AKT Signaling as a Novel Factor Associated with In Vitro Resistance of Human AML to Gemtuzumab Ozogamicin

Gemtuzumab ozogamicin (GO), an immunoconjugate between an anti-CD33 antibody and a calicheamicin-γ1 derivative, induces remissions and improves survival in a subset of patients with acute myeloid leukemia (AML). As the mechanisms underlying GO and calicheamicin-γ1 resistance are incompletely understood, we herein used flow cytometry-based single cell network profiling (SCNP) assays to study cellular responses of primary human AML cells to GO. Our data indicate that the extent of DNA damage is quantitatively impacted by CD33 expression and drug efflux activity. However, although DNA damage is required for GO-induced cytotoxicity, it is not sufficient for effective cell kill, suggesting that downstream anti-apoptotic pathways may function as relevant resistance mechanisms. Supporting this notion, we found activated PI3K/AKT signaling to be associated with GO resistance in vitro in primary AML cells. Consistently, the investigational AKT inhibitor MK-2206 significantly sensitized various human AML cells to GO or free calicheamicin-γ1 with particularly pronounced effects in otherwise GO or free calicheamicin-γ1 -resistant cells. Likewise, MK-2206 also sensitized primary AML cells to calicheamicin-γ1. Together, our findings illustrate the capacity of SCNP assays to discover chemotherapy-related biological pathways and signaling networks relevant to GO-induced genotoxic stress. The identification of AKT signaling as being associated with GO resistance in vitro may provide a novel approach to improve the in vivo efficacy of GO/calicheamicin-γ1 and, by extrapolation, other DNA damage-based therapeutics.


Introduction
Most patients with acute myeloid leukemia (AML) are currently expected to die from their disease or treatment-related toxicities [1][2][3][4]. The need to develop effective yet well-tolerated new therapies is therefore unquestioned. Monoclonal antibodies have raised high expectations to accomplish this goal, with gemtuzumab ozogamicin (GO), an immunoconjugate between a humanized anti-CD33 antibody and a toxic calicheamicin-c 1 derivative [5], being the clinically most widely exploited thus far.
Emerging data indicate that GO benefits a subset of AML patients. Initial phase 2 studies found an overall response rate of ,30% with GO monotherapy in relapsed adult AML and led to accelerated marketing approval in the U.S. in 2000 [5]. More recently, several large trials have suggested a clinical benefit when GO is added to standard chemotherapy for adults with newly diagnosed AML, in particular for those with favorable-risk and possibly intermediate-risk disease [6][7][8][9]. Nevertheless, GO is ineffective in many patients with AML. In fact, the lack of prespecified overall improvement in outcome, together with increased early mortality in the GO-containing arm, resulted in premature termination of the confirmatory randomized phase 3 trial conducted by the Southwest Oncology Group (SWOG; S0106) and, subsequently, withdrawal of the new drug application in the U.S. in 2010 [10]. Overall, this experience highlights the importance of understanding the factors associated with GO resistance to optimize the clinical use of this antibody-drug conjugate.
With GO, the antibody primarily facilitates cellular uptake of the calicheamicin-c 1 derivative, which is then released intracellularly and causes single-and double-stranded DNA damage ( Figure 1) [5]. Conceptually, the amount of intracellular, active calicheamicin is affected by cellular uptake, toxin release and activation, as well as drug inactivation/metabolism or extrusion.
Indeed, correlative and in vitro studies have shown that drug efflux mediated by P-glycoprotein (Pgp, MDR1) and, to a lesser degree, multidrug resistance protein (MRP1), mediate resistance to GO [5,11]. Similarly consistently, experimental studies revealed a striking, quantitative relationship between CD33 expression/ uptake and GO efficacy in engineered AML cell lines [12,13].
Conversely, the impact of DNA repair and downstream signaling pathways on GO-mediated cytotoxicity has not been examined in detail. To this end, single cell network profiling (SCNP) assays using multiparametric flow cytometry have emerged as a versatile tool to simultaneously study several specific biological pathways and signaling networks at the single cell level within the context of complex tissues (e.g., blood or bone marrow) without the need for isolation or purification of the cell populations of interest [14,15]. By characterizing cellular signaling responses following exposure to extrinsic modulators, signaling network integrity can be tested and dysfunctional properties that may not manifest in resting cells detected. We have recently demonstrated that dynamic single cell network profiles can serve as independent predictors of response to standard induction chemotherapy in newly diagnosed adult AML [16]. Herein, we demonstrate the usefulness of SCNP assays as a discovery tool to identify signaling pathways associated with responsiveness or resistance of primary AML specimens to GO in vitro and, consequently, novel pharmacological approaches that can overcome GO resistance.

Ethics Statement
In accordance with the Declaration of Helsinki, all patients (or guardians on behalf of the pediatric patients) provided written
Flow Cytometric SCNP Assays in Primary AML Cells SCNP assays were performed as described previously [24]. Briefly, aliquots of cryopreserved cells were thawed at 37uC, washed, resuspended in RPMI 1640/60% FBS, and mononuclear Figure 1. Functional characterization of GO-induced cytotoxicity in CD33 + cells. Scheme depicts the presumed mechanism of action of GO in CD33 + AML cells [5,11]. Experimentally measured components in our studies are shown in red: CD33 expression levels; drug efflux pump activity; cH2AX (extent of DNA damage); survival signaling pathways (PI3K/AKT, MEK/ERK, and JAK/STAT pathway); and cleaved PARP and cell membrane integrity (apoptosis/cell death). doi:10.1371/journal.pone.0053518.g001 cells isolated via ficoll density gradient. After sequential washing with RPMI 1640/60% FBS and RPMI 1640/1% FBS, cells were stained with amine aqua viability dye (see Table S1 for a complete list of reagents used and manufacturers) to distinguish viable from non-viable cells. Cells were then re-suspended in RPMI 1640/ 10% FBS and aliquoted at 100,000 cells/condition. Following a resting period of 1-2 hours at 37uC, cells were subjected to apoptosis or signaling pathway assays as described in detail below. Subsequently, cells were fixed with 1.6% paraformaldehyde for 10 minutes at 37uC, pelleted, permeabilized with 100% ice-cold methanol, and stored at 280uC. Cells were washed with FACS buffer (PBS, 0.5% BSA, 0.05% NaN 3 ), pelleted, and stained with cocktails of fluorochrome-conjugated antibodies. These cocktails included antibodies against cell surface markers for cell population gating (e.g. CD11b, CD33, CD34, and CD45) and up to 3 antibodies against intracellular signaling molecules for an 8-color flow cytometry assay. In these analyses, CD11b, CD34, and CD45 were consistently used in the SCNP assays while some specific conditions additionally included measurements of CD33 expression. Side-scatter properties and CD45 and/or CD33 expression were used to define the leukemic cell population. Antibodies against CD11b and CD34 were included to allow for further characterization of leukemic cell subsets but were not utilized for the analyses presented in this manuscript. Isotype controls or phosphopeptide blocking experiments were performed to characterize phospho-antibodies. Data was acquired on an LSR II and/ or CANTO II flow cytometers using the FACS DIVA software (BD Biosciences). All flow cytometry data were analyzed with FlowJo (TreeStar Software, Ashland, OR, USA) or WinList (Verity House Software, Topsham, ME, USA). Dead cells and debris were excluded by forward and side scatter properties combined with amine aqua viability dye exclusion. Leukemic cells were identified based side-scatter properties and expression of CD45 and/or CD33 as previously described [24,25], and analyzed for CD33 expression levels, drug-induced DNA damage and cytotoxicity, and modulator-induced signaling as follows: Quantification of CD33 expression. In pediatric specimens, CD33 was quantified using in-house biotin-conjugated CD33 followed by streptavidin-tagged Qdot605. In all adult specimens except AML-11, in which CD33-biotin-Qdot605 was not used because of limiting cell numbers, CD33 was quantified using PE-conjugated CD33, and CD33-biotin-Qdot605. To allow direct comparisons of CD33 expression levels between all specimens used in our studies, a linear regression model was construed between PE-conjugated and Qdot605-biotin-conjugated CD33 mean fluorescence intensities (MFIs), using AML samples and peripheral blood and bone marrow mononuclear cells from normal donors from our internal database with available data on both fluorophores, allowing calculation of equivalent Qdot605 MFI in specimen AML-11 using the equation: Qdot605 CD33 MFI = 0.69276(CD33 PE MFI) +176.05 (r = 0.94; see Figure S1).
Quantification of drug-induced DNA damage and cytotoxicity. Following incubation with GO (30 ng/mL, expressed as free calicheamicin-c 1 weight equivalents; Pfizer, New York, NY) with or without the drug efflux inhibitor, PSC833 (2 mM), for 6-48 hours or incubation with staurosporine (2.33 mg/ mL) for 6 hours, cells were restained with amine aqua viability dye prior to fixation and SCNP processing. Phosphorylation of histone H2AX at S139 (cH2AX) was used to quantify the extent of DNA damage in leukemic cells [26,27], whereas antibodies detecting cleaved PARP (cPARP[Asp214]) or cleaved caspase-3 (active caspase-3) and amine aqua viability dye were used to detect apoptotic and dead cells, respectively. The percentage of leukemic ''induced apoptotic/dead cells'', gated on leukemic/myeloid cells based on SSC and CD45/CD33 properties, was calculated as: [Live Untreated -Live Drug treated ] / [Live Untreated ], with ''live'' cells defined as cPARP 2/ aqua dye 2 . This metric ranges from values of 0 to 100% for each sample and normalizes for differences in sample quality or spontaneous apoptosis. The extent of GOinduced DNA damage was calculated as: % cH2AX + Drug treated -% cH2AX + Untreated .
Assessment of growth factor/cytokine-induced signaling in primary AML cells.  Table S2.

SCNP Assessment of Kinetics of DNA Damage in Human AML Cell Lines and Normal PBMCs
For kinetic assessment of GO induced DNA damage, human AML cell lines and normal PBMCs were incubated for 1-8 h with GO (30 ng/mL) with or without the drug efflux inhibitor, cyclosporin A (2.5 mg/mL), and processed as described above.

Western Blot Analysis of MK-2206-mediated Inhibition of AKT Signaling
Human AML cell lines were treated with MK-2206 (1 mM; partially provided by Merck & Co, Inc.; Whitehouse Station, NJ, and partially obtained from Selleck Chemicals, Houston, TX) or vehicle (DMSO) for 6 hours at 37uC in 5% CO 2 and air. The cells were then lysed in RIPA lysis buffer with Complete EDTA-free protease inhibitor cocktail (Roche, Indianapolis, IN, USA) on ice for 60 minutes and pre-cleared by centrifugation. 46 SDS sample buffer was added to RIPA soluble proteins to a final concentration of 16 SDS sample buffer. Samples were boiled, resolved by SDS-12%-PAGE, transblotted to nitrocellulose, and blots blocked with 5% non-fat dry milk in Tris-buffered saline. Blots were incubated with primary antibodies detecting p-AKT (S473) or total AKT (both CST) overnight at 4uC. After washing, incubation with HRP-conjugated secondary antibody for 1 hour at room temperature, and re-washing, immunoreactive signals were visualized with Amersham ECL Plus Western Blotting Detection System (GE Healthcare Biosciences, Pittsburgh, PA, USA) and exposed to autoradiography film (Genesee Scientific, San Diego, CA, USA).

Assessment of MK-2206-modulated GO and Free Calicheamicin-c 1 -induced Cytotoxicity in AML Cell Lines and Primary AML Cells
In experiments with human AML cell lines, cells were incubated with increasing concentrations of GO or free calicheamicin-c 1 (kindly provided by Wyeth-Ayerst [now Pfizer]) in the presence or absence of various doses of MK-2206. To partially reverse effluxmediated drug resistance, parallel GO-treated cultures of KG-1 cells were treated with a low, subsaturating concentration (25 mM) of the drug efflux inhibitor, PK11195 (Sigma Aldrich, St. Louis, MO, USA) [12,28,29]. In experiments with primary AML specimens, thawed aliquots of density gradient-separated mononuclear cells were incubated with increasing concentrations of calicheamicin-c 1 in the presence or absence of MK-2206. After 3 days at 37uC in 5% CO 2 and air, cell numbers and drug-induced cytotoxicity was determined by flow cytometry using 4',6diamidino-2-phenylindole (DAPI, Sigma Aldrich) to identify dead cells.

Statistical Considerations
Data on drug-induced cytotoxicity and DNA damage as well as SCNP are expressed as mean 6 SEM. Data on GO-induced cytotoxicity and DNA damage were correlated with CD33 expression levels using Pearson's linear correlation and expressed as correlation coefficient [95% confidence interval]. Two-way ANOVA for repeated measures was used to analyze cytotoxicity data in AML cell lines, which are shown as percent change in dead cells and cell numbers relative to parallel cultures treated without GO or free calicheamicin-c 1 but with corresponding amounts of MK-2206. All statistical analyses were performed with Prism or InStat (Graphpad, San Diego, CA); P,0.05 was considered statistically significant.

Basic Characterization of in vitro Sensitivity of Primary AML Specimens to GO
The postulated mechanism of action of GO implies a pivotal role of drug-induced DNA damage and intact downstream proand anti-apoptotic pathway activity [5]. As depicted in Figure 1, our SCNP assay focused on functional, quantitative measurements of DNA damage pathways as well as PI3K/AKT, MEK/ERK, and JAK/STAT signaling pathways in leukemic cells in response to in vitro stimulation of diagnostic specimens from 6 pediatric and 6 adult patients containing .78% blast cells in all cases (Table 1; AML-01-AML-12). First, the in vitro GO sensitivity of AML cells in these specimens was characterized. At the clinically relevant concentration of 30 ng/mL [30], GO treatment resulted in an induced apoptotic/dead cell fraction averaging 19.365.2% and 43.867.1% after continuous exposure for 24 and 48 hours, respectively ( Table 2). Using an arbitrary cut-off for the induced apoptotic/dead cell fraction of 15% at 24 hours, 5 specimens were classified as ''GO sensitive'', whereas 7 were classified as ''GO resistant''. The lack of apoptotic response in these GO resistant samples was likely directly due to insufficient intracellular GO concentrations rather than the consequence of dysfunctional apoptotic pathways, as parallel experiments with staurosporine, a classic activator of the mitochondrial apoptosis pathway [31], demonstrated robust apoptosis not only in GO-sensitive but also in most (5/6 tested) GO resistant samples ( Figure S2), establishing that the apoptotic machinery was generally intact in the tested AML specimens. Of note, among all patient specimens, there was no correlation between CD33 expression levels and GO-induced cytotoxicity at 24 hours (r = 0.181 [95% confidence interval: 20.439-0.684], P = 0.574) or 48 hours (r = 0.266 [20.397-0.747], P = 0.429). Importantly, GO failed to induce significant cytotoxicity after 24 or 48 hours in 2 cases (AML-07 and AML-08) with bright CD33 expression, indicating the presence of relevant resistance mechanisms that are unrelated to target antigen expression ( Figure 2).

Extent of DNA Damage Correlates with CD33 Expression Levels but not GO-induced Cytotoxicity
To identify the level at which cellular resistance to GO occurs, we first determined the kinetics of early GO-induced cH2AX in various CD33 + human AML cell lines (GDM-1, KG-1, and U937) and peripheral blood mononuclear cells from a healthy donor ( Figure S3). These studies indicated robust induction of cH2AX within 6 hours of exposure to GO or GO in combination with a drug efflux inhibitor, cyclosporine A. We therefore chose a 6 hour timepoint to quantify GO-induced DNA damage in individual primary AML specimens. As shown in Table 2, GO induced cH2AX within 6 hours of drug exposure in all primary AML specimens, with the extent of cH2AX induction being highly correlated to CD33 expression levels (r = 0.831 [0.492-0.951], P = 0.0008; Figure 2), indicating that CD33 expression is a limiting factor for the intracellular accumulation of the calicheamicin-c 1 derivative. In line with this notion, delayed induction of DNA damage was evident by 24 hours in many of the specimens with relatively lower CD33 expression ( Table 2, i.e., AML-03, AML-04, AML-05, and AML-10). As the calicheamicin-c 1 derivative is a substrate for ATP-binding cassette transporters, we predicted that drug efflux is a second factor that controls GO-induced DNA damage levels. To test this hypothesis, we studied GO-induced cH2AX levels upon co-treatment with the drug efflux inhibitor, PSC833 [32], in the specimens from pediatric patients (limited sample availability precluded testing in specimens from adult patients). We found that PSC833 increased cH2AX induction (at 6 hours: 46.0610.6% vs. 28.9611.0%, P = 0.0313 [Wilcoxon matched-pairs signed-rank test]), with very marked increases noted in 2/6 specimens (AML-02: increase from 6.8% to 30.9% at 6 hours; and AML-04: increase from 10.9% to 72.9% at 6 hours, respectively) but only minor effects seen in others (AML-05: increase from 23.6% to 31.0% at 6 hours; Figure S4). Together, these findings indicate that both CD33 expression levels and drug efflux play important roles in the extent of GO-induced DNA damage. Nevertheless, while induction of DNA damage appears a prerequisite for GO-induced cytotoxicity, it is not sufficient, as illustrated by 2 specimens in our cohort (AML-07 and AML-08), in which high levels of DNA damage were observed without subsequent apoptosis/cell death (Figure 3), thus suggesting that anti-apoptotic factors downstream of DNA damage are likely important for resistance of these AML cells to GO.

Association of Induced PI3K/AKT Signaling with in vitro GO Resistance
To identify downstream pathways that might affect GO cytotoxicity, we functionally assessed PI3K/AKT/mTOR, JAK/ STAT, and Ras/Raf/MEK signaling pathways using SCNP assays; for details regarding modulators and assessed targets, please see Supporting Table S2. Initial experiments in AML cell lines indicated that stem cell factor (SCF)-modulated PI3K pathway activity (as measured by levels of SCF-induced p-AKT and p-S6) was elevated in the GO-resistant GDM-1 but not the GO-sensitive U937 cells (p-AKT: mean log 2 -fold increase of 1.98 in GDM-1 cells vs. 20.11 in U937 cells; for p-S6: mean log 2 -fold increase of 1.00 for GDM-1 cells vs. 20.03 for U937 cells). We then used SCNP assays to assess these signaling pathways in the pediatric AML samples (the adult specimens lacked sufficient material for signaling analyses) using established SCNP methodology for primary human AML [24,33,34]. As shown in Figure 4 and Table S3, we found that SCF-modulated PI3K pathway activity was elevated in all 3 GO resistant samples relative to GO sensitive samples

Effect of AKT Inhibition on GO and Free Calicheamicin-c 1induced Cytotoxicity Against Human AML Cell Lines and Primary AML Cells
Taken together, these data suggest a potential role of PI3K/ AKT signaling in the mechanism of resistance to GO or, by extension, calicheamicin-c 1 -induced cytotoxicity, thus raising the possibility of using inhibitors of this signaling pathway as a novel means to increase the sensitivity of AML cells to calicheamicin-c 1based therapies. To test this hypothesis, we used MK-2206, an investigational small molecule allosteric inhibitor of AKT currently in Phase 2 clinical development for the treatment of various human malignancies including AML. Consistent with previous investigations on solid tumor cancer as well as acute lymphoblastic leukemia cells [35][36][37][38][39], treatment with MK-2206 (1 mM for 6 hours) indeed resulted in effective inhibition of S473 AKT phosphorylation while leaving total AKT levels unchanged in human AML cell lines, confirming target inhibition (data not shown). We initially assessed the effect of MK-2206 on GO and calicheamicin-c 1 -cytotoxicity in various human AML cell lines, which are relatively sensitive (HL-60, NB4) or resistant (TF-1, KG-1) to single agent GO or calicheamicin-c 1 . As shown in Figure 5, MK-2206 dose-dependently increased in vitro GO cytotoxicity in all 4 cell lines, with most marked effects noted in the GO-resistant TF-1 and KG-1 cell lines, suggesting that inhibition of PI3K/ AKT survival signaling can sensitize otherwise resistant AML cells  to GO-induced cytotoxicity. Of note, in KG-1 cells, which have active drug efflux, MK-2206 significantly sensitized the cells to GO cytotoxicity both in the absence as well as the presence of a drug efflux reversal agent, PK11195, supporting the relevance of PI3K/AKT pathway activation as a limiting factor for GO cytotoxicity even after inhibition of drug efflux. Consistent with the notion that GO-induced cytotoxic effects are primarily due to the calicheamicin-c 1 moiety rather than the anti-CD33 antibody,  comparable results were obtained when the effect of MK-2206 on cytotoxicity induced by free calicheamicin-c 1 was assessed in these cell lines ( Figure S5). Finally, to begin investigating the effects of AKT inhibition on GO and calicheamicin-c 1 -based treatment of primary AML, we treated 3 AML specimens with various doses of calicheamicin-c 1 in the presence or absence of a relatively nontoxic dose of MK-2206 (1 mM); limited cell numbers precluded the simultaneous testing of GO in these assays. As shown in Figure 6, the extent of calicheamicin-c 1 -induced cytotoxicity varied between these 3 specimens; nevertheless, in all 3 cases, MK-2206 enhanced the cytotoxic effects of calicheamicin-c 1 .

Discussion
Clinical studies conducted over the last decade have unequivocally demonstrated that GO provides clinical benefit in a subset of patients with AML while being largely ineffective in others [5]. Therefore, the ability to prospectively identify patients whose leukemias are resistant to GO, and unraveling the mechanisms underlying this resistance, would provide an important tool to optimize the clinical use of this antibody-drug conjugate. By simultaneously measuring multiple elements associated with cellular resistance to GO, including target antigen expression, drug-efflux mechanisms, extent of DNA damage, and cellular signaling networks, we show that SCNP assays offer a hypothesis-generating approach to discover novel biological features associated with GO sensitivity or resistance of human AML cells in vitro.
Using SCNP assays, the data from the current study support three major conclusions. First, DNA damage is required but not sufficient for GO-induced cytotoxicity. This finding is consistent with genotoxic responses previously observed in AML samples treated with other agents such as etoposide or cytarabine/ daunorubicin [24,40], and provides direct evidence for the significance of anti-apoptotic factors downstream of DNA damage as resistance factors to GO. Future studies on larger numbers of primary AML specimens will be required to test whether such anti-apoptotic mechanisms are indeed more relevant in adult AML, as perhaps suggested by our small dataset. Importantly, both CD33 expression levels and drug efflux affect the extent of GO-induced DNA damage, confirming previous studies demonstrating that these factors are pivotal determinants affecting the final intracellular accumulation of the calicheamicin-c 1 derivative [13]. The dependence of in vitro GO cytotoxicity on sufficient DNA damage, as determined by induced cH2AX levels, suggests that lack of cH2AX induction by GO could serve as an early biomarker of resistance to GO that could be available within hours after exposure to GO.
Second, our data are the first to indicate that anti-apoptotic pathways downstream of DNA damage contribute to in vitro cellular resistance to GO in primary AML samples. This finding supports a model in which the toxicity of the calicheamicin-c 1 moiety is critically modulated by the ability of the cell to repair DNA damage as well as the activity of downstream pro-and antiapoptotic pathways, and may offer a partial biological explanation for the observation that calicheamicin-c 1 in vitro sensitivity varies over 100 000-fold among individual primary AML cell samples [41].
Third, and most importantly, our studies identify activated PI3K/AKT signaling, measured after growth factor treatment, as a novel mechanism of resistance to GO and, by extension, calicheamicin-c 1 . AKT is downstream of PI3K and the primary effector molecule of the PI3K signaling cascade [8]. After activation via phosphorylation and translocation to the nucleus, AKT directly or indirectly affects the activity of several transcription factors. Accumulating evidence demonstrates that the PI3K/AKT signaling axis is crucial to many aspects of cell growth, survival, and apoptosis [8]. In AML, recent studies have demonstrated that PI3K/AKT signaling is frequently activated [42,43], and activated AKT is associated with poor outcome [44]. Of note, in a recent study, in which SCNP assays were used to develop classifiers for the prediction of clinical response to standard induction therapy in AML, elevated PI3K pathway signaling was consistently associated with therapeutic failure [16]. Based on these data, AKT has been identified as a rational drug target in AML. Our in vitro data with MK-2206 indicate that AKT signaling modulates GO/calicheamicin-c 1 cytotoxicity and is associated with cellular resistance to these drugs. In turn, inhibition of AKT activation can greatly increase GO/calicheamicin-c 1 sensitivity, suggesting a role of AKT inhibitors such as MK-2206 as chemosensitizers for GO or, more generally, calicheamicin-c 1 -based treatment strategies. Further studies will be required to fully understand the mechanistic details by which activation of this pathway interferes with GO/calicheamicin-c 1induced cytotoxicity.
Together, by identifying an association between PI3K/AKT signaling activation and in vitro GO and calicheamicin-c 1 resistance, our data illustrate the capacity of SCNP assays to functionally characterize the integrity of biological pathways and signaling networks relevant to cellular responses to genotoxins such as calicheamicin-c 1 -based antibody-drug conjugates in vitro in primary samples from patients with AML. Although future studies with larger numbers of patient specimens will be required to validate our studies and quantify the contribution of AKTmediated resistance to GO and calicheamicin-c 1 in detail, our data highlight the potential of SCNP assays to differentiate AML samples based on underlying biology which might be relevant to therapeutic interventions. Our data form the basis for future studies in which such assays are applied to AML samples from patients with documented clinical outcomes to validate findings from in vitro predictions. If validated, SCNP assays could serve to prospectively identify subsets of patients that are suitable for GObased therapy -a critical advancement toward optimized drug use -and may help in the discovery of additional therapeutic targets,. By monitoring multiple cellular characteristics (e.g. signaling in several survival pathways), SCNP assays may provide an ideal tool to prospectively inform about multiple GO-relevant resistance mechanisms simultaneously, and could help in the selection of the most appropriate chemosensitizing agents and drug combination strategies in patients under consideration for GO-containing therapy, thus further contributing to the individualization of AML treatment approaches. including drug efflux inhibitor PK11195 are also shown. After 3 days, viability (left-side panel) and cell numbers (right-side panel) was determined by flow cytometry. *P,0.05 as compared to medium alone; **P,0.01 as compared to medium alone; ***P,0.001 as compared to medium alone; ****P,0.0001 as compared to medium alone. doi:10.1371/journal.pone.0053518.g005

Supporting Information
Figure S1 Quantification of CD33 Qdot605 MFI in primary AML specimens. To compute the equivalent CD33 MFI value in the Qdot605 scale for sample AML-11 (which lacked this data point), a linear regression model was constructed comparing CD33 Qdot605 MFI with CD33 PE MFI and used to compute the equivalent Qdot605 MFI value for AML-11 based on its CD33 PE MFI value. AML samples and peripheral blood and bone marrow mononuclear cells from normal donors (from our internal database) with available data on both fluorophores (left table), was used to calculate a linear regression model between the CD33 Qdot605 and PE MFI scales (middle), allowing for computation of the equivalent CD33 Qdot605 MFI in specimen AML-11 using the equation: Qdot605-CD33 MFI = 0.69276(CD33-PE MFI) +176.05 (r = 0.94) (right). (TIFF) Figure S2 Effect of staurosporine on GO-resistant pediatric AML samples. Primary AML specimens were treated with staurosporine for 6 hours prior to flow cytometric assessment of apoptosis using cleaved caspase-3 (X-axis) and cleaved PARP (Y-axis). All GO-resistant samples except AML-10 showed robust apoptotic responses, as demonstrated by presence of .60-90% double positive cells upon treatment with staurosporine. Note: the apoptosis markers, cleaved caspase-3 and cleaved PARP, showed concordant results with an average of .90% of cells being either double positive or double negative for these markers. (TIFF) Figure S3 Kinetics of GO-induced DNA damage response in vitro. (A) Kinetics of GO-induced DNA damage measured by cH2AX levels. Treatment conditions are indicated by shape: GO alone (squares), drug efflux inhibitor (cyclosporine A, CsA) alone (circles), and GO in combination with cyclosporine A (crosses),.AML cell lines GDM-1 and KG-1 (left panels) were resistant to GO treatment alone with minimal induction of DNA damage at any time-points tested; however, U937 cells and primary myeloid PBMC (right panels) were sensitive to GO treatment alone with highest cH2AX levels observed at 6-8 hours.
Co-treatment of GO with cyclosporine A sensitized MDR+ KG-1 and GDM-1 cells to GO-induced DNA damage. (TIFF) Figure S4 Inhibition of drug efflux activity by PSC833 increases GO sensitivity in some AML samples. Drug transporter activity was assessed by co-treatment of GO and the pump efflux inhibitor, PSC833. DNA damage (cH2AX, X-axis) and apoptosis (cleaved PARP, Y-Axis) responses are shown for AML-02 (left) and AML-05 (right) in the presence of GO alone, PSC833 alone, or GO in combination with PSC833. While PSC833 co-treatment substantially increased GO induced apoptosis in AML-02, PSC833 co-treatment did not sensitize AML-05 to GO induced apoptosis. Circles highlight cH2AX+ cells (red) and apoptotic cPARP+ cells (green). and cell numbers (right-side panel) was determined by flow cytometry. *P,0.05 as compared to medium alone; **P,0.01 as compared to medium alone; ***P,0.001 as compared to medium alone; ****P,0.0001 as compared to medium alone. (TIFF)