1
|
Lybaek H, Robson M, de Leeuw N, Hehir-Kwa JY, Jeffries A, Haukanes BI, Berland S, de Bruijn D, Mundlos S, Spielmann M, Houge G. LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions. Autism Res 2022; 15:421-433. [PMID: 35088940 PMCID: PMC9305582 DOI: 10.1002/aur.2677] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/25/2022]
Abstract
LRFN5 is a regulator of synaptic development and the only gene in a 5.4 Mb mammalian‐specific conserved topologically associating domain (TAD); the LRFN5 locus. An association between locus structural changes and developmental delay (DD) and/or autism was suggested by several cases in DECIPHER and own records. More significantly, we found that maternal inheritance of a specific LRFN5 locus haplotype segregated with an identical type of autism in distantly related males. This autism‐susceptibility haplotype had a specific TAD pattern. We also found a male/female quantitative difference in the amount histone‐3‐lysine‐9‐associated chromatin around the LRFN5 gene itself (p < 0.01), possibly related to the male‐restricted autism susceptibility. To better understand locus behavior, the prevalence of a 60 kb deletion polymorphism was investigated. Surprisingly, in three cohorts of individuals with DD (n = 8757), the number of deletion heterozygotes was 20%–26% lower than expected from Hardy–Weinberg equilibrium. This suggests allelic interaction, also because the conversions from heterozygosity to wild‐type or deletion homozygosity were of equal magnitudes. Remarkably, in a control group of medical students (n = 1416), such conversions were three times more common (p = 0.00001), suggesting a regulatory role of this allelic interaction. Taken together, LRFN5 regulation appears unusually complex, and LRFN5 dysregulation could be an epigenetic cause of autism.
Collapse
Affiliation(s)
- Helle Lybaek
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Michael Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | | | | | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Diederik de Bruijn
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.,Institute of Clinical Medicine K2, Faculty of Medicine, University of Bergen, Bergen, Norway.,Honorary Chair of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| |
Collapse
|
2
|
de Bruijn DRH, van Dijk AHA, Pfundt R, Hoischen A, Merkx GFM, Gradek GA, Lybæk H, Stray-Pedersen A, Brunner HG, Houge G. Severe Progressive Autism Associated with Two de novo Changes: A 2.6-Mb 2q31.1 Deletion and a Balanced t(14;21)(q21.1;p11.2) Translocation with Long-Range Epigenetic Silencing of LRFN5 Expression. Mol Syndromol 2010; 1:46-57. [PMID: 20648246 DOI: 10.1159/000280290] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 12/02/2009] [Indexed: 01/12/2023] Open
Abstract
In a 19-year-old severely autistic and mentally retarded girl, a balanced de novo t(14;21)(q21.1;p11.2) translocation was found in addition to a de novo 2.6-Mb 2q31.1 deletion containing 15 protein-encoding genes. To investigate if the translocation might contribute to developmental stagnation at the age of 2 years with later regression of skills, i.e. a more severe phenotype than expected from the 2q31.1 deletion, the epigenetic status and expression of genes proximal and distal to the 14q21.1 breakpoint were investigated in Ebstein Barr Virus-transformed lymphoblast and primary skin fibroblast cells. The 14q21.1 breakpoint was found to be located between a cluster of 7 genes 0.1 Mb upstream, starting with FBXO33, and the single and isolated LRFN5 gene 2.1 Mb downstream. Only expression of LRFN5 appeared to be affected by its novel genomic context. In patient fibroblasts, LRFN5 expression was 10-fold reduced compared to LRFN5 expressed in control fibroblasts. In addition, a relative increase in trimethylated histone H3 lysine 9 (H3K9M3)-associated DNA starting exactly at the translocation breakpoint and going 2.5 Mb beyond the LRFN5 gene was found. At the LRFN5 promoter, there was a distinct peak of trimethylated histone H3 lysine 27 (H3K27M3)-associated DNA in addition to a diminished trimethylated histone H3 lysine 4 (H3K4M3) level. We speculate that dysregulation of LRFN5, a postsynaptic density-associated gene, may contribute to the patient's autism, even though 2 other patients with 14q13.2q21.3 deletions that included LRFN5 were not autistic. More significantly, we have shown that translocations may influence gene expression more than 2 Mb away from the translocation breakpoint.
Collapse
Affiliation(s)
- D R H de Bruijn
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|