Introduction The Tousled-like kinases 1 and 2 (TLK1 and TLK2) are involved in many fundamental processes, including DNA replication, cell cycle checkpoint recovery and chromatin remodelling. Mutations in TLK2 were recently associated with ‘Mental Retardation Autosomal Dominant 57’ (MRD57, MIM# 618050), a neurodevelopmental disorder characterised by a highly variable phenotype, including mild-to-moderate intellectual disability, behavioural abnormalities, facial dysmorphisms, microcephaly, epilepsy and skeletal anomalies.
Methods We re-evaluate whole exome sequencing and array-CGH data from a large cohort of patients affected by neurodevelopmental disorders. Using spatial proteomics (BioID) and single-cell gel electrophoresis, we investigated the proximity interaction landscape of TLK2 and analysed the effects of p.(Asp551Gly) and a previously reported missense variant (c.1850C>T; p.(Ser617Leu)) on TLK2 interactions, localisation and activity.
Results We identified three new unrelated MRD57 families. Two were sporadic and caused by a missense change (c.1652A>G; p.(Asp551Gly)) or a 39 kb deletion encompassing TLK2, and one was familial with three affected siblings who inherited a nonsense change from an affected mother (c.1423G>T; p.(Glu475Ter)). The clinical phenotypes were consistent with those of previously reported cases. The tested mutations strongly impaired TLK2 kinase activity. Proximal interactions between TLK2 and other factors implicated in neurological disorders, including CHD7, CHD8, BRD4 and NACC1, were identified. Finally, we demonstrated a more relaxed chromatin state in lymphoblastoid cells harbouring the p.(Asp551Gly) variant compared with control cells, conferring susceptibility to DNA damage.
Conclusion Our study identified novel TLK2 pathogenic variants, confirming and further expanding the MRD57-related phenotype. The molecular characterisation of missense variants increases our knowledge about TLK2 function and provides new insights into its role in neurodevelopmental disorders.
- genetic research
- loss of function mutation
- molecular biology
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THS and AB contributed equally.
Contributors MV-P, MSC, MG, MV and GA-G performed activity, localisation and BioID-MS analysis. LP wrote and edited the manuscript, interpreted exome data, collected the cases and performed variant confirmation, mRNA and splicing analysis. CA and VP performed the SCGE assay. EG interpreted exome data. DC, VAMG, KR, CC and GBF followed patients and collected their clinical information. SDR and JB performed exome sequencing. AB, TP, PD, AC, FCR and MT processed and analysed the WES data. THS and AB designed and supervised the project, analyzed data and wrote the manuscript.
Funding This research received funding specifically appointed to Department of Medical Sciences from the Italian Ministry for Education, University and Research (Ministero dell’Istruzione, dell’Università e della Ricerca—MIUR) under the programme 'Dipartimenti di Eccellenza 2018–2022' Project code D15D18000410001. MV-P was funded by an FPI fellowship from the Ministry of Science, Innovation and Universities (MCIU) and MSC by a Masters fellowship from the BIST and support from the IRB Barcelona. THS was funded by the MCIU (PGC2018-095616-B-I00/GINDATA and FEDER). MT was funded by Fondazione Bambino Gesù (Vite Coraggiose). The whole exome sequencing was performed as part of the Autism Sequencing Consortium and was supported by the NIMH (MH111661). Thanks to the MSPCF of IRB Barcelona, a principal unit in Proteored, PRB3, supported by PT17/0019 of the PE I+D+i 2013-2016, funded by SCIII and ERDF. This study makes use of data generated by the DECIPHER community. A full list of centres that contributed to the generation of the data is available from: http://decipher.sanger.ac.uk and via email from: email@example.com. Funding for the project was provided by the Wellcome Trust.
Competing interests None declared.
Patient consent for publication Parental/Guardian consent obtained.
Ethics approval The study protocol was approved by the internal Ethics Committee, according to the Declaration of Helsinki and informed consent was obtained from participating families.
Provenance and peer review Not commissioned; externally peer reviewed.
Data availability statement Data are available in a public, open access repository or included in the article or uploaded as supplementary information.
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