Molnes, J. | bioRxiv Science

bioRxiv2023

A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes

AimsMonogenic diabetes is characterized as a group of diseases caused by rare variants in single genes. Multiple genes have been described to be responsible for monogenic diabetes, but the information on the variants is not unified among different resources. In this work, we aimed to develop an automated pipeline that collects all the genetic variants associated with monogenic diabetes from different resources, unify the data and translate the genetic sequences to the proteins. MethodsThe pipeline developed in this work is written in Python with the use of Jupyter notebook. It consists of 6 modules that can be implemented separately. The translation step is performed using the ProVar tool also written in Python. All the code along with the intermediate and final results is available for public access and reuse. ResultsThe resulting database had 2701 genomic variants in total and was divided into two levels: the variants reported to have an association with monogenic diabetes and the variants that have evidence of pathogenicity. Of them, 2565 variants were found in the ClinVar database and the rest 136 were found in the literature showing that the overlap between resources is not absolute. ConclusionsWe have developed an automated pipeline for collecting and harmonizing data on genetic variants associated with monogenic diabetes. Furthermore, we have translated variant genetic sequences into protein sequences accounting for all protein isoforms and their variants. This allows researchers to consolidate information on variant genes and proteins associated with monogenic diabetes and facilitates their study using proteomics or structural biology. Our open and flexible implementation using Jupyter notebooks enables tailoring and modifying the pipeline and its application to other rare diseases. Research in contextO_LIMonogenic diabetes is a group of Mendelian diseases with an autosomal-dominant pattern of inheritance. C_LIO_LIMonogenic diabetes is mainly caused by rare genetic variants that are usually evaluated manually. C_LIO_LIThe data on the variants are stored in several resources and are not unified in terms of the genomic coordinates, alleles, and variant annotation. C_LIO_LIWhat can be done for the systematic evaluation of the variants and their protein consequences? C_LIO_LIIn this work, we have created an automated Jupyter notebook-based pipeline for the collection and unification of the variants associated with monogenic diabetes. C_LIO_LIThe database of the genetic variants was created and translated to all possible variant protein sequences. C_LIO_LIThese results will be used for the analysis of proteomics data and protein structure modeling. C_LI

bioinformatics↗

bioRxiv2021

Structural and biophysical characterization of HNF-1A as a tool to study MODY3 diabetes variants

Hepatocyte nuclear factor 1A (HNF-1A) is a transcription factor expressed in several embryonic and adult tissues, modulating expression of numerous target genes. Pathogenic variants in the HNF1A gene cause maturity-onset diabetes of the young 3 (MODY3 or HNF1A MODY), characterized by dominant inheritance, age of onset before 25-35 years of age, and pancreatic {beta}-cell dysfunction. A precise diagnosis alters management as insulin can be exchanged with sulfonylurea tablets and genetic counselling differs from polygenic forms of diabetes. More knowledge on mechanisms of HNF-1A function and the level of pathogenicity of the numerous HNF1A variants identified by exome sequencing is required for precise diagnostics. Here, we have structurally and biophysically characterized an HNF-1A protein containing both the DNA binding domain and the dimerization domain. We also present a novel approach to characterize HNF-1A variants. The folding and DNA binding capacity of two established MODY3 HNF-1A variant proteins (P112L, R263C) and one variant of unknown significance (N266S) were determined. All three variants showed reduced functionality compared to the wild-type protein. While the R263C and N266S variants displayed reduced binding to an HNF-1A target promoter, the P112L variant was unstable in vitro and in cells. Our results support and mechanistically explain disease causality for all investigated variants and allow for the dissection of structurally unstable and DNA binding defective variants. This points towards structural and biochemical investigation of HNF-1A being a valuable aid in reliable variant classification needed for precision diagnostics and management.

biochemistry↗