Impact of nsSNPs in human AIM2 and IFI16 gene: a comprehensive in silico analysis

AIM2 and IFI16 are the most studied members of AIM2-like receptors (ALRs) in humans and share a common N-Terminal PYD domain and C-terminal HIN domain. The HIN domain binds to dsDNA in response to the invasion of bacterial and viral DNA, and the PYD domain directs apoptosis-associated speck-like protein via protein-protein interactions. Hence, activation of AIM2 and IFI16 is crucial for protection against pathogenic assaults, and any genetic variation in these inflammasomes can dysregulate the human immune system. In this study, different computational tools were used to identify the most deleterious and disease-causing non-synonymous single nucleotide polymorphisms (nsSNPs) in AIM2 and IFI16 proteins. Molecular dynamic simulation was performed for the top damaging nsSNPs to study single amino acid substitution-induced structural alterations in AIM2 and IFI16. The observed results suggest that the variants G13V, C304R, G266R, and G266D for AIM2, and G13E and C356F are deleterious and affect structural integrity. We hope that the suggested deleterious nsSNPs and structural dynamics of AIM2 and IFI16 variants will guide future research to better understand the function of these variants with large-scale studies and may assist in fresher therapeutics focusing on these polymorphisms.Communicated by Ramaswamy H. Sarma.

Association of the rs3917647 polymorphism of the SELP gene with malnutrition in gastric cancer

BACKGROUND

Malnutrition and cachexia are common syndromes in patients with gastric cancer (GC) and are associated with poor quality of life and poor disease prognosis. However, there is still a lack of molecular factors that can predict malnutrition or cachexia in cancer. Studies have shown that among the potential contributors to the development of cancer cachexia, the level of the inflammatory response to P-selectin is regulated by single nucleotide polymorphisms (SNPs) located in the promoter region of the SELP gene. The aim of this study was to evaluate the association between the single nucleotide polymorphism (SNP)-2028 A/G of the SELP gene and malnutrition in patients receiving chemotherapy for gastric cancer (GC).

METHODS

The study group consisted of 220 GC patients treated with chemotherapy at Jinhua Municipal Central Hospital. DNA was extracted from peripheral leukocytes of whole blood samples using an animal DNA extraction kit. DNA was amplified using a 1.1 × T3 Super PCR mix, and loci corresponding to the peaks were genotyped using SNP1 software.

RESULTS

Patients carrying the A allele had a reduced risk of developing malnutrition compared to patients with the GG genotype (P < 0.001; OR = 3.411; 95% CI = 1.785-6.516). In addition, multivariate analysis indicated that the AA genotype significantly (more than 16-fold) reduced the risk of developing malnutrition (P < 0.001; OR = 0.062; 95% CI = 0.015-0.255).

CONCLUSION

SELP -2028A/G SNP may be a useful marker for assessing the risk of malnutrition in GC patients.

Putative functional non-coding polymorphisms in SELP significantly modulate sP-selectin levels, arterial stiffness and type 2 diabetes mellitus susceptibility

BACKGROUND

P-selectin, encoded by SELP, has been implicated as an important molecule in the development of arterial stiffness, consequently leading to vascular complications in T2DM. SELP polymorphisms and increased levels of soluble P-selectin (sP-selectin) have been shown to be associated with several inflammatory diseases. The present work was designed to assess nine putative functional non-coding SELP variants in relation to sP-selectin levels and arterial stiffness in T2DM.

METHODS

The genetic distribution of rs3917655, rs3917657, rs3917739, rs2235302, rs3917843 was determined by restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR). Genotyping of rs3917779 was performed by tetra primer amplification-refractory mutation system (ARMS)- PCR. Three SNPs i.e. rs3917853, rs3917854, rs3917855 were genotyped by Sanger sequencing. Construction of haplotypes was performed using PHASE software. The data thus obtained was analyzed by appropriate statistical tools.

RESULTS

Two non-coding variants i.e. rs3917657 and rs3917854 of SELP were found to be associated with 2 and 1.7 -fold risk of disease development respectively. However, one non-coding variant rs2235302 was found to provide protection against disease development. Furthermore, variant allele of rs3917854 in T2DM patients was found to be associated with 2.07-fold very high vascular risk. Non-coding haplotype GCAGGCCGC was conferring 4.14-fold risk of disease development. Furthermore, overall sP-selectin levels were higher in T2DM patients when segregated according to genotypes as well as haplotypes. Significant genotype- phenotype correlation was observed for rs3917655 as well as rs3917739 variant in patients and for rs3917854 in controls. In vascular risk categories, a significant genotype- phenotype correlation was observed for rs3917655 and rs2235302. Furthermore, patients with CCGGGCCGC haplotype in high risk category were observed with higher levels of sP-selectin as compared to other haplotypes (p < 0.05).

CONCLUSIONS

Non-coding SELP variants may significantly modulate sP-selectin levels, vascular risk and T2DM susceptibility.

Study of the Association of V640L (rs6133) Polymorphism in the Platelet P-selectin Gene with Acetylsalicylic Acid Resistance in Patients after Coronary Bypass Surgery

Aim.To study the association of V640L (rs6133) polymorphism in the P-selectin gene with acetylsalicylic acid (ASA) resistance in patients with coronary heart disease after coronary bypass surgery (CABG).Material and methods.The study included 104 patients aged 36-78 years (mean age 61.6±6.9 years) with stable angina pectoris: 61 (58.7%) patients had functional class II (according to Canadian Cardiovascular Society), 41 (39.4%) – class III and 2 (1.9%) – class IV. Atherosclerotic lesions of the coronary arteries were confirmed by coronary angiography. The antiplatelet therapy was stopped for at least 5 days before CABG. In the postoperative period, from the first day, all patients received 100 mg of ASA in enteric form, 61 patients received alone ASA therapy, 43 patients – combined antiplatelet therapy: ASA+clopidogrel (75 mg/day). The aggregation study was performed with an optical aggregometer, using 5 μM adenosinediphosphate (ADP) and 1 mM arachidonic acid inductors before CABG, on 1-3 day and on 8-10 day after surgical treatment. DNA samples were examined for the V640L (rs6133) polymorphism in the P-selectin gene by real-time polymerase chain reaction (PCR) using the allele-specific primers.

Results. The frequency of the homozygous GG genotype of the rs6133 polymorphism was 84.6%; heterozygous GT genotype – 15.4%. The amplitude of aggregation with ADP before CABG, on 1-3 day and on 8-10 day after CABG for carriers of homozygotes of allele G vs carriers of the allele T were: 47.9±19.3%, 44.5±17.8%, 30.1±13.2% vs 47.9±17.1%, 46.3±16.5%, 39.6±22.0%, respectively (p=0.497, 0.441 and 0.687, respectively). The amplitude of aggregation with arachidonic acid before CABG, on 1-3 day and on 8-10 day after CABG for carriers of homozygotesof allele G vs carriers of the allele T, were: 47.9±23.2%, 24.5±21.7%, 12.3±16.3% vs 54.3±17.8%, 29.7±23.7%,  11±10.9%, respectively (p=0.416, 0.825 and 0.872, respectively). In the first 10 days of the postoperative period, 6 thrombotic events (5.7%) were observed in the study group: 2 strokes and 4 perioperative myocardial infarctions. Five events occurred in the group of patients with the GG genotype, 1 event in the group of patients with the GT genotype.Conclusion. V640L (rs6133) polymorphism in the P-selectin gene is not associated with ASA resistance in patients with coronary artery disease after CABG. The T allele of the rs6133 polymorphism is not associated with increased platelet aggregation activity after CABG and does not increase the risk of adverse events in the first 10 days after CABG.

Relationship Between -2028 C/T SELP Gene Polymorphism, Concentration of Plasma P-Selectin and Risk of Malnutrition in Head and Neck Cancer Patients

Until today there is a lack of molecular factors, that could predict either cancer malnutrition or cachexia. Among potential mechanisms, that contribute to development of above syndromes, the systemic inflammatory response with overproduction of cytokines and adhesion molecules is the most likely. Recent papers suggested crucial role of P-selectin adhesion molecule in the initiation of leukocytes recruitment to the site of injury during inflammation, promotion of tumor aggressiveness and contribution to cancer cachexia. The aim of the study was to investigate SELP -2028 C/T polymorphism as a risk factor of malnutrition in 66 head and neck cancer (HNC) patients subjected to radiotherapy. Genotyping was conducted by real-time PCR method by means of TaqMan SNP Genotyping Assay. P-selectin Human ELISA Kit was used to determine P-selectin concentration in each extracted plasma samples. CC homozygous subjects had 4-fold higher risk score of being qualified as severely malnourished compared to other genotype carriers (p = 0.015). However, the TT homozygous patients were at lowest risk of severe weight loss >10% during the therapy period (OR = 0.20; p = 0.019). We also noted, that CC genotype carriers had significantly higher risk of early death incidence compared to CT or TT genotype (median survival time: 29 vs 34 months; HR = 3.02; p = 0.0085). Studied SELP -2028 C/T seems to be a novel attractive predictive factor of cancer malnutrition in HNC patients, perhaps in a future, patients carrying unfavorable CC genotype could be earlier scheduled for pharmaceutical intervention with parenterall nutrition, therefore they could be prevented from the development of severe malnutrition or even cachexia.

Association of SELP Polymorphisms with Soluble P-Selectin Levels and Vascular Risk in Patients with Type 2 Diabetes Mellitus: A Case-Control Study

P-selectin, an adhesion molecule, is encoded by SELP and known as biomarker of endothelial as well as platelet dysfunction. SELP polymorphisms (rs6136, rs6127, and rs6125) and raised levels of soluble P-selectin (sP-selectin) have been associated with several disease conditions. The present study was aimed to determine the association of SELP variants and sP-selectin levels as well as vascular risk in Type 2 diabetes mellitus (T2DM) patients. The frequency of rs6136, rs6127, and rs6125 was assessed by restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR). sP-selectin levels were measured using commercially available kits. Haplotypes were constructed using PHASE software. The data obtained from the above-said analyses was subjected to suitable statistical analyses. sP-selectin levels (ng/ml) were significantly higher in patients as compared to controls (p < 0.001). Out of total, 22% of patients were found to have very high vascular risk, 43.2% with high vascular risk, while 34.4% with moderate vascular risk. For both rs6136 and rs6127, frequency of variant allele was found to be significantly higher in patients as compared to controls and accounted for 2.4- and 1.5-fold risk of disease development, respectively. CAG was found to be associated with 4.5-fold risk towards disease development. In contrast, AGG was conferring the protective effect. Significantly high sP-levels were observed in patients with homozygous wild genotype of rs6136, all genotypes of rs6127, and heterozygous genotype of rs6125 as compared to respective controls. Significant difference was observed in P-selectin levels within moderate-risk category for rs6136. When compared between the categories, significant difference was observed for rs6136 and rs6127. Furthermore, patients with haplotypes AAA, AGA, and AGG were found to have significantly high sP-selectin levels as compared to controls. Significant difference in sP-selectin levels was observed within very high-risk as well as high-risk category. When compared between the categories, significant difference was observed for AGA and AGG haplotypes. The studied polymorphisms of SELP have shown significant association with sP-selectin levels as well as vascular risk in T2DM patients.