JMIR Publications

ABSTRACT

Background:

The TCF7L2 gene is a crucial genetic risk element for prevalent, polygenic Type 2 Diabetes (T2D). Although many research efforts emphasize intronic variants, infrequent non-synonymous single-nucleotide polymorphisms (nsSNPs) found in the coding region, especially within the HMG-box domain, are still mostly uninvestigated. This research seeks to explore the structural and functional impacts of these mutations on the Wnt/β-catenin signaling pathway and in the regulation of GLP-1.

Objective:

This study aims to understand how different changes in the TCF7L2 gene affect its structure and function and how these changes might lead to T2D. To do this, we will find new gene changes (nsSNPs) from a specific part of the genome using data from dbSNP and ClinVar. We will then look at how harmful these changes might be and how stable the proteins made by these genes are. We will create 3D models of the normal and changed versions of TCF7L2 and check if they work properly. We will also use computer simulations to see how well these proteins connect with β-catenin and the glucagon gene. We will run long simulations to check how stable these connections are over time. Finally, we will map these changes onto the Wnt signaling pathway to understand how they affect the process that leads to T2D.

Methods:

We examined sequence data from the NC_000010.11 region of human chromosome 10 (113151270..113151374) through computational genomics. We obtained missense mutations (such as rs176632 and rs183524814) from the dbSNP and ClinVar databases. Pathogenicity was estimated using SIFT and PolyPhen-2 through the Galaxy platform. We constructed the 3D models of both wild-type and mutated TCF7L2 proteins with PyMOL, assessed binding affinities with AutoDock Vina, and conducted 100 ns Molecular Dynamics (MD) simulations through GROMACS. Downstream signaling effects were charted in relation to the KEGG Wnt signaling pathway map map04310

Results:

Mutations like W480L caused notable steric interference in the HMG-box domain, diminishing thermodynamic stability (ΔΔG shift). Molecular docking revealed that the altered TCF7L2 protein exhibits a reduced binding affinity for β-catenin (ΔG = -8.2 kcal/mol) in contrast to the wild-type (ΔG = -10.5 kcal/mol). Additionally, the engagement with the proglucagon promoter DNA was weakened

Conclusions:

The missense mutations in the HMG-box domain interfere with TCF7L2's binding function, hindering Wnt-dependent transcription and GLP-1 secretion, thereby offering a molecular explanation for pancreatic β-cell dysfunction in T2D Clinical Trial: Not Applicable