ZBTB11 mutations

Inspired by a patient

Sumathipala D, Strømme P, Fattahi Z, Lüders T, Sheng Y, Kahrizi K, Einarsen IH, Sloan JL, Najmabadi H, van den Heuvel L, Wevers RA, Guerrero-Castillo S, Mørkrid L, Valayannopoulos V, Backe PH, Venditti CP, van Karnebeek CD, Nilsen H, Frengen E, Misceo D. ZBTB11 dysfunction: spectrum of brain abnormalities, biochemical signature and cellular consequences. Brain. 2022 Jul 29;145(7):2602-2616. doi: 10.1093/brain/awac034. PMID: 35104841; PMCID: PMC9337812.

Abstract

Bi-allelic pathogenic variants in ZBTB11 have been associated with intellectual developmental disorder, autosomal recessive 69 (MRT69; OMIM 618383). We report five patients from three families with novel, bi-allelic variants in ZBTB11. We have expanded the clinical phenotype of MRT69, documenting varied severity of atrophy affecting different brain regions and described combined malonic and methylmalonic aciduria as a biochemical manifestation. As ZBTB11 encodes for a transcriptional regulator, we performeded chromatin immunoprecipitation-sequencing targeting ZBTB11 in fibroblasts from patients and controls. Chromatin immunoprecipitation-sequencing revealed binding of wild-type ZBTB11 to promoters in 238 genes, among which genes encoding proteins involved in mitochondrial functions and RNA processing are over-represented. Mutated ZBTB11 showed reduced binding to 61 of the targeted genes, indicating that the variants act as loss of function. Most of these genes are related to mitochondrial functions. Transcriptome analysis of the patient fibroblasts revealed dysregulation of mitochondrial functions. In addition, we uncovered that reduced binding of the mutated ZBTB11 to ACSF3 leads to decreased ACSF3 transcript level, explaining combined malonic and methylmalonic aciduria. Collectively, these results expand the clinical spectrum of ZBTB11-related neurological disease and give insight into the pathophysiology in which the dysfunctional ZBTB11 affect mitochondrial functions and RNA processing contributing to the neurological and biochemical phenotypes.

Scala M, De Grandis E, Nobile G, Iacomino M, Madia F, Capra V, Nobili L, Zara F, Striano P. Biallelic ZBTB11 variants associated with complex neuropsychiatric phenotype featuring Tourette syndrome. Brain. 2023 Jan 5;146(1):e1-e4. doi: 10.1093/brain/awac323. PMID: 36068688; PMCID: PMC9825546.

No abstract. From the article:

In summary, we report a complex neuropsychiatric phenotype associated with ZBTB11 variants not strictly overlapping the previously described classic phenotype. However, milder phenotypes have been reported in subjects boring the homozygous c.154C>T (p.Arg52Trp) variant. These patients showed a mild cognitive impairment, subtle brain malformations, and no evident metabolic abnormalities, thus partially resembling our patient.1 The (p.Arg52Trp) change affects a conserved residue outside ZBTB11 functional domains and lies very close to the Arg34 residue, which is affected in our patient. Although further confirmation is needed, this would lead to suggest that variants located early in the ZBTB11 protein, outside the main functional domains, may be associated with a likely milder and more heterogeneous clinical phenotype.

Behavioural abnormalities reported in ZBTB11 patients include autism, stereotypies and ritualistic behaviour. The neuropsychiatric manifestations in our patient are instead suggestive of Tourette syndrome, a complex condition characterized by tics involving any part of the body (especially the face), usually starting in childhood and often improving in adult life.5 Although Tourette syndrome is a highly heritable disorder, it has complex genetics involving both common mildly deleterious and rare highly damaging variants in several crucial genes for neuronal function. Recently, a potentially relevant pathophysiological role has been suggested for genes encoding proteins involved in mitochondrial transport (NDE1, DISC1, OPA1), fusion (OPA1) and fission (ADCY). Of note, ZBTB11 variants were found to affect ZBTB11 binding to several target genes, including those encoding proteins involved in mitochondrial functions. This is also supported by the mitochondrial dysfunction observed in ZBTB11 patient fibroblasts, mainly resulting from the downregulation of genes implicated in the mitochondrial respiratory complex biogenesis and translation. Overall, these findings suggest a pathophysiological link between Tourette syndrome and the ZBTB11 variants detected in our patient. The lack of similar neuropsychiatric manifestations in other ZBTB11 patients might depend on several factors, including the localization of the variants, and further studies should confirm this association. However, our case raises the possibility that ZBTB11, as an essential transcriptional regulator, plays a role as a risk gene in Tourette syndrome...

Hence, our case raises the possibility that the phenotypical spectrum of MRT69 may be wider than expected based on previous reports, suggesting that patients harbouring biallelic variants in ZBTB11 may show a more heterogeneous neurodevelopmental and neuropsychiatric involvement. In particular, Tourette syndrome in our patient suggests a possible pathophysiological link between this condition and the mitochondrial dysfunction resulting from loss of function ZBTB11 variants. Further studies will play a pivotal role in the refinement of ZBTB11-related neuropsychiatric features and the investigation of the potential role of ZBTB11 as a risk gene for Tourette syndrome.

Fattahi Z, Sheikh TI, Musante L, Rasheed M, Taskiran II, Harripaul R, Hu H, Kazeminasab S, Alam MR, Hosseini M, Larti F, Ghaderi Z, Celik A, Ayub M, Ansar M, Haddadi M, Wienker TF, Ropers HH, Kahrizi K, Vincent JB, Najmabadi H. Biallelic missense variants in ZBTB11 can cause intellectual disability in humans. Hum Mol Genet. 2018 Sep 15;27(18):3177-3188. doi: 10.1093/hmg/ddy220. PMID: 29893856.

Abstract

Exploring genes and pathways underlying intellectual disability (ID) provides insight into brain development and function, clarifying the complex puzzle of how cognition develops. As part of ongoing systematic studies to identify candidate ID genes, linkage analysis and next-generation sequencing revealed Zinc Finger and BTB Domain Containing 11 (ZBTB11) as a novel candidate ID gene. ZBTB11 encodes a little-studied transcription regulator, and the two identified missense variants in this study are predicted to disrupt canonical Zn2+-binding residues of its C2H2 zinc finger domain, leading to possible altered DNA binding. Using HEK293T cells transfected with wild-type and mutant GFP-ZBTB11 constructs, we found the ZBTB11 mutants being excluded from the nucleolus, where the wild-type recombinant protein is predominantly localized. Pathway analysis applied to ChIP-seq data deposited in the ENCODE database supports the localization of ZBTB11 in nucleoli, highlighting associated pathways such as ribosomal RNA synthesis, ribosomal assembly, RNA modification and stress sensing, and provides a direct link between subcellular ZBTB11 location and its function. Furthermore, given the report of prominent brain and spinal cord degeneration in a zebrafish Zbtb11 mutant, we investigated ZBTB11-ortholog knockdown in Drosophila melanogaster brain by targeting RNAi using the UAS/Gal4 system. The observed approximate reduction to a third of the mushroom body size-possibly through neuronal reduction or degeneration-may affect neuronal circuits in the brain that are required for adaptive behavior, specifying the role of this gene in the nervous system. In conclusion, we report two ID families segregating ZBTB11 biallelic mutations disrupting Zn2+-binding motifs and provide functional evidence linking ZBTB11 dysfunction to this phenotype.

Wilson BC, Boehme L, Annibali A, Hodgkinson A, Carroll TS, Oakey RJ, Seitan VC. Intellectual disability-associated factor Zbtb11 cooperates with NRF-2/GABP to control mitochondrial function. Nat Commun. 2020 Oct 29;11(1):5469. doi: 10.1038/s41467-020-19205-x. PMID: 33122634; PMCID: PMC7596099.

Abstract

Zbtb11 is a conserved transcription factor mutated in families with hereditary intellectual disability. Its precise molecular and cellular functions are currently unknown, precluding our understanding of the aetiology of this disease. Using a combination of functional genomics, genetic and biochemical approaches, here we show that Zbtb11 plays essential roles in maintaining the homeostasis of mitochondrial function. Mechanistically, we find Zbtb11 facilitates the recruitment of nuclear respiratory factor 2 (NRF-2) to its target promoters, activating a subset of nuclear genes with roles in the biogenesis of respiratory complex I and the mitoribosome. Genetic inactivation of Zbtb11 resulted in a severe complex I assembly defect, impaired mitochondrial respiration, mitochondrial depolarisation, and ultimately proliferation arrest and cell death. Experimental modelling of the pathogenic human mutations showed these have a destabilising effect on the protein, resulting in reduced Zbtb11 dosage, downregulation of its target genes, and impaired complex I biogenesis. Our study establishes Zbtb11 as an essential mitochondrial regulator, improves our understanding of the transcriptional mechanisms of nuclear control over mitochondria, and may help to understand the aetiology of Zbtb11-associated intellectual disability.