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Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas [scMutiomics]

ABSTRACT: To investigate the mechanisms underlying cloned placenta hyperplasia, we employed single-nuclei RNA and ATAC-seq multi-omics at the critical window of placental overgrowth. Our work offers the first comprehensive and novel single-nuclei–level dissection of developmental barriers in SCNT placentas, demonstrating that genomic instability constitutes the principal determinant of SCNT placental dysfunction, and outlines a feasible approach to improve reproductive cloning outcomes.

ORGANISM(S): Mus musculus

PROVIDER: GSE305673 | GEO | 2026/06/18

REPOSITORIES: GEO

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Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas [ChIP-Seq]

Project description:To investigate the mechanisms underlying cloned placenta hyperplasia, we employed single-cell RNA and ATAC-seq multi-omics at the critical window of placental overgrowth. Our work offers the first comprehensive and novel single-cell–level dissection of developmental barriers in SCNT placentas, demonstrating that genomic instability constitutes the principal determinant of SCNT placental dysfunction, and outlines a feasible approach to improve reproductive cloning outcomes.

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Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas

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Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas

Project description:Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas

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Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas [scMutiomics]

Project description:Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas [scMutiomics]

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Identification of amniotic fluid metabolomic and placental transcriptomic changes associated with abnormal development of cloned pig fetuses

Project description:Piglets cloned by somatic cell nuclear transfer (SCNT) show a high incidence of malformations and a high death rate during the perinatal period. To investigate the underlying mechanisms for abnormal development of cloned pig fetuses, we compared body weight, amniotic fluid (AF) metabolome, and placental transcriptome between SCNT- and artificial insemination (AI)-derived pig fetuses. Results showed that the body weight of SCNT pig fetuses was significantly lower than that of AI pig fetuses. The identified differential metabolites between the two groups of AF were mainly involved in bile acids and steroid hormones. The levels of all detected bile acids in SCNT AF were significantly higher than those in AI AF. The increase in the AF bile acid levels in SCNT fetuses was linked with the downregulation of placental bile acid transporter expression and the abnormal development of placental folds (PFs), both of which negatively affected the transfer of bile acids from AF across the placenta into the mother's circulation. Alteration in the AF steroid hormone levels in cloned fetuses was associated with decreased expression of enzymes responsible for steroid hormone biosynthesis in the placenta. In conclusion, cloned pig fetuses undergo abnormal intrauterine development associated with alteration of bile acid and steroid hormone levels in AF, which may be due to the poor development of PFs and the erroneous expression of bile acid transporters and enzymes responsible for steroid hormone biosynthesis in the placentas.

2020-01-08 | MTBLS666 | MetaboLights

Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas [ChIP-Seq]

Project description:Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas [ChIP-Seq]

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Aberrant gene expression patterns in placentomes of cattle cloned by somatic cell nuclear transfer

Project description:Transcription profiling of placentomes derived from somatic cell nuclear transfer (SCNT), in vitro fertilization (IVF) and artificial insemination (AI) at or near term development was performed in order to better understand why SCNT and IVF often result in placental defects, hydrops and large offspring syndrome (LOS). Multivariate analysis of variance was used to distinguish the effects of SCNT, IVF and AI on gene expression, taking into account the effects of parturition, sex of the fetus, breed of dam, breed of fetus and disease status of the offspring. The differential expression of 21 physiologically important genes was confirmed using quantitative PCR. The largest effect on placentome gene expression was attributable to whether placentae were collected at term or preterm (whether the collection was due to disease or to obtain matching case-controls) followed by placentome source (AI, IVF or SCNT). Gene expression in SCNT placentomes was dramatically different from AI (N=336 genes; 276 >2-fold) and from IVF (N=733 genes; 162 >2-fold) placentomes. Functional analysis of differentially expressed genes (DEG) showed that IVF has significant effects on genes associated with cellular metabolism. In contrast, DEG associated with SCNT are involved in multiple pathways, including cell cycle, cell death, gene expression, posttranslational modification, molecular transport and connective tissue development. Many DEG were shared between the gene lists for IVF and SCNT comparisons, suggesting that common pathways are affected by the embryo culture methods used for IVF and SCNT. However, the many unique gene functions and pathways affected by SCNT suggest that cloned fetuses may be starved and accumulating toxic wastes due to placental insufficiency caused by reprogramming errors. Many of these genes are candidates for hydrops and LOS. Keywords: gene expression; development; SCNT; cloning; nuclear transfer; IVF; AI

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Loss of H3K27me3 imprinting in the Sfmbt2 miRNA cluster causes enlargement of cloned mouse placentas

Project description:Abnormal placentation in cloned animals remains an unsolved problem. We demonstrated the involvement of micro RNAs (miRNAs) in the abnormal enlargement (hyperplasia) of placentas in cloned mice. Using a comparative transcriptome analysis of cloned placentas, we noted the consistent upregulation of clustered miRNAs within Sfmbt2, a paternally expressed imprinted gene. This region was biallelically activated by loss of imprinting (LOI) in cloned placentas. Deletion of the maternal allele of the whole miRNA cluster resulted in the correction of their expression levels and upregulation of their putative target genes with antitumor or apoptotic functions. Consequently, the placental size was reduced to the normal level and histology was ameliorated. In contrast, correcting the expression of the LOI genes (Sfmbt2, Gab1, and Scl38a4) in cloned placentas had no impact on placental size. Thus, we identified that LOI of clustered miRNAs within Sfmbt2 in cloned placentas was the major cause of abnormal placental enlargement.

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Loss of H3K27me3 imprinting in the Sfmbt2 miRNA cluster causes enlargement of cloned mouse placentas

2020-02-29 | GSE129541 | GEO

Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium

Project description:A major unresolved issue in the cloning of mammals by somatic cell nuclear transfer (SCNT) is the mechanism by which the process fails after embryos are transferred to the uterus of recipients, prior to or during the implantation window. We investigated this problem by using RNA-seq to compare the transcriptomes in cattle conceptuses produced by SCNT and artificial insemination (AI) at d18 (pre-implantation) and d34 (post-implantation) of gestation. In addition, endometrium was profiled in order to identify the communication pathways that might be affected by the presence of a cloned conceptus, ultimately leading to mortality prior to or during the implantation window. At d18, the effects on the transcriptome associated with SCNT were massive, involving more than 5,000 differentially expressed genes (DEGs). Among them are 121 genes that have embryonic lethal phenotypes in mice, cause defects in trophoblast and placental development, and/or affect conceptus survival in mice. In endometria at d18, <0.4% of expressed genes were affected by the presence of a cloned conceptus, whereas at d34, ~36% and <0.7% of genes were differentially expressed in intercaruncular and caruncular tissues, respectively. Functional analysis of DEGs in placental and endometrial tissues suggests a major disruption of signaling between the cloned conceptus and the endometrium, particularly the intercaruncular tissue. Our results support a bottleneck model for cloned conceptus survival during the peri-implantation period determined by gene expression levels in extra-embryonic tissues and the endometrial response to altered signaling from clones.

2016-11-26 | GSE74152 | GEO

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