E-GEOD-39497 - Zinc finger nuclease knockouts of human ADP-glucokinase

Status
Released on 19 July 2012, last updated on 29 September 2015
Organism
Homo sapiens
Samples (10)
Array (1)
Protocols (8)
Description
Zinc finger nucleases (ZFN) are powerful tools for editing genes in cells. Here we use ZFNs to interrogate the biological function of human ADPGK, which encodes an ADP-dependent glucokinase (ADPGK), in tumour cell lines. The hypothesis tested is that ADPGK utilises ADP to phosphorylate glucose under conditions where ATP becomes limiting, such as hypoxia. We characterised two ZFN knockout clones in each of two tumour cell lines (H460 and HCT116). All four lines had frameshift mutations in all alleles at the target site in exon 1 of ADPGK, and were ADPGK-null by immunoblotting. ADPGK knockout had little or no effect on cell proliferation, but compromised the ability of H460 cells to survive siRNA silencing of hexokinase-2 under oxic conditions, with clonogenic survival falling from 21±3% for the parental line to 6.4±0.8% (p=0.002) and 4.3±0.8% (p=0.001) for the two knockouts. A similar increased sensitivity to clonogenic cell killing was observed under anoxia. No such changes were found when ADPGK was knocked out in HCT116 cells, for which the parental line was less sensitive than H460 to anoxia and to hexokinase-2 silencing. While knockout of ADPGK in HCT116 cells caused few changes in global gene expression, knockout of ADPGK in H460 cells caused notable up-regulation of mRNAs encoding cell adhesion proteins. Surprisingly, we could discern no effect on glycolysis as measured by glucose consumption or lactate formation under oxic or anoxic conditions, or extracellular acidification rate (Seahorse XF analyser) under oxic conditions in a variety of media. However, oxygen consumption rates were generally lower in the ADPGK knockouts, in some cases markedly so. Collectively, the results demonstrate that ADPGK can contribute to tumour cell survival under conditions of high glycolytic dependence, but the phenotype resulting from knockout of ADPGK is cell line dependent and appears to be unrelated to priming of glycolysis. Use Affymetrix microarrays to examine the effecs of knockout of the gene ADPGK using Zinc Finger nucleases in two cultured cell lines: (i) HCT116 cells (three wild type cultures compared to three ADPGK-knockout cultures), (ii) H460 cells (two wild type cultures compared to two ADPGK-knockout cultures). Ten microarrays in total.
Experiment type
transcription profiling by array 
Contacts
Cris Print <c.print@auckland.ac.nz>, Cristin Print, Jiechuang Su, Ron S Ronimus, Sean L McGee, Shona Morrison, Susan Richter, Tim Connor, William R Wilson
Citation
Expression and role in glycolysis of human ADP-dependent glucokinase. Richter S, Richter JP, Mehta SY, Gribble AM, Sutherland-Smith AJ, Stowell KM, Print CG, Ronimus RS, Wilson WR.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-39497.idf.txt
Sample and data relationshipE-GEOD-39497.sdrf.txt
Raw data (1)E-GEOD-39497.raw.1.zip
Processed data (1)E-GEOD-39497.processed.1.zip
Array designA-AFFY-141.adf.txt
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