Comprehensive transcriptomic analysis of long non-coding RNAs in bovine ovarian follicles and early embryos

Long non-coding RNAs (lncRNAs) have been the subject of numerous studies over the past decade. First thought to come from aberrant transcriptional events, lncRNAs are now considered a crucial component of the genome with roles in multiple cellular functions. However, the functional annotation and characterization of bovine lncRNAs during early development remain limited. In this comprehensive analysis, we review lncRNAs expression in bovine ovarian follicles and early embryos, based on a unique database comprising 468 microarray hybridizations from a single platform designed to target 7,724 lncRNA transcripts, of which 5,272 are intergenic (lincRNA), 958 are intronic, and 1,524 are antisense (lncNAT). Compared to translated mRNA, lncRNAs have been shown to be more tissue-specific and expressed in low copy numbers. This analysis revealed that protein-coding genes and lncRNAs are both expressed more in oocytes. Differences between the oocyte and the 2-cell embryo are also more apparent in terms of lncRNAs than mRNAs. Co-expression network analysis using WGCNA generated 25 modules with differing proportions of lncRNAs. The modules exhibiting a higher proportion of lncRNAs were found to be associated with fewer annotated mRNAs and housekeeping functions. Functional annotation of co-expressed mRNAs allowed attribution of lncRNAs to a wide array of key cellular events such as meiosis, translation initiation, immune response, and mitochondrial related functions. We thus provide evidence that lncRNAs play diverse physiological roles that are tissue-specific and associated with key cellular functions alongside mRNAs in bovine ovarian follicles and early embryos. This contributes to add lncRNAs as active molecules in the complex regulatory networks driving folliculogenesis, oogenesis and early embryogenesis all of which are necessary for reproductive success.

Standardization and validation of ATP luminometry as a diagnostic tool to assess the cleanliness of feeding equipment in preweaning calves

The objective of this cross-sectional study was to standardize a reliable and repeatable swabbing technique using ATP luminometry (light emission proportional to the amount of ATP with result provided in relative light units [RLU]) to describe the cleanliness of various feeding equipment used for preweaning calves in dairy farms. A total of 7 Québec commercial dairy herds were selected conveniently. Following visual hygiene scoring, the cleanliness of every available piece of feeding equipment was assessed using direct surface swabbing for buckets and nipples with Hygiena UltraSnap swabs. A liquid rinsing technique was used for esophageal feeders, bottles, and automatic milk feeders (AMF) with UltraSnap, AquaSnap, and MicroSnap swabs. To validate direct swabbing technique of buckets, a stage within and between operators was realized, as well as a conventional bacterial culture. A total of 519 swab samples were obtained from 201 pieces of equipment. The median (interquartile range) contamination in RLU for a bottle, esophageal feeder, AMF, bucket and nipple was 2 (1;6), 2 (0;12), 52 (19;269), 886 (128;7,230) and 899 (142;6,928), respectively. The direct swabbing technique, which consists in swabbing directly the surface of an equipment, showed excellent correlation for intrarater reliability (intraclass correlation (ICC) = 0.93; 95% CI: 0.88-0.96). The interoperator (2 sessions with 3 different operators) reliability also showed high correlation (ICC = 0.88; 95% CI: 0.78-0.94 for the first session, and ICC = 0.89; 95% CI: 0.79-0.95 for the second session). Luminometer values were positively associated with the visual score of esophageal feeders, AMF and buckets. A positive correlation between bacterial culture and direct swabbing of buckets was also found for the UltraSnap (rs = 0.653; 95% CI: 0.283-0.873; P = 0.0003) and MicroSnap (rs = 0.569, 95% CI: 0.309-0.765; P = 0.002). This study describes a standardized and practical on-farm swabbing technique for assessing the hygienic status of feeding equipment by luminometry, which can be integrated in the investigation of preweaning dairy calves problems.

Relationship between farm management strategies, reticuloruminal pH variations, and risks of subacute ruminal acidosis

Low reticuloruminal pH (rpH), often observed in subacute ruminal acidosis (SARA), may negatively affect rumen health and animal performance. To investigate the variability of rpH and the prevalence of SARA on commercial farms, we conducted an observational study on 110 early-lactation Holstein cows of different parities from 12 farms selected to cover a broad range of farm management strategies. The rpH of each cow was continuously monitored for 50 d using wireless boluses. To study the effects of animal and farm management characteristics on rpH, we used a multivariable mixed model analysis with the animal and farm as random effects. Automatic milking system and presence of corn silage in the ration were associated with a decrease in rpH of 0.37 and 0.20 pH units, respectively, whereas monensin supplementation was associated with an increase of 0.27 pH units. The rpH increased by 0.15 pH units during the first 60 d in milk. We defined a SARA-positive day as rpH below 5.8 (SARA5.8) or 6.0 (SARA6.0) for at least 300 min for 1 d. Using those definitions, during our study, a total of 38 (35%) and 65 (59%) cows experienced at least one episode of SARA5.8 and SARA6.0, respectively. The proportion of cows with at least one SARA-positive day varied among farms from 0 to 100%. Automatic milking system was associated with an increased risk of SARA5.8 (odds ratio: 10) and SARA6.0 (odds ratio: 11). The use of corn silage was associated with an increased risk of SARA5.8 (odds ratio: 21), whereas the use of monensin was associated with a decreased risk of SARA5.8 (odds ratio: 0.02). Our study shows that rpH is quite variable among farms, but also among animals on the same farm. We also show that multiple animal and farm characteristics are associated with rpH variability and the risk of SARA under commercial conditions.

Low level of the X-linked ribosomal protein S4 in human urothelial carcinomas is associated with a poor prognosis

AIM

We determined whether the Y-box binding protein-1 (YB-1) and its binding partner, the X-linked ribosomal protein S4 (RPS4X), are associated with clinical outcome in bladder cancer.

MATERIALS & METHODS

A population of 167 patients with muscle-invasive bladder tumor without evidence of metastasis at time of cystectomy was analyzed retrospectively. YB-1 and RPS4X expressions were evaluated immunohistochemically in tumors and analyzed for association with clinical variables and survival.

RESULTS

Kaplan-Meier and multivariate Cox regression analyses indicated that low expression of RPS4X was associated with a higher risk of death or disease recurrence. In contrast, YB-1 was not significantly associated with either recurrence-free or overall survival.

CONCLUSION

Low RPS4X expression is associated with poor disease-specific and recurrence-free survival in bladder cancer.

Global methylation profiling in serous ovarian cancer is indicative for distinct aberrant DNA methylation signatures associated with tumor aggressiveness and disease progression

OBJECTIVE

To characterize at high resolution the DNA methylation changes which occur in the genome of serous epithelial ovarian cancer (EOC) in association with tumor aggressiveness.

METHODS

Methylated DNA immunoprecipitation in combination with CpG island-tiling arrays was used to compare the methylation profiles of five borderline, five grade 1/stage III/IV, five grade 3/stage I and five grade 3/stage III/IV serous EOC tumors, to those of five normal human ovarian tissue samples.

RESULTS

We found widespread DNA hypermethylation that occurs even in low-malignant potential (borderline) tumors and which predominantly includes key developmental/homeobox genes. Contrary to DNA hypermethylation, significant DNA hypomethylation was observed only in grade 3 serous EOC tumors. The latter observation was further confirmed when comparing the DNA methylation profiles of primary cell cultures derived from matched tumor samples obtained prior to, and following chemotherapy treatment from two serous EOC patients with advanced disease. To our knowledge this is the first report that has shown the presence of massive DNA hypomethylation in advanced serous EOC, associated with tumor malignancy and disease progression.

CONCLUSIONS

Our data raise the concern that demethylating drugs that are currently being used in advanced EOC disease (representing the majority of serous EOC cases) might have adverse effects due to activation of oncogenes and prometastatic genes. Understanding the relative roles of hypomethylation and hypermethylation in cancer could have clear implications on the therapeutic use of agents targeting the DNA methylation machinery.

Annexin-1-mediated endothelial cell migration and angiogenesis are regulated by vascular endothelial growth factor (VEGF)-induced inhibition of miR-196a expression

Endothelial cell migration induced in response to vascular endothelial growth factor (VEGF) is an essential step of angiogenesis. It depends in part on the activation of the p38/MAPKAP kinase-2/LIMK1/annexin-A1 (ANXA1) signaling axis. In the present study, we obtained evidence indicating that miR-196a specifically binds to the 3'-UTR region of ANXA1 mRNA to repress its expression. In accordance with the role of ANXA1 in cell migration and angiogenesis, the ectopic expression of miR-196a is associated with decreased cell migration in wound closure assays, and the inhibitory effect of miR-196a is rescued by overexpressing ANXA1. This finding highlights the fact that ANXA1 is a required mediator of VEGF-induced cell migration. miR-196a also reduces the formation of lamellipodia in response to VEGF suggesting that ANXA1 regulates cell migration by securing the formation of lamellipodia at the leading edge of the cell. Additionally, in line with the fact that cell migration is an essential step of angiogenesis, the ectopic expression of miR-196a impairs the formation of capillary-like structures in a tissue-engineered model of angiogenesis. Here again, the effect of miR-196a is rescued by overexpressing ANXA1. Moreover, the presence of miR-196a impairs the VEGF-induced in vivo neo-vascularization in the Matrigel Plug assay. Interestingly, VEGF reduces the expression of miR-196a, which is associated with an increased level of ANXA1. Similarly, the inhibition of miR-196a with an antagomir results in an increased level of ANXA1. We conclude that the VEGF-induced decrease of miR-196a expression may participate to the angiogenic switch by maintaining the expression of ANXA1 to levels required to enable p38-ANXA1-dependent endothelial cell migration and angiogenesis in response to VEGF.