Altered Transcriptional Response Research Articles

Giredestrant reverses progesterone hypersensitivity driven by estrogen receptor mutations in breast cancer.

<i>ESR1</i> (estrogen receptor 1) hotspot mutations are major contributors to therapeutic resistance in estrogen receptor-positive (ER⁺) breast cancer. Such mutations confer estrogen independence to ERα, providing a selective advantage in the presence of estrogen-depleting aromatase inhibitors. In addition, <i>ESR1</i> mutations reduce the potency of tamoxifen and fulvestrant, therapies that bind ERα directly. These limitations, together with additional liabilities, inspired the development of the next generation of ERα-targeted therapeutics, of which giredestrant is a high-potential candidate. Here, we generated <i>Esr1</i> mutant-expressing mammary gland models and leveraged patient-derived xenografts (PDXs) to investigate the biological properties of the <i>ESR1</i> mutations and their sensitivity to giredestrant in vivo. In the mouse mammary gland, <i>Esr1</i> mutations promote hypersensitivity to progesterone, triggering pregnancy-like tissue remodeling and profoundly elevated proliferation. These effects were driven by an altered progesterone transcriptional response and underpinned by gained sites of ERα-PR (progesterone receptor) cobinding at the promoter regions of pro-proliferation genes. PDX experiments showed that the mutant ERα-PR proliferative program is also relevant in human cancer cells. Giredestrant suppressed the mutant ERα-PR proliferation in the mammary gland more so than the standard-of-care agents, tamoxifen and fulvestrant. Giredestrant was also efficacious against the progesterone-stimulated growth of <i>ESR1</i> mutant PDX models. In addition, giredestrant demonstrated activity against a molecularly characterized <i>ESR1</i> mutant tumor from a patient enrolled in a phase 1 clinical trial. Together, these data suggest that mutant ERα can collaborate with PR to drive protumorigenic proliferation but remain sensitive to inhibition by giredestrant.

HNF4A modulates glucocorticoid action in the liver.

SummaryThe glucocorticoid receptor (GR) is a nuclear receptor critical to the regulation of energy metabolism and inflammation. The actions of GR are dependent on cell type and context. Here, we demonstrate the role of liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver specificity of GR action. In mouse liver, the HNF4A motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodeled, with loss and gain of GR recruitment evident. Loss of chromatin accessibility at HNF4A-marked sites associates with loss of GR binding at weak GRE motifs. GR binding and chromatin accessibility are gained at sites characterized by strong GRE motifs, which show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is indicated by an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver.

Single-cell RNA sequencing reveals induction of distinct trained-immunity programs in human monocytes.

Trained immunity refers to the long-lasting memory traits of innate immunity. Recent studies have shown that trained immunity is orchestrated by sustained changes in epigenetic marks and metabolic pathways, leading to an altered transcriptional response to a second challenge. However, the potential heterogeneity of trained-immunity induction in innate immune cells has not been explored. In this study, we demonstrate cellular transcriptional programs in response to 4 different inducers of trained immunity in monocyte populations at single-cell resolution. Specifically, we identified 3 monocyte subpopulations upon the induction of trained immunity, and replicated these findings in an in vivo study. In addition, we found gene signatures consistent with these functional programs in patients with ulcerative colitis, sepsis, and COVID-19, suggesting the impact of trained-immunity programs in immune-mediated diseases.

Breaking IL7R Signaling-Induced Glucocorticoid Resistance By Small Molecule Inhibitors in T-Cell Acute Lymphoblastic Leukemia

▪T-lineage acute lymphoblastic leukemia (T-ALL) is considered as a high-risk disease entity that is associated with treatment resistance and relapse, and while there is only a 15% incidence of T-ALL among ALL patients, T-ALL represents 50% of patients that receive high-risk treatment based on residual disease levels during the initial phase of treatment. Glucocorticoids (GC) are cornerstone drugs in the treatment of ALL, and initial GC-responses strongly predict for survival and cure. However, cellular mechanisms of GC-resistance in ALL patients are poorly understood. We recently published our integrated genomics data for 69 primary T-ALL patient samples in relation to clinical outcome and in vitro drug responses (Li et al., PLoS Medicine, 2016).In that study, we identified activating mutations in the IL7R signaling pathway as cause of GC-resistance in T-ALL. Functional modeling of IL7R signaling mutations in two GC-sensitive T-ALL cell lines demonstrated that GC-resistance is not due to an altered transcriptional response by the glucocorticoid receptor NR3C1. We found that IL7R signaling mutations provoke strong MAPK and AKT signaling resulting in up-regulation of anti-apoptotic BCL2 family members and a shift in the molecular size of BIM, an essential pro-apoptotic molecule for GC-induced death. Another independent study linked strong induction of JAK/STAT signaling in response to interleukin-7 (IL7) to GC-resistance in T-ALL patients (Delgado-Martin et al., Leukemia, 2017).Following these observations, we now focus on improving our understanding on the role of BCL2 family members as effectors of GC-resistance downstream of IL7R signaling mutations and potential strategies to break GC-resistance. We generated inducible T-ALL cell lines that retain a GC-sensitive response following induction of wildtype IL7R or JAK1/3 molecules whereas these lines adopt a GC-resistant phenotype following (induced) expression of mutant IL7R, JAK1 or N/K-RAS molecules or wild-type RAS or AKT. Despite induced GC-resistance, up-regulation of total pro-apoptotic BIM levels is not affected following glucocorticoid exposure. Using specific targeted inhibitors, we found that ERK signaling becomes strongly activated downstream of most (mutant) IL7R-signaling molecules and phosphorylates pro-apoptotic BIM-L and BIM-EL isoforms at multiple residues, which are normally efficiently dephosphorylated by phosphatase PP2A. We currently use immuno-precipitation followed by mass-spectrometry to study the functional consequences of BIM phosphorylation that results in shifts among BCL2 family member interactions and GC-resistance and may point to novel strategies to break GC-resistance.The finding that GC-resistance arises from activated MEK-ERK and AKT suggests that a therapeutic regime combining GC-treatment with MEK, AKT or mTOR inhibitors may increase GC-responsiveness. We tested various compounds including the JAK1 inhibitor ruxolitinib, MEK inhibitors AZD5244 or trametinib, AKT inhibitor MK2206, mTOR inhibitors AZD8055 or everolimus or the dual kinase PI3K-mTOR inhibitor BEZ235 for their abilities to enhance GC-responsiveness of primary T-ALL patient samples using an in-vitro cytotoxicity assay (as measured by the combination index for the effective dose at which 50 percent of the leukemia cells are killed (ED50); see Figure). Despite 3 T-ALL patient samples tested that harbored IL7RA mutations, we found no proof for effectiveness of ruxolitinib to revert GC-resistance. This may possibly be due to a lack of cellular proliferation during in vitro drug sensitivity testing, implying that dormant leukemic stem cells are not killed by ruxolitinib. Both MEK inhibitors AZD6244 or trametinib synergistically enhanced prednisolone responsiveness in 5 out of 9 and 9 out of 10 patient samples, respectively. The AKT inhibitor MK2206 synergistically enhanced prednisolone sensitivity for 8 out of 11 patient samples, while mTOR inhibitors AZD-8055 and everolimus enhanced prednisolone responses in 10 out of 11 and 8 out of 8 patient samples, respectively (including two GC-resistant patients). The PI3K inhibitor NVPBEZ235 synergistically enhanced prednisolone sensitivity in 10 out of 11 patient samples.In conclusion, our data support the recommendation of including MEK, AKT, mTOR or dual PI3K/mTOR inhibitors to restore-or improve-GC-sensitivity of T-ALL cells to improve outcome. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Postoperative abdominal sepsis induces selective and persistent changes in CTCF binding within the MHC-II region of human monocytes.

BackgroundPostoperative abdominal infections belong to the most common triggers of sepsis and septic shock in intensive care units worldwide. While monocytes play a central role in mediating the initial host response to infections, sepsis-induced immune dysregulation is characterized by a defective antigen presentation to T-cells via loss of Major Histocompatibility Complex Class II DR (HLA-DR) surface expression. Here, we hypothesized a sepsis-induced differential occupancy of the CCCTC-Binding Factor (CTCF), an architectural protein and superordinate regulator of transcription, inside the Major Histocompatibility Complex Class II (MHC-II) region in patients with postoperative sepsis, contributing to an altered monocytic transcriptional response during critical illness.ResultsCompared to a matched surgical control cohort, postoperative sepsis was associated with selective and enduring increase in CTCF binding within the MHC-II. In detail, increased CTCF binding was detected at four sites adjacent to classical HLA class II genes coding for proteins expressed on monocyte surface. Gene expression analysis revealed a sepsis-associated decreased transcription of (i) the classical HLA genes HLA-DRA, HLA-DRB1, HLA-DPA1 and HLA-DPB1 and (ii) the gene of the MHC-II master regulator, CIITA (Class II Major Histocompatibility Complex Transactivator). Increased CTCF binding persisted in all sepsis patients, while transcriptional recovery CIITA was exclusively found in long-term survivors.ConclusionOur experiments demonstrate differential and persisting alterations of CTCF occupancy within the MHC-II, accompanied by selective changes in the expression of spatially related HLA class II genes, indicating an important role of CTCF in modulating the transcriptional response of immunocompromised human monocytes during critical illness.

Influenza-Induced Interferon Lambda Response Is Associated With Longer Time to Delivery Among Pregnant Kenyan Women.

Specific causes of preterm birth remain unclear. Several recent studies have suggested that immune changes during pregnancy are associated with the timing of delivery, yet few studies have been performed in low-income country settings where the rates of preterm birth are the highest. We conducted a retrospective nested case-control evaluation within a longitudinal study among HIV-uninfected pregnant Kenyan women. To characterize immune function in these women, we evaluated unstimulated and stimulated peripheral blood mononuclear cells in vitro with the A/California/2009 strain of influenza to understand the influenza-induced immune response. We then evaluated transcript expression profiles using the Affymetrix Human GeneChip Transcriptome Array 2.0. Transcriptional profiles of sufficient quality for analysis were obtained from 54 women; 19 of these women delivered <34 weeks and were defined as preterm cases and 35 controls delivered >37 weeks. The median time to birth from sample collection was 13 weeks. No transcripts were significantly associated with preterm birth in a case-control study of matched term and preterm birth (n = 42 women). In the influenza-stimulated samples, expression of IFNL1 was associated with longer time to delivery—the amount of time between sample collection and delivery (n = 54 women). A qPCR analysis confirmed that influenza-induced IFNL expression was associated with longer time to delivery. These data indicate that during pregnancy, ex vivo influenza stimulation results in altered transcriptional response and is associated with time to delivery in cohort of women residing in an area with high preterm birth prevalence.

The transcriptomic response to irinotecan in colon carcinoma bearing mice preconditioned by fasting.

BackgroundIrinotecan use is limited due to severe toxicity. Preconditioning by fasting (PBF) protects against side effects of irinotecan while preserving its antitumor activity. The mechanisms underlying the effects of PBF still need to be elucidated. Here, we investigated the transcriptional responses of PBF on irinotecan in both tumor and healthy liver tissue.Experimental approachMale BALB/c mice were subcutaneously injected with C26 colon carcinoma cells. Twelve days after tumor inoculation, two groups were fasted for three days and two groups were allowed food ad libitum (AL). Subsequently, both groups received one dose of irinotecan. Twelve hours after administration mice were sacrificed and blood, tumor and liver tissue were harvested. Blood samples were analyzed to determine liver, kidney and bone marrow function, tissues were used for transcriptome analyses.Key resultsThe AL irinotecan group showed worsened organ function and decreased leukocyte numbers. These effects were abated in PBF animals. PBF led to an altered transcriptional response in the liver of irinotecan-treated mice, including decreased cellular injury and increased stress resistance. Hepatic metabolism of irinotecan was also significantly changed due to PBF. The transcriptional response of tumor tissue observed after PBF was hardly affected compared to AL fed animals.ConclusionsTranscriptional changes after PBF to irinotecan treatment showed an improved protective stress response in healthy liver but not in tumor tissue, including changes in irinotecan metabolism. These data help to unravel the mechanisms underlying the effects of fasting on irinotecan and help to improve outcome of chemotherapeutic treatment in cancer patients.

In utero exposure to diesel exhaust particulates is associated with an altered cardiac transcriptional response to transverse aortic constriction and altered DNA methylation.

In utero exposure to diesel exhaust air pollution has been associated with increased adult susceptibility to heart failure in mice, but the mechanisms by which this exposure promotes susceptibility to heart failure are poorly understood. To identify the potential transcriptional effects that mediate this susceptibility, we have performed RNA sequencing analysis on adult hearts from mice that were exposed to diesel exhaust in utero and that have subsequently undergone transverse aortic constriction. We identified 3 target genes, Mir133a-2, Ptprf, and Pamr1, which demonstrate dysregulation after exposure and aortic constriction. Examination of expression patterns in human heart tissues indicates a correlation between expression and heart failure. We subsequently assessed DNA methylation modifications at these candidate loci in neonatal cultured cardiac myocytes after in utero exposure to diesel exhaust and found that the promoter for Mir133a-2 is differentially methylated. These target genes in the heart are the first genes to be identified that likely play an important role in mediating adult sensitivity to heart failure. We have also shown a change in DNA methylation within cardiomyocytes as a result of in utero exposure to diesel exhaust.-Goodson, J. M., Weldy, C. S., MacDonald, J. W., Liu, Y., Bammler, T. K., Chien, W.-M., Chin, M. T. In utero exposure to diesel exhaust particulates is associated with an altered cardiac transcriptional response to transverse aortic constriction and altered DNA methylation.

Abstract LB-010: Modeling the impact of mutations in ubiquitin pathway genes across human cancers

Abstract A number of ubiquitin pathway genes show a strikingly high frequency of somatic alterations across diverse human cancers. While several ubiquitin ligase genes with recurrent mutations or copy number alterations been studied in individual cancers, their role in many malignancies remains poorly understood. To better model the impact of ubiquitin pathway alterations, we developed a computational strategy for exploiting parallel phosphoproteomics and mRNA sequencing data for large tumor sets to link dysregulation of upstream signaling pathways with altered transcriptional response through the transcriptional circuitry. Our modeling allows us to interpret the impact of mutations and copy number events in terms of altered signaling and transcription factor (TF) activity. We used a multi-task learning strategy to jointly train phosphoprotein-TF interaction models across 10 human cancers for which large reverse-phase protein array and RNA-seq data sets are available through TCGA. We then applied a novel algorithmic approach to extract networks of signaling proteins and TFs whose inferred activities are correlated across tumors and whose dysregulation is associated with specific somatically altered ubiquitin pathway genes. Our analysis revealed both known and novel interactions of ubiquitin ligase genes with signaling pathways and transcriptional programs in a pan-cancer context. Citation Format: Hatice U. Osmanbeyoglu, Christina Leslie. Modeling the impact of mutations in ubiquitin pathway genes across human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-010. doi:10.1158/1538-7445.AM2017-LB-010

Hepatic transcriptional responses to copper in the three-spined stickleback are affected by their pollution exposure history

Some fish populations inhabiting contaminated environments show evidence of increased chemical tolerance, however the mechanisms contributing to this tolerance, and whether this is heritable, are poorly understood. We investigated the responses of two populations of wild three-spined stickleback (Gasterosteus aculeatus) with different histories of contaminant exposure to an oestrogen and copper, two widespread aquatic pollutants. Male stickleback originating from two sites, the River Aire, with a history of complex pollution discharges, and Siblyback Lake, with a history of metal contamination, were depurated and then exposed to copper (46μg/L) and the synthetic oestrogen ethinyloestradiol (22ng/L). The hepatic transcriptomic response was compared between the two populations and to a reference population with no known history of exposure (Houghton Springs, Dorset). Gene responses included those typical for both copper and oestrogen, with no discernable difference in response to oestrogen between populations. There was, however, some difference in the magnitude of response to copper between populations. Siblyback fish showed an elevated baseline transcription of genes encoding metallothioneins and a lower level of metallothionein induction following copper exposure, compared to those from the River Aire. Similarly, a further experiment with an F1 generation of Siblyback fish bred in the laboratory found evidence for elevated transcription of genes encoding metallothioneins in unexposed fish, together with an altered transcriptional response to 125μg/L copper, compared with F1 fish originating from the clean reference population exposed to the same copper concentration. These data suggest that the stickleback from Siblyback Lake have a differential response to copper, which is inherited by the F1 generation in laboratory conditions, and for which the underlying mechanism may include an elevation of baseline transcription of genes encoding metallothioneins. The genetic and/or epigenetic mechanisms contributing to this inherited alteration of metallothionein transcription have yet to be established.

Abstract 781: Modeling the impact of somatic alterations across human cancers

Abstract Large-scale cancer genomics projects like The Cancer Genome Atlas have generated a comprehensive catalog of somatic mutations and copy number aberrations across many tumor types, but the role of most frequently altered genes remains obscure. To better model the impact of these alterations, we developed a novel computational strategy for exploiting parallel phosphoproteomics and mRNA sequencing data for large tumor sets by linking dysregulation of upstream signaling pathways with altered transcriptional response through the transcriptional circuitry. Our modeling allows us to interpret the impact of somatic alterations in terms of functional outcomes such as altered signaling and transcription factor (TF) activity. We used this novel machine learning strategy to train phosphoprotein-TF interaction models across 12 human cancers for which large reverse-phase protein array and RNA-seq data sets are available through TCGA. First, we used this approach to identify shared and cancer-specific roles of TF/signaling regulators across cancer types. Then we performed a statistical analysis to associate frequent somatic aberrations with alterations in inferred TF and signaling protein activities. From our analysis, we gained many novel insights into cancer biology. We identified both known (e.g FOXO1 for breast cancer) and novel TF regulators of cancer (e.g. ELK1 for head and neck cancer). Many of these identified TF regulators were significantly associated with survival outcome in bladder urothelial, renal cell clear and endometrial carcinoma. Next we performed a comprehensive cross-cancer analysis and identified relationships between somatic alterations and downstream transcriptional effects and signaling pathway activation. We observed that specific molecular aberrations have different functional consequences in different cancer types. For example, PIK3CA mutations are associated with altered activities of a diverse set of TFs across cancers that are involved in cell cycle, apoptosis, metabolism and MAPK/ERK signaling. Notably, in cell line models, we validated some of the altered TFs predicted by our model. We showed that PIK3CA mutation leads to ELK1 activation in breast and head and neck cancer models. We further found that different set of TFs are associated with a specific mutation in different cancers due to the different background of genomic aberrations in each cancer. For example, KRAS mutations are associated with a distinct set of TFs depending of cancer-specific co-mutation profiles (e.g. co-mutations of KRAS and TP53 in lung adenocarcinoma and co-mutations of KRAS and APC in colorectal cancer). Our analysis revealed both known and novel interactions of frequently altered genes with signaling pathways and transcriptional programs in a pan-cancer context. Patterns of co-alterations across cancers may provide new insights relevant to targeted therapy and may be crucial to optimizing combination therapies. Citation Format: Hatice U. Osmanbeyoglu, Eneda Toska, José Baselga, Christina Leslie. Modeling the impact of somatic alterations across human cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 781.

An altered peripheral IL6 response in major depressive disorder

Major depressive disorder (MDD) is one of the most prevalent major psychiatric disorders with a lifetime prevalence of 17%. Recent evidence suggests MDD is not only a brain dysfunction, but a systemic disease affecting the whole body. Central and peripheral inflammatory changes seem to be a centerpiece of MDD pathology: a subset of patients show elevated blood cytokine and chemokine levels that partially normalize with symptom improvement over the course of anti-depressant treatment. As this inflammatory process in MDD is poorly understood, we hypothesized that the peripheral tissues of MDD patients will respond differently to inflammatory stimuli, resulting in an aberrant transcriptional response to elevated pro-inflammatory cytokines. To test this, we used MDD patient- and control-derived dermal fibroblast cultures to investigate their response to an acute treatment with IL6, IL1β, TNFα, or vehicle. Following RNA isolation and subsequent cDNA synthesis, quantitative PCR was used to determine the relative expression level of several families of inflammation-responsive genes. Our results showed comparable expression of the tested genes between MDD patients and controls at baseline. In contrast, MDD patient fibroblasts had a diminished transcriptional response to IL6 in all the gene sets tested (oxidative stress response, mitochondrial function, and lipid metabolism). We also found a significant increase in baseline and IL6 stimulated transcript levels of the IL6 receptor gene. This IL6 receptor transcript increase in MDD fibroblasts was accompanied by an IL6 stimulated increase in induction of SOCS3, which dampens IL6 receptor signaling. Altogether our results demonstrate that there is an altered transcriptional response to IL6 in MDD, which may represent one of the molecular mechanisms contributing to disease pathophysiology. Ultimately we hope that these studies will lead to validation of novel MDD drug targets focused on normalizing the altered IL6 response in patients.

Abstract LB-C04: Modeling the impact of somatic alterations across human cancers

Abstract Modeling the impact of somatic alterations across human cancers Hatice U. Osmanbeyoglu1, Christina S. Leslie1,* 1Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY Abstract Large-scale cancer genomics projects like The Cancer Genome Atlas have generated a comprehensive catalog of somatic mutations and copy number aberrations across many tumor types, but the role of some frequently altered genes remains obscure. To better model the impact of these alterations, we developed a computational strategy for exploiting parallel phosphoproteomics and mRNA sequencing data for large tumor sets to link dysregulation of upstream signaling pathways with altered transcriptional response through the transcriptional circuitry. Our modeling allows us to interpret the impact of mutations and copy number events in terms of altered signaling and transcription factor (TF) activity. We used a novel machine learning strategy to train phosphoprotein-TF interaction models across 10 human cancers for which large reverse-phase protein array and RNA-seq data sets are available through TCGA. We then applied a novel algorithmic approach to extract networks of signaling proteins and TFs whose inferred activities are correlated across tumors and whose dysregulation is associated with specific somatically altered genes. Our analysis revealed both known and novel interactions of frequently altered genes with signaling pathways and transcriptional programs in a pan-cancer context. Moreover, our algorithmic approach provides a general strategy for modeling the impact of recurrent mutations and copy number alterations on signaling pathways and transcriptional programs through pan-cancer analysis. Citation Format: Hatice U. Osmanbeyoglu, Christina Leslie. Modeling the impact of somatic alterations across human cancers. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-C04.

Adaptation of a polyphagous herbivore to a novel host plant extensively shapes the transcriptome of herbivore and host.

Generalist arthropod herbivores rapidly adapt to a broad range of host plants. However, the extent of transcriptional reprogramming in the herbivore and its hosts associated with adaptation remains poorly understood. Using the spider mite Tetranychus urticae and tomato as models with available genomic resources, we investigated the reciprocal genomewide transcriptional changes in both spider mite and tomato as a consequence of mite's adaptation to tomato. We transferred a genetically diverse mite population from bean to tomato where triplicated populations were allowed to propagate for 30 generations. Evolving populations greatly increased their reproductive performance on tomato relative to their progenitors when reared under identical conditions, indicative of genetic adaptation. Analysis of transcriptional changes associated with mite adaptation to tomato revealed two main components. First, adaptation resulted in a set of mite genes that were constitutively downregulated, independently of the host. These genes were mostly of an unknown function. Second, adapted mites mounted an altered transcriptional response that had greater amplitude of changes when re-exposed to tomato, relative to nonadapted mites. This gene set was enriched in genes encoding detoxifying enzymes and xenobiotic transporters. Besides the direct effects on mite gene expression, adaptation also indirectly affected the tomato transcriptional responses, which were attenuated upon feeding of adapted mites, relative to the induced responses by nonadapted mite feeding. Thus, constitutive downregulation and increased transcriptional plasticity of genes in a herbivore may play a central role in adaptation to host plants, leading to both a higher detoxification potential and reduced production of plant defence compounds.

P53 Contributes to Differentiating Gene Expression Following Exposure to Acetaminophen and Its Less Hepatotoxic Regioisomer Both In Vitro and In Vivo.

The goal of the present study was to compare hepatic toxicogenomic signatures across in vitro and in vivo mouse models following exposure to acetaminophen (APAP) or its relatively nontoxic regioisomer 3′-hydroxyacetanilide (AMAP). Two different Affymetrix microarray platforms and one Agilent Oligonucleotide microarray were utilized. APAP and AMAP treatments resulted in significant and large changes in gene expression that were quite disparate, and likely related to their different toxicologic profiles. Ten transcripts, all of which have been implicated in p53 signaling, were identified as differentially regulated at all time-points following APAP and AMAP treatments across multiple microarray platforms. Protein-level quantification of p53 activity aligned with results from the transcriptomic analysis, thus supporting the implicated mechanism of APAP-induced toxicity. Therefore, the results of this study provide good evidence that APAP-induced p53 phosphorylation and an altered p53-driven transcriptional response are fundamental steps in APAP-induced toxicity.

β‐actin knock‐out mouse embryonic fibroblasts show increased expression of LIM‐, CH‐, EFh‐domain containing proteins with predicted common upstream regulators

β-actin depletion from mouse embryonic fibroblasts results in an altered transcriptional response rendering these cells a myofibroblast like phenotype. The proteins and upstream regulatory factors responsible for this acquired phenotype, with prominent focal adhesions and stress fibres, are unknown. Data-mining of the changed proteome revealed that actin binding proteins associated with stress fiber or focal adhesion formation are overexpressed in the β-actin knock-out cells and that many of these contain CH-, LIM- or EFh- domains. Furthermore in silico analysis predicts potential common upstream regulators that may, at least partly, coordinate the altered transcriptional response.

A glimpse of the yeast Saccharomyces cerevisiae responses to NaCl stress

The budding yeast Saccharomyces cerevisiae has been widely used in fermentation and brewing industries. In industrial fermentation processes, the raw material often attaches certain NaCl or Na+ into bioreactor. High salinity represents an osmotic stress and specific ion toxicity for yeast cell. Protective biochemical reactions range from the synthesis of osmolyte to altered ion transportation, signal transduction, transcriptional response and translational response. This review will focus on responses of the yeast S. cerevisiae and mechanisms of adaptation to NaCl stress and offer a glimpse at the mechanisms of ion homeostasis, regulation of HOG (High Osmosis Glycerol) signaling pathway and the genomic expression response of the cells against the stress. Key words: Genomic expression response, HOG (High Osmosis Glycerol) signaling pathway, Saccharomyces cerevisiae, saline stress.

A glimpse of the yeast Saccharomyces cerevisiae responses to NaCl stress

The budding yeast Saccharomyces cerevisiae has been widely used in fermentation and brewing industries. In industrial fermentation processes, the raw material often attaches certain NaCl or Na+ into bioreactor. High salinity represents an osmotic stress and specific ion toxicity for yeast cell. Protective biochemical reactions range from the synthesis of osmolyte to altered ion transportation, signal transduction, transcriptional response and translational response. This review will focus on responses of the yeast S. cerevisiae and mechanisms of adaptation to NaCl stress and offer a glimpse at the mechanisms of ion homeostasis, regulation of HOG (High Osmosis Glycerol) signaling pathway and the genomic expression response of the cells against the stress. Key words: Genomic expression response, HOG (High Osmosis Glycerol) signaling pathway, Saccharomyces cerevisiae, saline stress.

Gene expression in response to ionizing radiation and family history of gastric cancer

Genes and molecular pathways involved in familial clustering of gastric cancer have not yet been identified. The purpose of the present study was to investigate gene expression changes in response to a cellular stress, and its link with a positive family history for this neoplasia. To this aim leukocytes of healthy first-degree relatives of gastric cancer patients and controls were challenged in vitro with ionizing radiation and gene expression evaluated 4 h later on microarrays with 1,800 cancer-related genes. Eight genes, mainly involved in signal transduction and cell cycle regulation, were differentially expressed in healthy relatives of gastric cancer cases. Functional class scoring by Gene Ontology classification highlighted two G-protein related pathways, implicated in the proliferation of neoplastic tissue, which were differentially expressed in healthy subjects with positive family history of gastric cancer. The relative expression of 84 genes related to these pathways was examined using the SYBR green-based quantitative real-time PCR. The results confirmed the indication of an involvement of G-protein coupled receptor pathways in GC familiarity provided by microarray analysis. This study indicates a possible association between familiarity for gastric cancer and altered transcriptional response to ionizing radiation.

Myocellular basis for tapering in competitive distance runners

The purpose of this study was to examine the effects of a 3-wk taper on the physiology of competitive distance runners. We studied seven collegiate distance runners (20+/-1 yr, 66+/-1 kg) before and after a 3-wk taper. The primary measures included 8-km cross-country race performance, gastrocnemius single muscle fiber size and function (peak force, shortening velocity, and power), baseline and exercise-induced gene expression 4 h after a standardized 8-km run, citrate synthase activity, and maximal and submaximal cardiovascular physiology (oxygen consumption, ventilation, heart rate, and respiratory exchange ratio). Race performance improved by 3% following taper (P<0.05). Myosin heavy chain (MHC) IIa fiber diameter (+7%, P<0.05), peak force (+11%, P=0.06), and absolute power (+9%, P<0.05) increased following taper. In addition to the MHC IIa adaptations, taper elicited a distinct postexercise gene response. Specifically, the induction of MuRF-1 was attenuated following taper, whereas MRF4, HSP 72, and MT-2A displayed an exaggerated response (P<0.05). No changes were observed in MHC I size or function, baseline gene expression, citrate synthase activity, or cardiovascular function. Our findings show that tapered training in competitive runners promoted MHC IIa fiber remodeling and an altered transcriptional response following the same exercise perturbation, with no adverse affects on aerobic fitness. Together, these results provide a myocellular basis for distance runners to taper in preparation for peak performance.