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BioAssay: AID 624256

HTS to identify compounds that promote myeloid differentiation with MLPCN compound set

Project Title: Discovering small molecules that overcome differentiation arrest in acute myeloid leukemia ..more
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AID: 624256
BioAssay Type: Primary, Primary Screening, Single Concentration Activity Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2012-06-04
Modify Date: 2012-06-18

Data Table ( Complete ):           Active    All
BioActive Compounds: 3720
Depositor Specified Assays
588701Summary of HTS to identify compounds that promote myeloid differentiationsummarySummary of HTS to identify compounds that promote myeloid differentiation.
UNMCMD Assay Overview:
Assay Support: 1 R03 DA032471-01
Project Title: Discovering small molecules that overcome differentiation arrest in acute myeloid leukemia
PI: David Sykes, PhD

Screening Center PI: Larry Sklar, PhD / UNMCMD
Screening Center Manager: Kristine Gouveia
Screening Lead: Mark Haynes, PhD
Assay Implementation: Mark Haynes, Stephanie Chavez

Chemistry Center PI: Stuart Schreiber, PhD / BIPDeC
Chemistry Center Manager: Patti Aha
Chemistry Lead: Tim Lewis

Assay Background and Significance:

The potential for successful differentiation therapy in acute leukemia was realized with the clinical development of all-trans retinoic acid (ATRA) and arsenic. ATRA and arsenic overcome the differentiation arrest imposed by the retinoic acid receptor alpha (RARa) fusion oncoprotein and treated leukemic promyelocytes terminally differentiate to mature neutrophils. These small molecules are remarkably well-tolerated by patients in comparison to traditional cytotoxic chemotherapy. Furthermore, incorporating ATRA into treatment regimens single-handedly improved the overall survival of patients with acute promyelocytic leukemia (APL) from 20% to 75% [1]. Unfortunately, differentiation therapy does not exist for the much larger fraction of non-APL acute myeloid leukemias where the standard of care results in an overall survival rate of only 25%.

The mammalian homeobox transcription factors contribute to lineage-specific hematopoietic differentiation, and their expression is tightly regulated during normal hematopoiesis. Though critical to early hematopoiesis, the expression of the HoxA cluster of genes is normally downregulated as cells mature [2]. The persistent, and inappropriate, expression of members of the HoxA cluster of genes has been described in the majority of acute myeloid leukemias. More specifically, HoxA9 has an important role in normal hematopoiesis and leukemogenesis. HoxA9 is directly involved in human leukemias as one partner of the fusion protein NUP98- HoxA9 [3]. In analyses of human AML, the level of HoxA9 expression has been correlated with poor prognostic karyotype [4] and inversely correlated with survival [5]. Furthermore, in patients with CML, a relatively higher level of HoxA9 expression was associated with transition from chronic phase to accelerated and blast phase [6]. More recently it has been shown that HoxA9 is critical to the small subset of lymphoid and myeloid leukemias that express fusion oncoproteins involving the mixed lineage leukemia (MLL) gene. Leukemias harboring MLL-rearrangements are a particularly poor prognosis subgroup of AML and depend on HoxA9 for proliferation and survival [7]. Overall, this suggests that HoxA9 dysregulation - via fusion with NUP98 or via inappropriate maintenance of HoxA9 expression - is a common pathway in the differentiation arrest in myeloid leukemia. This is an exciting possibility, as it suggests that by specifically targeting this pathway, one might be able to overcome differentiation arrest.

The identification of differentiation therapy has been hindered by the lack of a good model system of differentiation arrest in acute myeloid leukemia. Primary leukemic cells are difficult to isolate and culture, and their availability is limited. Leukemia cell lines (e.g. HL60, NB4, 32D) are readily available though their underlying mechanism of differentiation arrest is not known. Furthermore, these cell lines are only capable of incomplete differentiation and they differentiate in response to non-physiologic stimuli (e.g. DMSO, PMA). Finally, differentiation is cumbersome to assay in a high-throughput fashion, and previous studies have focused on complex screens using qPCR to monitor small changes in gene expression [8]. These problems have made it very difficult to adopt a system for the purpose of high-throughput screening to identify compounds which promote differentiation.

We have devised a novel cell-based assay with advantages over existing systems. The assay (1) provides an unlimited supply of cells, (2) the cells are derived from primary marrow, (3) the differentiation arrest is imposed by a single and clinically relevant oncoprotein, (4) the cells have a built-in marker of differentiation, and (5) when the oncoprotein is inactivated or inhibited, the cells are capable of recapitulating full and normal myeloid differentiation.
This assay will be used to identify small molecules that promote the differentiation of acute myeloid leukemia cells. Cells will be arrested in differentiation by the expression of HoxA9 from an estrogen receptor-HoxA9 construct. The screen will be conducted in the presence of estrogen so HoxA9 will be continuously expressed. The cells also contain a GFP construct regulated by the lysozyme promoter. Differentiated cells will express GFP. Small molecules that promote differentiation will be identified by green fluorescence. In order to eliminate compounds that are green fluorescent in nature or compounds that activate the expression of GFP, a MAC1-APC antibody will be used to detect true differentiation. True hits will be identified as those cells that are both green and red fluorescent.

Cells are cultured in RPMI supplemented with 10% fetal bovine serum, penicillin/streptomycin/L-glutamine, 5% conditioned media containing stem cell factor (SCF; approx. 100nanog/milliL), and beta-estradiol (0.5 microM). The conditioned media is generated by a Chinese Hamster Ovary (CHO) cell line that constitutively expresses and secretes SCF into the supernatant. On day 0, cells are suspended in mediumcontaining Pluronic-F68 (final 0.04%, Sigma P5556) and are dispensed into 384-well plates containing library compounds using an automated dispenser. The plates are incubated for four days under standard conditions (37 degrees-C, humidified, 5% CO2). On day 4, inert polystyrene beads (5 micron; Spherotech CPX) and anti-CD11b (clone M1/70, APC conjugate) are added and the plates are incubated for twenty minutes prior to analysis using high-throughput flow cytometry. Cell viability and green fluorescence is stable for 24 hours after the day 4 time point. Gating on the inert bead population provides a measure of sampling quality. The percent of GFP and APC positive live cells is used to determine whether the test compound has a differentiating effect.


The data are exported into a Microsoft Excel spreadsheet template, and the Normalized Percent Positive is calculated for each well as follows:
NORMALIZED PCT POS = 100*(Sample%X+ - DMSO%X+)/(PCntrl%X+ - DMSO%X+)
where %X+ is the percentage of the population in the positive region in GFP expression for either wells with Sample, DMSO control or Positive Control (5 microM fulvestrant).

Compounds were deemed active if NORMALIZED PCT POS is equal to or greater than PLATE CUTOFF.
PLATE CUTOFF = Average + 3*Standard Deviation
where Average and Standard Deviation are of the Normalized Percent Positive for the Negative Control (DMSO)wells on the plate.

1. Fenaux, P., et al., Effect of all transretinoic acid in newly diagnosed acute promyelocytic leukemia. Results of a multicenter randomized trial. European APL 91 Group. Blood, 1993. 82(11): p. 3241-9.
2. Lawrence, H.J., et al., The role of HOX homeobox genes in normal and leukemic hematopoiesis. Stem Cells, 1996. 14(3): p. 281-91.
3. Borrow, J., et al., The t(7;11)(p15;p15) translocation in acute myeloid leukaemia fuses the genes for nucleoporin NUP98 and class I homeoprotein HOXA9. Nat Genet, 1996. 12(2): p. 159-67.
4. Drabkin, H.A., et al., Quantitative HOX expression in chromosomally defined subsets of acute myelogenous leukemia. Leukemia, 2002. 16(2): p. 186-95.
5. Andreeff, M., et al., HOX expression patterns identify a common signature for favorable AML. Leukemia, 2008. 22(11): p. 2041-7.
6. Tedeschi, F.A. and F.E. Zalazar, HOXA9 gene expression in the chronic myeloid leukemia progression. Leuk Res, 2006. 30(11): p. 1453-6.
7. Faber, J., et al., HOXA9 is required for survival in human MLL-rearranged acute leukemias. Blood, 2009. 113(11): p. 2375-85.
8. Stegmaier, K., et al., Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation. Nat Genet, 2004. 36(3): p. 257-63.
Categorized Comment
BAO: version: 1.4b1080

BAO: bioassay specification: assay stage: primary

BAO: bioassay specification: assay biosafety level: bsl2

BAO: bioassay specification: assay measurement type: endpoint assay

BAO: bioassay specification: assay readout content: assay readout method: regular screening

BAO: bioassay specification: assay readout content: content readout type: single readout

BAO: detection technology: fluorescence: flow cytometry

BAO: bioassay specification: bioassay type: functional: reporter gene

BAO: bioassay specification: assay footprint: microplate: 384 well plate

BAO: bioassay specification: assay measurement throughput quality: single concentration single measurement

BAO: format: cell-based format

BAO: format detail: assay phase characteristic: homogeneous assay

BAO: meta target: organism name: Mus musculus

BAO: meta target detail: cell line specification: cell modification: transfection: stable transfection

BAO: meta target detail: cell line specification: growth mode: suspension

Result Definitions
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1NORMALIZED PCT POS (10μM**)Percent response based on range of positive GFP expression population in DMSO control versus positive controlFloat%
2PCT POSPercent of population in the positive area for GFP expressionFloat%
3PCT DOUBLE POSPercent of population in the double positive area, both GFP expression and MAC1-APC antibody binding.Float%
4PLATE_CUTOFFCutoff for determining hit compound based on Average + 3xStandard Deviation of the NORMALIZED PCT POSFloat%
5Z_PRIMEZprime for compound plate based on percent positive in the GFP expressionFloat%

** Test Concentration.
Additional Information
Grant Number: 1 R03 DA032471-01

Data Table (Concise)