Genetics, genomics and personalized medicine in Type 2 diabetes: a perspective on the Arab region

A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa

Copy number variation (CNV) is considered as the most frequent type of structural variation in the human genome. Some CNVs can act on human phenotype diversity, encompassing rare Mendelian diseases and genomic disorders. The North African populations remain underrepresented in public genetic databases in terms of single-nucleotide variants as well as for larger genomic mutations. In this study, we present the first CNV map for a North African population using the Affymetrix Genome-Wide SNP (single-nucleotide polymorphism) array 6.0 array genotyping intensity data to call CNVs in 102 Tunisian healthy individuals. Two softwares, PennCNV and Birdsuite, were used to call CNVs in order to provide reliable data. Subsequent bioinformatic analyses were performed to explore their features and patterns. The CNV map of the Tunisian population includes 1083 CNVs spanning 61.443 Mb of the genome. The CNV length ranged from 1.017 kb to 2.074 Mb with an average of 56.734 kb. Deletions represent 57.43% of the identified CNVs, while duplications and the mixed loci are less represented. One hundred and three genes disrupted by CNVs are reported to cause 155 Mendelian diseases/phenotypes. Drug response genes were also reported to be affected by CNVs. Data on genes overlapped by deletions and duplications segments and the sequence properties in and around them also provided insights into the functional and health impacts of CNVs. These findings represent valuable clues to genetic diversity and personalized medicine in the Tunisian population as well as in the ethnically similar populations from North Africa.

Genetics and genomics studies in type 2 diabetes: A brief review of the current scenario in the Arab region

BACKGROUND

Type 2 diabetes (T2D) is a polygenic and multi-factorial complex disease, the challenge to find genetic markers that could explain the risk of development of this disease still remains unresolved. The Arab region is one among the populations with a high prevalence of T2D and a large number of studies have been carried out in exploring the genetic factors associated with T2D risk.

AIM

To summarize the recent developments in the Arab world based on the recent studies that had looked into genetic factors associated with the development of T2D in the Arab populations.

METHODS

A systematic literature search was conducted to identify studies published between 2015 and 2018 reporting genetic factors or polymorphisms associated with the risk of T2D in the Arab world. The online databases PubMed and Web of Science were used to perform the literature search.

CONCLUSION

The present study has evaluated 14 studies published during the year 2015-2018. Studies from Egypt, Iraq, Jordan, Oman, Qatar, Saudi Arabia, Tunisia, and United Arab Emirates had been explored studying the associations of GIPR, ADIPOQ, FTO, (GRCh38.p12), MLXIP, AKNAD1, KCNJ11 CDKAL1, CDKN2A/2B, TCF7L2, ACE, SNAP25, ELMO1, VDR, KCTD8, GABRA4 and PRKD1 genes with T2D development.

TCF7L2 Gene Polymorphisms and Susceptibility to Type 2 Diabetes Mellitus, A Pilot Study

Transcription factor 7-like 2 (TCF7L2) variants are known risk factors of type 2 diabetes (T2DM).However, this association is not consistent among different populations. The current study aimed at investigating the relationship between rs 7903146, rs 12255372 variants of TCF7L2 and susceptibility to T2DM and different metabolic parameters in a cohort of Egyptian type 2 diabetic patients. This case control study included 60 diabetic patients and 60 matched unrelated healthy controls. Genotyping was performed by using Real Time-PCR. The frequency of genotypes, alleles, anthropometric measures, glycemic indices, HOMA-IR and lipid profile were evaluated in patients and control. Regarding rs 7903146, TT genotype was more frequent in healthy controls (43.3%) than diabetic patients (20%) (OR = 0.291, 95% CI = 0.108-0.788, P = 0.015). T allele was more frequent in healthy control (61.7%) than diabetic patients (44.2%) and it was associated with lower risk of diabetes (OR = 0.492, 95% CI = 0.294-0.823, P = 0.007).However, there was no significant difference between patients with CC, CT and TT genotypes of rs7903146 regarding HbA1C (p=0.549), HOMA-IR (p=0.359), total cholesterol (p=0.482). In contrast, T allele of rs12255372 had no significant relation to diabetes risk (OR = 0.602, 95% CI = 0.361-1.005, P = 0.052). There was no statistically significant difference of frequency of any rs12255372 genotypes between cases and controls In addition, patients with GG,GT, TT genotypes of rs12255372 had no significant difference regarding HbA1C (p=0.393), HOMA-IR (p=0.985), total cholesterol (p=0.368). The study confirmed the association of TCF7L2 (rs 7903146) and T2DM, while failed to detect any association between TCF7L2 (rs 12255372) and susceptibility to T2DM. No significant difference in respect to metabolic parameters between different genotypes of rs7930146 and rs12255372.

Genetic and epigenetic modifications in the pathogenesis of diabetic retinopathy: a molecular link to regulate gene expression

Intensification in the frequency of diabetes and the associated vascular complications has been a root cause of blindness and visual impairment worldwide. One such vascular complication which has been the prominent cause of blindness; retinal vasculature, neuronal and glial abnormalities is diabetic retinopathy (DR), a chronic complicated outcome of Type 1 and Type 2 diabetes. It has also become clear that "genetic" variations in population alone can't explain the development and progression of diabetes and its complications including DR. DR experiences engagement of foremost mediators of diabetes such as hyperglycemia, oxidant stress, and inflammatory factors that lead to the dysregulation of "epigenetic" mechanisms involving histone acetylation and histone and DNA methylation, chromatin remodeling and expression of a complex set of stress-regulated and disease-associated genes. In addition, both elevated glucose concentration and insulin resistance leave a robust effect on epigenetic reprogramming of the endothelial cells too, since endothelium associated with the eye aids in maintaining the vascular homeostasis. Furthermore, several studies conducted on the disease suggest that the modifications of the epigenome might be the fundamental mechanism(s) for the proposed metabolic memory' resulting into prolonged gene expression for inflammation and cellular dysfunction even after attaining the glycemic control in diabetics. Henceforth, the present review focuses on the aspects of genetic and epigenetic alterations in genes such as vascular endothelial growth factor and aldose reductase considered being associated with DR. In addition, we discuss briefly the role of the thioredoxin-interacting protein TXNIP, which is strongly induced by high glucose and diabetes, in cellular oxidative stress and mitochondrial dysfunction potentially leading to chromatin remodeling and ocular complications of diabetes. The identification of disease-associated genes and their epigenetic regulations will lead to potential new drugs and gene therapies as well as personalized medicine to prevent or slow down the progression of DR.