Variations in TAP1 and PSMB9 Genes Involved in Antigen Processing and Presentation Increase the Risk of Vitiligo in the Saudi Community

Background

The antigen processing 1 (TAP1) and proteasome 20S subunit beta 9 (PSMB9) genes are associated with strong susceptibility to many autoimmune diseases. Here, we explored whether TAP1/PSMB9 genetic variants, individually or combined, affected susceptibility to the complex, autoimmune-based skin disorder vitiligo.

Methods

Samples of genomic DNA from buccal cells of 172 patients with vitiligo and 129 healthy controls were analyzed using TaqMan™ genotyping assays for the TAP1 rs1135216 (A>G) and PSMB9 rs17587 (A>G) single nucleotide polymorphisms (SNPs). SNPStats software (https://www.snpstats.net) was utilized to choose the best interactive inheritance mode for selected SNPs.

Results

The genotype frequencies for the TAP1 rs1135216 and PSMB9 rs17587 SNPs were in Hardy-Weinberg equilibrium for cases (P= 0.11 and P= 0.10, respectively) but not for controls (P< 0.05). The TAP1 rs1135216 (D637G) and PSMB9 rs17587 (R60H) SNPs increased the risk of vitiligo four-fold and two-fold, respectively (odds ratio [OR]= 4.6; 95% confidence interval [CI], 3.2-6.5; P< 0.0001 and OR= 2.2; 95% CI, 1.5-3.1; P< 0.0001). The recessive model (G/G-D/G versus D/D) and the codominant model (R/R versus R/H) were the best models of inheritance for the rs113526 and rs17587 SNPs, respectively (OR= 16.4; 95% CI, 2.0-138; P= 0.0006 and OR= 1.7; 95% CI, 0.3-1.8; P= 0.013). Vulgaris, focal vulgaris, and acryl/acrofacial were the most common vitiligo subtypes in our sample (51%, 21%, and 19%, respectively). Heterozygous rs113526 (637D/G) and rs17587 (60R/H) were the most common genotypes in most vitiligo subtypes. The heterozygous 637D/G genotype and the 637G variant allele were significantly more common in patients with active disease than in patients with stable disease (P= 0.000052 and P= 0.0063, respectively).

Conclusion

Our findings suggest a crucial role for TAP1 rs1135216 and PSMB9 rs17587 in the risk and progression of vitiligo in the Saudi community. Genomic analyses are needed to identify more candidate genes and more genetic variants associated with vitiligo.

Variations in TAP1 and PSMB9 Genes Involved in Antigen Processing and Presentation Increase the Risk of Vitiligo in the Saudi Community

BACKGROUND

The antigen processing 1 (TAP1) and proteasome 20S subunit beta 9 (PSMB9) genes are associated with strong susceptibility to many autoimmune diseases. Here, we explored whether TAP1/PSMB9 genetic variants, individually or combined, affected susceptibility to the complex, autoimmune-based skin disorder vitiligo.

METHODS

Samples of genomic DNA from buccal cells of 172 patients with vitiligo and 129 healthy controls were analyzed using TaqMan™ genotyping assays for the TAP1 rs1135216 (A>G) and PSMB9 rs17587 (A>G) single nucleotide polymorphisms (SNPs). SNPStats software (https://www.snpstats.net) was utilized to choose the best interactive inheritance mode for selected SNPs.

RESULTS

The genotype frequencies for the TAP1 rs1135216 and PSMB9 rs17587 SNPs were in Hardy-Weinberg equilibrium for cases (P= 0.11 and P= 0.10, respectively) but not for controls (P< 0.05). The TAP1 rs1135216 (D637G) and PSMB9 rs17587 (R60H) SNPs increased the risk of vitiligo four-fold and two-fold, respectively (odds ratio [OR]= 4.6; 95% confidence interval [CI], 3.2-6.5; P< 0.0001 and OR= 2.2; 95% CI, 1.5-3.1; P< 0.0001). The recessive model (G/G-D/G versus D/D) and the codominant model (R/R versus R/H) were the best models of inheritance for the rs113526 and rs17587 SNPs, respectively (OR= 16.4; 95% CI, 2.0-138; P= 0.0006 and OR= 1.7; 95% CI, 0.3-1.8; P= 0.013). Vulgaris, focal vulgaris, and acryl/acrofacial were the most common vitiligo subtypes in our sample (51%, 21%, and 19%, respectively). Heterozygous rs113526 (637D/G) and rs17587 (60R/H) were the most common genotypes in most vitiligo subtypes. The heterozygous 637D/G genotype and the 637G variant allele were significantly more common in patients with active disease than in patients with stable disease (P= 0.000052 and P= 0.0063, respectively).

CONCLUSION

Our findings suggest a crucial role for TAP1 rs1135216 and PSMB9 rs17587 in the risk and progression of vitiligo in the Saudi community. Genomic analyses are needed to identify more candidate genes and more genetic variants associated with vitiligo.

Risk of Colorectal Carcinoma May Predispose to the Genetic Variants of the GST, CYP450, and TP53 Genes Among Nonsmokers in the Saudi Community

PURPOSE

Colorectal carcinoma (CRC) represents a considerable public health burden in Saudi Arabia. Several candidate genes and genetic variants have been associated with morbidity and mortality among patients with CRC. We explored whether allelic variants of the GSTM1, GSTT1, CYP450 (rs4646903 and rs1048943), and TP53 (rs1042522) genes predisposed nonsmoking Saudi individuals to increased risk for CRC.

PATIENTS AND METHODS

DNA from buccal cells of 158 participants (80 with CRC and 78 healthy controls) were analyzed for five SNPs using conventional PCR and TaqMan genotyping assays. The SNPStats software was utilized to choose the best interactive inheritance mode for selected SNPs (https://www.snpstats.net).

RESULTS

The mean age of diagnosis was 62.4±13.5 years (range, 40-83 years), with those aged 71-80 years and those aged 40-50 years accounting for the most diagnoses (35.7% and 28.6% of diagnosis, respectively). The GSTM1 and TP53 rs1042522 SNPs were associated with CRC (OR= 3.7; P< 0.0001, and OR= 1.6; P= 0.033, respectively). A plausible contribution to CRC was observed for the GSTM1 and TP53 rs1042522 SNPs (x ² _Yates= 14.7; P= 0.00013, and x ² _Yates= 11.2; P= 0.0008, respectively), while the GSTT1 null variant did not affect risk. Heterozygosity in the CYP450 (rs4646903 and rs1048943 SNPs) was associated with a significant risk for CRC. The GSTM1/GSTT1 and CYP450 rs4646903/rs1048943 SNP pairs were in linkage disequilibrium, and the associations were statistically significant (P= 0.01 and P= 4.6x10^‒7, respectively).

CONCLUSION

The GSTM1 and TP53 rs1042522 variants can increase the development of CRC in Saudi nonsmokers. Even the presence of one copy of a variant allele in the CYP1A1 gene can predispose CRC risk. Additional studies should also examine other SNP combinations with lifestyle factors that may help prevent, rather than facilitate, colorectal tumorigenesis.

Molecular characterization of exonic rearrangements and frame shifts in the dystrophin gene in Duchenne muscular dystrophy patients in a Saudi community

BACKGROUND

In individuals with Duchenne muscular dystrophy (DMD), exon skipping treatment to restore a wild-type phenotype or correct the frame shift of the mRNA transcript of the dystrophin (DMD) gene are mutation-specific. To explore the molecular characterization of DMD rearrangements and predict the reading frame, we simultaneously screened all 79 DMD gene exons of 45 unrelated male DMD patients using a multiplex ligation-dependent probe amplification (MLPA) assay for deletion/duplication patterns. Multiplex PCR was used to confirm single deletions detected by the MLPA.

RESULTS

There was an obvious diagnostic delay, with an extremely statistically significant difference between the age at initial symptoms and the age of clinical evaluation of DMD cases (t value, 10.3; 95% confidence interval 5.95-8.80, P < 0.0001); the mean difference between the two groups was 7.4 years. Overall, we identified 147 intragenic rearrangements: 46.3% deletions and 53.7% duplications. Most of the deletions (92.5%) were between exons 44 and 56, with exon 50 being the most frequently involved (19.1%). Eight new rearrangements, including a mixed deletion/duplication and double duplications, were linked to seven cases with DMD. Of all the cases, 17.8% had duplications with no hot spots. In addition, confirmation of the reading frame hypothesis helped account for new DMD rearrangements in this study. We found that 81% of our Saudi patients would potentially benefit from exon skipping, of which 42.9% had a mutation amenable to skipping of exon 51.

CONCLUSIONS

Our study could generate considerable data on mutational rearrangements that may promote future experimental therapies in Saudi Arabia.

TNF-238 polymorphism may predict bronchopulmonary dysplasia among preterm infants in the Egyptian population

Bronchopulmonary dysplasia (BPD) remains as a major and increasing burden in Egypt.

RATIONALE

To determine whether alleles of TNFα-238G > A affect the risk of BPD or the severity of BPD in preterm infants in Egypt.

STUDY DESIGN

We prospectively genotyped 220 premature neonates (birth weight <1,500 g and gestational age 26-32 weeks) for the -238 polymorphism, and assessed the clinical risk factors for BPD in our study populations. Infants with BPD were mechanically ventilated.

RESULTS

Infants who developed BPD (n = 120) had a younger gestational age (31.0 ± 2.1 weeks vs. 34.3 ± 1.5 weeks) and lower birth weight (1,490 ± 360 g vs. 1,880 ± 520 g) than infants who did not develop BPD (n = 100). Results of antenatal steroid supplementation, surfactant therapy, or sepsis might affect the genetic modulation of BPD. The -238G > A polymorphism was associated with a twofold risk of BPD (OR = 2.86; 95% confidence interval, 1.35-3.83). Despite the dominance of the G allele in the Egyptian population, the -238A allele was more common among infants with BPD (23%) than among infants without BPD (15%). The A allele occurred less often in infants with mild BPD (9%) than in infants with severe (39%) or moderate (52%). The AA genotype occurred in 15% of cases but in none of the controls.

CONCLUSION

The TNFα -238G > A polymorphism-particularly the presence of an A allele-should be evaluated as a biomarker to predict the clinical outcome of preterm infants with BPD in Egypt. Even the presence of one copy of this mutant allele appears to be sufficient to influence the severity of disease.

Deletion mutations in Duchenne muscular dystrophy (DMD) in Western Saudi children

Duchenne and Becker muscular dystrophy (DMD and BMD) are caused, in the majority of cases, by deletions in the dystrophin gene (DMD). The disease is an X-linked neuromuscular diseases typically caused by disrupting (DMD) or non-disrupting (BMD) the reading frame in the dystrophin (DMD) gene. In the present study, amplifications of the genomic DNAs of unrelated 15 Saudi DMD males were carried out using multiplex polymerase chain reaction (PCR) for nine-hotspot regions of exons 4, 8, 12, 17, 19, 44, 45, 48 and 51. We detected six Saudi patients having deletions in a frequency of 40%. The frequency of deletions in exon 51 (20%) was the most common deletion frequently associated with our Saudi sample males. Exons 19, 45, and 48 were present in a frequency of 6.7% each. All deletions were recognized as an individual exonic deletions, while no gross deletion where detected. Finally, the molecular deletions in the Saudi males was expected to be characterized by a moderate frequency among different populations due to the geographical KSA region, which it is in the crossroad of intense migrations and admixture of people coming from continental Asia, Africa, and even Europe. In conclusion, attempts to include an extra DNA samples might reflect a valid vision of the deletions within the high frequency deletion regions (HFDR's) in the DMD gene mutations in KSA.

Helicobacter pylori cagA and iceA genotypes status and risk of peptic ulcer in Saudi patients

OBJECTIVE

To determine the prevalence of cagA+ and iceA genotypes among Helicobacter pylori (H. pylori) isolates from a group of Saudi patients with gastric complaints, and to find out any significant correlation between these strains and severe gastric clinical outcomes such as peptic ulcer and gastric cancer in Saudi population.

METHODS

A total of 1104 gastric biopsies from 368 patients who presented with symptoms suggestive of chronic gastritis, peptic ulcer disease, or gastric carcinoma were taken from the main hospitals in the Western region of Saudi Arabia from July 2004 to July 2005. We cultured the samples for H. pylori and a polymerase chain reaction was carried out to check for the presence or absence of cagA gene and the status of iceA genotypes.

RESULTS

Among the 368 suspected patients to be infected with H. pylori by means of clinical features and endoscopic findings; 103 (28%) were positive using culture technique. The relation of the presence of cagA and the development of cases to gastritis and ulcer was statistically significant (p=0.0001). Furthermore, this study revealed that 100% of ulcer cases were infected with iceA1 with a statistically significant correlation (p=0.0001), while 94.6% of gastritis and 90.9% of normal were infected with iceA2 (p=0.0001). Moreover cagA+/iceA1 combined genotypes was statistically correlated with peptic ulcer (100%) but not cagA-/iceA1 (0%; p=0.0001).

CONCLUSION

Certain H. pylori genotypes were more virulent than others. Multiple clinical implications based on these finding might be studied further.

Relationship between Helicobacter pylori vacA genotypes status and risk of peptic ulcer in Saudi patients

OBJECTIVE

To determine if there is a significant correlation between different Helicobacter pylori (H. pylori) vacA genotypes strains and severe gastric clinical outcomes.

METHODS

A total of 1104 gastric biopsies from 368 patients who presented with symptoms suggestive of chronic gastritis or peptic ulcer were taken from the main hospitals in the western region of Saudi Arabia from July 2004 to July 2005. These samples were cultured for H. pylori, and a polymerase chain reaction (PCR) was carried out to determine vacA genotypes status.

RESULTS

One hundred and three (28%) patients were positive for H. pylori using culture technique. The distribution of vacA genotypes was 13 for vacAs1m1, 47 for vacAs1m2 and 43 for vacAs2m2. None of the clinical isolates were vacAs2m1 positive. The study showed a significant correlation between the vacAs1m2 genotype and gastritis cases, and a significant correlation between vacAs1m1 genotype and ulcer cases.

CONCLUSION

The results of this study might be used for the identification of high-risk patients who are infected by vacAs1m1 genotype H. pylori strains.

Chlamydia pneumoniae seropositivity and risk of developing coronary heart disease in Western Saudi Arabia

OBJECTIVES

To estimate the seroprevalence of IgG and IgA antibodies against Chlamydia pneumoniae (C. pneumoniae) among a sample of the Saudi population, and to evaluate whether there is a relationship between seropositivity to chronic infection with C. pneumoniae and the manifestation of symptomatic coronary heart disease (CHD).

METHODS

We collected 273 sera samples from CHD patients and 273 sera samples from healthy matched controls from the Western region of Saudi Arabia during the period from November 2004 to May 2005. We tested anti-chlamydial IgG and IgA antibodies using enzyme-linked immunosorbent assay technique.

RESULTS

We found 239 (87.5%) patients and 213 (78%) controls positive for C. pneumoniae IgG antibodies. However, 58 (21.2%) patients and 55 (23.9%) controls were positive for C. pneumoniae IgA antibodies. These results indicate a significant correlation between the presence of IgG antibodies and the development of CHD (p=0.003). Data of this study showed that the presence of IgG antibodies has a 2-fold increase risk in development of CHD. We found no significant correlation between the existence of IgA antibodies and CHD.

CONCLUSION

Our study indicates that C. pneumoniae infection plays an important role in the development of CHD in the Saudi community, emphasizing the importance of developing strategies for prevention and control against this type of bacterial infection. However, we need further study throughout the Kingdom to approve these results in all regions.

Accuracy of current oxacillin sensitivity tests routinely used in hospitals in Western Saudi Arabia

OBJECTIVE

To determine the accuracy of the current oxacillin resistant Staphylococcus aureus (S. aureus) detection test used in Makkah hospitals in comparison with the National Committee for Clinical Laboratory Standards (NCCLS) method.

METHODS

A total of 500 S. aureus clinical isolates and it's oxacillin sensitivity patterns were collected from the 4 main hospitals in Makkah, Kingdom of Saudi Arabia between April 2003 and January 2004. The oxacillin sensitivity of these clinical isolates were re-examined using the NCCLS standard method and confirmed using polymerase chain reaction (PCR) technique.

RESULTS

Of 500 clinical isolates, 103 (20.6%) were resistant to oxacillin using NCCLS standard method but they were sensitive according to the current hospital routine sensitivity test method. The PCR technique confirmed the presence of mecA gene in 88/103 isolates appeared to be methicillin-resistant S. aureus (MRSA) using NCCLS standard technique.

CONCLUSION

A significant percentage of MRSA are currently misdiagnosed in accordance with the current routine sensitivity method. In addition, some mecA negative and oxacillin resistant strains (according to the NCCLS standard method) can be misdiagnosed by using PCR technique. These findings emphasis the urgent need to comply with the recommended NCCLS guidelines for detection of oxacillin resistance. Moreover, the PCR technique can not be used as a single diagnostic tool for detection of MRSA.

Vitamin D receptor, HER-2 polymorphisms and risk of prostate cancer in men with benign prostate hyperplasia

OBJECTIVE

Prostate cancer (PRCa) is one of the most common causes of cancer death in men and determinants of PRCa risk remain largely unidentified. Benign prostatic hyperplasia (BPH) is found in the majority of ageing men and has been associated with PRCa. Many candidate genes have been suggested to be involved in PRCa, such as those that are central to cellular growth and differentiation in the prostate gland. The vitamin D receptor (VDR) and HER-2 protooncogene have been shown to be involved in the regulation of cell proliferation and differentiation in prostate cells. Genetic variations of these genes could be useful to detect BPH patients that have a higher risk of developing PRCa. This study used a case-control design to assess the predictive value of 3 polymorphisms in VDR (TaqI and FokI) and HER-2 (Val655Ile) to determine the risk of developing PRCa in patients with BPH.

METHODS

Polymorphisms were detected by RFLP analysis. The study evaluated 28 patients who presented with PRCa at least 6 years after the diagnosis of BPH and 56 matched patients with BPH who did not progress to PRCa over a comparable period. The study was carried out in University of Aberdeen, Foresterhill, Aberdeen, United Kingdom in the year 2002.

RESULTS

Among the case group, 89% had a TT TaqI genotype, whereas 57% of control had this genotype (odds ratio [OR] = 5.16, 95% confidence interval [CI] = 1.46-18.22). A similar pattern was seen for the FokI genotype, although this was not statistically significant (OR = 2.33, 95% CI = 0.86-6.29). The frequency of the HER-2 Ile/Ile genotype was higher in cases (79%) compared to control subjects (66%), although this was not statistically significant (OR = 1.94, 95% CI = 0.67-5.63).

CONCLUSION

This study shows that the VDR TaqI polymorphism is associated with a group of men with BPH who are at an increase risk of PRCa, providing a potential tool to assist prediction strategies for this important disease.

Length and somatic mosaicism of CAG and GGN repeats in the androgen receptor gene and the risk of prostate cancer in men with benign prostatic hyperplasia

BACKGROUND

The most common malignancy in men worldwide is cancer of the prostate and determinants of prostate cancer (PRCa) risk remain largely unidentified. Many candidate genes may be involved in PRCa, such as those that are central to cellular growth and differentiation in the prostate gland. We analysed the polymorphic CAG and GGN repeats sequence in exon 1 of the AR gene to determine if the number of repeats might be an indicator of PRCa risk in patients with BPH.

METHODS

The study evaluated 28 patients who presented with PRCa at least 6 years after the diagnosis of BPH and 56 matched patients with BPH who did not progress to PRCa over a comparable period.

RESULTS

This study showed no evidence for association between the size of AR CAG and GGN repeats and the risk of the development of PRCa in patients with BPH. However, BPH patients with AR CAG instability had a 12-fold increased risk in development of PRCa.

CONCLUSIONS

While independent confirmation is required in further studies, these results provide a potential tool to assist prediction strategies for this important disease.

CYP3A4 and VDR gene polymorphisms and the risk of prostate cancer in men with benign prostate hyperplasia

Prostate cancer (PRCa) is one of the most common causes of cancer death in men and determinants of PRCa risk remain largely unidentified. Benign prostatic hyperplasia (BPH) is found in the majority of ageing men and has been associated with PRCa. Many candidate genes have been suggested to be involved in PRCa, such as those that are central to cellular growth and differentiation in the prostate gland. The vitamin D receptor (VDR) and CYP3A4 have been shown to be involved in the regulation of cell proliferation and differentiation in prostate cells. Genetic variations of these genes have been associated with PRCa in case-control studies and may be useful to detect BPH patients that have a higher risk of developing PRCa. The association between CYP3A4 and VDR TaqI SNPs and the risk of developing PRCa have been investigated in this study by determining the variant genotype frequencies of both SNPs in 400 patients with BPH who have been followed clinically for a median of 11 years. The results of this study showed that the incidence rate of PRCa was higher in BPH patients having CYP3A4 variant genotype compared to those with wild type (relative risk (RR)=2.7; 95% CI=0.77-7.66). No association between variant genotype and risk of developing PRCa was observed with the VDR TaqI variant genotype. In addition, the results of combined genotype analysis of these two SNPs showed a borderline significant association between CYP3A4 and VDR TaqI combined variant genotypes and PRCa risk (RR=3.43; 95% CI=0.99-11.77). While independent confirmation is required in further studies, these results provide a potential tool to assist prediction strategies for this important disease.

CYP3A4 promoter variant is associated with prostate cancer risk in men with benign prostate hyperplasia

Prostate cancer (PRCa) is one of the most common causes of cancer death in men and determinants of PRCa risk remain largely unidentified. Benign prostatic hyperplasia (BPH) is found in the majority of ageing men and has been linked with PRCa. CYP3A4 may influence PRCa through its role in testosterone metabolism. This nested case-control study assessed a CYP3A4 single nucleotide polymorphism as a risk factor for developing PRCa in patients with BPH. The CYP3A4 variant allele identified men with BPH who are at increased risk of progressing to PRCa (odds ratio 6.3, 95% CI 2.3-17.3), providing a potential tool to assist prediction strategies for this disease.