Gender and ethnicity modify the association between the CYP1A2 rs762551 polymorphism and habitual coffee intake: evidence from a meta-analysis.

The association between the single nucleotide polymorphism rs762551 in the cytochrome P450 family 1, subfamily A2 gene (CYP1A2) and caffeine consumption remains controversial. We conducted a meta-analysis to clarify this potential association. Twelve studies were selected from articles retrieved from the and Google Scholar databases, and the data were analyzed to determine the odds ratio (OR) of genotypes AA (conferring fast caffeine metabolism) vs AC + CC (conferring slow caffeine metabolism). Comparisons were made between 6161 high caffeine consumers and 3219 low caffeine consumers. The overall analysis showed a significant association between genotype AA and coffee intake  [OR = 1.13, 95% confidence interval (CI) = 1.03-1.24; Q = 19.23, P = 0.06; I2 = 43%]. In subgroup analyses, the association was also found within male, younger, and Caucasian subjects (OR = 1.21, 95%CI = 1.08- 1.35; OR = 1.71, 95%CI = 1.18-2.48; OR = 1.29, 95%CI = 1.12-1.49, respectively) but not in female, older, and Asian subjects (OR = 0.98, 95%CI = 0.83-1.15; OR = 0.83, 95%CI = 0.56-1.22; OR = 0.91, 95%CI = 0.71-1.17, respectively). Therefore, the rs762551 AA genotype may lead to higher coffee intake, especially in males, younger age groups, and individuals of Caucasian ethnicity. Our data highlight the need to test other CYP1A2 polymorphisms showing significance in genome-wide association studies to clarify the association with caffeine intake in the Asian population.

Mn-SOD 47 CC genotype in combination with high tea consumption may prevent complications in Tunisian type-2 diabetes.

Reactive oxygen species metabolizing enzymes may play an important role in the prevention of type-2 diabetes (T2D) complications. We analyzed the association between Cu/Zn-SOD +35 A/C, Mn-SOD T47C, and CAT -21 A/T gene polymorphisms and complications, in combination with tea consumption in Tunisian T2D. A sample of 366 T2D subjects was enrolled in this study. All participants were asked about tea consumption and frequency. Anthropometric, clinical, and routine biochemical characteristics were obtained from subjects' updated medical records. Malondialdehyde, as an early marker of lipid peroxidation, was measured in plasma samples. Urinary polyphenol derivatives (UPDs), as a marker of polyphenols intake, were assessed by the Folin-Ciocalteu assay. SODs and CAT genotypes were determined by conventional restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) methods. From all subjects, the results showed that in high tea consumers (>3 cups/day), the frequency of the Mn-SOD 47 CC genotype was significantly higher in T2D without complications compared with T2D with complications (P = 0.03; OR = 0.284; 95%CI = 0.086-0.939). However, no significant associations were observed with Cu/Zn-SOD +35 A/C or CAT -21 A/T genes polymorphisms. Additionally, the evaluation of UPDs showed that individuals carrying the Mn-SOD 47 CC genotype and consuming more than three cups of tea per day present significantly higher UPDs (P = 0.038). In conclusion, the Mn-SOD 47 C variant in combination with high tea consumption may provide protection against complications in T2D.

Bias toward a 1:1 ratio in primer-introduced restriction analysis PCR: mechanism and minimization.

Primer-introduced restriction analysis is widely used in molecular genetics. However, several studies have reported inconsistent data regarding sequencing, mainly among heterozygous samples. This discrepancy may be related to the bias towards a 1:1 ratio typically observed in heterozygous digestion products. In this study, we investigated the mechanism and minimization of this observed bias. Three mismatched polymerase chain reaction (PCR) models were analyzed by testing different PCR conditions and reaction mixtures. For EPHX1 gene rs1051740 single-nucleotide polymorphism PCR, DNA concentration, denaturation and elongation time, annealing temperature, and cycle number significantly influenced product ratios. For SERPINA1 gene PIMmalton deletion (ΔPhe52) and CHRNA3 gene rs1051730 single-nucleotide polymorphism PCRs, significant bias fluctuations were observed only for the annealing temperature and cycle number conditions. The relevance of these results to the amplification efficiency parameter is discussed. Rather than reducing the observed bias, our data provide evidence of a counterbalance for preferential amplification, depending on cycle number, annealing temperature, and amplification efficiency alteration. Our results are relevant for application to primer-introduced restriction analysis PCR assays.

Relationship between glutathione S-transferase P1 polymorphisms and chronic obstructive pulmonary disease in a Tunisian population.

Chronic obstructive pulmonary disease (COPD) is a multifactorial disease with possible genetic predisposition and involvement of various environmental factors. Several candidate genes have been reported as potentially associated with this lung disease. The glutathione S-transferase P1 gene (GSTP1) was proposed to be involved in susceptibility to develop COPD. It belongs to the GST family, which is a group of phase II enzymes that catalyze the glutathione conjugation of many endogenous and exogenous electrophilic compounds, such as carcinogens, therapeutic drugs, environmental toxins, and oxidative stress products. We conducted a case-control study to investigate genetic polymorphisms of this enzyme [exon 5 (Ile105Val) and exon 6 (Ala114Val)] in 234 unrelated COPD cases and 182 healthy controls from a Tunisian population. Genotyping was carried out using polymerase chain reaction and restriction fragment length polymorphism methods. GSTP1 Ala114/Val114 and Val114/Val114 genotypes were not found in either patients or healthy controls. However, there were differences in the distribution of various exon 5 GSTP1 genotypes between COPD patients and healthy controls. GSTP1 Val105/Val105 was significantly more common in patients compared to controls (OR = 2.67; 95%CI = 1.45-4.92; P = 0.0013). Multivariate logistic regression analysis confirmed a significant relationship between the mutant genotype and COPD (OR = 2.58; 95%CI = 1.31-5.09; P = 0.026), after adjustment for classic risk factors. Analysis of variance showed no correlation between age, body-mass index, pack-years, percentage of predicted FEV1 values, and any of the GSTP1 genotypes. We conclude that subjects with GSTP1 Val105 allele are at higher risk of COPD.

[Biochemical and molecular diagnosis of alpha 1 antitrypsin deficiency in a Tunisian family]. / Diagnostic biochimique et moléculaire du déficit en alpha 1 antitrypsine dans une famille tunisienne.

Our study investigated alpha 1 antitrypsin deficiency (AATD) diagnosis in a family originated from central Tunisia and showing a familial history of asthma. Biochemical and genetic diagnosis for AATD was performed according to current diagnostic standards. AAT level quantification in affected individuals showed plasma AAT levels consistent with intermediate AATD (ranged from 0.91 to 1.04 g/L). The molecular analysis was assessed using the genotyping of the most prevalent PI*S and PI*Z SERPINA1 mutations and the sequencing of AAT coding exons for rare AATD variants detection. No PI*S or PI*Z deficient variants were seen in this family. Sequencing results showed the inheritance of the deficient rare variant PI*M(wurzburg) (P369S) at the heterozygous state in the mother and two affected siblings. However, AATD status remains unexplained in the third affected case, with no mutations detected in the AAT coding exons.

[Alpha 1 antitrypsin polymorphism associated to asthma and emphysema in a central Tunisian population]. / Polymorphisme de l'alpha 1 antitrypsine associé à l'asthme et l'emphysème pulmonaire dans une population du centre tunisien.

INTRODUCTION: more than 100 alleles have been described on the alpha 1 antitrypsin gene. Normal variants (PiM1, PiM2 and PiM3) encodes AAT molecules which are different but functional and normally secreted. The more frequent risk variants are PiS and PiZ. In this study, an AAT polymorphism analysis in correlation with pulmonary diseases was conducted. MATERIAL AND METHODS: analyses were performed on 96 asthmatics, 67 emphysema cases and 318 control subjects. Alpha 1 antitrypsin phenotypes were studied by quantitative determination of AAT concentration and isoelectrofocusing. Genotyping was performed by RFLP PCR. RESULTS: PiM1, PiM2, PiM3, PiS and PiZ allelic frequencies were calculated (0.7395, 0.2291, 0.0156, 0.0104, 0.0052 in asthmatics; 0.7547, 0.1716, 0.0298, 0.0298, 0.0149 in emphysema patients and 0.8030, 0.1525, 0.0408, 0.006, 0.0000 in controls, respectively). Results showed an increase in PiM2 allele frequencies in both patients' groups compared to controls. Allelic frequencies difference is significant only with the asthmatic group (p=0,0179). PiS and PiZ deficiency alleles are more prevalent in the emphysema (0.0298, 0.0149) than in the asthmatic subjects (0.0104, 0.0052). Meanwhile, no significant difference in PiS and PiZ allelic frequencies was observed between patients and controls. CONCLUSION: PiM2 allele can be considered as genetic risk factor for asthma. PiS and PiZ alleles are very rare in Tunisia in comparison with the European population, leading to a very small contribution in pulmonary diseases pathogenesis in Tunisia.

[C3 complement polymorphism in patients suffering from obstructive chronic bronchopneumopathy in Tunisia]. / Polymorphisme du C3 du complément chez des patients atteints de bronchopneumopathie chronique obstructive en Tunisie.

We analysed the C3*S and C3*F polymorphism of the third component of the complement (C3), first at the protein level by the electrophoresis of the plasma on agarose gel and second on the gene level by the ARMS PCR technique. We determined the phenotypic and genotypic frequencies of the C3 on a sample of 90 patients suffering from the obstructive chronic bronchopneumopathy (OCBP) disease. Comparisons have been done with frequencies observed on a control sample of 437 healthy individuals from the Tunisian population in order to establish a putative correlation between the polymorphism studied and the disease. Frequencies of the C3*S and C3*F alleles in OCBP patients are 0,788 and 0,212 respectively. They are not significantly different from those observed in control sample (0,834 and 0,152 respectively). Therefore, no correlation is observed between the C3 polymorphism and the risk of developing the OCBP disease.

[Clinical, biologic and molecular characteristics of two Tunisian MPS IV A patients]. / Etude de la maladie de Morquio A dans une famille tunisienne présentant deux enfants atteints.

Mucopolysaccharidosis type IV A (MPS IV A) is an autosomal recessive disorder resulting from the deficient activity of the lysosomal enzyme, N-acetylgalactosamine-6-sulfate sulfatase (GALNS) and the progressive lysosomal accumulation of keratane sulfate. Clinically, the MPS IV A differs from the other MPS by the localisation of the keratane sulfate in skelet and in eyes associated to the conservation of a normal intelligence. To date, the characterization and purification of the GALNS gene made a research for pathogenic mutations in patients with MPS IV A easier. These mutations are responsible of severe, intermediate or mild phenotype. The aim for this work was the research of clinical, biologic and molecular characteristics of two Tunisian MPS IV A patients who were offsprings of consanguineous mating. Enzymatic and urinary diagnostics suggested a MPS IV A phenotype. A novel homozygous mutation IVS1+1G-A was identified by direct sequencing in the GALNS gene of the two patients. Identification of GALNS mutations provide genotype/phenotype correlations and permit the precision of anomalies responsible of Morquio A phenotype in concerned families.

[COPD characteristics in subjects carrying the rare alpha-1 antitrypsin variant PIMMmalton]. / Aspects de la BPCO chez les porteurs de la mutation déficitaire rare de l'alpha-1 antitrypsine PIMMmalton.

INTRODUCTION: Several studies have investigated the clinical feature of COPD in subjects carrying the common alpha-1 antitrypsin deficiency mutations PIS and PIZ. However, there are few data on COPD due to rarer deficient variants. In this study, we aimed to explore the features of COPD in subjects carrying the PIMMmalton mutation, which is the most prevalent alpha-1 antitrypsin variant in Tunisia. MATERIAL AND METHODS: Five individuals, heterozygous for PIMMmalton were analyzed and compared to 97 non-deficient COPD patients. Demographic data as well as clinical and functional outcomes from subjects were collected. Blood gases and plasma alpha-1 antitrypsin levels were recorded. RESULTS: PIMMmalton subjects did not show any significant difference in terms of predicted FEV1 (35±13.2%), predicted forced vital capacity (34.2±9.6%) and FEV1 decline (148.6±114mL/year) compared to usual COPD patients (respectively 41.7±17.2%, P=0.500; 43.8±18.8%, P=0.300; 197.9±191mL/year, P=0.800). However, PaO2 was significantly reduced in PIMMmalton subjects (58.8±4.0mmHg) compared to usual COPD (69.9±10.6mmHg; P=0.029) and those patients with chronic bronchitis and centrolobular emphysema (71.0±10.9mmHg; P=0.038). CONCLUSION: PIMMmalton subjects were significantly hypoxic, similar to that observed in PiZZ homozygous rather than observed in heterozygous individuals.

[Molecular analysis and prenatal diagnosis of beta-thalassemia: about our experience in central Tunisia]. / Analyse moléculaire et diagnostic prénatal de la beta-thalassémie: à propos de notre expérience en Tunisie centrale.

Beta-thalassemia, by its high frequency and its heterogeneity, constitutes a real problem of health in Tunisia. Prenatal diagnosis by DNA analysis represents the only reality for couples at risk. The denaturant gradient (urea and formamide) on polyacrylamide gel electrophoresis has been performed in our laboratory, using psoralen as chemical clamps. This method is simple, reliable, safe, rapid, without radioactivity and has a reasonable cost (chemical clamps). Even if it needs an informatic modelization in other laboratories, this method seems to be adapted to our economic and work conditions and to the molecular heterogeneity of the Tunisian beta-thalassemia. We present the results of an epidemiological molecular study on 75 patients with beta-thalassemia and the results of ten prenatal diagnosis. The molecular lesions codon 39 (C-T) and IVS1 nt2 (T-G) are the most frequent in our study. This technical approach provides genetic counselling for at risk families by offering prenatal diagnosis (reducing as possible the cost and the delay of the result) after prealable family study and identification of the mutation(s).

Alpha 1 antitrypsin polymorphism in the Tunisian population with special reference to pulmonary disease.

OBJECTIVES: The study investigated alpha 1 antitrypsin (AAT) gene polymorphism in the Tunisian population. We aimed to analyze the correlation between Pi polymorphism and the risk of developing chronic obstructive pulmonary disease (COPD). PATIENTS AND METHODS: We focused our study on two samples originating from the Tunisian centre: 318 healthy controls and 90 patients suffering from COPD. Data analysis was investigated by AAT level quantification, serum isoelectric focusing (IEF) and RFLP-PCR performed with PiS and PiZ allele specific primers. RESULTS: We calculated PiM1, PiM2, PiM3, PiS and PiZ allele frequencies in patients and controls. The difference in allele frequencies is significant only for the PiM2 allele (P=0.00378). In COPD patients, we note the presence of PiZ allele. This allele mainly observed in European populations, is rare in sub-Saharian populations and not described in North Africa. CONCLUSION: PiZ allele is found in COPD sample and never in Tunisian controls. However, no significant difference in PiZ allele frequency between patients and controls can be concluded. PiM2 allele, which is considered as "normal" variant can be associated with COPD risk.