Abstract
Herein, we report on a large Polish family presenting with a classical triphalangeal thumb–polysyndactyly syndrome (TPT-PS). This rare congenital limb anomaly is generally caused by microduplications encompassing the Sonic Hedgehog (SHH) limb enhancer, termed the zone of polarizing activity (ZPA) regulatory sequence (ZRS). Recently, a pathogenic variant in the pre-ZRS (pZRS), a conserved sequence located near the ZRS, has been described in a TPT-PS Dutch family. We performed targeted ZRS sequencing, array comparative genomic hybridization, and whole-exome sequencing. Next, we sequenced the recently described pZRS region. Finally, we performed a circular chromatin conformation capture-sequencing (4C-seq) assay on skin fibroblasts of one affected family member and control samples to examine potential alterations in the SHH regulatory domain and functionally characterize the identified variant. We found that all affected individuals shared a recently identified pathogenic point mutation in the pZRS region: NC_000007.14:g.156792782C>G (GRCh38/hg38), which is the same as in the Dutch family. The results of 4C-seq experiments revealed increased interactions within the whole SHH regulatory domain (SHH-LMBR1 TAD) in the patient compared to controls. Our study expands the number of TPT-PS families carrying a pathogenic alteration of the pZRS and underlines the importance of routine pZRS sequencing in the genetic diagnostics of patients with TPT-PS or similar phenotypes. The pathogenic mutation causative for TPT-PS in our patient gave rise to increased interactions within the SHH regulatory domain in yet unknown mechanism.
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The datasets for this article are not publicly available due to concerns regarding participants’ anonymity. Requests to access the datasets should be directed to the corresponding author.
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Funding
A.S.-S. was supported by the Polish National Science Centre (grant: UMO-2016/21/D/NZ5/00064). A. Jankowski was supported by the Polish National Agency for Academic Exchange (Polish Returns 2019). A. Jamsheer was supported by the Polish National Science Centre (grant: UMO-2016/22/E/NZ5/00270).
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AJ and KM recruited and clinically diagnosed the patients. AJ critically revised the manuscript, designed and supervised the study. JW.P.P and AS-S designed the study and drafted the manuscript. AS-S designed and performed the 4C-seq experiments and analyzed the data. EB-O prepared Figs. 1, 2, and 3 and critically revised the manuscript. AJ performed bioinformatics and differential analysis of the 4C-seq data. PN, FM, CA.vN, R-JH. G and AdK performed the genetic analysis. All authors have read and approved the final manuscript.
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The study was approved by the Bioethics Committee at Poznan University of Medical Sciences (no. 459/17) according to the Good Clinical Practice and Polish law and by the Medical Ethics Committee of the Erasmus University Medical Centre in Rotterdam, the Netherlands (MEC-2015-12).
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Communicated by Shuhua Xu.
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Potuijt, J.W.P., Sowinska-Seidler, A., Bukowska-Olech, E. et al. The pZRS non-coding regulatory mutation resulting in triphalangeal thumb–polysyndactyly syndrome changes the pattern of local interactions. Mol Genet Genomics 297, 1343–1352 (2022). https://doi.org/10.1007/s00438-022-01921-2
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DOI: https://doi.org/10.1007/s00438-022-01921-2