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Modelling the developmental spliceosomal craniofacial disorder Burn-McKeown syndrome using induced pluripotent stem cells

ABSTRACT: The craniofacial developmental disorder Burn-McKeown Syndrome (BMKS) is caused by biallelic variants in the pre-messenger RNA splicing factor gene TXNL4A/DIB1. The majority of affected individuals with BMKS have a 34 base pair deletion in the promoter region of one allele of TXNL4A combined with a loss-of-function variant on the other allele, resulting in reduced TXNL4A expression. However, it is unclear how reduced expression of this ubiquitously expressed spliceosome protein results in craniofacial defects during development. Here we reprogrammed peripheral mononuclear blood cells from a BMKS patient and her unaffected mother into induced pluripotent stem cells (iPSCs) and differentiated the iPSCs into induced neural crest cells (iNCCs), the key cell type required for correct craniofacial development. BMKS patient-derived iPSCs proliferated more slowly than both mother- and unrelated control-derived iPSCs, and RNA-Seq analysis revealed significant differences in gene expression and alternative splicing. Patient iPSCs displayed defective differentiation into iNCCs compared to maternal and unrelated control iPSCs, in particular a delay in undergoing an epithelial-to-mesenchymal transition (EMT). RNA-Seq analysis of differentiated iNCCs revealed widespread gene expression changes and mis-splicing in genes relevant to craniofacial and embryonic development that highlight a dampened response to WNT signalling, the key pathway activated during iNCC differentiation. Furthermore, we identified the mis-splicing of TCF7L2 exon 4, a key gene in the WNT pathway, as a potential cause of the downregulated WNT response in patient cells. Additionally, mis-spliced genes shared common physical properties such as length, splice site strengths and sequence motifs, suggesting that splicing of particular subsets of genes is particularly sensitive to changes in TXNL4A expression. Together, these data provide the first insight into how reduced TXNL4A expression in BMKS patients might compromise splicing and NCC function, resulting in defective craniofacial development in the embryo.

ORGANISM(S): Homo sapiens

PROVIDER: GSE149369 | GEO | 2020/08/05

REPOSITORIES: GEO

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Project description:Purpose: Heterozygous mutations in SNRPB, an essential core component of the five small ribonucleoprotein particles of the spliceosome, are responsible for craniofacial and rib defects in patients with Cerebrocostomandibular Syndrome (CCMS). However, why the mutations in SNRPB causes tissue specific CCMS abnormalities such as craniofacial defects are unknown. We hypothesize that splicing of tissue specific transcripts required for craniofacial development is disrupted due to SNRPB deficiency, during embryonic development. The purpose of the study was to identify those developmentally important transcripts that are dysregulated due to Snrpb mutation. Methods: We mated Snrpbloxp mice that we have developed with commercially available Wnt-1-Cre2 transgenic mice to remove one allele of Snrpb from neural crest cells. The mutant (Snrpb \ncc+/-) embryos showed craniofacial abnormalities at E9.5 and onward. We collected morphologically normal embryos at E9.0 for both Snrpb wildtype and Snrpbncc+/- mutants. We pooled two embryo heads of similar somites for each genotype and extracted the RNA for RNAseq. Results: We found that Snrpbncc+/- mutants show aberrant splicing that includes both increased exon skipping and intron retention. A strong tendency towards increased exon skipping and intron inclusion in the mutant samples were observed; there were more SE (273 in Het versus 83 in WT) and RI (191 in Het versus 21 in WT). We identified 13 transcripts required for craniofacial development or stem cell development with significant increases in exon skipping including Smad2, Rere and Pou2f1. From pathway analysis of differentially expressed genes, we found they were associated with the spliceosome and the P53-pathway. We also found an increase in splicing of two P53 regulator, Mdm2 and Mdm4. Conclusions: We propose that abnormal splicing underlies the defects found in Snrpbncc+/-mutant embryos. We confirmed differential splicing of the P53 regulators, Mdm2 and Mdm4 and identified several transcripts important for craniofacial development which were abnormally spliced in Snrpbncc+/- embryos.

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Modelling the developmental spliceosomal craniofacial disorder Burn-McKeown syndrome using induced pluripotent stem cells

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