Impact of maternal age and in vitro maturation on the transcriptome of denuded human oocytes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666614 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12746700_1.fastq.gz | Fastqsanger.gz | |||
| SRR12746700_2.fastq.gz | Fastqsanger.gz | |||
| SRR12746701_1.fastq.gz | Fastqsanger.gz | |||
| SRR12746701_2.fastq.gz | Fastqsanger.gz | |||
| SRR12746702_1.fastq.gz | Fastqsanger.gz |
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Project description:While the oocytes’ transcriptome is predominantly determined by maturation stage, transcripts related to specific pathways such as chromosome segregation, mitochondria and RNA processing are affected by age after in vitro maturation of denuded oocytes.
2021-03-24 | GSE158802 | GEO
Project description:Study Question: What effects do maternal age and oocyte maturation stage have on the human oocyte transcriptome that may be associated with oocyte developmental potential? Summary Answer: Although polyadenylated transcript abundance changes during human oocyte maturation irrespective of age, young (YNG) and advanced maternal age (AMA) metaphase II (MII) oocytes exhibit divergent transcriptomes. What is known already: Maternal age and maturation stage affect oocyte polyadenylated transcript abundance in human oocytes. Although RNA-Seq analysis of single human MII oocytes has been conducted, comparison of the germinal vesicle (GV) and MII oocyte transcriptomes has not been investigated using RNA-Seq, a technique that could provide novel insight into oocyte maturation and age-associated aberrations in gene expression. Participants / materials, settings, methods: Patients undergoing infertility treatment at the Colorado Center for Reproductive Medicine (Lone Tree, CO, USA) underwent ovarian stimulation with FSH and received hCG for final follicular maturation prior to ultrasound guided egg retrieval. Unused GV oocytes obtained at retrieval were donated for transcriptome analysis. Single oocytes were stored (at -80°C in PicoPure RNA Extraction Buffer; Thermo Fisher Scientific, USA) immediately upon verification of immaturity or after undergoing in vitro oocyte maturation (24 hour incubation), representing GV and MII samples, respectively. After isolating RNA and generating single oocyte RNA-Seq libraries (SMARTer Ultra Low Input RNA HV kit; Clontech, USA), Illumina sequencing (100 bp paired-end reads in HiSeq 2500) and bioinformatics analysis (CLC Genomics Workbench, DESeq2, Weighted Gene Correlation Network Analysis (WGCNA), 3’UTR motif analysis, Ingenuity Pathway Analysis) were performed. Main results and the role of chance: Within the 12,770 expressed genes in human oocytes (reads per kilobase per million mapped reads (RPKM) > 0.4 in at least 3 of 5 replicates for a minimum of one sample type), 458 and 3,506 genes significantly (adjusted p < 0.05 and log2 fold change > 1) increased and decreased in polyadenylated transcript abundance during oocyte maturation, respectively. The differentially expressed genes were enriched (FDR < 0.05) for biological functions and canonical pathways related to cell cycle and mitochondrial function. The majority (76%) and minority (25%) of up- and down-regulated transcripts with a complete 3’UTR were predicted to be targets of cytoplasmic polyadenylation (910 total genes), respectively. Differential gene expression analysis between young and advanced maternal age oocytes (within stage) identified 1 and 255 genes that significantly differed (adjusted p < 0.1 and log2 fold change > 1) in polyadenylated transcript abundance for GV and MII oocytes, respectively. These genes included CDK1, NLRP5, and PRDX1, which have been reported to affect oocyte developmental potential and be markers of oocyte quality. Despite similarity in transcript abundance between GV oocytes irrespective of age, divergent expression patterns emerged during oocyte maturation. These age-specific differentially expressed genes were enriched (FDR < 0.05) for functions and pathways associated with mitochondria, cell cycle, and cytoskeleton. Gene modules generated by WGCNA (based on gene expression) and patient traits related to oocyte quality (e.g. age and blastocyst development) were determined to be correlated (p < 0.05) and enriched (FDR < 0.05) for functions and pathways associated with oocyte maturation. Limitations, reasons for caution: The human oocytes used in the current study were obtained from patients with varying causes of infertility (e.g. decreased oocyte quality and oocyte quality-independent factors), possibly affecting oocyte gene expression. Oocytes in this study were retrieved at the GV stage following hCG administration and the MII oocytes were derived by in vitro maturation of patient oocytes, which has the benefit of identifying intrinsic differences between samples, but may not be completely representative of in vivo matured oocytes. Thus, these factors should be considered when interpreting the results. Wider Implications of the findings: Transcriptome profiles of young and advanced maternal age oocytes, particularly at the MII stage, suggest aberrant transcript abundance contributes to the age-associated decline in fertility.
2018-04-12 | GSE95477 | GEO
Project description:STUDY QUESTION: Does maternal age affect the maturated oocyte quality and the fol-lowing development after fertilization in human? SUMMARY ANSWER: Maternal age affects the quality of maturated oocytes by altering the stored mRNA levels in human, such as TOP2B. WHAT IS KNOWN ALREADY: Intracellular mRNAs in maturated oocytes are tran-scripted from the maternal genome during oogenesis and important for the zygotic genome activation (ZGA) after fertilization. Microarray data showed that maternal age affected polyadenylated transcript abundance in human oocytes. These genes are involved in in signaling pathway related to cell cycle regulation, chromosome alignment. However, which genes are the key genes affected by maternal age and important for the development after fertilization had not been reported. Therefore, single-cell RNA sequencing (scRNA-Seq) technology is employed in this study to screen the key genes affected by maternal age in human maturated oocytes. STUDY DESIGN, SIZE, DURATION: We isolated mRNA from maturated (MII) oo-cytes donated by IVF or ICSI patients (three oocytes from young (≤ 30 years) and three oocytes from advanced maternal age (≥ 40 years) patients) undergoing controlled ovarian stimulation. Thus, a total of six maturated oocytes were individually processed for scRNA-seq analysis. The key genes screened from scRNA-seq analysis are confirmed using mouse model. PARTICIPANTS/MATERIALS, SETTING, METHODS: Patients undergoing infertility treatment at the Yuhuangding Hospital of Yantai underwent ovarian stimulation with FSH and received hCG for final follicular maturation prior to ul-trasound guided oocyte retrieval. We isolated RNA, generated single cell RNA-seq librar-ies (Smart-Seq2) and sequenced by Illumina Hiseq X-ten platform with 150 bp paired-end. Bioinformatics analysis of the sequencing data was done to find the biological processes and key genes that led to the decline in the quality of oocytes with advanced maternal age. To validate the findings, we used mouse model and validated candidate genes by RT-PCR and knockdown experiments. MAIN RESULTS AND THE ROLE OF CHANCE: We identified 1439 genes differentially expressed between older and younger women's maturated oocytes (|foldchange|>2, P < 0.05). These genes are significantly enriched with annotations related to transporter activity, cytoskeleton, oxidative stress, catalytic activity, immune function, cellular senescence and biosynthesis. The key candidate gene TOP2B was found by protein interaction network analysis, and knockdown verification on young mouse maturated oocytes showed that TOP2B was a key gene affecting the oocyte quality and disturbing early embryo development. LARGE SCALE DATA Raw data from this study can be accessed through GSE. LIMITATIONS, REASONS FOR CAUTION: The human maturated oocytes used in this study were from patients with different causes of infertility and may affect oocyte gene expression. In addition, the study was based on a lim-ited number of patients, and there are possible natural biological variance existed in human samples. WIDER IMPLICATIONS OF THE FINDINGS: For the first time, we used scRNA-seq to detect global gene transcriptome of maturated oocytes in young and older women. These results are useful to indicate the molecular mechanisms of female ovary aging and establishing a criterion to evaluate the quality of oocytes in women with advanced maternal age. STUDY FUNDING/COMPETING INTERESTS: This research was supported by the National Key Research and Development Program of China (2018YFC1004304, 2016YFA0100203), Medical and Health Science Technology Development Plan Project of Shandong Province (Grant#. 2017WS566). There are no competing interests.
2019-01-19 | GSE125300 | GEO
Project description:The long-standing view of 'immortal germ line versus mortal soma' poses a fundamental question in biology concerning how oocytes age in molecular terms. A mainstream hypothesis is that maternal aging of oocytes has its roots in gene transcription. Investigating the proteins resulting from mRNA translation would reveal how far the levels of functionally available proteins correlate with mRNAs, and would offer novel insight into the changes oocytes undergo during maternal aging. Gene ontology semantic analysis reveals the high similarity of the detected proteome (2,324 proteins) to the transcriptome (22,334 mRNAs), though not all proteins have a cognate mRNA. Concerning their dynamics, 4-fold changes of abundance are more frequent in the proteome (3%) than the transcriptome (0.05%), with correlation. Whereas proteins associated with the nucleus (e.g. structural maintenance of chromosomes, spindle-assembly checkpoints) are largely represented among those that change in oocytes during maternal aging; proteins associated with oxidative stress/damage (e.g. superoxide dismutase) are infrequent. These quantitative alterations are either impoverishing or enriching. Using gene ontology analysis, these alterations do not relate in any simple way to the classic signature of aging known from somatic tissues. We conclude that proteome analysis of mouse oocytes may not be surrogated with transcriptome analysis, given the lack of correlation. Furthermore, we conclude that the classic features of aging may not be transposed from somatic tissues to oocytes in a one-to-one fashion. Overall, there is more to the maternal aging of oocytes than mere cellular deterioration exemplified by the notorious increase of meiotic aneuploidy. Three pools of 20 zona-enclosed B6C3F1 oocytes from each age group were subjected for experiment.
2014-04-15 | E-GEOD-42959 | biostudies-arrayexpress
Project description:The proper mammalian oocytes maturation is recognized as reaching MII stage and accumulation of mRNA and proteins in cell cytoplasm following fertilization. The proper course of folliculogenesis and oogenesis is orchestrated with morphogenesis significantly influencing further zygote formation and embryos growth. This study was aimed to determinate new transcriptomic markers of porcine oocytes morphogenesis associated with cell maturation capacity. We used microarrays to detail the global programme of gene expression underlying changes before and after in vitro maturation of oocytes in sus scrofa
2017-03-31 | GSE97246 | GEO
Project description:We analyzed the functions of ERK in maternal mRNA degradation in mouse oocytes. By comparing the degradation of transcripts in WT oocytes and KO oocytes, we are able to know the defects in maternal mRNA clearance in ERK-deleted oocytes, and identified the ERK target genes in oocyte maturation.
2016-12-16 | GSE92317 | GEO
Project description:The long-standing view of 'immortal germ line versus mortal soma' poses a fundamental question in biology concerning how oocytes age in molecular terms. A mainstream hypothesis is that maternal aging of oocytes has its roots in gene transcription. Investigating the proteins resulting from mRNA translation would reveal how far the levels of functionally available proteins correlate with mRNAs, and would offer novel insight into the changes oocytes undergo during maternal aging. Gene ontology semantic analysis reveals the high similarity of the detected proteome (2,324 proteins) to the transcriptome (22,334 mRNAs), though not all proteins have a cognate mRNA. Concerning their dynamics, 4-fold changes of abundance are more frequent in the proteome (3%) than the transcriptome (0.05%), with correlation. Whereas proteins associated with the nucleus (e.g. structural maintenance of chromosomes, spindle-assembly checkpoints) are largely represented among those that change in oocytes during maternal aging; proteins associated with oxidative stress/damage (e.g. superoxide dismutase) are infrequent. These quantitative alterations are either impoverishing or enriching. Using gene ontology analysis, these alterations do not relate in any simple way to the classic signature of aging known from somatic tissues. We conclude that proteome analysis of mouse oocytes may not be surrogated with transcriptome analysis, given the lack of correlation. Furthermore, we conclude that the classic features of aging may not be transposed from somatic tissues to oocytes in a one-to-one fashion. Overall, there is more to the maternal aging of oocytes than mere cellular deterioration exemplified by the notorious increase of meiotic aneuploidy.
2014-04-15 | GSE42959 | GEO
Project description:An increase in the incidence of aneuploidy is well documented with increasing maternal age, in particular in human females. Remarkably, little is known regarding the underlying molecular basis for the age-associated increase in aneuploidy, which is a major source of decreased fertility in humans. Using mouse as a model system we find that eggs obtained from old mice (60-70 weeks of age) display a 6-fold increase in the incidence of hyperploidy as assessed by chromosome spreads. Expression profiling of transcripts in oocytes and eggs obtained from young and old mice reveals that approximately 5% of the transcripts are differentially expressed in oocytes obtained from old females when compared to oocytes obtained from young females (6-12 weeks of age) and that this fraction increases to approximately 33% in eggs. The latter finding indicates that the normal pattern of degradation of maternal mRNAs that occurs during oocyte maturation is dramatically altered in eggs obtained from old mice and could therefore be a contributing source to the decline in fertility. Analysis of the differentially expressed transcripts also indicated that the strength of the spindle assembly checkpoint is weakened and that higher errors of microtubule-kinetochore interactions constitute part of molecular basis for the age-associated increase in aneuploidy in females. Last, BRCA1 expression is reduced in oocytes obtained from old females and RNAi-mediated reduction of BRCA1 in oocytes obtained from young females results in perturbing spindle formation and chromosome congression following maturation Experiment Overall Design: We profiled the global gene expression in GV & MII oocyte by maternal aging, and identified the genes differentially expressed.
2008-06-18 | E-GEOD-11667 | biostudies-arrayexpress
Project description:We aimed to reveal gene expression profiles of human oocytes at each maturation stage by single cell RNA-seq analyses. We investigated transcriptomes of immature oocytes at the germinal vesicle (GV) stage, maturating oocytes at the metaphase I (MI) stage and in vitro matured oocytes at the metaphase II (MII) stage.
2022-05-09 | GSE166533 | GEO
Project description:Fully grown oocytes remain transcriptionally quiescent, yet many maternal mRNAs are synthesized and retained in growing oocytes. We now know that maternal mRNAs are stored in a structure called the mitochondria associated ribonucleoprotein domain (MARDO). But the components and functions of MARDO remain elusive. Here, we found that LSM14B knockout prevents the proper storage and timely clearance of mRNAs (including Cyclin B1, Btg4, and other mRNAs that are translationally activated during meiotic maturation), specifically by disrupting MARDO assembly during oocyte growth and meiotic maturation. With decreased levels of storage and clearance, the LSM14B knockout oocytes failed to enter meiosis II, ultimately resulting in female infertility. Our results demonstrate the function of LSM14B in MARDO assembly, couple the MARDO with mRNA clearance and oocyte meiotic maturation
2023-10-17 | PXD042761 | Pride