Combining resources to obtain a comprehensive survey of the bovine embryo transcriptome through deep sequencing and microarrays

Robert, Claude; Nieminen, Julie; Dufort, Isabelle; Gagné, Dominic; Grant, Jason R.; Cagnone, Gaël; Plourde, Dany; Nivet, Anne‐Laure; Fournier, Éric; Paquet, Éric R.; Blazejczyk, Michal; Rigault, Philippe; Juge, Nicolas; Sirard, Marc‐André

doi:10.1002/mrd.21364

Cited by 95 publications

(83 citation statements)

References 42 publications

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“…An embryo-specific microarray from Agilent Technologies (Santa Clara, CA, USA) was used in collaboration with the EmbryoGENE platform (Université Laval, Québec, Canada), comprised of a total of 42 242 probes, as described by Robert et al (2011).…”

Section: Microarray-based Transcriptome Studymentioning

confidence: 99%

Insulin exposure during in vitro bovine oocyte maturation changes blastocyst gene expression and developmental potential

Laskowski

Humblot

Sirard

et al. 2017

Reprod. Fertil. Dev.

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Abstract. Metabolic imbalance impairs fertility, because changes in concentrations of metabolites and hormones in the blood and follicular fluid create an unfavourable environment for early embryonic development. Insulin is a key metabolic hormone known for its effects on fertility: insulin concentrations are increased during energy balance disturbances in diabetes or metabolic syndrome. Still, insulin is frequently used at supraphysiological concentrations for embryo in vitro culture with unknown consequences for the developmental potential of the offspring. In the present study we investigated the effects of insulin exposure during in vitro bovine oocyte maturation on developmental rates, embryo quality and gene expression. Supplementation of the maturation media with insulin at 10 or 0.1 mg mL À1 decreased blastocyst rates compared with an insulin-free control (19.8 AE 1.3% and 20.4 AE 1.3% vs 23.8 AE 1.3%, respectively; P , 0.05) and led to increased cell numbers (nearly 10% more cells on Day 8 compared with control; P , 0.05). Transcriptome analysis revealed significant upregulation of genes involved in lipid metabolism, nuclear factor (erythroid-derived 2)-like 2 (NRF2) stress response and cell differentiation, validated by quantitative polymerase chain reaction. To conclude, the results of the present study demonstrate that insulin exposure during in vitro oocyte maturation has a lasting effect on the embryo until the blastocyst stage, with a potential negative effect in the form of specific gene expression perturbations.

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Section: Microarray-based Transcriptome Studymentioning

confidence: 99%

Insulin exposure during in vitro bovine oocyte maturation changes blastocyst gene expression and developmental potential

Laskowski

Humblot

Sirard

et al. 2017

Reprod. Fertil. Dev.

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“…All datasets were generated using the EmbryoGENE bovine transcriptome microarray (24). Each experiment focused on a specific cell-type within the ovarian follicle: granulosa cells (21), cumulus cells (5), and the GVBD oocyte (18).…”

Section: Data Retrievalmentioning

confidence: 99%

Transcriptome meta-analysis of three follicular compartments and its correlation with ovarian follicle maturity and oocyte developmental competence in cows

Khan

Landry

Fournier

et al. 2016

Physiological Genomics

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Sirard MA. Transcriptome meta-analysis of three follicular compartments and its correlation with ovarian follicle maturity and oocyte developmental competence in cows. Physiol Genomics 48: 633-643, 2016. First published July 8, 2016 doi:10.1152/physiolgenomics.00050.2016.-Oocyte developmental competence in superstimulated cows is dependent in part on the duration of the FSH coasting. FSH coasting refers to superstimulation with FSH (2 days of endogenous FSH following follicle ablation and 3 days of FSH injections) followed by no FSH for a specific duration. The optimal duration varies among individuals. FSH coasting appears to modulate the transcriptome of different follicular compartments, which cooperate as a single functional unit. However, the integrative effects of FSH coasting on different follicular compartments remain ambiguous. Meta-analysis of three independent transcriptome studies, each focused on a single cell type (granulosa, cumulus, and oocyte) during FSH coasting, allowed the identification of 12 gene clusters with similar time-course expression patterns in all three compartments. Network analysis identified HNF4A (involved in metabolic functions) and ELAVL1 (an RNA-binding protein) as hub genes regulated respectively upward and downward in the clusters enriched at the optimal coasting time, and APP (involved in mitochondrial functions) and COPS5 (a member of the COP9 signalosome) as hub genes regulated respectively upwards and downwards in the clusters enriched progressively throughout the coasting period. We confirmed the effects on HNF4A downstream targets (TTR, PPL) and other hub genes (ELAVL1, APP, MYC, and PGR) in 30 cows with RT-quantitative PCR. The correlation of hub gene expression levels with FSH coasting indicated that a combination of these genes could predict oocyte competence with 83% sensitivity, suggesting that they are potential biomarkers of follicle differentiation. These findings could be used to optimize FSH coasting on an individual basis. ovarian follicle; oocyte competence; transcriptomics; meta-analysis; FSH coasting ASSISTED REPRODUCTIVE TECHNOLOGIES have been used successfully in a wide range of research and clinical applications. However, the success rate remains low, despite increasing research efforts (19). Better understanding of ovarian physiology and of the acquisition of oocyte developmental competence in particular is needed to improve the efficiency of fertility treatments in the clinical setting and in livestock production.

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“…Labeling efficiency was measured using the Nano-Drop ND-1000. Samples (nZ12) were hybridized individually on EmbryoGENE's bovine 44K microarray (Robert et al 2011). Each hybridization was performed in the following design: for each cow individually, each coasting time was compared with others (i.e.…”

Section: Sample Labeling and Microarray Hybridizationmentioning

confidence: 99%

Changes in granulosa cells' gene expression associated with increased oocyte competence in bovine

Nivet¹,

Vigneault²,

Blondin³

et al. 2013

Reproduction

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One of the challenges in mammalian reproduction is to understand the basic physiology of oocyte quality. It is believed that the follicle status is linked to developmental competence of the enclosed oocyte. To explore the link between follicles and competence in cows, previous research at our laboratory has developed an ovarian stimulation protocol that increases and then decreases oocyte quality according to the timing of oocyte recovery post-FSH withdrawal (coasting). Using this protocol, we have obtained the granulosa cells associated with oocytes of different qualities at selected times of coasting. Transcriptome analysis was done with Embryogene microarray slides and validation was performed by real-time PCR. Results show that the major changes in gene expression occurred from 20 to 44 h of coasting, when oocyte quality increases. Secondly, among upregulated genes (20-44 h), 25% were extracellular molecules, highlighting potential granulosa signaling cascades. Principal component analysis identified two patterns: one resembling the competence profile and another associated with follicle growth and atresia. Additionally, three major functional changes were identified: i) the end of follicle growth (BMPR1B, IGF2, and RELN), involving interactions with the extracellular matrix (TFPI2); angiogenesis (NRP1), including early hypoxia, and potentially oxidative stress (GFPT2, TF, and VNN1) and ii) apoptosis (KCNJ8) followed by iii) inflammation (ANKRD1). This unique window of analysis indicates a progressive hypoxia during coasting mixed with an increase in apoptosis and inflammation. Potential signaling pathways leading to competence have been identified and will require downstream testing. This preliminary analysis supports the potential role of the follicular differentiation in oocyte quality both during competence increase and decrease phases.Reproduction (2013) 145 555-565

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Combining resources to obtain a comprehensive survey of the bovine embryo transcriptome through deep sequencing and microarrays

Cited by 95 publications

References 42 publications

Insulin exposure during in vitro bovine oocyte maturation changes blastocyst gene expression and developmental potential

Insulin exposure during in vitro bovine oocyte maturation changes blastocyst gene expression and developmental potential

Transcriptome meta-analysis of three follicular compartments and its correlation with ovarian follicle maturity and oocyte developmental competence in cows

Changes in granulosa cells' gene expression associated with increased oocyte competence in bovine

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