Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome

Large/abnormal offspring syndrome (LOS/AOS) is a congenital overgrowth syndrome reported in ruminants produced by assisted reproduction (ART-LOS) which exhibit global disruption of the epigenome and transcriptome. LOS/AOS shares phenotypes and epigenotypes with the human congenital overgrowth condition Beckwith-Wiedemann syndrome. We have reported that LOS occurs spontaneously (SLOS), however, to date, no study has been conducted to determine if SLOS has the same methylome epimutations as ART-LOS. In this study, we performed whole genome bisulfite sequencing to examine global DNA methylation in SLOS and ART-LOS tissues. We observed unique patterns of global distribution of differentially methylated regions (DMRs) over different genomic contexts, such as promoters, CpG islands and surrounding regions, and repetitive sequences from different treatment groups. In addition, we identified hundreds of LOS-vulnerable DMRs across different cattle breeds when analyzing four idependent LOS experiments together. Specifically, there are 25 highly vulnerable DMRs that could potentially serve as molecular markers for the diagnosis of LOS, including at the promoters of DMRT2 and TBX18, at the imprinted gene bodies of IGF2R, PRDM8, and BLCAP/NNAT, and at multiple CpG islands. We also observed tissue-specific DNA methylation patterns between muscle and blood, and conservation of ART-induced DNA methylation changes between muscle and blood. We conclude that as in ART-LOS, alterations of the epigenome are involved in the etiology of SLOS. In addition, SLOS and ART-LOS share some similarities in methylome epimutations. Whole genome bisulfite sequencing (WGBS) for tissues (mainly blood and muscle) of bovine calves from control and treatment groups. Animals from the US include three from the control group, eight from the SLOS group, and three which are relatives to one SLOS animal. Animals from Spain (ES) include three from the control group, four from the ART group, three from the reproductive fluid (RF) group, and two from the RF_necropsy group.

大/异常子代综合征（Large/abnormal offspring syndrome, LOS/AOS）是一类在辅助生殖技术繁育的反刍动物中被报道的先天性过度生长综合征（ART-LOS），该病症伴随表观基因组与转录组的全局紊乱。LOS/AOS与人类先天性过度生长疾病贝克威思-威德曼综合征（Beckwith-Wiedemann syndrome）共享表型与表观表型特征。此前已有研究报道自发性LOS（SLOS）的存在，但截至目前尚无研究探讨SLOS是否与ART-LOS具有相同的甲基化组表观突变。本研究通过全基因组亚硫酸氢盐测序（whole genome bisulfite sequencing, WGBS）分析了SLOS与ART-LOS组织的全局DNA甲基化水平。我们观察到不同处理组的差异甲基化区域（differentially methylated regions, DMRs）在启动子、CpG岛及其侧翼区域、重复序列等不同基因组语境下呈现独特的全局分布模式。此外，在整合4项独立LOS实验的分析中，我们在不同牛品种中鉴定出数百个易感LOS的DMRs，其中25个高易感DMRs可作为LOS诊断的潜在分子标志物，包括DMRT2与TBX18的启动子区域、IGF2R、PRDM8及BLCAP/NNAT的印记基因本体区域，以及多个CpG岛。我们还发现肌肉与血液之间存在组织特异性的DNA甲基化模式，且ART诱导的DNA甲基化改变在肌肉与血液中具有保守性。综上，与ART-LOS一致，表观基因组改变同样参与SLOS的发病机制；此外，SLOS与ART-LOS在甲基化组表观突变方面存在部分相似性。本研究的测序样本来自对照组与处理组牛犊的组织（主要为血液与肌肉）：美国来源样本包含3只对照个体、8只SLOS个体，以及3只与某只SLOS动物存在亲缘关系的个体；西班牙（ES）来源样本包含3只对照个体、4只ART组个体、3只生殖液（RF）组个体，以及2只RF尸检组个体。