be assessed for prognostic and preventive purposes in clinical care.
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Affiliation(s)
- Vivi-Anne Oxelius
- Department of Pediatrics and Institute of Laboratory Medicine, Department of Clinical Immunology, University Hospital, Lund University, Lund, Sweden
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17
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Association of GWAS-Supported Variants rs2200733 and rs6843082 on Chromosome 4q25 with Ischemic Stroke in the Southern Chinese Han Population. J Mol Neurosci 2015; 56:585-92. [DOI: 10.1007/s12031-015-0520-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/10/2015] [Indexed: 12/25/2022]
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18
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Bader DM, Wilkening S, Lin G, Tekkedil MM, Dietrich K, Steinmetz LM, Gagneur J. Negative feedback buffers effects of regulatory variants. Mol Syst Biol 2015; 11:785. [PMID: 25634765 PMCID: PMC4332157 DOI: 10.15252/msb.20145844] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mechanisms conferring robustness against regulatory variants have been controversial. Previous studies suggested widespread buffering of RNA misexpression on protein levels during translation. We do not find evidence that translational buffering is common. Instead, we find extensive buffering at the level of RNA expression, exerted through negative feedback regulation acting in trans, which reduces the effect of regulatory variants on gene expression. Our approach is based on a novel experimental design in which allelic differential expression in a yeast hybrid strain is compared to allelic differential expression in a pool of its spores. Allelic differential expression in the hybrid is due to cis-regulatory differences only. Instead, in the pool of spores allelic differential expression is not only due to cis-regulatory differences but also due to local trans effects that include negative feedback. We found that buffering through such local trans regulation is widespread, typically compensating for about 15% of cis-regulatory effects on individual genes. Negative feedback is stronger not only for essential genes, indicating its functional relevance, but also for genes with low to middle levels of expression, for which tight regulation matters most. We suggest that negative feedback is one mechanism of Waddington's canalization, facilitating the accumulation of genetic variants that might give selective advantage in different environments.
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Affiliation(s)
- Daniel M Bader
- Computational Genomics, Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Stefan Wilkening
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Gen Lin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manu M Tekkedil
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Kim Dietrich
- Computational Genomics, Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julien Gagneur
- Computational Genomics, Gene Center, Ludwig Maximilians University, Munich, Germany
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Ma L, Chen J, Song X, Yuan H, Wang Y, Wu Y, Wang Z. Evidence that the genetic polymorphism rs1412115 on chromosome 10 is associated with risk for oral squamous cell carcinoma. Gene 2015; 560:137-9. [PMID: 25639357 DOI: 10.1016/j.gene.2015.01.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/22/2015] [Accepted: 01/26/2015] [Indexed: 01/13/2023]
Abstract
A genome-wide association study on schizophrenia in Jewish population discovered a novel single nucleotide polymorphism (SNP), rs1412115, on chromosome 10. It has been proved that neuropilin-1 (NRP-1) gene located on chromosome 10, tightly close to rs1412115, is associated with increased risk for oral squamous cell carcinoma (OSCC). In the present study, we hypothesized that SNP rs1412115:A>G is associated with increased risk for OSCC. We therefore genotyped this polymorphism in 295 patients with OSCC and 594 cancer-free controls in the Chinese Han population, using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectroscopy. The pooled odds ratio was 1.42 (95% confidence interval [CI]=1.01-1.99, p=0.042) for carriers with the A version of the allele (AA and AG) compared with GG, and 1.46 (95% CI=1.02-2.09, p=0.036) for AG compared with GG. Our data provide evidence that the rs1412115: A>G polymorphism increases the risk of OSCC in Chinese Han populations. Larger population-based studies are needed to confirm these results.
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Affiliation(s)
- Lu Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China; Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Jie Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China; Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Xiaomeng Song
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China; Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Hua Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China; Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Yuqun Wang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Yunong Wu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China; Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Zilu Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China.
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Pandey JP, Kistner-Griffin E, Radwan FF, Kaur N, Namboodiri AM, Black L, Butler MA, Carreón T, Ruder AM. Immunoglobulin genes influence the magnitude of humoral immunity to cytomegalovirus glycoprotein B. J Infect Dis 2014; 210:1823-6. [PMID: 24973460 DOI: 10.1093/infdis/jiu367] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a risk factor for many human diseases, but among exposed individuals, not everyone is equally likely to develop HCMV-spurred diseases, implying the presence of host genetic factors that might modulate immunity to this virus. Here, we show that antibody responsiveness to HCMV glycoprotein B (gB) is significantly associated with particular immunoglobulin GM (γ marker) genotypes. Anti-HCMV gB antibody levels were highest in GM 17/17 homozygotes, intermediate in GM 3/17 heterozygotes, and lowest in GM 3/3 homozygotes (28.2, 19.0, and 8.1 µg/mL, respectively; P=.014). These findings provide mechanistic insights in the etiopathogenesis of HCMV-spurred diseases.
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Affiliation(s)
| | - Emily Kistner-Griffin
- Department of Public Health Sciences, Medical University of South Carolina, Charleston
| | | | | | | | | | - Mary Ann Butler
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
| | - Tania Carreón
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
| | - Avima M Ruder
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
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21
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22
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Kang M, Ding X, Xu M, Zhu H, Liu S, Wang M, Wu D, Tong N, Gong W, Zhou J, Zhang Z. Genetic variation rs10484761 on 6p21.1 derived from a genome-wide association study is associated with gastric cancer survival in a Chinese population. Gene 2014; 536:59-64. [DOI: 10.1016/j.gene.2013.11.087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/06/2013] [Accepted: 11/25/2013] [Indexed: 12/13/2022]
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Oxelius VA, Pandey JP. Human immunoglobulin constant heavy G chain (IGHG) (Fcγ) (GM) genes, defining innate variants of IgG molecules and B cells, have impact on disease and therapy. Clin Immunol 2013; 149:475-86. [PMID: 24239836 DOI: 10.1016/j.clim.2013.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/23/2013] [Accepted: 10/02/2013] [Indexed: 12/15/2022]
Abstract
The distinguished alternative GM allotypes localized in immunoglobulin constant heavy G chain IGHG (Fcγ) (GM) genes on chromosome 14q32.3 define two unique variants of respectively IgG3, IgG1 and IgG2 subclasses, with different structures and functions. The IGHG allele (allotypes), expressed in homozygous or heterozygous forms, are assessed by new serological methods. Fixed combinations of γ3, γ1 and γ2 allotypes constitute the haplotypes, which are indirect markers of B cells. We highlight the role of homozygous IGHG genes with restricted qualities of IgG subclass molecules and B cells. These common Mendelian IGHG genes respond differently to allergens and infections, both bacterial and viral, and to active and passive immunotherapies. IGHG genes have an impact on diseases such as allergy, immunodeficiency, autoimmunity and malignancy. Association/linkage of different IGHG genes gives information about risk/protection, good or bad prognosis, for improvement of clinical care. The IGHG gene map of healthy Caucasians is registered.
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Affiliation(s)
- Vivi-Anne Oxelius
- Department of Pediatrics and Institute of Laboratory Medicine, Department of Clinical Immunology, University Hospital, Lund University, Lund, Sweden.
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24
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Pandey JP. Immunoglobulin GM allotypes as effect modifiers of cytomegalovirus-spurred neuroblastoma. Cancer Epidemiol Biomarkers Prev 2013; 22:1927-30. [PMID: 24008491 DOI: 10.1158/1055-9965.epi-13-0612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An uncommon immunoglobulin GM (γ marker) genotype has been reported to be strongly associated with susceptibility to neuroblastoma, but the mechanism(s) underlying this association is not known. Increasing evidence implicates human cytomegalovirus (HCMV) in the pathogenesis of neuroblastoma. HCMV has evolved a large repertoire of sophisticated strategies to evade host immunosurveillance. Particular GM alleles modulate an immunoevasion strategy of HCMV and contribute to humoral immunity to HCMV epitopes, attributes that provide possible mechanistic explanations for their involvement in the etiopathogenesis of neuroblastoma and explain, at least partially, why a common virus causes/spurs an uncommon cancer.
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Affiliation(s)
- Janardan P Pandey
- Author's Affiliation: Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina
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Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet 2013; 9:e1003447. [PMID: 23717210 PMCID: PMC3662561 DOI: 10.1371/journal.pgen.1003447] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 02/28/2013] [Indexed: 12/21/2022] Open
Abstract
Genetic diversity across different human populations can enhance understanding of the genetic basis of disease. We calculated the genetic risk of 102 diseases in 1,043 unrelated individuals across 51 populations of the Human Genome Diversity Panel. We found that genetic risk for type 2 diabetes and pancreatic cancer decreased as humans migrated toward East Asia. In addition, biliary liver cirrhosis, alopecia areata, bladder cancer, inflammatory bowel disease, membranous nephropathy, systemic lupus erythematosus, systemic sclerosis, ulcerative colitis, and vitiligo have undergone genetic risk differentiation. This analysis represents a large-scale attempt to characterize genetic risk differentiation in the context of migration. We anticipate that our findings will enable detailed analysis pertaining to the driving forces behind genetic risk differentiation. The environment humans inhabit has changed many times in the last 100,000 years. Migration and dynamic local environments can lead to genetic adaptations favoring beneficial traits. Many genes responsible for these adaptations can alter disease susceptibility. Genes can also affect disease susceptibility by varying randomly across different populations. We have studied genetic variants that are known to modify disease susceptibility in the context of worldwide migration. We found that variants associated with 11 diseases have been affected to an extent that is not explained by random variation. We also found that the genetic risk of type 2 diabetes has steadily decreased along the worldwide human migration trajectory from Africa to America.
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Affiliation(s)
- Erik Corona
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Rong Chen
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Martin Sikora
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Alexander A. Morgan
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Chirag J. Patel
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Aditya Ramesh
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Atul J. Butte
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
- * E-mail:
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26
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Pandey JP. Genetic markers of immunoglobulin G as potential risk factors for IgG4-related disease. J Rheumatol 2013; 39:2048. [PMID: 23028031 DOI: 10.3899/jrheum.120671] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Pandey JP, Li Z. The forgotten tale of immunoglobulin allotypes in cancer risk and treatment. Exp Hematol Oncol 2013; 2:6. [PMID: 23425356 PMCID: PMC3598368 DOI: 10.1186/2162-3619-2-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 02/13/2013] [Indexed: 11/10/2022] Open
Abstract
Monoclonal antibody (mAb) has fulfilled the promise of being the "Magic Bullet" in oncology with the clinical success of mAbs against CD20, Her-2/neu, epidermal growth factor receptor, vascular endothelial cell growth factor and others in a variety of cancers. Most manufacturers of mouse-human chimeric antibodies (and most immunologists) have treated the constant region of human immunoglobulin (Ig) as if it were naturally monomorphic and therefore not immunogenic in humans. In fact, the constant region of Ig heavy and light chain is highly polymorphic, and yet Ig haplotypes are usually not defined by genome-wide association studies nor are they considered to be important for optimizing mAb therapy. We hereby summarize evidence that Ig allotypes are important and biologically relevant in that they contribute to the etiopathogenesis of many malignant, infectious, and autoimmune diseases. Because Ig allotypes differ from each other in engaging Fc receptor, we argue that future development of effective mAb therapy for cancer should take a patient-specific approach by using the correct allotype for each patient to maximize the efficacy of this therapy.
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Affiliation(s)
- Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA.
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28
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Chen J, Meng Y, Zhou J, Zhuo M, Ling F, Zhang Y, Du H, Wang X. Identifying candidate genes for Type 2 Diabetes Mellitus and obesity through gene expression profiling in multiple tissues or cells. J Diabetes Res 2013; 2013:970435. [PMID: 24455749 PMCID: PMC3888709 DOI: 10.1155/2013/970435] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/30/2013] [Accepted: 10/25/2013] [Indexed: 12/18/2022] Open
Abstract
Type 2 Diabetes Mellitus (T2DM) and obesity have become increasingly prevalent in recent years. Recent studies have focused on identifying causal variations or candidate genes for obesity and T2DM via analysis of expression quantitative trait loci (eQTL) within a single tissue. T2DM and obesity are affected by comprehensive sets of genes in multiple tissues. In the current study, gene expression levels in multiple human tissues from GEO datasets were analyzed, and 21 candidate genes displaying high percentages of differential expression were filtered out. Specifically, DENND1B, LYN, MRPL30, POC1B, PRKCB, RP4-655J12.3, HIBADH, and TMBIM4 were identified from the T2DM-control study, and BCAT1, BMP2K, CSRNP2, MYNN, NCKAP5L, SAP30BP, SLC35B4, SP1, BAP1, GRB14, HSP90AB1, ITGA5, and TOMM5 were identified from the obesity-control study. The majority of these genes are known to be involved in T2DM and obesity. Therefore, analysis of gene expression in various tissues using GEO datasets may be an effective and feasible method to determine novel or causal genes associated with T2DM and obesity.
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Affiliation(s)
- Junhui Chen
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yuhuan Meng
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
- Chinese PLA General Hospital, Beijing 100853, China
| | - Jinghui Zhou
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Min Zhuo
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Fei Ling
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yu Zhang
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510555, China
| | - Hongli Du
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
- *Hongli Du:
| | - Xiaoning Wang
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
- Chinese PLA General Hospital, Beijing 100853, China
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Genetic variants at 10q23 are associated with risk of head and neck cancer in a Chinese population. Oral Oncol 2012; 49:332-5. [PMID: 23151416 DOI: 10.1016/j.oraloncology.2012.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 10/14/2012] [Accepted: 10/21/2012] [Indexed: 11/20/2022]
Abstract
BACKGROUND A recent genome-wide association study (GWAS) focused on esophageal squamous cell carcinoma (ESCC) has identified several susceptible regions (5q11, 21q22, 6p21 10q23, and 12q24) in Chinese population. We hypothesized that single nucleotide polymorphisms (SNPs) identified in these regions for ESCC were also associated with the risk of head and neck cancer (HNC) which share similar risk factors with ESCC. METHODS To test this hypothesis, we genotyped three SNPs (rs2274223, rs2014300 and rs10484761) in a case-control study with 503 HNC cases and 900 cancer-free controls in a Chinese population. RESULTS We found that rs2274223 was associated with a significantly increased risk of HNC in our population [GG vs. AA: adjusted odds ratio (OR)=1.86, 95% confidence interval (CI)=1.09-3.16; GG vs. (AG/AA): adjusted OR=1.85, 95% CI=1.09-3.12], and the effect appeared to be more prominent among drinkers (P=0.024) and patients with oral cavity cancer (P=0.019). In contrast, rs2014300 and rs10484761 variant were not observed any significantly association with risk of HNC. CONCLUSIONS These results indicate that rs2274223 may be a marker SNP for HNC susceptibility in Chinese population.
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Parmeggiani F, Romano MR, Costagliola C, Semeraro F, Incorvaia C, D'Angelo S, Perri P, De Palma P, De Nadai K, Sebastiani A. Mechanism of inflammation in age-related macular degeneration. Mediators Inflamm 2012; 2012:546786. [PMID: 23209345 PMCID: PMC3504473 DOI: 10.1155/2012/546786] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/02/2012] [Indexed: 12/16/2022] Open
Abstract
Age-related macular degeneration (AMD) is a multifactorial disease that represents the most common cause of irreversible visual impairment among people over the age of 50 in Europe, the United States, and Australia, accounting for up to 50% of all cases of central blindness. Risk factors of AMD are heterogeneous, mainly including increasing age and different genetic predispositions, together with several environmental/epigenetic factors, that is, cigarette smoking, dietary habits, and phototoxic exposure. In the aging retina, free radicals and oxidized lipoproteins are considered to be major causes of tissue stress resulting in local triggers for parainflammation, a chronic status which contributes to initiation and/or progression of many human neurodegenerative diseases such as AMD. Experimental and clinical evidences strongly indicate the pathogenetic role of immunologic processes in AMD occurrence, consisting of production of inflammatory related molecules, recruitment of macrophages, complement activation, microglial activation and accumulation within those structures that compose an essential area of the retina known as macula lutea. This paper reviews some attractive aspects of the literature about the mechanisms of inflammation in AMD, especially focusing on those findings or arguments more directly translatable to improve the clinical management of patients with AMD and to prevent the severe vision loss caused by this disease.
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31
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Doris PA. Genetic susceptibility to hypertensive renal disease. Cell Mol Life Sci 2012; 69:3751-63. [PMID: 22562581 PMCID: PMC3422437 DOI: 10.1007/s00018-012-0996-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 12/21/2022]
Abstract
Hypertensive renal disease occurs at increased frequency among the relatives of patients with this disease compared to individuals who lack a family history of disease. This suggests a heritable risk in which genetic variation may play a role. These observations have motivated a search for genetic variation contributing to this risk in both experimental animal models and in human populations. Studies of animal models indicate the capacity of natural genetic variants to contribute to disease risk and have produced a few insights into the disease mechanism. In its current phase, human population genetic studies have sought to associate genetic variation with disease in large populations by testing genotypes at a large number of common genetic variations in the genome, expecting that common genetic variants contributing to renal disease risk will be identified. These genome-wide association studies (GWAS) have been productive and are a clear technical success; they have also identified narrowly defined loci and genes containing variation contributing to disease risk. Further extension and refinement of these GWAS are likely to extend this success. However, it is also clear that few additional variants with substantial effects accounting for the greatest part of heritability will be uncovered by GWAS. This raises an interesting biological question regarding where the remaining unaccounted heritable risk may be located. At present, much consideration is being given to this question and to the challenge of testing hypotheses that lead from the various alternative mechanisms under consideration. One result of the progress of GWAS is likely to be a renewed interest in mechanisms by which related individuals can share and transmit traits independently of Mendelian inheritance. This paper reviews the current progress in this area and considers other mechanisms by which familial aggregation of risk for renal disease may arise.
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Affiliation(s)
- Peter A Doris
- Institute of Molecular Medicine, University of Texas HSC at Houston, Houston, TX 77030, USA.
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32
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Pandey JP, Kistner-Griffin E, Iwasaki M, Bu S, Deepe R, Black L, Kasuga Y, Hamada GS, Tsugane S. Genetic markers of immunoglobulin G and susceptibility to breast cancer. Hum Immunol 2012; 73:1155-8. [PMID: 22884983 DOI: 10.1016/j.humimm.2012.07.340] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/16/2012] [Accepted: 07/30/2012] [Indexed: 01/18/2023]
Abstract
Immunoglobulin GM allotypes, antigenic determinants of γ chains, are encoded by three very closely linked codominant genes on chromosome 14q32. Particular GM alleles/haplotypes are associated with antibody responses to certain tumor antigens and contribute to the cytotoxicity of breast cancer cells, but their possible role in susceptibility to this malignancy has not been adequately examined. Using a matched case-control design, we genotyped a large (1710 subjects) study population from Japan and Brazil for several GM alleles to determine whether these determinants are associated with susceptibility to breast cancer. After adjusting for the potential confounders, the GM 3 allele of IgG1 was significantly associated with susceptibility to breast cancer in white subjects from Brazil (OR=2.07, CI 1.16-3.71; p=0.0147). These data show that Caucasians with the GM 3 allele are over twice as likely to develop breast cancer as those who lack this allele. Since this allele modulates an immune evasion strategy of cytomegalovirus, the results also shed light on the possible mechanism underlying the reported involvement of this virus in the etiology of breast cancer.
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Affiliation(s)
- Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425-2230, USA.
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33
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Lara-Pezzi E, Dopazo A, Manzanares M. Understanding cardiovascular disease: a journey through the genome (and what we found there). Dis Model Mech 2012; 5:434-43. [PMID: 22730474 PMCID: PMC3380707 DOI: 10.1242/dmm.009787] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cardiovascular disease (CVD) is a major cause of mortality and hospitalization worldwide. Several risk factors have been identified that are strongly associated with the development of CVD. However, these explain only a fraction of cases, and the focus of research into the causes underlying the unexplained risk has shifted first to genetics and more recently to genomics. A genetic contribution to CVD has long been recognized; however, with the exception of certain conditions that show Mendelian inheritance, it has proved more challenging than anticipated to identify the precise genomic components responsible for the development of CVD. Genome-wide association studies (GWAS) have provided information about specific genetic variations associated with disease, but these are only now beginning to reveal the underlying molecular mechanisms. To fully understand the biological implications of these associations, we need to relate them to the exquisite, multilayered regulation of protein expression, which includes chromatin remodeling, regulatory elements, microRNAs and alternative splicing. Understanding how the information contained in the DNA relates to the operation of these regulatory layers will allow us not only to better predict the development of CVD but also to develop more effective therapies.
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Affiliation(s)
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones, Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
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34
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Abstract
Familial risk in hypertensive renal disease has stimulated a search for genetic variation contributing to this risk. The current phase of population genetic studies has sought to associate genetic variation with disease in large populations by testing genotypes at a large number of common genetic variations in the genome, expecting that common genetic variants contributing to renal disease risk will be identified. These genome-wide association studies (GWAS) have been productive and are a clear technical success. It is also clear that narrowly defined loci and genes containing variation contributing to disease risk have been identified. Further extension and refinement of these GWAS are likely to extend this success. However, it is also clear that few if any variants with substantial effects accounting for the greatest part of heritability will be uncovered by GWAS. This raises an interesting biological question regarding where the remaining heritable risk may be located. One result of the progress of GWAS is likely to be a renewed interest in mechanisms by which related individuals can share and transmit traits independently of Mendelian inheritance. This paper reviews current progress in this area and considers other mechanisms by which familial aggregation of risk for renal disease may arise.
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Affiliation(s)
- Michael C Braun
- Division of Pediatric Nephrology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA
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35
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Deepe RN, Kistner-Griffin E, Martin JN, Deeks SG, Pandey JP. Epistatic interactions between Fc (GM) and FcγR genes and the host control of human immunodeficiency virus replication. Hum Immunol 2011; 73:263-6. [PMID: 22213007 DOI: 10.1016/j.humimm.2011.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/21/2011] [Accepted: 12/06/2011] [Indexed: 10/14/2022]
Abstract
Host genetic factors are thought to contribute to the interindividual differences in the control of human immunodeficiency virus (HIV) replication. The aim of the present investigation was to determine whether genes encoding GM and KM allotypes-genetic markers of immunoglobulin γ and κ chains, respectively-and those encoding Fcγ receptor (FcγR) IIa and IIIa are associated with the host control of HIV replication. A case-control design was employed among HIV-infected subjects, with a group that spontaneously controlled HIV replication ("controllers") as cases (n = 73) and those who did not control replication as controls (n = 100). Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism, direct DNA sequencing, and TaqMan genotyping assays. In Caucasian Americans, certain combinations of FcγR and GM genotypes were differentially distributed between controllers and noncontrollers. Among the noncarriers of the FcγRIIa arginine allele, GM21 noncarriers had over 7-fold greater odds of being controllers than the carriers of this allele (odds ratio [OR] = 7.47). These GM determinants also interacted with FcγRIIIa alleles. Among the carriers of the FcγRIIIa valine allele, GM21 noncarriers had over 3-fold greater odds of being controllers than the carriers of this allele (OR = 3.26). These results demonstrate epistatic interactions of genes on chromosomes 14 (GM) and 1 (FcγR) in influencing the control of HIV replication.
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Affiliation(s)
- Raymond N Deepe
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
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Chapman BP, Roberts B, Duberstein P. Personality and longevity: knowns, unknowns, and implications for public health and personalized medicine. J Aging Res 2011; 2011:759170. [PMID: 21766032 PMCID: PMC3134197 DOI: 10.4061/2011/759170] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/19/2011] [Indexed: 11/23/2022] Open
Abstract
We review evidence for links between personality traits and longevity. We provide an overview of personality for health scientists, using the primary organizing framework used in the study of personality and longevity. We then review data on various aspects of personality linked to longevity. In general, there is good evidence that higher level of conscientiousness and lower levels of hostility and Type D or "distressed" personality are associated with greater longevity. Limited evidence suggests that extraversion, openness, perceived control, and low levels of emotional suppression may be associated with longer lifespan. Findings regarding neuroticism are mixed, supporting the notion that many component(s) of neuroticism detract from life expectancy, but some components at some levels may be healthy or protective. Overall, evidence suggests various personality traits are significant predictors of longevity and points to several promising directions for further study. We conclude by discussing the implications of these links for epidemiologic research and personalized medicine and lay out a translational research agenda for integrating the psychology of individual differences into public health and medicine.
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Affiliation(s)
- Benjamin P. Chapman
- Laboratory of Personality and Development and Rochester Health Decision Making Group, Department of Psychiatry, University of Rochester Medical Center, 300 Crittenden, Rochester, NY 14607, USA
| | - Brent Roberts
- Personality Interest Group, Department of Psychology, University of Illinoi, Rochester, NY 14607, USA
| | - Paul Duberstein
- Laboratory of Personality and Development and Rochester Health Decision Making Group, Department of Psychiatry, University of Rochester Medical Center, 300 Crittenden, Rochester, NY 14607, USA
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Pandey JP. Genetic and Viral Etiology of Glioblastoma—a Unifying Hypothesis. Cancer Epidemiol Biomarkers Prev 2011; 20:1061-3. [DOI: 10.1158/1055-9965.epi-11-0247] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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