scholarly journals Gene-signatures predict biologically relevant dose-response potencies in phenotypic assays

2019 ◽  
Author(s):  
Steffen Renner ◽  
Christian Bergsdorf ◽  
Rochdi Bouhelal ◽  
Magdalena Koziczak-Holbro ◽  
Andrea Marco Amati ◽  
...  
Keyword(s):  
Dose Response ◽  
R Package ◽  
Gene Signature ◽  
Inhibitory Effect ◽  
Single Individual ◽  
Biologically Relevant ◽  
Camp Generation ◽  
Relevant Dose ◽  
Agonistic Activity ◽  
Highly Correlated

AbstractMultiplexed gene-signature-based phenotypic assays are increasingly used for the identification and profiling of small molecule-tool compounds and drugs. Here we introduce a method (provided as R-package) for the quantification of the dose-response potency of a gene-signature as EC50 and IC50 values.Two signaling pathways were used as models to validate our methods: beta-adrenergic agonistic activity on cAMP generation (dedicated dataset generated for this study) and EGFR inhibitory effect on cancer cell viability. In both cases, potencies derived from multi-gene expression data were highly correlated with orthogonal potencies derived from cAMP and cell growth readouts, and superior to potencies derived from single individual genes.Our results show that gene-signature potencies are a novel valid alternative to conventional readouts for compound potency quantification, in particular in scenarios where no other established readouts are available.

scholarly journals NoRCE: non-coding RNA sets cis enrichment tool

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan
Keyword(s):  
Expression Patterns ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Fruit Fly ◽  
Relevant Information ◽  
R Package ◽  
Data Repository ◽  
Biologically Relevant ◽  
Gene Sets ◽  
Data Files

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

scholarly journals The effects of human leptin fragment(126-140) on pituitary functions in man

2003 ◽  
pp. 407-412 ◽  
Author(s):  
K Hanew
Keyword(s):  
Dose Response ◽  
Area Under The Curve ◽  
Inhibitory Effect ◽  
Pituitary Hormones ◽  
Pituitary Function ◽  
Gh Secretion ◽  
Combined Administration ◽  
The Mean ◽  
Spontaneous Secretion ◽  
Control Study

OBJECTIVE: The effects of human leptin fragment(126-140) on pituitary function in eight healthy, non-obese men were studied. METHODS AND DESIGN: The effects of the fragment on spontaneous secretion of pituitary hormones and endogenous leptin, as well as on GHRH-induced GH secretion were examined. RESULTS: After the administration of the fragment (50 microg i.v. for 150 min), the mean nadir value and 45 min value were significantly lower than that of the control study. Endogenous leptin levels did not decrease significantly following the administration of the leptin fragment. Other pituitary hormones were not affected by the fragment. The area under the curve of the GH response to GHRH(1-44)NH(2) (10 microg, i.v. from 0 to 75 min) was also significantly inhibited by the combined administration of the leptin fragment (100 microg i.v. from -30 to 75 min) (P<0.001). Three subjects were re-examined with larger doses of the leptin fragment (200-400 microg), and even greater GH suppression was observed. CONCLUSIONS: These results indicate that human leptin fragment(126-140) has an inhibitory role in GH secretion, since when administered exogenously this fragment significantly suppressed spontaneous and, in a dose-response manner, GHRH-induced GH secretion. Clear effects of the fragment on other pituitary hormones and an inhibitory effect on endogenous leptin secretion were not observed in this study.

Adenosine A1 receptor-mediated inhibition of vasopressin action in inner medullary collecting duct

1994 ◽  
Vol 266 (5) ◽  
pp. F791-F796 ◽  
Author(s):  
R. M. Edwards ◽  
W. S. Spielman
Keyword(s):  
Receptor Agonist ◽  
Collecting Duct ◽  
Basolateral Membrane ◽  
Inhibitory Effect ◽  
Dependent Manner ◽  
Camp Accumulation ◽  
Concentration Dependent Manner ◽  
Cgs 21680 ◽  
Camp Generation ◽  
A1 Receptor

We examined the effects of adenosine and adenosine analogues on arginine vasopressin (AVP)-induced increases in osmotic water permeability (Pf; micron/s) and adenosine 3',5'-cyclic monophosphate (cAMP) accumulation in rat inner medullary collecting ducts (IMCDs). When added to the bath, the A1 receptor agonist N6-cyclohexyladenosine (CHA) produced a rapid and reversible inhibition of AVP-stimulated (10 pM) Pf (1,781 +/- 195 to 314 +/- 85 microns/s at 0.3 microM CHA; n = 9). The inhibitory effect of CHA was concentration dependent, with a 50% inhibitory concentration of 10 nM. The effect of CHA was inhibited by prior exposure of IMCDs to the A1 receptor antagonist 1,3-dipropylxanthine-8-cyclopentylxanthine (DP-CPX; 1 microM) or by preincubation with pertussis toxin. CHA had no effect on cAMP-induced increases in Pf. In addition to CHA, adenosine and the nonselective agonist 5'-(N-ethylcarboxamido)-adenosine (NECA) inhibited AVP-dependent Pf by > or = 70%, whereas the A2 receptor agonist CGS-21680 had no effect. Luminal adenosine (0.1 mM) had no effect on basal or AVP-stimulated Pf. CHA, NECA, and adenosine but not CGS-21680 inhibited AVP-stimulated cAMP accumulation in a concentration-dependent manner (50% inhibitory concentrations 0.1–300 nM). The inhibitory effect of CHA on AVP-stimulated cAMP accumulation was attenuated by DPCPX. We conclude that adenosine, acting at the basolateral membrane, inhibits AVP action in the IMCD via interaction with A1 receptors. The inhibition occurs proximal to cAMP generation and likely involves an inhibitory G protein.

scholarly journals Hormetic Concentrations of Hydrogen Peroxide but Not Ethanol Induce Cross-Adaptation to Different Stresses in Budding Yeast

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Halyna M. Semchyshyn
Keyword(s):  
Hydrogen Peroxide ◽  
Dose Response ◽  
Budding Yeast ◽  
Regulatory Protein ◽  
Colony Growth ◽  
Inhibitory Effect ◽  
Cross Resistance ◽  
Mild Stress ◽  
Low Concentrations ◽  
Cross Adaptation

The biphasic-dose response of microorganisms to hydrogen peroxide is a phenomenon of particular interest in hormesis research. In different animal models, the dose-response curve for ethanol is also nonlinear showing an inhibitory effect at high doses but a stimulatory effect at low doses. In this study, we observed the hormetic-dose response to ethanol in budding yeastS. cerevisiae. Cross-protection is a phenomenon in which exposure to mild stress results in the acquisition of cellular resistance to lethal stress induced by different factors. Since both hydrogen peroxide and ethanol at low concentrations were found to stimulate yeast colony growth, we evaluated the role of one substance in cell cross-adaptation to the other substance as well as some weak organic acid preservatives. This study demonstrates that, unlike ethanol, hydrogen peroxide at hormetic concentrations causes cross-resistance ofS. cerevisiaeto different stresses. The regulatory protein Yap1 plays an important role in the hormetic effects by low concentrations of either hydrogen peroxide or ethanol, and it is involved in the yeast cross-adaptation by low sublethal doses of hydrogen peroxide.

scholarly journals Contrasting Roles of Ang II and ACEA in the Regulation of IL10 and IL1β Gene Expression in Primary SHR Astroglial Cultures

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 3012
Author(s):  
Dhanush Haspula ◽  
Michelle A. Clark
Keyword(s):  
Gene Expression ◽  
Wistar Rats ◽  
Gene Signature ◽  
Brain Regions ◽  
Inhibitory Effect ◽  
Ang Ii ◽  
Cannabinoid Type 1 Receptor ◽  
Il10 Gene ◽  
Cerebellar Astrocytes

Angiotensin (Ang) II is well-known to have potent pro-oxidant and pro-inflammatory effects in the brain. Extensive crosstalk between the primary Ang II receptor, Ang type 1 receptor (AT1R), and the cannabinoid type 1 receptor (CB1R) has been demonstrated by various groups in the last decade. Since activation of glial CB1R has been demonstrated to play a key role in the resolution of inflammatory states, we investigated the role of Ang II (100 nM) and/or ACEA (10 nM), a potent CB1R-specific agonist in the regulation of inflammatory markers in astrocytes from spontaneously hypertensive rats (SHR) and Wistar rats. Astrocytes were cultured from brainstems and cerebellums of SHR and Wistar rats and assayed for IL1β and IL10 gene expression and secreted fraction, in treated and non-treated cells, by employing qPCR and ELISA, respectively. mRNA expression of both IL10 and IL1β were significantly elevated in untreated brainstem and cerebellar astrocytes isolated from SHR when compared to Wistar astrocytes. No changes were observed in the secreted fraction. While ACEA-treatment resulted in a significant increase in IL10 gene expression in Wistar brainstem astrocytes (Log2FC ≥ 1, p < 0.05), its effect in SHR brainstem astrocytes was diminished. Ang II treatment resulted in a strong inhibitory effect on IL10 gene expression in astrocytes from both brain regions of SHR and Wistar rats (Log2FC ≤ −1, p < 0.05), and an increase in IL1β gene expression in brainstem astrocytes from both strains (Log2FC ≥ 1, p < 0.05). Co-treatment of Ang II and ACEA resulted in neutralization of Ang II-mediated effect in Wistar brainstem and cerebellar astrocytes, but not SHR astrocytes. Neither Ang II nor ACEA resulted in any significant changes in IL10 or IL1β secreted proteins. These data suggest that Ang II and ACEA have opposing roles in the regulation of inflammatory gene signature in astrocytes isolated from SHR and Wistar rats. This however does not translate into changes in their secreted fractions.

scholarly journals Oscillations of cyclic nucleotide concentrations in relation to the excitability of Dictyostelium cells

1979 ◽  
Vol 81 (1) ◽  
pp. 33-47 ◽  
Author(s):  
G. Gerisch ◽  
D. Malchow ◽  
W. Roos ◽  
U. Wick
Keyword(s):  
Signal Processing ◽  
Cyclic Amp ◽  
Adenylate Cyclase ◽  
Inhibitory Effect ◽  
Camp Concentration ◽  
Surface Receptors ◽  
Camp Generation ◽  
Adenylate Cyclase Activation ◽  
Signal Input ◽  
Extracellular Camp

Aggregating cells of Dictyostelium discoideum are able to release cyclic AMP periodically. The oscillations of cAMP generation are associated with changes in adenylate cyclase activity. Cyclic AMP receptors on the cell surface are functionally coupled to the oscillating system as evidenced by phase shifts that are induced by small pulses of extracellular cAMP. An important element of the oscillating system is the signal processing from surface receptors to the adenylate cyclase. This pathway exhibits adaptation resulting in the suppression of responses to constant, elevated concentrations of cAMP. The signal input for adenylate cyclase activation is, therefore, a change in the extracellular cAMP concentration with time. Oscillations in the absence of detectable changes of intra- or extracellular cAMP concentrations suggest the possibility that there is a metabolic network in D. discoideum cells that undergoes oscillations without coupling to adenylate cyclase. Cyclic GMP concentrations oscillate with a slight phase difference in advance of that of cAMP, suggesting that the two nucleotide cyclases might not be activated by the same mechanism. Elevation of extracellular calcium exerts an inhibitory effect on the accumulation of cAMP and on the second of the two cGMP peaks.

Hearing Foreign Voices: Does Knowing What is Said Affect Visual-Masked-Speech Detection?

Perception ◽  
10.1068/p3466 ◽  
2003 ◽  
Vol 32 (1) ◽  
pp. 111-120 ◽  
Author(s):  
Jeesun Kim ◽  
Chris Davis
Keyword(s):  
High Frequency ◽  
Signal Amplification ◽  
Inhibitory Effect ◽  
Cognitive Factors ◽  
Large Impact ◽  
Perceptual Integration ◽  
Speech Detection ◽  
Detection Ability ◽  
Sensory Enhancement ◽  
Highly Correlated

We investigated audio-visual (AV) perceptual integration by examining the effect of seeing the speaker's synchronised moving face on masked-speech detection ability. Signal amplification and higher-level cognitive accounts of an AV advantage were contrasted, the latter by varying whether participants knew the language of the speaker. An AV advantage was shown for sentences whose mid-to-high-frequency acoustic envelope was highly correlated with articulator movement, regardless of knowledge of the language. For low-correlation sentences, knowledge of the language had a large impact; for participants with no knowledge of the language an AV inhibitory effect was found (providing support for reports of a compelling AV illusion). The results indicate a role for both sensory enhancement and higher-level cognitive factors in AV speech detection.

Inhibitory effect of ethacrynic acid on chloride permeability

1976 ◽  
Vol 231 (5) ◽  
pp. 1485-1489 ◽  
Author(s):  
R Motais ◽  
JL Cousin
Keyword(s):  
Hydrophobic Interaction ◽  
Ethacrynic Acid ◽  
Chloride Transport ◽  
Direct Proof ◽  
Inhibitory Effect ◽  
Ringer Solution ◽  
Relative Activity ◽  
Chloride Permeability ◽  
Sh Group ◽  
Highly Correlated

Ethacrynic acid inhibits anion movements in ox red blood cells. The I50 for chloride is 7 X 10(-6) M. The inhibitory effect is instantaneous and completely reversed by washing the cells with a Ringer solution, suggesting that reaction with a membrane SH group is not involved in this process. Direct proof that ethacrynic acid does not act by its reactivity with thiol groups is given by experiments with dihydroethacrynic acid, a derivative that lacks the ability to combine with SH groups: the characteristics of inhibition are strictly identical (instantaneous and reversible; I50 equals 9 X 10(-6) M). All the phenoxyacetic derivatives tested were also more or less inhibitory. The relative activity of all the derivatives was highly correlated with their liposolubility, indicating that hydrophobic interaction is important in determining drug effect and influence of steric factors is minimal. The data suggest that inhibition essentially results from a hydrophobic interaction between ethacrynic acid and apolar regions of the membrane protein allowing chloride transport.

scholarly journals Development of a Predictive Immune-Related Gene Signature Associated With Hepatocellular Carcinoma Patient Prognosis

2020 ◽  
Vol 27 (1) ◽  
pp. 107327482097711
Author(s):  
Jiasheng Lei ◽  
Dengyong Zhang ◽  
Chao Yao ◽  
Sheng Ding ◽  
Zheng Lu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Cox Regression ◽  
R Package ◽  
Gene Signature ◽  
Differentially Expressed ◽  
Related Gene ◽  
Patient Cohort ◽  
Immune Related Gene ◽  
Related Risk

Background: Hepatocellular carcinoma (HCC) remains the third leader cancer-associated cause of death globally, but the etiological basis for this complex disease remains poorly clarified. The present study was thus conceptualized to define a prognostic immune-related gene (IRG) signature capable of predicting immunotherapy responsiveness and overall survival (OS) in patients with HCC. Methods: Five differentially expressed IRG associated with HCC were established the immune-related risk model through univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. Patients were separated at random into training and testing cohorts, after which the association between the identified IRG signature and OS was evaluated using the “survival” R package. In addition, maftools was leveraged to assess mutational data, with tumor mutation burden (TMB) scores being calculated as follows: (total mutations/total bases) × 106. Immune-related risk term abundance was quantified via “ssGSEA” algorithm using the “gsva” R package. Results: HCC patients were successfully stratified into low-risk and high-risk groups based upon a signature composed of 5 differentially expressed IRGs, with overall survival being significantly different between these 2 groups in training cohort, testing cohort and overall patient cohort ( P = 1.745e-06, P = 1.888e-02, P = 4.281e-07). No association was observed between TMB and this IRG risk score in the overall patient cohort ( P = 0.461). Notably, 19 out of 29 immune-related risk terms differed substantially in the overall patient dataset. These risk terms mainly included checkpoints, human leukocyte antigens, natural killer cells, dendritic cells, and major histocompatibility complex class I. Conclusion: In summary, an immune-related prognostic gene signature was successfully developed and used to predict survival outcomes and immune system status in patients with HCC. This signature has the potential to help guide immunotherapeutic treatment planning for patients affected by this deadly cancer.

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