Time-dependent effects of Pochonia chlamydosporia endophytism on gene expression profiles of colonized tomato roots

Benzene is used as a general purpose solvent. Benzene metabolism starts from phenol and ends with p-benzoquinone and o-benzoquinone. Liver injury inducted by benzene still remains a toxicologic problem. Tumor related genes and immune responsive genes have been studied in patients suffering from benzene exposure. However, gene expression profiles and pathways related to its hepatotoxicity are not known. This study reports the results obtained in the liver of BALB/C mice (SLC, Inc., Japan) administered 0.05 ml/100 g body weight of 2% benzene for six days. Serum, ALT, AST and ALP were determined using automated analyzer (Fuji., Japan). Histopathological observations were made to support gene expression data. c-DNA microarray analyses were performed using Affymetrix Gene-chip system. After six days of benzene exposure, twenty five genes were down regulated whereas nineteen genes were up-regulated. These gene expression changes were found to be related to pathways of biotransformation, detoxification, apoptosis, oxidative stress and cell cycle. It has been shown for the first time that genes corresponding to circadian rhythms are affected by benzene. Results suggest that gene expression profile might serve as potential biomarkers of hepatotoxicity during benzene exposure.

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Photo-caged agonists of the nuclear receptors RARγ and TRβ provide unique time-dependent gene expression profiles for light-activated gene patterning

Bioorganic & Medicinal Chemistry ◽

10.1016/j.bmc.2004.08.022 ◽

2004 ◽

Vol 12 (22) ◽

pp. 5949-5959 ◽

Cited By ~ 15

Author(s):

Kristian H. Link ◽

Federico G. Cruz ◽

Hai-Fen Ye ◽

Kathryn E. O’Reilly ◽

Sarah Dowdell ◽

...

Keyword(s):

Gene Expression ◽

Nuclear Receptors ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Time Dependent ◽

Gene Patterning

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Abstract P744: Gene Transcript Clusters Distinguish Time-Dependent Expression Patterns in Monocytes, Neutrophils and Whole Blood After Ischemic Stroke Injury

Stroke ◽

10.1161/str.52.suppl_1.p744 ◽

2021 ◽

Vol 52 (Suppl_1) ◽

Author(s):

Paulina Carmona-Mora ◽

Glen C Jickling ◽

Xinhua Zhan ◽

Marisa Hakoupian ◽

Heather Hull ◽

...

Keyword(s):

Gene Expression ◽

Ischemic Stroke ◽

Whole Blood ◽

Temporal Dynamics ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Time Dependent ◽

Gene Transcript ◽

Time Points

Introduction: After ischemic stroke (IS), peripheral leukocytes infiltrate the damaged region and modulate the response to injury. We previously showed that peripheral blood cells display different gene expression profiles after IS and these transcriptional programs reflect the changes in immune processes in response to IS. Dissecting the temporal dynamics of gene expression after IS improves our understanding of the changes of molecular and cellular pathways involved in acute brain injury. Methods: We analyzed the transcriptomic profiles of 33 IS patients in isolated monocytes, neutrophils and whole blood. RNA-sequencing was performed on all the stroke samples as well as 12 controls with vascular risk factors (diabetes and/or hypertension and/or hypercholesterolemia). To identify differentially expressed genes, subjects were split into time points (TPs) from stroke onset (TP1= 0-24 h; TP2= 24-48 h; and TP3= > 48 h), and controls were assigned TP0. A linear regression model including time and the interaction of diagnosis x TP with cutoff of p<0.02 and fold-change>|1.2| was used. Time dependent changes were analyzed using artificial neural networks to identify clusters of genes that behave in a similar way across TPs. Results: Unique patterns of temporal expression were distinguished for the three sample types. These include genes not expressed in TP0 that peak only within the first 24 h, others that peak or decrease in TP2 and TP3, and more complex patterns. Genes that peak at TP1 in monocytes and neutrophils are related to cell adhesion and leukocyte differentiation/migration, respectively. Early peaks in whole blood occur in genes related to transcriptional regulation. In monocytes, interleukin pathways are enriched across all TPs, whereas there is a trend of suppression after 24 h in neutrophils. The inflammasome pathway is enriched in the earlier TPs in neutrophils, while not enriched in monocytes until over 48 hours. Conclusion: Our analyses on gene expression dynamics and cluster patterns allow identification of key genes and pathways at different time points following ischemic injury that are valuable as IS biomarkers and may be possible treatment targets.

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