Association of interleukin 1 receptor antagonist intron 2 variable number of tandem repeats polymorphism with vitiligo susceptibility in Gujarat population

Background: Vitiligo is a multifactorial, polygenic, autoimmune skin disorder caused by selective destruction of melanocytes. Interleukin 1 receptor antagonist intron 2 polymorphism was found to be associated with various autoimmune disorders. Aims: We aimed to investigate the association of interleukin 1 receptor antagonist intron 2 variable number of tandem repeats polymorphism (rs2234663) with vitiligo to assess interleukin 1 receptor antagonist transcript levels and to perform possible genotype–phenotype correlation. Methods: Three hundred and seven vitiligo patients and 316 controls were enrolled in the study, genotyping of interleukin 1 receptor antagonist rs2234663 was performed by polymerase chain reaction, and relative gene expression of interleukin 1 receptor antagonist was carried out in peripheral blood mononuclear cells from patients (n = 36) and controls (n = 36) by real-time-PCR. Results: A significant difference was observed in the frequency of interleukin 1 receptor antagonist *A (1/2) genotype among patients with active and stable vitiligo (P = 0.0172). Interleukin 1 receptor antagonist*A (2/2) genotype and allele frequencies were significantly different between SV patients and controls (P = 0.0246 and P = 0.0046, respectively). Significant difference was also observed for interleukin 1 receptor antagonist*A2 (allele) in active and stable vitiligo patients (P = 0.0060). However, other comparisons did not show any significant difference in genotype and allele frequencies. Moreover, interleukin 1 receptor antagonist*A (3/2) genotype was observed only in patients whereas interleukin 1 receptor antagonist*A (5/2) was observed only in controls. Gene expression analysis showed no significant difference in interleukin 1 receptor antagonist transcript levels in patients compared to controls (P = 0.5962). Interestingly, genotype–phenotype correlation analysis revealed that individuals with IL1RN*A (2/2) exhibited higher interleukin 1 receptor antagonist expression compared to other major genotypes interleukin 1 receptor antagonist*A (1/2) (P = 0.01) and interleukin 1 receptor antagonist*A (1/1) (P = 0.03). Limitations: More case-control studies on interleukin 1 receptor antagonist rs2234663 polymorphism and gene expression from different ethnic populations are required to explore the impact of interleukin 1 receptor antagonist in vitiligo susceptibility. Conclusion: Interleukin 1 receptor antagonist*A2 might be a risk factor for progressive vitiligo.

Application of Single-nucleotide Polymorphism and Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats Analyses to Clinical Mycobacterium tuberculosis Isolates from Korea / 대한진단검사의학회지

BACKGROUND: Single-nucleotide polymorphism (SNP) analysis is a powerful strategy for large-scale molecular population studies examining phylogenetic relationships among bacterial strains. Mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) can be easily digitized to share data among laboratories. This study applied SNP and MIRU-VNTR analyses for molecular strain typing of Mycobacterium tuberculosis isolates collected throughout Korea. METHODS: We studied 102 clinical M. tuberculosis isolates, including 6 paired strains, collected from 11 university hospitals in Korea in 2008 and 2009. SNPs were detected using hairpin primer assays, and then, MIRU-VNTR analysis was performed. RESULTS: Thirty-five SNPs contained polymorphisms that helped differentiate the 96 tested isolates. The isolates were classified into 15 clusters. The Beijing family strains were distributed within closely related clusters in the SNP dendrogram. For MIRU-VNTR analysis, the 96 isolates were divided into 12 groups. The discriminatory index in 8 of these groups (MIRU-10, -23, -26, and -31; ETR-A, -B, -C, and -F) was high (Hunter-Gaston diversity index > 0.6). Unlike the SNP method, MIRU-VNTR analysis did not identify any notable localizations of Beijing or non-Beijing family isolates in specific clusters. CONCLUSIONS: SNP and MIRU-VNTR analyses are surrogate molecular strain-typing methods for M. tuberculosis in Korea where Beijing family isolates are predominant.

Prevalence of chimerism after non-myeloablative hematopoietic stem cell transplantation / Prevalência do quimerismo após transplante de células hematopoiéticas não-mieloablativo

Context and objective: Non-myeloablative hematopoietic stem cell transplantation (NMA-HSCT) is performed in onco-hematological patients who cannot tolerate ablative conditioning because of older age or comorbidities. This approach does not completely eliminate host cells and initially results in mixed chimerism. Long-term persistence of mixed chimerism results in graft rejection and relapse. Involvement of graft-versus-host disease is concomitant with complete chimerism and graft-versus-tumor effect. The aim of this study was to evaluate the prevalence of chimerism in onco-hematological patients who underwent NMA-HSCT. Desingn and setting: Observational clinical study on chimerism status after human leukocyte antigen-identical NMA-HSCT at the Discipline of Hematology and Hemotherapy of Universidade Federal de São Paulo. Methods: We sequentially analyzed the amplification of APO-B, D1S80, DxS52, FVW, 33.6, YNZ-2 and H-ras primers using variable number of tandem repeats (VNTR) on 17 pairs and fluorescent in situ hybridization (FISH) with the XY probe and SRY primer on 13 sex-unmatched pairs. RESULTS: The informativeness of the primers using VNTR was 60 percent for APO-B, 75 percent D1S80, 36 percent DxS52, 14 percent FVW, 40 percent YNZ-22 and 16 percent H-ras. The SRY primer was informative in female receptors with male donors. The XY-FISH method was informative in 100 percent of the sex-unmatched pairs. Conclusion: These methods were sensitive and informative. In VNTR, the association of APO-B with D1S80 showed 88 percent informativeness. The quantitative FISH method was more sensitive, but had the disadvantage of only being used for sex-unmatched pairs.

Contexto e objetivo: O transplante de células hematopoiéticas não-mieloablativo é realizado em pacientes com doenças onco-hematológicas que não suportam condicionamentos ablativos devido à elevada idade ou ao acometimento por comorbidades. Esta abordagem não elimina completamente as células do hospedeiro, resultando, inicialmente, em quimerismo misto. A persistência do quimerismo misto na evolução de longo prazo resulta na rejeição ao enxerto e recaída. O acometimento pela doença do enxerto contra hospedeiro é concomitante ao quimerismo completo e ao efeito enxerto versus tumor. O objetivo deste estudo foi avaliar a prevalência do quimerismo em doenças onco-hematológicas tratadas com o transplante não-mieloablativo de células hematopoiéticas. Tipo de estudo e local: Estudo clínico observacional do estado de quimerismo após transplante antígenos leucocitários humanos-idêntico não-mieloabaltivo realizado na Disciplina de Hematologia e Hemoterapia da Universidade Federal de São Paulo. Métodos: Analisamos sequencialmente a amplificação dos primers APO-B, D1S80, DxS52, FVW, 33,6, YNZ-22, H-ras pelo VNTR (variable number of tandem repeats) em 17 pares e FISH (fluorescent in situ hybridization) pela sonda XY e do primer SRY em 13 pares de não relacionados a sexo. Resultado: A informatividade dos primers pelo VNTR foi de 60 por cento para APO-B; 75 por cento D1S80; 36 por cento DxS52; 14 por cento FVW; 40 por cento YNZ-22 e 16 por cento H-ras. O primer SRY foi informativo em receptores femininos com doadores masculinos. O método XY-FISH foi informativo em 100 por cento dos pares de não relacionado a sexo. Conclusão: Estes métodos foram sensíveis e informativos. No VNTR, a associação do APO-B com D1S80 mostrou 88 por cento de informatividade. O FISH, método quantitativo, foi mais sensível, porém com desvantagem de ser usado somente nos pares não relacionados a sexo.

Variable Number of Tandem Repeats (VNTR) Disparity between Donor and Recipient has a Potential to Predict the Outcomes of HLA-identical Allogeneic Stem Cell Transplantation

BACKGROUND: Detection of variable number of tandem repeats (VNTR) between recipient and donor has been adopted to monitor the degree of chimerism after allogeneic stem cell transplantation (SCT). In allogeneic SCT, besides MHC-disparity, the disparity of various polymorphous proteins encoded by several genes may play a critical role in the pathogenesis of graft-versus-host disease (GVHD). However, the biologic effect of VNTR disparity has been scarcely studied. METHODS: We analyzed 84 patients receiving SCT from HLA-identical sibling (n=68) or unrelated donors (n=16). Enrolled diseases included AML 48, ALL 8, CML 15, NHL 10, and high-risk MDS 3. The PCR was performed to amplify 3 VNTR regions (D1S80, D1S111, and D17S5). RESULTS: We observed strong correlation between the D1S80 disparity and transplant outcomes in terms of OS (P=0.0179) or non-relapse mortality (NRM) (P=0.0305), but not for D1S111 or D17S5 disparity. The D1S80-fully matched pair showed a better OS (72% vs 38%) and lower NRM (17% vs 50%) compared to partially matched or mismatched pairs. In multivariate analyses, D1S80-fully matched pair was found to be independent favorable prognostic factor for OS (P=0.03) or NRM (P=0.05). In addition, the D1S80 disparity was significantly associated with the myeloid engraftment speed (P=0.01) or the occurrence of gut chronic GVHD (P=0.05). CONCLUSION: Our data suggest that disparities in D1S80-located on chromosome1-seemed to be associated with increased incidence of gut chronic GVHD and NRMs, thus suggesting the existence of unknown genes of minor histocompatibility antigens targeting gut or cytokine/cytokine receptor on chromosome 1.

AMPLIFICATION FRAGMENT LENGTH POLYMORPHISIM OF p33. 4 LOCUS AND ITS APPLICATION TO FORENSIC SCIENCE PRACTICE / 中国法医学杂志

DNA extracted from 100 unrelated Chinese were detected by using the Polymerase Chain Reaction (PCR), mini polyacryl gel vertical electrophorese and silver staining techniques at the p33. 4 locus. Among 100 unrelated individuals, 8 alleles were detected,Foster-Freeman BIOTRAC system indicated that the number of copies of the tandem repeats in different allele was 7, 10 to 15 respectively.There was a rare allele whose copy number was more than 13 but less than 14. The allele fragmehtlength varied from 603 to 1115bp,the allele freqency 0.5 % ~ 53. 5 %,heterozygosity 64 %,DP value84. 5 %. Pedigree analysis indicated that alleles of p33. 4 locus obey Mendel's Laws. Successful typingof various tissues and single hair folicle had confirmed that this technique is suitable for personal identification. In addition, by using Chelex we had established an alterntive method for extracting DNAfrom biological materials,whlch is rapid and easy to perform.