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Gene Expression Profiling of Single Embryos, Significant Effects of In Vitro Maturation, Fertilization and Culture

ABSTRACT: In vitro production (IVP) has been shown to affect embryonic gene expression and often result in large offspring syndrome (LOS) in cattle and sheep. To dissect the effects of in vitro maturation, fertilization and culture, we compared the expression profiles of single bovine blastocysts generated by: 1) in vitro maturation, fertilization and culture (IVF); 2) in vivo maturation, fertilization and in vitro culture (IVD); and 3) in vivo maturation, fertilization and development (AI). To conduct expression profiling, total RNA was isolated from individual embryos, linearly amplified and hybridized to a custom bovine cDNA microarray containing approximately 6,300 unique genes. There were 306, 367 and 200 genes differentially expressed between the AI and IVD, IVF and IVD and AI and IVF comparisons, respectively. Interestingly, 44 differentially expressed genes were identified between the AI embryos and both the IVF and IVD embryos, making these potential candidates for LOS. There were 60 genes differentially expressed between the IVF embryos and the AI and IVD embryos. The Gene Ontology category “RNA processing” was over-represented among the genes that were down-regulated in the IVF embryos, indicating an effect of in vitro oocyte maturation/fertilization on embryonic gene expression. A culture effect on the expression of genes involved in translation was also observed by the comparison of AI to IVD embryos. Keywords: developmental condition

ORGANISM(S): Bos taurus

PROVIDER: GSE8807 | GEO | 2008/05/05

SECONDARY ACCESSION(S): PRJNA102119

REPOSITORIES: GEO

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Gene Expression Profiling of Single Embryos, Significant Effects of In Vitro Maturation, Fertilization and Culture

Project description:In vitro production (IVP) has been shown to affect embryonic gene expression and often result in large offspring syndrome (LOS) in cattle and sheep. To dissect the effects of in vitro maturation, fertilization and culture, we compared the expression profiles of single bovine blastocysts generated by: 1) in vitro maturation, fertilization and culture (IVF); 2) in vivo maturation, fertilization and in vitro culture (IVD); and 3) in vivo maturation, fertilization and development (AI). To conduct expression profiling, total RNA was isolated from individual embryos, linearly amplified and hybridized to a custom bovine cDNA microarray containing approximately 6,300 unique genes. There were 306, 367 and 200 genes differentially expressed between the AI and IVD, IVF and IVD and AI and IVF comparisons, respectively. Interestingly, 44 differentially expressed genes were identified between the AI embryos and both the IVF and IVD embryos, making these potential candidates for LOS. There were 60 genes differentially expressed between the IVF embryos and the AI and IVD embryos. The Gene Ontology category M-bM-^@M-^\RNA processingM-bM-^@M-^] was over-represented among the genes that were down-regulated in the IVF embryos, indicating an effect of in vitro oocyte maturation/fertilization on embryonic gene expression. A culture effect on the expression of genes involved in translation was also observed by the comparison of AI to IVD embryos. Reference design with dye swap. 43 individual embryos were analyzed.

2008-05-04 | E-GEOD-8807 | biostudies-arrayexpress

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

2007-12-21 | GSE8923 | GEO

Interferon tau-dependent and independent effects of the bovine conceptus on the endometrial transcriptome: effect of conceptus origin and sex

Project description:This study aimed to identify bovine conceptus-induced modifications to the endometrial transcriptome both dependent and independent of interferon tau (IFNT), dependent on conceptus origin [in vitro fertilization (IVF) or artifical insemination (AI) derived blastocysts] and dependent on conceptus sex. Major findings include identification of genes differentially expressed in endometrium in response to the conceptus but independent of IFNT and genes differentially expressed in endometrium in response to AI vs. IVF and male vs. female conceptuses.

2018-08-17 | GSE118672 | GEO

LncRNA affects epigenetic reprogramming of porcine embryo development by regulating global epigenetic modification

Project description:The key lncRNAs that regulate embryo development were screened through analyzing expression pattern of lncRNA in porcine in vivo fertilization (IVV) embryos. By knocking down lncRNA expression in in vitro fertilization (IVF) embryos, we investigated its function and mechanism of regulating embryonic development. The RNAseq was curry out to explore the genes influenced by lncT(LOC102165808).

2022-08-30 | GSE207258 | GEO

TFAP2C affects epigenetic reprogramming of porcine embryo development by regulating global epigenetic modification

Project description:By knocking down TFAP2C expression in in vitro fertilization (IVF) embryos, we investigated its function and mechanism of regulating embryonic development. The RNAseq was curry out to explore the genes influenced by TFAP2C

2023-09-05 | GSE230288 | GEO

Comparison between caruncles and intercaruncles in AI, IVF-ET and SCNT pregnancies

Project description:Implantation is crucial for placental development whose quality will directly impact fetal growth and pregnancy success with possible consequences on post-natal health. We postulated that early perturbations of the conceptus-maternal environment communication may alter the endometrium physiology that could account for the final reproductive outcome. Using cattle as an animal model, we compared gene expression profiles of the endometrial caruncular and intercaruncular areas at implantation in three types of pregnancies, namely artificial insemination (AI), in vitro fertilization with embryo transfer (IVF-ET) or somatic cell nuclear transfer (SCNT). Less than 35% of the differentially regulated genes were found to be common between AI, IVF-ET, and SCNT conditions. Compared to AI, numerous biological functions and several canonical pathways and genes were found to be significantly affected in IVF-ET or SCNT, with a major impact on metabolism and immune function in SCNT. Our data show that endometrium can fine-tune its physiology and could be considered as a biological sensor in response to pregnancy manipulations. Determining the limits of the endometrial plasticity should bring new insights on the contribution of the maternal compartment to the issue of pregnancy. Keywords: Fluorescence Microarray 30 samples

2010-06-20 | E-GEOD-14047 | biostudies-arrayexpress

Identification of large offspring syndrome during pregnancy through maternal blood transcriptome analyses

Project description:In vitro production of bovine embryos can result in large/abnormal offspring syndrome (LOS), a condition characterized by macrosomia, macroglossia, exomphalos and placental abnormalities. LOS can lead to the death of dam and calf. Currently, no test exists to identify LOS pregnancies. We hypothesized that maternal blood markers are useful to identify LOS. Bovine fetuses were generated by artificial insemination (control) or produced in vitro. Surgical fetal collections performed on d56 or d105. Maternal blood was collected on gestation d55 and d105. On d56 and d105, fetuses produced in vitro weighing greater than 97th percentile of the AI weight were considered as LOS. To determine whether maternal blood may be used to identify LOS on d55 and/or d105 of gestation, leukocyte mRNA from 23 pregnant females was isolated and sequenced using a short-read platform. Unsupervised clustering grouped 20 samples by animal (n=10 heifers) rather than by stage of pregnancy. Leukocyte gene expression analyses revealed >3,500 differentially expressed genes in females carrying the two largest LOS fetuses. In summary, our study suggests that transcript amount of ATF7IP from d105 maternal leukocytes may be useful to identify extreme cases of LOS.

2022-06-29 | GSE179946 | GEO

Effect of intra-cytoplasmic sperm injection (ICSI) on gene expression and development of mouse preimplantation embryos

Project description:Background: In vitro culture of preimplantation mouse embryos is associated with changes in gene expression. It is however not known if the method of fertilization affects the global pattern of gene expression. Method: We compared gene expression and development of mouse blastocysts produced by intra-cytoplasmic sperm injection and cultured in Whitten’s medium (ICSIWM) or KSOM medium with amino acids (ICSIKSOMaa) with control blastocysts flushed out of the uterus on post coital day 3.5 (In vivo). Global pattern of gene expression was assessed using the Affymetrix 430 2.0 chip. In addition we compared gene expression in embryos generated in IVF or ICSI using WM. Results: Blastocysts resulting from ICSI fertilization have a reduction in the number of trophoblastic and inner cell mass cells compared to in vivo generated embryos. Approximately 1000 genes are different between ICSI blastocyst and in vivo blastocysts; proliferation, apoptosis and morphogenetic pathways are the most common pathways altered after in vitro culture. Unexpectedly, only 41 genes were statistically different between embryo cultured in suboptimal conditions (WM) or optimal conditions (KSOMaa). Conclusion: The method of fertilization plays a more important role in shaping the transcriptome of the developing mouse embryo than the culture media used.

2010-11-10 | GSE23009 | GEO

AI versus IVF-ET & AI versus SCNT

Project description:Implantation is crucial for placental development which directly impacts fetal growth and pregnancy success with possible consequences on post-natal health. We postulated that early perturbations of the conceptus-maternal environment communication may alter the endometrium physiology that could account for the final reproductive outcome. Using cattle as an animal model, we compared gene expression profiles of the endometrial caruncular and intercaruncular areas during the critical period of implantation in three types of pregnancies: artificial insemination (AI), in vitro fertilization with embryo transfer (IVF-ET) or somatic cell nuclear transfer (SCNT). Less than 35% of the differentially expressed genes were found to be common between AI, IVF-ET, and SCNT conditions. Compared to AI, numerous biological functions and several canonical pathways and genes were found to be significantly affected in IVF-ET or SCNT, with a major impact on metabolism and immune function in SCNT. Our data show that the endometrium can fine-tune its physiology and could be considered as a biological sensor in response to pregnancy manipulations. Determining the limits of the endometrial plasticity should bring new insights on the contribution of the maternal compartment to the pregnancy outlet. Keywords: Fluorescence Microarray - Dye switch loop design 44 samples

2009-10-31 | E-GEOD-14050 | biostudies-arrayexpress

A temporal extracellular transcriptome atlas of human preimplantation development

Project description:We develop a non-invasive method for comprehensive characterization of the extracellular RNAs (exRNA) in a single droplet of spent media that was used to culture human in vitro fertilization (IVF) embryos. We generate and provide as a resource the temporal extracellular transcriptome atlas of human preimplantation development (TETA). TETA consists of 245 exRNA sequencing datasets, corresponding to 245 collections of spent media at five developmental stages.

2023-11-14 | GSE227442 | GEO

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