Characteristics, tissue-specific expression, and hormonal regulation of expression of tyrosine aminotransferase in the avian female reproductive tract

Transcriptome analysis of the uterovaginal junction containing sperm storage tubules in heat-stressed breeder hens

Sperm storage tubules (SSTs) in the uterovaginal junction (UVJ) of the oviduct are major sites of sperm storage after artificial insemination or mating. Female birds may regulate sperm motility in the UVJ. Heat stress can decrease the reproductive ability of broiler breeder hens. However, its effects on UVJ remain unclear. Changes in gene expression aid in understanding heat stress-affected molecular mechanisms. Herein, we wanted to conduct a comparative transcriptomic analysis to identify the differentially expressed genes (DEGs) in the UVJ of breeder hens under thermoneutral (23°C) and heat stress (36°C for 6 h) conditions. The results indicated that cloacal temperatures and respiratory rates were significantly increased in heat-stressed breeder hens (P < 0.05). Total RNA was extracted from the hen UVJ tissues containing SSTs after heat exposure. Transcriptome analysis identified 561 DEGs, including 181 upregulated DEGs containing heat shock protein (HSP) transcripts and 380 downregulated DEGs containing immune-related genes, such as interleukin 4-induced 1, radical S-adenosyl methionine domain containing 2, and 2'-5'-oligoadenylate synthetase like, in heat-stressed hens. Gene Ontology analysis revealed the significantly enriched terms involving HSPs. Kyoto Encyclopedia of Genes and Genomes analysis identified 9 significant pathways, including the protein processing in endoplasmic reticulum (11 genes including HSPs), neuroactive ligand-receptor interaction (13 genes including luteinizing hormone/choriogonadotropin receptor), biosynthesis of amino acids (4 genes including tyrosine aminotransferase), ferroptosis (3 genes including heme oxygenase 1), and nitrogen metabolism (carbonic anhydrase [CA]-12 and CA6) pathways. Protein-protein interaction network analysis of DEGs revealed 2 large networks, one containing upregulated HSPs and the other containing downregulated interferon-stimulating genes. Overall, heat stress inhibits innate immunity in the UVJ tissues of broiler chickens, and heat-stressed chickens protect their cells by increasing the expression levels of HSPs. The identified genes are potential candidates for further exploration of the UVJ in heat-stressed hens. The identified molecular pathways and networks increase our understanding of the sperm storage reservoirs (UVJ containing SSTs) within the reproductive tract and may be used to prevent heat stress-induced fertility loss in breeder hens.

Estimates of Genomic Heritability and the Marker-Derived Gene for Re(Production) Traits in Xinggao Sheep

Xinggao sheep are a breed of Chinese domestic sheep that are adapted to the extremely cold climatic features of the Hinggan League in China. The economically vital reproductive trait of ewes (litter size, LS) and productive traits of lambs (birth weight, BWT; weaning weight, WWT; and average daily gain, ADG) are expressed in females and later in life after most of the selection decisions have been made. This study estimated the genetic parameters for four traits to explore the genetic mechanisms underlying the variation, and we performed genome-wide association study (GWAS) tests on a small sample size to identify novel marker trait associations (MTAs) associated with prolificacy and growth. We detected two suggestive significant single-nucleotide polymorphisms (SNPs) associated with LS and eight significant SNPs for BWT, WWT, and ADG. These candidate loci and genes also provide valuable information for further fine-mapping of QTLs and improvement of reproductive and productive traits in sheep.

The study of candidate genes in the improvement of egg production in ducks – a review

Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.

Ovarian transcriptomic analysis of black Muscovy duck at the early, peak and late egg-laying stages

Ovarian development is a complex process involving many genes and pathways. A well-developed ovary is essential for poultry to keep high egg production and egg fertility. In order to better understand the mechanism of egg production performance, a comparative transcriptomic analysis was performed on ovaries of black Muscovy ducks at the early (BE), peak (BP) and late laying (BL) stages. 1683 DEGs were identified from BL-vs-BE, BL-vs-BP and BP-vs-BE, and the up-regulated genes were 41, 835, 260, the down-regulated genes were 60, 255, 730, respectively. Besides, there were 32, 20 and 424 DEGs co-expressed in the two comparison groups, and 11 DEGs were co-expressed in the three comparison groups. HOXA10, HtrA3, StAR, ZP2 and TAT were found to be involved in the regulation of ovarian development were significantly differentially expressed at different laying stages, which helped to regulate ovarian maturation and egg production. Moreover, we discovered several important functional pathways, such as steroid hormone biosynthesis and ovarian steroidogenesis, that appear to be much more active in the BP ovary compared to those of the BE and BL. Furthermore, 17 coding and 244 non-coding new transcripts were detected in the three comparison groups, the gene structures were optimized and the gene annotation informations were improved. These findings will provide a solid foundation on ovarian development in black Muscovy ducks and other poultry animals at different laying stages, and help to understand the complex molecular and cellular mechanisms of ovary.

Targeting glioma-initiating cells via the tyrosine metabolic pathway

OBJECTIVE

Despite an aggressive multimodal therapeutic regimen, glioblastoma (GBM) continues to portend a grave prognosis, which is driven in part by tumor heterogeneity at both the molecular and cellular levels. Accordingly, herein the authors sought to identify metabolic differences between GBM tumor core cells and edge cells and, in so doing, elucidate novel actionable therapeutic targets centered on tumor metabolism.

METHODS

Comprehensive metabolic analyses were performed on 20 high-grade glioma (HGG) tissues and 30 glioma-initiating cell (GIC) sphere culture models. The results of the metabolic analyses were combined with the Ivy GBM data set. Differences in tumor metabolism between GBM tumor tissue derived from within the contrast-enhancing region (i.e., tumor core) and that from the peritumoral brain lesions (i.e., tumor edge) were sought and explored. Such changes were ultimately confirmed at the protein level via immunohistochemistry.

RESULTS

Metabolic heterogeneity in both HGG tumor tissues and GBM sphere culture models was identified, and analyses suggested that tyrosine metabolism may serve as a possible therapeutic target in GBM, particularly in the tumor core. Furthermore, activation of the enzyme tyrosine aminotransferase (TAT) within the tyrosine metabolic pathway influenced the noted therapeutic resistance of the GBM core.

CONCLUSIONS

Selective inhibition of the tyrosine metabolism pathway may prove highly beneficial as an adjuvant to multimodal GBM therapies.

PD-1-Associated Gene Expression Signature of Neoadjuvant Trastuzumab-Treated Tumors Correlates with Patient Survival in HER2-Positive Breast Cancer

The therapeutic HER2-targeting antibody trastuzumab has been shown to elicit tumor immune response in a subset of HER2-positive (HER2+) breast cancer. We performed genomic and immunohistochemical profiling of tumors from eight patients who have completed multiple rounds of neoadjuvant trastuzumabb to identify predictive biomarkers for trastuzumab-elicited tumor immune responses. Immunohistochemistry showed that all tumors had an activated tumor immune microenvironment positive for nuclear NF-κB/p65RelA, CD4, and CD8 T cell markers, but only four out of eight tumors were positive for the PD-1 immune checkpoint molecule, which is indicative of an exhausted immune environment. Exome sequencing showed no specific driver mutations correlating with PD-1 positivity. Hierarchical clustering of the RNA sequencing data revealed two distinct groups, of which Group 2 represented the PD-1 positive tumors. A gene expression signature that was derived from this clustering composed of 89 genes stratified HER2+ breast cancer patients in the TCGA dataset and it was named PD-1-Associated Gene Expression Signature in HER2+ Breast Cancer (PAGES-HBC). Patients with the Group 2 PAGES-HBC composition had significantly more favorable survival outcomes with mortality reduced by 83% (hazard ratio 0.17; 95% CI, 0.05 to 0.60; p = 0.011). Analysis of three longitudinal samples from a single patient showed that PAGES-HBC might be transiently induced by trastuzumab, independent of clonal tumor expansion over time. We conclude that PAGES-HBC could be further developed as a prognostic predictor of trastuzumab response in HER2+ breast cancer patients and be potentially used as an alternative biomarker for anti-PD-1 therapy trials.

A Map of the microRNA Regulatory Networks Identified by Experimentally Validated microRNA-Target Interactions in Five Domestic Animals: Cattle, Pig, Sheep, Dog, and Chicken

Domestic animals are members of the broader ecological context, in which humans are situated. Yet, genomics and systems science research have lagged behind and been relatively underappreciated in domestic animals compared to human genetics/genomics. Harnessing big data calls for omics data mapping studies in a broad range of mammals. To this end, microRNAs (miRNAs) regulate posttranscriptional expression of target genes, hence, governing different biological pathways and physiological processes. The knowledge of miRNA regulatory networks and maps is important for understanding regulation of gene expression and functions in both humans and domestic animals. However, complete miRNA regulatory networks have not yet been described in all species, particularly in domestic animals. We report here an original analysis so as to map the miRNA regulatory networks in domestic animals based on miRNA-target interactions (MTIs). Validated MTIs for five species; cattle, pig, sheep, dog, and chicken were extracted from the miRTarBase. miRNA regulomes were visualized using the Cytoscape software. The data in cattle, chicken, and pig were sufficient to visualize networks, identify central molecules, and subnetworks associated with the same phenotype; however, the MTI data in dog and sheep are still limited. We found several hub genes with large number of interactions, for example, 1 miRNA (bta-miR-17-5p) interacting with 27 genes and 7 miRNAs interacting with the same gene (tumor necrosis factor [TNF]) in cattle. In addition, two single-nucleotide polymorphisms were identified within the seed region of a previously demonstrated MTI, namely, between HMGB3 (high mobility group box 3) gene and bta-miR-17-5p. In summary, this miRNA regulome mapping study will enable and guide further studies of genome function in mammals with a view to applications in human as well as veterinary medicine. Furthermore, these miRNA regulomes can help to clarify fundamental pathways in cell biology and reveal molecular insights on phenotypic trait variability in common complex diseases and response phenotypes of drugs or other health interventions for precision medicine in the future.