Subjects and sample collection.
In this case-control study, semen samples were collected from 128 idiopathic male infertility and 77 fertile men without any history of infertility in their first-degree family as a healthy control group. All semen samples prepared from Fatemeh Al-Zahra IVF and Pastor Laboratory (Babol, Mazandaran, Iran), and stored at -20°C for other use. The infertile men who referred to Fatemeh Al-Zahra IVF and Pastor Laboratory had no history of cryptorchidism, orchitis, infectious disease, diabetes mellitus, drug abuse, obstruction of the vas deferens, varicocele, abnormal profiles of luteinizing hormone (LH), follicle-stimulating hormone (FSH) and testosterone, abnormal karyotype as well as Y-chromosome microdeletion. In addition, the infertile men’s women had no problem in their reproductive systems. Also, there was no sign of coronary heart disease (CHD), atherosclerosis, liver diseases, hypertension, diabetes and cancer in all fertile and subfertile cases which are paraxonase-affecting diseases. The semen analysis was evaluated according to the world health organization [32] guidelines with respect to sperm motility (normal ≥ 25%) concentration (normal ≥ 20× 106 spermatozoa/ml), and normal morphology (normal ≥ 14%).
This study was confirmed by the principles outlined in the Declaration of Helsinki and approved by the ethics committees of University of Mazandaran (#IR.UMZ.REC.1399.033).
DNA extraction and PON1 L55M genotyping.
Genomic DNA was extracted from semen samples by a conventional salting-out method, which described by Mwer et al. [33] and then stored in -20°C until to use. The PON1 L55M (NM_000446.7: c.163T > A) gene polymorphisms were genotyped using polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP).
One pair of primers were designed using with oligo primer analysis software ver. 7.0 and were listed as follows: forward primer: 5´-GAAGAGTGATGTATAGCCCCAGTT, reverse primer: 5´-AGTGGGCATGGGTATACAGAAA. The amplification reactions were carried out in a total volume of 25 µl consisting: 100 ng (2 µl) genomic DNA, 10 pmol (1 µl) of each primer, 2.5 µl of 10X PCR buffer, 0.5 µl of four mixed dNTPs (10 mM, Cinnagen Inc, Iran), 1µl of MgCl2 (50 mM, Cinnagen Inc, Iran), 0.25 µl of 5U/µl Taq DNA polymerase (Cinnagene, Co., Iran). PCR program was used for the amplification: 5 min at 94°C, 32 cycles of 30s at 94°C, 30s at 56°C, 30s at 72°C and finally extension step 5 min at 72°C. PON1 gene rs854560 polymorphism was amplified by PCR and then genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. For the PCR RFLP analysis, PCR products were digested with Hin1II restriction enzyme (Thermo Fisher Scientific, USA). The restriction reactions were carried out in a total volume of 10 µl containing: 5µl PCR product (~ 100ng); 3µl DNAase free H2O; 1.5 µl 10X fast digest green buffer and 0.5µl (~ 3 Units) of the restriction enzymes. These components were incubated 5min at 37°C. Restriction fragments were separated by 1.5% agarose gel electrophoresis and visualized by UV-transilluminators after staining with 1 µg/ml ethidium bromide [34]. Function of Hin1II restriction enzyme, PCR amplification product sizes and genotyping map are summarized in Figure. 1b.
TAC, MDA and PON1 activities.
Total antioxidant capacity (TAC) level was measured by its ability to reduce Fe3+ to Fe2+ using the ferric reducing ability of plasma (FRAP) method [35]. Malondialdehyde (MDA) level determined by its reaction with thiobarbituric acid (TBA) at 100°C [36]. Procedure these methods in semen fluid and described by Fallah et al [37].
The PONase activity was assessed spectrophotometrically using paraoxon (Sigma Chem, USA) as substrate and the absorbance was recorded at 412 nm, because of 4 -nitrophenol formation [38]. Briefly, the paraxonase activity was measured at 25°C during 3 min after 10 µl of seminal plasma were added to each well containing 150 µl of Tris-Cl (100 mM, pH 8.5) buffer including 2 mM CaCl2 and 6 mM of paraoxon. All results are expressed in U/ml which is defined as 1 nmol of 4- nitrophenol formed per minute. The PON1 enzymatic activity was calculated by using the molar extinction coefficient 18 053 M−¹ cm−¹.
Statistical analysis.
Statistical analysis of difference in allele and genotype frequencies between controls and infertility groups were performed by using SPSS ver. 26.0 (SPSS, Inc., Chicago, IL, USA) software. After assessing the normality of the constant variables, using the Shapiro-Wilk test, quantitative data were presented as mean ± SD (normally distributed data) however qualitative variables were represented as a number or percentage. The Hardy–Weinberg equilibrium (HWE) test was used to estimate genotype frequencies. Results were revealed by odds ratios (ORs) and 95% confidence intervals (CI). Both clinical and laboratory data were checked for their correlation with PON1 polymorphism. A p-value less than 0.05 (typically ≤ 0.05) were accepted to be statistically significant.
in silico analysis.
L55M is one of the most studied polymorphisms has been associated with PON1 levels and activity. In this study, some bioinformatics tools were used to investigate the molecular effects of this substitution. To prediction the effects of L55M substitution on the structure and function on PON1 protein, the PolyPhen-2 in silico prediction server (http://genetics.bwh.harvard.edu/pph2/index.shtml) was used. SIFT server is an online tool to predict if an amino acid substitution effects on protein function (https://sift.bii.a-star.edu.sg/). The MutPred server which is based on SIFT, was developed to classify amino acid substitutions (AAS) as benign or disease-associated (http://mutpred.mutdb.org/).To determine the effect of mutation on protein stability and structure according to free energy change value (ΔΔG), I-Mutant 2.0 online server was used (https://folding.biofold.org/i-mutant/i-mutant2.0.html). SNP & GO is an online server which predict human disease-related Mutations in proteins by determination of Reliability Index (RI) (https://snps-and-go.biocomp.unibo.it/snps-and-go/). To determine the effect of this polymorphism on m-RNA secondary structure SNAP software was used. For the purpose of finding PON1 expression in different tissues and the relationship between rs854560 polymorphism and PON1 expression levels in testis, GTEx portal was used. Kyte-Doolittle scale was used for detection protein hydrophobic and hydrophilic tendencies before and after mutation.