Zhuang Jianlong, Li Yanqing, Chen Yu'e, Zhang Hegan, Liu Shufen, Hu Manman, Chen Chunnuan
Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China.
Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China.
BMC Genomics. 2025 Feb 5;26(1):113. doi: 10.1186/s12864-025-11297-3.
Split-hand/foot malformation (SHFM) is a congenital disability characterized by the absence or hypoplasia of the central ray of the hands and/or feet. This study reports a causative variant in the TP63 gene in a Chinese family exhibiting limb anomalies associated with SHFM4.
Enrolled in this study was a Chinese family with limb anomalies without any other clinical features. Karyotype analysis and chromosomal microarray analysis (CMA) were conducted to identify chromosomal abnormalities. Whole exome sequencing (WES) was utilized to investigate sequence variants, while RNA sequencing assessed differentially expressed genes, with findings confirmed through quantitative PCR (qPCR).
Karyotype analysis and CMA revealed no chromosomal abnormalities in the family. Subsequently, WES identified a rare heterozygous variant of NM_003722.5: c.956G > A (p.Arg319His) in the TP63 gene in the proband, which was inherited from her father who also presented with limb deformities. However, both of the sister and grandfather of the proband had the same variant but exhibited normal limb morphology. RNA sequencing results demonstrated an increased expression level of TP63 and its downstream genes (PERP, CDH3, and DLX5) compared with the controls, indicating an enrichment of cell adhesion molecules the differentially expressed genes in the patient. However, significant differences were noted only for the CDH3 and DLX5 genes in qPCR analysis (p<0.05).
This study identifies, for the first time, the TP63 gene variant c.956G > A (p.Arg319His) as a causative factor for SHFM4 in Chinese individuals with incomplete penetrance. In addition, we hypothesize that the p.Arg319His variant functions as a gain-of-function variant, leading to the upregulation of cell adhesion target genes. Such upregulation then disrupts the p63-Dlx signaling pathway and causes AER stratification failure.
裂手/裂足畸形（SHFM）是一种先天性残疾，其特征是手和/或脚的中央射线缺失或发育不全。本研究报告了一个中国家庭中TP63基因的致病变异，该家庭表现出与SHFM4相关的肢体异常。
本研究纳入了一个无任何其他临床特征的肢体异常中国家庭。进行了核型分析和染色体微阵列分析（CMA）以鉴定染色体异常。利用全外显子组测序（WES）研究序列变异，同时RNA测序评估差异表达基因，结果通过定量PCR（qPCR）得到证实。
核型分析和CMA显示该家庭无染色体异常。随后，WES在先证者的TP63基因中鉴定出一种罕见的杂合变异NM_003722.5:c.956G＞A（p.Arg319His），该变异遗传自她同样有肢体畸形的父亲。然而，先证者的姐姐和祖父都有相同的变异，但肢体形态正常。RNA测序结果表明，与对照组相比，患者中TP63及其下游基因（PERP、CDH3和DLX5）的表达水平升高，表明差异表达基因中细胞粘附分子富集。然而，qPCR分析中仅CDH3和DLX5基因存在显著差异（p<0.05）。
本研究首次确定TP63基因变异c.956G＞A（p.Arg319His）是中国个体中SHFM4的致病因素，且具有不完全外显率。此外，我们假设p.Arg319His变异作为一种功能获得性变异，导致细胞粘附靶基因上调。这种上调随后破坏p63-Dlx信号通路并导致顶外胚层嵴分层失败。
