Functional genomics identifies novel and diverse molecular targets of nutrients in vivo

Abstract Genomic responses to nutrients are important determinants of physiological and pathological functions of living systems. Many of these responses are mediated by changes in mRNA concentrations that are primarily regulated by gene transcription. Transcriptional networks that regulate the expression and activities of transcription factors and structural genes in response to nutrients need to be defined. The tools of functional genomics and bioinformatics offer powerful means to address these needs. The application of global mRNA profiling tools to define genome-wide responses to nutrients and micronutrients with a primary focus on in vivo genomic responses of vital organs of laboratory mice is reviewed here. The studies show that major and minor nutrients affect the expression of mRNAs that are related to aging and inflammation, and chemically diverse micronutrients such as polyphenols and tocopherols may exert their effects through modulating the expression of functionally related genes.

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Genome-wide microarray investigation of molecular targets and signaling networks in response to high-LET neutron in in vivo-mimic spheroid of human carcinoma

Molecular & Cellular Toxicology ◽

10.1007/s13273-012-0002-z ◽

2012 ◽

Vol 8 (1) ◽

pp. 9-18 ◽

Cited By ~ 3

Author(s):

Jee Young Kwon ◽

Jung Min Kim ◽

Young Hoon Ji ◽

Young Rok Seo

Keyword(s):

Molecular Targets ◽

Signaling Networks ◽

Human Carcinoma ◽

Genome Wide ◽

High Let

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HIF1/2-exerted control over glycolytic gene expression is not functionally relevant for glycolysis in human leukemic stem/progenitor cells

Cancer & Metabolism ◽

10.1186/s40170-019-0206-y ◽

2019 ◽

Vol 7 (1) ◽

Cited By ~ 1

Author(s):

Albertus T. J. Wierenga ◽

Alan Cunningham ◽

Ayşegül Erdem ◽

Nuria Vilaplana Lopera ◽

Annet Z. Brouwers-Vos ◽

...

Keyword(s):

Gene Expression ◽

Progenitor Cells ◽

Lactate Production ◽

Glucose Consumption ◽

Transcriptional Networks ◽

Metabolic State ◽

Hematopoietic Stem ◽

Genome Wide ◽

Xenograft Mice

Abstract Background Hypoxia-inducible factors (HIF)1 and 2 are transcription factors that regulate the homeostatic response to low oxygen conditions. Since data related to the importance of HIF1 and 2 in hematopoietic stem and progenitors is conflicting, we investigated the chromatin binding profiles of HIF1 and HIF2 and linked that to transcriptional networks and the cellular metabolic state. Methods Genome-wide ChIPseq and ChIP-PCR experiments were performed to identify HIF1 and HIF2 binding sites in human acute myeloid leukemia (AML) cells and healthy CD34+ hematopoietic stem/progenitor cells. Transcriptome studies were performed to identify gene expression changes induced by hypoxia or by overexpression of oxygen-insensitive HIF1 and HIF2 mutants. Metabolism studies were performed by 1D-NMR, and glucose consumption and lactate production levels were determined by spectrophotometric enzyme assays. CRISPR-CAS9-mediated HIF1, HIF2, and ARNT−/− lines were generated to study the functional consequences upon loss of HIF signaling, in vitro and in vivo upon transplantation of knockout lines in xenograft mice. Results Genome-wide ChIP-seq and transcriptome studies revealed that overlapping HIF1- and HIF2-controlled loci were highly enriched for various processes including metabolism, particularly glucose metabolism, but also for chromatin organization, cellular response to stress and G protein-coupled receptor signaling. ChIP-qPCR validation studies confirmed that glycolysis-related genes but not genes related to the TCA cycle or glutaminolysis were controlled by both HIF1 and HIF2 in leukemic cell lines and primary AMLs, while in healthy human CD34+ cells these loci were predominantly controlled by HIF1 and not HIF2. However, and in contrast to our initial hypotheses, CRISPR/Cas9-mediated knockout of HIF signaling did not affect growth, internal metabolite concentrations, glucose consumption or lactate production under hypoxia, not even in vivo upon transplantation of knockout cells into xenograft mice. Conclusion These data indicate that, while HIFs exert control over glycolysis but not OxPHOS gene expression in human leukemic cells, this is not critically important for their metabolic state. In contrast, inhibition of BCR-ABL did impact on glucose consumption and lactate production regardless of the presence of HIFs. These data indicate that oncogene-mediated control over glycolysis can occur independently of hypoxic signaling modules.

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