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Wenzler AN, van de Loo B, van der Velde N, van Schoor NM. The Effect of Genetic Variations in the Vitamin D Receptor Gene on the Course of Depressive Symptoms. J Nutr 2024; 154:2255-2263. [PMID: 38692355 DOI: 10.1016/j.tjnut.2024.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/03/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Evidence on the association between single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) and depressive symptoms is inconclusive. OBJECTIVES The primary aim of the study was to investigate the association between SNPs in the VDR gene and depressive symptoms. METHODS In a sample of older adults from the Longitudinal Ageing Study Amsterdam (n = 922), depressive symptoms were assessed using the Centre for Epidemiological Studies Depression scale (CES-D scale) at baseline and after 3, 6, and 10 y of follow-up. Blood samples for SNP and serum 25-hydroxyvitamin D3 (25(OH)D3) determination were obtained at baseline. The association between 13 SNPs in the VDR gene and the course of depressive symptoms were evaluated using linear mixed models. The interaction between SNPs and serum 25(OH)D3 in relation to depressive symptoms was evaluated using multiple linear regression. RESULTS No SNPs were associated with the course of depressive symptoms. Significant interactions between serum 25(OH)D3 and SNPs in the VDR gene were found. Stratified analysis revealed that within the GG genotype strata, 10 nmol/L higher serum 25(OH)D3 was associated with 0.27 (95% CI: -0.50, -0.04) and 0.23 (95% CI: -0.48, 0.02) lower scores on the CES-D scale for Cdx-2 and 1b-G-886A, respectively. This association was not found in persons having the GA or AA genotype. CONCLUSIONS No SNPs are associated with the course of depressive symptoms. Stratified analysis shows that the effect of serum 25(OH)D3 concentrations on depressive symptoms is different among genotypes of Cdx-2 and 1b-G-886A. Future research should elucidate on the function of Cdx-2 and 1b-G-886A to describe their effect.
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Affiliation(s)
- Ana Neeltje Wenzler
- Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science Department, Amsterdam, The Netherlands.
| | - Bob van de Loo
- Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science Department, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Internal Medicine, Section of Geriatric Medicine Department, Amsterdam, The Netherlands; Amsterdam Public Health Research Institute, Ageing and Later Life Department, Amsterdam, The Netherlands
| | - Natalie van der Velde
- Amsterdam UMC location University of Amsterdam, Internal Medicine, Section of Geriatric Medicine Department, Amsterdam, The Netherlands; Amsterdam Public Health Research Institute, Ageing and Later Life Department, Amsterdam, The Netherlands
| | - Natasja M van Schoor
- Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science Department, Amsterdam, The Netherlands; Amsterdam Public Health Research Institute, Ageing and Later Life Department, Amsterdam, The Netherlands
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Naidoo L, Arumugam T, Ramsuran V. Host Genetic Impact on Infectious Diseases among Different Ethnic Groups. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2300181. [PMID: 38099246 PMCID: PMC10716055 DOI: 10.1002/ggn2.202300181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/11/2023] [Indexed: 12/17/2023]
Abstract
Infectious diseases such as malaria, tuberculosis (TB), human immunodeficiency virus (HIV), and the coronavirus disease of 2019 (COVID-19) are problematic globally, with high prevalence particularly in Africa, attributing to most of the death rates. There have been immense efforts toward developing effective preventative and therapeutic strategies for these pathogens globally, however, some remain uncured. Disease susceptibility and progression for malaria, TB, HIV, and COVID-19 vary among individuals and are attributed to precautionary measures, environment, host, and pathogen genetics. While studying individuals with similar attributes, it is suggested that host genetics contributes to most of an individual's susceptibility to disease. Several host genes are identified to associate with these pathogens. Interestingly, many of these genes and polymorphisms are common across diseases. This paper analyzes genes and genetic variations within host genes associated with HIV, TB, malaria, and COVID-19 among different ethnic groups. The differences in host-pathogen interaction among these groups, particularly of Caucasian and African descent, and which gene polymorphisms are prevalent in an African population that possesses protection or risk to disease are reviewed. The information in this review could potentially help develop personalized treatment that could effectively combat the high disease burden in Africa.
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Affiliation(s)
- Lisa Naidoo
- School of Laboratory Medicine and Medical SciencesCollege of Health SciencesUniversity of KwaZulu‐NatalDurban4041South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical SciencesCollege of Health SciencesUniversity of KwaZulu‐NatalDurban4041South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical SciencesCollege of Health SciencesUniversity of KwaZulu‐NatalDurban4041South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA)University of KwaZulu‐NatalDurban4041South Africa
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3
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Al-Gharrawi ANR, Anvari E, Fateh A. Association of ApaI rs7975232 and BsmI rs1544410 in clinical outcomes of COVID-19 patients according to different SARS-CoV-2 variants. Sci Rep 2023; 13:3612. [PMID: 36869206 PMCID: PMC9983525 DOI: 10.1038/s41598-023-30859-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/02/2023] [Indexed: 03/05/2023] Open
Abstract
A growing body of research has shown how important vitamin D is in the prognosis of coronavirus disease 19 (COVID-19). The vitamin D receptor is necessary for vitamin D to perform its effects, and its polymorphisms can help in this regard. Therefore, we aimed to evaluate whether the association of ApaI rs7975232 and BsmI rs1544410 polymorphisms in different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants were influential in the outcomes of COVID-19. The polymerase chain reaction-restriction fragment length polymorphism method was utilized to determine the different genotypes of ApaI rs7975232 and BsmI rs1544410 in 1734 and 1450 patients who had recovered and deceased, respectively. Our finding revealed that the ApaI rs7975232 AA genotype in the Delta and Omicron BA.5 and the CA genotype in the Delta and Alpha variants were associated with higher mortality rate. Also, the BsmI rs1544410 GG genotype in the Delta and Omicron BA.5 and the GA genotype in the Delta and Alpha variants were related to a higher mortality rate. The A-G haplotype was linked with COVID-19 mortality in both the Alpha and Delta variants. The A-A haplotype for the Omicron BA.5 variants was statistically significant. In conclusion, our research revealed a connection between SARS-CoV-2 variants and the impacts of ApaI rs7975232 and BsmI rs1544410 polymorphisms. However, more research is still needed to substantiate our findings.
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Affiliation(s)
| | - Enayat Anvari
- Clinical Research Development Unit, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Science, Ilam, Iran.
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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4
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[Vitamin D and polymorphisms of VDR and GC genes in the severity and mortality from COVID-19. A systematic review]. NUTR HOSP 2022; 39:1397-1407. [PMID: 36327123 DOI: 10.20960/nh.04299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Introduction Previous studies have pointed to a possible relationship between vitamin D deficiency and the severity of the disease promoted by SARS-CoV-2, reducing respiratory and cardiovascular complications caused by a hyperreaction of the immune system known as "cytokine storm". This vitamin exerts multiple functions that depend on the presence and levels of different proteins, such as the vitamin D receptor (VDR) and the vitamin D binding protein (DBP), and the existence of single nucleotide polymorphisms (SNPs) of the genes that encode these proteins. The objective of this review is to assess whether some VDR and GC SNPs are risk factors for the most severe forms of COVID-19 disease and whether they condition the response to vitamin D supplementation. A search was performed in PubMed, Google Scholar and Scielo, finding that genotypes in patients affected by COVID-19, were rarely performed, although some studies find a relationship between different alleles and the severity of the disease. The ApaI polymorphism of the VDR gene stands out, as the minor allele "a" increases the risk of mortality from COVID-19 (OR = 11.828, CI: 2,493-56,104, p = 0.002). Results divergency in the efficacy of vitamin D supplementation suggest the need for a larger number of studies. In conclusion, the study of VDR and GC polymorphisms seems essential to effectively treat vitamin D deficiency and particularly to protect against COVID-19. Well-designed studies are needed to elucidate whether plasma vitamin D levels play a role of casuality or causality.
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5
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Resino S, Jiménez-Sousa MÁ, Blanco J, Pacheco YM, del Romero J, Peraire J, Virseda-Berdices A, Muñoz-Gómez MJ, Galera-Peñaranda C, García-Fraile LJ, Benito JM, Rallón N. DBP rs7041 and DHCR7 rs3829251 are Linked to CD4+ Recovery in HIV Patients on Antiretroviral Therapy. Front Pharmacol 2022; 12:773848. [PMID: 35115928 PMCID: PMC8804497 DOI: 10.3389/fphar.2021.773848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/09/2021] [Indexed: 12/03/2022] Open
Abstract
Background: The lack of the recovery of CD4+ T-cells (CD4+ recovery) among immunodeficiency virus (HIV)-infected patients on antiretroviral therapy (ART) is not well known. We aimed to analyze the association between single nucleotide polymorphisms (SNPs) underlying vitamin D metabolism and the CD4+ recovery in naïve HIV-infected patients who started ART with low baseline CD4+. Methods: We conducted a retrospective study in 411 naïve individuals with plasma HIV load >200 copies/mL and CD4+ <200 cells/mm3. During 24 months of follow-up, all patients had plasma HIV load <50 copies/mL. DNA genotyping was performed using the Sequenom MassARRAY platform. The outcome variable was the change in CD4+ during the study. Results: CD4+ recovery was higher in patients carrying DBP rs7041 AA genotype (AA versus CC/AC) and DHCR7 rs3829251 AA genotype (AA versus GG/AG) (p-value < 0.05). DBP rs7041 AA genotype was linked to increase in CD4+ (adjusted arithmetic mean ratio (aAMR) = 1.22; q-value = 0.011), increase in CD4+ ≥P75th [adjusted odds ratio (aOR) = 2.31; q-value = 0.005], slope of CD4+ recovery (aAMR = 1.25; q-value = 0.008), slope of CD4+ recovery ≥ P75th (aOR = 2.55; q-value = 0.005) and achievement of CD4+ ≥500 cells/mm3 (aOR = 1.89; q-value = 0.023). Besides, DHCR7 rs3829251 AA genotype was related to increase in CD4+ (aAMR = 1.43; q-value = 0.031), increase in CD4+ ≥P75th (aOR = 3.92; q-value = 0.030), slope of CD4+ recovery (aAMR = 1.40; q-value = 0.036), slope of CD4+ recovery ≥ P75th (aOR = 3.42; q-value = 0.031) and achievement of CD4+ ≥500 cells/mm3 (aOR = 5.68; q-value = 0.015). Conclusion: In summary, DHCR7 rs3829251 and DBP rs7041 polymorphisms were associated with CD4+ recovery in HIV-infected patients who started cART with low CD4+ T-cell counts.
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Affiliation(s)
- Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Salvador Resino,
| | - María Ángeles Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Julià Blanco
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Virología e Inmunología Celular, IrsiCaixa AIDS Research Institute, Badalona, Spain
| | - Yolanda M. Pacheco
- Laboratorio de Inmunología, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - Jorge del Romero
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Madrid, Spain
| | - Joaquim Peraire
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina Interna, Hospital Universitari de Tarragona Joan XXIII, Tarragona, Spain
| | - Ana Virseda-Berdices
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - María José Muñoz-Gómez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Galera-Peñaranda
- Departamento de Medicina Interna, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Lucio Jesus García-Fraile
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina Interna, Hospital Universitario de La Princesa, Madrid, Spain
| | - José M. Benito
- Laboratorio de Investigación Del VIH y la Hepatitis Viral, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Norma Rallón
- Laboratorio de Investigación Del VIH y la Hepatitis Viral, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Hospital Universitario Rey Juan Carlos, Móstoles, Spain
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6
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Yadav U, Kumar P, Rai V. FokI polymorphism of the vitamin D receptor (VDR) gene and susceptibility to tuberculosis: Evidence through a meta-analysis. INFECTION GENETICS AND EVOLUTION 2021; 92:104871. [PMID: 33901685 DOI: 10.1016/j.meegid.2021.104871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Tuberculosis is one of the top ten causes of deaths worldwide. The deficiency of vitamin D was reported to be associated with the increased susceptibility of tuberculosis. Various previous reports were published to check the association of FokI polymorphism of the vitamin D receptor gene with tuberculosis risk. But their results were inconsistent so, we performed a meta-analysis to know the exact relation of the two. METHODS Different databases were screened up to November 2020 with the keywords "Vitamin D receptor", "VDR", and "FokI", along with "Tuberculosis" and "TB" to find the suitable articles. All the statistical analyses were performed by the Open Meta-Analyst program and all p-values were two-tailed with a significance level of 0.05. RESULTS No statistically significant association was observed in the allele contrast model (ORfvs.F = 1.11, 95%CI = 0.99-1.24, p = 0.05, I2 = 73.46%), in the dominant model (ORff+Ffvs.FF = 1.11, 95%CI = 0.96-1.28, p = 0.14, I2 = 71.39%), and in the co-dominant model (ORFfvs.FF = 1.05, 95%CI = 0.92-1.21, p = 0.41, I2 = 65.97%). However, a significant association was found in the homozygote model (ORffvs.FF = 1.32, 95%CI = 1.03-1.69, p = 0.02, I2 = 67.02%) and in the recessive model (ORFF+Ff vs.ff = 1.26, 95%CI = 1.03-1.54, p = 0.02, I2 = 58.01%). Further analysis was performed on the bases of the ethnicity. In Asian population a significant association was found in the homozygote model (ORffvs.FF = 1.57, 95%CI = 1.12-2.21, p = 0.008, I2 = 70.37%) and in the recessive model (ORFF+Ff vs.ff = 1.43, 95%CI = 1.08-1.89, p = 0.01, I2 = 63.13%). CONCLUSION In conclusion, a significant association of FokI with tuberculosis susceptibility was found in the overall analysis and in the Asian population.
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Affiliation(s)
- Upendra Yadav
- Human Molecular Genetics Laboratory, Department of Biotechnology, VBS Purvanchal University, Jaunpur, UP, India
| | - Pradeep Kumar
- Human Molecular Genetics Laboratory, Department of Biotechnology, VBS Purvanchal University, Jaunpur, UP, India
| | - Vandana Rai
- Human Molecular Genetics Laboratory, Department of Biotechnology, VBS Purvanchal University, Jaunpur, UP, India.
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7
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Silva RCD, Alves NMP, Pereira JJDS, Coelho AVC, Arraes LC, Brandão LAC, Crovella S, Silva JDA. VDR polymorphisms influence immunological response in HIV-1+ individuals undergoing antiretroviral therapy. Genet Mol Biol 2019; 42:351-356. [PMID: 31259360 PMCID: PMC6726152 DOI: 10.1590/1678-4685-gmb-2017-0289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 08/14/2018] [Indexed: 12/25/2022] Open
Abstract
Vitamin D exerts an immuno-modulatory activity on several immune system cells
through the vitamin D receptor (VDR). Herein, we verified that age and a
therapeutic regimen containing protease inhibitors are associated with failures
in antiretroviral therapies (ARVs). In addition, we assessed whether a
VDR SNP (rs11568820: C allele and CC genotype) and GC
(rs2228570-rs11568820) allelic combinations are associated with immunological
failure (p < 0.05). Our findings suggest a possible role of
VDR SNPs on immunological failure in HIV-1+ individuals
undergoing regular ARVs.
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Affiliation(s)
- Ronaldo Celerino da Silva
- Laboratorio de Immunopatologyia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Neyla Maria Pereira Alves
- Laboratorio de Immunopatologyia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.,Departamento of Patologia, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Jorge José de Souza Pereira
- Laboratorio de Immunopatologyia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.,Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Antonio Victor Campos Coelho
- Laboratorio de Immunopatologyia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.,Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Luiz Cláudio Arraes
- Instituto de Medicina Integral de Pernambuco Professor Fernando Figueira, Recife, PE, Brazil
| | - Lucas André Cavalcanti Brandão
- Laboratorio de Immunopatologyia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.,Departamento of Patologia, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Sergio Crovella
- Laboratorio de Immunopatologyia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.,Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Jaqueline de Azevêdo Silva
- Laboratorio de Immunopatologyia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.,Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
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8
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Xu X, Shen M. Associations between vitamin D receptor genetic variants and tuberculosis: a meta-analysis. Innate Immun 2019; 25:305-313. [PMID: 30987490 PMCID: PMC6830906 DOI: 10.1177/1753425919842643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We performed a meta-analysis to evaluate potential associations between
vitamin D receptor (VDR) genetic variants and
tuberculosis (TB). Systematic literature research was conducted in
PubMed, Web of Science, and Embase. We calculated odds ratios (ORs)
and 95% confidence intervals (CIs) to estimate strength of
associations in all possible genetic models, and P
values ≤ 0.05 were considered to be statistically significant. In
total, 42 studies were enrolled for analyses. Pooled overall analyses
suggested that VDR rs1544410 (dominant model:
P = 0.02; allele model:
P = 0.03) and rs731236 (dominant model:
P = 0.04; recessive model:
P = 0.02; allele model: P = 0.01)
variants were significantly associated with TB. Further subgroup
analyses by ethnicity revealed that rs1544410 (dominant and allele
models) and rs731236 (dominant, recessive, and allele models) variants
were both significantly associated with TB in South Asians. When we
stratified data by type of disease, positive results were detected for
rs7975232 variant in EPTB (dominant, recessive, over-dominant, and
allele models) subgroup, and for rs2228570 variant in PTB (dominant,
recessive, and allele models) and EPTB (dominant, recessive,
over-dominant, and allele models) subgroups. Our meta-analysis
supported that rs7975232, rs1544410, rs2228570, and rs731236 variants
might serve as genetic biomarkers of certain types of TB.
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Affiliation(s)
- Xun Xu
- Department of Infectious Diseases, Yu Yao People's Hospital, Yuyao, China
| | - Minghao Shen
- Department of Infectious Diseases, Yu Yao People's Hospital, Yuyao, China
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9
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Jiménez-Sousa MA, Jiménez JL, Fernández-Rodríguez A, Brochado-Kith O, Bellón JM, Gutierrez F, Díez C, Bernal-Morell E, Viciana P, Muñoz-Fernández MA, Resino S. VDR rs2228570 Polymorphism Is Related to Non-Progression to AIDS in Antiretroviral Therapy Naïve HIV-Infected Patients. J Clin Med 2019; 8:jcm8030311. [PMID: 30841566 PMCID: PMC6463017 DOI: 10.3390/jcm8030311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/28/2022] Open
Abstract
Background: Vitamin D is a fundamental regulator of host defenses by activating genes related to innate and adaptive immunity. In this study, we analyzed the association among single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene, with clinical patterns of AIDS progression in antiretroviral treatment (ART)-naïve HIV-infected patients. Methods: We conducted a retrospective study in 667 HIV-infected patients, who were classified within three groups according to their AIDS progression pattern (183 long-term non-progressors (LTNPs), 334 moderate progressors (MPs), and 150 rapid progressors (RPs)). Five VDR SNPs (rs11568820, rs4516035, rs2228570, rs1544410, and rs7975232) were genotyped using Agena Bioscience’s MassARRAY platform. Results: Significant association results were found for rs2228570. Within all HIV patients, the presence of T allele at VDR rs2228570 SNP was protective against AIDS progression (ordinal outcome) under additive (adjusted odds ratio (aOR) = 0.75; p = 0.009), dominant (aOR = 0.69; p = 0.015), and codominant (aOR = 0.56; p = 0.017) inheritance models. In addition, the same allele was protective under additive and codominant inheritance models when we compared with LTNPs vs. RPs [aOR = 0.64 (p = 0.019) and aOR = 0.37 (p = 0.018), respectively] and when we compared MPs vs. RPs [aOR = 0.72 (p = 0.035) and aOR = 0.45 (p = 0.028), respectively]. Conclusions: The VDR rs2228570 T allele was related to a lower AIDS progression pattern in ART-naïve HIV-infected patients. These findings expand upon the knowledge about HIV pathogenesis in untreated HIV-infected patients with different clinical outcomes.
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Affiliation(s)
- María A Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
| | - José Luis Jiménez
- Plataforma de Laboratorio, Hospital General Universitario "Gregorio Marañón", 28007 Madrid, Spain.
- Fundación para la Investigación Biomédica, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), 28007 Madrid, Spain.
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
| | - Oscar Brochado-Kith
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
| | - José María Bellón
- Fundación para la Investigación Biomédica, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), 28007 Madrid, Spain.
| | - Félix Gutierrez
- Unidad de Enfermedades Infecciosas, Hospital General de Elche & Universidad Miguel Hernández, 03202 Alicante, Spain.
| | - Cristina Díez
- Servicio Microbiología, Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario Gregorio Marañon, 28007 Madrid, Spain.
| | - Enrique Bernal-Morell
- Servicio de Enfermedades Infecciosas, Hospital General Universitario Reina Sofia, 30003 Madrid, Spain.
| | - Pompeyo Viciana
- Servicio de Enfermedades Infecciosas, Hospital Virgen del Rocío, 41013 Seville, Spain.
| | - María A Muñoz-Fernández
- Sección Inmunología, Laboratorio Inmuno Biología Molecular, Hospital General Universitario Gregorio Marañón, IiSGM, and Spanish HIV HGM BioBank, 28007 Madrid, Spain.
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28007 Madrid, Spain.
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
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10
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Laplana M, Royo JL, Fibla J. Vitamin D Receptor polymorphisms and risk of enveloped virus infection: A meta-analysis. Gene 2018; 678:384-394. [PMID: 30092343 DOI: 10.1016/j.gene.2018.08.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/04/2018] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Vitamin-D plays a role regulating the immune response against to viral infection. In this sense, vitamin-D deficiency may confer increased susceptibility to enveloped virus infection such as HIV, Hepatitis, Dengue and Respiratory Syncytial virus infection, among others. Vitamin D activity is mediated by its receptor (VDR), which acts as a transcription factor modulating the expression of genes triggering the response against viruses. To date, six major VDR polymorphisms (Cdx, A1012G, FokI, BsmI, ApaI and TaqI) have been studied in the context of viral infection susceptibility. Reported studies show controversial results probably due to statistical lack of power and population genetic differences. AIMS To do a systematic review of the published data and to perform a meta-analysis examining the role of six VDR polymorphisms on infection susceptibility to enveloped virus. RESULTS From all markers and virus considered an association of FokI polymorphism with RSV infection emerges as significant. The worldwide distribution of risk T-allele reveals a lower prevalence in African populations that runs parallel with the relative lower incidence of RSV-associated severe ALRI in children <1 year described in African samples. CONCLUSION The results disclose FokI polymorphism as a relevant variant capturing the association of VDR polymorphisms with viral infection.
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Affiliation(s)
- Marina Laplana
- Department of Basic Medical Sciences, University of Lleida and Institute of Biomedical Research of Lleida (IRBLleida), Lleida, Spain.
| | - José Luis Royo
- Department of Basic Medical Sciences, University of Lleida and Institute of Biomedical Research of Lleida (IRBLleida), Lleida, Spain
| | - Joan Fibla
- Department of Basic Medical Sciences, University of Lleida and Institute of Biomedical Research of Lleida (IRBLleida), Lleida, Spain.
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Stein CM, Sausville L, Wejse C, Sobota RS, Zetola NM, Hill PC, Boom WH, Scott WK, Sirugo G, Williams SM. Genomics of human pulmonary tuberculosis: from genes to pathways. CURRENT GENETIC MEDICINE REPORTS 2017; 5:149-166. [PMID: 29805915 DOI: 10.1007/s40142-017-0130-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Purpose of review Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major public health threat globally. Several lines of evidence support a role for host genetic factors in resistance/susceptibility to TB disease and MTB infection. However, results across candidate gene and genome-wide association studies (GWAS) are largely inconsistent, so a cohesive genetic model underlying TB risk has not emerged. Recent Findings Despite the difficulties in identifying consistent genetic associations, genetic studies of TB and MTB infection have revealed a few well-documented loci. These well validated genes are presented in this review, but there remains a large gap in how these genes translate into better understanding of TB. To address this, we present a pathway based extension of standard association analyses, seeding the results with the best validated genes from candidate gene and GWAS studies. Summary Several pathways were significantly enriched using pathway analyses that may help to explain population patterns of TB risk. In conclusion, we advocate for novel approaches to the study of host genetic analysis of TB that extend traditional association approaches.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Cleveland, OH.,Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - Lindsay Sausville
- Department of Population and Quantitative Health Sciences, Cleveland, OH
| | - Christian Wejse
- Dept of Infectious Diseases/Center for Global Health, Aarhus University, Aarhus, Denmark
| | - Rafal S Sobota
- The Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, IL
| | - Nicola M Zetola
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA 19104, USA.,Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Medicine, University of Botswana, Gaborone, Botswana
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - William K Scott
- Department of Human Genetics and Genomics, University of Miami School of Medicine, Miami, FL
| | - Giorgio Sirugo
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland, OH
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A reappraised meta-analysis of the genetic association between vitamin D receptor BsmI (rs1544410) polymorphism and pulmonary tuberculosis risk. Biosci Rep 2017; 37:BSR20170247. [PMID: 28533426 PMCID: PMC5463263 DOI: 10.1042/bsr20170247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 01/11/2023] Open
Abstract
BsmI (rs1544410) polymorphism located in intron 8 at the 3′-end of the vitamin D receptor (VDR) gene is known to be involved in the regulation of mRNA stability. Many studies evaluated the possible correlation between VDR BsmI polymorphism and the risk of pulmonary tuberculosis (PTB), and reported conflicting results. In the present study, an updated meta-analysis was performed to evaluate the above-said association. PubMed, Embase, and Google Scholar web-databases were searched for the relevant studies and a meta-analysis was performed by calculating pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) for all the genetic models. A total of 19 studies comprising 3644 controls and 2635 cases were included in the present study. Overall no association of PTB in allelic contrast (b compared with B: P=0.285; OR =0.909, 95% CI =0.762–1.083), homozygous (bb compared with BB: P=0.881; OR =0.975, 95% CI =0.700–1.359), heterozygous (bB compared with BB: P=0.834; OR =1.017, 95% CI =0.872–1.185), dominant (bb compared with BB + Bb: P=0.451; OR =0.954, 95% CI =0.843–1.079) and recessive (bb + Bb compared with BB: P=0.983; OR =1.002, 95% CI =0.868–1.156) genetic models in comparison with wild-type allele and genotype BB were observed. However, variant allele (b compared with B: P=0.001; OR =2.289, 95% CI =1.661–3.154) showed increased risk of PTB in Asians. In conclusion, VDR BsmI polymorphism is not a risk factor for PTB in overall population. However, this polymorphism may be interrelated to an increased risk of PTB amongst Asians.
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Abstract
ABSTRACT
Familial risk of tuberculosis (TB) has been recognized for centuries. Largely through studies of mono- and dizygotic twin concordance rates, studies of families with Mendelian susceptibility to mycobacterial disease, and candidate gene studies performed in the 20th century, it was recognized that susceptibility to TB disease has a substantial host genetic component. Limitations in candidate gene studies and early linkage studies made the robust identification of specific loci associated with disease challenging, and few loci have been convincingly associated across multiple populations. Genome-wide and transcriptome-wide association studies, based on microarray (commonly known as genechip) technologies, conducted in the past decade have helped shed some light on pathogenesis but only a handful of new pathways have been identified. This apparent paradox, of high heritability but few replicable associations, has spurred a new wave of collaborative global studies. This review aims to comprehensively review the heritability of TB, critically review the host genetic and transcriptomic correlates of disease, and highlight current studies and future prospects in the study of host genomics in TB. An implicit goal of elucidating host genetic correlates of susceptibility to
Mycobacterium tuberculosis
infection or TB disease is to identify pathophysiological features amenable to translation to new preventive, diagnostic, or therapeutic interventions. The translation of genomic insights into new clinical tools is therefore also discussed.
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Cao Y, Wang X, Cao Z, Cheng X. Vitamin D receptor gene FokI polymorphisms and tuberculosis susceptibility: a meta-analysis. Arch Med Sci 2016; 12:1118-1134. [PMID: 27695504 PMCID: PMC5016579 DOI: 10.5114/aoms.2016.60092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 05/27/2015] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION The association between FokI polymorphism of vitamin D receptor (VDR) and tuberculosis (TB) susceptibility has been investigated previously; however, the results were inconsistent and conflicting. In the present study, a meta-analysis was performed to assess the relationship between VDR FokI gene polymorphism and the risk of TB. MATERIAL AND METHODS Databases including PubMed and Embase were searched for genetic association studies of FokI polymorphism of vitamin D receptor (VDR) and TB. Data were extracted by two independent authors and the pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to assess the strength of the association between VDR FokI gene polymorphism and TB risk. Meta-regression and subgroup analyses were performed to identify the source of heterogeneity. RESULTS Thirty-four studies with a total of 5669 cases and 6525 controls were reviewed in the present meta-analysis. A statistically significant correlation was found between VDR FokI gene polymorphism and increased TB risk in two comparison models: the homozygote model (ff vs. FF: OR = 1.37, 95% CI: 1.17-1.60; Pheterogeneity = 0.001) and the recessive model (ff vs. Ff + FF: OR = 1.32, 95% CI: 1.14-1.52; Pheterogeneity = 0.006). Meta-regression found no source contributing to heterogeneity. However, sub-group analyses revealed that there was a statistically increased TB risk in the East and Southeast Asian population. CONCLUSIONS Synthesis of the available studies suggests that homozygosity for the FokI polymorphism of the VDR gene might be associated with an increased TB risk, especially in the East and Southeast Asian population. Additional well-designed, larger-scale epidemiological studies among different ethnicities are needed.
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Affiliation(s)
- Yan Cao
- Key Laboratory of Tuberculosis Prevention and Treatment, and Beijing Key Laboratory of New Techniques for Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis, 309th Hospital, Beijing, China
| | - Xinjing Wang
- Key Laboratory of Tuberculosis Prevention and Treatment, and Beijing Key Laboratory of New Techniques for Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis, 309th Hospital, Beijing, China
| | - Zhihong Cao
- Key Laboratory of Tuberculosis Prevention and Treatment, and Beijing Key Laboratory of New Techniques for Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis, 309th Hospital, Beijing, China
| | - Xiaoxing Cheng
- Key Laboratory of Tuberculosis Prevention and Treatment, and Beijing Key Laboratory of New Techniques for Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis, 309th Hospital, Beijing, China
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Huang L, Liu C, Liao G, Yang X, Tang X, Chen J. Vitamin D Receptor Gene FokI Polymorphism Contributes to Increasing the Risk of Tuberculosis: An Update Meta-Analysis. Medicine (Baltimore) 2015; 94:e2256. [PMID: 26705207 PMCID: PMC4697973 DOI: 10.1097/md.0000000000002256] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The association between vitamin D receptor (VDR) FokI polymorphism and tuberculosis (TB) risk remains a matter of debate. Potential selection bias exists in most studies using HIV-positive TB patients.An update meta-analysis was carried out to derive a more reliable assessment of the association between FokI polymorphisms and TB risk, especially in HIV-negative TB patients. All major databases from inception to June 2015 were searched for all publications that studied the association between FokI polymorphism and TB risk. The odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) were calculated according to the frequencies of genotypes.In total, 32 studies with 4894 cases and 5319 controls were included in this meta-analysis. In the overall analysis, the estimated OR was 1.34 (95% CI=1.091-1.646, P = 0.005) in the best genetic model (recessive model, ff vs fF+FF) with moderate heterogeneity (I = 32.2%, P = 0.043). In the subgroup analysis stratified by HIV status, significant associations were found only in the HIV-negative TB group (OR = 1.60, 95% CI = 1.180-2.077, P = 0.002; I = 29.5%, and P = 0.141 for heterogeneity). In the subgroup analysis stratified by ethnicity, significant associations were found in the Asian group (OR = 1.65, 95% CI = 1.205-2.261, P = 0.002; I = 43.9%, and P = 0.024 for heterogeneity), but not in the Caucasian group (OR = 1.09, 95% CI = 0.762-1.547, P = 0.649; I = 0.0%, and P = 0.740 for heterogeneity) and African group (OR = 0.99, 95% CI = 0.726-1.341, P = 0.934; I = 43.9%, and P = 0.024 for heterogeneity).This meta-analysis confirms that VDR FokI polymorphism contributes to the risk of TB, especially in HIV-negative TB patients and in the Asian group. Further studies are required to clarify the role of the FokI polymorphism in HIV-positive TB and in other ethnic groups.
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Affiliation(s)
- Liling Huang
- From the Department of Clinical Laboratory (LH, XY); Department of Tuberculosis (CL); Department of Central Laboratory (GL, XT); Department of Science and Education, Longtan Hospital of Guangxi Zhuang Automomous Region, Liuzhou, Guangxi, People's Republic of China (JC)
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Xu C, Tang P, Ding C, Li C, Chen J, Xu Z, Mao Y, Wu M, Zhao J. Vitamin D Receptor Gene FOKI Polymorphism Contributes to Increasing the Risk of HIV-Negative Tuberculosis: Evidence from a Meta-Analysis. PLoS One 2015; 10:e0140634. [PMID: 26485279 PMCID: PMC4618110 DOI: 10.1371/journal.pone.0140634] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/29/2015] [Indexed: 12/15/2022] Open
Abstract
Background Vitamin D receptor (VDR) gene FokI polymorphism have been studied in relation to tuberculosis (TB) in many populations and provided inconsistent results. In this study, we carried out a meta-analysis to derive a more reliable assessment on FokI polymorphism and the risk of HIV-negative TB. Methods The Embase, PubMed, and Cochrane Library databases were used to undertake a comprehensive systematic literature review of all current published VDR gene FOKI association studies aimed at the risk of TB up to June 30, 2015. Odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) were used to measure the strength of the models. Results A total of 14 studies (1,668 cases and 1,893 controls) were retrieved in the meta-analysis. The pooled OR was 1.60 (95% = 1.28–1.97, P<0.001; I2 = 29.5%, and P = 0.141 for heterogeneity) in the best genetic model (recessive model: ff vs. fF+FF). In the subgroup analysis by ethnicities, a significantly increased risk was found in the Asian group (OR = 1.82, 95% CI = 1.42–2.33, P<0.001; I2 = 31.0%, and P = 0.150 for heterogeneity) in the recessive model. Similarly, significant associations were also found in the polymerase chain reaction-restriction fragment length polymorphism group, high-quality studies, and the population based or hospital based groups. Moderate heterogeneity was found in this study. Conclusion Our results suggested that VDR FokI polymorphism contributes to increasing the risk of TB in HIV-negative individuals, especially in the Asian region. Further studies on this topic in other races are expected to be conducted in future.
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Affiliation(s)
- Chun Xu
- Department of Cardiothoracic Surgery, The First Hospital Affiliated to Soochow University, Soochow, Jiangsu, People's Republic of China
| | - Peijun Tang
- Department of Tuberculosis, The Affiliated Infectious Hospital of Soochow University, Soochow, Jiangsu, People's Republic of China
| | - Cheng Ding
- Department of Cardiothoracic Surgery, The First Hospital Affiliated to Soochow University, Soochow, Jiangsu, People's Republic of China
| | - Chang Li
- Department of Cardiothoracic Surgery, The First Hospital Affiliated to Soochow University, Soochow, Jiangsu, People's Republic of China
| | - Jun Chen
- Department of Cardiothoracic Surgery, The First Hospital Affiliated to Soochow University, Soochow, Jiangsu, People's Republic of China
| | - Zhenlei Xu
- Department of Cardiothoracic Surgery, The First Hospital Affiliated to Soochow University, Soochow, Jiangsu, People's Republic of China
| | - Yi Mao
- Department of Cardiothoracic Surgery, The First Hospital Affiliated to Soochow University, Soochow, Jiangsu, People's Republic of China
| | - Meiying Wu
- Department of Tuberculosis, The Affiliated Infectious Hospital of Soochow University, Soochow, Jiangsu, People's Republic of China
- * E-mail: (JZ); (MW)
| | - Jun Zhao
- Department of Cardiothoracic Surgery, The First Hospital Affiliated to Soochow University, Soochow, Jiangsu, People's Republic of China
- * E-mail: (JZ); (MW)
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Facchini L, Venturini E, Galli L, Martino MD, Chiappini E. Vitamin D and tuberculosis: a review on a hot topic. J Chemother 2015; 27:128-38. [DOI: 10.1179/1973947815y.0000000043] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Salimi S, Farajian-Mashhadi F, Alavi-Naini R, Talebian G, Narooie-Nejad M. Association between vitamin D receptor polymorphisms and haplotypes with pulmonary tuberculosis. Biomed Rep 2014; 3:189-194. [PMID: 26075071 DOI: 10.3892/br.2014.402] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/11/2014] [Indexed: 11/05/2022] Open
Abstract
The vitamin D receptor (VDR) is an important factor in activating immune response in different infectious diseases. The aim of the present study was to investigate the association between the VDR gene polymorphisms and pulmonary tuberculosis (PTB). The case control study was performed on 120 PTB patients and 131 healthy controls. Genetic analysis was performed by polymerase chain reaction and the restriction fragment length polymorphism method. The VDR Fok1 Ff genotype was associated with TB and the risk of PTB was two times higher in individuals with the Ff genotype. A higher frequency of f allele was observed in PTB patients and therefore, the f allele may be a risk factor for PTB susceptibility. There were no associations between the Taq1 and Bsm1 polymorphisms and PTB. In addition, haplotype analysis showed that the f-T-B and f-t-b haplotypes (Fok1, Taq1 and Bsm1) may have the potential to increase PTB susceptibility. In conclusion, the Ff genotype and f allele of the VDR Fok1 polymorphism were associated with PTB susceptibility. In addition, the f-T-B and f-t-b haplotypes may be the susceptible haplotypes for PTB.
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Affiliation(s)
- Saeedeh Salimi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran ; Departments of Clinical Biochemistry and Zahedan University of Medical Sciences, Zahedan 9816743175, Iran
| | - Farzaneh Farajian-Mashhadi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran ; Departments of Pharmacology, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran
| | - Roya Alavi-Naini
- Infectious Diseases and Tropical Medicine Research Center, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran ; School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran
| | - Golbarg Talebian
- Infectious Diseases and Tropical Medicine Research Center, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran
| | - Mehrnaz Narooie-Nejad
- Department of Genetics, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran ; Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran
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Areeshi MY, Mandal RK, Akhter N, Panda AK, Haque S. Evaluating the Association between TaqI Variant of Vitamin D Receptor Gene and Susceptibility to Tuberculosis: A Meta-analysis. Toxicol Int 2014; 21:140-7. [PMID: 25253922 PMCID: PMC4170554 DOI: 10.4103/0971-6580.139791] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES Vitamin D has been shown to hamper the growth of Mycobacterium tuberculosis in macrophages. The actions of vitamin D are exerted through a vitamin D receptor (VDR). The genetic variant TaqI of VDR has been implicated in tuberculosis (TB) risk in several case-control studies. However, these studies have shown inconsistent results. Hence, a meta-analysis was conducted to investigate the potential relationship between VDR TaqI polymorphism and risk of developing TB. MATERIALS AND METHODS We performed a quantitative synthesis for published studies based upon the relationship between TaqI polymorphism and TB risk from PubMed (Medline) and Embase databases. The meta-analysis was performed and pooled odds ratios (ORs) and 95% confidence intervals (CIs) were estimated for all genetic models. RESULTS A total of 21 studies including 2,960 TB cases and 3,894 controls were included in this study. The pooled analysis demonstrated no evidence of association between VDR TaqI genotypes and risk of TB in any of the genetic models; variant (t vs T: P = 0.618; OR = 1.051, 95% CI = 0.864-1.278), homozygous (tt vs TT: P = 0.120; OR = 1.336, 95% CI = 0.927-1.924), heterozygous (Tt vs TT: P = 0.925; OR = 0.988, 95% CI = 0.774-1.262), dominant model (tt + Tt vs TT: P = 0.805; OR = 1.032, 95% CI = 0.805-1.322), and recessive model (tt vs TT + Tt: P = 0.180; OR = 1.229, 95% CI = 0.909-1.660). No publication bias was detected during the analysis. CONCLUSIONS Overall findings of this meta-analysis suggest that genetic polymorphism TaqI of VDR gene may not contribute to the risk of TB. However, future larger studies with group of populations are warranted to analyze this relationship.
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Affiliation(s)
- Mohammed Y Areeshi
- Research Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Raju K Mandal
- Department of Urology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Aditya K Panda
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha
| | - Shafiul Haque
- Department of Biosciences, Jamia Millia Islamia, (A Central University), New Delhi, India
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Areeshi MY, Mandal RK, Panda AK, Haque S. Vitamin D Receptor ApaI Gene Polymorphism and Tuberculosis Susceptibility: A Meta-Analysis. Genet Test Mol Biomarkers 2014; 18:323-9. [DOI: 10.1089/gtmb.2013.0451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Raju Kumar Mandal
- Department of Urology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Aditya K. Panda
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Shafiul Haque
- Gene Expression Laboratory, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
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Hu J, Qiu Z, Zhang L, Cui F. Kallikrein 3 and vitamin D receptor polymorphisms: potentials environmental risk factors for prostate cancer. Diagn Pathol 2014; 9:84. [PMID: 24755043 PMCID: PMC4022449 DOI: 10.1186/1746-1596-9-84] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 03/15/2014] [Indexed: 12/31/2022] Open
Abstract
Objective To investigate the relationship and interaction of the single nucleotide polymorphisms (SNPs) of KLK3 and VDR and environmental factors with the predisposition to prostate cancer within Chinese population. Methods The comparison between 108 patients and 242 healthy people was carried out by using the TaqMan/MGB Probe Technology to determine the genotypes of KLK3(rs2735839 is located between KLK2 and KLK3) and VDR (rs731236 is located exon 9). Univariate and multivariate logistic regression model were used to assess the connection of genetic polymorphisms and environmental risk factors with PCa by collecting demographic information, as well as BMI, consumption of cigarettes, alcohol, and tea, exercise, and other environmental risk factors. Results The appearing frequencies of AA, AG, and GG genotypes at the SNPs rs2735839 (A/G) for KLK3 were 13.89%, 62.96% and 23.15% in PCa and 37.19%, 44.63%, 18.18% in control, respectively; these two groups are statistically different (P = 0.00). While the appearing frequencies of TT, TC, and CC genotypes at the SNPs rs731236 (T/C) for VDR were 88.89%, 9, 26%, 1.85% and 90.50%, 9.10%, 0.40% in control, respectively, with no significant statistical difference between the two group. The study confirmed decreasing risk in tea drinkers (OR = 0.58, 95% CI = 0.35-0.96). Conclusions Our studies indicate that environmental factor-tea drinking is associated with the development of PCa. The habit of drinking tea is a protective factor against PCa. The SNPs rs2735839 for KLK3 is strongly related to the development of PCa, while the SNPs rs731236 for VDR is not. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9759981571058803.
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Affiliation(s)
| | | | | | - Feilun Cui
- Department of Urology, People's Hospital Affiliated of Jiangsu University, Zhenjiang 212002, Jiangsu, China.
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Laplana M, Sánchez-de-la-Torre M, Puig T, Caruz A, Fibla J. Vitamin-D pathway genes and HIV-1 disease progression in injection drug users. Gene 2014; 545:163-9. [PMID: 24768180 DOI: 10.1016/j.gene.2014.04.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/17/2014] [Indexed: 11/27/2022]
Abstract
Vitamin-D has pleiotropic effects on calcium and bone metabolism, cellular growth control, cell differentiation and modulation of both innate and acquired immune response. Previous studies revealed the association of vitamin-D receptor gene (VDR) polymorphism with infection diseases including HIV-1 infection. To assess for association between polymorphisms of vitamin-D pathway genes CYP27B1, vitamin-D binding protein (VDBP) and VDR with HIV-1 infection, disease progression to acquired immunodeficiency syndrome (AIDS) was analysed according to CDC93 criteria in a cohort of 185 HIV-1 seroprevalent patients belonging to the injection drug users. Genotype data was obtained from rs10877012, rs3782130 and rs4646536 markers at CYP27B1 locus; rs7041 and rs4588 at VDBP locus; and rs11568820, rs4516035, rs2228570, rs1544410 and rs17878969 at VDR locus. Distribution of genotypes between patients grouped by outcome was compared by contingency table analysis. Marker-marker interaction was assessed by a MDR analysis. Assuming an additive model for VDR markers, a Kaplan-Meier survival analysis was employed to evaluate association with disease progression. Among vitamin-D pathway genes, VDR locus reveals specific 5'UTR and 3'UTR diplotype combinations associated with both, slower and faster progression to AIDS. Marker-marker interaction analysis indicates a strong interaction between VDR markers and a redundant effect for CYP27B1 markers. According to our results, VDR locus association follows an additive model in which increased genetic risk score for the VDR is directly correlated with AIDS progression rates. Our data supports a role of vitamin-D pathway gene variability on HIV-1 disease progression.
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Affiliation(s)
- Marina Laplana
- Unitat de Genètica Humana, Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Catalonia, Spain; Genetic of Complex Disease Research Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), Lleida, Catalonia, Spain
| | - Manuel Sánchez-de-la-Torre
- Unitat de Genètica Humana, Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Catalonia, Spain
| | - Teresa Puig
- Servei de Medicina Interna, Hospital Universitari Arnau de Vilanova, Lleida, Catalonia, Spain
| | - Antonio Caruz
- Immunogenetics Unit, Faculty of Sciences, University of Jaén, Jaén, Spain
| | - Joan Fibla
- Unitat de Genètica Humana, Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Catalonia, Spain; Genetic of Complex Disease Research Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), Lleida, Catalonia, Spain.
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Khalilullah SA, Harapan H, Hasan NA, Winardi W, Ichsan I, Mulyadi M. Host genome polymorphisms and tuberculosis infection: What we have to say? EGYPTIAN JOURNAL OF CHEST DISEASES AND TUBERCULOSIS 2013; 63:173-185. [PMID: 26966339 DOI: 10.1016/j.ejcdt.2013.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Several epidemiology studies suggest that host genetic factors play important roles in susceptibility, protection and progression of tuberculosis infection. Here we have reviewed the implications of some genetic polymorphisms in pathways related to tuberculosis susceptibility, severity and development. Large case-control studies examining single-nucleotide polymorphisms (SNPs) in genes have been performed in tuberculosis patients in some countries. Polymorphisms in natural resistance-associated macrophage protein 1 (NRAMP1), toll-like receptor 2 (TLR2), interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), interleukin-1 receptor antagonist (IL-1RA), IL-10, vitamin D receptor (VDR), dendritic cell-specific ICAM-3-grabbing non-integrin (DC-SIGN), monocyte chemoattractant protein-1 (MCP-1), nucleotide oligomerization binding domain 2 (NOD2), interferon-gamma (IFN-γ), inducible nitric oxide synthase (iNOS), mannose-binding lectin (MBL) and surfactant proteins A (SP-A) have been reviewed. These genes have been variably associated with tuberculosis infection and there is strong evidence indicating that host genetic factors play critical roles in tuberculosis susceptibility, severity and development.
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Affiliation(s)
| | - Harapan Harapan
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Tropical Disease Center, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia
| | - Nabeeh A Hasan
- Research Affiliate, Centre for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Wira Winardi
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Graduate Institute of Medical Science, Taipei Medical University, Taipei, Taiwan
| | - Ichsan Ichsan
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Tropical Disease Center, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Institute of Medical Microbiology and National Reference Center for Systemic Mycosis, University Medical Center Goettingen, Goettingen, Germany
| | - Mulyadi Mulyadi
- Pulmonology Department, School of Medicine, Syiah Kuala University, Banda Aceh, Indonesia
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Chen C, Liu Q, Zhu L, Yang H, Lu W. Vitamin D receptor gene polymorphisms on the risk of tuberculosis, a meta-analysis of 29 case-control studies. PLoS One 2013; 8:e83843. [PMID: 24349552 PMCID: PMC3862802 DOI: 10.1371/journal.pone.0083843] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 11/17/2013] [Indexed: 11/18/2022] Open
Abstract
The relationship of four potentially functional polymorphisms of the vitamin D receptor (VDR) gene, ApaI, BsmI, FokI and TaqI , with tuberculosis susceptibility were considered. The aim of this meta-analysis was to explore the association between the four polymorphisms and tuberculosis risk in different ethnic backgrounds. Eligible case-control studies that were catalogued before April 1st 2013 were enrolled, and the heterogeneity between the studies was evaluated using a χ2 based Q-test. Fixed and random effect models were built to evaluate the association of the four polymorphisms with the risk of tuberculosis, and the association between the four polymorphisms and tuberculosis was expressed as the odds ratio (OR) and 95% confidence interval (CI). Finally, twenty nine qualified studies were enrolled for this meta-analysis that included 6179 tuberculosis cases and 6585 healthy controls. The variant homozygote genotype of the FokI polymorphism was associated with a significantly increased risk of tuberculosis when compared to the heterozygote and wild type homozygote genotypes in the Chinese population (ff vs. Ff+FF: ORrecessive=1.97, 95%CI: 1.32-2.93, Pbonferroni=0.0032; heterogeneity test: χ2=0.24, P=0.62). For European subjects, the homozygote and heterozygote genotypes of the BsmI polymorphism were associated with a significantly decreased risk of tuberculosis when compared to the wild type homozygote (bb+Bb vs. BB: ORdominant=0.41, 95%CI, 0.22-0.76, Pbonferroni=0.02; heterogeneity test: χ2=2.59, P=0.11). Based on the above results, we conclude that variants of the VDR gene that are homozygous for the FokI polymorphism might be more susceptible to tuberculosis in Chinese. Furthermore, larger sample studies are warranted to confirm the protective effects of BsmI variants on tuberculosis in the Europeans.
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Affiliation(s)
- Cheng Chen
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Haitao Yang
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
- * E-mail:
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Abstract
BACKGROUND Vitamin D deficiency is common in HIV infection and has been associated with advanced disease. This study investigated whether vitamin D-related genetic variants were associated with disease progression in HIV-infected children. METHODS The Fok-I (C/T), Bsm-I (G/A), GC (A/C), DHCR7 (G/T) and CYP2R1 (G/A) genetic variants were detected by real-time polymerase chain reaction in HIV-infected children who participated in the Pediatric AIDS Clinical Trials Group P152 and P300 protocols, which predated the availability of effective combination antiretroviral therapy. The primary endpoints included time to progression to the first HIV-related disease endpoint (≥2 opportunistic infection, weight growth failure) or death, which constituted the progression-free survival. Analyses were performed for age>2 years and ≤2 years separately adjusting for race and treatment effect. RESULTS Of the 998 children evaluated, 139 experienced HIV disease progression. For children>2 years, rapid disease progression was associated with the DHCR7 G allele compared with the T allele (G/G vs. T/T: hazard ratio [HR]=5.0, P = 0.035; G/T vs. T/T: HR=4.5, P=0.042; G/G+G/T vs. T/T: HR=4.8, P=0.036) and the Bsm-I A allele compared with the G allele (A/G vs. G/G: HR=2.2, P=0.014 and A/G+A/A vs. G/G: HR=2.0, P=0.026). In children≤2 years, the Bsm-I A allele increased the risk of disease progression in Hispanics (A/A vs. G/A+G/G: HR=2.8, P=0.03 and A/A vs. G/G: HR=2.8, P=0.046) and whites (A/A vs. G/G: HR=6.6, P=0.025 and A/A vs. G/A+G/G: HR=3.6, P=0.038). CONCLUSIONS Vitamin D-related host genetic variants that alter the availability and activity of vitamin D are associated with risk of HIV disease progression in children and may vary by age and race.
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Sortica VA, Cunha MG, Ohnishi MDO, Souza JM, Ribeiro-dos-Santos ÂKC, Santos SEB, Hutz MH. Role of IL6, IL12B and VDR gene polymorphisms in Plasmodium vivax malaria severity, parasitemia and gametocytemia levels in an Amazonian Brazilian population. Cytokine 2013; 65:42-7. [PMID: 24139871 DOI: 10.1016/j.cyto.2013.09.014] [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: 05/28/2013] [Revised: 09/09/2013] [Accepted: 09/19/2013] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To investigate the influence of IL6, IL12B and VDR single nucleotide polymorphisms (SNPs) in uncomplicated Plasmodium vivax infection symptoms intensity, parasitemia and gametocytemia levels in a Brazilian Amazonian population. METHODS A total of 167 malaria patients infected by P. vivax have parasitemia and gametocytemia levels estimated before treatment. Fourteen clinical symptoms were evaluated and included in a principal component analysis to derive a clinical symptom index. Patients were genotyped for IL6-174C>G, IL12B 735T>C, 458A>G, 159A>C, and VDR FokI, TaqI, BsmI SNPs by Taqman 5' nuclease assays. A General Linear Model analysis of covariance with age, gender, exposure period and infection history and genetic ancestry was performed to investigate the association of genotypes with parasitemia and gametocytemia levels and with a clinical symptom index. RESULTS Higher parasitemia levels were observed in IL6-174C carriers (p=0.02) whereas IL12B CGT haplotype carriers presented lower parasitemia levels (p=0.008). VDR TaqIC/BsmIA haplotype carriers showed higher gametocyte levels than non-carriers (p=0.013). Based on the clinical index values the IL6-174C>G polymorphism was associated with malaria severity. The IL6-174C carriers presented a more severe clinical index when compared to GG homozygotes (p=0.001). CONCLUSION The present study suggests that IL6, IL12 and VDR influence severity, parasitemia and gametocytemia clearance in P. vivax infections, and highlights their potential role in malaria immune response in an Amazonian population.
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Affiliation(s)
- Vinicius A Sortica
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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López Campos GN, Velarde Félix JS, Sandoval Ramírez L, Cázares Salazar S, Corona Nakamura AL, Amaya Tapia G, Prado Montes de Oca E. Polymorphism in cathelicidin gene (CAMP) that alters Hypoxia-inducible factor (HIF-1α::ARNT) binding is not associated with tuberculosis. Int J Immunogenet 2013; 41:54-62. [DOI: 10.1111/iji.12080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/01/2013] [Accepted: 07/15/2013] [Indexed: 12/27/2022]
Affiliation(s)
- G. N. López Campos
- In silico Laboratory; Pharmaceutical and Medical Biotechnology Unit; Research Center in Technology and Design Assistance of Jalisco State (CIATEJ, AC); National Council of Science and Technology; Guadalajara Mexico
| | - J. S. Velarde Félix
- Biology Academic Unit; Sinaloa Autonomous University (UAS); Culiacán México
- Genomic Medicine Center; Dr. Bernardo J. Gastelum Culiacán Primary Care Hospital; Health Ministry (SS); Culiacán Mexico
| | - L. Sandoval Ramírez
- Genetics Division; Western Biomedical Research Center; National Institute of Social Security (CIBO-IMSS); Guadalajara Mexico
| | - S. Cázares Salazar
- Biology and Chemistry Sciences Faculty; Sinaloa Autonomous University (FCQB-UAS); Culiacán Mexico
| | - A. L. Corona Nakamura
- Infectology Service; External Attention Medical Unit (UMAE); Western National Medical Center (CMNO); Specialty Hospital; National Institute of Social Security (IMSS); Guadalajara Mexico
| | - G. Amaya Tapia
- Infectology Service; Primary Care Western Hospital; Health Ministry of Jalisco State (SSJ); Guadalajara Mexico
| | - E. Prado Montes de Oca
- In silico Laboratory; Pharmaceutical and Medical Biotechnology Unit; Research Center in Technology and Design Assistance of Jalisco State (CIATEJ, AC); National Council of Science and Technology; Guadalajara Mexico
- Molecular Biology Laboratory; Biosecurity Area, Pharmaceutical and Medical Biotechnology Unit; Research Center in Technology and Design Assistance of Jalisco State (CIATEJ, AC); National Council of Science and Technology (CONACYT); Guadalajara Mexico
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Wu YJ, Yang X, Wang XX, Qiu MT, You YZ, Zhang ZX, Zhu SM, Xu L, Tang FL. Association of vitamin D receptor BsmI gene polymorphism with risk of tuberculosis: a meta-analysis of 15 studies. PLoS One 2013; 8:e66944. [PMID: 23825591 PMCID: PMC3692555 DOI: 10.1371/journal.pone.0066944] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/12/2013] [Indexed: 11/19/2022] Open
Abstract
Background Genetic variations in vitamin D receptor (VDR) may contribute to tuberculosis (TB) risk. Many studies have investigated the association between VDR BsmI gene polymorphism and TB risk, but yielded inconclusive results. Methodology/Principal Findings We performed a comprehensive meta-analysis of 15 publications with a total of 2309 cases and 3568 controls. We assessed the strength of the association between VDR BsmI gene polymorphism and TB risk and performed sub-group analyses by ethnicity, sample size and Hardy–Weinberg equilibrium (HWE). We found a statistically significant correlation between VDR BsmI gene polymorphism and decreased TB risk in four comparison models: allele model (b vs. B: OR = 0.78, 95% CI = 0.67, 0.89; Pheterogeneity = 0.004), homozygote model (bb vs. BB: OR = 0.61, 95% CI = 0.43, 0.87; Pheterogeneity = 0.001), recessive model (bb vs. Bb+BB: OR = 0.70, 95% CI = 0.56, 0.88; Pheterogeneity = 0.005) and dominant model (bb+Bb vs. BB: OR = 0.77, 95% CI = 0.61, 0.97; Pheterogeneity = 0.010), especially in studies based on Asian population. Sub-group analyses also revealed that there was a statistically decreased TB risk in “small” studies (<500 participants) and studies with PHWE>0.5. Meta-regression and stratification analysis both showed that the ethnicity and sample size contributed to heterogeneity. Conclusions This meta-analysis suggests that VDR BsmI gene polymorphism is associated with a significant decreased TB risk, especially in Asian population.
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Affiliation(s)
- Yu-jiao Wu
- Department of Pharmacy, Changzhou Third People’s Hospital, Changzhou, China
- College of Pharmacy, Soochow University, Suzhou, China
| | - Xin Yang
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Nanjing, China
| | - Xiao-xiao Wang
- Department of Bio-statistics, Georgia Health Science University, Augusta, Georgia, United States of America
| | - Man-Tang Qiu
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Nanjing, China
| | - Yi-zhong You
- Department of Pharmacy, Changzhou First People’s Hospital, Changzhou, China
| | - Zhi-xin Zhang
- Department of Pulmonary Tuberculosis, Changzhou Third People’s Hospital, Changzhou, China
| | - Shan-mei Zhu
- Department of Pharmacy, Changzhou Third People’s Hospital, Changzhou, China
| | - Lin Xu
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Nanjing, China
- * E-mail: (LX); (F-lT)
| | - Feng-lei Tang
- Department of Pharmacy, Changzhou Third People’s Hospital, Changzhou, China
- * E-mail: (LX); (F-lT)
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Bandiera S, Cartault F, Jannot AS, Hatem E, Girard M, Rifai L, Loiseau C, Munnich A, Lyonnet S, Henrion-Caude A. Genetic variations creating microRNA target sites in the FXN 3'-UTR affect frataxin expression in Friedreich ataxia. PLoS One 2013; 8:e54791. [PMID: 23382970 PMCID: PMC3559822 DOI: 10.1371/journal.pone.0054791] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/14/2012] [Indexed: 11/18/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a severe neurodegenerative disease caused by GAA repeat expansion within the first intron of the frataxin gene. It has been suggested that the repeat is responsible for the disease severity due to impaired transcription thereby reducing expression of the protein. However, genotype-phenotype correlation is imperfect, and the influence of other gene regions of the frataxin gene is unknown. We hypothesized that FRDA patients may harbor specific regulatory variants in the 3'-UTR. We sequenced the 3'-UTR region of the frataxin gene in a cohort of 57 FRDA individuals and 58 controls. Seven single nucleotide polymorphisms (SNPs) out of 19 were polymorphic in our case-control sample. These SNPs defined several haplotypes with one reaching 89% of homozygosity in patients versus 24% in controls. In another cohort of 47 FRDA Reunionese patients, 94% patients were found to be homozygous for this haplotype. We found that this FRDA 3'-UTR conferred a 1.2-fold decrease in the expression of a reporter gene versus the alternative haplotype configuration. We established that differential targeting by miRNA could account for this functional variability. We specifically demonstrated the involvement of miR-124 (i.e hsa-mir-124-3p) in the down-regulation of FRDA-3'-UTR. Our results suggest for the first time that post-transcriptional regulation of frataxin occurs through the 3'-UTR and involves miRNA targeting. We propose that the involvement of miRNAs in a FRDA-specific regulation of frataxin may provide a rationale to increase residual levels of frataxin through miRNA-inhibitory molecules.
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Affiliation(s)
- Simonetta Bandiera
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - François Cartault
- INSERM U781 Hôpital Necker–Enfants Malades, Paris, France
- Département de Génétique, Centre Hospitalier Régional de La Réunion, Saint-Denis, La Réunion, France
| | - Anne-Sophie Jannot
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Elie Hatem
- INSERM U781 Hôpital Necker–Enfants Malades, Paris, France
| | - Muriel Girard
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Laila Rifai
- Department of Medical Genetics, National Institute of Health, Rabat, Morocco
| | | | - Arnold Munnich
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Stanislas Lyonnet
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Alexandra Henrion-Caude
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
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Non-HLA gene polymorphisms and their implications on dengue virus infection. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2013. [DOI: 10.1016/j.ejmhg.2012.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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Abstract
Tuberculosis (TB) is a leading cause worldwide of human mortality attributable to a single infectious agent. Recent studies targeting candidate genes and "case-control" association have revealed numerous polymorphisms implicated in host susceptibility to TB. Here, we review current progress in the understanding of causative polymorphisms in host innate immune genes associated with TB pathogenesis. We discuss genes encoding several types of proteins: macrophage receptors, such as the mannose receptor (MR, CD206), dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN, CD209), Dectin-1, Toll-like receptors (TLRs), complement receptor 3 (CR3, CD11b/CD18), nucleotide oligomerization domain 1 (NOD1) and NOD2, CD14, P2X7, and the vitamin D nuclear receptor (VDR); soluble C-type lectins, such as surfactant protein-A (SP-A), SP-D, and mannose-binding lectin (MBL); phagocyte cytokines, such as tumor necrosis factor (TNF), interleukin-1β (IL-1β), IL-6, IL-10, IL-12, and IL-18; chemokines, such as IL-8, monocyte chemoattractant protein 1 (MCP-1), RANTES, and CXCL10; and other important innate immune molecules, such as inducible nitric oxide synthase (iNOS) and solute carrier protein 11A1 (SLC11A1). Polymorphisms in these genes have been variably associated with susceptibility to TB among different populations. This apparent variability is probably accounted for by evolutionary selection pressure as a result of long-term host-pathogen interactions in certain regions or populations and, in part, by lack of proper study design and limited knowledge of molecular and functional effects of the implicated genetic variants. Finally, we discuss genomic technologies that hold promise for resolving questions regarding the evolutionary paths of the human genome, functional effects of polymorphisms, and corollary impacts of adaptation on human health, ultimately leading to novel approaches to controlling TB.
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Affiliation(s)
- Abul K. Azad
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology
| | - Wolfgang Sadee
- Department of Pharmacology, Program in Pharmacogenomics, The Ohio State University, Columbus, Ohio, USA
| | - Larry S. Schlesinger
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology
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Price P, Haddow LJ, Affandi J, Agarwal U, Easterbrook PJ, Elliott J, French M, Kumar M, Moosa MYS, Oliver B, Singh S, Sola M, Saphonn V, Vun MC. Short communication: Plasma levels of vitamin D in HIV patients initiating antiretroviral therapy do not predict immune restoration disease associated with Mycobacterium tuberculosis. AIDS Res Hum Retroviruses 2012; 28:1216-9. [PMID: 22280097 DOI: 10.1089/aid.2011.0272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Immune restoration disease associated with Mycobacterium tuberculosis (TB IRD) is clinically important among HIV patients commencing antiretroviral therapy in countries where tuberculosis is endemic. Vitamin D affects dendritic cell and T cell function and the antimicrobial activity of monocytes. Plasma levels of vitamin D and polymorphisms in the vitamin D receptor may affect tuberculosis, and HIV infection associates with vitamin D deficiency. Here we assess whether plasma vitamin D levels may predict TB IRD. Samples were available from prospective studies of TB IRD in Cambodia (26 cases), India (19 cases), and South Africa (29 cases). IRD cases and controls from each site were similar in age and baseline CD4(+) T cell count. Plasma samples were assessed using 25(OH) vitamin D immunoassay plates. DNA samples were available from a subset of patients and were genotyped for the VDR FokI (F/f) [C/T, rs10735810] SNP. When data from each cohort were pooled to assess ethnic/geographic differences, 25(OH)D levels were higher in Cambodian than Indian or South African patients (p<0.0001) and higher in South African than Indian patients (p<0.0001). TB IRD was not associated with differences in levels of 25(OH)D in any cohort (p=0.36-0.82), irrespective of the patients' prior TB diagnoses/treatment. Carriage of the minor allele of VDR FokI (F/f) was marginally associated with TB IRD in Indian patients (p=0.06) with no association in Cambodians. Neither plasma levels of vitamin D nor the vitamin D allele will usefully predict TB IRD in diverse populations from TB endemic regions.
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Affiliation(s)
- Patricia Price
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Australia.
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Higa GM, Hicks J, Isabella C. Adjudication of the alleged role of vitamin d in the antimicrobial pathway. SCIENTIFICA 2012; 2012:129516. [PMID: 24278668 PMCID: PMC3820478 DOI: 10.6064/2012/129516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/13/2012] [Indexed: 06/02/2023]
Abstract
Dynamic interactions between microorganism and host have evolved in such a way that while microbial pathogens are the cause of many human infections, a symbiotic relationship is also known to exist. Another important anomaly is that exposure to pathogenic organisms does not necessarily result in development of clinical disease. The latter conclusion infers that susceptibility to infectious disease can be modified by host-related factors. Arguably the two most prominent factors are genetic variability and immunologic status of the exposed individual. Because of the Human Genome and the HapMap projects, developments in genotyping technology have brought the possibility of identifying associations between specific genetic alterations and common diseases closer to reality. In addition, a growing body of evidence suggests vitamin D has an important contributory role in the antimicrobial pathway.
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Affiliation(s)
- Gerald M. Higa
- Schools of Pharmacy and Medicine and the Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Jason Hicks
- School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
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Qidwai T, Jamal F, Khan MY. DNA Sequence Variation and Regulation of Genes Involved in Pathogenesis of Pulmonary Tuberculosis. Scand J Immunol 2012; 75:568-87. [DOI: 10.1111/j.1365-3083.2012.02696.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Raghavan S, Alagarasu K, Selvaraj P. Immunogenetics of HIV and HIV associated tuberculosis. Tuberculosis (Edinb) 2012; 92:18-30. [PMID: 21943869 DOI: 10.1016/j.tube.2011.08.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/08/2011] [Indexed: 11/28/2022]
Affiliation(s)
- S Raghavan
- Department of Immunology, Tuberculosis Research Centre (ICMR), Mayor V.R. Ramanathan Road, Chetput, Chennai 600031, India
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Zhang C, Zhao L, Ma L, Lv C, Ding Y, Xia T, Wang J, Dou X. Vitamin D status and expression of vitamin D receptor and LL-37 in patients with spontaneous bacterial peritonitis. Dig Dis Sci 2012; 57:182-8. [PMID: 21755299 DOI: 10.1007/s10620-011-1824-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 06/30/2011] [Indexed: 12/11/2022]
Abstract
BACKGROUND Vitamin D, which exerts its effect through vitamin D receptor (VDR), and LL-37, a vitamin D-dependent antimicrobial peptide, are involved in many infectious diseases. AIM The objective of this study was to evaluate whether vitamin D status and expressions of VDR and LL-37 are involved in the pathogenesis of spontaneous bacterial peritonitis (SBP). METHODS Serum and ascitic fluid 25-dihydroxyvitamin D [25(OH)D] concentrations and levels of VDR and LL-37 in peritoneal leukocytes were measured by ELISA and real-time PCR methods in cirrhotic patients with SBP (n = 19) and cirrhotic patients with simple ascites (n = 28). The correlations between these levels and clinical variables were evaluated. RESULTS Cirrhotic patients with ascites showed low vitamin D concentrations in both serum and ascitic fluid. Lower serum vitamin D concentrations were observed in cirrhotic patients with Child-Pugh C class. 25(OH)D concentrations in ascitic fluid were positive correlated with that in serum (r = 0.74, P < 0.001). The SBP group showed significantly higher levels of both VDR and LL-37 mRNA expressions in peritoneal leukocytes than the simple ascites group (P = 0.005 and P = 0.003, respectively). In the SBP group, VDR and LL-37 expressions in peritoneal leukocytes were positively correlated (r = 0.70, P = 0.001). CONCLUSIONS Vitamin D insufficiency was universal among cirrhotic patients with ascites, and the situation was more severe with more serious cirrhosis. Expressions of peritoneal leukocytes VDR and LL-37 genes were simultaneously up-regulated in cirrhotic patients with SBP when compared with cirrhotic patients with simple ascites. It is indicated that the vitamin D-VDR system and its downstream gene, LL-37, are involved in the pathogenesis and antibacterial immune response to SBP.
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Affiliation(s)
- Chong Zhang
- Department of Infectious Diseases, Shengjing Hospital Affiliated to China Medical University, Shenyang 110004, China
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Prostate cancer susceptibility Loci identified on chromosome 12 in African Americans. PLoS One 2011; 6:e16044. [PMID: 21358824 PMCID: PMC3040176 DOI: 10.1371/journal.pone.0016044] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/06/2010] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PCa) is a complex disease that disproportionately affects African Americans and other individuals of African descent. A number of regions across the genome have been associated to PCa, most of them with moderate effects. A few studies have reported chromosomal changes on 12p and 12q that occur during the onset and development of PCa but to date no consistent association of the disease with chromosome 12 polymorphic variation has been identified. In order to unravel genetic risk factors that underlie PCa health disparities we investigated chromosome 12 using ancestry informative markers (AIMs), which allow us to distinguish genomic regions of European or West African origin, and tested them for association with PCa. Additional SNPs were genotyped in those areas where significant signals of association were detected. The strongest signal was discovered at the SNP rs12827748, located upstream of the PAWR gene, a tumor suppressor, which is amply expressed in the prostate. The most frequent allele in Europeans was the risk allele among African Americans. We also examined vitamin D related genes, VDR and CYP27B1, and found a significant association of PCa with the TaqI polymorphism (rs731236) in the former. Although our results warrant further investigation we have uncovered a genetic susceptibility factor for PCa in a likely candidate by means of an approach that takes advantage of the differential contribution of parental groups to an admixed population.
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Tripathi G, Sharma R, Sharma RK, Gupta SK, Sankhwar SN, Agrawal S. Vitamin D receptor genetic variants among patients with end-stage renal disease. Ren Fail 2010; 32:969-77. [DOI: 10.3109/0886022x.2010.501934] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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