Multiomic approaches identify a rare CCG repeat expansion in BCLAF3 in neurodevelopmental disorders.
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LaFlamme Christy W, Clarkson Chris, Ibañez Kristina, Wang Jin-Yuan, Sengupta Soham, Lord Jenny, Valentine Virginia, Bonkowski Emily S, Almanza Fuerte Edith P, Olszewski Athena R, Ghosh Sourav, Jadhav Bharati, Mack Taralynn, Lin Jiadong, Gibson Sophia B, van Hagen Johanna M, Alders Mariëlle, Martin-Geary Alexandra, Gu Bida, Kharbanda Mira, Banka Siddharth, Stuart Helen M, Webster Andrew R, Hosokawa Akimoto, Dashnow Harriet, Bajpai Richa, Pruett-Miller Shondra M, Chaisson Mark J P, Miller Danny E, Whiffin Nicola, Eichler Evan E, Sisodiya Sanjay M, Houlden Henry, Sharp Andrew J, Sadikovic Bekim, Valentine Marc, Sadleir Lynette G, Tucci Arianna, Mefford Heather C
Аннотация
METHODS: We used patient-derived fibroblasts and neuronal models from a family with BCLAF3 repeat expansions to generate multiomic data and investigate downstream molecular consequences of the repeat expansion. To identify additional affected individuals with BCLAF3 repeat expansions, we screened methylation arrays (n = 12,375) and short-read genomes (n = 15,963) from probands with neurodevelopmental presentations. We also characterized BCLAF3 repeat expansions in the general population using long-read sequencing data (n = 793) and population-level short-read sequencing data (n = 410,076).
RESULTS: Long-read sequencing validated hypermethylation of expanded repeats. Patient-derived cells showed repressed BCLAF3 RNA and protein expression. We show that the BCLAF3 CCG repeat expansion constitutes a previously uncharacterized fragile site (FRAXG) that shifts the surrounding chromatin compartment from open euchromatin to closed heterochromatin. Using our multiomic screening approaches, we identified three additional unrelated males and one related male cousin with long-read sequencing validated (n = 2) or short-read sequencing predicted (n = 2) repeat expansions. In one family, the BCLAF3 repeats segregate with more severe phenotypes than expected for the primary diagnoses. Long-read sequencing in three carrier mothers showed skewed X-inactivation against the repeat expansion, highlighting the potential deleterious effect of an allele with an expansion. Expansions were absent in long-read sequencing data from control populations. Assessment of the BCLAF3 repeat expansion in the UK Biobank indicates that it may be ~ 20X rarer than FMR1 repeat expansions.
CONCLUSIONS: CCG repeat expansions in the 5'UTR of BCLAF3 likely constitute a novel genetic etiology associated with X-linked neurodevelopmental phenotypes in males. Future work will be essential to delineate the phenotypic spectrum and determine a disease pathomechanism.