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Nazarov IB, Zilov DS, Gordeev MN, Potapenko EV, Yeremenko N, Tomilin AN. Transcriptional Coactivator BOB1 (OBF1, OCA-B) Modulates the Specificity of DNA Recognition by the POU-Domain Factors OCT1 and OCT2 in a Monomeric Configuration. Biomolecules 2024; 14:123. [PMID: 38254723 PMCID: PMC10812921 DOI: 10.3390/biom14010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
BOB1, a mammalian lymphocyte-specific transcriptional coactivator of the transcription factors OCT1 and OCT2 (OCT1/2), plays important roles in normal immune responses, autoimmunity, and hematologic malignancies. The issue of a DNA sequence preference change imposed by BOB1 was raised more than two decades ago but remains unresolved. In this paper, using the EMSA-SELEX-Seq approach, we have reassessed the intrinsic ability of BOB1 to modulate the specificity of DNA recognition by OCT1 and OCT2. Our results have reaffirmed previous conclusions regarding BOB1 selectivity towards the dimer configuration of OCT1/2. However, they suggest that the monomeric configuration of these factors, assembled on the classical octamer ATGCAAAT and related motifs, are the primary targets of BOB1. Our data further specify the DNA sequence preference imposed by BOB1 and predict the probability of ternary complex formation. These results provide an additional insight into the action of BOB1-an essential immune regulator and a promising molecular target for the treatment of autoimmune diseases and hematologic malignancies.
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Affiliation(s)
- Igor B. Nazarov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Danil S. Zilov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Mikhail N. Gordeev
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Evgenii V. Potapenko
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
- University of Haifa, Haifa 3498838, Israel
| | - Nataliya Yeremenko
- Center for Research in Transplantation and Translational Immunology UMR1064, 30 Bd Jean Monnet, Nantes University, CEDEX 01, 44093 Nantes, France;
| | - Alexey N. Tomilin
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
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Antontseva EV, Degtyareva AO, Korbolina EE, Damarov IS, Merkulova TI. Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis. Vavilovskii Zhurnal Genet Selektsii 2023; 27:662-675. [PMID: 37965371 PMCID: PMC10641029 DOI: 10.18699/vjgb-23-77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 11/16/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most common type of variation in the human genome. The vast majority of SNPs identified in the human genome do not have any effect on the phenotype; however, some can lead to changes in the function of a gene or the level of its expression. Most SNPs associated with certain traits or pathologies are mapped to regulatory regions of the genome and affect gene expression by changing transcription factor binding sites. In recent decades, substantial effort has been invested in searching for such regulatory SNPs (rSNPs) and understanding the mechanisms by which they lead to phenotypic differences, primarily to individual differences in susceptibility to diseases and in sensitivity to drugs. The development of the NGS (next-generation sequencing) technology has contributed not only to the identification of a huge number of SNPs and to the search for their association (genome-wide association studies, GWASs) with certain diseases or phenotypic manifestations, but also to the development of more productive approaches to their functional annotation. It should be noted that the presence of an association does not allow one to identify a functional, truly disease-associated DNA sequence variant among multiple marker SNPs that are detected due to linkage disequilibrium. Moreover, determination of associations of genetic variants with a disease does not provide information about the functionality of these variants, which is necessary to elucidate the molecular mechanisms of the development of pathology and to design effective methods for its treatment and prevention. In this regard, the functional analysis of SNPs annotated in the GWAS catalog, both at the genome-wide level and at the level of individual SNPs, became especially relevant in recent years. A genome-wide search for potential rSNPs is possible without any prior knowledge of their association with a trait. Thus, mapping expression quantitative trait loci (eQTLs) makes it possible to identify an SNP for which - among transcriptomes of homozygotes and heterozygotes for its various alleles - there are differences in the expression level of certain genes, which can be located at various distances from the SNP. To predict rSNPs, approaches based on searches for allele-specific events in RNA-seq, ChIP-seq, DNase-seq, ATAC-seq, MPRA, and other data are also used. Nonetheless, for a more complete functional annotation of such rSNPs, it is necessary to establish their association with a trait, in particular, with a predisposition to a certain pathology or sensitivity to drugs. Thus, approaches to finding SNPs important for the development of a trait can be categorized into two groups: (1) starting from data on an association of SNPs with a certain trait, (2) starting from the determination of allele-specific changes at the molecular level (in a transcriptome or regulome). Only comprehensive use of strategically different approaches can considerably enrich our knowledge about the role of genetic determinants in the molecular mechanisms of trait formation, including predisposition to multifactorial diseases.
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Affiliation(s)
- E V Antontseva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A O Degtyareva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E E Korbolina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I S Damarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T I Merkulova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Verhasselt H, Stelmach P, Domin M, Jung D, Hagemann A, Manthey I, Bachmann HS. Characterization of the promoter of the human farnesyltransferase beta subunit and the impact of the transcription factor OCT-1 on its expression. Genomics 2022; 114:110314. [DOI: 10.1016/j.ygeno.2022.110314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/14/2021] [Accepted: 02/09/2022] [Indexed: 11/24/2022]
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Degtyareva AO, Antontseva EV, Merkulova TI. Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. Int J Mol Sci 2021; 22:6454. [PMID: 34208629 PMCID: PMC8235176 DOI: 10.3390/ijms22126454] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
The vast majority of the genetic variants (mainly SNPs) associated with various human traits and diseases map to a noncoding part of the genome and are enriched in its regulatory compartment, suggesting that many causal variants may affect gene expression. The leading mechanism of action of these SNPs consists in the alterations in the transcription factor binding via creation or disruption of transcription factor binding sites (TFBSs) or some change in the affinity of these regulatory proteins to their cognate sites. In this review, we first focus on the history of the discovery of regulatory SNPs (rSNPs) and systematized description of the existing methodical approaches to their study. Then, we brief the recent comprehensive examples of rSNPs studied from the discovery of the changes in the TFBS sequence as a result of a nucleotide substitution to identification of its effect on the target gene expression and, eventually, to phenotype. We also describe state-of-the-art genome-wide approaches to identification of regulatory variants, including both making molecular sense of genome-wide association studies (GWAS) and the alternative approaches the primary goal of which is to determine the functionality of genetic variants. Among these approaches, special attention is paid to expression quantitative trait loci (eQTLs) analysis and the search for allele-specific events in RNA-seq (ASE events) as well as in ChIP-seq, DNase-seq, and ATAC-seq (ASB events) data.
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Affiliation(s)
- Arina O. Degtyareva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Elena V. Antontseva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Tatiana I. Merkulova
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Roos D, de Boer M. Mutations in cis that affect mRNA synthesis, processing and translation. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166166. [PMID: 33971252 DOI: 10.1016/j.bbadis.2021.166166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022]
Abstract
Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.
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Affiliation(s)
- Dirk Roos
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Martin de Boer
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands
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Del Pinto R, Pietropaoli D, Monaco A, Desideri G, Ferri C, Grassi D. Non-pharmacological Strategies Against Systemic Inflammation: Molecular Basis and Clinical Evidence. Curr Pharm Des 2020; 26:2620-2629. [PMID: 32242777 DOI: 10.2174/1381612826666200403122600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
Systemic inflammation is a common denominator to a variety of cardiovascular (CV) and non-CV diseases and relative risk factors, including hypertension and its control, metabolic diseases, rheumatic disorders, and those affecting the gastrointestinal tract. Besides medications, a non-pharmacological approach encompassing lifestyle changes and other complementary measures is mentioned in several updated guidelines on the management of these conditions. We performed an updated narrative review on the mechanisms behind the systemic impact of inflammation and the role of non-pharmacological, complementary measures centered on lowering systemic phlogosis for preserving or restoring a good global health. The central role of genetics in shaping the immune response is discussed in conjunction with that of the microbiome, highlighting the interdependence and mutual influences between the human genome and microbial integrity, diversity, and functions. Several plausible strategies to modulate inflammation and restore balanced crosstalk between the human genome and the microbiome are then recapitulated, including dietary measures, active lifestyle, and other potential approaches to manipulate the resident microbial community. To date, evidence from high-quality human studies is sparse to allow the unconditioned inclusion of understudied, though plausible solutions against inflammation into public health strategies for global wellness. This gap claims further focused, well-designed research targeted at unravelling the mechanisms behind future personalized medicine.
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Affiliation(s)
- Rita Del Pinto
- University of L'Aquila, Department of Life, Health, and Environmental Sciences, San Salvatore Hospital, L'Aquila, Italy
| | - Davide Pietropaoli
- University of L'Aquila, Department of Life, Health, and Environmental Sciences, San Salvatore Hospital, L'Aquila, Italy
| | - Annalisa Monaco
- University of L'Aquila, Department of Life, Health, and Environmental Sciences, San Salvatore Hospital, L'Aquila, Italy
| | - Giovambattista Desideri
- University of L'Aquila, Department of Life, Health, and Environmental Sciences, San Salvatore Hospital, L'Aquila, Italy
| | - Claudio Ferri
- University of L'Aquila, Department of Life, Health, and Environmental Sciences, San Salvatore Hospital, L'Aquila, Italy
| | - Davide Grassi
- University of L'Aquila, Department of Life, Health, and Environmental Sciences, San Salvatore Hospital, L'Aquila, Italy
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Boechat N, Carvalho RCC, Ferreira MDLG, Coutinho JP, Sa PM, Seito LN, Rosas EC, Krettli AU, Bastos MM, Pinheiro LCS. Antimalarial and anti-inflammatory activities of new chloroquine and primaquine hybrids: Targeting the blockade of malaria parasite transmission. Bioorg Med Chem 2020; 28:115832. [PMID: 33166927 DOI: 10.1016/j.bmc.2020.115832] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
Malaria is a disease that requires new drugs not only to fight Plasmodium but also to reduce symptoms of infection such as fever and inflammation. A series of 21 hybrid compounds were designed from chloroquine (CQ) and primaquine (PQ) linked to the pharmacophoric group present in phenylacetic anti-inflammatory drugs. These compounds were designed to have dual activity: namely, to be capable of killing Plasmodium and still act on the inflammatory process caused by malaria infection. The compounds were assayed with nine different biological methods. The carbonylated CQ derivative 6 (n = 3; R1 = Cl) was more potent than CQ in vitro, and 8 (n = 4; R1 = H) reduced P. berghei parasitemia up to 37% on day 7. The carbonylated PQ derivative 17 (R = Br) was slightly less potent than PQ. The gem-difluoro PQ derivative 20 (R = Cl) exhibited high transmission blockade of the malaria sporogonic cycle in mosquitoes. Compounds 6 and 20 dose-dependently reduced nitric oxide (NO) production and inhibited TNFα production by LPS-stimulated J774A.1 macrophages. Our results indicate a viable and interesting approach in planning new chemical entities that act as transmission-blocking drugs for treating malaria caused by P. falciparum and P. vivax and the anti-inflammatory process related to this disease.
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Affiliation(s)
- Nubia Boechat
- Laboratorio de Sintese de Farmacos, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz. Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil.
| | - Rita C C Carvalho
- Laboratorio de Sintese de Farmacos, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz. Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
| | - Maria de Lourdes G Ferreira
- Laboratorio de Sintese de Farmacos, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz. Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
| | - Julia Penna Coutinho
- Centro de Pesquisas Rene Rachou, CPqRR - FIOCRUZ, Fundacao Oswaldo Cruz, Belo Horizonte, MG 30190-002, Brazil
| | - Paula M Sa
- Laboratorio de Sintese de Farmacos, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz. Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
| | - Leonardo N Seito
- Departamento de Farmacologia, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz, Brazil
| | - Elaine C Rosas
- Departamento de Farmacologia, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz, Brazil
| | - Antoniana U Krettli
- Centro de Pesquisas Rene Rachou, CPqRR - FIOCRUZ, Fundacao Oswaldo Cruz, Belo Horizonte, MG 30190-002, Brazil
| | - Monica M Bastos
- Laboratorio de Sintese de Farmacos, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz. Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
| | - Luiz C S Pinheiro
- Laboratorio de Sintese de Farmacos, Instituto de Tecnologia em Farmacos, Farmanguinhos - FIOCRUZ, Fundacao Oswaldo Cruz. Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
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Ferreira L, Soares MAM, Rodrigues MT, de Araujo JLS, de Melo ALP, Gasparino E, Garcia OSR. UCP2 and PPARG gene polymorphisms and their association with milk yield and composition traits in goats. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Takechi T, Hirota T, Fujii K, Nakahara T, Sakai T, Maeda N, Furue M, Ieiri I. Effect of Genetic Polymorphisms of Human SLC22A3 in the 5'-flanking Region on OCT3 Expression and Sebum Levels in Human Skin. J Dermatol Sci 2020; 101:4-13. [PMID: 33168399 DOI: 10.1016/j.jdermsci.2020.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/30/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Human organic cation transporter 3 (OCT3,SLC22A3) mediates the uptake of many important endogenous substances and basic drugs, and has been identified as one of the transporters that are highly expressed in human skin. However, the mechanisms responsible for variability in mRNA expression, and the role of SLC22A3 in human skin is not clear. OBJECTIVE We examined the effects of the single nucleotide polymorphisms ofSLC22A3 on the variability in SLC22A3 expression and sebum levels in humans. METHODS Immunostaining of OCT3 in human skin was performed. We analyzed the association of promoter variants with the SLC22A3 mRNA expression levels in human skins. Luciferase, knockdown, chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay were employed to investigate transcriptional regulation of SLC22A3 expression. Effects of the identified variant on sebum levels were evaluated in healthy volunteers. RESULTS Immunohistochemistry revealed marked expressions of OCT3 in the basal epidermis, sebaceous glands, hair follicles, and sweat glands of human skin. SLC22A3 mRNA levels were significantly lower in skin samples with homozygotes for -1603A/A than in those for -1603 G/G. The analysis of p53 binding to -1603 G > A in the promoter ofSLC22A3 suggested that -1603 G > A down-regulates SLC22A3 gene expression by decreased p53 binding in the vicinity of the -1603 site. In humans, squalene levels in samples from the back at the baseline were significantly lower in homozygotes for -1603A/A than in those for -1603 G/G. CONCLUSION These results suggest that the genetic variant contributes to the variability of expression and activities of OCT3 in human skin.
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Affiliation(s)
- Tomoki Takechi
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan; Drug Development Research Laboratories, Kyoto R&D Center, Maruho Co., Ltd., Kyoto, Japan
| | - Takeshi Hirota
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazushi Fujii
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Nakahara
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuya Sakai
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Natsumi Maeda
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Masutaka Furue
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ichiro Ieiri
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
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Al-Khatib SM, Abdo N, Al-Eitan LN, Al-Mistarehi AHW, Zahran DJ, Kewan TZ. LTA, LEP, and TNF-a Gene Polymorphisms are Associated with Susceptibility and Overall Survival of Diffuse Large B-Cell lymphoma in an Arab Population: A Case-Control Study. Asian Pac J Cancer Prev 2020; 21:2783-2791. [PMID: 32986381 PMCID: PMC7779465 DOI: 10.31557/apjcp.2020.21.9.2783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Indexed: 01/08/2023] Open
Abstract
Objective: In this study, we aimed to explore the relationship between five selected proinflammatory and immune-mediated genes (TNF rs1800629G>A, rs361525G>A, rs1799964T>C, LTA rs1800683G>A, rs909253A>G, TNFAIP8 rs1042541C>T, LEPR rs1327118G>C, and LEP rs2167270G>A) and the risk and overall survival of DLBCL patients within the Jordanian Arab population. Methods: One hundred twenty-five patients (125) diagnosed with DLBCL at the King Abdullah University Hospital (KAUH) between 2013 and 2018 and 238 healthy cancer-free control subjects with similar geographic and ethnic backgrounds to the patients were included in the study. Genomic DNA was extracted from the formalin-fixed paraffin-embedded tissues of the subjects and from peripheral blood samples of the controls. The Sequenom MassARRAY® sequencer system (iPLEX GOLD) was used. The analyses included assessments of population variability and survival. Results: Our study showed significant differences in the distribution of the studied polymorphisms of DLBCL between the patients and controls for TNF rs1800629G>A, LTA rs909253 G>A and LEP rs2167270 G>A. TNF rs1800629G>A (p = 0.01), in which the G allele harbors a higher risk of DLBCL (GG and GA genotypes when compared with AA genotype) (p = 0.044). The LTA rs909253 A>G polymorphism is associated with a higher risk of DLBCL in the allelic model (p = .004). LEP rs2167270 G>A polymorphism is associated with a decreased risk of DLBCL in the recessive mode models (p = .03). Subjects with the dominant model for TNF-a rs1799964 (TT genotype in comparison with the combined TT/TC genotype) and patients with the homozygous genotype (GG) of rs361525 have better overall survival rates. Conclusion: Our results confirmed the diversity and the heterogeneity of the disease. Although the study has a limitation because of its relatively small size, it clearly emphasizes the significance of ancestry and genetic composition as the determinants of DLBCL risk and behavior.
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Affiliation(s)
- Sohaib M Al-Khatib
- Department of Pathology and Laboratory Medicine Jordan University of Science and Technology Irbid, Jordan
| | - Nour Abdo
- Department of Public Health, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Laith N Al-Eitan
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Abdel-Hameed W Al-Mistarehi
- Department of Family Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Deeb Jamil Zahran
- Department of Internal Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Tariq Zuheir Kewan
- Department of Internal Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan.,Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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Chandra A, Farrell C, Wilson H, Dervenoulas G, De Natale ER, Politis M. Aquaporin-4 polymorphisms predict amyloid burden and clinical outcome in the Alzheimer's disease spectrum. Neurobiol Aging 2020; 97:1-9. [PMID: 33068891 DOI: 10.1016/j.neurobiolaging.2020.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 02/03/2023]
Abstract
Clearance of amyloid-β (Aβ) from the brain is hypothesized to be mediated by the glymphatic system through aquaporin-4 (AQP4) water channels. Genetic variation of AQP4 may impact water channel function, Aβ clearance, and clinical outcomes. We examined whether single-nucleotide polymorphisms (SNPs) of the AQP4 gene were related to Aβ neuropathology on [18F]Florbetapir PET in 100 Aβ positive late mild cognitive impairment (LMCI) or Alzheimer's disease (AD) patients and were predictive of clinical outcome in prodromal AD patients. AQP4 SNP rs72878794 was associated with decreased Aβ uptake, whereas rs151244 was associated with increased Aβ uptake, increased risk of conversion from MCI and LMCI to AD, and an increased 4-year rate of cognitive decline in LMCI. AQP4 genetic variation was associated with Aβ accumulation, disease stage progression, and cognitive decline. This variation may correspond to changes in glymphatic system functioning and brain Aβ clearance and could be a useful biomarker in predicting disease burden for those on the dementia spectrum.
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Affiliation(s)
- Avinash Chandra
- Neurodegeneration Imaging Group, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Chloe Farrell
- Neurodegeneration Imaging Group, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Heather Wilson
- Neurodegeneration Imaging Group, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK; Neurodegeneration Imaging Group, University of Exeter Medical School, London, UK
| | - George Dervenoulas
- Neurodegeneration Imaging Group, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK; Department of Neurology, Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust, London, UK
| | - Edoardo Rosario De Natale
- Neurodegeneration Imaging Group, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK; Neurodegeneration Imaging Group, University of Exeter Medical School, London, UK
| | - Marios Politis
- Neurodegeneration Imaging Group, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK; Neurodegeneration Imaging Group, University of Exeter Medical School, London, UK.
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Georgescu AM, Banescu C, Azamfirei R, Hutanu A, Moldovan V, Badea I, Voidazan S, Dobreanu M, Chirtes IR, Azamfirei L. Evaluation of TNF-α genetic polymorphisms as predictors for sepsis susceptibility and progression. BMC Infect Dis 2020; 20:221. [PMID: 32171247 PMCID: PMC7071754 DOI: 10.1186/s12879-020-4910-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/19/2020] [Indexed: 12/12/2022] Open
Abstract
Background The goal of the study was to evaluate a potential role for tumor necrosis factor alpha (TNF-α) genetic variability as biomarker in sepsis. In particular, we aimed to determine if single nucleotide polymorphisms (SNPs) of TNF-α gene are associated with sepsis in terms of risk, severity and outcome. Methods We performed a prospective study on 163 adult critically ill septic patients (septic shock 65, sepsis 98, further divided in 40 survivors and 123 deceased) and 232 healthy controls. Genotyping of TNF-α SNPs (-308G/A, -238G/A, -376G/A and +489G/A) was performed for all patients and controls and plasma cytokine levels were measured during the first 24 h after sepsis onset. Results TNF-α +489G/A A-allele carriage was associated with significantly lower risk of developing sepsis and sepsis shock (AA+AG vs GG: OR = 0.53; p = 0.004; 95% CI = 0.34–0.82 and OR = 0.39; p = 0.003; 95% CI = 0.21–0.74, respectively) but not with sepsis-related outcomes. There was no significant association between any of the other TNF-α promoter SNPs, or their haplotype frequencies and sepsis or septic shock risk. Circulating TNF-α levels were higher in septic shock; they were not correlated with SNP genotype distribution; GG homozygosity for each polymorphism was correlated with higher TNF-α levels in septic shock. Conclusions TNF-α +489G/A SNP A-allele carriage may confer protection against sepsis and septic shock development but apparently does not influence sepsis-related mortality. Promoter TNF-α SNPs did not affect transcription and were not associated with distinct sepsis, septic shock risk or outcomes.
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Affiliation(s)
- Anca Meda Georgescu
- Infectious Diseases Clinic, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
| | - Claudia Banescu
- Genetics Laboratory, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania.
| | - Razvan Azamfirei
- Johns Hopkins School of Medicine, Johns Hopkins University, 733 N Broadway, Baltimore, MD, 21202, USA
| | - Adina Hutanu
- Immunology Laboratory, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
| | - Valeriu Moldovan
- Genetics Laboratory, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
| | - Iudita Badea
- Department of Anesthesiology and Intensive Care, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
| | - Septimiu Voidazan
- Department of Epidemiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
| | - Minodora Dobreanu
- Immunology Laboratory, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
| | - Ioana Raluca Chirtes
- Infectious Diseases Clinic, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
| | - Leonard Azamfirei
- Department of Anesthesiology and Intensive Care, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 38 Gh. Marinescu St, 540139, Targu Mures, Romania
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Mbagwu SI, Lannes N, Walch M, Filgueira L, Mantel PY. Human Microglia Respond to Malaria-Induced Extracellular Vesicles. Pathogens 2019; 9:pathogens9010021. [PMID: 31878288 PMCID: PMC7168629 DOI: 10.3390/pathogens9010021] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
Microglia are the chief immune cells of the brain and have been reported to be activated in severe malaria. Their activation may drive towards neuroinflammation in cerebral malaria. Malaria-infected red blood cell derived-extracellular vesicles (MiREVs) are produced during the blood stage of malaria infection. They mediate intercellular communication and immune regulation, among other functions. During cerebral malaria, the breakdown of the blood–brain barrier can promote the migration of substances such as MiREVs from the periphery into the brain, targeting cells such as microglia. Microglia and extracellular vesicle interactions in different pathological conditions have been reported to induce neuroinflammation. Unlike in astrocytes, microglia–extracellular vesicle interaction has not yet been described in malaria infection. Therefore, in this study, we aimed to investigate the uptake of MiREVs by human microglia cells and their cytokine response. Human blood monocyte-derived microglia (MoMi) were generated from buffy coats of anonymous healthy donors using Ficoll-Paque density gradient centrifugation. The MiREVs were isolated from the Plasmodium falciparum cultures. They were purified by ultracentrifugation and labeled with PKH67 green fluorescent dye. The internalization of MiREVs by MoMi was observed after 4 h of co-incubation on coverslips placed in a 24-well plate at 37 °C using confocal microscopy. Cytokine-gene expression was investigated using rt-qPCR, following the stimulation of the MoMi cells with supernatants from the parasite cultures at 2, 4, and 24 h, respectively. MiREVs were internalized by the microglia and accumulated in the perinuclear region. MiREVs-treated cells increased gene expression of the inflammatory cytokine TNFα and reduced gene expression of the immune suppressive IL-10. Overall, the results indicate that MiREVs may act on microglia, which would contribute to enhanced inflammation in cerebral malaria.
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Affiliation(s)
- Smart Ikechukwu Mbagwu
- Anatomy Unit, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
- Department of Anatomy, Faculty of Basic Medical Sciences, Nnamdi Azikiwe University, Nnewi Campus, Nnewi 435101, Nigeria
- Correspondence: (S.I.M.); (L.F.)
| | - Nils Lannes
- Anatomy Unit, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Michael Walch
- Anatomy Unit, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Luis Filgueira
- Anatomy Unit, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
- Correspondence: (S.I.M.); (L.F.)
| | - Pierre-Yves Mantel
- Anatomy Unit, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
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Guru Vishnu P, Bhattacharya TK, Bhushan B, Paswan C, Rajendra Prasad A, Divya D. Genetic polymorphism in core promoter sequence of ACTRIIB gene and association analysis with growth traits in chicken. Reprod Domest Anim 2019; 54:1330-1340. [PMID: 31310035 DOI: 10.1111/rda.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 07/06/2019] [Indexed: 11/29/2022]
Abstract
Molecular breeding exploiting candidate genes is burgeoning reproductive approach to improve growth traits in poultry. The activin type IIB receptor (ACTRIIB) is a negative growth regulator, modulating action of many muscle growth regulators. PCR-single-strand conformation polymorphism was employed to unravel polymorphism in promoter region of the ACTRIIB gene and delineate its association with growth traits in Aseel and control broiler (CB). Analysis of 5' promoter region (1122bp) of ACTRIIB gene identified five SNPs, that is g. [56 G > C (SNP1), 352A > C (SNP2), 580G > A (SNP3), 625C > T (SNP4) and 962C > T (SNP5)] at SMAD, paired box 7 homeodomain binding motif, GC box and bHLH-PAS type transcription factors in CB and Aseel. CB had significantly higher body weight (BW) and average daily gain (ADG) at all SNP sites, except at SNP 1. The haplotype construction resulted 8 haplotypes in CB and Aseel population. The BW and ADG differed significantly (p < .05) at all ages in CB and Aseel. The diplotypes H1H8 and H1H4 manifested higher BW and ADG, while diplotypes H3H8 and H3H7 displayed BW and ADG at each age in both lines (p < .05). Aseel exhibited higher expression of ACTRIIB gene than CB by 70.17, 4.83, 1.41, 2.38, 5.13, 1.20, 2.90, 6.53 and 11.75 times for h1h2, h1h3, h1h4, h1h6, h1h7, h1h8 h3h4, h3h7 and h3h8, respectively. The H3H8 and H3H7 diplotypes exhibited higher level of mRNA and protein than H1H8 and H1H4. The regulatory upstream region of ACTRIIB gene demonstrates high degree of genetic diversity and can be harnessed as potential marker in genetic selection programmes for increasing meat production.
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Affiliation(s)
| | | | - Bharat Bhushan
- Division of Animal Genetics & Breeding, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Chandan Paswan
- Avian Molecular Genetics Laboratory, ICAR-Directorate of Poultry Research, Hyderabad, India
| | - Athe Rajendra Prasad
- Division of Animal Genetics & Breeding, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Devara Divya
- Avian Molecular Genetics Laboratory, ICAR-Directorate of Poultry Research, Hyderabad, India
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Passan S, Goyal S, Bhat MA, Singh D, Vanita V. Association of TNF-α gene alterations (c.-238G>A, c.-308G>A, c.-857C>T, c.-863C>A) with primary glaucoma in north Indian cohort. Gene 2019; 709:25-35. [PMID: 31132515 DOI: 10.1016/j.gene.2019.05.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/27/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Tumor Necrosis Factor-alpha (TNF-α) a pleuripotent pro-inflammatory cytokine, is involved in retinal ganglion cells apoptosis in glaucoma. Thus present study aimed to analyze the association of TNF-α promoter region alterations (c.-238G>A (rs361525), c.-308G>A (rs1800629), c.-857C>T (rs1799724) and c.-863C>A (rs1800630)) with glaucoma in north Indian cohort. METHODS Present hospital based case control study involved 286 glaucoma patients (Primary Open Angle Glaucoma [POAG], Primary Angle Closure Glaucoma [PACG], Primary Congenital Glaucoma [PCG]) and 300 controls. TNF-α gene alteration (c.-238G>A (also referred as c.-418G>A; NM_000594.3)), c.-308G>A (c.-488G>A; NM_000594.3), c.-857C>T (c.-1037C>T; NM_000594.3) and c.-863C>A (c.-1043C>A; NM_000594.3) harboring regions were PCR amplified and sequenced by Sanger sequencing. Allele frequency and genotype distribution in glaucoma cases and controls were compared using chi-square test and genetic association tested using different genetic models. RESULTS Statistically significant genotype and allelic association was observed between glaucoma cases and controls for c.-308G>A and c.-863C>A alterations (p = 0.001, p = 0.001; p = 0.001, p = 0.001 respectively). AA genotype of c.-308G>A conferred ~7 fold increased risk towards glaucoma (OR = 6.82, 95% CI = 2.82-16.53, p = 0.001). c.-863C>A alteration under dominant, recessive and co-dominant genetic models conferred ~2 fold increased risk for glaucoma. However, no association for c.-238G>A and c.-857C>T variants with glaucoma was observed. Further, three haplotypes (GGCA, GACC and GACA) (OR = 0.48, 95% CI = 0.35-0.67, p = 0.001; OR = 0.58, 95% CI = 0.36-0.91, p = 0.019 and OR = 0.16, 95% CI = 0.05-0.51, p = 0.002, respectively) conferred protective role towards glaucoma. CONCLUSIONS Present study is the first to indicate significant association of c.-308G>A and c.-863C>A alterations with glaucoma in cases from north Indian cohort. Also it is the first study from India to analyze the association and interaction of four promoter region alterations (c.-238G>A, c.-308G>A, c.-857C>T and c.-863C>A) in TNF-α resulting in three protective haplotypes.
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Affiliation(s)
- Shruti Passan
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Shiwali Goyal
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Mohd Akbar Bhat
- Multidisciplinary Research Unit, Government Medical College, Amritsar, Punjab, India
| | - Daljit Singh
- Dr. Daljit Singh Eye Hospital, Amritsar, Punjab, India
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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Neavin DR, Lee JH, Liu D, Ye Z, Li H, Wang L, Ordog T, Weinshilboum RM. Single Nucleotide Polymorphisms at a Distance from Aryl Hydrocarbon Receptor (AHR) Binding Sites Influence AHR Ligand-Dependent Gene Expression. Drug Metab Dispos 2019; 47:983-994. [PMID: 31292129 PMCID: PMC7184190 DOI: 10.1124/dmd.119.087312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/07/2019] [Indexed: 12/17/2022] Open
Abstract
Greater than 90% of significant genome-wide association study (GWAS) single-nucleotide polymorphisms (SNPs) are in noncoding regions of the genome, but only 25.6% are known expression quantitative trait loci (eQTLs). Therefore, the function of many significant GWAS SNPs remains unclear. We have identified a novel type of eQTL for which SNPs distant from ligand-activated transcription factor (TF) binding sites can alter target gene expression in a SNP genotype-by-ligand–dependent fashion that we refer to as pharmacogenomic eQTLs (PGx-eQTLs)—loci that may have important pharmacotherapeutic implications. In the present study, we integrated chromatin immunoprecipitation-seq with RNA-seq and SNP genotype data for a panel of lymphoblastoid cell lines to identify 10 novel cis PGx-eQTLs dependent on the ligand-activated TF aryl hydrocarbon receptor (AHR)—a critical environmental sensor for xenobiotic (drug) and immune response. Those 10 cis PGx-eQTLs were eQTLs only after AHR ligand treatment, even though the SNPs did not create/destroy an AHR response element—the DNA sequence motif recognized and bound by AHR. Additional functional studies in multiple cell lines demonstrated that some cis PGx-eQTLs are functional in multiple cell types, whereas others displayed SNP-by-ligand–dependent effects in just one cell type. Furthermore, four of those cis PGx-eQTLs had previously been associated with clinical phenotypes, indicating that those loci might have the potential to inform clinical decisions. Therefore, SNPs across the genome that are distant from TF binding sites for ligand-activated TFs might function as PGx-eQTLs and, as a result, might have important clinical implications for interindividual variation in drug response.
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Affiliation(s)
- Drew R Neavin
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Jeong-Heon Lee
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Zhenqing Ye
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Hu Li
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Tamas Ordog
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
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Carrasco Pro S, Dafonte Imedio A, Santoso CS, Gan KA, Sewell JA, Martinez M, Sereda R, Mehta S, Fuxman Bass JI. Global landscape of mouse and human cytokine transcriptional regulation. Nucleic Acids Res 2019; 46:9321-9337. [PMID: 30184180 PMCID: PMC6182173 DOI: 10.1093/nar/gky787] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/21/2018] [Indexed: 12/24/2022] Open
Abstract
Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through three decades of studies to generate a comprehensive database, CytReg, reporting 843 and 647 interactions between TFs and cytokine genes, in human and mouse respectively. By integrating CytReg with other functional datasets, we determined general principles governing the transcriptional regulation of cytokine genes. In particular, we show a correlation between TF connectivity and immune phenotype and disease, we discuss the balance between tissue-specific and pathogen-activated TFs regulating each cytokine gene, and cooperativity and plasticity in cytokine regulation. We also illustrate the use of our database as a blueprint to predict TF-disease associations and identify potential TF-cytokine regulatory axes in autoimmune diseases. Finally, we discuss research biases in cytokine regulation studies, and use CytReg to predict novel interactions based on co-expression and motif analyses which we further validated experimentally. Overall, this resource provides a framework for the rational design of future cytokine gene regulation studies.
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Affiliation(s)
- Sebastian Carrasco Pro
- Department of Biology, Boston University, Boston, MA 02215, USA.,Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | | | | | - Kok Ann Gan
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | | | - Rebecca Sereda
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Shivani Mehta
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Juan Ignacio Fuxman Bass
- Department of Biology, Boston University, Boston, MA 02215, USA.,Bioinformatics Program, Boston University, Boston, MA 02215, USA
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Haplotypes of TNF α/ β Genes Associated with Sex-Specific Paranoid Schizophrenic Risk in Tunisian Population. DISEASE MARKERS 2018; 2018:3502564. [PMID: 30627222 PMCID: PMC6304811 DOI: 10.1155/2018/3502564] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/24/2018] [Accepted: 11/04/2018] [Indexed: 01/30/2023]
Abstract
Several medical research findings have announced a strong association between the biology of cytokines and various brain activities. Since growing evidences suggest the crucial and complex role of the tumor necrosis factor in the CNS, we have hypothesized that functional genetic variants of the LTA and TNFA genes (LTA +252A/G (rs909253) and TNFA -857C/T (rs1799724) and TNFA -238G/A (rs361525)) may be involved in the predisposition to schizophrenia. This research is based on a case-control study. The RFLP-PCR genotyping was conducted on a Tunisian population composed of 208 patients and 208 controls. We found a strong significant overrepresentation of the minor alleles (G, T, and A, respectively) in all patients compared with controls (p = 0.003, OR = 1.55; p = 0.005, OR = 1.78; and p = 0.0001, OR = 1.74, respectively). This correlation was confirmed for male but not for female patients. Interestingly, the frequencies of the minor alleles were significantly more common among patients with paranoid schizophrenia when compared with controls (p = 0.003, OR = 1.75; p = 5 · 10-6, OR = 3.04; and p = 4 · 10-6, OR = 2.35, respectively). This potential association was confirmed by a logistic binary regression analysis only for the development of the paranoid form of schizophrenia (p = 0.001/OR = 2.6; p = 0.0002/OR = 3.2; and p = 0.0004/OR = 3.1, respectively) and remained not significant for the other subtypes. Moreover, our study showed an important association between GCA haplotype and the development of this pathological form (p = 10-4, OR = 3.71). In conclusion, our results proved a significant association between the three polymorphisms and paranoid schizophrenia, at least in the Tunisian population, suggesting a substantially increased risk for paranoid schizophrenia with dominant inheritance of these three minor alleles.
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Yen TY, Shih WL, Huang YC, Lee JT, Huang LM, Chang LY. Polymorphisms in enterovirus 71 receptors associated with susceptibility and clinical severity. PLoS One 2018; 13:e0206769. [PMID: 30395634 PMCID: PMC6218064 DOI: 10.1371/journal.pone.0206769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/18/2018] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE To evaluate the association of enterovirus 71 (EV71) susceptibility and clinical severity with polymorphisms in EV71 receptors, including human scavenger receptor class B member 2 (SCARB2), P-selectin glycoprotein ligand-1 (PSGL-1), and annexin II (ANXA2). METHODS We enrolled laboratory-confirmed EV71 cases and healthy age- and gender-matched controls in Taiwan from 2000 to 2012. We detected genetic polymorphisms in SCARB2, PSGL-1, and ANXA2 and correlated the results with EV71 susceptibility and severity. RESULTS We collected 599 EV71 cases and 98 controls. Among EV71 patients, the male to female ratio was 1.61, and the mean age was 2.99±2.47 years. For clinical severity, 117 (19.6%) had severe central nervous system involvement with or without cardiopulmonary failure. For outcomes, 46 (7.7%) had sequelae, and 14 (2.3%) died. SCARB2 polymorphisms (rs6824953 and rs11097262) were associated with susceptibility to EV71 infection (OR 1.60, 95% CI 1.07-2.39; and OR 1.64, 95% CI 1.09-2.47, respectively). PSGL-1 polymorphisms (rs7137098 and rs8179137) were significantly associated with severe EV71 infection (OR 1.46, 95% CI 1.1-1.96; and OR 1.47, 95% CI 1.07-2.03, respectively). CONCLUSIONS SCARB2 polymorphisms (rs6824953 and rs11097262) might be associated with EV71 susceptibility. PSGL-1 polymorphisms (rs7137098 and rs8179137) were associated with severe EV71 infection.
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Affiliation(s)
- Ting-Yu Yen
- Department of Pediatrics, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
| | - Wei-Liang Shih
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yi-Chuan Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jian-Te Lee
- Department of Pediatrics, National Taiwan University Hospital, Yun-Lin Branch, Yunlin, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Luan-Yin Chang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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20
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Wilson KD, Ochoa LF, Solomon OD, Pal R, Cardona SM, Carpio VH, Keiser PH, Cardona AE, Vargas G, Stephens R. Elimination of intravascular thrombi prevents early mortality and reduces gliosis in hyper-inflammatory experimental cerebral malaria. J Neuroinflammation 2018; 15:173. [PMID: 29866139 PMCID: PMC5987620 DOI: 10.1186/s12974-018-1207-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Cerebral malaria (CM) is the most lethal outcome of Plasmodium infection. There are clear correlations between expression of inflammatory cytokines, severe coagulopathies, and mortality in human CM. However, the mechanisms intertwining the coagulation and inflammation pathways, and their roles in CM, are only beginning to be understood. In mice with T cells deficient in the regulatory cytokine IL-10 (IL-10 KO), infection with Plasmodium chabaudi leads to a hyper-inflammatory response and lethal outcome that can be prevented by anti-TNF treatment. However, inflammatory T cells are adherent within the vasculature and not present in the brain parenchyma, suggesting a novel form of cerebral inflammation. We have previously documented behavioral dysfunction and microglial activation in infected IL-10 KO animals suggestive of neurological involvement driven by inflammation. In order to understand the relationship of intravascular inflammation to parenchymal dysfunction, we studied the congestion of vessels with leukocytes and fibrin(ogen) and the relationship of glial cell activation to congested vessels in the brains of P. chabaudi-infected IL-10 KO mice. METHODS Using immunofluorescence microscopy, we describe severe thrombotic congestion in these animals. We stained for immune cell surface markers (CD45, CD11b, CD4), fibrin(ogen), microglia (Iba-1), and astrocytes (GFAP) in the brain at the peak of behavioral symptoms. Finally, we investigated the roles of inflammatory cytokine tumor necrosis factor (TNF) and coagulation on the pathology observed using neutralizing antibodies and low-molecular weight heparin to inhibit both inflammation and coagulation, respectively. RESULTS Many blood vessels in the brain were congested with thrombi containing adherent leukocytes, including CD4 T cells and monocytes. Despite containment of the pathogen and leukocytes within the vasculature, activated microglia and astrocytes were prevalent in the parenchyma, particularly clustered near vessels with thrombi. Neutralization of TNF, or the coagulation cascade, significantly reduced both thrombus formation and gliosis in P. chabaudi-infected IL-10 KO mice. CONCLUSIONS These findings support the contribution of cytokines, coagulation, and leukocytes within the brain vasculature to neuropathology in malaria infection. Strikingly, localization of inflammatory leukocytes within intravascular clots suggests a mechanism for interaction between the two cascades by which cytokines drive local inflammation without considerable cellular infiltration into the brain parenchyma.
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Affiliation(s)
- Kyle D Wilson
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Lorenzo F Ochoa
- Center for Biomedical Engineering, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Olivia D Solomon
- Center for Biomedical Engineering, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Rahul Pal
- Center for Biomedical Engineering, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Sandra M Cardona
- Department of Biology, One UTSA Circle, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Victor H Carpio
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Philip H Keiser
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0435, USA
| | - Astrid E Cardona
- Department of Biology, One UTSA Circle, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Gracie Vargas
- Center for Biomedical Engineering, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA.,Department of Neuroscience and Cell Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Robin Stephens
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA. .,Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0435, USA. .,Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555, USA.
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Law WD, Fogarty EA, Vester A, Antonellis A. A genome-wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve. BMC Genomics 2018; 19:311. [PMID: 29716548 PMCID: PMC5930951 DOI: 10.1186/s12864-018-4692-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/17/2018] [Indexed: 12/29/2022] Open
Abstract
Background Identifying functional non-coding variation is critical for defining the genetic contributions to human disease. While single-nucleotide polymorphisms (SNPs) within cis-acting transcriptional regulatory elements have been implicated in disease pathogenesis, not all cell types have been assessed and functional validations have been limited. In particular, the cells of the peripheral nervous system have been excluded from genome-wide efforts to link non-coding SNPs to altered gene function. Addressing this gap is essential for defining the genetic architecture of diseases that affect the peripheral nerve. We developed a computational pipeline to identify SNPs that affect regulatory function (rSNPs) and evaluated our predictions on a set of 144 regions in Schwann cells, motor neurons, and muscle cells. Results We identified 28 regions that display regulatory activity in at least one cell type and 13 SNPs that affect regulatory function. We then tailored our pipeline to one peripheral nerve cell type by incorporating SOX10 ChIP-Seq data; SOX10 is essential for Schwann cells. We prioritized 22 putative SOX10 response elements harboring a SNP and rapidly validated two rSNPs. We then selected one of these elements for further characterization to assess the biological relevance of our approach. Deletion of the element from the genome of cultured Schwann cells—followed by differential gene expression studies—revealed Tubb2b as a candidate target gene. Studying the enhancer in developing mouse embryos revealed activity in SOX10-positive cells including the dorsal root ganglia and melanoblasts. Conclusions Our efforts provide insight into the utility of employing strict conservation for rSNP discovery. This strategy, combined with functional analyses, can yield candidate target genes. In support of this, our efforts suggest that investigating the role of Tubb2b in SOX10-positive cells may reveal novel biology within these cell populations. Electronic supplementary material The online version of this article (10.1186/s12864-018-4692-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William D Law
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Elizabeth A Fogarty
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aimée Vester
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA. .,Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Neurology, University of Michigan Medical School, 3710A Medical Sciences II, 1241 E. Catherine St. SPC 5618, Ann Arbor, MI, 48109, USA.
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Role of IL-1β, IL-6 and TNF-α cytokines and TNF-α promoter variability in Plasmodium vivax infection during pregnancy in endemic population of Jharkhand, India. Mol Immunol 2018; 97:82-93. [DOI: 10.1016/j.molimm.2018.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/18/2018] [Accepted: 03/22/2018] [Indexed: 12/17/2022]
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Ramírez-Bello J, Cadena-Sandoval D, Mendoza-Rincón JF, Barbosa-Cobos RE, Sánchez-Muñoz F, Amezcua-Guerra LM, Sierra-Martínez M, Jiménez-Morales S. Tumor necrosis factor gene polymorphisms are associated with systemic lupus erythematosus susceptibility or lupus nephritis in Mexican patients. Immunol Res 2018; 66:348-354. [DOI: 10.1007/s12026-018-8993-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Genetic Polymorphisms in Cytokine Genes in Colombian Patients with Ocular Toxoplasmosis. Infect Immun 2018; 86:IAI.00597-17. [PMID: 29426041 DOI: 10.1128/iai.00597-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/22/2018] [Indexed: 01/23/2023] Open
Abstract
Toxoplasmosis is caused by infection with the protozoan parasite Toxoplasma gondii, which has the capacity to infect all warm-blooded animals worldwide. Toxoplasmosis is a major cause of visual defects in the Colombian population; however, the association between genetic polymorphisms in cytokine genes and susceptibility to ocular toxoplasmosis has not been studied in this population. This work evaluates the associations between polymorphisms in genes coding for the cytokines tumor necrosis factor alpha (TNF-α) (rs1799964, rs1800629, rs1799724, rs1800630, and rs361525), interleukin 1β (IL-1β) (rs16944, rs1143634, and rs1143627), IL-1α (rs1800587), gamma interferon (IFN-γ) (rs2430561), and IL-10 (rs1800896 and rs1800871) and the presence of ocular toxoplasmosis (OT) in a sample of a Colombian population (61 patients with OT and 116 healthy controls). Genotyping was performed with the "dideoxynucleotide (ddNTP) primer extension" technique. Functional-effect predictions of single nucleotide polymorphisms (SNPs) were done by using FuncPred. A polymorphism in the IL-10 gene promoter (-1082G/A) was significantly more prevalent in OT patients than in controls (P = 1.93e-08; odds ratio [OR] = 5.27e+03; 95% confidence interval [CI] = 3.18 to 8.739; Bonferroni correction [BONF] = 3.48e-07). In contrast, haplotype "AG" of the IL-10 gene promoter polymorphisms (rs1800896 and rs1800871) was present at a lower frequency in OT patients (P = 7e-04; OR = 0.10; 95% CI = 0.03 to 0.35). The +874A/T polymorphism of IFN-γ was associated with OT (P = 3.37e-05; OR = 4.2; 95% CI = 2.478 to 7.12; BONF = 6.07e-04). Haplotype "GAG" of the IL-1β gene promoter polymorphisms (rs1143634, rs1143627, and rs16944) appeared to be significantly associated with OT (P = 0.0494). The IL-10, IFN-γ, and IL-1β polymorphisms influence the development of OT in the Colombian population.
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Ahouty B, Koffi M, Ilboudo H, Simo G, Matovu E, Mulindwa J, Hertz-Fowler C, Bucheton B, Sidibé I, Jamonneau V, MacLeod A, Noyes H, N’Guetta SP. Candidate genes-based investigation of susceptibility to Human African Trypanosomiasis in Côte d'Ivoire. PLoS Negl Trop Dis 2017; 11:e0005992. [PMID: 29059176 PMCID: PMC5695625 DOI: 10.1371/journal.pntd.0005992] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/02/2017] [Accepted: 09/25/2017] [Indexed: 01/31/2023] Open
Abstract
Human African Trypanosomiasis (HAT) or sleeping sickness is a Neglected Tropical Disease. Long regarded as an invariably fatal disease, there is increasing evidence that infection by T. b. gambiense can result in a wide range of clinical outcomes, including latent infections, which are long lasting infections with no parasites detectable by microscopy. The determinants of this clinical diversity are not well understood but could be due in part to parasite or host genetic diversity in multiple genes, or their interactions. A candidate gene association study was conducted in Côte d’Ivoire using a case-control design which included a total of 233 subjects (100 active HAT cases, 100 controls and 33 latent infections). All three possible pairwise comparisons between the three phenotypes were tested using 96 SNPs in16 candidate genes (IL1, IL4, IL4R, IL6, IL8, IL10, IL12, IL12R, TNFA, INFG, MIF, APOL1, HPR, CFH, HLA-A and HLA-G). Data from 77 SNPs passed quality control. There were suggestive associations at three loci in IL6 and TNFA in the comparison between active cases and controls, one SNP in each of APOL1, MIF and IL6 in the comparison between latent infections and active cases and seven SNP in IL4, HLA-G and TNFA between latent infections and controls. No associations remained significant after Bonferroni correction, but the Benjamini Hochberg false discovery rate test indicated that there were strong probabilities that at least some of the associations were genuine. The excess of associations with latent infections despite the small number of samples available suggests that these subjects form a distinct genetic cluster different from active HAT cases and controls, although no clustering by phenotype was observed by principle component analysis. This underlines the complexity of the interactions existing between host genetic polymorphisms and parasite diversity. Since it was first identified, human African trypanosomiasis (HAT) or sleeping sickness has been described as invariably fatal. Recent data however suggest that infection by T. b. gambiense can result in a wide range of clinical outcomes in its human host including long lasting infections, that can be detected by the presence of antibodies, but in which parasites cannot be seen by microscopy; these cases are known as latent infections. While the factors determining, this varied response have not been clearly characterized, the effectors of the immune responses have been partially implicated as key players. We collected samples from people with active HAT, latent infections and controls in endemic foci in the Côte d’Ivoire. We tested the role of single nucleotide polymorphisms (SNPs) in 16 genes on susceptibility/resistance to HAT by means of a candidate gene association study. There was some evidence that variants of the genes for IL4, IL6, APOL1, HLAG, MIF and TNFA modified the risk of developing HAT. These proteins regulate the inflammatory response to many infections or are directly involved in killing the parasites. In this study, the results were statistically weak and would be inconclusive on their own, however other studies have also found associations in these genes, increasing the chance that the variants that we have identified play a genuine role in the response to trypanosome infection in Côte D’Ivoire.
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Affiliation(s)
- Bernardin Ahouty
- Laboratoire de Génétique, Félix Houphouët Boigny University, Abidjan, Côte d’Ivoire
| | - Mathurin Koffi
- Unité de Recherche en Génétique et Epidémiology Moléculaire, Jean Lorougnon Guédé University, Daloa, Côte d’Ivoire
- * E-mail:
| | - Hamidou Ilboudo
- Unité Maladies à Vecteurs et Biodiversité, Centre International de Recherche-Développement sur l’Elevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
| | - Gustave Simo
- Department of Biochemistry, University of Dchang, Dchang, Cameroon
| | - Enock Matovu
- School of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- School of Veterinary Medicine, Makerere University, Kampala, Uganda
| | | | - Bruno Bucheton
- Unité Mixte de Recherche 177 IRD-CIRAD, Institut de Recherche pour le Développement, Montpellier, France
| | - Issa Sidibé
- Unité Maladies à Vecteurs et Biodiversité, Centre International de Recherche-Développement sur l’Elevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
| | - Vincent Jamonneau
- Unité Mixte de Recherche 177 IRD-CIRAD, Institut de Recherche pour le Développement, Montpellier, France
- Unité de Recherche Glossines et Trypanosomes, Institut Pierre Richet, Bouaké, Côte d’Ivoire
| | - Annette MacLeod
- Wellcome Center for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
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Pabalan N, Chaisri S, Tabunhan S, Tarasuk M, Jarjanazi H, Steiner T. Associations of tumor necrosis factor-α-308 polymorphism with dengue infection: A systematic review and meta-analysis. Acta Trop 2017; 173:17-22. [PMID: 28495402 DOI: 10.1016/j.actatropica.2017.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 01/18/2023]
Abstract
Inconsistency of reported associations between the tumor necrosis factor-alpha-308 (TNFα-308) polymorphism (rs1800629) and dengue virus infection prompted a meta-analysis, to obtain more precise estimates. A literature search yielded 14 case-control studies. We calculated pooled odds ratios (OR) and 95% confidence intervals in three groups according to severity, dengue fever (DF), dengue hemorrhagic fever (DHF) and dengue (DEN) using standard genetic models. Pooled ORs were subjected to modifier treatment where re-analysis was confined to Hardy-Weinberg compliant (HWC) studies. Heterogeneity of outcomes warranted examining their sources with outlier treatment. In subgroup analysis, we compared Asian and South/Central American (SCA)/Brazilian effects. Overall pooled outcomes yielded no significant effects (OR 0.66-1.44, P=0.08-0.96). In the dominant-codominant model, pooled effects were heterogeneous (I2=47%-71%) which was lost/reduced (I2=0%-43%) when outlier treatment was applied. This also yielded significant associations (OR 0.68-0.77, P=0.02-0.05). Our results are best seen in the Asian subgroup, which in itself already yielded significant effects in DEN (OR 0.62-0.67, P=0.01-0.02). These reduced risk findings were significant from the tests of interaction (P=0.001-0.02) which highlights the protective effects of TNFα-308 among Asians. TNFα-308 effects on dengue are based on significance and non-heterogeneity of the post-outlier outcomes in the dominant and codominant models. Here, pooled effects may also be ethnic specific, where Asians are protected but not SCA. Both modified and Asian effects are up to 38% protective.
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Nguyen TN, Baaklini S, Koukouikila-Koussounda F, Ndounga M, Torres M, Pradel L, Ntoumi F, Rihet P. Association of a functional TNF variant with Plasmodium falciparum parasitaemia in a congolese population. Genes Immun 2017; 18:152-157. [DOI: 10.1038/gene.2017.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 11/09/2022]
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Marquet S. Overview of human genetic susceptibility to malaria: From parasitemia control to severe disease. INFECTION GENETICS AND EVOLUTION 2017; 66:399-409. [PMID: 28579526 DOI: 10.1016/j.meegid.2017.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
Malaria is a life-threatening blood disease caused by the protozoan Plasmodium. Infection may lead to several different patterns of symptoms in the host: asymptomatic state, uncomplicated disease or severe disease. Severe malaria occurs mostly in young children and is a major cause of death. Disease is thought to result from the sequestration of parasites in the small blood vessels of the brain and the deregulation of key immune system elements. The cellular and molecular regulatory mechanisms underlying the pathogenesis of disease are however not fully understood. What is known it is that the genetic determinants of the host play an important role in the severity of the disease and the outcome of infection. Here we review the most convincing results obtained through genetic epidemiology studies concerning the genetic control of malaria in human caused by Plasmodium falciparum infection. The identification of genes conferring susceptibility or resistance to malaria might improve diagnosis and treatment.
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Affiliation(s)
- Sandrine Marquet
- Aix-Marseille University, INSERM, GIMP, Labex ParaFrap, Marseille, France.
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29
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Shabani E, Ouma BJ, Idro R, Bangirana P, Opoka RO, Park GS, Conroy AL, John CC. Elevated cerebrospinal fluid tumour necrosis factor is associated with acute and long-term neurocognitive impairment in cerebral malaria. Parasite Immunol 2017; 39. [PMID: 28453871 DOI: 10.1111/pim.12438] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 04/24/2017] [Indexed: 12/25/2022]
Abstract
Systemic tumour necrosis factor-α (TNF-α) may contribute to the pathogenesis of cerebral malaria (CM) by promoting endothelial activation and parasite sequestration. However, less is known about the role of central nervous system (CNS) TNF-α in CM. We assessed plasma (n=249) and cerebrospinal fluid (CSF) (n=167) TNF-α levels in Ugandan children with CM, plasma TNF-α in Ugandan community control children (n=198) and CSF TNF-α in North American control children who had recovered from leukaemia (n=13). Plasma and CSF TNF-α were measured by magnetic bead assay. We compared plasma and CSF TNF-α levels in children with CM to mortality, acute and chronic neurologic deficits and long-term neurocognitive impairment. Plasma and CSF TNF-α levels were higher in CM than control children (P<.0001 for both). CSF TNF-α levels were higher in children who had neurologic deficits at discharge or 6-month follow-up (P≤.05 for both). Elevated CSF but not plasma TNF-α was associated with longer coma duration (Spearman's rho .18, P=.02) and deficits in overall cognition in children 5 years and older (β coefficient -.74, 95% CI -1.35 to -0.13, P=.02). The study findings suggest that CNS TNF-α may be involved in the development of acute and chronic neurologic and cognitive sequelae in children with CM.
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Affiliation(s)
- E Shabani
- Department of Pediatrics, Division of Global Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Ryan White Center for Pediatric Infectious Disease and Global Health, Department of Pediatrics, Indiana University, Indianapolis, IN, USA
| | - B J Ouma
- Department of Microbiology, Makerere University, Kampala, Uganda
| | - R Idro
- Department of Pediatrics and Child Health, Makerere University, Kampala, Uganda
| | - P Bangirana
- Department of Psychiatry, Makerere University, Kampala, Uganda
| | - R O Opoka
- Department of Pediatrics and Child Health, Makerere University, Kampala, Uganda
| | - G S Park
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - A L Conroy
- Ryan White Center for Pediatric Infectious Disease and Global Health, Department of Pediatrics, Indiana University, Indianapolis, IN, USA
| | - C C John
- Department of Pediatrics, Division of Global Pediatrics, University of Minnesota, Minneapolis, MN, USA.,Ryan White Center for Pediatric Infectious Disease and Global Health, Department of Pediatrics, Indiana University, Indianapolis, IN, USA
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Dittmar D, Schuttelaar ML. Immunology and genetics of tumour necrosis factor in allergic contact dermatitis. Contact Dermatitis 2017; 76:257-271. [DOI: 10.1111/cod.12769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/16/2016] [Accepted: 01/02/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Daan Dittmar
- Department of Dermatology; University Medical Centre Groningen, University of Groningen; 9700 RB Groningen The Netherlands
| | - Marie L. Schuttelaar
- Department of Dermatology; University Medical Centre Groningen, University of Groningen; 9700 RB Groningen The Netherlands
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Frequency of TNFA, INFG, and IL10 Gene Polymorphisms and Their Association with Malaria Vivax and Genomic Ancestry. Mediators Inflamm 2016; 2016:5168363. [PMID: 27999453 PMCID: PMC5143728 DOI: 10.1155/2016/5168363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/14/2016] [Accepted: 09/27/2016] [Indexed: 02/08/2023] Open
Abstract
Polymorphisms in cytokine genes can alter the production of these proteins and consequently affect the immune response. The trihybrid heterogeneity of the Brazilian population is characterized as a condition for the use of ancestry informative markers. The objective of this study was to evaluate the frequency of -1031T>C, -308G>A and -238G>A TNFA, +874 A>T IFNG and -819C>T, and -592C>A IL10 gene polymorphisms and their association with malaria vivax and genomic ancestry. Samples from 90 vivax malaria-infected individuals and 51 noninfected individuals from northern Brazil were evaluated. Genotyping was carried out by using ASO-PCR or PCR/RFLP. The genomic ancestry of the individuals was classified using 48 insertion/deletion polymorphism biallelic markers. There were no differences in the proportions of African, European, and Native American ancestry between men and women. No significant association was observed for the allele and genotype frequencies of the 6 SNPs between malaria-infected and noninfected individuals. However, there was a trend toward decreasing the frequency of individuals carrying the TNF-308A allele with the increasing proportion of European ancestry. No ethnic-specific SNPs were identified, and there was no allelic or genotype association with susceptibility or resistance to vivax malaria. Understanding the genomic mechanisms by which ancestry influences this association is critical and requires further study.
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Olaniyan SA, Amodu OK, Bakare AA, Troye-Blomberg M, Omotade OO, Rockett KA. Tumour necrosis factor alpha promoter polymorphism, TNF-238 is associated with severe clinical outcome of falciparum malaria in Ibadan southwest Nigeria. Acta Trop 2016; 161:62-7. [PMID: 27178813 DOI: 10.1016/j.actatropica.2016.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 01/24/2023]
Abstract
Tumour necrosis factor (TNF) - α has been shown to play an important role in the pathogenesis of falciparum malaria. Two TNF promoter polymorphisms, TNF-308 and TNF-238 have been associated with differential activity and production of TNF. In order to investigate the association between TNF-308 and TNF-238 and the clinical outcome of malaria in a Nigerian population, the two TNF polymorphisms were analysed using Sequenom iPLEX Platform. A total of 782 children; 283 children with uncomplicated malaria, 255 children with severe malaria and 244 children with asymptomatic infection (controls) were studied. The distribution of TNF-308 and TNF-238 genotypes were consistent with the Hardy-Weinberg equilibrium. Distribution of both TNF polymorphisms differed significantly across all clinical groups (TNF-308: p=0.007; TNF-238: p=0.001). Further tests for association with severe malaria using genotype models controlling for age, parasitaemia and HbAS showed a significant association of the TNF-238 polymorphism with susceptibility to severe malaria (95% CI=1.43-6.02, OR=2.94, p=0.003237) The GG genotype of TNF-238 significantly increased the risk of developing cerebral malaria from asymptomatic malaria and uncomplicated malaria (95% CI=1.99-18.17, OR=6.02, p<0.001 and 95% CI=1.78-8.23, OR=3.84, p<0.001 respectively). No significant association was found between TNF-308 and malaria outcome. These results show thegenetic association of TNF-238 in the clinical outcome of malaria in Ibadan, southwest Nigeria. These findings add support to the role of TNF in the outcome of malaria infection. Further large scale studies across multiple malaria endemic populations will be required to determine the specific roles of TNF-308 and TNF-238 in the outcome of falciparum malaria infection.
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Thada S, Ponnana M, Sivangala R, Joshi L, Alasandagutti M, Ansari MSS, Schumann RR, Valluri V, Gaddam S. Polymorphisms of IFN-γ (+874A/T) and IL-12 (+1188A/C) in tuberculosis patients and their household contacts in Hyderabad, India. Hum Immunol 2016; 77:559-65. [PMID: 27108964 DOI: 10.1016/j.humimm.2016.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/12/2016] [Accepted: 04/20/2016] [Indexed: 01/27/2023]
Abstract
Several cytokine gene variants have shown to be associated with host susceptibility to infectious diseases including tuberculosis (TB). High rates of transmission were identified within household members of TB patients. In this study, we examined whether single nucleotide polymorphisms of IFN-γ +874A/T and IL-12 +1188A/C affect susceptibility to TB. Genomic DNA from patients with active disease, their household contacts HHC and healthy controls HC was genotyped for IFN-γ +874A/T and IL-12 +1188A/C SNPs by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). IFN-γ +874 AA and AT genotypes were significantly with different frequencies in patients and total HHC as compared to HC (p<0.0001). In patients IL-12 +1188 AC and CC genotypes were associated with TB (p<0.003, p<0.008). In total HHC AC, CC genotypes and both alleles (A&C) were significantly different as compared to HC (p<0.004, p<0.001, p<0.034) and the same result was obtained when HHC were stratified into related (p<0.02, p<0.001) and unrelated (p<0.009, p<0.017) individuals. Allelic frequencies, however, were significant only in related contacts (p<0.021). Generalized multifactor dimensionality reduction method (GMDR) testing revealed high risk combinations of several genotypes in IFN-γ & IL-12 genes. Our findings suggest an important role of genetic variations of IFN-γ and IL-12 for susceptibility to TB.
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Affiliation(s)
- Shruthi Thada
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India; Institute for Microbiology and Hygiene, Charite University Medical Center, Berlin, Germany
| | - Meenakshi Ponnana
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India
| | - Ramya Sivangala
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India
| | - Lavanya Joshi
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India
| | | | | | - Ralf R Schumann
- Institute for Microbiology and Hygiene, Charite University Medical Center, Berlin, Germany
| | - Vijayalakshmi Valluri
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India; LEPRA India - Blue Peter Public Health & Research Centre, Cherlapally, Hyderabad, Andhra Pradesh, India
| | - Sumanlatha Gaddam
- Bhagwan Mahavir Medical Research Centre, Hyderabad, Andhra Pradesh, India; Department of Genetics, Osmania University Hyderabad, Telangana, India.
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Zimring JC, Spitalnik SL. Pathobiology of Transfusion Reactions. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2015; 10:83-110. [DOI: 10.1146/annurev-pathol-012414-040318] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James C. Zimring
- Puget Sound Blood Center Research Institute, Seattle, Washington 98102;
- Departments of Laboratory Medicine and Internal Medicine, Division of Hematology, University of Washington, Seattle, Washington 98195
| | - Steven L. Spitalnik
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032
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Cañas CA, Tobón GJ, Bonilla-Abadía F. The importance of evolution in the development and course of rheumatoid arthritis. Med Hypotheses 2014; 82:784-91. [PMID: 24746382 DOI: 10.1016/j.mehy.2014.03.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/24/2014] [Indexed: 12/29/2022]
Abstract
Rheumatoid arthritis (RA) is a complex autoimmune disease of recent evolutionary origin. Genetic drift determines diverse polymorphisms implicated in the susceptibility to RA including the major histocompatibility complex (MHC) class II genes in the so-called shared epitope. These genes originated after the divergence between Homo and Pan from their common ancestry Ardipithecus ramidus about 5 million years ago. Natural selection determined the particular changes in the legs (bipedal position), hands, neck, brain and eusociality in humans which influence the clinical presentation of RA. In this article, we hypothesized that the origin and course of RA may be explainable in the light of evolution.
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Affiliation(s)
- C A Cañas
- Rheumatology Unit, Fundación Valle del Lili, Universidad ICESI, Cali, Colombia
| | - G J Tobón
- Rheumatology Unit, Fundación Valle del Lili, Universidad ICESI, Cali, Colombia.
| | - F Bonilla-Abadía
- Rheumatology Unit, Fundación Valle del Lili, Universidad ICESI, Cali, Colombia; Human Molecular Genetics Laboratory, Universidad del Valle, Cali, Colombia
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Shafia S, Sofi FA, Dilafroze, Rasool R, Javeed S, Shah ZA. The association between TNFα gene polymorphisms and susceptibility to rheumatoid arthritis in an ethnic Kashmiri population: relationship with disease activity and severity markers. Int J Rheum Dis 2014; 19:362-9. [PMID: 24382334 DOI: 10.1111/1756-185x.12270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM The aim of our study was to determine the genetic associations between polymorphisms of the TNFα gene (-308G/A and -238G/A) with disease susceptibility and severity in patients with rheumatoid arthritis (RA) in an ethnic Kashmiri population. METHODS Allele and genotype frequencies of TNFα-308G/A and TNFα-238G/A polymorphisms were compared between 150 RA patients and 200 healthy controls by using polymerase chain reaction - restriction fragment length polymorphism method. Demographic, clinical and serological data were prospectively evaluated. Disease activity score (DAS28) was also assessed. RESULTS We did not find any significant association between TNFα-308G/A and TNFα-238G/A polymorphism and RA risk (P > 0.05), but TNFα-308GG genotype was associated significantly with rheumatoid factor seropositivity (P < 0.01) and TNFα-238GA genotype was associated with swollen joint count < 5 (P = 0.04) as well as with less severe disease activity as measured by DAS28 score (P = 0.02). CONCLUSION Our findings suggest the possible roles of TNFα-308GG and TNFα-238GA as important determinants for the development of certain manifestations and disease severity in RA in ethnic Kashmiri population.
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Affiliation(s)
- Syed Shafia
- Department of Immunology and Molecular Medicine, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, India
| | - Fayaz A Sofi
- Division of Rheumatology, Department of General Medicine, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, India
| | - Dilafroze
- Department of Immunology and Molecular Medicine, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, India
| | - Roohi Rasool
- Department of Immunology and Molecular Medicine, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, India
| | - Sheikh Javeed
- Department of Physical Medicine and Rehabilitation, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, India
| | - Zafar A Shah
- Department of Immunology and Molecular Medicine, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, India
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Hernandez-Valladares M, Rihet P, Iraqi FA. Host susceptibility to malaria in human and mice: compatible approaches to identify potential resistant genes. Physiol Genomics 2014; 46:1-16. [DOI: 10.1152/physiolgenomics.00044.2013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
There is growing evidence for human genetic factors controlling the outcome of malaria infection, while molecular basis of this genetic control is still poorly understood. Case-control and family-based studies have been carried out to identify genes underlying host susceptibility to malarial infection. Parasitemia and mild malaria have been genetically linked to human chromosomes 5q31-q33 and 6p21.3, and several immune genes located within those regions have been associated with malaria-related phenotypes. Association and linkage studies of resistance to malaria are not easy to carry out in human populations, because of the difficulty in surveying a significant number of families. Murine models have proven to be an excellent genetic tool for studying host response to malaria; their use allowed mapping 14 resistance loci, eight of them controlling parasitic levels and six controlling cerebral malaria. Once quantitative trait loci or genes have been identified, the human ortholog may then be identified. Comparative mapping studies showed that a couple of human and mouse might share similar genetically controlled mechanisms of resistance. In this way, char8, which controls parasitemia, was mapped on chromosome 11; char8 corresponds to human chromosome 5q31-q33 and contains immune genes, such as Il3, Il4, Il5, Il12b, Il13, Irf1, and Csf2. Nevertheless, part of the genetic factors controlling malaria traits might differ in both hosts because of specific host-pathogen interactions. Finally, novel genetic tools including animal models were recently developed and will offer new opportunities for identifying genetic factors underlying host phenotypic response to malaria, which will help in better therapeutic strategies including vaccine and drug development.
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Affiliation(s)
| | - Pascal Rihet
- UMR1090 TAGC, INSERM, Marseille, France
- Aix-Marseille University, Marseille, France; and
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
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Apinjoh TO, Anchang-Kimbi JK, Njua-Yafi C, Mugri RN, Ngwai AN, Rockett KA, Mbunwe E, Besingi RN, Clark TG, Kwiatkowski DP, Achidi EA. Association of cytokine and Toll-like receptor gene polymorphisms with severe malaria in three regions of Cameroon. PLoS One 2013; 8:e81071. [PMID: 24312262 PMCID: PMC3842328 DOI: 10.1371/journal.pone.0081071] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/08/2013] [Indexed: 11/23/2022] Open
Abstract
P. falciparum malaria is one of the most widespread and deadliest infectious diseases in children under five years in endemic areas. The disease has been a strong force for evolutionary selection in the human genome, and uncovering the critical human genetic factors that confer resistance to the disease would provide clues to the molecular basis of protective immunity that would be invaluable for vaccine development. We investigated the effect of single nucleotide polymorphisms (SNPs) on malaria pathology in a case- control study of 1862 individuals from two major ethnic groups in three regions with intense perennial P. falciparum transmission in Cameroon. Twenty nine polymorphisms in cytokine and toll-like receptor (TLR) genes as well as the sickle cell trait (HbS) were assayed on the Sequenom iPLEX platform. Our results confirm the known protective effect of HbS against severe malaria and also reveal a protective effect of SNPs in interleukin-10 (IL10) cerebral malaria and hyperpyrexia. Furthermore, IL17RE rs708567 GA and hHbS rs334 AT individuals were associated with protection from uncomplicated malaria and anaemia respectively in this study. Meanwhile, individuals with the hHbS rs334 TT, IL10 rs3024500 AA, and IL17RD rs6780995 GA genotypes were more susceptible to severe malarial anaemia, cerebral malaria, and hyperpyrexia respectively. Taken together, our results suggest that polymorphisms in some immune response genes may have important implications for the susceptibility to severe malaria in Cameroonians. Moreover using uncomplicated malaria may allow us to identify novel pathways in the early development of the disease.
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Affiliation(s)
- Tobias O. Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
- * E-mail:
| | | | - Clarisse Njua-Yafi
- Department of Animal Biology and Physiology, University of Yaounde I, Yaounde, Cameroon
| | - Regina N. Mugri
- Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
| | - Andre N. Ngwai
- Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
| | - Kirk A. Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Eric Mbunwe
- Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
- Diabetes Research Center, Brussels Free University, Brussels, Belgium
| | - Richard N. Besingi
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - Taane G. Clark
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dominic P. Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Eric A. Achidi
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
- Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
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Torres-Espíndola LM, Velázquez-Cruz R, Falfán-Valencia R, Chavez-Pacheco JL, Salcedo-Vargas M, de Jesús Nambo-Lucio M, Salinas-Lara C, Alemón-Medina R, Granados-Montiel J, Reyes-Servín MA, Granados J, de Jesús Castillejos-López M. Genetic polymorphism of tumor necrosis factor promoter region and susceptibility to develop Hodgkin lymphoma in a Mexican population. Leuk Lymphoma 2013; 55:1295-9. [PMID: 24033107 DOI: 10.3109/10428194.2013.842982] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hodgkin lymphoma (HL) is a rare neoplasm of the lymphatic system, in which inflammation and allelic variants in cytokines have been proposed as etiological factors. Epstein-Barr virus infection is often associated as a risk factor in HL and since cytokines are involved in the humoral response to viral infection. Our aim was to study the association between single nucleotide polymorphisms (SNPs) located in the tumor necrosis factor (TNF) gene (- 376G> A, - 238G> A and 581G> A) in a sample of Mexican patients (56 cases) and their susceptibility to develop HL, comparing these SNPs among healthy individuals (127 controls). Frequencies for TNF - 238G> A and TNF 581G> A showed no significant differences between cases and controls. However, the proportion of cases with the GA genotype of - 376 SNP showed a significant difference as compared to controls, odds ratio = 4.41 (95% confidence interval: 1.21-16.6), p = 0.02. We found that in this group of patients from Mexico the SNP - 376G> A in TNF shows an association with higher risk for HL.
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Affiliation(s)
- Luz María Torres-Espíndola
- PhD Graduate Program in Biological Sciences, National Autonomous University of Mexico , Mexico City , Mexico
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Li M, Wang Y, Gu Y. Quantitative assessment of the influence of tumor necrosis factor alpha polymorphism with gastritis and gastric cancer risk. Tumour Biol 2013; 35:1495-502. [PMID: 24072494 DOI: 10.1007/s13277-013-1206-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 09/16/2013] [Indexed: 12/18/2022] Open
Abstract
Tumor necrosis factor alpha (TNFA) is an important molecule in inflammatory, infectious, and tumoral processes. Inflammation is one of the early phases in the development of gastric cancer (GC). Therefore, several studies have examined the association of polymorphism in TNFA with gastritis and GC risk. A functional polymorphism, -308G>A (rs1800629), which is located in the promoter of TNFA gene, has been suggested to alter the production of TNF-α and influence cancer risk. To date, a number of studies have been carried out to investigate the relationship between the polymorphism and gastritis or GC susceptibility, but the results were conflicting. To investigate this inconsistency, we performed a meta-analysis of 36 studies for TNFA -308G>A polymorphism to evaluate the effect of TNFA on genetic susceptibility for gastritis and GC. An overall random-effects per-allele odds ratio of 1.16 (95 % confidence interval 1.04-1.29, P = 0.008) was found for the polymorphism. Significant results were also observed using dominant or recessive genetic models. In the subgroup analyses by ethnicity, significant results were found in Caucasians, whereas no significant associations were found among East Asians and other ethnic populations. No associations between the polymorphism and gastritis were observed. In addition, our data indicate that TNFA is involved in GC susceptibility and confers its effect primarily in diffuse type of tumors. Besides, -308G>A polymorphism was found to be significantly associated with both cardiac and noncardiac tumors. This meta-analysis demonstrated that the TNFA -308G>A polymorphism is a risk factor for developing GC, but the associations vary in different ethnic populations.
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Affiliation(s)
- Ming Li
- Department of General Surgery, Qingpu Branch of Zhongshan Hospital, Fudan University, 1158 East Gongyuan Road, Shanghai, 201700, People's Republic of China,
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Ghesquières H, Maurer MJ, Casasnovas O, Ansell SM, Larrabee BR, Lech-Maranda E, Novak AJ, Borrel AL, Slager SL, Brice P, Allmer C, Brion A, Ziesmer SC, Morschhauser F, Habermann TM, Gaillard I, Link BK, Stamatoullas A, Fermé C, Dogan A, Macon WR, Audouin J, Cerhan JR, Salles G. Cytokine gene polymorphisms and progression-free survival in classical Hodgkin lymphoma by EBV status: results from two independent cohorts. Cytokine 2013; 64:523-31. [PMID: 24008079 DOI: 10.1016/j.cyto.2013.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 06/18/2013] [Accepted: 08/06/2013] [Indexed: 12/29/2022]
Abstract
BACKGROUND Cytokines are important immune mediators of classical Hodgkin lymphoma (CHL) pathogenesis, and circulating levels at diagnosis may help predict prognosis. Germline single nucleotide polymorphisms (SNPs) in immune genes have been correlated with cytokine production and function. METHODS We investigated whether selected germline SNPs in IL10 (rs1800890, rs1800896, rs1800871, rs1800872), TNFA (rs1800629), IL6 (rs1800795), ILRN (rs419598), INFG (rs2430561) and CCL17 (rs223828) were associated with circulating levels of related cytokines at diagnosis and progression-free survival (PFS) in CHL. Patients were from France (GELA, N=464; median age=32years) and the United States (Iowa/Mayo Specialized Program Of Research Excellence [SPORE], N=239; median age=38years); 22% of 346 CHL cases with EBV tumor status were positive. RESULTS There was no association with any of the SNPs with cytokine levels. Overall, there was no association of any of the SNPs with PFS. In exploratory analyses by EBV status, TNFA rs1800629 (HRAA/AG=2.41; 95%CI, 1.17-4.94) was associated with PFS in EBV-negative GELA patients, with similar trends in the SPORE patients (HRAA/AG=1.63; 95%CI, 0.61-4.40). In a meta-analysis of the two studies, TNFA (HRAA/AG=2.11; 95%CI, 1.18-3.77; P=0.01) was statistically significant, and further adjustment for the international prognostic system did not alter this result. CONCLUSIONS This study showed that germline variation in TNFA was associated with CHL prognosis for EBV-negative patients, which will require confirmation. These results support broader studies on the differential impact of genetic variation in immune genes on EBV-positive vs. EBV-negative CHL pathogenesis.
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Affiliation(s)
- Hervé Ghesquières
- Onco-Hematology, Centre Léon Bérard, UMR CNRS 5239, Université Lyon 1, Lyon, France; Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
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Waters JP, Pober JS, Bradley JR. Tumour necrosis factor in infectious disease. J Pathol 2013; 230:132-47. [PMID: 23460469 DOI: 10.1002/path.4187] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 02/15/2013] [Accepted: 02/23/2013] [Indexed: 12/12/2022]
Abstract
TNF signals through two distinct receptors, designated TNFR1 and TNFR2, which initiate diverse cellular effects that include cell survival, activation, differentiation, and proliferation and cell death. These cellular responses can promote immunological and inflammatory responses that eradicate infectious agents, but can also lead to local tissue injury at sites of infection and harmful systemic effects. Defining the molecular mechanisms involved in TNF responses, the effects of natural and experimental genetic diversity in TNF signalling and the effects of therapeutic blockade of TNF has increased our understanding of the key role that TNF plays in infectious disease.
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Affiliation(s)
- John P Waters
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
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Polymorphic genetic variation in immune system genes: a study of two populations of Espirito Santo, Brazil. Mol Biol Rep 2013; 40:4843-9. [PMID: 23666056 PMCID: PMC7088621 DOI: 10.1007/s11033-013-2582-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 04/29/2013] [Indexed: 11/25/2022]
Abstract
Mapping single nucleotide polymorphisms (SNPs) in genes potentially involved in immune responses may help understand the pathophysiology of infectious diseases in specific geographical regions. In this context, we have aimed to analyze the frequency of immunogenetic markers, focusing on genes CD209 (SNP -336A/G), FCγRIIa (SNP -131H/R), TNF-α (SNP -308A/G) and VDR (SNP Taq I) in two populations of the Espirito Santo State (ES), Brazil: general and Pomeranian populations. Peripheral blood genomic DNA was extracted from one hundred healthy individuals of the general population and from 59 Pomeranians. Polymorphic variant identification was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP). SNP genotype frequencies were in Hardy–Weinberg Equilibrium. There was no statistically significant difference in allelic and genotypic distributions between the two populations studied. Statistically significant differences were observed for SNP genotype distribution in genes CD209, TNF-α and VDR when comparing the ES populations with other Brazilian populations. This is the first report of CD209, FcγRIIa, TNF-α and VDR allelic frequencies for the general and Pomeranian populations of ES.
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Chuansumrit A, Anantasit N, Sasanakul W, Chaiyaratana W, Tangnararatchakit K, Butthep P, Chunhakan S, Yoksan S. Tumour necrosis factor gene polymorphism in dengue infection: association with risk of bleeding. Paediatr Int Child Health 2013; 33:97-101. [PMID: 23925283 DOI: 10.1179/2046905512y.0000000049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND A single nucleotide polymorphism located at the promoter -308A of tumour necrosis factor-alpha (TNF-α) gene may affect transcription and increase cytokine production, leading to the severe manifestation of dengue virus infection. AIM To study the association of the TNF-α -308A allele and the severity of patients with dengue infection. METHODS 112 patients suspected of having dengue infection and 106 normal controls were enrolled in the study. Mean (SD) age was 10.4 (3.6) years. In all, 19 and 82 patients were diagnosed with dengue fever (DF) and dengue haemorrhagic fever (DHF), respectively, while 11 were diagnosed with other febrile illnesses (OFIs). They were tested for the polymorphisms at the promoter -308 position of the TNF-α gene and their TNF-α levels were measured. RESULTS In the patients with dengue infection (14/202, 6.9%) with OFIs (1/22, 4.5%) and in normal controls (17/212, 8.0%), the frequency of the TNF-α -308A allele was not significantly different. Moreover, no statistically significant difference was found in patients with various clinical manifestations of dengue infection involving DF (5.3%, 2/38), DHF grade I (5.0%, 2/40), DHF grade II (9.5%, 4/42), DHF grade III (2.5%, 1/40) and DHF grade IV (11.9%, 5/42). However, patients with dengue infection and significant bleeding manifestations, apart from petechiae and ecchymosis, tended to have a higher frequency of the TNF-α -308A allele (11.8%, 9/76) than those without significant bleeding manifestations (5/126, 4.0%) (P = 0.056). The levels of TNF-α were additionally measured in 67 patients but the results failed to demonstrate a functional effect in the transcriptional rate of the TNF-α -308A allele. CONCLUSION In patients with dengue infection there is an association between the TNF-α -308A allele and the risk of bleeding. The test may be used as one of the predictors of the severity of dengue infection.
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Affiliation(s)
- Ampaiwan Chuansumrit
- Department of Pediatrics, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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Abstract
Legionella pneumophila is a facultative intracellular pathogen that is an important cause of pneumonia. Although host factors that may predispose to acquisition of Legionnaire's Disease (LD) include comorbid illnesses (e.g., diabetes, chronic lung disease), age, male sex, and smoking, many individuals have no identifiable risk factors. Some studies suggest that genetic factors may enhance susceptibility to LD. In this chapter we discuss current techniques and scientific methods to identify genetic susceptibility factors. These genetic studies provide insight into the human immune response to intracellular pathogens and may improve strategies for treatment and vaccine development.
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Affiliation(s)
- William R Berrington
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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Possible influence of resistance to malaria in clinical presentation of rheumatoid arthritis: biological significance of natural selection. ARTHRITIS 2012; 2012:670579. [PMID: 23209898 PMCID: PMC3504378 DOI: 10.1155/2012/670579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/21/2012] [Indexed: 01/02/2023]
Abstract
Rheumatoid arthritis (RA) is a common autoimmune disease that affects all ethnic groups. Genetic factors, mainly HLA alleles, are highly associated with increased risk to develop RA. However, there are few available data about the role of these genetic polymorphisms in the prevalence or severity of RA in the Afrodescendant population, who have evolutionarily and by natural selection developed mutations that allowed them to acquire resistance to infectious diseases like malaria. Some of the mechanisms, by which this resistance was developed as a product of natural selection, are involved in different forms of immunological response, many of them of a well-known importance in the pathophysiology of RA. This paper focuses on presenting the known mechanisms of resistance to malaria and their possible contribution to the pathophysiology of RA, including "loss-of-function" mutations, lack of expression of chemokine receptors, decrease of immune complexes clearance by asplenia, or increase of immune reactivity mediated by B cells, among other mechanisms in this special group of patients.
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Aarnink A, Bonhomme M, Blancher A. Positive selection in the major histocompatibility complex class III region of cynomolgus macaques (Macaca fascicularis) of the Philippines origin. ACTA ACUST UNITED AC 2012; 81:12-8. [PMID: 23134469 DOI: 10.1111/tan.12028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/25/2012] [Accepted: 10/10/2012] [Indexed: 11/30/2022]
Abstract
The cynomolgus macaque (Macaca fascicularis) is a model of choice among primates for the study of local adaptation processes because of its mixed and wide insular and continental distribution. In a previous study, by using 12 markers [5 microsatellites located in the major histocompatibility complex (MHC) region and 7 outside MHC], we have detected a signal of positive selection on the microsatellite DRACA located inside the gene DRA. In order to refine the location of this signal of positive selection in the MHC region, we studied the genetic diversity of 36 markers (18 microsatellites spread across the MHC region and 18 autosomal microsatellites outside MHC) in a sample of 254 individuals from four populations (Vietnam, Java, the Philippines, and Mauritius). We estimated for each locus the deviation of F(st) from a neutral model by using two methods based on contrasted demographic models. The two approaches showed a signal of positive selection in the MHC class III region that is much more significant than the one previously reported for the marker DRACA which could have been influenced by a hitchhiking effect due to its proximity with the class III region.
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Affiliation(s)
- A Aarnink
- Laboratoire d'Immunogénétique Moléculaire, EA 3034, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse 3, France
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Khanizadeh S, Ravanshad M, Mohebbi SR, Naghoosi H, Abrahim Tahaei M, Mousavi Nasab SD, Romani S, Azimzadeh P, Sanati A, Zali MR. Polymorphisms within the Promoter Region of the Gamma Interferon (IFN-γ) Receptor1 Gene are Associated with the Susceptibility to Chronic HBV Infection in an Iranian Population. HEPATITIS MONTHLY 2012; 12:e7283. [PMID: 23300496 PMCID: PMC3539059 DOI: 10.5812/hepatmon.7283] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/15/2012] [Accepted: 09/15/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND chronic hepatitis B virus (HBV) infection is a multifactorial disease that can result in serious clinical complications. Host genetic background especially the genes that encode immunologic factors like INF-γ and its receptor (IFN-γ R) are critical in the pathogenesis of infection. OBJECTIVES The current study aimed to investigate the association between two single nucleotide polymorphisms (SNPs) at positions -611 and -56 within the promoter region of gamma interferon receptor1 gene (IFN-γ R1) and chronic HBV infection. MATERIALS AND METHODS Genomic DNA from peripheral blood samples of 200 chronically HBV infected patients and 200 healthy blood donors, as controls, were collected and genomic DNA was extracted by phenol-chloroform method and DNA analysis genotype identification was performed by PCR-RFLP. RESULTS The results indicated that both SNP's frequency had a significant difference in the patient and control groups. At position -56, TT genotype was associated with patient group and P value was 0.002 and at position -611, GG genotype was further observed in control group and P value was 0.006. CONCLUSIONS Presence of G allele at position -611 within promoter of IFN-γ R1 gene in the enrolled population for the study was related to lower risk of disease, and presence of T allele at position -56 was also related to susceptibility to chronic HBV infection. Men had higher frequency of chronic HBV infection, which might be the result of high risk behavior.
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Affiliation(s)
- Sayyad Khanizadeh
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, IR Iran
| | - Mehrdad Ravanshad
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, IR Iran
- Corresponding author: Mehrdad Ravanshad, Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box: 14115-331, Tehran, IR Iran. Tel.: +98-2182883836, Fax: +98-2182883581, E-mail:
| | - Seyed Reza Mohebbi
- Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Seyed Reza Mohebbi, Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran. P.O. Box: 14115-331, Tehran, IR Iran. Tel.: +98-2122432515, Fax: +98-2122432516, E-mail:
| | - Hamed Naghoosi
- Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Mohamad Abrahim Tahaei
- Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran
| | | | - Sara Romani
- Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Pedram Azimzadeh
- Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Azar Sanati
- Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Mohammad Reza Zali
- Research Center for Gastroenterology and Liver Disease, Shaheed Beheshti University of Medical Sciences, Tehran, IR Iran
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TNF-α Polymorphisms in Juvenile Idiopathic Arthritis: Which Potential Clinical Implications? Int J Rheumatol 2012; 2012:756291. [PMID: 23133455 PMCID: PMC3485518 DOI: 10.1155/2012/756291] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 07/13/2012] [Accepted: 08/03/2012] [Indexed: 02/06/2023] Open
Abstract
Whether tumor necrosis factor alpha (TNF-α) gene polymorphisms (SNPs) influence disease susceptibility and treatment of patients with juvenile idiopathic arthritis (JIA) is presently uncertain. TNF-α is one of the most important cytokine involved in JIA pathogenesis. Several single nucleotide polymorphisms (SNPs) have been identified within the region of the TNF-α gene but only a very small minority have proven functional consequences and have been associated with susceptibility to JIA. An association between some TNF-α SNPs and adult rheumatoid arthritis (RA) susceptibility, severity and clinical response to anti-TNF-α treatment has been reported. The most frenquetly studied TNF-α SNP is located at -308 position, where a substitution of the G allele with the rare A allele has been found. The presence of the allele -308A is associated to JIA and to a poor prognosis. Besides, the -308G genotype has been associated with a better response to anti-TNF-α therapy in JIA patients, confirming adult data. Psoriatic and oligoarticular arthritis are significantly associated to the -238 SNP only in some works. Studies considering other SNPs are conflicting and inconclusive. Large scale studies are required to define the contribution of TNF-α gene products to disease pathogenesis and anti-TNF-α therapeutic efficacy in JIA.
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