Cleavage-stage arrest in human embryos substantially limits the success rate of infertility treatment, with maternal-to-zygotic transition (MZT) abnormalities being a potential contributor. However, the underlying mechanisms and regulators remain unclear. Here, by performing allelic transcriptome analysis on human preimplantation embryos, we accurately quantified MZT progression by allelic ratio and identified a fraction of 8-cell embryos, at the appropriate developmental time point and exhibiting normal morphology, were in transcriptionally arrested status. Furthermore, we identified PAIRED (PRD)-like homeobox transcription factors divergent paired-related homeobox (DPRX) and arginine-fifty homeobox (ARGFX) as factors involved in MZT, whose deficiency severely impairs MZT and lineage specification and leads to aberrant retention of histone acetylation. By reversing the acetylation retention caused by DPRX and ARGFX defects, embryonic arrest can be partially rescued. Our study identifies factors involved in human MZT and elucidates the etiology underlying human cleavage-stage arrest.

Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.

AbstractPre-implantation genetic testing for aneuploidy (PGT-A) is used in approximately half of in vitro fertilization cycles. Given the limited understanding of the genetics of human embryos, the current use of PGT-A is based on biologically uncertain assumptions and unvalidated guidelines, leading to the possibility of disposing of embryos with pregnancy potential. We isolated and sequenced all single cells (1133) from in vitro cultured 20 human blastocysts. We found that all blastocysts exhibited mosaicism with mitotic-induced aneuploid cells and showed an ~25% aneuploidy rate per embryo. Moreover, 70% (14/20) of blastocysts contained ‘chromosome-complementary’ cells, suggesting genetic mosaicism is underestimated in routine PGT-A. Additionally, the analysis of 20,945 single cells from day 8–14 embryos (in vitro cultured) and embryonic/fetal organs showed that 97% of the analyzed embryos/organs were mosaic. Over 96% of their aneuploid cells harbored ≤ 2 chromosome errors. Our findings have revealed a high prevalence of mosaicism in human embryos.

Infertility has become a global health issue, with the number of people suffering from the disease increasing year by year, and ART offering great promise for infertility treatment. However, the regulation of early embryonic development is complicated and a series of processes takes place, including the maternal-to-zygotic transition. In addition, developmental arrest is frequently observed during human early embryonic development. In this study, we performed single-cell RNA sequencing on a biopsied blastomere from human eight-cell embryos and tracked the developmental potential of the remaining cells. To compare the sequencing results between different eight-cell embryos, we have combined the research data of this project with the data previously shared in the database and found that cells from the same embryo showed a higher correlation. Additionally, the transcriptome of embryos with blastocyst formation failure was significantly different from developed embryos, and the gene expression as well as cell signaling pathways related to embryonic development were also altered. In particular, the expression of some maternal and zygotic genes in the failed blastocyst formation group was significantly altered: the overall expression level of maternal genes was significantly higher in the failed blastocyst than the developed blastocyst group. In general, these findings provide clues for the causes of human embryonic arrest after the eight-cell stage, and they also provide new ideas for improving the success rate of ART in clinical practice.

Abstract Pre-implantation Genetic Testing for Aneuploidy (PGT-A) is widely used in half of in vitro fertilization (IVF) cycles, leading to the unwarranted disposal of embryos with pregnancy potential. Due to the limited understanding of genetics of human embryo, current PGT-A is built on biologically uncertain assumptions and on unvalidated guidelines1. Here, we sequenced all single cells (1,072) from 20 human blastocysts and analyzed 13,897 single cells from post-implantation embryos as well as fetal organs. Unexpectedly, all blastocysts contained mitotic aneuploid cells and showed about 25% aneuploidy rate per embryo. Among the 20 blastocysts, 70% (14/20) contained chromosome ‘complementary’ cells, suggesting the possible underestimation of mosaicism in traditional PGT-A. All the post-implantation embryos and fetal organs were mosaic, and over 80% of their aneuploid cells harbored ≤ 2 chromosome errors. Our findings showed all human embryos are naturally aneuploid-mosaic and this may provide guidance to the implementation of PGT-A in clinical practice.

Pneumonia induced by severe acute respiratory coronavirus 2 (SARS-CoV-2) via ACE2 receptor may affect many organ systems like lung, heart and kidney. An autopsy report revealed positive SARS-Cov-2 detection results in ovary, however, the developmental-stage-specific and cell-type-specific risk in fetal primordial germ cells (PGCs) and adult women ovary remained unclear. In this study, we used single-cell RNA-sequencing (scRNA-seq) datasets spanning several developmental stages of ovary including PGCs and cumulus-oocyte complex (COC) to investigate the potential risk of SARS-CoV-2 infection. We found that PGCs and COC exhibited high ACE2 expression. More importantly, the ratio of ACE2 -positive cells was sharply up-regulated in primary stage and ACE2 was expressed in all oocytes and cumulus cells in preovulatory stage, suggesting the possible risk of SARS-CoV-2 infection in follicular development. CatB/L, not TMPRSS2, was identified to prime for SARS-CoV-2 entry in follicle. Our findings provided insights into the potential risk of SARS-CoV-2 infection during folliculogenesis in adulthood and the possible risk in fetal PGCs.

The worldwide infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacts human health and life on multiple levels.People infected with SARS-CoV-2 suffer from physical disorders and psychological distress.At present,no direct evidence indicates that SARS-CoV-2 negatively influences human reproduction,and the possibility that gametes and embryos are affected requires further investigation.To evaluate the potential effects of SARS-CoV-2 infection on human reproduction and fetal health,this review summarizes the basic and clinical research of SARS-CoV-2 on reproduction up to date,hoping to offer guid-ance and advice to people at reproductive age and provide clues for the prevention and treatment of associated diseases.

Transcriptomic and epigenetic alterations during early embryo development have been proven to play essential roles in regulating the cell fate. Nowadays, advances in single-cell transcriptomics and epigenomics profiling techniques provide large volumes of data for understanding the molecular regulatory mechanisms in early embryos and facilitate the investigation of assisted reproductive technology as well as preimplantation genetic testing. However, the lack of integrated data collection and unified analytic procedures greatly limits their usage in scientific research and clinical application. Hence, it is necessary to establish a database integrating the regulatory information of human and mouse early embryos with unified analytic procedures. Here, we introduce DevOmics (http://devomics.cn/), which contains normalized gene expression, DNA methylation, histone modifications (H3K4me3, H3K9me3, H3K27me3, H3K27ac), chromatin accessibility and 3D chromatin architecture profiles of human and mouse early embryos spanning six developmental stages (zygote, 2cell, 4cell, 8cell, morula and blastocyst (ICM, TE)). The current version of DevOmics provides Search and Advanced Search for retrieving genes a researcher is interested in, Analysis Tools including the differentially expressed genes (DEGs) analysis for acquiring DEGs between different types of samples, allelic explorer for displaying allele-specific gene expression as well as epigenetic modifications and correlation analysis for showing the dynamic changes in different layers of data across developmental stages, as well as Genome Browser and Ortholog for visualization. DevOmics offers a user-friendly website for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryos.

Being infected by SARS-CoV-2 may cause damage to multiple organs in patients, such as the lung, liver and heart. Angiotensin-converting enzyme 2(ACE2), reported as a SARS-CoV-2 receptor, is also expressed in human male testes. This suggests a potential risk in human male reproductive system. However, the characteristics of ACE2-positive cells and the expression of other SARS-CoV-2 process-related genes are still worthy of further investigation. Here, we performed singlecell RNA seq(scRNA-seq) analysis on 853 male embryo primordial germ cells(PGCs) and 2,854 normal testis cells to assess the effects of the SARS-CoV-2 virus on the male reproductive system from embryonic stage to adulthood. We also collected and constructed the scRNA-seq library on 228 Sertoli cells from three non-obstructive azoospermia(NOA) patients to assess the effects at disease state. We found that ACE2 expressing cells existed in almost all testis cell types and Sertoli cells had highest expression level and positive cells ratio. Moreover, ACE2 was also expressed in human male PGCs. In adulthood, the level of ACE2 expression decreased with the increase of age. We also found that ACE2 positive cells had high expressions of stress response and immune activation-related genes. Interestingly, some potential SARS-CoV-2 process-related genes such as TMPRSS2, BSG, CTSL and CTSB had different expression patterns in the same cell type. Furthermore, ACE2 expression level in NOA donors’ Sertoli cells was significantly decreased. Our work would help to assess the risk of SARS-CoV-2 infection in the male reproductive system.

BackgroundThe 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.MethodsIn 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.FindingsWe 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.InterpretationDifferent 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 sourcesThis study was funded by National Natural Science Foundation of China (81730038; 81521002), 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.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the world, leading to large-scale population infection. Angiotensin-converting enzyme 2 (ACE2) is the receptor of both severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. However, it is still controversial whether vertical transmission exists. In order to investigate the potential risk of SARS-CoV-2 vertical transmission, we explored ACE2 and TMPRSS2 (encoding transmembrane protease serine 2) expression patterns in peri-implantation embryos and the maternal–fetal interface using previously published single-cell transcriptome data. The results showed that day 6 (D6) trophectoderm (TE) cells in peri-implantation embryos, as well as syncytiotrophoblast (STB) at 8 weeks of gestation (STB_8W) and extravillous trophoblast (EVT) cells at 24 weeks of gestation (EVT_24W) in the maternal–fetal interface, strongly co-expressed ACE2 and TMPRSS2, indicating a SARS-CoV-2 infection susceptibility. The ACE2 positive-expressing cells in the three cell types mentioned above were found to share common characteristics, which were involved in autophagy and immune-related processes. ACE2 showed no gender bias in post-implantation embryos but showed a significant gender difference in D6_TE, D6 primitive endoderm (PE) cells, and ACE2 positive-expressing STBs. These findings suggest that there may be different SARS-CoV-2 infection susceptibilities of D6 embryos of different genders and during the gestation of different genders. Our results reveal potential SARS-CoV-2 infection risks during embryo transfer, peri-implantation embryo development, and gestation.

Preimplantation genetic diagnosis (PGD) of genetic diseases, combined with human leukocyte antigen (HLA) typing (PGD-HLA), is a useful technique to have healthy offspring that are compatible with a sibling for hematopoietic stem cells transplantation (HSCT) to treat their genetic diseases. Here, we report a new strategy using single nucleotide polymorphism (SNP) linkage analysis for monogenic disease PGD combined with HLA typing, to simultaneously obtain the information of chromosomal aneuploidy, target mutations and HLA typing through a single low-depth next generation sequencing (NGS) procedure. In this study, five couples with probands underwent SNP linkage analysis for PGD-HLA typing were recruited. Within these five couples, two couples fortunately harvested four unaffected and HLA matched embryos with their siblings. After embryo transfer, two healthy neonates were born successfully. Subsequently, cord blood hematopoietic stem cells obtained from these two neonates were collected and frozen for treating their sick siblings. This novel strategy could provide abundant and specific SNPs for each family, therefore linkage information adjacent and even within HLA clusters were apparent. This study offers a highly flexible and precise method which could eliminate misdiagnosis caused by chromosomal recombination of the HLA gene, thus potentially benefit the success rate of HSCT.

Previous studies reported inconsistent evidence about some phenotypic traits of females in human opposite-sex twins (opposite-sex females [OSF]) being distinct from females in same-sex twins (SSF). Comparatively, less evidence showed significant differences between males in OS twins (opposite-sex males [OSM]) and males in same-sex twins (SSM). The twin testosterone transfer hypothesis suggests that prenatal exposure of testosterone in utero may be a possible explanation for the differential traits in OSF; however, the underlying mechanism is unknown. Here, we investigated the potential epigenetic effects of hormone interactions and their correlation to the observed phenotypic traits. In the study, DNA methylomic data from 54 newborn twins and histone modification data (H3K4me3, H3K4me1, H3K27me3, and H3K27ac) from 14 newborn twins, including same-sex females (SSF), OS twins, and same-sex males (SSM) were generated. We found that OSF were clearly distinguishable from SSF by DNA methylome, while OSM were distinguishable from SSM by H3K4me1 and H3K4me3. To be more specific, compared to SSF, OSF showed a stronger correlation to males (OSM and SSM) in genome-wide DNA methylation. Further, the DNA methylomic differences between OSF and SSF were linked to the process involving cognitive functions and nervous system regulation. The differential H3K4me3 between OSM and SSM was linked to immune responses. These findings provide epigenetic evidence for the twin testosterone transfer hypothesis and offer novel insights on how prenatal hormone exposure in utero may be linked to the reported differential traits of OS twins.

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 potential for elevated risks of ART-related disorders persists in adult life, and the underlying epigenetic mechanisms are largely uncharacterized. Here, we recruited 100 nuclear families and profiled the DNA methylomes, genome-wide histone modifications and transcriptomes to clarify the inherent extra risks attributable to specific ART procedures. We discovered that IVF-ET seemed to introduce less disturbance into the infant epigenome than IVF-FET or ICSI-ET did. Furthermore, we noted approximately half of the DNA methylomic changes in ART-conceived offspring could be explained by parental background biases. Through removal of the parental effect, we confirmed that ART per se would introduce minor DNA methylation changes locally. More importantly, we found that ART-induced epigenomic alterations were highly enriched in the processes which might contribute to increased incidence of preeclampsia during pregnancy and metabolic syndrome in offspring. Overall, our study provides an epigenetic basis for the potential long-term health risks in ART-conceived offspring that reinforces the need to review all methods of human ART.