Differentially expressed genes in adipocytokine signaling pathway of adipose tissue in pregnancy

Identification of Genomic Signatures in Bullmastiff Dogs Using Composite Selection Signals Analysis of 23 Purebred Clades

Dog breeds represent canine sub-populations with distinctive phenotypic features and limited genetic diversity. We have established a resource to study breed-specific genetic diversity. Utilising genetic resources within our laboratory biobank, public domain genotype data and the phylogenetic framework of 23 breed clades, the primary objective for this study was to identify genomic regions that differentiate the Bullmastiff breed. Through application of a composite index analysis (CSS), genomic signatures were identified in Bullmastiffs when compared to the formative breeds, Mastiffs and Bulldogs, and to 22 other breed groups. Significant regions were identified on 15 chromosomes, with the most differentiated regions found on CFA1, CFA9, and CFA18. These regions may reflect genetic drift following establishment of the breed or the effects of selective breeding during development of the modern Bullmastiff. This was supported by analysis of genes from the identified genomic regions, including 458 genes from the multi-clade analysis, which revealed enriched pathways that may be related to characteristic traits and distinct morphology of the breed. The study demonstrates the utility of the CSS method in breed-specific genome analysis and advances our understanding of genetic diversity in Bullmastiff dogs.

Polystyrene nanoplastics affect transcriptomic and epigenomic signatures of human fibroblasts and derived induced pluripotent stem cells: Implications for human health

Plastic pollution is increasing at an alarming rate yet the impact of this pollution on human health is poorly understood. Because human induced pluripotent stem cells (hiPSC) are frequently derived from dermal fibroblasts, these cells offer a powerful platform for the identification of molecular biomarkers of environmental pollution in human cells. Here, we describe a novel proof-of-concept for deriving hiPSC from human dermal fibroblasts deliberately exposed to polystyrene (PS) nanoplastic particles; unexposed hiPSC served as controls. In parallel, unexposed hiPSC were exposed to low and high concentrations of PS nanoparticles. Transcriptomic and epigenomic signatures of all fibroblasts and hiPSCs were defined using RNA-seq and whole genome methyl-seq, respectively. Both PS-treated fibroblasts and derived hiPSC showed alterations in expression of ESRRB and HNF1A genes and circuits involved in the pluripotency of stem cells, as well as in pathways involved in cancer, inflammatory disorders, gluconeogenesis, carbohydrate metabolism, innate immunity, and dopaminergic synapse. Similarly, the expression levels of identified key transcriptional and DNA methylation changes (DNMT3A, ESSRB, FAM133CP, HNF1A, SEPTIN7P8, and TTC34) were significantly affected in both PS-exposed fibroblasts and hiPSC. This study illustrates the power of human cellular models of environmental pollution to narrow down and prioritize the list of candidate molecular biomarkers of environmental pollution. This knowledge will facilitate the deciphering of the origins of environmental diseases.

A prognostic model based on tumor microenvironment-related lncRNAs predicts therapy response in pancreatic cancer

Pancreatic cancer is an aggressive malignant tumor with high mortality and a low survival rate. The immune and stromal cells that infiltrate in the tumor microenvironment (TME) significantly impact immunotherapy and drug responses. Therefore, we identify the TME-related lncRNAs to develop a prognostic model for predicting the therapy efficacy in pancreatic cancer patients. Firstly, we identified differentially expressed genes (DEGs) for weighted gene co-expression network analysis (WGCNA) to identify the TME-related module eigengenes. According to the module eigengenes, the TME-related prognostic lncRNAs were screened through the univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox analyses to construct a prognostic risk score (RS) model. Next, the predictive power of this model was evaluated by the time-dependent receiver operating characteristic (ROC) curve and Kaplan-Meier analyses. In addition, functional enrichment, immune cell infiltration, and somatic mutation analyses were performed. Finally, tumor immune dysfunction and exclusion (TIDE) score and drug sensitivity analyses were applied to predict therapy response. In this study, 11 TME-related prognostic lncRNAs were identified to develop the prognostic RS model. According to the RS, the low-risk patients had a better prognosis, lower rates of somatic mutation, lower TIDE scores, and higher sensitivity to gemcitabine and paclitaxel compared to high-risk patients. The findings above suggested that low-risk patients may benefit more from immunotherapy, and high-risk patients may benefit more from chemotherapy. Within this study, we established a prognostic RS model based on 11 TME-related lncRNAs, which may help improve clinical decision-making.

Brief high fat high sugar diet results in altered energy and fat metabolism during pregnancy in mice

During pregnancy several maternal adaptations occur in order to support the growing fetus which are further exacerbated by gestational diabetes mellitus (GDM). Previously we developed a mouse model of GDM, however we did not evaluate alterations to energy and fat metabolism. We have also shown that alterations in lipid metabolism are mediated by adrenomedullin (ADM) in normal and GDM pregnancies. Our objectives were: (1) evaluate energy and fat homeostasis in our GDM mouse model and (2) determine if ADM may play a role in these changes. Female mice were placed on either control (P-CD) or high fat, high sucrose diet (P-HFHS) 1 week prior to and throughout pregnancy. Mice were placed into comprehensive lab animal monitoring system (CLAMS) chambers throughout pregnancy. Visceral adipose tissue (VAT) was collected at d17.5 of pregnancy for analysis. Energy Expenditure was significantly increased (p < 0.05) in P-HFHS dams compared to all other groups. VAT ex-vivo lipolysis was increased (p < 0.05) in P-HFHS compared to P-CD dams. VAT gene expression of ADM receptors Crlr, Ramp2, and Ramp3 was increased (p < 0.05) in P-HFHS dams. ADM dose dependently increased ex vivo lipolysis. This data further validates our animal model of GDM and is usefulness in investigating the pathophysiology of GDM.

Gut Microbiome Associated with the Psychoneurological Symptom Cluster in Patients with Head and Neck Cancers

Cancer patients experience a cluster of co-occurring psychoneurological symptoms (PNS) related to cancer treatments. The gut microbiome may affect severity of the PNS via neural, immune, and endocrine signaling pathways. However, the link between the gut microbiome and PNS has not been well investigated in cancer patients, including those with head and neck cancers (HNCs). This pilot study enrolled 13 patients with HNCs, who reported PNS using the Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (CTCAEs). Stool specimens were collected to analyze patients' gut microbiome. All data were collected pre- and post-radiation therapy (RT). Associations between the bacterial abundances and the PNS clusters were analyzed using the linear discriminant analysis effect size; functional pathway analyses of 16S rRNA V3-V4 bacterial communities were conducted using Tax4fun. The high PNS cluster had a greater decrease in microbial evenness than the low PNS cluster from pre- to post-RT. The high and low PNS clusters showed significant differences using weighted UniFrac distance. Those individuals with the high PNS cluster were more likely to have higher abundances in phylum Bacteroidetes, order Bacteroidales, class Bacteroidia, and four genera (Ruminiclostridium9, Tyzzerella, Eubacterium_fissicatena, and DTU089), while the low PNS cluster had higher abundances in family Acidaminococcaceae and three genera (Lactococcus, Phascolarctobacterium, and Desulfovibrio). Both glycan metabolism (Lipopolysaccharide biosynthesis) and vitamin metabolism (folate biosynthesis and lipoic acid metabolism) were significantly different between the high and low PNS clusters pre- and post-RT. Our preliminary data suggest that the diversity and abundance of the gut microbiome play a potential role in developing PNS among cancer patients.

Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F2-Crossbred Bulls

Intramuscular fat (IMF) is a meat quality indicator associated with taste and juiciness. IMF deposition, influenced by genetic and non-genetic factors, occurs through a transcriptionally coordinated process of adipogenesis. MicroRNAs (miRNAs) are transcriptional regulators of vital biological processes, including lipid metabolism and adipogenesis. However, in bovines, limited data on miRNA profiling and association with divergent intramuscular fat content, regulated exclusively by genetic parameters, have been reported. Here, a microarray experiment was performed to identify and characterize the miRNA expression pattern in the Musculus longissimus dorsi of F₂-cross (Charolais × German Holstein) bulls with high and low IMF. A total of 38 differentially expressed miRNAs (DE miRNAs), including 33 upregulated and 5 downregulated (corrected p-value ≤ 0.05, FC ≥ ±1.2), were reported. Among DE miRNAs, the upregulated miRNAs miR-105a/b, miR-695, miR-1193, miR-1284, miR-1287-5p, miR-3128, miR-3178, miR-3910, miR-4443, miR-4445 and miR-4745, and the downregulated miRNAs miR-877-5p, miR-4487 and miR-4706 were identified as novel fat deposition regulators. DE miRNAs were further analyzed, along with previously identified differentially expressed genes (DEGs) from the same samples and predicted target genes, using multiple bioinformatic approaches, including target prediction tools and co-expression networks, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. We identified DE miRNAs and their gene targets associated with bovine intramuscular adipogenesis, and we provide a basis for further functional investigations.

Comparison of Transcriptome Profiles of the Fungus Botrytis cinerea and Insect Pest Bradysia odoriphaga in Response to Benzothiazole

Benzothiazole (BT) has a strong inhibitory effect on the growth and development of a wide spectrum of fungi and insects, such as Botrytis cinerea and Bradysia odoriphaga, that cause serious losses in agriculture. To investigate the underlying antifungal and insecticidal mechanisms of BT, RNA-seq analysis was performed for B. cinerea after BT treatment for 12, 24, and 48 h and for B. odoriphaga after BT treatment for 6 and 24 h. In B. cinerea, the pectin degradation process was inhibited, suggesting a low utilization of carbohydrate sources. As the treatment time was extended, the cell walls of B. cinerea thickened, and increases in melanin synthesis and ion transport were observed. In B. odoriphaga, signaling pathways including MAPK, insulin, adipocytokine, forkhead box class O, and peroxisome proliferator-activated receptor were activated at 6 h, and phosphoenolpyruvate carboxykinase was the core gene in the signal transduction pathways that responded to BT; digestive system and melanogenesis genes were obviously altered at 24 h. In addition, we identified several insecticidal target genes, such as trypsin, aminopeptidase N, and tyrosinase. Benzothiazole significantly affected nutrient metabolism, especially carbohydrate metabolism, in both species, and the pentose and glucuronate interconversions pathway was shared by both species, although the individual genes were different in each species. Overall, our results suggested that BT was a melanogenesis disrupter for the insect but an activator for the fungus. Our findings are helpful for deeply exploring the genes targeted by BT and for developing new pesticide compounds with unique mechanisms of action.

Transcriptome profiling reveals male- and female-specific gene expression pattern and novel gene candidates for the control of sex determination and gonad development in Xenopus laevis

Xenopus laevis is an amphibian (frog) species widely used in developmental biology and genetics. To unravel the molecular machinery regulating sex differentiation of Xenopus gonads, we analyzed for the first time the transcriptome of developing amphibian gonads covering sex determination period. We applied microarray at four developmental stages: (i) NF50 (undifferentiated gonad during sex determination), (ii) NF53 (the onset of sexual differentiation of the gonads), (iii) NF56 (sexual differentiation of the gonads), and (iv) NF62 (developmental progression of differentiated gonads). Our analysis showed that during the NF50, the genetic female (ZW) gonads expressed more sex-specific genes than genetic male (ZZ) gonads, which suggests that a robust genetic program is realized during female sex determination in Xenopus. However, a contrasting expression pattern was observed at later stages (NF56 and NF62), when the ZW gonads expressed less sex-specific genes than ZZ gonads, i.e., more genes may be involved in further development of the male gonads (ZZ). We identified sexual dimorphism in the expression of several functional groups of genes, including signaling factors, proteases, protease inhibitors, transcription factors, extracellular matrix components, extracellular matrix enzymes, cell adhesion molecules, and epithelium-specific intermediate filaments. In addition, our analysis detected a sexually dimorphic expression of many uncharacterized genes of unknown function, which should be studied further to reveal their identity and if/how they regulate gonad development, sex determination, and sexual differentiation. Comparison between genes sex-specifically expressed in developing gonads of Xenopus and available transcriptome data from zebrafish, two reptile species, chicken, and mouse revealed significant differences in the genetic control of sex determination and gonad development. This shows that the genetic control of gonad development is evolutionarily malleable.

Exploring the Genetic Correlation Between Growth and Immunity Based on Summary Statistics of Genome-Wide Association Studies

The relationship between growth and immune phenotypes has been presented in the context of physiology and energy allocation theory, but has rarely been explained genetically in humans. As more summary statistics of genome-wide association studies (GWAS) become available, it is increasingly possible to explore the genetic relationship between traits at the level of genome-wide summary statistics. In this study, publicly available summary statistics of growth and immune related traits were used to evaluate the genetic correlation coefficients between immune and growth traits, as well as the cause and effect relationship between them. In addition, pleiotropic variants and KEGG pathways were identified. As a result, we found negative correlations between birthweight and immune cell count phenotypes, a positive correlation between childhood head circumference and eosinophil counts (EO), and positive or negative correlations between childhood body mass index and immune phenotypes. Statistically significant negative effects of immune cell count phenotypes on human height, and a slight but significant negative influence of human height on allergic disease were also observed. A total of 98 genomic regions were identified as containing variants potentially related to both immunity and growth. Some variants, such as rs3184504 located in SH2B3, rs13107325 in SLC39A8, and rs1260326 located in GCKR, which have been identified to be pleiotropic SNPs among other traits, were found to also be related to growth and immune traits in this study. Meanwhile, the most frequent overlapping KEGG pathways between growth and immune phenotypes were autoimmune related pathways. Pleiotropic pathways such as the adipocytokine signaling pathway and JAK-STAT signaling pathway were also identified to be significant. The results of this study indicate the complex genetic relationship between growth and immune phenotypes, and reveal the genetic background of their correlation in the context of pleiotropy.

Effects of Conjugated Linoleic Acid Supplementation on the Expression Profile of miRNAs in Porcine Adipose Tissue

Conjugated linoleic acids (CLAs) play a major role in adipocyte differentiation and lipid metabolism in animals. MicroRNAs (miRNAs) appear to be involved in many biological processes in adipose tissue. However, the specific influence on miRNAs by CLA supplementation in porcine adipose tissue remains unclear. Thus, we continuously added 1.5% CLA to the pig diet from the embryo stage to the finishing period and conducted a high-throughput sequencing approach to analyse the changes in adipose tissue miRNAs. We identified 283 known porcine miRNAs, and 14 miRNAs were differentially expressed in response to CLA treatment. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the targets of the 14 differentially expressed miRNAs were involved in the Wnt signalling pathway. The CLA treatment downregulated the gene expression of PPARγ, C/EBPα, FAS, and FATP1 in both subcutaneous and abdominal fat tissues; the analysis showed that ssc-miR-21 expression was significantly correlated with PPARγ expression (p < 0.05), and speculated that ssc-miR-21 might influence adipogenesis through PPARγ. In conclusion, our study analysed the miRNA profiles in porcine adipose tissues by CLA treatment, and demonstrated that miRNAs are important regulators of fat lipogenesis. This study provides valuable information for the molecular regulatory mechanism of CLA on adipose tissue.

Flow cytometric single cell analysis reveals heterogeneity between adipose depots

Understanding adipose tissue heterogeneity is hindered by the paucity of methods to analyze mature adipocytes at the single cell level. Here, we report a system for analyzing live adipocytes from different adipose depots in the adult mouse. Single cell suspensions of buoyant adipocytes were separated from the stromal vascular fraction and analyzed by flow cytometry. Compared to other lipophilic dyes, Nile Red uptake effectively distinguished adipocyte populations. Nile Red fluorescence increased with adipocyte size and granularity and could be combined with MitoTracker® Deep Red or fluorescent antibody labeling to further dissect adipose populations. Epicardial adipocytes exhibited the least mitochondrial membrane depolarization and highest fatty-acid translocase CD36 surface expression. In contrast, brown adipocytes showed low surface CD36 expression. Pregnancy resulted in reduced mitochondrial membrane depolarisation and increased CD36 surface expression in brown and epicardial adipocyte populations respectively. Our protocol revealed unreported heterogeneity between adipose depots and highlights the utility of flow cytometry for screening adipocytes at the single cell level.

Expression of selected genes related to energy mobilisation and insulin resistance in dairy cows

The physiological and metabolic adaptation characterising the transition period in the dairy cows is developed by a complex modulation of different metabolic pathways as well as the expression of selected tissue-specific gene. The aim of this study was to evaluate the age effect on expression of selected genes in adipose, hepatic and muscle tissues in dairy cows during their transition period using the quantitative real-time PCR. Twenty-two pluriparous dairy cows were divided into three groups in relation to age: Group A (38 ± 2 months); Group B (52 ± 2 months) and Group C (80 ± 8 months). Lower levels of peroxisome proliferator-activated receptor gamma and higher levels of adiponectin were found in adipose tissue in Group C than Groups A and B (P < 0.05). Higher levels of solute carrier family 2/facilitated glucose transporter member 4 were found in muscle in Group C than Group A (P < 0.001) and Group B (P < 0.05). The present study showed in dairy cows that the expression of selected genes associated with mobilisation of energy and with insulin resistance are influenced by age demonstrating and highlighting the importance of a genomics approach to assess the metabolic status of dairy cows during the transition period.

Down but Not Out: The Role of MicroRNAs in Hibernating Bats

MicroRNAs (miRNAs) regulate many physiological processes through post-transcriptional control of gene expression and are a major part of the small noncoding RNAs (snRNA). As hibernators can survive at low body temperatures (Tb) for many months without suffering tissue damage, understanding the mechanisms that enable them to do so are of medical interest. Because the brain integrates peripheral physiology and white adipose tissue (WAT) is the primary energy source during hibernation, we hypothesized that both of these organs play a crucial role in hibernation, and thus, their activity would be relatively increased during hibernation. We carried out the first genomic analysis of small RNAs, specifically miRNAs, in the brain and WAT of a hibernating bat (Myotis ricketti) by comparing deeply torpid with euthermic individual bats using high-throughput sequencing (Solexa) and qPCR validation of expression levels. A total of 196 miRNAs (including 77 novel bat-specific miRNAs) were identified, and of these, 49 miRNAs showed significant differences in expression during hibernation, including 33 in the brain and 25 in WAT (P≤0.01 &│logFC│≥1). Stem-loop qPCR confirmed the miRNA expression patterns identified by Solexa sequencing. Moreover, 31 miRNAs showed tissue- or state-specific expression, and six miRNAs with counts >100 were specifically expressed in the brain. Putative target gene prediction combined with KEGG pathway and GO annotation showed that many essential processes of both organs are significantly correlated with differentially expressed miRNAs during bat hibernation. This is especially evident with down-regulated miRNAs, indicating that many physiological pathways are altered during hibernation. Thus, our novel findings of miRNAs and Interspersed Elements in a hibernating bat suggest that brain and WAT are active with respect to the miRNA expression activity during hibernation.