Physiol Genomics [journal]
- Transcriptome meta-analysis of three follicular compartments and its correlation with ovarian follicle maturity and oocyte developmental competence in cows. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jul 8.:physiolgenomics.00050.2016.
Oocyte developmental competence in super-stimulated cows is dependent in part on the duration of the FSH coasting. FSH coasting refers to super-stimulation with FSH (two days of endogenous FSH following follicle ablation and three days of FSH injections) followed by no FSH for a specific duration. The optimal duration varies among individuals. FSH coasting appears to modulate the transcriptome of different follicular compartments, which cooperate as a single functional unit. However, the integrative effects of FSH coasting on different follicular compartments remain ambiguous. Meta-analysis of three independent transcriptome studies each focused on a single cell type (granulosa, cumulus and oocyte) during FSH coasting allowed the identification of 12 gene clusters with similar time-course expression patterns in all three compartments. Network analysis identified HNF4A (involved in metabolic functions) and ELAVL1 (an RNA-binding protein) as hub genes regulated respectively upwards and downwards in the clusters enriched at the optimal coasting time, and APP (involved in mitochondrial functions) and COPS5 (a member of the COP9 signalosome) as hub genes regulated respectively upwards and downwards in the clusters enriched progressively throughout the coasting period. We confirmed the effects on HNF4A downstream targets (TTR, PPL) and other hub genes (ELAVL1, APP, MYC and PGR) in 30 cows using RT-qPCR. The correlation of hub gene expression levels with FSH coasting indicated that a combination of these genes could predict oocyte competence with 83% sensitivity, suggesting that they are potential biomarkers of follicle differentiation. These findings could be used to optimize FSH coasting on an individual basis.
- Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jul 8.:physiolgenomics.00023.2016.
The strength of associations between various exposures (e.g., diet, tobacco, chemopreventive agents) and colorectal cancer risk may partially depend on the complex interaction between epithelium and stroma across anatomic subsites. Unfortunately, baseline data describing genome-wide coding and long-noncoding gene expression profiles in the healthy colon specific to tissue type and location are lacking. Therefore, colonic mucosal biopsies from 10 healthy participants who were enrolled in a clinical study to evaluate effects of lignan supplementation on gut resiliency were used to characterize the site-specific global gene expression signatures associated with stromal versus epithelial cells in the sigmoid colon and rectum. Using RNAseq, we demonstrate that tissue type and location patterns of gene expression and upstream regulatory pathways are distinct. For example, consistent with a key role of stroma in the crypt niche, mRNAs associated with immunoregulatory and inflammatory processes (i.e., CXCL14, ANTXR1), smooth muscle contraction (CALD1), proliferation and apoptosis (GLP2R, IGFBP3), and modulation of extracellular matrix (MMP2, COL3A1, MFAP4) were all highly expressed in the stroma. In comparison, HOX genes (HOXA3, HOXD9, HOXD10, HOXD11, and HOXD-AS2, a HOXD cluster antisense RNA 2), and WNT5B expression were also significantly higher in sigmoid colon as compared to the rectum. These findings provide strong impetus for considering colorectal tissue subtypes and location in future observational studies and clinical trials designed to evaluate the effects of exposures on colonic health.
- A rapid conditional targeted ablation model for hemolytic anemia in the rat. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jul 1.:physiolgenomics.00026.2016.
Effective methods for cell ablation are important tools for examining the anatomical, functional and behavioral consequences of selective loss of specific cell types in animal models. We have developed an ablation system based on creating genetically modified animals that express human CD59 (hCD59), a membrane receptor, and administering intermedilysin (ILY), a toxin produced by Streptococcus intermedius, which binds specifically to hCD59 to induce cell lysis. As proof-of-concept in the rat, we generated an anemia model, SD-Tg(CD59-HBA1)Bryd, which expresses hCD59 on erythrocytes. Hemolysis is a common complication of inherited or acquired blood disorders, which can result in cardiovascular compromise and death. A rat model which can replicate hemolysis through specific ablation of erythrocytes would allow further study of disease and novel treatments. In vitro, complete lysis of erythrocytes expressing hCD59 was observed at and above 250 pM ILY while no lysis was observed in wild type erythrocytes at any ILY concentration (8-1000 pM). In vivo, ILY intravenous injection (100 ng/g body weight) dramatically reduced the hematocrit within 10 minutes, with a mean hematocrit reduction of 43% compared to 1.4% in the saline control group. Rats injected with ILY at 500 ng/g intraperitoneally developed gross signs of anemia. Histopathology confirmed anemia and revealed hepatic necrosis, with microthrombi present. These studies validate the hCD59-ILY cell ablation technology in the rat and provide the scientific community with a new rapid conditional targeted ablation model for hemolytic anemia and hemolysis-associated sequelae.
- The role of the hypothalamic-pituitary-adrenal axis in modulating seasonal changes in immunity. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jun 24.:physiolgenomics.00006.2016.
Seasonal changes in environmental conditions are accompanied by significant adjustment of multiple biological processes. In temperate regions, the day fraction, or photoperiod, is a robust environmental cue that synchronizes seasonal variations in neuroendocrine and metabolic function. In this work, we propose a semi-mechanistic mathematical model that considers the influence of seasonal photoperiod changes as well as cellular and molecular adaptations to investigate the seasonality of immune function. Our model predicts that the circadian rhythms of cortisol, our pro-inflammatory mediator and its receptor exhibit seasonal differences in amplitude and phase; oscillating at higher amplitudes in the winter season with peak times occurring later in the day. Furthermore, the reduced photoperiod of winter coupled with seasonal alterations in physiological activity induces a more exacerbated immune response to acute stress; simulated in our studies as the administration of an acute dose of endotoxin. Our findings are therefore in accordance with experimental data that reflect the predominance of a pro-inflammatory state during the winter months. These changes in circadian rhythm dynamics may play a significant role in the seasonality of disease incidence and regulate the diurnal and seasonal variation of disease symptom severity.
- Intrauterine growth restriction inhibits expression of eukaryotic elongation factor 2 kinase, a 1 regulator of protein translation. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jun 17.:physiolgenomics.00045.2016.
Nutrient deprivation suppresses protein synthesis by blocking peptide elongation. Transcriptional upregulation and activation of eukaryotic elongation factor 2 kinase (eEF2K) blocks peptide elongation by phosphorylating eukaryotic elongation factor 2 (eEF2). Previous studies examining placentas from intrauterine growth restricted (IUGR) newborn infants show decreased eEF2K expression and activity despite chronic nutrient deprivation. However, the effect of IUGR on hepatic eEF2K expression in the fetus is unknown. We, therefore, examined the transcriptional regulation of hepatic eEF2K gene expression in a Sprague-Dawley rat model of IUGR. We found decreased hepatic eEF2K mRNA and protein levels in IUGR offspring at birth compared to control, consistent with previous placental observations. Furthermore, the CpG island (CGI) within the eEF2K promoter demonstrated increased methylation at a critical USF 1/2 transcription factor binding site. In vitro methylation of this binding site caused near complete loss of eEF2K promoter activity, designating this promoter as methylation sensitive. The eEF2K promotor in IUGR offspring also lost the protective histone covalent modifications associated with unmethylated CGIs. In addition, the +1 nucleosome was displaced 3' and RNA polymerase loading was reduced at the IUGR eEF2K promoter. Our findings provide evidence to explain why IUGR-induced chronic nutrient deprivation does not result in the upregulation of eEF2K gene transcription.
- Interactions between the colonic transcriptome, metabolome and microbiome in mouse models of obesity-induced intestinal cancer. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jun 17.:physiolgenomics.00034.2016.
Obesity is a significant risk factor for colorectal cancer (CRC); however, the relative contribution of high-fat consumption and excess adiposity remains unclear. It is becoming apparent that obesity perturbs both the intestinal microbiome and gut metabolome, and each has the potential to induce pro-tumorigenic changes in the epithelial transcriptome. The physiologic consequences and the degree to which these different biologic systems interact remain poorly defined. To better understand the mechanisms by which obesity drives colonic tumorigenesis, we profiled the colonic epithelial transcriptome of high fat (HF) diet-induced and genetically-induced (DbDb) obese mice with a genetic predisposition to intestinal tumorigenesis (Apc(1638N)). 266 and 584 genes were differentially expressed in the colonic mucosa of HF and DbDb mice respectively. These genes mapped to pathways involved in immune function, and cellular proliferation and cancer. Furthermore, Akt was central within the networks of interacting genes identified in both gene sets. Co-expression analysis comparing associations between the colonic transcriptome and microbiome revealed that three bacterial taxa previously correlated with tumor burden were significantly correlated with a gene module enriched for Akt-related genes. Similarly, co-expression analysis of the colonic transcriptome and metabolome found that adenosine, which was negatively associated with inflammatory markers and tumor burden, was also correlated with a gene module enriched with Akt regulators. Our findings provide evidence that high-fat consumption and excess adiposity result in changes in the colonic transcriptome that, although distinct, both appear to converge on Akt signaling. Such changes could be mediated by alterations in the colonic microbiome and metabolome.
- Comprehensive coverage of cardiovascular disease data in the Disease Portals at the Rat Genome Database. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jun 10.:physiolgenomics.00046.2016.
Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and Quantitative Trait Loci (QTLs) thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared using in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality.
- Relationship of Disease-Associated Gene Expression to Cardiac Phenotype is Buffered by Genetic Diversity and Chromatin Regulation. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jun 10.:physiolgenomics.00035.2016.
Re-expression of fetal genes is a hallmark of transcriptional change in cardiac hypertrophy models. How this remodeling is affected by the common genetic variation present in populations is unknown. We examined the role of genetics, as well as contributions of chromatin proteins, to regulate cardiac gene expression and heart failure susceptibility. We examined gene expression in 84 genetically distinct inbred strains of control and isoproterenol-treated mice, which exhibited varying degrees of disease. Unexpectedly, fetal gene expression was not correlated with hypertrophic phenotypes. Unbiased modeling identified 74 predictors of heart mass after isoproterenol-induced stress, but these predictors did not enrich for any cardiac pathways. However, expanded analysis of fetal genes and chromatin remodelers as groups correlated significantly with individual systemic phenotypes. Yet, cardiac transcription factors and genes shown by gain/loss of function studies to contribute to hypertrophic signaling did not correlate with cardiac mass or function in disease. Because the relationship between gene expression and phenotype was strain-specific, we examined genetic contribution to expression. Strikingly, strains with similar transcriptomes in the basal heart did not cluster together in the isoproterenol state, providing comprehensive evidence that there are different genetic contributors to physiological and pathological gene expression. Furthermore, the divergence in transcriptome similarity versus genetic similarity between strains is organ-specific and genome-wide, suggesting chromatin is the critical buffer between genetics and gene expression. Fetal gene regulation is buffered by genetic variation and is not predictive of disease. Cardiac gene expression is influenced in the basal and disease states through chromatin.
- Preeclampsia, of mice and women. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jun 3.:physiolgenomics.00125.2015.
Preeclampsia (PE) is a devastating disorder of pregnancy that affects up to 8% of pregnant women in the United States (1). The diagnosis of PE is made by the presentation of new onset hypertension, ≥140mmHg systolic blood pressure (BP) or ≥90mmHg diastolic BP, and either proteinuria or another accompanying sign/symptom, such as renal insufficiency, thrombocytopenia, hepatic dysfunction, pulmonary edema or cerebral/visual impairment (2-4). These signs can occur suddenly and without warning. PE that presents before 34 weeks of gestation is considered early-onset and carries a greater risk for perinatal morbidity/mortality than late-onset PE that occurs at or after 34 weeks of gestation (2,3). At this time there is no cure for PE and the only effective treatment is delivery of the baby and placenta. If allowed to progress to eclampsia (PE with neurologic involvement), seizures will occur and possibly death through stroke. PE also carries the risk of significant fetal and neonatal morbidity/mortality in addition to long term health risks for mother and child (5). Despite significant research efforts to accurately predict, diagnose, and treat PE, a cure eludes us. Elucidating the pathophysiological mechanisms that can cause PE will aid in our ability to accurately prevent, manage, and treat PE in order to avoid maternal and fetal losses. Intense research efforts are focused on PE and the mouse has proven to be a useful animal model for investigating molecular mechanisms that may hold the key to unraveling the mysteries of PE in women.
- Genome-wide identification of quantitative trait transcripts for blood traits in the liver samples of a White Duroc × Erhualian F2 pig resource population. [JOURNAL ARTICLE]
- Physiol Genomics 2016 Jun 3.:physiolgenomics.00123.2015.
Blood cell counts are important clinical indicators for health status. The liver plays a crucial role in food digestion and metabolism and is also a blood-forming organ. Here, we conducted a whole-genome quantitative trait transcript (QTT) analysis on 497 liver samples for 16 hematological traits in a White Duroc × Erhualian F2 pig resource population. A total of 20,108 transcripts were explored to detect their association with hematological traits. By using Spearman correlation coefficients, we identified 1,267 QTTs for these 16 hematological traits at the significance threshold of P < 0.001. We found eight candidate genes for erythrocyte and leukocyte-related traits by a look-up of human and pig and genome-wide association study results. Further, we constructed co-expression networks for leukocyte-related QTTs using weighted gene co-expression analysis. These QTTs were clustered into two to eight modules. The highest connection strength in intra-modules was identified in a module for white blood cell count. In the module, USP18, RSAD2 and OAS1 appeared to be important genes involved in interferon-stimulated innate immune system. The findings improve our understanding of intrinsic relationships between the liver and blood cells and provide novel insights into the potential therapeutic targets of hematologic diseases.