Integrated transcriptome and proteome analyses unveil cytoskeletal alterations in an endothelial model of monogenic diabetes.

BACKGROUND: HNF1A-MODY is a subtype of monogenic diabetes caused by mutations in the hepatocyte nuclear factor-1 homeobox A (HNF1A) gene. While the role of HNF1A in pancreatic beta cells has been extensively studied, its role in other cell types, such as endothelial cells (ECs), is less understood. Despite the pharmacologically controlled glycemia in HNF1A-MODY patients, still cardiovascular disorders and other endothelial dysfunction diseases, such as retinopathy, are quite common. Therefore, the aim of the current study was to look for potential molecular alterations in the ECs related to HNF1A-MODY disease. METHODS: To understand the molecular pathways underlying this effect, ECs from three sets of human pluripotent stem cells (hiPSC-ECs) were used – two isogenic and one patient set. The patient set consisted of four hiPSCs lines with two healthy/control lines and two hiPSCs lines derived from HNF1A-MODY patients. The control isogenic set has a control (healthy) and two CRISPR/Cas9-mutated hiPSCs lines, with monoallelic or biallelic mutations in the HNF1A. The patient isogenic set consists of HNF1A-MODY patient hiPSCs line and two repaired (control) lines. All these lines were subsequently differentiated toward ECs (hiPSC-ECs) and used for global transcriptome, global proteome, and other functional analyses. Additionally, selected results were confirmed in primary ECs, where HNF1A expression was silenced. RESULTS: The integrated global transcriptome and proteome analyses of the control isogenic set (mutated versus unmutated), show differences in actin-based cytoskeleton, general metabolism, and proteoglycan-related genes. All HNF1A-mutated hiPSC-ECs had shorter glycocalyx layer in comparison to their control counterparts. The same phenotype can be mimicked by silencing the HNF1A in primary ECs. Additionally, HNF1A-mutated control isogenic lines showed increased migratory potential, which aligns with a decrease in the actin stress fibres. Similarly, increased migration is observed after HNF1A silencing in patient-specific hiPSC-ECs or in primary ECs. CONCLUSIONS: Taken together, these results reveal for the first time that mutations in the HNF1A cause proteomic and transcriptomic changes in ECs that affect their function through reduction of the glycocalyx layer and changes in the cell migration. Cumulatively, these changes could account for signs of endothelial dysfunction in HNF1A-MODY patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01615-z.