Exploring by whole exome sequencing patients with initial diagnosis of Rubinstein–Taybi syndrome: the interconnections of epigenetic machinery disorders

Abstract

Rubinstein–Taybi syndrome (RSTS) is an autosomal-dominant neurodevelopmental disease affecting 1:125,000 newborns characterized by intellectual disability, growth retardation, facial dysmorphisms and skeletal abnormalities. RSTS is caused by mutations in genes encoding for writers of the epigenetic machinery: CREBBP (~ 60%) or its homologous EP300 (~ 10%). No causative mutation is identified in up to 30% of patients. We performed whole-exome sequencing (WES) on eight RSTS-like individuals who had normal high-resolution array CGH testing and were CREBBP- and EP300-mutation -negative, to identify the molecular cause. In four cases, we identified putatively causal variants in three genes (ASXL1, KMT2D and KMT2A) encoding members of the epigenetic machinery known to be associated with the Bohring–Opitz, Kabuki and Wiedemann–Steiner syndromes. Each variant is novel, de novo, fulfills the ACMG criteria and is predicted to result in loss-of-function leading to haploinsufficiency of the epi-gene. In two of the remaining cases, homozygous/compound heterozygous variants in XYLT2 and PLCB4 genes, respectively, associated with spondyloocular and auriculocondylar 2 syndromes and in the latter an additional candidate variant in XRN2, a gene yet unrelated to any disease, were detected, but their pathogenicity remains uncertain. These results underscore the broad clinical spectrum of Mendelian disorders of the epigenetic apparatus and the high rate of WES disclosure of the genetic basis in cases which may pose a challenge for phenotype encompassing distinct syndromes. The overlapping features of distinct intellectual disability syndromes reflect common pathogenic molecular mechanisms affecting the complex regulation of balance between open and closed chromatin.

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Acknowledgements

We thank the patients’ families for participating in this study. CG thanks the Italian Association of Rubinstein–Taybi patients “RTS Una Vita Speciale ONLUS” for its support and Dr. Giordano, Dr. Ficcadenti, Dr. Cavaliere, Dr. Vitiello for providing clinical data of patients #76, #88, #118 and #169, respectively. This work was supported by University of Milan young researcher grant to CG (Dotazione d’Ateneo linea 2 del piano di sostegno alla ricerca), by Associazione “RTS Una Vita Speciale ONLUS” (project #DigiRare) to CG and by a Ministry of Health grant to Istituto Auxologico Italiano IRCCS (08C623_2016) to PF.

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Contributions

TP and CG: conceived the project. DM, EB, MP, SS, CP, GV, MF, AB, MS: contributed to patient recruitment and/or provided biological samples. GN, PM, EDF, EAC, MCG, IL, PF: contributed to molecular analyses. UWCMG, MJB, DAN, JDS: performed bioinformatics analyses. PM, GN, CG, TP: performed data analysis and interpretation. GN, LL, TP and CG: wrote the manuscript. All authors: approved the manuscript.

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Correspondence to Cristina Gervasini.

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Supplemental Table S1: list of mutations so far described for ASXL1 gene (DOCX 17 KB)

Supplemental Table S2: list of mutations so far described for KMT2D gene (DOCX 34 KB)

Supplemental Table S3: list of mutations so far described for KMT2A gene (DOCX 17 KB)

Supplemental Table S4: variants detected in RSTS-like patients with unclear pathogenetic role. Position and type of the pathogenic variants are indicated (DOCX 15 KB)

Supplemental Table S5: Clinical signs of patients #76, #88, #118 and #169 compared to typical features of RSTS (DOCX 16 KB)

Supplementary material 6 (DOCX 39 KB)

Supplemental Fig. S1: Gene distribution of described ASXL1, KMT2A and KMT2D mutations. Colored rectangles represent the main protein domains. Dashed lines indicate start and stop codons. Known mutations are depicted as red = truncating, blue = missense, green = inframe indel. Intragenic positions of variants identified in the present work are indicated in black. GPviz software was used to visualize mutations (TIF 248 KB)

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Negri, G., Magini, P., Milani, D. et al. Exploring by whole exome sequencing patients with initial diagnosis of Rubinstein–Taybi syndrome: the interconnections of epigenetic machinery disorders. Hum Genet 138, 257–269 (2019). https://doi.org/10.1007/s00439-019-01985-y

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