Do major histocompatibility complex tag single nucleotide polymorphisms accurately identify HLA-B27 in the Turkish population?

OBJECTIVE: To evaluate the performance of human leukocyte antigen (HLA)-B27 tag single nucleotide polymorphisms (SNPs) by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP). METHODS: We genotyped three SNPs (rs116488202, rs13202464 and rs4349859). The primers were designed using Primer3 algorithm via primer-BLAST interface. PCR products were digested by using NlaIII, BmrI and TaqαI enzymes. Quality control was performed by DNA sequence analysis. RESULTS: In total, 207 patients with ankylosing spondylitis and 32 healthy controls were included in the study. The sensitivity and specificity of SNPs rs116488202 and rs4349859 in identifying HLA-B27 were identical and adequate at 0.946 and 1.000, respectively. On the other hand, the sensitivity and specificity for rs13202464 was 0.878 and 0.934, respectively. The presence of another SNP (rs141774149) in close proximity to rs116488202 complicated the analysis for RFLP and required that we sequence all the T allele carrying samples. CONCLUSION: The SNPs rs116488202 and rs4349859 may have a place in the identification of HLA-B27 in the Turkish population; however, methods other than PCR-RFLP should be considered.

Investigation of the association between ATP2B4 and ATP5B genes with colorectal cancer.

Colorectal cancer (CRC) develops as a multi-step process which results from gradual accumulation of mutations in proto-oncogenes, tumor suppressor, and DNA repair genes. Mortality rate of CRC is very high. Therefore, development of alternative diagnostic methods which can be used in the early diagnosis is crucial. ATP2B4 gene encodes one of the four isoforms of p-type ATPase PMCA enzyme and bears critical importance in maintaining the balance of intracellular calcium homeostasis by providing the export of calcium ions out of the cell. ATP5B encodes a subunit of the mitochondrial ATP synthase which is an f-type ATPase. In this study, the relationship between ATP2B4 and ATP5B genes and CRC regarding gene expression was investigated. Study groups were constructed from a number of 50 patients (25 males, 25 females) with the mean age of 55.68 ± 9.4 and the gene expression levels in the healthy and cancerous tissues of the patients were compared by using semi-quantitative PCR and Real-Time PCR methods. As a result, in patients with rectum tumors, there was a significant relationship between ATP2B4 gene expression and the tumor location and in patients younger than 45 years, ATP5B gene expressions were detected significantly higher in tumor tissues by using RT-PCR. However, no significant relationship was detected in terms of expression differences of ATP2B4 and ATP5B genes between cancerous and healthy tissues of the CRC patients. ATP2B4 and ATP5B genes might have indirect associations in CRC pathogenesis and the investigation of their interactions with DNA repair and other related genes may help in understanding of CRC formation.