Molecular and cellular issues of KMT2A variants involved in Wiedemann-Steiner syndrome

Abstract

Variants in KMT2A, encoding the histone methyltransferase KMT2A, are a growing cause of intellectual disability (ID). Up to now, the majority of KMT2A variants are non-sense and frameshift variants causing a typical form of Wiedemann-Steiner syndrome. We studied KMT2A gene in a cohort of 200 patients with unexplained syndromic and non-syndromic ID and identified four novel variants, one splice and three missense variants, possibly deleterious. We used primary cells from the patients and molecular approaches to determine the deleterious effects of those variants on KMT2A expression and function. For the putative splice variant c.11322-1G>A, we showed that it led to only one nucleotide deletion and loss of the C-terminal part of the protein. For two studied KMT2A missense variants, c.3460C>T (p.(Arg1154Trp)) and c.8558T>G (p.(Met2853Arg)), located at the cysteine-rich CXXC domain and the transactivation domain of the protein, respectively, we found altered KMT2A target genes expression in patient's fibroblasts compared to controls. Furthermore, we found a disturbed subcellular distribution of KMT2A for the c.3460C>T mutant. Taken together, our results demonstrated the deleterious impact of the splice variant and of the missense variants located at two different functional domains and suggested reduction of KMT2A function as the disease-causing mechanism.

Expanding the phenotype of Wiedemann‐Steiner syndrome: Craniovertebral junction anomalies

“…The predominant findings were vertebral segmentation defects (9/11), involving different cervical vertebrae and various degrees of fusion of the vertebral bodies and/or posterior elements. The most common was cervical C2/C3 vertebral fusion (7/11), also reported in Baer et al, 2018 andLebrun et al, 2018; one individual had a more severe C1/C2 vertebral fusion, while another had a combination of C2/C3 and C1/occiput fusion.…”

“…We have recently resolved the diagnosis of a patient who, in addition to typical WDSTS features, presented with cervical C2/C3 vertebral fusion and small foramen magnum. At the same time, anomalies of the craniovertebral junction (CVJ) have been reported in a few other WDSTS patients (Baer et al, 2018;Feldman, Dlouhy, Lah, Payne, & Weaver, 2019;Lebrun et al, 2018), suggesting that they may warrant inclusion among the WDSTS-associated features.…”

Description of the molecular and phenotypic spectrum of Wiedemann-Steiner syndrome in Chinese patients

“…Other 5 recurrent variants, including p.Arg1154Trp [ 11 ], p.Cys1155Tyr [ 11 , 22 ], p.Gly1168Asp [14, this study], p.Arg1633* [ 2 , 11 ] and p.Arg2480* [ 7 , 11 ] were also identified. Although we did not find hotspot variation region, it is noteworthy that only missense variants (7/17) occurred in the cysteine-rich CXXC zinc finger domain (Additional file 2 : Table S2), which is predicted to selectively bind to unmethylated CpG-containing stretches of the target genes [ 10 ]. Previous studies suggested that patients who harbor the missense variant in the CXXC DNA binding domain may show more severe neurodevelopmental delay [ 10 , 14 ].…”

“…Although we did not find hotspot variation region, it is noteworthy that only missense variants (7/17) occurred in the cysteine-rich CXXC zinc finger domain (Additional file 2 : Table S2), which is predicted to selectively bind to unmethylated CpG-containing stretches of the target genes [ 10 ]. Previous studies suggested that patients who harbor the missense variant in the CXXC DNA binding domain may show more severe neurodevelopmental delay [ 10 , 14 ]. Indeed, in our cohort, Patient 5 (p.Gly1168Asp) has the most severe anomalies in neurological development.…”

“…It is speculated that missense variants of the KMT2A gene are more likely to cause WDSTS by a dominant negative effect [ 23 ]. The hypothesis is supported by the fact that upregulation of the KMT2A gene transcription in patient with p.Arg1154Trp and site-specific DNA methylation changes driven by KMT2A missense variants [ 9 , 10 ], which might explain the missense variants in the CXXC DNA binding domain linked to a more severe neurophenotypes. Nevertheless, more functional study need be performed to figure out the molecular mechanism, especially why there were only missense variants in this domain.…”