Integrated multi-omics reveal epigenomic disturbance of assisted reproductive technologies in human offspring

Abstract

Background The births of more than 8 million infants have been enabled globally through assisted reproductive technologies (ARTs), including conventional in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) with either fresh embryo transfer (ET) or frozen embryo transfer (FET). However, the safety issue regarding ARTs has drawn growing attention with accumulating observations of rising health risks, and underlying epigenetic mechanisms are largely uncharacterized. Methods In order to clarify epigenetic risks attributable to ARTs, we profiled DNA methylome on 137 umbilical cord blood (UCB) and 158 parental peripheral blood (PPB) samples, histone modifications (H3K4me3, H3K4me1, H3K27me3 and H3K27ac) on 33 UCB samples and transcriptome on 32 UCB samples by reduced representation bisulfite sequencing (RRBS), chromatin immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq), respectively. Findings We revealed that H3K4me3 was the most profoundly impacted by ICSI and freeze-thawing operation compared with the other three types of histone modifications. IVF-ET seemed to introduce less disturbance into infant epigenomes than IVF-FET or ICSI-ET did. ARTs also decreased the similarity of DNA methylome within twin pairs, and we confirmed that ART per se would introduce conservative changes locally through removal of parental effect. Importantly, those unique and common alterations induced by different ART procedures were highly enriched in the processes related to nervous system, cardiovascular system and glycolipid metabolism etc., which was in accordance with those findings in previous epidemiology studies and suggested some unexplored health issues, including in the immune system and skeletal system. Interpretation Different ART procedures can induce local and functional epigenetic abnormalities, especially for DNA methylation and H3K4me3, providing an epigenetic basis for the potential long-term health risks in ART-conceived offspring. Funding sources This study was funded by National Natural Science Foundation of China (81,730,038; 81,521,002), National Key Research and Development Program (2018YFC1004000; 2017YFA0103801; 2017YFA0105001) and Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16020703). Yang Wang was supported by Postdoctoral Fellowship of Peking-Tsinghua Center for Life Science.

Comparison of Histone H3K4me3 between IVF and ICSI Technologies and between Boy and Girl Offspring

“…Similar findings were recently reported by Chen and colleagues [24], who found that H3K4me3, but not H3K4me1, H3K27me3, or H3K27ac, showed differences in newborn CBMC from natural conception and ART groups. Herein, we found ICSI placentas showed lower levels of H3K4me3 than naturally conceived placentas.…”

“…Besides, H3K4me3 is the most affected histone modification in the in vitro culture system [27]. A previous study suggested that H3K4me3 may potentially serve as a marker for evaluating the influence of ARTs [24].…”

Environmental Exposures around Conception: Developmental Pathways Leading to Lifetime Disease Risk

“…However, whilst there is evidence of ART affecting human birth weight [128] and associating with adverse cardiometabolic health in offspring [129][130][131], there are many confounders that complicate interpretation, including parental infertility status and varied demographics, the introduction of improved protocols over time and differences between clinics and the relatively young age of offspring born to date. Moreover, while epigenetic abnormalities are detected in ART offspring [132], variations in DNA methylation, potentially symptomatic of later disease, may not be permanent and can resolve by adulthood [133].…”

OUP accepted manuscript

“…Normalized normative adult peripheral blood RRBS profiles were obtained from GSE136849 (Table 1 ) ( 37 ). Because the RRBS dataset coordinates are based on the GRCh38/hg38 human genome assembly, they were converted to the GRCh37/hg19 assembly using liftover from the UCSC.…”

“…Predictors were tested on several independent blood-based datasets: normative samples from the GSE132203, GSE125105 and ARIES cohorts, as well as clinical and matching control samples from the Klinefelter (47,XXY), Turner (45,X) and 47,XXX syndrome cohorts ( 63–65 ). The region-based predictor was also tested in the blood RRBS dataset ( 37 ). All test results are presented in Table 3 .…”