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BioAssay: AID 686971

qHTS for induction of synthetic lethality in tumor cells producing 2HG: qHTS for the HT-1080-IDH1KD cell line

Unbiased genomic sequencing for 22 glioma genomes found recurrent mutation of IDH1 on chromosome 2q33, a gene encoding the cytosolic isoform of IIDH1 associated with the tri-carboxylic acid cycle (TCA) that catalyzes the oxidative decarboxylation of isocitrate, yielding alpha-ketoglutarate and CO2 via NADP+ to NADPH conversion. Subsequent studies confirmed the recurrent IDH mutations in up to 70% more ..
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 Tested Compounds
 Tested Compounds
All(364452)
 
 
Active(7438)
 
 
Inactive(327961)
 
 
Inconclusive(29128)
 
 
 Tested Substances
 Tested Substances
All(364851)
 
 
Active(7452)
 
 
Inactive(328241)
 
 
Inconclusive(29158)
 
 
 Related BioAssays
 Related BioAssays
AID: 686971
Data Source: NCGC (IDH1-lethal-IDH1KD)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2013-05-06
Modify Date: 2013-05-09

Data Table ( Complete ):           View Active Data    View All Data
BioActive Compounds: 7438
Related Experiments
AIDNameTypeComment
686970qHTS for induction of synthetic lethality in tumor cells producing 2HG: qHTS for the HT-1080-NT fibrosarcoma cell lineConfirmatorydepositor-specified cross reference
686972qHTS for inhibitors of synthetic-lethal in tumor cells producing 2HG: SummarySummarydepositor-specified cross reference
Description:
Unbiased genomic sequencing for 22 glioma genomes found recurrent mutation of IDH1 on chromosome 2q33, a gene encoding the cytosolic isoform of IIDH1 associated with the tri-carboxylic acid cycle (TCA) that catalyzes the oxidative decarboxylation of isocitrate, yielding alpha-ketoglutarate and CO2 via NADP+ to NADPH conversion. Subsequent studies confirmed the recurrent IDH mutations in up to 70% of secondary gliomas and in 10% of AML cases [1]. In addition, the somatic mutation of cancer-associated IDH1 is a point mutation resulting in various amino-acid substituents at Arginine132 (IDH1 R132), a key residue found in the enzyme's active site that when mutated, results in the loss-of-function in metabolizing isocitrate but confers a gain-of-function to produce the oncometabolite 2-hydroxyglutarate (2HG) [2]. This in effect defines IDH1 as an oncogene and provides an extraordinary opportunity to discover chemical probes against mutant IDH1 that may translate into much needed new therapies for glioma and AML patients.

This assay aims to perform a synthetic-lethal screen for chemical probes specific for 2HG-producing tumor cells using matched paired cell lines (1) HT-1080-NT fibrosarcoma cell line that overproduces 2HG and (2) HT-1080-IDH1KD cell line which has IDH1 expression knocked-down. Desirable compounds are toxic to the NT fibrosarcoma cell line but not to the IDH1KD cell line. The data in this AID corresponds to the results of the qHTS against the HT-1080 IDH1KD cell line.

[1] Dang L, Jin S, Su SM. IDH mutations in glioma and acute myeloid leukemia. Trends of Mol Med. 2010; 16(9): 387-97.
[2] Dang L et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature. 2010; 465(7300):966.

Molecular Libraries Probe Production Centers Network [MLPCN]
NIH Chemical Genomics Center [NCGC]
MLPCN Grant: RO3 DA032129
Assay Submitter (PI): Lenny Dang Ph.D., Agios Pharmaceuticals
Protocol
Suspensions of trypsinized HT-1080-IDH1KD cells were dispensed into white, tissue culture-treated, solid 1536-well plates at 5uL/well (750 cells/well final concentration) in RPMI medium supplemented with 5% FBS. Plates were incubated at 37 degrees C for 2 hours, after which 23 nL of compounds or DMSO were delivered to each well using a pin tool. Plates were then incubated at 37 degrees C for an additional 48 hours. CellTiter-Glo viability reagent (Promega) was dispensed into wells (2.5uL/well) and incubated at room temperature for 10 minutes. The plates were measured on a PerkinElmer ViewLux plate reader for luminescent signal (clear filter, 1 sec exp.). DMSO-treated control wells and media-only (no cells) control wells were used to normalize %Activity of identified toxic compounds; DMSO-treated wells corresponded to 0%Activity (100% viability), while media-only controls were used to normalize 100%Activity (0% viability). To minimize variability between cell lines, both HT-1080-NT and HT-1080-IDH1KD lines were dispensed and treated with identical compound series in single batches.
Concentration-response curves were fitted to the signals arising from the resulting luminescence. The concentration-effect curves were then classified based on curve quality (r2), response magnitude and degree of measured activity, and compounds were subsequently categorized based on their curve class. Active (toxic) compounds showed concentration-dependent decreases in luminescence, concordant with a decrease in ATP levels and overall cell number. Inactive compounds showed no effect on total luminescence.
Comment
Compound Ranking:
1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.
Categorized Comment - additional comments and annotations
From PubChem:
Assay Cell Type: HT 1080
From ChEMBL:
Assay Format: Cell-based
Assay Type: Functional
Result Definitions
Show more
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1PhenotypeIndicates type of activity observed: inhibitor, activator, fluorescent, cytotoxic, inactive, or inconclusive.String
2Potency*Concentration at which compound exhibits half-maximal efficacy, AC50. Extrapolated AC50s also include the highest efficacy observed and the concentration of compound at which it was observed.FloatμM
3EfficacyMaximal efficacy of compound, reported as a percentage of control. These values are estimated based on fits of the Hill equation to the dose-response curves.Float%
4Analysis CommentAnnotation/notes on a particular compound's data or its analysis.String
5Activity_ScoreActivity score.Integer
6Curve_DescriptionA description of dose-response curve quality. A complete curve has two observed asymptotes; a partial curve may not have attained its second asymptote at the highest concentration tested. High efficacy curves exhibit efficacy greater than 80% of control. Partial efficacies are statistically significant, but below 80% of control.String
7Fit_LogAC50The logarithm of the AC50 from a fit of the data to the Hill equation (calculated based on Molar Units).Float
8Fit_HillSlopeThe Hill slope from a fit of the data to the Hill equation.Float
9Fit_R2R^2 fit value of the curve. Closer to 1.0 equates to better Hill equation fit.Float
10Fit_InfiniteActivityThe asymptotic efficacy from a fit of the data to the Hill equation.Float%
11Fit_ZeroActivityEfficacy at zero concentration of compound from a fit of the data to the Hill equation.Float%
12Fit_CurveClassNumerical encoding of curve description for the fitted Hill equation.Float
13Excluded_PointsWhich dose-response titration points were excluded from analysis based on outlier analysis. Each number represents whether a titration point was (1) or was not (0) excluded, for the titration series going from smallest to highest compound concentrations.String
14Max_ResponseMaximum activity observed for compound (usually at highest concentration tested).Float%
15Activity at 0.0007804147 uM (0.000780415μM**)% Activity at given concentration.Float%
16Activity at 0.00282 uM (0.00281981μM**)% Activity at given concentration.Float%
17Activity at 0.00702 uM (0.00702378μM**)% Activity at given concentration.Float%
18Activity at 0.012 uM (0.0117803μM**)% Activity at given concentration.Float%
19Activity at 0.015 uM (0.0147191μM**)% Activity at given concentration.Float%
20Activity at 0.022 uM (0.0218916μM**)% Activity at given concentration.Float%
21Activity at 0.066 uM (0.0659391μM**)% Activity at given concentration.Float%
22Activity at 0.190 uM (0.189642μM**)% Activity at given concentration.Float%
23Activity at 0.295 uM (0.295005μM**)% Activity at given concentration.Float%
24Activity at 0.370 uM (0.369706μM**)% Activity at given concentration.Float%
25Activity at 0.587 uM (0.587058μM**)% Activity at given concentration.Float%
26Activity at 1.290 uM (1.29μM**)% Activity at given concentration.Float%
27Activity at 1.835 uM (1.83477μM**)% Activity at given concentration.Float%
28Activity at 2.587 uM (2.58678μM**)% Activity at given concentration.Float%
29Activity at 4.921 uM (4.92099μM**)% Activity at given concentration.Float%
30Activity at 8.047 uM (8.04673μM**)% Activity at given concentration.Float%
31Activity at 9.239 uM (9.23932μM**)% Activity at given concentration.Float%
32Activity at 15.70 uM (15.7008μM**)% Activity at given concentration.Float%
33Activity at 32.30 uM (32.3μM**)% Activity at given concentration.Float%
34Activity at 46.09 uM (46.0854μM**)% Activity at given concentration.Float%
35Activity at 64.71 uM (64.715μM**)% Activity at given concentration.Float%
36Activity at 92.20 uM (92.2μM**)% Activity at given concentration.Float%
37Compound QCNCGC designation for data stage: 'qHTS', 'qHTS Verification', 'Secondary Profiling'String

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: DA032129

Data Table (Concise)
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