Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Cryopreserved bovine oviductal epithelial cells survival, growth, and ability to support early embryo development

National audienc

Oviductal exosome supplementation improves bovine in vitro blastocyst yield and quality

National audienc

N-3 polyunsaturated fatty acid DHA during IVM affected oocyte developmental competence in cattle

Remerciements :Pôle STAR (Services Techniques d'Appui à la Recherche), Inra, UMR PRC, 37380 Nouzilly, Centre Val de LoireThe positive effect of n-3 poly-unsaturated fatty acids (FA) on fertility in ruminants seems to be partly mediated through direct effects on the oocyte developmental potential. We aimed to investigate whether supplementation with physiological levels of docosahexaenoic acid (DHA, C22:6 n-3 PUFA) during in vitro maturation (IVM) has an effect on oocyte maturation and in vitro embryo development in cattle. We showed that DHA (0, 1, 10 or 100 μM) had no effect on oocyte viability or maturation rate after 22 h IVM. Incubation of oocyte-cumulus complexes (OCC) with 1 μM DHA during IVM significantly increased (p&lt;0.05) oocyte cleavage rate as compared to control (86.1% vs. 78.8%, respectively) and the &gt;4-cell embryo rate at day 2 after parthenogenetic activation (PA) (39.1% vs. 29.7%, respectively). Supplementation with 1 μM DHA during IVM also induced a significant increase in the blastocyst rate at day 7 after in vitro fertilization (IVF) as compared to control (30.6% vs. 17.6%, respectively) and tended to increase the number of cells in the blastocysts (97.1 ± 4.9 vs. 81.2 ± 5.3, respectively; p = 0.08). On the contrary, 10 μM DHA had no effects, whereas 100 μM DHA significantly decreased the cleavage rate compared to control (69.5% vs.78.8%, respectively) and the &gt;4-cell embryo rate at day 2 after PA (19.5% vs. 29.7%). As was shown by real-time PCR, negative effects of 100 μM DHA were associated with significant increase of progesterone synthesis by OCCs, a three-fold increase in expression level of FA transporter CD36 and a two-fold decrease of FA synthase FASN genes in cumulus cells (CC) of corresponding oocytes. DHA at 1 and 10 μM had no effect on expression of those and other key lipid metabolism-related genes in CC. In conclusion, administration of a low physiological dose of DHA (1μM) during IVM may have beneficial effects on oocyte developmental competence in vitro without affecting lipid metabolism gene expression in surrounding cumulus cells, contrarily to 100 μM DHA which diminished oocyte quality associated with perturbation of lipid and steroid metabolism in CC

Effect of oviductal fluid on bovine oocyte zona pellucida hardening and sperm binding, and on early embryo development

International audienc

Characterization of bovine oviductal exosomes from in vivo and in vitro origin

National audienc

Early development of bovine embryos is influenced by the origin of feeders during in vitro culture

National audienceThe early development of embryo is clearly impacted by its environment and more specifically by the oviduct secretions in vivo. In cattle, an in vitro model of co-culture of bovine oviduct epithelial cells (BOEC) with the embryo has been developed to mimic the in vivo oviduct/embryo crosstalk. On the other hand, several other co-culture systems were previously developed including co-culture with monkey VERO fibroblasts to improve bovine embryo quality. Nevertheless, to the best of our knowledge, no comparison of co-culture systems using BOEC and other cells has been done yet to analyze if there is a specific impact of BOEC on bovine embryo. To answer to this question, we compared the influence of BOEC as well as VERO cells on bovine early development. Because co-culture with BOEC cells require culture at 20%O2, we included two control conditions: embryos cultured at 20%O2 and embryos cultured at 5% O2 in SOF medium + 5% SVF. No difference of cleavage rates were observed. No difference in the timing and rate of 16 cell stage development were observed despite this stage just follows EGA which is very sensitive to environmental conditions. Blastocyst rates are currently analyzed. To have new insight on the embryo quality at the 16-cell stage, a high throughput transcriptomic analysis was developed. Therefore, a new bovine microarray was designed including more than 26 700 transcripts and 250 retroviral EST. Considering an adjusted p value < 0.05, only one gene was differentially expressed between 5% O2 and 20%O2 conditions. Thus, 16-cell embryos seem to not respond to the induced oxidative stress. The direct comparison of the two co-culture conditions revealed only 19 differential expressed genes. Nevertheless, the presence of VERO or BOEC induced differential expression of 125 and 1162 genes respectively when compared to 5% O2 and 1209 and 2186 genes respectively when compared to 20% O2. Interestingly functional analysis using DAVID software pointed to different biological pathways according to the cell types used for co-culture. Further analyses at the blastocyst stage will be necessary to clarify the differential impact of cell types used in co-culture systems on embryo quality

Steroid hormones regulate sperm-oviduct interactions in the bovine

After insemination in the cow, a sperm reservoir is formed within the oviducts, allowing the storage then progressive release of spermatozoa toward the ovulated oocyte. In order to investigate the hormonal regulation of these events in vitro, the ovarian steroids 17beta-estradiol (E2) and progesterone (P4) were added at various concentrations to monolayers of bovine oviduct epithelial cells (BOEC) before or during co-incubation with spermatozoa. Main findings demonstrate that: (1) a 18-h pretreatment of BOEC with 100 pg/mL and 100 ng/mL of E2 decreased by 25% the ability of BOEC to bind spermatozoa after 10 min, and for the highest dose of E2, 60 min of co-incubation; (2) P4 at concentrations of 10, 100 and 1000 ng/mL induced the release within 60 min of 32 to 47% of bound spermatozoa from BOEC; this sperm releasing effect was maintained after a 18-h pretreatment of BOEC with 100 pg/mL of E2; (3) E2 in concentrations above 100 pg/mL inhibited the releasing effect of P4 on bound sperm in a dose-dependent manner; (4) spermatozoa bound to then released from BOEC by the action of P4 induced higher cleavage and blastocyst rates after in vitro fertilization than the control group. These results support the hypothesis that the dynamic changes in steroid hormones around the time of ovulation regulate the formation of the sperm reservoir and the timed delivery of capacitated spermatozoa to the site of fertilization

Interception of exosomal messages between the oviduct and the embryo: What are they tweeting about?

International audienc