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GSE26801
Saccharomyces cerevisiae
2 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
The ARV1-encoded protein mediates sterol transport from the endoplasmic reticulum (ER) to the plasma membrane. Yeast ARV1 mutants accumulate multiple lipids in the ER and are sensitive to pharmacological modulators of both sterol and sphingolipid metabolism. Using fluorescent and electron microscopy, we demonstrate sterol accumulation, subcellular membrane expansion, elevated lipid droplet formation and vacuolar fragmentation in ARV1 mutants. Motif-based regression analysis of ARV1 deletion transcription profiles indicates activation of Hac1p, an integral component of the UPR. Accordingly, we show constitutive splicing of HAC1 transcripts, induction of a UPR reporter and elevated expression of UPR targets in ARV1 mutants. IRE1, encoding the unfolded protein sensor in the ER lumen, exhibits a lethal genetic interaction with ARV1, indicating a viability requirement for the UPR in cells lacking ARV1. Surprisingly, ARV1 mutants expressing a variant of Ire1p defective in sensing unfolded proteins are viable. Moreover these strains also exhibit constitutive HAC1 splicing that interacts with DTT-mediated perturbation of protein folding. These data suggest a component of UPR induction in arv1? strains is distinct from protein misfolding. Decreased ARV1 expression in murine macrophages also results in UPR induction, particularly up-regulation of activating transcription factor-4, C/EBP homologous protein (CHOP) and apoptosis. Cholesterol loading or inhibition of cholesterol esterification further elevated CHOP expression in ARV1 knockdown cells. Thus, loss or down-regulation of ARV1 disturbs membrane and lipid homeostasis resulting in a disruption of ER integrity, one consequence of which is induction of the UPR.
Publication Title
Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response.
Sample Metadata Fields
No sample metadata fields
View Samples- Macaca mulatta
- 21 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
This study was designed to provide a genome-wide analysis of the effects of luteinizing hormone (LH) ablation/replacement versus steroid ablation/replacement on gene expression in the developed corpus luteum (CL) in primates during the menstrual cycle. Naturally cycling, female rhesus monkeys were left untreated (Control; n = 4) or received one of the following treatments for three days beginning on Day 9 of the luteal phase: daily injection of the gonadotropin-releasing hormone (GnRH) antagonist (Antide; n = 5), Antide + recombinant human LH (A+LH; n = 4), Antide + LH + the 3b-HSD antagonist Trilostane (A+LH+TRL; n = 4), and Antide + LH + TRL + progesterone replacement with a synthetic progestin R5020 (A+LH+TRL+ R5020; n = 5). On Day 12 of the luteal phase, CL were removed and samples of RNA from individual CL were fluorescently labeled and hybridized to Affymetrix rhesus macaque total genome microarrays. The greatest number of altered transcripts was associated with the ablation/replacement of LH, while ablation/replacement of progestin affected fewer transcripts. Replacement of LH during Antide treatment restored expression of most transcripts to control levels. Real-time PCR validation of a subset of transcripts revealed that most expression patterns were similar between microarray and real-time PCR. Analysis of protein levels were subsequently determined for 2 of the transcripts differentially expressed by real-time PCR. This is the first genome-wide analysis of LH and steroid regulation of gene transcription in the developed primate CL. Further analysis of novel transcripts identified in this data set can clarify the relative role for LH and steroids in CL maintenance and luteolysis.
Publication Title
The effects of luteinizing hormone ablation/replacement versus steroid ablation/replacement on gene expression in the primate corpus luteum.
Sample Metadata Fields
No sample metadata fields
View Samples- Macaca mulatta
- 12 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Luteolysis of the corpus luteum (CL) during non-fertile cycles involves a cessation of progesterone (P4) synthesis (functional regression) and subsequent structural remodeling. The molecular processes responsible for initiation of luteal regression in the primate CL are poorly defined. Therefore, a genomic approach was utilized to systematically identify differentially expressed genes in the rhesus macaque CL during spontaneous luteolysis. CL were collected prior to (days 10-11 post-LH surge, mid-late [ML] stage) or during (days 14-16, late stage) functional regression. Based on P4 levels, late stage CL were subdivided into functional late (FL, serum P4 > 1.5 ng/ml) and functionally-regressed late (FRL, serum P4 < 0.5 ng/ml) groups (n=4 CL/group). Total RNA was isolated, labeled and hybridized to Affymetrix genome microarrays that contain elements representing the entire rhesus macaque transcriptome. With the ML stage serving as the baseline, there were 681 differentially expressed transcripts (>2-fold change; p< 0.05) that could be categorized into three primary patterns of expression: 1) increasing from ML through FRL, 2) decreasing from ML through FRL, and 3) increasing ML to FL, followed by a decrease in FRL. Ontology analysis revealed potential mechanisms and pathways associated with functional and/or structural regression of the macaque CL. Quantitative real-time PCR was used to validate microarray expression patterns of 13 genes with the results being consistent between the two methodologies. Protein levels were found to parallel mRNA profiles in 4 of 5 differentially expressed genes analyzed by Western blot. Thus, this database will facilitate the identification of mechanisms involved in primate luteal regression.
Publication Title
Dynamic changes in gene expression that occur during the period of spontaneous functional regression in the rhesus macaque corpus luteum.
Sample Metadata Fields
Sex
View Samples- Macaca mulatta
- 18 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
The molecular and cellular processes required for development, function, and regression of the primate corpus luteum (CL) are poorly defined. We hypothesized that there are dynamic changes in gene expression occurring during the CL lifespan, which represent proteins and pathways critical to its regulation. Therefore, a genomic approach was utilized to systematically identify differentially expressed genes in the rhesus macaque CL during the luteal phase of natural menstrual cycles. CL were collected between days 3-5 (early stage), 7-8 (mid), 10-12 (mid-late), 14-16 (late), or 18-19 (very-late) after the midcycle LH surge. From the early through very-late stages, 3234 transcripts were differentially expressed, with 879 occurring from the early through late stages that encompass the processes of luteinization, maintenance, and functional regression. To characterize gene changes most relevant to these processes, ontology analysis was performed using the list of 879 differentially expressed transcripts. Four main groups of related genes were identified with relevance to luteal physiology including: 1) immune function; 2) hormone and growth factor signaling; 3) steroidogenesis; and 4) prostaglandin biosynthesis, metabolism, and signaling. A subset of genes representing each of the four major categories was selected for validation of microarray results by quantitative real-time PCR. Results in mRNA levels were similar between the two methodologies for 17 of 18 genes. Additionally, protein levels for 3 genes were determined by Western blot analysis to parallel mRNA levels. This database will facilitate the identification of many novel or previously underappreciated pathways that regulate the structure and function of the primate CL.
Publication Title
Systematic determination of differential gene expression in the primate corpus luteum during the luteal phase of the menstrual cycle.
Sample Metadata Fields
Sex
View Samples- Macaca mulatta
- 20 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
To explore chorionic gonadotropin (CG)-regulated gene expression in the primate corpus luteum (CL), adult female rhesus macaques were treated with a model of simulated early pregnancy (SEP). Total RNA was isolated from individual CL and hybridized to Affymetrix GeneChip Rhesus Macaque Genome Arrays The level of 1192 transcripts changed expression > 2-fold (one-way ANOVA, FDR correction; P<0.05) during SEP when compared to Day 10 untreated controls, and the majority of changes occurred between Days 10 and 12 of SEP. To compare transcript levels between SEP rescued and regressing CL, previously banked rhesus GeneChip array data from the mid- to late and very late luteal phase were analyzed with time-matched intervals in SEP. Comparing RMA-normalized transcripts from the natural cycle with those from luteal rescue revealed 7677 transcripts changing in expression pattern >2 fold (one-way ANOVA, FDR correction; P<0.05) between the two groups. Clustering of samples revealed that the SEP samples possessed the most related transcript expression profiles. Regressed CL (days 18-19, around menses) were the most unlike all other CL. The most affected KEGG pathway was Steroid Biosynthesis, and most significantly absent pathways following SEP treatment includes groups of genes whose products promote cell-death. By further comparing the genome-wide changes in luteal gene expression during rescue in SEP, with those in CL during luteolysis in the natural menstrual cycle, it is possible to identify key regulatory pathways promoting fertility.
Publication Title
Microarray analysis of the primate luteal transcriptome during chorionic gonadotrophin administration simulating early pregnancy.
Sample Metadata Fields
Sex, Specimen part
View Samples- Macaca mulatta
- 33 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
The LH-like molecule chorionic gonadotropin (CG) is secreted by the macaque conceptus during and following implantation, rescuing the CL from impending regression and extending its functional lifespan in early pregnancy for approximately two weeks. CG binds to the same receptor as LH; i.e., LHCGR, and promotes production of steroids and other factors such as relaxin (RLN1). Our research group recently used Affymetrix rhesus macaque total genome arrays to compare the effects of CG on the luteal transcriptome from rhesus females during simulated early pregnancy (SEP) with changes during luteal regression in the non-fecund menstrual cycle. This analysis demonstrated that CG-rescue affected expression levels of 4,500 mRNA transcripts between days 10 and 15 of the luteal phase. Previous analyses indicated that a portion of the transcriptome in the macaque CL of the menstrual cycle was regulated indirectly by LH via the local actions of steroid hormones, including progesterone (P). Therefore, this study was designed to distinguish CG-regulated luteal genes that are dependent versus independent of local steroid (P) action. A protocol of increasing dosages of hCG (SEP) was begun on day 9 of the luteal phase in rhesus females combined with concurrent administration of the 3BHSD inhibitor trilostane (TRL) +/- the synthetic progestin (P) R5020. CL were collected on day 10 (no treatment) of the luteal phase to serve as a baseline comparison (n=8), 1 day of SEP (Day 10+hCG+/-TRL+/-R5020) and 6 days of SEP (Day 15+hCG+/-TRL+/-R5020); n=4/group. In the presence of CG, treatment with TRL reduced serum P levels to less than 1 ng/ ml after 1 day and all of the Day 15+h+TRL-treated females initiated menses before CL collection. The isolated CL were processed for total RNA and hybridized to microarrays. Compared to hCG treatment alone, 50 significantly altered mRNA transcripts were identified on day 10, rising to 95 on day 15 (P<0.05, 2-fold change in gene expression). The mRNA levels for several genes were validated in CL by real-time PCR. RNL1 levels increased with CG-treatment, but were not affected by steroid ablation, similar to previously reported relaxin protein expression. Steroid-sensitive genes included CDH11, IL1RN, INSL3, LDLR, OPA1, SERPINE1, SFRP4, and TNSF13B1; however differential sensitivity was observed and effects of steroid ablation and P replacement varied by day. Expression of some genes (e.g., 3BHSD2, ADAMTS1, ADAMTS5, MMP9, STAR, and VEGFA) previously identified as steroid regulated in the macaque CL during the menstrual cycle were not significantly altered by steroid ablation and P replacement during CG exposure in SEP. These data indicate that the majority of CG-regulated luteal transcripts are differentially expressed independently of local steroid actions. The proportion of steroid sensitive mRNA transcripts in the presence of CG is much smaller than in the presence of LH during the non-fecund cycle. Nevertheless, the steroid-regulated genes in the macaque CL may be essential during early pregnancy, based on the previous report that TRL treatment initiates premature structural regression of the CL during SEP. These data reinforce the concept that the structure, function, and regulation of the rescued CL in early pregnancy is different from the CL of the menstrual cycle.
Publication Title
Effects of steroid ablation and progestin replacement on the transcriptome of the primate corpus luteum during simulated early pregnancy.
Sample Metadata Fields
Sex, Specimen part
View Samples- Macaca mulatta
- 12 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Parthenogenetic embryonic stem cells (PESCs) may have future utility in cell replacement therapies. We examined genome-wide mRNA expression profiles of monkey PESCs relative to ESCs derived from fertilized embryos. Several known paternally-imprinted genes were in the highly down-regulated group in PESCs compared to ESCs. Allele specific expression analysis of paternally-imprinted genes, i.e., those genes whose expression is down-regulated in PESCs, led to the identification of one novel candidate that was exclusively expressed from a paternal allele. Our findings suggest that PESCs could be used as a model for studying genomic imprinting and in the discovery of novel imprinted genes.
Publication Title
Discovery of a novel imprinted gene by transcriptional analysis of parthenogenetic embryonic stem cells.
Sample Metadata Fields
Sex, Specimen part
View Samples- Macaca mulatta
- 8 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
This study examined the small antral follicles (SAFs) in ovaries of young adult rhesus monkeys following consumption of a western-style diet (WSD), with or without chronically elevated androgen levels since before puberty. Cholesterol or testosterone (T; n=6/group) implants were placed subcutaneously beginning at 1 yr of age, with addition of a WSD (high fat/fructose) at 5.5 yrs. Ovaries from treated females and age-matched controls were collected at 7 yrs of age. Compared to controls, consumption of a WSD, with and without T treatment, increased the numbers of SAFs per ovary (P<0.001), due to the presence of more atretic follicles (P<0.01). Immunostaining for the cellular proliferation markers (pRb and pH3) was greater in granulosa cells of healthy SAFs (P<0.01), while staining for the cell cycle inhibitor (p21) was higher in atretic SAFs (P<0.01). Intense CYP17A1 staining was observed on the theca of SAFs from WSD+/- T groups, compared to controls. Microarray analyses of the transcriptome in SAFs isolated from a subgroup (n=3/grp) of WSD and WSD+T treated females and controls consuming a standard diet, identified mRNA levels for 1944 genes changed >2-fold (p<0.05) among the three groups. Pathway analyses identified several gene pathways altered by WSD and/or WSD+T associated with lipid, carbohydrate and lipid metabolism, plus ovarian processes. Alterations of several SAF mRNAs are similar to those observed in follicular cells from women with PCOS. These data indicate chronic exposure to a WSD in the presence and absence of chronically elevated T alters structure and function of SAFs within primate ovaries.
Publication Title
Western-style diet, with and without chronic androgen treatment, alters the number, structure, and function of small antral follicles in ovaries of young adult monkeys.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hyperactivation of phosphatidylinositol-3 kinase (PI3K) promotes escape from hormone dependence in estrogen receptor-positive breast cancer.
Publication Title
Hyperactivation of phosphatidylinositol-3 kinase promotes escape from hormone dependence in estrogen receptor-positive human breast cancer.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Macaca mulatta
- 19 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Experiments were designed to evaluate changes in the transcriptome (mRNA levels) in the ovulatory, luteinizing follicle of rhesus monkeys, using a controlled ovulation (COv) model that permits analysis of the naturally selected, dominant follicle at specific intervals (0, 12, 24, 36 hours) after exposure to an ovulatory (exogenous hCG) stimulus during the menstrual cycle. Total RNA was prepared from individual follicles (n=4-8/timepoint), with an aliquot used for microarray analysis (AffymetrixTM Rhesus Macaque Genome Array) and the remainder applied to quantitative real-time PCR (q-PCR) assays. The microarray data from individual samples distinctly clustered according to timepoints, and ovulated follicles displayed markedly different expression patterns from unruptured follicles at 36 h. Between timepoint comparisons revealed profound changes in mRNA expression profiles. The dynamic pattern of mRNA expression for steroidogenic enzymes (CYP17A, CYP19A, HSD3B2, HSD11B1, HSD11B2), StAR, and gonadotropin receptors (LHCGR, FSHR) as determined by microarray analysis correlated precisely with those from blinded q-PCR assays. Patterns of mRNA expression for EGF-like factors (AREG, EREG) and processes (HAS2, TNFAIP6) implicated in cumulus-oocyte maturation/expansion were also comparable between assays. Thus, several mRNAs displayed the expected expression pattern for purported theca (e.g., CYP17A, AREG), granulosa (CYP19A, FSHR), cumulus (HAS2, TNFAIP6) cell, and surface epithelium (HSD11B) related genes in the rodent/primate preovulatory follicle. This database will be of great value in analyzing molecular and cellular pathways associated with periovulatory events in the primate follicle (e.g. follicle rupture, luteinization, inflammatory response, and angiogenesis), and for identifying novel gene products controlling mammalian fertility.
Publication Title
Dynamics of the transcriptome in the primate ovulatory follicle.
Sample Metadata Fields
Sex, Specimen part
View Samples