Analysis of Common SNPs across Continents Reveals Major Genomic Differences between Human Populations

A computational and structural approach to identify malignant non-synonymous FOXM1 single nucleotide polymorphisms in triple-negative breast cancer

The proliferation-specific oncogenic transcription factor, FOXM1 is overexpressed in primary and recurrent breast tumors across all breast cancer (BC) subtypes. Intriguingly, FOXM1 overexpression was found to be highest in Triple-negative breast cancer (TNBC), the most aggressive BC with the worst prognosis. However, FOXM1-mediated TNBC pathogenesis is not completely elucidated. Single nucleotide polymorphisms (SNPs) are the most common genetic variations causing functional and structural aberrations in proteins enhancing cancer susceptibility. This computational investigation attempted to identify the malignant FOXM1 non-synonymous SNPs (nsSNPs) and evaluate their role in affecting the conformational and functional stability, evolutionary conservation, post-translational modifications, and malignant susceptibility of the protein. Out of a huge data pool of 8826 FOXM1 SNPs using several in-silico sequence-based tools and structural approaches, four SNPs viz. E235Q, R256C, G429E and S756P were identified as pathogenic nsSNPs and among the shortlisted variants molecular dynamics simulations identified E235Q as the most damaging malignant SNP, followed by S756P. Additionally, the defective drug and DNA binding motif of E235Q and S756P were also determined in our study. Thus, although further in-vitro validations are awaited the findings of this in-silico work can be used as a blueprint for malignant nsSNP identification of FOXM1 aiding in clinical TNBC therapeutics.

Association between gene polymorphisms and glaucoma susceptibility among Africans: a systematic review and meta-analysis

PURPOSE

This study sought to analyze the effect of allele mutations and gene functions specific to glaucoma susceptibility among Africans.

METHODS

Potentially relevant studies were retrieved from major bibliographic databases (PubMed, Scopus, and Web of Science). Data were extracted and study-specific estimates were meta-analyzed using various models to obtain pooled results.

RESULTS

A total of 11 studies were included in the study. The studies included a total of 3,191 cases with glaucoma and 3,013 controls across all variants. There is no association between the E396E variants of the myocilin (MYOC) gene and an increased likelihood of susceptibility to POAG (OR: 0.91 [95% CI 0.42 to 1.97]). The R141L variant of the Lysyl Oxidase Like 1 (LOXL1) gene is associated with an approximately 3-fold increased likelihood of susceptibility to exfoliative syndrome/exfoliative glaucoma (XFS/XFG) (OR: 2.68 [95% CI 0.04 to 198.94]). There is no association between the G153D variant of the LOXL1 gene and an increased likelihood of susceptibility to XFS/XFG (OR: 0.42 [95% CI 0.02 to 7.65]). The rs59892895*C variant of the Amyloid Beta Precursor Protein Binding Family B Member 2 (APBB2) is associated with a 34% increased likelihood of susceptibility to POAG (OR: 1.34 [95% CI 1.13 to 1.58]).

CONCLUSION

Although progress has been made in understanding the genetic basis of the pathogenesis of glaucoma, several gene mutations related to glaucoma pathogenesis in Africans are yet to be discovered, especially those associated with the pathogenesis of POAG, the most prevalent glaucoma subtype in Africa.

Association between cytokine polymorphisms and recurrent pregnancy loss: A review of current evidence

Cytokines are a type of protein that play an important role in the immune response and can also affect many physiological processes in the body. Cytokine polymorphisms refer to genetic variations or mutations that occur within the genes that code for cytokines, which may affect the level of cytokine production and function. Some cytokine polymorphisms have been associated with an increased risk of developing certain diseases, while others may be protective or have no significant effect on health. In recent years, the role of cytokine polymorphisms in the development of recurrent pregnancy loss (RPL) has been studied. RPL or miscarriage is defined as the occurrence of two or more consecutive pregnancy losses before the 20th week of gestation. There are diverse causes leading to RPL, including genetic, anatomical, hormonal, and immunological factors. With regard to cytokine polymorphisms, a few of them have been found to be associated with an increased risk of RPL, for instance, variations in the genes that code for interleukin-6, tumor necrosis factor-alpha, and interleukin-10. The exact mechanisms by which cytokine polymorphisms affect the risk of recurrent miscarriage are still being studied, and further research is essential to fully understand this complex condition. This brief review aims to summarize the recent literature on the association between cytokine polymorphisms and RPL.

An elevated level of interleukin-17A in a Senegalese malaria cohort is associated with rs8193038 IL-17A genetic variant

Malaria infection is a multifactorial disease partly modulated by host immuno-genetic factors. Recent evidence has demonstrated the importance of Interleukin-17 family proinflammatory cytokines and their genetic variants in host immunity. However, limited knowledge exists about their role in parasitic infections such as malaria. We aimed to investigate IL-17A serum levels in patients with severe and uncomplicated malaria and gene polymorphism's influence on the IL-17A serum levels. In this research, 125 severe (SM) and uncomplicated (UM) malaria patients and 48 free malaria controls were enrolled. IL-17A serum levels were measured with ELISA. PCR and DNA sequencing were used to assess host genetic polymorphisms in IL-17A. We performed a multivariate regression to estimate the impact of human IL-17A variants on IL-17A serum levels and malaria outcomes. Elevated serum IL-17A levels accompanied by increased parasitemia were found in SM patients compared to UM and controls (P < 0.0001). Also, the IL-17A levels were lower in SM patients who were deceased than in those who survived. In addition, the minor allele frequencies (MAF) of two IL-17A polymorphisms (rs3819024 and rs3748067) were more prevalent in SM patients than UM patients, indicating an essential role in SM. Interestingly, the heterozygous rs8193038 AG genotype was significantly associated with higher levels of IL-17A than the homozygous wild type (AA). According to our results, it can be concluded that the IL-17A gene rs8193038 polymorphism significantly affects IL-17A gene expression. Our results fill a gap in the implication of IL-17A gene polymorphisms on the cytokine level in a malaria cohort. IL-17A gene polymorphisms also may influence cytokine production in response to Plasmodium infections and may contribute to the hyperinflammatory responses during severe malaria outcomes.

Genetic association of vitamin D receptor gene with female infertility

BACKGROUND

Infertility is defined as failure to achieve a clinical pregnancy after 12 months of unprotected intercourse. It affects 15% of couples globally and 22% of couples within Pakistan. Female infertility can be caused by numerous genetic or environmental factors including hormone imbalances and exposure to chemicals or radiation. The prevalence of vitamin D deficiency among the adult population was reported to be 14-59% with a higher prevalence in Asian countries. Furthermore, the expression of Vitamin D receptor (VDR) can play a vital role in the reproductive organs of females. Hence, the aim of our present study was to check the association of VDR polymorphisms with infertile females. For this purpose, blood samples were collected for genotyping of four known VDR mutations [FokI (rs2228570), TaqI (rs731236), ApaI (rs7975232), and BsmI (rs1544410)] via PCR-based RFLP assay.

RESULTS

Genotyping indicated that FokI, TaqI, and ApaI are associated with infertility (p = 0.004*, p = 0.013*, and p = 0.033*, respectively). However, BsmI did not show any significance. Multinomial regression analysis indicated that FokI heterozygous genotypes increase the risk of infertility by 2.5 times (hetero: OR = 2.5, 95%, p = 0.001*) as compared to wild type. Heterozygous genotypes of TaqI and ApaI were found to play a protective role and reduce the risk of infertility by 58 and 52%, respectively [TaqI: OR = 0.42, 95%, p = 0.004*, ApaI: OR = 0.48, 95%, p = 0.01*, respectively] as compared to wild type. Multinomial logistic regression analysis was also performed for allelic data as well.

CONCLUSION

Thus, it could be summarized that among the studied polymorphisms of VDR, FokI SNP greatly increased the risk of infertility, while TaqI and ApaI genotypes protect from infertility. However, BsmI does not influence the risk of infertility in Pakistani females.

Special Issue "Feature Papers in Population and Evolutionary Genetics and Genomics"

Theodosius Dobzhansky famously wrote in 1973 that "nothing in biology makes sense except in the light of evolution" [...].

Linking single nucleotide polymorphisms to signaling blueprints in abdominal aortic aneurysms

Abdominal aortic aneurysms (AAA) is a multifactorial complex disease with life-threatening consequences. While Genome-wide association studies (GWAS) have revealed several single nucleotide polymorphisms (SNPs) located in the genome of individuals with AAA, the link between SNPs with the associated pathological signals, the influence of risk factors on their distribution and their combined analysis is not fully understood. We integrated 86 AAA SNPs from GWAS and clinical cohorts from the literature to determine their phenotypical vulnerabilities and association with AAA risk factors. The SNPs were annotated using snpXplorer AnnotateMe tool to identify their chromosomal position, minor allele frequency, CADD (Combined Annotation Dependent Depletion), annotation-based pathogenicity score, variant consequence, and their associated gene. Gene enrichment analysis was performed using Gene Ontology and clustered using REVIGO. The plug-in GeneMANIA in Cytoscape was applied to identify network integration with associated genes and functions. 15 SNPs affecting 20 genes with a CADD score above ten were identified. AAA SNPs were predominantly located on chromosome 3 and 9. Stop-gained rs5516 SNP obtained high frequency in AAA and associated with proinflammatory and vascular remodeling phenotypes. SNPs presence positively correlated with hypertension, dyslipidemia and smoking history. GO showed that AAA SNPs and their associated genes could regulate lipid metabolism, extracellular matrix organization, smooth muscle cell proliferation, and oxidative stress, suggesting that part of these AAA traits could stem from genetic abnormalities. We show a library of inborn SNPs and associated genes that manifest in AAA. We uncover their pathological signaling trajectories that likely fuel AAA development.