Our aim was to determine whether protein tyrosine phosphatase nonreceptor 22 (PTPN22) C1858T polymorphism (rs2476601) is associated with susceptibility to juvenile idiopathic arthritis (JIA). MEDLINE and EMBASE databases were searched to identify articles in which PTPN22 C1858T polymorphism was reported to be identified in JIA patients and controls. A meta-analysis was conducted to evaluate the association between PTPN22 C1858T polymorphism and RA using allelic contrast. Trial sequential analysis (TSA) was performed. Sixteen separate comparisons involving 5696 JIA patients and 9483 controls (a total of 15,179 subjects) were considered in this meta-analysis. A meta-analysis was performed with all JIA patients as well as JIA patients in each ethnic group. Meta-analysis revealed an association between the T allele of PTPN22 C1858T polymorphism and JIA in all subjects (OR, 1.322; 95% CI, 1.233–1.418; p < .001). Analysis after stratification by ethnicity indicated that the T allele was significantly associated with JIA in the European population (OR, 1.312; 95% CI, 1.2211–1.410; p < .001). However, analysis performed in the non-European population showed no significant association between the T allele and JIA. TSA indicated that the observed association between the PTPN22 polymorphism and JIA in all subjects and the European population is consistent with the existing evidence. This meta-analysis confirms that PTPN22 C1858T polymorphism is associated with susceptibility to JIA in Europeans, and that no additional studies are needed to verify these results. However, current evidence in the non-European population is insufficient, and further studies are warranted.
{"title":"Association between PTPN22 C1858T polymorphism and juvenile idiopathic arthritis: A meta-analysis update with trial sequential analysis","authors":"Young Ho Lee, Gwan Gyu Song","doi":"10.1111/iji.12590","DOIUrl":"10.1111/iji.12590","url":null,"abstract":"<p>Our aim was to determine whether protein tyrosine phosphatase nonreceptor 22 (<i>PTPN22</i>) C1858T polymorphism (rs2476601) is associated with susceptibility to juvenile idiopathic arthritis (JIA). MEDLINE and EMBASE databases were searched to identify articles in which <i>PTPN22</i> C1858T polymorphism was reported to be identified in JIA patients and controls. A meta-analysis was conducted to evaluate the association between <i>PTPN22</i> C1858T polymorphism and RA using allelic contrast. Trial sequential analysis (TSA) was performed. Sixteen separate comparisons involving 5696 JIA patients and 9483 controls (a total of 15,179 subjects) were considered in this meta-analysis. A meta-analysis was performed with all JIA patients as well as JIA patients in each ethnic group. Meta-analysis revealed an association between the T allele of <i>PTPN22</i> C1858T polymorphism and JIA in all subjects (OR, 1.322; 95% CI, 1.233–1.418; <i>p</i> < .001). Analysis after stratification by ethnicity indicated that the T allele was significantly associated with JIA in the European population (OR, 1.312; 95% CI, 1.2211–1.410; <i>p</i> < .001). However, analysis performed in the non-European population showed no significant association between the T allele and JIA. TSA indicated that the observed association between the <i>PTPN22</i> polymorphism and JIA in all subjects and the European population is consistent with the existing evidence. This meta-analysis confirms that <i>PTPN22</i> C1858T polymorphism is associated with susceptibility to JIA in Europeans, and that no additional studies are needed to verify these results. However, current evidence in the non-European population is insufficient, and further studies are warranted.</p>","PeriodicalId":14003,"journal":{"name":"International Journal of Immunogenetics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40545162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ali Jafarpoor, Seyed Mohammad Jazayeri, Farah Bokharaei-Salim, Angila Ataei-Pirkooh, Azam Ghaziasadi, Saber Soltani, Ahmadreza Sadeghi, Shima Sadeghipoor Marvi, Vahdat Poortahmasebi, Seyed Mahmood Seyed Khorrami, Mandana Hasanzad, Negar Parsania, Sina Nagozir, Narges Mokhtari, Ali Parsania, Asma Bahrami, Mohammad Hossein Nadjarha, Reza Pakzad, Masoud Parsania
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the pathogenesis is unclear. Host genetic background is one of the main factors influencing the patients' susceptibility to several viral infectious diseases. This study aimed to investigate the association between host genetic polymorphisms of two genes, including vitamin D receptor (VDR) and vitamin D binding protein (DBP), and susceptibility to COVID-19 in a sample of the Iranian population. This case-control study enrolled 188 hospitalized COVID-19 patients as the case group and 218 suspected COVID-19 patients with mild signs as the control group. The VDR (rs7975232, rs731236 and rs2228570) and DBP (rs7041) gene single nucleotide polymorphisms (SNPs) were genotyped by Polymerase Chain Reaction Restriction – Fragment Length Polymorphism (PCR-RFLP) method. A significant association between rs2228570 SNP in the VDR gene and the susceptibility of COVID-19 was found between case and control groups. The CT genotype (Heterozygous) of rs2228570 C > T polymorphism showed significant association with a 3.088 fold increased odds of COVID-19 (p < .0001; adjusted OR: 3.088; 95% CI: 1.902–5.012). In addition, a significant association between CC genotype of rs2228570 CT polymorphism and increased odds of COVID-19 in male and female groups (p = .001; adjusted OR: 3.125; 95% CI: 1.630–5.991 and p = .002; adjusted OR: 3.071; 95% CI: 1.485–6.354 respectively) were determined. Our results revealed no significant differences in the frequency of genotype and allele of VDR (rs7975232 and rs731236) and DBP (rs7041) between SARS-CoV-2-infected patients and controls (p > .05). Our results showed that polymorphism of VDR (rs2228570) probably could influence individual susceptibility to COVID-19. The polymorphisms of VDR (rs7975232 and rs731236) and DBP (rs7041) were not associated with SARS-CoV-2 infection susceptibility.
{"title":"VDR gene polymorphisms are associated with the increased susceptibility to COVID-19 among iranian population: A case-control study","authors":"Ali Jafarpoor, Seyed Mohammad Jazayeri, Farah Bokharaei-Salim, Angila Ataei-Pirkooh, Azam Ghaziasadi, Saber Soltani, Ahmadreza Sadeghi, Shima Sadeghipoor Marvi, Vahdat Poortahmasebi, Seyed Mahmood Seyed Khorrami, Mandana Hasanzad, Negar Parsania, Sina Nagozir, Narges Mokhtari, Ali Parsania, Asma Bahrami, Mohammad Hossein Nadjarha, Reza Pakzad, Masoud Parsania","doi":"10.1111/iji.12585","DOIUrl":"10.1111/iji.12585","url":null,"abstract":"<p>Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the pathogenesis is unclear. Host genetic background is one of the main factors influencing the patients' susceptibility to several viral infectious diseases. This study aimed to investigate the association between host genetic polymorphisms of two genes, including vitamin D receptor (VDR) and vitamin D binding protein (DBP), and susceptibility to COVID-19 in a sample of the Iranian population. This case-control study enrolled 188 hospitalized COVID-19 patients as the case group and 218 suspected COVID-19 patients with mild signs as the control group. The VDR (rs7975232, rs731236 and rs2228570) and DBP (rs7041) gene single nucleotide polymorphisms (SNPs) were genotyped by Polymerase Chain Reaction Restriction – Fragment Length Polymorphism (PCR-RFLP) method. A significant association between rs2228570 SNP in the VDR gene and the susceptibility of COVID-19 was found between case and control groups. The CT genotype (Heterozygous) of rs2228570 C > T polymorphism showed significant association with a 3.088 fold increased odds of COVID-19 (<i>p</i> < .0001; adjusted OR: 3.088; 95% CI: 1.902–5.012). In addition, a significant association between CC genotype of rs2228570 CT polymorphism and increased odds of COVID-19 in male and female groups (<i>p</i> = .001; adjusted OR: 3.125; 95% CI: 1.630–5.991 and <i>p</i> = .002; adjusted OR: 3.071; 95% CI: 1.485–6.354 respectively) were determined. Our results revealed no significant differences in the frequency of genotype and allele of VDR (rs7975232 and rs731236) and DBP (rs7041) between SARS-CoV-2-infected patients and controls (<i>p</i> > .05). Our results showed that polymorphism of VDR (rs2228570) probably could influence individual susceptibility to COVID-19. The polymorphisms of VDR (rs7975232 and rs731236) and DBP (rs7041) were not associated with SARS-CoV-2 infection susceptibility.</p>","PeriodicalId":14003,"journal":{"name":"International Journal of Immunogenetics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9350092/pdf/IJI-49-243.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40612857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The following sequences have been submitted to the Nomenclature Committee since the January, February and March 2022 nomenclature update (Marsh, 2022) and, following agreed policy, have been assigned official allele designations (Marsh et al., 2010). Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case, you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. In addition, the sequence for the allele C*16:15:01 has been extended to become a new C*16 protein variant. The allele name C*16:15:01has been abandoned and the sequence renamedC*16:201. Furthermore, the allele DPA1*02:64 was found to have an alternative start codon, and has had theQ suffix added, to becomeDPA1*02:64Q. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IPD-IMGT/HLADatabase using the sequence submission tool provided (Robinson et al., 2020). The IPD-IMGT/HLA Databasemay be accessed via theWorldWideWeb at: www.ebi.ac.uk/ ipd/imgt/hla.
{"title":"Nomenclature for factors of the HLA system, update April, May and June 2022","authors":"Steven G. E. Marsh","doi":"10.1111/iji.12591","DOIUrl":"10.1111/iji.12591","url":null,"abstract":"The following sequences have been submitted to the Nomenclature Committee since the January, February and March 2022 nomenclature update (Marsh, 2022) and, following agreed policy, have been assigned official allele designations (Marsh et al., 2010). Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case, you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. In addition, the sequence for the allele C*16:15:01 has been extended to become a new C*16 protein variant. The allele name C*16:15:01has been abandoned and the sequence renamedC*16:201. Furthermore, the allele DPA1*02:64 was found to have an alternative start codon, and has had theQ suffix added, to becomeDPA1*02:64Q. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IPD-IMGT/HLADatabase using the sequence submission tool provided (Robinson et al., 2020). The IPD-IMGT/HLA Databasemay be accessed via theWorldWideWeb at: www.ebi.ac.uk/ ipd/imgt/hla.","PeriodicalId":14003,"journal":{"name":"International Journal of Immunogenetics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40612858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nitin Kumar, Manminder Kaur, Gurjinderpal Singh, Srishti Valecha, Rubanpal Khinda, Mario Di Napoli, Monica Singh, Puneetpal Singh, Sarabjit Mastana
Despite strong genetic implications of NLRP3 inflammasome, its examination as genetic determinant of ischaemic stroke (IS) remains to be done in Punjab, which has been investigated in this study. In this case control study, 400 subjects (200 IS patients, 200 stroke free controls) were included. Contributions of 5 single nucleotide polymorphisms (SNPs) including a functional SNP within NLRP3 gene (rs10754558, rs4612666, rs2027432, rs3738488 and rs1539019) for the risk of IS were investigated through genetic models after correcting the effect of significant variables. Plasma levels of three pro-inflammatory markers, that is, C-reactive protein (CRP), interleukin-1beta (IL-1β) and interleukin-18 (IL-18) were measured by enzyme-linked immunosorbent assays (ELISA). Minor alleles of 3 out of 5 SNPs (rs10754558, rs4612666 and rs1539019) exhibited association with IS risk in additive, recessive and multiplicative models. Multivariable regression analysis confirmed that higher levels of systolic blood pressure (β ± SE: 1.42 ± 0.57, p = .013), CRP (β ± SE: 1.22 ± 0.41, p = .003), IL-1β (β ± SE: 1.78 ± 0.88, p = .043) and IL-18 (β ± SE: 1.13 ± 0.49, p = .021) were independent risk predictors for IS. Haplotype analysis revealed a susceptibility putative haplotype GTGTA, which approximately doubled the IS risk (OR: 1.98, 95% CI: 1.12–3.78, p = .04) in dominant mode after adjusting the effect with confounding variables. This susceptibility putative haplotype GTGTA was significantly associated with increased concentrations of CRP (β = 1.21, p = .014) and IL-1β (β = 1.53, p = .034) in dose-dependent manner (less in carriers of 1 copy than those who had 2 copies of GTGTA).
The present study has revealed a susceptibility putative haplotype GTGTA within NLRP3 gene, carriers of which have double the risk of IS by having increased plasma levels of CRP and IL-1β in a dose-dependent manner.
{"title":"A susceptibility putative haplotype within NLRP3 inflammasome gene influences ischaemic stroke risk in the population of Punjab, India","authors":"Nitin Kumar, Manminder Kaur, Gurjinderpal Singh, Srishti Valecha, Rubanpal Khinda, Mario Di Napoli, Monica Singh, Puneetpal Singh, Sarabjit Mastana","doi":"10.1111/iji.12589","DOIUrl":"10.1111/iji.12589","url":null,"abstract":"<p>Despite strong genetic implications of NLRP3 inflammasome, its examination as genetic determinant of ischaemic stroke (IS) remains to be done in Punjab, which has been investigated in this study. In this case control study, 400 subjects (200 IS patients, 200 stroke free controls) were included. Contributions of 5 single nucleotide polymorphisms (SNPs) including a functional SNP within NLRP3 gene (rs10754558, rs4612666, rs2027432, rs3738488 and rs1539019) for the risk of IS were investigated through genetic models after correcting the effect of significant variables. Plasma levels of three pro-inflammatory markers, that is, C-reactive protein (CRP), interleukin-1beta (IL-1β) and interleukin-18 (IL-18) were measured by enzyme-linked immunosorbent assays (ELISA). Minor alleles of 3 out of 5 SNPs (rs10754558, rs4612666 and rs1539019) exhibited association with IS risk in additive, recessive and multiplicative models. Multivariable regression analysis confirmed that higher levels of systolic blood pressure (<i>β</i> ± SE: 1.42 ± 0.57, <i>p</i> = .013), CRP (<i>β</i> ± SE: 1.22 ± 0.41, <i>p</i> = .003), IL-1β (<i>β</i> ± SE: 1.78 ± 0.88, <i>p</i> = .043) and IL-18 (<i>β</i> ± SE: 1.13 ± 0.49, <i>p</i> = .021) were independent risk predictors for IS. Haplotype analysis revealed a susceptibility putative haplotype GTGTA, which approximately doubled the IS risk (OR: 1.98, 95% CI: 1.12–3.78, <i>p</i> = .04) in dominant mode after adjusting the effect with confounding variables. This susceptibility putative haplotype GTGTA was significantly associated with increased concentrations of CRP (<i>β</i> = 1.21, <i>p</i> = .014) and IL-1β (<i>β</i> = 1.53, <i>p</i> = .034) in dose-dependent manner (less in carriers of 1 copy than those who had 2 copies of GTGTA).</p><p>The present study has revealed a susceptibility putative haplotype GTGTA within NLRP3 gene, carriers of which have double the risk of IS by having increased plasma levels of CRP and IL-1β in a dose-dependent manner.</p>","PeriodicalId":14003,"journal":{"name":"International Journal of Immunogenetics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ff/a5/IJI-49-260.PMC9546049.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40613817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Breast cancer is one of the leading causes of cancer mortality. Growing evidence indicates that interleukins and its polymorphisms are involved in the pathogenesis of breast cancer. Variable number of tandem repeat (VNTR) polymorphism can affect transcription rate, mRNA stability and also the resulting protein expression and activity. Hence, present study aimed to assess the possible association between interleukin-1 receptor antagonist (IL-1Ra) VNTR polymorphism, and breast cancer susceptibility in Iranian population. A total of 300 Iranian individuals, 150 breast cancer patients and 150 age-matched healthy women, were included in this study. DNA extracted by salting out method and genotyping was done using the polymerase chain reaction. The frequency of the allele 2(5% vs. 22%) and the 2/2 genotype (22% vs. 46%) of IL-1Ra VNTR polymorphism was significantly higher in healthy control compared to breast cancer patient: therefore, A2 allele may play a protective role against breast cancer and its progression (p = .0001 and OR = 0.105, 95% CI: [0.044–0.248]). The allele 2 and 2/2 genotype of the IL-Ra VNTR polymorphism can be a protective factor against breast cancer susceptibility.
乳腺癌是导致癌症死亡的主要原因之一。越来越多的证据表明,白细胞介素及其多态性参与了乳腺癌的发病机制。可变数目串联重复序列(VNTR)多态性可以影响转录率、mRNA的稳定性以及由此产生的蛋白的表达和活性。因此,本研究旨在评估白细胞介素-1受体拮抗剂(IL-1Ra) VNTR多态性与伊朗人群乳腺癌易感性之间的可能关联。这项研究共包括300名伊朗人、150名乳腺癌患者和150名年龄匹配的健康妇女。用盐析法提取DNA,用聚合酶链反应进行基因分型。与乳腺癌患者相比,健康对照组IL-1Ra VNTR多态性等位基因2(5% vs 22%)和2/2基因型(22% vs 46%)的频率显著高于乳腺癌患者,因此A2等位基因可能对乳腺癌及其进展具有保护作用(p = 0.0001, OR = 0.105, 95% CI:[0.044-0.248])。IL-Ra VNTR多态性的等位基因2和2/2基因型可能是乳腺癌易感性的保护因素。
{"title":"Association between interleukin-1 receptor antagonist (IL-1ra) VNTR, gene polymorphism and breast cancer susceptibility in Iranian population: Experimental and web-based analysis","authors":"Reza Ibrahimi, Mostafa Ibrahimi, Behzad jamalzei, Mohammad Esmaeil Akbari, Mohsen Navari, Maryam Moossavi, Milad Khorasani","doi":"10.1111/iji.12584","DOIUrl":"10.1111/iji.12584","url":null,"abstract":"<p>Breast cancer is one of the leading causes of cancer mortality. Growing evidence indicates that interleukins and its polymorphisms are involved in the pathogenesis of breast cancer. Variable number of tandem repeat (VNTR) polymorphism can affect transcription rate, mRNA stability and also the resulting protein expression and activity. Hence, present study aimed to assess the possible association between interleukin-1 receptor antagonist (IL-1Ra) VNTR polymorphism, and breast cancer susceptibility in Iranian population. A total of 300 Iranian individuals, 150 breast cancer patients and 150 age-matched healthy women, were included in this study. DNA extracted by salting out method and genotyping was done using the polymerase chain reaction. The frequency of the allele 2(5% vs. 22%) and the 2/2 genotype (22% vs. 46%) of IL-1Ra VNTR polymorphism was significantly higher in healthy control compared to breast cancer patient: therefore, A2 allele may play a protective role against breast cancer and its progression (<i>p</i> = .0001 and OR = 0.105, 95% CI: [0.044–0.248]). The allele 2 and 2/2 genotype of the IL-Ra VNTR polymorphism can be a protective factor against breast cancer susceptibility.</p>","PeriodicalId":14003,"journal":{"name":"International Journal of Immunogenetics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40524906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jaqueline De Azevêdo Silva, Suelen Cristina de Lima, Thiago Sotero Fragoso, Catarina Addobbati Jordão Cavalcanti, Alexandre Domingues Barbosa, Maria Eduarda de Albuquerque Borborema, Thays Maria Costa de Lucena, Angela Luzia Branco Pinto Duarte, Sergio Crovella, Paula Sandrin-Garcia