Association of SLC11A1 polymorphisms with anthropometric and biochemical parameters describing Type 2 Diabetes Mellitus

Abstract

Diabetes, a leading cause of death globally, has different types, with Type 2 Diabetes Mellitus (T2DM) being the most prevalent one. It has been established that variations in the SLC11A1 gene impact risk of developing infectious, inflammatory, and endocrine disorders. This study is aimed to investigate the association between the SLC11A1 gene polymorphisms (rs3731864 G/A, rs3731865 C/G, and rs17235416 + TGTG/- TGTG) and anthropometric and biochemical parameters describing T2DM. Eight hundred participants (400 in each case and control group) were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and amplification-refractory mutation system-PCR (ARMS-PCR) methods. Lipid profile, fasting blood sugar (FBS), hemoglobin A1c level, and anthropometric indices were also recorded for each subject. Findings revealed that SLC11A1-rs3731864 G/A, -rs17235416 (+ TGTG/- TGTG) were associated with T2DM susceptibility, providing protection against the disease. In contrast, SLC11A1-rs3731865 G/C conferred an increased risk of T2DM. We also noticed a significant association between SLC11A1-rs3731864 G/A and triglyceride levels in patients with T2DM. In silico evaluations demonstrated that the SLC11A2 and ATP7A proteins also interact directly with the SLC11A1 protein in Homo sapiens. In addition, allelic substitutions for both intronic variants disrupt or create binding sites for splicing factors and serve a functional effect. Overall, our findings highlighted the role of SLC11A1 gene variations might have positive (rs3731865 G/C) or negative (rs3731864 G/A and rs17235416 + TGTG/- TGTG) associations with a predisposition to T2DM.

Figure 1

Loci of the studied SLC11A1 gene polymorphisms on chromosome 2 (2q35).

Figure 2

Gel photograph of SLC11A1–rs3731864 G/A (A), –rs3731865 G/C (B), and –rs17235416 + TGTG/− TGTG (C) polymorphisms.

Figure 3

Web-based analysis of the impact of studied intronic variants on the pattern of splicing processes using the SpliceAid database. rs3731864 mutant (A), rs3731864 wild-type (B), rs3731865 mutant (C), rs3731865 wild-type (D). G to A substitution in the rs3731864 position disrupts the binding sites of some splicing factors including SC35, SF2/ASF, hnRNP f, hnRNP H3, hnRNP H1, and hnRNP H2. On the contrary, nucleotid change on the position of rs3731865 creates binding site for SF2/ASF and hnRNP H3 facors.

Figure 4

Illustration of sequence conservation. WebLogo illustrated the conservation of the DNA sequences around SLC11A1–rs3731864 G/A, –rs3731865 G/C, and –rs17235416 + TGTG/− TGTG variations loci. The red vertical line indicates the positions of the variants loci in humans and the conservation of wild alleles across multiple mammalian species. The high nucleotide symbols indicate more conservation, while the small and more diverse ones show less conservation.

Figure 5

The PPI network of the SLC11A1 protein. Colored lines between proteins indicate evidence of various types of interactions. Regarding “Known Interactions”, the blue lines represents interactions based on curated databases and the purple lines highlight interactions based on experimentally determined. Regarding “Predicted Interactions”, the green lines show interactions based on gene neighborhood; the red lines indicate gene fusions; and the dark blue, represents gene co-occurrence. Regarding “Others,” the yellow lines represents interaction based on text mining; the black lines show co-expression; and the light blue lines represent protein homology. The above classification information was obtained using STRING. STRING imports protein association knowledge from databases of physical interactions and databases of curated biological pathway knowledge (MINT, HPRD, BIND, DIP, BioGRID, KEGG, Reactome, IntAct, EcoCyc, NCI-Nature Pathway Interaction Database, and GO). A PPI analysis was conducted using inBio Discover™ to investigate the possible interactions between SLC11A1 and other proteins. The PPI analysis was conducted using inBio Discover™ to investigate possible interactions between SLC11A1 and other proteins. Our Bioinformatics results showed that some of the genes that have direct interaction with SLC11A1, including ATP7A, FGB, FGA, SLC11A2, and SLC40A1, can also play important roles in the course of T2DM, and this makes SLC11A1 a hub protein that can regulate different signaling pathways involved in the pathogenesis of T2DM. PPI protein–protein interaction, SLC11A1 solute carrier family 11 member 1, SLC11A2 solute carrier family 11 member 2, SLC25A37 solute carrier family 25 member 37, SLC31A2 solute carrier family 31 member 2, SLC34A1 solute carrier family 34 member 1, SLC34A2, solute carrier family 34 member 2, SLC40A1 solute carrier family 40 member 1, ATOX1 antioxidant 1 copper chaperone, ATP7A ATPase copper transporting alpha, HAMP hepcidin antimicrobial peptide, FGA fibrinogen alpha chain, FGB fibrinogen beta chain, FGG fibrinogen gamma chain, F2 coagulation factor II, thrombin, SPL1 squamosa promoter binding protein-like 1, IRF8 interferon regulatory factor 8, GATA2 GATA binding protein 2, TTN titin, NEB nebulin, TRIM63 tripartite motif containing 63, ACTN2 actinin alpha 2, TCAP titin-cap.