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Lu T, Wang M, Liu N, Zhang S, Shi L, Bao L, Luo F, Shi L, Liu S, Yao Y. Transporter Associated with Antigen Processing 1 Gene Polymorphisms Increase the Susceptibility to Tuberculosis. Pharmgenomics Pers Med 2023; 16:325-336. [PMID: 37077653 PMCID: PMC10108862 DOI: 10.2147/pgpm.s404339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/31/2023] [Indexed: 04/21/2023] Open
Abstract
Purpose Tuberculosis (TB) is known to result from a complex interaction between the host immune response and Mycobacterium infection. The transporter associated with antigen processing (TAP) plays an important role in the processing and presentation pathways for the Mycobacterium tuberculosis (M. tb) antigen. To investigate the possible association of the TAP1 and TAP2 genes with TB. Patients and Methods A total of 449 TB patients and 435 control subjects were included in this study, and single nucleotide polymorphisms (SNPs) in the TAP gene, as well as TAP1 and TAP2 alleles, were genotyped. Results TAP gene association analysis of TB diseases showed that rs41551515-T in the TAP1 gene was significantly associated with susceptibility to TB (P=7.96E-04, OR=4.124, 95% CI: 1.683-10.102), especially pulmonary TB (PTB, P=6.84E-04, OR=4.350, 95% CI: 1.727-10.945), and the combination of rs1057141-T-rs1135216-C in the TAP1 gene significantly increased the risk of TB susceptibility (P=5.51E-05, OR=10.899, 95% CI: 2.555-46.493). Five novel TAP1 alleles were detected in Yunnan Han people, and the allele frequency of TAP1*unknown_3 (rs41555220-rs41549617-rs1057141-rs1135216-rs1057149-rs41551515: C-A-T-C-C-T) was notably increased in all TB patients, including in the PTB and EPTB subgroups, and was significantly associated with the risk of susceptibility to TB. However, no association between the TAP2 gene and TB was found in this study. Conclusion Host genetic variants of rs41551515-T and the combination rs1057141-T-rs1135216-C, as well as TAP1*unknown_3 may play a critical role in susceptibility to TB disease.
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Affiliation(s)
- Tianchang Lu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Minyi Wang
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
- School of Life Science, Yunnan University, Kunming, 650500, People’s Republic of China
| | - Nannan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Shuqiong Zhang
- Department of Clinical Laboratory, The Third People’s Hospital of Kunming, Kunming, 650041, People’s Republic of China
| | - Lei Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Ling Bao
- Department of Clinical Laboratory, The Third People’s Hospital of Kunming, Kunming, 650041, People’s Republic of China
| | - Feng Luo
- Department of Clinical Laboratory, The Third People’s Hospital of Kunming, Kunming, 650041, People’s Republic of China
| | - Li Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Shuyuan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
- Correspondence: Shuyuan Liu, Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China, Tel +86 871 68334483, Email
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, 650118, People’s Republic of China
- Yufeng Yao, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, 650118, People’s Republic of China, Tel +86 871 68335632, Email
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Tao Y, Han X, Liu N, Shi L, Shi L, Liu S, Yao Y. Association study of TAP and HLA-I gene combination with chronic hepatitis C virus infection in a Han population in China. Int J Immunogenet 2022; 49:169-180. [PMID: 35485366 DOI: 10.1111/iji.12574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/08/2022] [Accepted: 04/03/2022] [Indexed: 11/28/2022]
Abstract
Host immune system genes play key roles in the progression of chronic hepatitis C virus (HCV) infection. Transporters associated with antigen processing (TAP) play an important role in the loading of viral peptides onto MHC class I molecules. This study aimed to investigate the association between TAP gene polymorphisms and chronic HCV in a Chinese Han population. A total of 232 chronic hepatitis C (CHC) patients and 362 healthy individuals were recruited from the Han population in Yunnan province in southwest China, and a TaqMan SNP genotyping assay was used to detect six single nucleotide polymorphisms (SNPs) of TAP1 and three SNPs of TAP2 genes. The association of the TAP gene with CHC was analysed at the allele, genotype, and haplotype levels. There were no significant differences in the allele and genotype frequencies of these SNPs in the TAP gene between CHC patients and controls after Bonferroni correction. A novel TAP1 allele (TAP1*unknown_1: rs41555220-rs41549617-rs1057141-rs1135216-rs1057149-rs41551515: G-G-A-G-G-G) was only present in the CHC group, and this allele significantly increased susceptibility to CHC (p = .005, odds ratio [OR] = 11.105. 95% confidence interval [CI]: 1.362-90.558). Homozygous TAP1*03:01/TAP1*03:01 was observed only in the CHC group that exhibited an obvious risk for CHC (p = .002, OR = 9.637, 95% CI: 1.153-80.574). And the haplotype TAP1*unknown_1-TAP2*01:01 was only present in the CHC group and indicated a significant risk for CHC (p = .002, OR = 9.498, 95% CI: 1.140-79.149). We observed significant interactions among HLA-A, -B,C, TAP1, and TAP2 alleles, and combination analysis revealed that the combination of TAP1*01:01-TAP2*01:01-HLA-B*35:01 was only present in the control group (2.2%) and resulted in significantly increased resistance to CHC (p = .002, OR = 0.096, 95% CI: 0.012-0.759). Whereas, the combination of TAP1*01:01-TAP2*01:01-HLA-C*07:02 and TAP1*03:01-TAP2*01:01-HLA-C*01:02 increased the susceptibility to CHC significantly (p = .001, OR = 2.016, 95% CI: 1.309-3.106 and p = .002, OR = 8.070, 95% CI: 1.018-63.997, respectively). Our results indicated that TAP and HLA-I may exert a combined effect on CHC susceptibility in the Chinese Han population.
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Affiliation(s)
- Yufen Tao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Xue Han
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Nannan Liu
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Lei Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Li Shi
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Shuyuan Liu
- Department of Immunogenetics, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
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Association between TAP gene polymorphisms and tuberculosis susceptibility in a Han Chinese population in Guangdong. Mol Genet Genomics 2022; 297:779-790. [PMID: 35325275 PMCID: PMC8943507 DOI: 10.1007/s00438-022-01885-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/08/2022] [Indexed: 12/02/2022]
Abstract
Tuberculosis (TB) is an important public health problem. Studies indicated that TAP plays a key role in the presentation and transport of antigenic peptides during anti-M.tb infection. Given the important biological role of the TAP gene involved in anti-M.tb infection, a family-based case–control study including 133 tuberculosis patients, 107 healthy household contacts, and 173 healthy controls was conducted to assess the association between TAP gene polymorphisms and TB susceptibility. The basic information of subjects and their blood samples were collected. Four SNPs including rs1135216, rs1057141, rs241447, and rs3819721 were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP). Our results suggested that BMI, residence, bedroom crowding, indoor humidity, fitness activities, history of smoking, and TB exposure history were associated with the occurrence of tuberculosis (P < 0.05). A significant association was observed between the TAP1 rs1135216 CT/CC genotype and increased TB risk, and the ORs were 2.56 (95% CI 1.31–4.99) and 6.73 (95% CI 1.33–34.02), respectively. TAP2 rs3819721 GG genotype carriers also showed an increased risk of TB when compared TB patients to healthy household contacts. Haplotype analysis revealed that the haplotype CT at rs1057141 and rs1135216 (OR = 11.34, 95% CI 1.49–86.56; OR = 7.45, 95% CI 1.43–38.76), as well as TA at rs241447 and rs3819721 (OR = 2.20, 95% CI 1.07–4.56) had a significantly increased risk of TB. The genetic risk scores (GRS) analysis of the four loci indicated that the risk of tuberculosis increased with increasing GRS scores in TB vs HHC (Ptrend = 0.010) and in TB vs HC (Ptrend = 0.001). In conclusion, our findings suggested that the SNPs of rs1135216 and rs3819721 were associated with TB susceptibility among the tuberculosis-prone families in the Chinese Han population and the risk of developing tuberculosis increases with the number of risk alleles, which could help identify high-risk groups in time and take scientific preventive measures. Further cohort studies with large samples are needed to validate the role of TAP gene variants on TB susceptibility.
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Cazarez-Navarro G, Palomares-Marín J, Rodríguez-Preciado SY, Pereira-Suárez AL, Martínez-López E, Bacilio-Medrano EA, Huerta-Olvera S, Hernández-Cañaveral II. Association of TAP1 1177A>G and 2090A>G gene polymorphisms with latent tuberculosis infections in sheltered populations, in the metropolitan area of Guadalajara, Mexico: a pilot study. Rev Inst Med Trop Sao Paulo 2021; 63:e55. [PMID: 34231820 PMCID: PMC8266304 DOI: 10.1590/s1678-9946202163055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/26/2021] [Indexed: 11/21/2022] Open
Abstract
Latent tuberculosis infection (LTBI) is a condition that has no clinical signs and symptoms. LTBI patients are characterized by persistent immune responses to Mycobacterium tuberculosis, and approximately 5-10% of these infected individuals will develop active TB at some point in their lives. The antigen transporter associated with antigen processing (TAP1) is a protein involved in the transport of the antigen from the cytoplasm to the endoplasmic reticulum by means of the association with MHC class I molecules. It plays a fundamental role in the immune response, promoting the clearance of intracellular pathogens. Our pilot study aimed to determine the association between TAP1 gene 1177A>G (rs1057141) and 2090A>G (rs1135216) genetic polymorphisms with susceptibility to LTBI. In this case-control study, 153 individuals from shelters were analyzed (46 were LTBI-positive and 92 were controls). Genotyping of the rs11352216 (2090A>G) and rs1057141 (1177A>G) gene IDs was performed using the Applied Biosystems Step One Thermal Cycler Real-Time PCR allelic discrimination technology. The haplotypic analyses were performed with the Arlequin 3.5 program. Social assistance centers and shelters that serve vulnerable populations represent high-risk sites due to overcrowding and the impaired nutritional status of their residents. The G allele (OR=1.99, CI=1.109-3.587, p=0.021) and the GG genotype of rs11352216 (A>G) were associated with susceptibility to LTBI, according to the codominant genetic model (OR=8.32, CI=1.722-61.98, p=0.007). The rs1057141 (A>G) polymorphism was not associated with LTBI risk. The results suggest that carriers of the G allele of rs1135216 (A>G) are susceptible to LTBI.
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Affiliation(s)
- Gerardo Cazarez-Navarro
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud Guadalajara, Departamento de Microbiología y Patología, Guadalajara, Jalisco, Mexico
| | - Jaime Palomares-Marín
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud Guadalajara, Departamento de Microbiología y Patología, Guadalajara, Jalisco, Mexico
| | - Sergio Yair Rodríguez-Preciado
- Universidad de Guadalajara, Centro Universitario de los Valles, Departamento de Ciencias de la Salud, Ameca, Jalisco, Mexico
| | - Ana Laura Pereira-Suárez
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud Guadalajara, Departamento de Microbiología y Patología, Guadalajara, Jalisco, Mexico
| | - Erika Martínez-López
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud, Departamento de Biología Molecular y Genómica, Guadalajara, Jalisco, Mexico
| | | | - Selene Huerta-Olvera
- Universidad de Guadalajara, Centro Universitario de la Ciénega, Departamento de Ciencias Médicas y de la Vida, Ocotlán, Jalisco, Mexico
| | - Iván Isidro Hernández-Cañaveral
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud Guadalajara, Departamento de Microbiología y Patología, Guadalajara, Jalisco, Mexico
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Associations of genetic variants at TAP1 and TAP2 with pulmonary tuberculosis risk among the Chinese population. Epidemiol Infect 2021; 149:e79. [PMID: 33736739 PMCID: PMC8080186 DOI: 10.1017/s0950268821000613] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis (TB) is a common infectious disease, and the present study aims to explore the associations of single nucleotide polymorphisms (SNPs) at rs1135216 and rs1057141 of transporter-associated antigen processing (TAP1) and rs2228396 of TAP2 with pulmonary tuberculosis (PTB) risk. A case-control study including 168 smear-positive PTB cases and 251 controls was conducted. Genotyping of the SNPs at rs1135216, rs1057141 and rs2228396 was performed, and their associations with PTB risk were analysed with SPSS software version 19.0. After conducting stratification for age, a significant association was detected for rs1057141 with increased PTB risk (OR = 0.17, 95% CI 0.04-0.79) among those aged ≥60 years. For those aged <60 years, a marginally significant association was detected between rs1135216 TC/CC and PTB risk (OR = 1.97, 95% CI 0.93-4.19). Haplotype analysis revealed that the haplotype AT at rs1135216 and rs2228396, as well as AAT at rs1057141, rs1135216 and rs2228396, was associated with increased PTB risk, and the ORs were 2.83 (95% CI 1.30-6.14) and 2.89 (95% CI 1.34-6.27), respectively. Rs1057141 is a genetic predictor of reduced PTB risk for those aged ≥60 years, while rs1135216 might be a potential genetic predictor for those aged <60 years. Haplotype AT at rs1135216 and rs2228396, as well as AAT at rs1057141, rs1135216 and rs2228396, is a genetic marker that may predict PTB risk.
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Palomares-Marin J, Govea-Camacho LH, Araujo-Caballero V, Cazarez-Navarro G, Rodriguez-Preciado SY, Ortiz-Hernandez E, Martinez-Lopez E, Muñoz-Valle JF, Hernandez-Cañaveral II. Association between the TAP1 gene polymorphisms and recurrent respiratory papillomatosis in patients from Western Mexico: A pilot study. J Clin Lab Anal 2021; 35:e23712. [PMID: 33507546 PMCID: PMC8059727 DOI: 10.1002/jcla.23712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 02/05/2023] Open
Abstract
Background Recurrent respiratory papillomatosis (RRP) is a respiratory tract disease that affects children and adults and is characterized by the recurrent proliferation of multiple papillomas. The etiologic agent is the human papillomavirus, mainly genotypes 6 and 11. Furthermore, polymorphisms in TAP1 appear to influence the selection of antigenic peptides and the transport process to the rough endoplasmic reticulum, for their subsequent presentation to T lymphocytes, an essential process against viral diseases and tumor processes. Previous studies have shown that individuals with those polymorphisms are susceptible to immune, infectious, and tumor‐related diseases. The present study aimed to determine the association between the TAP1 rs1057141 (c.1177A>G) and rs1135216 (c.2090A>G) single nucleotide polymorphisms (SNPs) and RRP. Methods A case–control study was carried out on a group of 70 individuals (35 controls and 35 patients). RRP diagnosis, HPV genotyping, and viral load were determined through histology and PCR. SNPs rs1057141 and rs1135216 were identified through allelic discrimination, using real‐time PCR. The haplotypic analyses were performed using the Arlequin 3.5 program. Results HPV‐6 and HPV‐11 were the genotypes found in the samples. In the polymorphism analysis, rs1057141 showed no significant differences (p = 0.049, CI = 0.994–7.331). In contrast, a significant difference was found in rs1135216 (p = 0.039, OR = 2.4) in the allelic analysis, as well as in the dominant (p = 0.027, OR = 3.06), codominant (p = 0.033, OR = 3.06), and additive model (p = 0.043, OR = 2.505) in subjects with the G allele. Conclusion The G allele in rs1135216 was associated with a genetic risk of susceptibility for RRP in a population in Western Mexico.
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Affiliation(s)
- Jaime Palomares-Marin
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Luis Humberto Govea-Camacho
- Servicio de Otorrinolaringología, Cabeza y uello, Centro Médico Nacional de Occidente, IMSS, Guadalajara, México
| | - Vania Araujo-Caballero
- Servicio de Otorrinolaringología, Cabeza y uello, Centro Médico Nacional de Occidente, IMSS, Guadalajara, México
| | - Gerardo Cazarez-Navarro
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Sergio Yair Rodriguez-Preciado
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Enrique Ortiz-Hernandez
- Servicio de Otorrinolaringología, Hospital Civil de Guadalajara Fray Antonio Alcalde, Guadalajara, México
| | - Erika Martinez-Lopez
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Jose Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ivan Isidro Hernandez-Cañaveral
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
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Analysis of transporter associated with antigen presentation (TAP) genes polymorphisms with HIV-1 infection. Mol Cell Biochem 2019; 464:65-71. [PMID: 31732831 PMCID: PMC6949311 DOI: 10.1007/s11010-019-03649-x] [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: 05/28/2019] [Accepted: 11/03/2019] [Indexed: 01/02/2023]
Abstract
Human leukocyte antigen (HLA) class I molecules of the human major histocompatibility complex (MHC) play an important role in modulating immune response. HLA class I molecules present antigenic peptides to CD8+ T cells and thereby play a role in the immune surveillance of cells infected with viruses. TAP1 and TAP2 are MHC-II-encoded genes necessary for the generation of a cellular immune response and polymorphism of these genes can influence the specificity of peptides preferentially presented by the MHC class I molecules and the outcome of the immune response. Several studies implicated genetic variation in TAP genes to various immune-mediated and infectious diseases. To determine the correlation between HIV-1 infection and the TAP1 and TAP2 genes polymorphisms, we performed PCR–RFLP assay of these genes in 500 HIV-1 seropositives and the matched seronegative individuals. Statistical analysis of the data disclosed no correlation between TAP1 (C/T intron 7) gene polymorphism and HIV-1/AIDS disease. However, the current results demonstrated that the heterozygous A/G [OR (95% CI) 1.39 (1.06–1.83), P = 0.0171] and homozygous G/G [OR (95% CI) 3.38(1.56–7.46), P = 0.0010] variants of TAP2 (A/G exon 11) (T665A) gene are positively associated with an increased risk of HIV-1/AIDS infection. This case–control analysis might suggest a possible role of TAP2 (A/G exon 11) (T665A) gene in the susceptibility to HIV-1 infection and disease outcome among North Indian patients.
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The influence of TAP1 and TAP2 gene polymorphisms on TAP function and its inhibition by viral immune evasion proteins. Mol Immunol 2018; 101:55-64. [DOI: 10.1016/j.molimm.2018.05.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 01/03/2023]
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Meng J, Li W, Zhang M, Hao Z, Fan S, Zhang L, Liang C. An update meta-analysis and systematic review of TAP polymorphisms as potential biomarkers for judging cancer risk. Pathol Res Pract 2018; 214:1556-1563. [PMID: 30082158 DOI: 10.1016/j.prp.2018.07.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/26/2018] [Accepted: 07/22/2018] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Transporter associated with antigen processing protein (TAP) is a heterodimer protein consist of TAP1 and TAP2, act a pivotal part in the immune surveillance. In recent days, controversial relationships were reported between TAP polymorphisms and cancer risk, thus, a systematic meta-analysis was performed to resolve this discrepancy. METHODS We searched the PubMed, EMbase, Web of Science, CNKI and Wanfang databases, the cited references were also manually searched again, covering all the papers published until March 25, 2018. Quality assessment was conducted using the Newcastle-Ottawa Scale. All the meta-analysis was conducted with Stata version 12.0 software to assess the strength of the association. RESULTS 4719 cases and 4215 controls from 24 case-control studies related to TAP polymorphisms were enrolled. There was no significant association between TAP1-rs1135216, TAP1-rs4148873, TAP2-rs2228396, TAP2-rs241447 and TAP2-rs4148873 and cancer sensibility. Interestingly, a significant positive association was observed between TAP2 rs4148876 C/T polymorphism and increase cancer risk in homozygote and recessive models. Further in-silico results indicated the expression of TAP2 in cancer tissue is higher than that in normal tissue (cervical cancer, TPM = 70.2 vs. 24.0 respectively, P < 0.01; acute myeloid leukemia, TPM = 52.5 vs. 8.8 respectively, P < 0.01), and influence the survival time of acute myeloid leukemia patients (Log-rank P < 0.05). CONCLUSIONS Our finding suggested that TAP1-rs1135216, TAP1-rs4148873, TAP2-rs2228396, TAP2-rs241447 and TAP2-rs4148873 might not be involved in cancer risk, but the T allele of TAP2-rs4148876 might be a potential biomarker for judging cancer risk, and larger-scale studies are required to confirm our findings.
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Affiliation(s)
- Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China; Graduate School of Anhui Medical University, Hefei, Anhui, China
| | - Wanzhen Li
- Graduate School of Anhui Medical University, Hefei, Anhui, China
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China; Graduate School of Anhui Medical University, Hefei, Anhui, China
| | - Zongyao Hao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Song Fan
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China.
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Abstract
Gastrointestinal tuberculosis (TB) is a fascinating disease which can be observed both in the clinical context of active pulmonary disease and as a primary infection with no pulmonary involvement. It represents a significant clinical challenge because of the resurgence of TB as well as the diagnostic challenges it poses. A high clinical suspicion remains the most powerful tool in an era of medicine when reliance on diagnostic technology increases. Antimicrobial therapy is the mainstay of therapy, but surgical and endoscopic interventions are frequently required for intestinal TB. Gastrointestinal TB is truly the "great mimic" and continues to require the astute clinical acumen of skillful clinicians to diagnose and treat.
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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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Roh EY, Yoon JH, Shin S, Song EY, Park MH. Association of TAP1 and TAP2 genes with susceptibility to pulmonary tuberculosis in Koreans. APMIS 2015; 123:457-64. [DOI: 10.1111/apm.12373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/06/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Eun Youn Roh
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
- Department of Laboratory Medicine; Seoul National University Boramae Medical Center; Seoul Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
- Department of Laboratory Medicine; Seoul National University Boramae Medical Center; Seoul Korea
| | - Sue Shin
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
- Department of Laboratory Medicine; Seoul National University Boramae Medical Center; Seoul Korea
| | - Eun Young Song
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
| | - Myoung Hee Park
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
- Korea Organ Donation Agency Laboratory; Seoul Korea
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Sahajpal R, Kandoi G, Dhiman H, Raj S, Scaria V, Bhartiya D, Hasija Y. HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau112. [PMID: 25502817 PMCID: PMC5630898 DOI: 10.1093/database/bau112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tuberculosis (TB) is an infectious disease caused by fastidious pathogen Mycobacterium tuberculosis. TB has emerged as one of the major causes of mortality in the developing world. Role of host genetic factors that modulate disease susceptibility have not been studied widely. Recent studies have reported few genetic loci that provide impetus to this area of research. The availability of tools has enabled genome-wide scans for disease susceptibility loci associated with infectious diseases. Till now, information on human genetic variations and their associated genes that modulate TB susceptibility have not been systematically compiled. In this work, we have created a resource: HGV&TB, which hosts genetic variations reported to be associated with TB susceptibility in humans. It currently houses information on 307 variations in 98 genes. In total, 101 of these variations are exonic, whereas 78 fall in intronic regions. We also analysed the pathogenicity of the genetic variations, their phenotypic consequences and ethnic origin. Using various computational analyses, 30 variations of the 101 exonic variations were predicted to be pathogenic. The resource is freely available at http://genome.igib.res.in/hgvtb/index.html. Using integrative analysis, we have shown that the disease associated variants are selectively enriched in the immune signalling pathways which are crucial in the pathophysiology of TB. Database URL:http://genome.igib.res.in/hgvtb/index.html
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Affiliation(s)
- Ruchika Sahajpal
- Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | - Gaurav Kandoi
- Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | - Heena Dhiman
- Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | - Sweety Raj
- Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | | | - Vinod Scaria
- Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | - Deeksha Bhartiya
- Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India, GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India and Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
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Ozbas-Gerceker F, Bozman N, Gezici S, Pehlivan M, Yilmaz M, Pehlivan S, Oguzkan-Balci S. Association of TAP1 and TAP2 Gene Polymorphisms with Hematological Malignancies. Asian Pac J Cancer Prev 2013; 14:5213-7. [DOI: 10.7314/apjcp.2013.14.9.5213] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Timofeev AV, Kuzmenko YV, Zharkova II, Starodubova ES, Karpov VL. Activation of transcription of immunoproteasome subunit genes in murine monocytes infected with different mycobacterial strains. Mol Biol 2013. [DOI: 10.1134/s0026893313020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shinde V, Marcinek P, Rani DS, Sunder SR, Arun S, Jain S, Nath I, Thangaraj K, Velavan TP, Valluri VL. Genetic evidence of TAP1 gene variant as a susceptibility factor in Indian leprosy patients. Hum Immunol 2013; 74:803-7. [PMID: 23395648 DOI: 10.1016/j.humimm.2013.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 12/07/2012] [Accepted: 01/14/2013] [Indexed: 02/08/2023]
Abstract
The heterodimeric transporter associated with antigen processing (TAP) gene loci is known to play a vital role in immune surveillance. We investigated a possible association of gene polymorphisms both in TAP1 and TAP2 in a cohort of clinically classified leprosy patients (n=222) and in ethnically matched controls (n=223). The TAP1 and TAP2 genes were genotyped for four single nucleotide polymorphisms TAP1 (rs1057141 Iso333Val and rs1135216 Asp637Gly) and TAP2 (rs2228396 Ala565Thr and rs241447 Ala665Thr) by direct sequencing and ARMS-PCR. The minor allele of TAP1 637G contributes to an increased risk to leprosy compared to controls (OR: 1.68, 95% CI 1.2-2.36, P=0.0057). An increased risk for the variant minor allele of the TAP1 637G to multibacillary (BL+LL) or paucibacillary (BT+TT) infections was also observed [multibacillary vs. controls (OR: 1.56, 95% CI 1.07-2.28, P=0.054); paucibacillary vs. controls (OR: 1.92, 95% CI 1.21-3.01, P=0.013)]. In the dominant model, the genotypes of the TAP1 rs1135216AG+GG additionally contributed to an increased risk. Overall our findings demonstrate that the TAP1 gene variant (rs1135216 Asp637Gly) influences the susceptibility to clinically classified leprosy patients in Indian population.
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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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