Chromosomal abnormalities in hepatic cysts point to novel polycystic liver disease genes

Autosomal dominant polycystic liver disease (ADPLD) is caused by mutations in PRKCSH, SEC63, and LRP5, while autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1, and PKD2. Liver cyst development in these disorders is explained by somatic loss-of-heterozygosity (LOH) of the wild type allele in the developing cyst. We hypothesize that we can use this mechanism to identify novel disease genes that reside in LOH regions. In this study, we aim to map abnormal genomic regions using high-density SNP microarrays to find novel polycystic liver disease genes. We collected 46 cysts from 23 patients with polycystic or sporadic hepatic cysts, and analyzed DNA from those cysts using high-resolution microarray (n=24) or Sanger sequencing (n=22). We here focused on regions of homozygosity on the autosomes (>3.0Mb), and large CNVs (>1.0Mb). We found frequent LOH in PRKCSH (22/29), and PKD1/PKD2 (2/3) cysts of patients with known heterozygous germline variants in the respective genes. In the total cohort, 12/23 patients harbored abnormalities outside of familiar areas. In individual ADPLD cases, we identified germline events: a 2q13 complex rearrangement resulting in BUB1 haploinsufficiency, a 47XXX karyotype, chromosome 9q copy number loss, and LOH on chromosome 3p. The latter region was overlapping with an LOH region identified in two other cysts. Unique germline and somatic abnormalities occur frequently in and outside of known genes underlying cysts. Each liver cyst has a unique genetic makeup. LOH driver gene BUB1 may imply germline causes of genetic instability in PLD. 24 liver cysts from 23 patients常染色体显性遗传性多囊肝病 (Autosomal dominant polycystic liver disease, ADPLD) 由PRKCSH、SEC63及LRP5基因的突变引发，而常染色体显性遗传性多囊肾病 (Autosomal dominant polycystic kidney disease, ADPKD) 则由PKD1与PKD2基因的突变所致。此类疾病中肝囊肿的发生机制，可通过发育中的囊肿内野生型等位基因发生体细胞杂合性缺失 (somatic loss-of-heterozygosity, LOH) 得到解释。我们提出假说：可依托该机制鉴定位于LOH区域内的新型疾病基因。本研究旨在通过高密度单核苷酸多态性 (Single Nucleotide Polymorphism, SNP) 微阵列绘制异常基因组区域，以发现新型多囊肝病相关基因。我们从23名罹患多囊性或散发性肝囊肿的患者体内采集了46个囊肿样本，并分别采用高分辨率微阵列（n=24）或桑格测序 (Sanger sequencing, n=22) 对这些囊肿的DNA进行分析。本研究聚焦于常染色体上的长片段纯合区域（>3.0Mb）以及大片段拷贝数变异 (Copy Number Variations, CNVs, >1.0Mb)。我们发现，在已知对应基因存在杂合生殖系变异的患者囊肿中，PRKCSH（22/29）及PKD1/PKD2（2/3）囊肿常出现LOH现象。在全部研究队列中，12/23的患者存在已知基因区域之外的基因组异常。在个别ADPLD病例中，我们鉴定出了多种生殖系事件：包括导致BUB1单倍体剂量不足的2q13区域复杂重排、47XXX核型、9号染色体q区段拷贝数缺失，以及3号染色体p区段的LOH。其中后者的区域与另外两个囊肿中鉴定出的LOH区域存在重叠。独特的生殖系与体细胞异常频繁出现于已知囊肿易感基因的区域内外。每一个肝囊肿都具备独特的遗传特征。作为LOH驱动基因的BUB1可能提示了多囊肝病中遗传不稳定性的生殖系诱因。本研究纳入了来自23名患者的24个肝囊肿样本。