Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction

Abstract

Background Kabuki syndrome is a genetic disorder that affects several body systems and presents with variations in symptoms and severity. The syndrome is named for a common phenotype of faces resembling stage makeup used in a Japanese traditional theatrical art named kabuki. The most frequent cause of this syndrome is mutations in the H3K4 family of histone methyltransferases while a smaller percentage results from genetic alterations affecting the histone demethylase, KDM6A. Because of the rare presentation of the latter form of the disease, little is known about how missense changes in the KDM6A protein sequence impact protein function. Results In this study, we use molecular mechanic and molecular dynamic simulations to enhance the annotation and mechanistic interpretation of the potential impact of eleven KDM6A missense variants found in Kabuki syndrome patients. These variants (N910S, D980V, S1025G, C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W, and R1351Q) are predicted to be pathogenic, likely pathogenic or of uncertain significance by sequence-based analysis. Here, we demonstrate, for the first time, that although Kabuki syndrome missense variants are found outside the functionally critical regions, they could affect overall function by significantly disrupting global and local conformation (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), chemical environment (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), and/or molecular dynamics of the catalytic domain (all variants). In addition, our approaches predict that many mutations, in particular C1153R, could allosterically disrupt the key enzymatic interactions of KDM6A. Conclusions Our study demonstrates that the KDM6A Kabuki syndrome variants may impair histone demethylase function through various mechanisms that include altered protein integrity, local environment, molecular interactions and protein dynamics. Molecular dynamics simulations of the wild type and the variants are critical to gain a better understanding of molecular dysfunction. This type of comprehensive structure- and MD-based analyses should help develop improved impact scoring systems to interpret the damaging effects of variants in this protein and other related proteins as well as provide detailed mechanistic insight that is not currently predictable from sequence alone.

Structural bioinformatics enhances the interpretation of somatic mutations in KDM6A found in human cancers

“…We focus more on the local chemical environment and geometry of the key reactive groups. The influence of the p K a shift has been already noticed and presented in our publication [13] . However, the influence of local geometry has not been explored.…”

“…Next, additional information comes from the RMSFs of each amino acid, which highlights the flexible regions of the systems. Atomic RMSFs from the average structure in the trajectory were calculated for each residue and plotted as shown in our publication [13] . Finally, we computed the time-dependent binding free energy for all cases as well as radius of gyration (Rg) and dynamic solvent accessible-accessible surface area (SASA) using the protocols implemented in the Discovery Studio.…”

“…Correct annotations of these variations are vital for understanding its underlying molecular mechanisms and better diagnostic management and treatment for the patients. Importantly, only 15 KDM6A variants in the demethylase domain found to cause Kabuki syndrome have been carefully studied [13] , [14] , while the complete repertoire of mutations found in cancer is broad and remains poorly understood. Consequently, this study was designed specifically to begin filling this knowledge gap in the field of genomics and precision oncology.…”

Novel KDM6A mutation in a Chinese infant with Kabuki syndrome: A case report

“…Both KDM6A and KMT2D are components of the activation signal cofactor complex whose function is to remove inhibitory epigenetic markers and deposit activated methylation markers on the chromatin, and then recruit RNA polymerase II complex to activate chromatin[ 19 ]. A previous study demonstrated that the KDM6A KS variants might impair functions of the histone demethylase through various mechanisms, including alteration of the protein integrity, local environment, molecular interactions and protein dynamics[ 20 ]. KDM6A protein plays a critical role in cell differentiation, development, and cancer, and is also important in differentiation of embryonic stem cells and development of various tissues, and alteration of KDM6A protein functions and expression results in developmental defects, growth retardation, multiple congenital organ malformations, and hematological and immunological anomalies[ 21 ].…”

Correction to: Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction

“…After the publication of the original article [ 1 ], the authors became aware of the work by Petrizzelli et al, 2020 [ 2 ]. The two studies truly represent independent works, for which contents are different.…”