Effects of signal transducer and activator of transcription (STAT) genes STAT1 and STAT3 genotypic combinations on fertilization and embryonic survival rates in Holstein cattle

Gene expression of pregnancy-associated glycoproteins-1 (PAG-1), interferon-tau (IFNt) and interferon stimulated genes (ISGs) as diagnostic and prognostic markers of maternal-fetal cellular interaction in buffalo cows

The aim of this study was to determine the presence of Pregnancy-associated glycoprotein -1 (PAG-1) mRNA expression in the maternal circulation of pregnant buffaloes during the early stage of pregnancy. Contemporaneously, the mRNA expression levels of Interferon-tau (IFNt) and some Interferon stimulated genes (ISGs) (interferon stimulated gene 15 ubiquitin-like modifier interferon, ISG15; Mixoviruses resistance 1 and 2, MX1 and MX2; 2',5'-oligoadenylate synthase 1,OAS1) were evaluated in order to expand our knowledge of the molecular processes involved in the early stages of pregnancy and to identify potential biomarkers of maternal-fetal cellular interaction in buffalo. The study was conducted on 38 synchronized and artificially inseminated buffalo cows (d 0), divided ex post into 3 groups: Pregnant (n = 17), Non-pregnant (n = 15) and Embryo mortality (n = 6). Blood samples were collected on d 14, 19, 28 and 40 after artificial insemination (AI) for peripheral blood mononuclear cells (PBMCs) isolation. Expression levels of mRNA of PAG-1, IFNt, ISG15. MX1, MX2 and OAS1 were measured using RT-qPCR. No significant changes were observed in IFNt and PAG gene expressions between groups, while significant differences (p < 0.001) were found for ISG15, MX1, MX2, and OAS1. Pairwise comparisons revealed that the differences between groups occurred on days 19 and 28 post-AI. ISG15 proved to have the best diagnostic performance for distinguishing between pregnant animals and animals that experienced embryo mortality with the ROC analysis. According to the results of the univariate analyses, day 19 was identified as the most indicative to discriminate between groups while the most reliable genes for this differentiation were ISG15, MX1 and MX2. MX2 proved to be the best gene for discriminating pregnant buffaloes using the discriminant analysis, while MX1 was the gene that best predicted embryo mortality. Our results showed that among PAG-1, IFNt and ISGs expression as diagnostic and prognostic markers of maternal-fetal cellular interaction in buffalo cows, ISGs proved to be the best peripheral biomarkers for predicting pregnancy and embryonic mortality during the peri-implantation period. These insights into the mechanisms behind maternal-fetal interaction and the development of a method for the early detection of embryo distress may enable us to implement effective strategies to support embryo survival.

Genomic Regions Associated with Milk Composition and Fertility Traits in Spring-Calved Dairy Cows in New Zealand

The objective of this study was to identify genomic regions and genes that are associated with the milk composition and fertility traits of spring-calved dairy cows in New Zealand. Phenotypic data from the 2014–2015 and 2021–2022 calving seasons in two Massey University dairy herds were used. We identified 73 SNPs that were significantly associated with 58 potential candidate genes for milk composition and fertility traits. Four SNPs on chromosome 14 were highly significant for both fat and protein percentages, and the associated genes were DGAT1, SLC52A2, CPSF1, and MROH1. For fertility traits, significant associations were detected for intervals from the start of mating to first service, the start of mating to conception, first service to conception, calving to first service, and 6-wk submission, 6-wk in-calf, conception to first service in the first 3 weeks of the breeding season, and not in calf and 6-wk calving rates. Gene Ontology revealed 10 candidate genes (KCNH5, HS6ST3, GLS, ENSBTAG00000051479, STAT1, STAT4, GPD2, SH3PXD2A, EVA1C, and ARMH3) that were significantly associated with fertility traits. The biological functions of these genes are related to reducing the metabolic stress of cows and increasing insulin secretion during the mating period, early embryonic development, foetal growth, and maternal lipid metabolism during the pregnancy period.

Major locus on ECA18 influences effectiveness of GonaCon vaccine in feral horses

Contraceptive vaccines are used to reduce birth rates in wild and feral animal populations. While the immunocontraceptive GonaCon-Equine has proven effective in reducing fertility among female feral horses, there is individual variation in the duration of infertility following treatment. To identify genetic factors influencing the effectiveness of GonaCon-Equine, we conducted a genome-wide association study of 88 mares from a feral population genotyped using the Illumina GGP Equine 70k SNP array. Contraceptive treatment schedules and long-term foaling rates have been recorded for each individual. We used mixed linear models to control for relatedness among mares. We found a significant association (p < 5 ×10^-8) with a locus on equine chromosome 18. The most likely candidate genes in this region are STAT1 and STAT4, which are both involved in immune system function. Variation in STAT function could affect the immune response to the vaccine, leading to variation in contraceptive efficacy. Additional SNPs reaching a less stringent threshold of significance (p < 5 ×10^-6) were located on other chromosomes near known immune system genes, supporting the hypothesis that variation in immunocontraceptive efficacy can be attributed to genetic variation in immune response rather than fertility genes.

Global Transcriptional Profiling of Granulosa Cells from Polycystic Ovary Syndrome Patients: Comparative Analyses of Patients with or without History of Ovarian Hyperstimulation Syndrome Reveals Distinct Biomarkers and Pathways

Ovarian hyperstimulation syndrome (OHSS) is often a complication of polycystic ovarian syndrome (PCOS), the most frequent disorder of the endocrine system, which affects women in their reproductive years. The etiology of OHSS is multifactorial, though the factors involved are not apparent. In an attempt to unveil the molecular basis of OHSS, we conducted transcriptome analysis of total RNA extracted from granulosa cells from PCOS patients with a history of OHSS (n = 6) and compared them to those with no history of OHSS (n = 18). We identified 59 significantly dysregulated genes (48 down-regulated, 11 up-regulated) in the PCOS with OHSS group compared to the PCOS without OHSS group (p-value < 0.01, fold change >1.5). Functional, pathway and network analyses revealed genes involved in cellular development, inflammatory and immune response, cellular growth and proliferation (including DCN, VIM, LIFR, GRN, IL33, INSR, KLF2, FOXO1, VEGF, RDX, PLCL1, PAPPA, and ZFP36), and significant alterations in the PPAR, IL6, IL10, JAK/STAT and NF-κB signaling pathways. Array findings were validated using quantitative RT-PCR. To the best of our knowledge, this is the largest cohort of Saudi PCOS cases (with or without OHSS) to date that was analyzed using a transcriptomic approach. Our data demonstrate alterations in various gene networks and pathways that may be involved in the pathophysiology of OHSS. Further studies are warranted to confirm the findings.

Seasonal variation in the morphokinetics of in-vitro-derived bovine embryos is associated with the blastocyst developmental competence and gene expression

Summer heat stress is a major cause of reduced development of preimplantation embryos. Nevertheless, seasonal effects on embryo morphokinetics have been less studied. We used a non-invasive time-lapse system that allows continuous monitoring of embryos to study the seasonal impact on embryo morphokinetics. The experiments were performed during the cold and the hot seasons. Cumulus-oocyte complexes were aspirated from ovaries, in-vitro-matured, and fertilized. Putative zygotes were cultured in an incubator equipped with a time-lapse system. The cleavage and blastocyst formation rates were lower in the hot vs. the cold season (p < 0.01). The kinetics of the embryos differed between seasons, reflected by a delay in the second cleavage in the hot vs. the cold season (p < 0.03). The distribution of the embryos into different morphological grades (good, fair, and poor) throughout the first three cleavages differed between seasons, with a higher proportion of good-grade embryos in the hot season (p < 0.03). Cleaved embryos were categorized as either normal or abnormal, based on their first cleavage pattern. Normal cleavage was defined as when the first cleavage resulted in two equal blastomeres and further classified as either synchronous or asynchronous, according to their subsequent cleavages. Abnormal cleavage was defined as when the embryo directly cleaved into more than two blastomeres, it cleaved unequally into two unevenly sized blastomeres, or when the fusion of already divided blastomeres occurred. The proportion of abnormally cleaved embryos was higher in the hot season vs. the cold one (p < 0.01), reflected by a higher proportion of unequally cleaved embryos (p < 0.02). In the cold season, abnormally cleaved embryos had a lower potential to develop into blastocysts relative to their normally cleaved counterparts (p < 0.001). Blastocysts that developed in the cold and the hot seasons differed in the expression of genes that related to the cell cycle (STAT1; p < 0.01), stress (HSF1; p < 0.03), and embryo development (ZP3; p < 0.05). A higher expression level was recorded for the STAT1 and UHRF1 genes in blastocysts that developed from unequally vs. the synchronously cleaved embryos (p < 0.04). We provide the first evidence for a seasonal effect on embryo morphokinetics, which might explain the reduced embryo development during the hot season.

The impact of STAT3 and phospho-STAT3 expression on the prognosis and clinicopathology of ovarian cancer: a systematic review and meta-analysis

Purpose

STAT3 and p-STAT3 are often overexpressed in various human tumours and participate in cancer development and progression. However, whether STAT3/p-STAT3 expression is associated with clinicopathologic characteristics and has prognostic significance for people suffering from ovarian cancer remains controversial. We conducted a systematic review and meta-analyses to clarify the associations between STAT3/p-STAT3 expression and clinicopathologic characteristics and prognostic factors of ovarian cancer.

Methods

A systematic electronic search in the PubMed, Embase, CNKI, and Wanfang databases was conducted to identify relevant articles published before 3 April 2021. All statistical analyses were performed using Stata 15.1.

Results

We included 16 eligible studies incorporating 1747 ovarian cancer patients. The expression of STAT3/p-STAT3 was upregulated in ovarian cancer samples versus normal ovarian tissue, benign tumours and borderline tumours (OR = 10.14, p < 0.00001; OR = 9.08, P < 0.00001; OR = 4.01, p < 0.00001, respectively). STAT3/p-STAT3 overexpression was significantly correlated with FIGO stage (I-II vs. III-IV) (OR = 0.36, p < 0.00001), tumour grade (G1 + G2 vs. G3) (OR = 0.55; p = 0.001) and lymph node metastasis (yes vs. no) (OR = 3.39; p < 0.00001). High STAT3/p-STAT3 expression was correlated with poorer prognosis of ovarian cancer patients for both overall survival (OS) (HR = 1.67, p < 0.00001) and progression-free survival (PFS) (HR = 1.40, p = 0.007).

Conclusion

The present meta-analysis indicated that high STAT3/p-STAT3 expression is likely predictive of an unfavourable prognosis in ovarian cancer patients. Nonetheless, prospective trials are required to confirm these associations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13048-021-00918-6.

Expression of miR-135a-5p and its target gene JAK2 in spermatozoa of patients with asthenozoospermia

This study aimed to identify the molecular mechanism by which JAK2 mRNA and microRNA-135a-5p (miR-135a-5p) affect asthenozoospermia. The expression levels of JAK2 mRNA in the spermatozoa of 30 asthenozoospermia patients and 30 normal controls were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). MiR-135a-5p that targeted JAK2 mRNA was predicted by bioinformatics. A dual luciferase reporter vector containing miR-135a-5p 3'UTR was constructed. The binding of miR-135a-5p to JAK2 mRNA was verified by luciferase reporter assay. The protein expression levels of JAK2 and STAT3 in spermatozoa were examined by Western bolt. The relative expression levels of JAK2 mRNA and protein in the asthenozoospermia group were significantly lower than those of the normal group. MiR-135a-5p overexpression inhibited JAK2 mRNA and protein expression by targeting JAK2 mRNA 3'UTR. Correlation analysis showed that miR-135a-5p level was significantly negatively correlated with progressive sperm motility, while JAK2 mRNA level was significantly positively correlated with progressive sperm activity. Low expression of JAK2 mRNA and high expression of miR-135a-5p were related to asthenozoospermia and male infertility.

Identification of novel candidate genes for age at first calving in Nellore cows using a SNP chip specifically developed for Bos taurus indicus cattle

The age at first calving has a great economic impact on the beef cattle system and calving at 24 months is an objective of selection for a more efficient herd. However, an age at first calving around 36 months has been observed for Nellore cattle in Brazil. Thus, a genome-wide association study (GWAS) was carried out with 8376 records of age at first calving and 3239 animals genotyped with the GGP-Indicus 35K, which has been developed specifically for Bos taurus indicus. The weighted single-step genomic best linear unbiased prediction method was used, with adjacent SNPs (single nucleotide polymorphisms) in genomic windows of 1.0 Mb. After quality control, 3239 (2161 males and 1078 females) animals genotyped for 30,519 SNPs were used in GWAS analysis. The average and standard deviation of age at first calving were 1041.7 and 140.6 days, respectively. The heritability estimate was 0.10 ± 0.02. The GWAS analysis found seven genomic regions in BTA1, 2, 5, 12, 18, 21, and 24, which explained a total of 11.24% of the additive genetic variance of age at first calving. In these regions were found 62 protein coding genes, and the genes HSD17B2, SERPINA14, SERPINA1, SERPINA5, STAT1, NFATC1, ATP9B, CTDP1, THPO, ECE2, PSMD2, EIF4G1, EIF2B2, DVL3, POLR2H, TMTC2, and GPC6 are possible candidates for age at first birth due their function. Moreover, two molecular functions ("serine-type endopeptidase inhibitor activity" and "negative regulation of endopeptidase activity") were significant, which depend on several serpin genes. The use of a SNP chip developed especially for Bos taurus indicus allowed to find genomic regions for age at first calving, which are close to QTLs previously reported for other reproduction-related traits. Future studies can reveal the causal variants and their effects on reproductive precocity of Nellore cows.

Genome-wide association and genomic prediction for scrotal circumference in Hereford and Braford bulls

Scrotal circumference (SC) is widely used as a selection criterion for bulls in breeding programs, since it is easily assessed and correlated with several desirable reproductive traits. The objectives of this study were: to perform a genome-wide association study (GWAS) to identify genomic regions associated with SC adjusted for age (SCa) and for both age and weight (SCaw); to select Tag SNPs from GWAS to construct low-density panel for genomic prediction; and to compare the prediction accuracy of the SC through different methods for Braford and Hereford bulls from the same genetic breeding program. Data of SC from 18,172 bulls (30.4 ± 3.7 cm) and of genotypes from 131 sires and 3,545 animals were used. From GWAS, the top 1% of 1-Mb windows were observed on chromosome (BTA) 2, 20, 7, 8, 15, 3, 16, 27, 6 and 8 for SCa and on BTA 8, 15, 16, 21, 19, 2, 6, 5 and 10 for SCaw, representing 17.4% and 18.8% of the additive genetic variance of SCa and SCaw, respectively. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene functions related to the SCa and SCaw. The genomic enhancement methods, especially single step GBLUP, that combined phenotype and pedigree data with direct genomic values generated gains in accuracy in relation to pedigree BLUP, suggesting that genomic predictions should be applied to improve genetic gain and to narrow the generation interval compared to traditional methods. The proposed Tag-SNP panels may be useful for lower-cost commercial genomic prediction applications in the future, when the number of bulls in the reference population increases for SC in Hereford and Braford breeds.

Approaches to Identify Pregnancy Failure in Buffalo Cows

Simple Summary

Embryonic mortality and pregnancy failures still represent a major issue in domestic livestock production, particularly in dairy cattle. Despite the presence of extensive work in this research area, there is still no effective, accurate and practical method able to determine timing and viability of embryo specifically during early gestation. Indeed, technologies and techniques for predicting pregnancy success must continue to be developed. The aim of this work was to find the best strategy to diagnose pregnancy failures in buffalo cows in order to improve farm reproductive management. Among the methods compared in this study (ultrasonography, progesterone, PAGs), pregnancy-associated glycoproteins (PAGs) seem to be the best marker for predicting embryonic mortality between 25 and 40 days of gestation to be utilized as a diagnostic tool to improve reproductive management in buffalo farms.

Abstract

The aim of this work was to find the best strategy to diagnose pregnancy failures in buffalo. A total of 109 animals belonging to a buffalo herd subjected to a synchronization and artificial insemination (AI) program were enrolled in this study. Blood samples were collected at days 0, 14, 25, 28 and 40 after AI for the determination of progesterone (P4) and pregnancy-associated glycoproteins (PAGs) by the radioimmunoassay (RIA) method. Transrectal ultrasonography was performed on day 25, 28 and 40 after AI to monitor pregnancy. The animals included in the data analysis were assigned ex post in pregnant (n = 50) and mortality (n = 12) groups. By ultrasonography, the predictive sign of mortality was the heartbeat. At day 25, the PAGs concentration was significant in predicting embryonic mortality with respect to ultrasonography and P4, at the cut-off of 1.1 ng/mL. At day 28, either PAGs, at a cut-off of 2.2 ng/mL, or ultrasonography, with no detection of heartbeat, were highly predictive of embryonic mortality. PAGs were the best marker (p < 0.05) for predicting embryonic mortality between 25 and 40 days of gestation in buffalo. Its utilization as a diagnostic tool can influence management decisions in order to improve farm reproductive management.

Pre-clinical investigation of STAT3 pathway in bladder cancer: Paving the way for clinical translation

Effective cancer therapy requires identification of signaling networks and investigating their potential role in proliferation and invasion of cancer cells. Among molecular pathways, signal transducer and activator of transcription 3 (STAT3) has been of importance due to its involvement in promoting proliferation, and invasion of cancer cells, and mediating chemoresistance. In the present review, our aim is to reveal role of STAT3 pathway in bladder cancer (BC), as one of the leading causes of death worldwide. In respect to its tumor-promoting role, STAT3 is able to enhance the growth of BC cells via inhibiting apoptosis and cell cycle arrest. STAT3 also contributes to metastasis of BC cells via upregulating of MMP-2 and MMP-9 as well as genes in the EMT pathway. BC cells obtain chemoresistance via STAT3 overexpression and its inhibition paves the way for increasing efficacy of chemotherapy. Different molecular pathways such as KMT1A, EZH2, DAB2IP and non-coding RNAs including microRNAs and long non-coding RNAs can function as upstream mediators of STAT3 that are discussed in this review article.

Transcriptome profile and association study revealed STAT3 gene as a potential quality marker of bovine gametes

The present study was aimed to investigate differences in molecular signatures in oocytes derived from Holstein-Friesian heifers with different genetic merit for fertility, euthanized during day 0 or day 12 of the estrous cycle. Moreover, association between single nucleotide polymorphisms (SNPs) of ODC1 and STAT3 genes and bull fertility traits was investigated. The gene expression patterns were analyzed using cDNA array and validated with quantitative real-time polymerase chain reaction (PCR). The result revealed that several genes have shown not only to be regulated by fertility merit but also by the day of oocyte recovery during the estrous cycle. The STAT3 gene was found to be upregulated in oocytes recovered from animals with high fertility merit at both day 0 and day 12. Some other genes like PTTG1, ODC1 and TUBA1C were downregulated at day 0 and upregulated at day 12 in high, compared with low, fertility merit recovered oocytes. In contrast, the transcript abundance of TPM3 was upregulated at day 0 and downregulated at day 12 in high, compared with low, fertility merit recovered oocytes. In addition, ODC1 and STAT3 were found to be associated (P < 0.05) with sperm quality traits as well as flow cytometry parameters. Therefore, the expression of several candidate genes including ODC1 and STAT3 was related to the genetic merit of the cow. In addition polymorphisms in these two genes were found to be associated with bull semen quality.

STAT3: A Potential Drug Target for Tumor and Inflammation

STAT (Signal Transducers and Activators of Transcription) is a cellular signal transcription factor involved in the regulation of many cellular activities, such as cell differentiation, proliferation, angiogenesis in normal cells. During the study of the STAT family, STAT3 was found to be involved in many diseases, such as high expression and sustained activation of STAT3 in tumor cells, promoting tumor growth and proliferation. In the study of inflammation, it was found that it plays an important role in the anti-inflammatory and repairing of damage tissues. Because of the important role of STAT3, a large number of studies have been obtained. At the same time, after more than 20 years of development, STAT3 has also been used as a target for drug therapy. And the discovery of small molecule inhibitors also promoted the study of STAT3. Since STAT3 has been extensively studied in inflammation and tumor regulation, this review presents the current state of research on STAT3.

Sex affects immunolabeling for histone 3 K27me3 in the trophectoderm of the bovine blastocyst but not labeling for histone 3 K18ac

The mammalian embryo displays sexual dimorphism in the preimplantation period. Moreover, competence of the embryo to develop is dependent on the sire from which the embryo is derived and can be modified by embryokines produced by the endometrium such as colony stimulating factor 2 (CSF2). The preimplantation period is characterized by large changes in epigenetic modifications of DNA and histones. It is possible, therefore, that effects of sex, sire, and embryo regulatory molecules are mediated by changes in epigenetic modifications. Here it was tested whether global levels of two histone modifications in the trophectoderm of the bovine blastocyst were affected by sex, sire, and CSF2. It was found that amounts of immunolabeled H3K27me3 were greater (P = 0.030) for male embryos than female embryos. Additionally, labeling for H3K27me3 and H3K18ac depended upon the bull from which embryos were derived. Although CSF2 reduced the proportion of embryos developing to the blastocyst, there was no effect of CSF2 on labeling for H3K27me3 or H3K18ac. Results indicate that the blastocyst trophoctoderm can be modified epigenetically by embryo sex and paternal inheritance through alterations in histone epigenetic marks.

Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues

Transcription factors (TFs) are a special class of DNA-binding proteins that orchestrate gene transcription by recruiting other TFs, co-activators or co-repressors. Their combinatorial interplay in higher organisms maintains homeostasis and governs cell identity by finely controlling and regulating tissue-specific gene expression. Despite the rich literature on the importance of cooperative TFs for deciphering the mechanisms of individual regulatory programs that control tissue specificity in several organisms such as human, mouse, or Drosophila melanogaster, to date, there is still need for a comprehensive study to detect specific TF cooperations in regulatory processes of cattle tissues. To address the needs of knowledge about specific combinatorial gene regulation in cattle tissues, we made use of three publicly available RNA-seq datasets and obtained tissue-specific gene (TSG) sets for ten tissues (heart, lung, liver, kidney, duodenum, muscle tissue, adipose tissue, colon, spleen and testis). By analyzing these TSG-sets, tissue-specific TF cooperations of each tissue have been identified. The results reveal that similar to the combinatorial regulatory events of model organisms, TFs change their partners depending on their biological functions in different tissues. Particularly with regard to preferential partner choice of the transcription factors STAT3 and NR2C2, this phenomenon has been highlighted with their five different specific cooperation partners in multiple tissues. The information about cooperative TFs could be promising: i) to understand the molecular mechanisms of regulating processes; and ii) to extend the existing knowledge on the importance of single TFs in cattle tissues.

Co-Expression Network Analysis Identifies miRNA⁻mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites

MicroRNAs (miRNA) regulate mRNA networks to coordinate cellular functions. In this study, we constructed gene co-expression networks to detect miRNA modules (clusters of miRNAs with similar expression patterns) and miRNA–mRNA pairs associated with blood (triacylglyceride and nonesterified fatty acids) and milk (milk yield, fat, protein, and lactose) components and milk fatty acid traits following dietary supplementation of cows’ diets with 5% linseed oil (LSO) (n = 6 cows) or 5% safflower oil (SFO) (n = 6 cows) for 28 days. Using miRNA transcriptome data from mammary tissues of cows for co-expression network analysis, we identified three consensus modules: blue, brown, and turquoise, composed of 70, 34, and 86 miRNA members, respectively. The hub miRNAs (miRNAs with the most connections with other miRNAs) were miR-30d, miR-484 and miR-16b for blue, brown, and turquoise modules, respectively. Cell cycle arrest, and p53 signaling and transforming growth factor–beta (TGF-β) signaling pathways were the common gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched for target genes of the three modules. Protein percent (p = 0.03) correlated with the turquoise module in LSO treatment while protein yield (p = 0.003) and milk yield (p = 7 × 10⁻⁰⁴) correlated with the turquoise model, protein and milk yields and lactose percent (p < 0.05) correlated with the blue module and fat percent (p = 0.04) correlated with the brown module in SFO treatment. Several fatty acids correlated (p < 0.05) with the blue (CLA:9,11) and brown (C4:0, C12:0, C22:0, C18:1n9c and CLA:10,12) modules in LSO treatment and with the turquoise (C14:0, C18:3n3 and CLA:9,11), blue (C14:0 and C23:0) and brown (C6:0, C16:0, C22:0, C22:6n3 and CLA:10,12) modules in SFO treatment. Correlation of miRNA and mRNA data from the same animals identified the following miRNA–mRNA pairs: miR-183/RHBDD2 (p = 0.003), miR-484/EIF1AD (p = 0.011) and miR-130a/SBSPON (p = 0.004) with lowest p-values for the blue, brown, and turquoise modules, respectively. Milk yield, protein yield, and protein percentage correlated (p < 0.05) with 28, 31 and 5 miRNA–mRNA pairs, respectively. Our results suggest that, the blue, brown, and turquoise modules miRNAs, hub miRNAs, miRNA–mRNA networks, cell cycle arrest GO term, p53 signaling and TGF-β signaling pathways have considerable influence on milk and blood phenotypes following dietary supplementation of dairy cows’ diets with 5% LSO or 5% SFO.

STAT3, stem cells, cancer stem cells and p63

Signal Transducer and Activator of Transcription 3 (STAT3) is a transcription factor with many important functions in the biology of normal and transformed cells. Its regulation is highly complex as it is involved in signaling pathways in many different cell types and under a wide variety of conditions. Besides other functions, STAT3 is an important regulator of normal stem cells and cancer stem cells. p63 which is a member of the p53 protein family is also involved in these functions and is both physically and functionally connected with STAT3. This review summarizes STAT3 function and regulation, its role in stem cell and cancer stem cell properties and highlights recent reports about its relationship to p63.

Multiple-trait genomewide mapping and gene network analysis for scrotal circumference growth curves in Brahman cattle

Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals. Because SC is a sex-limited trait, identifying the underlying genomics of growth curve parameters will allow selection across both males and females. We reported the first multitrait genomewide association study (GWAS) of estimated growth curve parameters for SC data in Brahman cattle. Five widely used nonlinear models were tested to fit a total of 3,612 SC records, measured at 6, 12, 18, and 24 mo of age. The von Bertalanffy model, individually fitted for each animal, best fit this SC data. Parameter estimates SC at maturity (A) and K as well as SC at all ages were jointly analyzed in a GWAS to identify 1-Mb regions most strongly associated with each trait. Heritabilities were 0.25 for K and 0.32 for A and ranged from 0.51 to 0.72 for SC at 6 (SC6), 12 (SC12), 18 (SC18), and 24 mo of age (SC24). An overlapping window on chromosome 14 explaining around 0.8% of genetic variance for K, SC12, SC18, and SC24 was observed. The major positional candidate genes within 1 Mb upstream and downstream of this overlapping window were , , , and . Windows of 1 Mb explaining more than 0.4% of each trait on chromosomes 1, 3, 6, 7, 14, 17, 18, 24, 25, and 26 were identified. Pathways and net-work analyses were indicated through transcription factors playing a role on fertility traits: , , , , , , and . Further validation studies on larger populations or other breeds are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with scrotal growth and male fertility in cattle.

An invertebrate signal transducer and activator of transcription 5 (STAT5) ortholog from the disk abalone, Haliotis discus discus: Genomic structure, early developmental expression, and immune responses to bacterial and viral stresses

Signal transducer and activator of transcription (STAT) family members are key signaling molecules that transduce cellular responses from the cell membrane to the nucleus upon Janus kinase (JAK) activation. Although seven STAT members have been reported in mammals, very limited information on STAT genes in molluscans is available. In this study, we identified and characterized a STAT paralog that is homologous to STAT5 from the disk abalone, Haliotis discus discus, and designated as AbSTAT5. Comparison of the deduced amino acid sequence for AbSTAT5 (790 amino acids) with other counterparts revealed conserved residues important for functions and typical domain regions, including the N-terminal domain, coiled-coil domain, DNA-binding domain, linker domain, and Src homology 2 (SH2) domains as mammalian counterparts. Analysis of STAT phylogeny revealed that AbSTAT5 was clustered with the molluscan subgroup in STAT5 clade with distinct evolution. According to the genomic structure of AbSTAT5, the coding sequence was distributed into 20 exons with 19 introns. Immunologically essential transcription factor-binding sites, such as GATA-1, HNF, SP1, C/EBP, Oct-1, AP1, c-Jun, and Sox-2, were predicted at the 5'-proximal region of AbSTAT5. Expression of AbSTAT5 mRNA was detected in different stages of embryonic development and observed at considerably higher levels in the morula and late veliger stages. Tissue-specific expressional studies revealed that the highest level of AbSTAT5 transcripts was detected in hemocytes, followed by gill tissues. Temporal expressions of AbSTAT5 were analyzed upon live bacterial (Vibrio parahemolyticus and Listeria monocytogenes), viral (viral hemorrhagic septicemia virus), and pathogen-associated molecular pattern (lipopolysaccharides and Poly I:C) stimulations, and significant elevations indicated immune modulation. These results suggest that AbSTAT5 may be involved in maintaining innate immune responses from developmental to adult stages in the disk abalone. Further, this study provides a basis for structural and functional exploration of STAT members in the invertebrate JAK/STAT signaling pathway.

The role of STAT3 in autophagy

Autophagy is an evolutionarily conserved process in eukaryotes that eliminates harmful components and maintains cellular homeostasis in response to a series of extracellular insults. However, these insults may trigger the downstream signaling of another prominent stress responsive pathway, the STAT3 signaling pathway, which has been implicated in multiple aspects of the autophagic process. Recent reports further indicate that different subcellular localization patterns of STAT3 affect autophagy in various ways. For example, nuclear STAT3 fine-tunes autophagy via the transcriptional regulation of several autophagy-related genes such as BCL2 family members, BECN1, PIK3C3, CTSB, CTSL, PIK3R1, HIF1A, BNIP3, and microRNAs with targets of autophagy modulators. Cytoplasmic STAT3 constitutively inhibits autophagy by sequestering EIF2AK2 as well as by interacting with other autophagy-related signaling molecules such as FOXO1 and FOXO3. Additionally, the mitochondrial translocation of STAT3 suppresses autophagy induced by oxidative stress and may effectively preserve mitochondria from being degraded by mitophagy. Understanding the role of STAT3 signaling in the regulation of autophagy may provide insight into the classic autophagy model and also into cancer therapy, especially for the emerging targeted therapy, because a series of targeted agents execute antitumor activities via blocking STAT3 signaling, which inevitably affects the autophagy pathway. Here, we review several of the representative studies and the current understanding in this particular field.

Integrating Genomics with Nutrition Models to Improve the Prediction of Cattle Performance and Carcass Composition under Feedlot Conditions

Cattle body composition is difficult to model because several factors affect the composition of the average daily gain (ADG) of growing animals. The objective of this study was to identify commercial single nucleotide polymorphism (SNP) panels that could improve the predictability of days on feed (DOF) to reach a target United States Department of Agriculture (USDA) grade given animal, diet, and environmental information under feedyard conditions. The data for this study was comprised of crossbred heifers (n = 681) and steers (n = 836) from commercial feedyards. Eleven molecular breeding value (MBV) scores derived from SNP panels of candidate gene polymorphisms and two-leptin gene SNP (UASMS2 and E2FB) were evaluated. The empty body fat (EBF) and the shrunk body weight (SBW) at 28% EBF (AFSBW) were computed by the Cattle Value Discovery System (CVDS) model using hip height (EBF_HH and AFSBW_HH) or carcass traits (EBF_CT and AFSBW_CT) of the animals. The DOF_HH was calculated when AFSBW_HH and ADG_HH were used and DOF_CT was calculated when AFSBW_CT and ADG_CT were used. The CVDS estimates dry matter required (DMR) by individuals fed in groups when observed ADG and AFSBW are provided. The AFSBW_CT was assumed more accurate than the AFSBW_HH because it was computed using carcass traits. The difference between AFSBW_CT and AFSBW_HH, DOF_CT and DOF_HH, and DMR and dry matter intake (DMI) were regressed on the MBV scores and leptin gene SNP to explain the variation. Our results indicate quite a large range of correlations among MBV scores and model input and output variables, but MBV ribeye area was the most strongly correlated with the differences in DOF, AFSBW, and DMI by explaining 8, 13.2 and 6.5%, respectively, of the variation. This suggests that specific MBV scores might explain additional variation of input and output variables used by nutritional models in predicting individual animal performance.

Uncovering influence links in molecular knowledge networks to streamline personalized medicine

OBJECTIVES

We developed Resource Description Framework (RDF)-induced InfluGrams (RIIG) - an informatics formalism to uncover complex relationships among biomarker proteins and biological pathways using the biomedical knowledge bases. We demonstrate an application of RIIG in morphoproteomics, a theranostic technique aimed at comprehensive analysis of protein circuitries to design effective therapeutic strategies in personalized medicine setting.

METHODS

RIIG uses an RDF "mashup" knowledge base that integrates publicly available pathway and protein data with ontologies. To mine for RDF-induced Influence Links, RIIG introduces notions of RDF relevancy and RDF collider, which mimic conditional independence and "explaining away" mechanism in probabilistic systems. Using these notions and constraint-based structure learning algorithms, the formalism generates the morphoproteomic diagrams, which we call InfluGrams, for further analysis by experts.

RESULTS

RIIG was able to recover up to 90% of predefined influence links in a simulated environment using synthetic data and outperformed a naïve Monte Carlo sampling of random links. In clinical cases of Acute Lymphoblastic Leukemia (ALL) and Mesenchymal Chondrosarcoma, a significant level of concordance between the RIIG-generated and expert-built morphoproteomic diagrams was observed. In a clinical case of Squamous Cell Carcinoma, RIIG allowed selection of alternative therapeutic targets, the validity of which was supported by a systematic literature review. We have also illustrated an ability of RIIG to discover novel influence links in the general case of the ALL.

CONCLUSIONS

Applications of the RIIG formalism demonstrated its potential to uncover patient-specific complex relationships among biological entities to find effective drug targets in a personalized medicine setting. We conclude that RIIG provides an effective means not only to streamline morphoproteomic studies, but also to bridge curated biomedical knowledge and causal reasoning with the clinical data in general.

Postpartal subclinical endometritis alters transcriptome profiles in liver and adipose tissue of dairy cows

Transcriptome alterations in liver and adipose tissue of cows with subclinical endometritis (SCE) at 29 d postpartum were evaluated. Bioinformatics analysis was performed using the Dynamic Impact Approach by means of KEGG and DAVID databases. Milk production, blood metabolites (non-esterified fatty acids, magnesium), and disease biomarkers (albumin, aspartate aminotransferase) did not differ greatly between healthy and SCE cows. In liver tissue of cows with SCE, alterations in gene expression revealed an activation of complement and coagulation cascade, steroid hormone biosynthesis, apoptosis, inflammation, oxidative stress, MAPK signaling, and the formation of fibrinogen complex. Bioinformatics analysis also revealed an inhibition of vitamin B3 and B6 metabolism with SCE. In adipose, the most activated pathways by SCE were nicotinate and nicotinamide metabolism, long-chain fatty acid transport, oxidative phosphorylation, inflammation, T cell and B cell receptor signaling, and mTOR signaling. Results indicate that SCE in dairy cattle during early lactation induces molecular alterations in liver and adipose tissue indicative of immune activation and cellular stress.

Genes of the transforming growth factor-beta signalling pathway are associated with pre-implantation embryonic development in cattle

One of the main factors affecting cattle fertility is pre-implantation development of the bovine embryo, which is a complex process regulated by various signal-transduction pathways. The transforming growth factor-β (TGF-β) signalling system, which is responsible for many biological processes including cell proliferation, differentiation and apoptosis, also is involved in embryo development. We hypothesized that altered expression of TGF-β genes in pre-implantation bovine embryos is associated with morphological abnormalities of these embryos. To test this hypothesis, we produced embryos in vitro and classified them at the blastocyst stage as either normally developed blastocysts or degenerates (growth-arrested embryos). The expression patterns of 25 genes from the TGF-β pathway were assessed using quantitative real time PCR. Ten genes showed differential expression between the two embryo groups, four genes displayed similar expressional profiles, and 11 genes had no detectable expression. An altered expression profile was statistically significant for 10 of the 14 expressed genes, and all were up-regulated in degenerate embryos vs. blastocysts. Furthermore, genomic association analysis of the cows from which embryos were produced revealed a significant association of ID3 and BMP4 polymorphisms--two of the most significant differentially expressed genes--with fertilization rate and blastocyst rate, respectively. Taken together, we conclude that TGF-β pathway genes, especially BMP4 and ID3 play a vital function in the regulation of pre-implantation embryo development at both embryo and maternal levels. Hence, these genes may be suitable as genetic markers for embryo development and fertility in cattle.

JAK-1 rs2780895 C-related genotype and allele but not JAK-1 rs10789166, rs4916008, rs2780885, rs17127114, and rs3806277 are associated with higher susceptibility to asthma

BACKGROUND

Asthma, one major respiratory consequence, might be caused by a complex interaction between multiple candidate genes and environmental factors. Herein, we aimed to investigate whether Janus kinase (JAK)-1 gene polymorphisms are associated with asthma susceptibility.

MATERIALS AND METHODS

Patients were divided into two groups: (1) asthma (n=117) and (2) nonasthma (n=60). The JAK-1 polymorphisms (rs2780895, rs10789166, rs4916008, rs2780885, rs17127114, and rs3806277) were amplified by polymerase chain reaction and detected by electrophoresis after restriction enzyme (HpyCH4IV, Tsp45I, HpaII, XmnI, MspI, and HpaII) digestions. Genotypes, allelic frequencies, and association of haplotypes in both groups were compared.

RESULTS

JAK-1 rs2780895 gene polymorphism is associated with susceptibility to asthma. Distributions of JAK-1 rs2780895*CC/CT/TT and C/T allele in both groups are: (1) 80/4/16% and 82/18%; (2) 48/45/7% and 71/29%. Other 5 JAK-1 SNPs (rs10789166, rs4916008, rs2780885, rs17127114, and rs3806277) are not associated with asthma susceptibilities. Distributions of JAK-1 rs10789166*AA/AG/GG, rs4916008*CC/CT/TT, rs2780885*CC/CT/TT, rs17127114*AA/AG/GG, rs3806277*AA/AG/GG in both groups are: (1) 50/40/10%, 42/49/9%, 50/40/10%, 9/37/54%, 8/35/57%; (2) 43/50/7%, 40/50/10%, 50/43/7%, 7/48/45%, 6/42/52%. Haplotype analyses for JAK-1 gene polymorphisms (rs2780895-rs10789166-rs4916008-rs2780885-rs17127114-rs3806277) revealed that JAK-1 haplotypes are not associated with asthma susceptibilities.

CONCLUSIONS

JAK-1 rs2780895 C-related genotype and allele are associated with higher susceptibility to asthma. JAK-1 rs10789166, rs4916008, rs2780885, rs17127114, and rs3806277 single-nucleotide polymorphisms are not associated with asthma development. Some JAK-related genetic variations might be associated with asthma pathogenesis, which deserve further surveys.

Polymorphisms in genes of the somatotrophic axis are independently associated with milk production, udder health, survival and animal size in Holstein-Friesian dairy cattle

The somatotrophic axis consisting of pituitary-derived growth hormone and circulating insulin-like growth factor 1 has been well established as key regulators of animal health, metabolism, lactation, fertility, body composition and growth rate. The aim of this study was to simultaneously quantify the associations between SNPs in candidate genes of the somatotrophic axis (i.e., IGF-1, GH1 and GHR) with performance traits in Holstein-Friesian (HF) dairy cattle. Both novel SNPs identified previously by this group alongside other published SNPs within these genes were analysed for associations with performance in dairy cattle. Multiple regression analyses regressing genetic merit of up to 848 HF sires on novel SNPs (n = 76) and published SNPs (n = 33) were undertaken using weighted animal mixed linear models. Twenty-three SNPs were significantly associated with at least one of 18 traits analysed and involved in milk production, udder health, fertility and growth. Eight traits including milk fat composition, carcass conformation, stature, chest width, body depth, rump width, carcass and cull cow weight were independently associated with SNPs in two genes. Furthermore, for several traits including milk fat yield, somatic cell count, survival and carcass fat, SNPs in all three genes were independently associated with performance. Milk fat yield and carcass fat showed the highest number of independent associations across all three genes with five SNPs associated with both traits. The cumulative effects of the favourable alleles of all five SNPs across GH1, GHR and IGF-1 result in an increase of 5.9 kg and 28.6 units of milk fat and carcass fat, respectively. Cow survival was associated with a single SNP in each of the three genes with a cumulative allele effect of 1.5%. Independent effects of polymorphisms in GH1, GHR and IGF-1 reinforce the central role of the somatotrophic axis on animal development and performance.