1

Title: 5-Azacitidine Induces NOXA to Prime AML Cells for Venetoclax-

mediated Apoptosis

Authors: Sha Jin1*, Dan Cojocari1*, Julie J. Purkal1, Relja Popovic2, Nari N. Talaty3, Yu Xiao1,

Larry R. Solomon1,4, Erwin R. Boghaert1, Joel D. Leverson5 & Darren C. Phillips1#

Authors and Affiliations: 1Oncology Discovery/2Genomics Research Center/3Drug Discovery

Science and Technologies/4Former AbbVie Employee/5Oncology Development, AbbVie Inc., 1

North Waukegan Rd., North Chicago, IL 60064. *Authors contributed equally. # Corresponding

author

Running Title: Aza-induced NOXA prime AML for Venetoclax-mediated Apoptosis

Funding: The design, study conduct, and financial support for this research were provided by

AbbVie Inc. AbbVie Inc. participated in the interpretation of data, review, and approval of this

publication.

Disclosure of Conflicts of Interest: DC, SJ, JP, RP, NT, YX, ERB, JDL, and DCP are

employees of AbbVie. LRS is a former employee of AbbVie and was employed during the

duration of this study. SJ, JP, RP, NT, YX, LRS, ERB, JDL & DCP are stockholders of AbbVie

Inc. The design study conduct, and financial support for this research were provided by AbbVie.

AbbVie Inc. participated in the interpretation of data, review, and approval of the publication.

Corresponding author:

Darren C. Phillips, PhD

AbbVie Inc., 1 North Waukegan Road, North Chicago, IL 60064.

Phone: 847-938-8508;

Fax: 847-935-5165;

E-mail: Darren.Phillips@AbbVie.com

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Therapeutic Relevance

The FDA recently approved the combination of venetoclax with HMAs in elderly AML patients;

however, the molecular mechanism behind the combinatorial activity is unknown. We show that

5-Aza and venetoclax provided added anti-tumorigenic benefit relative to either agent alone in

pre-clinical models of AML. We characterize the 5-Aza-mediated apoptotic priming of AML

cells linked to the induction of the pro-apoptotic protein NOXA and its binding to anti-apoptotic

BCL-2 family proteins. This study uncovers a non-epigenetic mechanism for the combinatorial

activity between venetoclax and 5-Aza, and highlights a central role for NOXA in venetoclax-

induced apoptosis.

3

Abstract

Purpose: Acute myeloid leukemia (AML) patients frequently do not respond to conventional

therapies. Leukemic cell survival and treatment resistance has been attributed to the

overexpression of B-cell lymphoma 2 (BCL-2) and aberrant DNA hypermethylation. In a Phase-

Ib study in elderly AML patients, combining the BCL-2 selective inhibitor venetoclax with

hypomethylating agents (HMAs) azacitidine (5-Aza) or decitabine resulted in 67% overall

response rate; however, the underlying mechanism for this activity is unknown.

Experimental Design: We studied the consequences of combining two therapeutic agents:

venetoclax and 5-Aza, in AML preclinical models and primary patient samples. We measured

expression changes in the integrated stress response (ISR) and the BCL-2 family by western blot

and qPCR. Subsequently we engineered PMAIP1 (NOXA)- and BBC3 (PUMA)-deficient AML

cell lines using CRISPR-Cas9 methods to understand their respective role in driving the

venetoclax/5-Aza combinatorial activity.

Results: In this study, we demonstrate that venetoclax and 5-Aza act synergistically to kill AML

cells in vitro and display combinatorial anti-tumor activity in vivo. We uncover a novel non-

epigenetic mechanism for 5-Aza-induced apoptosis in AML cells through transcriptional

induction of the pro-apoptotic BH3-only protein NOXA. This induction occurred within hours of

treatment and was mediated by the ISR pathway. NOXA was detected in complex with anti-

apoptotic proteins, suggesting that 5-Aza may be “priming” the AML cells for venetoclax-

induced apoptosis. PMAIP1 knockout confirmed its major role in driving venetoclax and 5-Aza

synergy.

Conclusions: These data provide a novel non-epigenetic mechanism of action for 5-Aza and its

combinatorial activity with venetoclax through the ISR-mediated induction of PMAIP1.

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Introduction

Acute myeloid leukemia (AML) is a clonal hematologic malignancy characterized by genomic

heterogeneity and epigenetic changes, including aberrant DNA methylation (1).

Hypomethylating agents (HMAs), such as the cytidine analogues 5-Azacitidine (5-Aza) and

decitabine, demonstrate single-agent activity in 25-50% of myelodysplastic syndrome (MDS) (2)

and myeloproliferative neoplasm (MPN) (3) patients, and is active in about 15-29% of AML

(4,5). Following cellular uptake, 5-Aza is metabolized and incorporated into both DNA and RNA

to drive distinct cellular responses. Many of 5-Aza’s epigenetic effects can be attributed to its

incorporation into DNA to deplete DNA methyltransferase (DNMTs) and drive DNA

hypomethylation (6,7). However, 80-90% of 5-Aza is incorporated into RNA (8-10), which may

drive non-epigenetic effects (11,12) including apoptosis (13,14). This may account for some of

5-Aza’s clinical activity since DNA hypomethylation is not predictive of clinical response to 5-

Aza in myeloid malignancies (15).

Apoptosis is primarily regulated at the mitochondrial level by the B-cell lymphoma protein-2

(BCL-2) family of proteins. This collection of cell death regulators is divided into three groups

that each contains at least one BCL-2 homology (BH) motif (BH1-4). The pro-apoptotic “BH3-

only” proteins BIM, BID, PUMA, NOXA, BAD, BIK, BMF and HRK, and the ”multidomain

effector” proteins BAX and BAK are activated or induced by various cell death stimuli that drive

mitochondrial outer membrane permeabilization (MOMP) and subsequently apoptosis (16). The

anti-apoptotic members (BCL-2, BCL-XL, MCL-1, BCL-W, and BCL2-A1) possess BH3-

binding grooves that function to constrain the “BH3-only” and multidomain effectors. Aberrant

expression and/or function of BCL-2 family proteins are integral to tumorigenesis and

therapeutic resistance by enabling malignant cells to evade apoptosis (16,17). Deletion of the

genes encoding the BH3-only proteins BIM (BCL2L11), PUMA (BBC3) or NOXA (PMAIP1)

can drive resistance to various apoptosis stimuli (18-22) and accelerates tumorigenesis in mouse

models of hematologic malignancies (23-25). Similarly, BCL-2 overexpression is a clinical

feature of human hematologic malignancies (26-28) that exacerbates the malignant state (29) and

drives apoptosis resistance phenotypes (30), including that induced by 5-Aza (13). Consequently,

targeting apoptosis signaling, and in particular BCL-2 itself, has emerged as a tractable

therapeutic approach in oncology.

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Venetoclax (ABT-199) is a highly selective, orally bioavailable BCL-2 inhibitor that induces

apoptosis in BCL-2-dependent tumor cells (31), and is approved by the FDA in the USA for use

in patients with small lymphocytic lymphoma or chronic lymphocytic leukemia, who have tried

at least one therapy (32). Further, in a phase-II monotherapy study in R/R AML patients,

venetoclax has demonstrated an overall response rate (ORR) of 19% (33), providing the

foundation for combinational studies in AML. Subsequent phase-Ib data in treatment-naive AML

patients indicate that combining venetoclax with 5-Aza or decitabine results in an ORR of 67%

(34), compared to the historical ORR of 15-29% with HMAs treatment alone (5,35-37). These

encouraging data have led to the initiation of randomized phase-III trials to evaluate venetoclax

activity in combination with 5-Aza in elderly treatment-naïve AML patients ineligible for

standard induction therapy (M15-656, NCT02993523). However, the underlying mechanism for

the combinational activity observed between venetoclax and 5-Aza is unknown.

Herein, we demonstrate that acute 5-Aza treatment drives combinatorial activity with venetoclax

independent of epigenetic effects (6,7). Specifically, we determine that, at pharmacologically

relevant concentrations (38), 5-Aza activates the integrated stress response (ISR) pathway to

induce expression of the canonical target DDIT3, as well as the BH3-only proteins NOXA

(PMAIP1) and PUMA (BBC3) in human AML cell lines, priming them for apoptosis

independent of DNA demethylation. We subsequently demonstrate that NOXA induction is not

only required for the synergy observed between 5-Aza and venetoclax, but PMAIP1 deletion

significantly impacts the kinetics and depth of response to either agent alone or in combination.

Together, these data provide a rationale for an ongoing randomized phase-III clinical trial

evaluating venetoclax activity in combination with 5-Aza (M15-656, NCT02993523), and

advocates for the assessment of PMAIP1 and DDIT3 gene induction in patients treated with 5-

Aza and venetoclax as potential biomarkers of response.

6

Materials and Methods

Cell culture and reagents

AML cell lines: OCI-AML5 (RRID:CVCL_1620), SET-2 (CVCL_2187), PL-21 (CVCL_2161),

SKM-1 (CVCL_0098), MOLM-13 (CVCL_2119), SKNO-1 (CVCL_2196), SHI-1

(CVCL_2191), NOMO-1 (CVCL_1609) were purchased from DSMZ (Braunschweig,

Germany); and HEL (CVCL_2481), U-937 (CVCL_0007), MV4-11 (CVCL_0064), Kasumi-1

(CVCL_0589), KG-1 (CVCL_0374), THP-1 (CVCL_0006) were purchased from ATCC

(Manassas, VA) and cultivated for 1-10 passages in RPMI-1640 medium, 20mM HEPES

(Gibco) supplemented with penicillin/streptomycin and 10% fetal bovine serum (FBS;

Invitrogen). Cells were grown at 37°C in a humidified atmosphere with 5% CO2. All cell lines

were tested for authenticity by short tandem repeat (STR) profiling and mycoplasma by the

AbbVie Core Cell Line Facility. Primary AML cells from peripheral blood were purchased from

Discovery Life Sciences, collected with informed consent from patients, and cultured overnight

in media described above, plus 30 U/ml of IL-2, prior to 5-Aza treatment. AML-340 and AML-

343 [stage M2] were newly diagnosed, untreated; AML-69 had previous treatment: gemtuzumab

ozogamicin and decitabine, treatment at time of collection: venetoclax; AML-3667 treatment at

time of collection: mercaptopurine. Venetoclax and 5-Aza were obtained from AbbVie chemical

library. ISRIB (trans-isomer) was purchased from Selleck Chemicals (S7400).

Cell viability

AML cell lines were seeded at 10,000 cells per well in 96-well plates and treated with 5-Aza and

or venetoclax for 24 hours. For combinatorial studies, cells were treated in matrix of 9 dose of

venetoclax (10 µM, 1:3 dilutions) and 3 doses of 5-Aza, 0.3, 1, and 3 µM. Cell viability was

subsequently determined using CellTiter-Glo reagent as described by the manufacturer’s

instructions (Promega Inc.). The effective concentration (EC50) to induce 50% cell death were

determined by nonlinear regression algorithms using Prism 7.03 (GraphPad Software).

Western blotting

AML cells were treated with 0.3, 1, 3, 10, or 30 µM of 5-Aza for 24 hours. To inhibit caspase

activation, cells were pre-treated with 40 µM Z-VAD-fmk for 1 hour prior to treatment with 5-

Aza for a further 24 hours. Protein concentration was quantified using Pierce bicinchoninic acid

7

assay (BCA) (ThermoFisher Scientific) and equal amounts of each cellular protein samples were

separated with 4-12% SDS-PAGE (Invitrogen) and blotted to nitrocellulose or PVDF

membranes (Invitrogen). The blots were incubated with the following primary antibodies: anti-

BIM (Cell Signaling Technology Cat# 2933, RRID:AB_1030947), anti-BCL-2 (Abcam Cat#

ab32124, RRID:AB_725644), anti-BCL-XL (Abcam Cat# ab32370, RRID:AB_725655), anti-

MCL-1 Cell Signaling Technology Cat# 94296, RRID:AB_2722740), anti-PUMA (Abcam Cat#

ab9645, RRID:AB_296538), anti-NOXA (Abcam Cat# ab13654, RRID:AB_300536), anti-

PARP (BD Biosciences Cat# 556494, RRID:AB_396433), anti-caspase-3 (Abcam Cat#

ab13585, RRID:AB_300480), ani-DNMT1 (Cell Signaling Technology Cat# 5032,

RRID:AB_10548197), anti-ATF4 (Cell Signaling Technology Cat# 11815, RRID:AB_2616025),

anti-CHOP (Cell Signaling Technology Cat# 2895, RRID:AB_2089254), anti-eIF2α (Cell

Signaling Technology Cat# 2103, RRID:AB_836874), anti-phospho-eIF2α (S51) (Cell Signaling

Technology Cat# 3398, RRID:AB_2096481), anti-β-actin (Sigma-Aldrich Cat# A2228,

RRID:AB_476697) and anti-GAPDH (Abcam Cat# ab110305, RRID:AB_10861081). The blots

were imaged using the Odyssey CLx (Li-Cor) following incubation in with the IRDye secondary

antibodies (LI-COR Bio, AB_10795014; AB_10796098). Approximate protein molecular size

calculated from protein size standards in Image Studio 5.0 (LI-COR).

Immunoprecipitation

Cells were pretreated with 40 µM zVAD-fmk 1 hours prior to treatment with 0.3, 1, 3, or 10 µM

of 5-Aza for a further 24 hours. Cellular proteins were extracted and centrifuged in 1 % CHAPs

buffer. Cell lysates (250 µg) were incubated with 3 µg of biotinylated anti-BCL-2 (US

Biological, Cat# B0807-06F), or BCL-XL (R&D systems, Cat# DYC894-2) or MCL-1 (BD

Bioscience, Cat# 624008 custom biotinylation) or IgG control (US Biological, B1750-06X)

antibodies in the presence of protease inhibitors (complete tablets, Roche) overnight at 4°C.

Streptavidin beads (Sigma) were added to precipitate complexes containing BCL-2, BCL-XL or

MCL-1 prior to separation by SDS-PAGE.

DNA methylation analysis

AML cells were treated with 0.3 or 3 µM of 5-Aza for 24 hours or 7 days, replenished on days 0,

2, 4, and 6. For methylation analysis, 500 ng of DNA was denatured by heating the sample at

100°C. Samples were treated with 5 units of Nuclease P1 (Sigma) in reaction buffer (5mM

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ZnCl2, 50mM NaCl) at 50°C for one hour. Samples were further treated with 0.002 units of

phosphodiesterase I (Sigma) at 37°C for 2 hours followed by treatment with 0.5 U of alkaline

phosphatase (Invitrogen) for one hour at 37°C. The samples were diluted 3-fold to dilute out the

salts and enzymes, and injected into a Acquity UPLC HSS T3 2.1 mm x 50 mm column (1.8 µm

particle size) (Waters Cat # 186003538). Samples were run on a Shimadzu Nexera-X2 UHPLC

coupled to an ABSciex 6500 Triple Quadrupole Mass Spectrometer. Quantification was

performed using the Analyst 1.6.2 Workstation software using the intelliquan algorithm in a

multiple reaction monitoring (MRM) mode. All runs included standard curves for 5-hmC, 5-mC

and 5-dC. Linear regression was performed to obtain slopes and intercepts, which were used to

calculate the actual % 5-mdC and % 5-hmdC values. All standards and samples were matrix

matched and treated with same dilutions.

Cell line-derived xenograft models of AML

SKM1.FP1 is a cell line derived from a subcutaneous tumor generated by the injection 2 x 106 of

SKM-1 cells (DSMZ). SKM1.FP1 and MV4-11 (ATCC) were cultured as described above.

Female Fox Chase SCID Beige (RRID: IMSR_CRL:250; for SKM1.FP1; 8-10 weeks, 18-20 g)

and female Fox Chase SCID (RRID: IMSR_CRL:236; for MV4-11; 8-10 weeks, 18-20 g) mice

were purchased from Charles River Laboratories (Wilmington, MA). Body weights upon arrival

were 18-20 g. Food and water were provided ad libitum. Animals were on the light phase of a

12 h light: 12 h dark cycle. All animal studies were conducted in accordance with the guidelines

established by the AbbVie Institutional Animal Care and Use Committee. In flank xenograft

experiments, mice were inoculated with 2 x 106 (SKM1.FP1) or 5 x 106 (MV4-11) cells

subcutaneously into the right flank. Mice were injected with a 0.1 mL inoculum of 1:1 cell

mixture in culture media and Matrigel (BD Biosciences, Bedford, MA). When tumors reached

approximately 225 mm3, the mice were size-matched into treatment and control groups. Mice

were treated QDx14 PO 50 mg/kg with venetoclax, Q7Dx3 IV 8 mg/kg with 5-Aza or

combination of both. Venetoclax was formulated in 60 % phosal 50 propylene glycol (PG), 30 %

polyethylene glycol (PEG) 400 and 10 % ethanol, and 5-Aza was formulated with 0.9 % sodium

chloride. Tumor volume was measured twice per week with electronic calipers and calculated

according to the formula, (L x W2)/2. All treatment groups consisted of 8 mice per group.

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Caspase-3/-7 activity time course

96-well clear bottom black polystyrene microplates (Corning) were coated with CellTAK

(Corning) as recommended by the manufacturer. For each well, 5x104 cells were seeded in 50 µl

of RPMI media then placed in the tissue culture incubator for 20 minutes. The IncuCyte

Caspase-3/-7 Red Apoptosis Assay Reagent (Sartorius) and the compounds were dispensed into

the corresponding wells and dilutions using the D300 Digital Dispenser (Tecan). The assay plate

was then placed in the IncuCyte ZOOM (Sartorius) and programmed to take 4 images per well at

a 1-hour interval for 24 hours. Data was analyzed using the IncuCyte Zoom 2017 software and

plotted as the number of red objects (aCasp-3/7+) per well divided by area (in µm2) occupied by

the cells, per well.

RT-qPCR

1.0x107 cells, for AML cell lines, and 2.5x105 cells per well, for primary AML cells, were

treated with DMSO or 0.3, 1, or 3µM of 5-Aza, for 6 and 24 hours, at which point the cells were

washed with 10 ml of cold DPBS and spun down at 4°C, 300rcf for 5 min. The supernatant was

removed, and the cells were lysed with 400ul of RLT buffer containing β-mercaptoethanol. RNA

was isolated using Qiagen RNeasy Plus Mini Kit (74134) for cell lines, and Micro Kit (74034)

for primary samples, as recommended by manufacturer. cDNA was prepared from 3 µg of

purified RNA using iScript® Reverse Transcription Supermix (Bio-Rad) protocol. qPCR was

performed on 2 µl of cDNA reaction, TaqMan® Fast Advanced (Life Technologies, #4444557)

in 20 µl final volume. The following PrimeTime® qPCR Probe were manufactured by Integrated

DNA Technologies (IDT, Coralville, IA): HEX dye probe RPLP0 (reference gene,

Hs.PT.39a.22214824); 6-FAM probes: PMAIP1 (Hs.PT.58.21318159), BBC3

(Hs.PT.5839966045), DDIT3 (Hs.PT.58.39204289.g), CDKN1A (Hs.PT.47.2442322)

(Supplementary Table S1). The cDNA standards (5-fold dilutions) were prepared from AML5

and Kasumi-1 cells treated with SN-38 for 24 hours. qPCR was performed in 96-well PCR plates

(Bio-Rad) on the Bio-Rad CFX 96. Gene expression (ΔΔCq) was quantified on the Bio-Rad

CFX Manager 3.1. Target 6-FAM probes were normalized to HEX-GAPDH control gene and

relative to vehicle control treated 0 µM 5-Aza.

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Knockout cell lines

Genomic editing for elimination of BBC3 (PUMA) and PMAIP1 (NOXA) was done using the

ALT-R® CRISPR-Cas9 system from Integrated DNA Technologies (IDT, Coralville, IA). All

reagents were from IDT, and RNP complexes were formed as described by IDT. Briefly, the

CRIPSR RNA (crRNA) (Supplemental Table 1) was annealed to tracRNA labeled with ATTO™

550 fluorescent reagent. The annealed product was combined with Alt-R® S.p. Cas9 Nuclease

V3 (IDT) and subsequently introduced into the OCI-AML5, Kasumi-1, and MV4-11 cells by

electroporation. The electroporation was done with a NEON Transfection System (Thermo

Fisher) containing 2x106 cells using the following settings: OCI-AML5 (1x30ms pulse@1500V),

Kasumi-1 (1x20ms pulse@1700V), MV4-11 (1x20ms pulse@1700V). Transfection efficiency

was monitored using the ATTO™ 550 fluorescent reagent. At 24 hours following transfection,

the top 5% ATTO™ 550+ cells were sorted by fluorescence-activated flow cytometry (BD

FACSAria Fusion) under sterile conditions as a single cell per well of a 96-well plate and was

used to isolate clonal cell lines. The expression of either NOXA or PUMA protein was

monitored using PAGE-western analysis. Genomic DNA from clones that showed lack of

expression of the intended target was amplified with PCR primers flanking the site of the target

CRISPR crRNA. Primers for PCR and sequencing are shown in Supplementary Table S2. The

sequencing data was analyzed using Vector NTI Express (Thermo Fisher) to confirm successful

genomic editing.

Statistical analysis

Data shown as mean and standard error of the mean (s.e.m.) of at least 3 independent

experiments and two technical replicates. Groups were statistically compared using Student’s t

test or one-way and two-way ANOVA for multiple comparison using Prism 7.03 (GraphPad

Software). Asterisks on graphs denote a significant difference (*p < 0.05), and ns for not

significant (ns, p>0.05). Spearman correlation and linear fit ± 95% confidence intervals was used

for correlation of gene expression and bliss sums. The Bliss independence model was used to

evaluate combinatorial activity, positive integers indicating synergy (39). Bliss scores were

calculated for each combination in the dose matrix and totaled to give a “Bliss sum” value.

11

Results

Chronic or acute 5-Aza treatment synergizes with venetoclax in pre-clinical models of AML

5-Aza is a known DNA hypomethylation agent (40). To determine its hypomethylating potential

in vitro, we treated AML cell lines with various doses of 5-Aza, replenished every 48 hours, over

a total period of 7 days. No difference in methylation was observed within the first 24 hours of

treatment of Kasumi-1 or SET-2 cells (Supplementary Fig. S1A). However, 5-Aza treatment for

7 days at the 300 nM dose, was able to decrease global DNA methylation in four AML cell lines

tested (Fig. 1A). When these 5-Aza pre-treated cells were then exposed to venetoclax for an

additional 24 hours, OCI-AML5, Kasumi-1, and MV4-11 cell lines were found to be more

sensitive to venetoclax compared to the DMSO pre-treated cells (Fig. 1B). In contrast, the SHI-1

and SET-2 cell lines were not sensitized to venetoclax (Supplementary Fig. S1B). In humans, 5-

Aza has an elimination half-life of approximately 4 hours, reaching maximum plasma

concentrations of approximately 11 µM, with intravenous dosing of 75 mg/m2 (38). To capture

these acute clinical parameters in vitro in the context of venetoclax co-treatment, we measured

the kinetics and number of cells with active caspase-3/-7 (aCasp-3/-7+) immediately following

the addition of the two agents to OCI-AML5 and MV4-11. The combination of 5-Aza and

venetoclax resulted in a rapid induction in the number of aCasp-3/-7+ cells that was greater than

either agent alone (Fig. 1C). To further explore this observation, we evaluated the acute

combinatorial activity of venetoclax and 5-Aza in a panel of 14 AML cell lines treated for 24

hours at various doses of either agent. In this setting, 5-Aza significantly sensitized the AML cell

lines to venetoclax-induced cell death (Fig. 1D, Supplementary Fig. S1C) and showed

synergistic activity in 12 out of 14 AML cell lines, as measured by the Bliss independence model

(39) (Fig. 1E). To further validate this observation, we generated cell line-derived mouse

xenografts of SKM-1 and MV4-11 and treated the mice with either 5-Aza (3 times every 7 days),

venetoclax (daily for 14 days), or the combination of 5-Aza and venetoclax (Fig. 1F). In both

xenograft models, the tumor growth inhibition caused by the combination of the two agents was

increased as compared to the either agent alone, consistent with the reduction of cell survival in

vitro.

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5-Aza upregulates NOXA and PUMA in AML cell lines

To identify a molecular mechanism of 5-Aza in promoting apoptosis in combination with

venetoclax, we characterized the protein expression levels of both pro-apoptotic and anti-

apoptotic BCL-2 family members by western blot following 5-Aza treatment for 24 hours.

Through its previously reported target-binding activity (7), 5-Aza completely depleted the

DNMT1 protein. This was associated with a concomitant dose- and time-dependent increase in

NOXA and PUMA protein expression (Fig. 2A, Supplementary Fig. S2). To examine whether

the up-regulation of PUMA and NOXA was a cause or consequence of cell death, we pre-treated

the cells with the pan-caspase inhibitor Z-VAD-fmk to abrogate the induction of apoptosis. In

the presence of Z-VAD-fmk and 5-Aza, a robust up-regulation of NOXA and PUMA was

detected (Fig. 2B). Further, qPCR indicated that 5-Aza was able to significantly increase both

PMAIP1 (NOXA) and BBC3 (PUMA) transcripts in a dose-dependent manner as early as 6 hours

post-treatment, with longer treatment periods of up to 24 hours being associated with a further

increase in BBC3 expression in the OCI-AML5, Kasumi-1 and MV4-11 cell lines (Fig. 2C).

Interestingly, synergy between venetoclax and 5-Aza significantly correlated with the 5-Aza

induction of PMAIP1 and BBC3 transcripts in a broader AML cell line panel, and was

independent of TP53 status (Fig. 2D) (41,42). Similarly, primary AML patient cells treated with

increasing doses of 5-Aza resulted in an upregulation of BBC3 (3/4 patient samples) and

PMAIP1 (4/4 patient samples) after 6 hours, with elevated BBC3 expression maintained at 24

hours post-treatment in 2 of 4 patient specimens (Fig. 2E). Chronic 5-Aza treatment did not have

any significant effect on the gene expression or methylation, as the promoter regions for both

PMAIP1 and BBC3 genes were unmethylated (Supplementary Fig. S3A) and their transcript

levels were unaltered (Supplementary Fig. S3B) in a sample of AML cell lines. The rapid

induction of these two transcripts at 6 hours, coupled with the low baseline methylation of either

PMAIP1 or BBC3 and absence of methylation changes following 5-Aza treatment, collectively

indicated a non-epigenetic mechanism for transcriptional induction.

5-Aza primes the anti-apoptotic proteins with NOXA and PUMA.

To determine the functional consequence of NOXA and PUMA upregulation, we measured the

binding of these two proteins to the anti-apoptotic proteins BCL-2, BCL-XL and MCL-1 in AML

cell lines after 5-Aza treatment, by immunoprecipitation. The amount of NOXA bound to BCL-2

in Kasumi-1 and MV4-11 cells, and NOXA bound to MCL-1 in Kasumi-1, OCI-AML5 and

13

MV4-11 cells increased in a dose-dependent fashion following 5-Aza treatment (Fig. 3).

Although to a lesser degree than MCL-1, PUMA binding to BCL-2 and BCL-XL was also

increased. These results collectively indicate that 5-Aza enhances the amount of BH3-only

proteins found in complex with the anti-apoptotic BCL-2 family members.

The Integrated Stress Response induces NOXA following 5-Aza acute treatment.

5-Aza has been shown to also inhibit protein synthesis through RNA incorporation (11). The

integrated stress response (ISR) pathway is induced by various stress signals, including

proteotoxic stress. During conditions of severe stress, the ISR’s main effector, activating

transcription factor 4 (ATF4), can tip the cell towards death through transcriptional induction of

pro-apoptotic targets (43). As the transcriptional upregulation of both BBC3 and PMAIP1

appeared to occur in a p53-independent manner (Fig. 2D), we postulated that the transcription

factor ATF4 may play a role in the induction of these transcripts. ATF4 has been reported to bind

to the PMAIP1 promoter to induce its transcription (44,45). The protein levels of ATF4 increased

significantly when the AML cell lines were exposed to 5-Aza for 24 hours (Fig. 4A). This was

indicative of ISR pathway activation and was confirmed by upstream phosphorylation of serine

51 (S51) on the alpha subunit of the eukaryotic Initiation Factor 2 (eIF2α) (Fig. 4A). In addition,

we observed significant induction of a transcriptional target of ATF4, CCAAT-enhancer-binding

protein homologous protein (CHOP). In agreement with the upregulation of CHOP at the protein

level (Fig.4A, Supplementary Fig. S4A), its transcript, DDIT3, was also induced in a dose-

dependent manner by 5-Aza after 6 hours treatment of AML cell lines (Fig. 4B) and primary

AML patient samples ex vivo (Fig. 4C), although the level of DDIT3 induction was reduced after

24 hours 5-Aza treatment (Fig. 4C). The level of DDIT3 induction also correlated significantly

with the synergy observed between venetoclax and 5-Aza combination in 14 AML cell lines

(Fig. 4D). Finally, to explore whether the ISR pathway may be responsible for the induction of

PMAIP1 and BBC3, we used ISRIB, a small molecule that acts as a potent inhibitor of this

pathway by reversing the effect of eIF2α phosphorylation (46). OCI-AML5 cells were treated for

6 hours with ISRIB, 5-Aza, or ISRIB and 5-Aza in combination. As expected, 5-Aza induced the

PMAIP1, BBC3, and DDIT3 transcripts; however, in the presence of ISRIB, the 5-Aza-mediated

induction of all three transcripts was significantly suppressed (Fig. 4E, Supplementary Fig. S4B).

ISRIB partially rescued AML cells from 5-Aza-induced death (Supplementary Fig S4C). ISRIB

also induced significant resistance to the venetoclax+5-Aza combinatorial cell killing (Fig. 4F);

14

enhancing the venetoclax AUC (Fig. 4G) and reducing the synergy between these two agents

(Supplementary Fig. S4D).

Deletion of PMAIP1 abrogates 5-Aza and venetoclax combinatorial activity.

The 5-Aza-mediated induction of NOXA and PUMA, as well as their subsequent binding to the

anti-apoptotic BCL-2 family members, suggested a role in priming the AML cells for apoptosis.

To understand the importance of NOXA and PUMA in this context, CRISPR/cas9 technology

was employed to respectively delete PMAIP1 (Fig. 5A) and BBC3 (Supplementary Fig. S5A).

Following deletion of the PMAIP1 gene, no consistent changes were observed in the expression

of other BCL-2 family members across cell lines (Fig. 5A). The OCI-AML5, Kasumi-1, and

MV4-11 PMAIP1-/- cell lines were each more resistant to venetoclax-induced cell death

compared to their respective parental cell lines. The Kasumi-1 and MV4-11 PMAIP1-/- cell lines

were also more resistant to 5-Aza-induced cell death (Fig. 5B). In agreement with the cell

viability data, the kinetics of induction and number of aCasp-3/-7+ cells in PMAIP1-deficient cell

lines were substantially reduced in response to either venetoclax or 5-Aza treatment (Fig. 5C).

Since venetoclax and 5-Aza induced broad synergistic cell killing in AML cell lines, we assessed

the impact of PMAIP1 deletion on this combination. PMAIP1 deletion reduced the magnitude of

cell death resulting from combined venetoclax/5-Aza treatment in MV4-11, OCI-AML5, and

Kasumi-1 cells (Fig. 6A), which was associated with a loss of venetoclax potency (EC50) in the

presence of increasing concentrations of 5-Aza (Fig. 6B) and the abrogation of synergy (Fig. 6C)

Lastly, we hypothesized that PUMA might also play a role in priming the cells for apoptosis. The

gene encoding PUMA, BBC3, was deleted in the parental and the PMAIP1-/- cell lines, OCI-

AML5 and MV4-11. The crRNA was designed to target both BH3-containing isoforms of

PUMA, alpha and beta. Western blot analysis indicated complete absence of PUMA at the

protein level (Supplementary Fig. S5A). Unlike the PMAIP1-/- cell lines, the BBC3-/- OCI-AML-

3 and MV4-11 cell lines responded similarly to venetoclax and/or 5-Aza as the parental cell lines

(Supplementary Fig. S5B, S5C). Additionally, BBC3 deletion in the PMAIP1-/- AML cell lines

did not further impact the response of PMAIP1-/- cells to the venetoclax/5-Aza combination as

measured by cell viability (Supplementary Fig. S5B). Taken together, our findings show that,

although both NOXA and PUMA are induced by 5-Aza treatment of AML cell lines, only

NOXA is critical in sensitizing the AML cells to 5-Aza/venetoclax-induced apoptosis.

15

Discussion

Venetoclax has been approved by the FDA for use in the treatment of elderly AML patients

(aged ≥ 75 yrs.) in combination with 5-Aza who are ineligible for induction therapy based on the

significant improvement in overall response rates (34). Herein we utilize pre-clinical models of

AML to provide mechanistic insights into the clinical activity observed between 5-Aza and

venetoclax. At physiologically relevant concentrations (38), we demonstrate that 5-Aza

combines with venetoclax in AML cell lines via non-epigenetic mechanisms requiring the

induction of NOXA via the integrated stress response pathway.

Treatment of AML cell lines with the combination of venetoclax and 5-Aza induced the rapid

induction of apoptosis that was greater than either 5-Aza or venetoclax as single agents, both in

terms of rate and magnitude of response. This corresponded with broad synergistic cell killing

observed across a panel of AML cell lines that was also reflected in vivo, where the co-treatment

of MV4-11 and SKM-1 xenograft models with 5-Aza and venetoclax inhibited tumor growth

superior to either agent alone. The rapid kinetics (<24 hours) of apoptosis associated with the

combinatorial activity between venetoclax and 5-Aza indicate that although DNMT1 expression

is eliminated, the resulting cell death was independent of changes in DNA methylation, which

required a week of continuous treatment. Similarly, acute cell death was previously reported in

AML patient cells treated ex vivo for 24 hours with the venetoclax/5-Aza combination (47),

aligning with the rapid blast clearance observed within 24-72h post-treatment in AML patients

treated with this combination therapy (48).

In the acute treatment setting, 5-Aza did not affect the expression of anti-apoptotic proteins, but

it significantly induced the expression of the pro-apoptotic BH3-only proteins PUMA and

NOXA, independent of their respective gene methylation status. Several mechanisms beyond

hypomethylation have been proposed to be responsible for 5-Aza’s activity (12-14), including

DNA damage (11). However, although PMAIP1 and BBC3 are both p53 response genes

(21,22,49,50), they were both induced independent of TP53 status following 5-Aza treatment,

and were not associated with changes in p53 phosphorylation status (data not shown). We

subsequently hypothesized that the induction of these BH3-only proteins was not a result of

DNA incorporation by 5-Aza (7,40), but rather a consequence of RNA incorporation (8-10) and

inhibition of protein synthesis (11), which may result in activation of ISR. The regulatory region

16

of PMAIP1 contains the binding sites for over 40 different transcription factors and co-activators

including those mediated by DNA damage, hypoxia, epigenetic regulation, metabolic stress,

proteasome inhibition, autophagy and ISR. One of these transcription factors and ISR

component, ATF4, induces PMAIP1 transcription and enhances the expression of NOXA

protein in a p53-independent manner, following treatment of cells with proteotoxic agents

(44,45). Exposure of AML cell lines to 5-Aza resulted in the activation of the ISR pathway, as

evident by CHOP and ATF4 induction coupled with phosphorylation of eIF2 (S51).

Subsequent pharmacologic inhibition of ISR prevented the 5-Aza-mediated induction in

PMAIP1, BBC3 and DDIT3. Importantly, the degree of PMAIP1, BBC3 or DDIT3 expression

induced following 5-Aza treatment correlated with the degree of synergy observed between

venetoclax and 5-Aza in AML cell lines in vitro. A recent study identified that the venetoclax

and 5-Aza combination killed leukemic stem cells from AML patients by decreasing amino acid

uptake and mitochondrial respiration (47). Interestingly, amino acid deprivation activates the ISR

through general control nonderepressible-2 kinase (GCN2) signaling (43), offering a potential

mechanism for the ISR activation observed in our study.

The capacity of the anti-apoptotic BCL-2 family members to sequester or buffer elevations in

their pro-apoptotic counterparts through direct protein-protein interactions, functions to thwart

the execution of apoptosis (16). In this context, MCL-1 functions as a resistance factor to

venetoclax, operating in part as a sink to sequester BH3-only proteins released from BCL-2 upon

venetoclax binding (51). 5-Aza enhanced the association of NOXA with MCL-1 in a dose-

dependent fashion, potentially neutralizing the anti-apoptotic capacity of this protein similar to

one of several mechanisms ascribed to the activity of bortezomib in combination with venetoclax

in multiple myeloma (52). Although full-length NOXA binds MCL-1 with a Kd of 3.4 nM, it also

possesses a dissociation constant of 250 nM for BCL-2 (53). Reflecting these data, 5-Aza

treatment also consistently enhanced the interactions between NOXA and BCL-2 in AML cell

lines, providing an additional mechanism by which this hypomethylating agent may potentially

prime AML cells for apoptosis induction by venetoclax. 5-Aza-mediated PMAIP1 induction

correlated with venetoclax/5-Aza synergy in AML cell lines in vitro; the failure to induce

PMAIP1 associated with the poor combinatorial activity observed between these two agents in

THP-1 and SET-2 cells.

17

To further understand the impact of NOXA or PUMA on the combinatorial activity between

venetoclax and 5-Aza, we utilized gene editing technology to delete PMAIP1 and/or BBC3,

respectively, in OCI-AML-5, Kasumi-1 and MV4-11 cells. PMAIP1 deletion, but not BBC3

deletion, significantly inhibited the synergy between venetoclax and 5-Aza, additionally reducing

the kinetics and magnitude of caspase-3/-7 activation when compared to the parental cell lines.

BBC3 deletion did not inhibit apoptosis induced by either venetoclax or 5-Aza and did not

further enhance the resistance to venetoclax activity mediated by PMAIP1 deletion. Although

these data contrast with DNA damage-induced apoptosis, where PUMA drives most of the

apoptosis with partial contributions from NOXA (54), our observations that PMAIP deletion

restricts apoptosis induced by venetoclax single-agent treatment aligns with recent studies

demonstrating that elevated PMAIP1 expression is responsible for enhanced sensitivity to

venetoclax in pre-clinical models of diffuse large B-cell lymphoma (55) and neuroblastoma (56).

What’s more, loss of PMAIP1 inhibited 5-Aza induced cell death in two of three AML cell lines

assessed, complementing data that demonstrate NOXA peptides can discriminate the clinical

responses of AML, MDS and MDS/PMN patients treated with 5-Aza (13).

Collectively, these data indicate that NOXA expression is a key determinant of venetoclax

activity, both as a monotherapy and in the combination setting with 5-Aza. Additionally, this

work demonstrates that, at pharmacologically relevant concentrations, 5-Aza induces NOXA

through the ISR pathway to sensitize AML cells to venetoclax in pre-clinical models of this

malignancy. These data provide a rational behind the ongoing randomized phase III clinical trial

evaluating the activity of venetoclax in combination with 5-Aza in treatment-naïve subjects with

AML who are ineligible for induction therapy (M15-656, NCT02993523). Consequently,

understanding the association of NOXA and CHOP expression in AML patients in relation to

venetoclax clinical activity is of significant interest.

18

Acknowledgements

We would like to acknowledge Loren M Lasko from AbbVie Oncology Discovery for his

technical expertise in single cell sorting of the knockout cells.

19

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24

Figure Legends

Fig. 1 | Chronic or acute 5-Aza synergizes with venetoclax in AML cell lines in vitro and

provides added benefit over either agent alone in xenograft models of AML.

A. AML cell lines MV4-11, OCI-AML5, SET-2 and SHI-1 were treated with 300 nM of 5-Aza on

day 0, 2, 4, and 6, followed by measurements of relative 5-methylcytosine (mC) in DNA on day 7

(n=3, *p<0.05, ns: not significant). B. The 5-Aza pre-treated cells (7 days, 300 nM) were washed

and treated with the indicated doses of venetoclax for 24 hours, at which point cell viability was

assayed (n=3). C. Cells with active caspase-3/-7 (aCasp-3/-7+) were counted over time following

treatment with venetoclax, 5-Aza (3µM) and venetoclax in combination with 5-Aza in OCI-AML5

and MV4-11 cell lines (n=3). D. AML cell lines SKM-1, PL-21, OCI-AML5, and MV4-11 were

co-treated with the indicate doses of 5-Aza and venetoclax for 24 hours at which point cell viability

was assayed (n≥3). E. Synergistic activity between 5-Aza and venetoclax was quantified using the

Bliss independence model and the total synergy across the combination matrix determined (Bliss

Sum; n≥3). F. SKM-1 and MV4-11 xenograft models were treated (grey bar) with 5-Aza (8 mg/kg,

QD7x3, IV), venetoclax (50 mg/kg, QDx14, PO) or venetoclax in combination with 5-Aza, and

the effect on tumor growth determined. Data are presented as the mean tumor volume ± s.e.m

obtained from 8 mice per treatment group.

25

Fig. 2 | 5-Aza upregulates NOXA and PUMA in AML cells independent of cell death.

A. AML cell lines were treated with 5-Aza for 24 hours and the effect on the expression of BCL-

2 family members, caspase-3, PARP, DNMT1 and β-actin determined by western blot analysis.

Approximate protein molecular size calculated from protein size standards. B. OCI-AML5,

MOLM-13, and MV4-11 cells were pre-treated with 40 µM Z-VAD-fmk for 1 hour prior to

treatment with 5-Aza for a further 24 hours, and the impact on MCL-1, PUMA, NOXA, caspase-

3, PARP, DNMT1 and β-actin determined by western blot analysis. C. AML cell lines were treated

with 5-Aza for 6 and 24 hours and the effect on PMAIP1 (NOXA) and BBC3 (PUMA) gene

expression was quantified using qPCR. (n=3) D. Fold-change in PMAIP1 and BBC3 gene

expression by 5-Aza (3 µM, 6 hours) was correlated with the Bliss sum of the 5-Aza and

venetoclax combination for a panel of 15 AML cell lines. The cell lines were classified by TP53

status labeled in black, for wild-type, and in red, for mutated/null TP53 gene. (n=3, dotted line:

95% confidence bands of the best-fit line) E. Primary cells from AML patients were treated ex

vivo with 5-Aza at the indicated concentrations and timepoints, and the effect on PMAIP1 (NOXA)

and BBC3 (PUMA) gene expression was quantified using qPCR. Reported percent blasts from

pathology and treatment (Tx) status.

26

Fig. 3 | 5-Aza enhances the amount of NOXA and PUMA in complex with BCL-2 and

MCL-1 in AML cell lines.

OCI-AML5, Kasumi-1, and MV4-11 cells were pre-treated with 40 µM Z-VAD-fmk for 1 hour

prior to treatment with 5-Aza for an additional 24 hours. The association of PUMA or NOXA with

MCL-1, BCL-2 or BCL-XL was determined by immunoprecipitation (IP) and subsequent western

immunoblot (IB) analysis as described in the materials and methods.

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Fig. 4 | 5-Aza activates the Integrated Stress Response (ISR) pathway to transcriptionally

induce PMAIP1 and BBC3.

A. OCI-AML5 and Kasumi-1 and MV4-11 cell lines were treated with increasing doses of 5-Aza

for 24 hours and the ISR pathway activation was measured by immunoblotting for CHOP, ATF4

proteins and phosphorylation of eIF2α at serine 51. Total eIF2α was used as control for total

protein loading. #denotes non-specific band. Approximate protein molecular size calculated using

protein size standards. B. AML cell lines were treated with 5-Aza for 6 and 24 hours and the effect

on PMAIP1 (NOXA) and BBC3 (PUMA) gene expression was quantified using qPCR (n=3). C.

Primary cells from AML patients were treated ex vivo with 5-Aza at the indicated concentrations

and timepoints and the effect on DDIT3 gene expression was quantified using qPCR. Reported

percent blasts from pathology, and treatment (Tx) status. D. Fold-change in PMAIP1 and BBC3

gene expression was correlated with the Bliss sum of the 5-Aza and venetoclax combination for a

panel of 15 AML cell lines (n=3). E. OCI-AML5 cells treated with 5-Aza alone (3 µM PMAIP1,

DDIT3 or 10 µM for BBC3) or in combination with ISRIB (200 nM) for 6 hours followed by

quantification of PMAIP1, BBC3, DDIT3 transcripts using qPCR (n=3, *p<0.05). F. venetoclax

dose-response curve treated with increasing doses of 5-Aza in the presence of DMSO or ISRIB

(200nM) (n=3). G. Area under the curve of the dose-response curves from (F) for OCI-AML5,

Kasumi-1 and MV4-11 cell lines (n=3, *p<0.05).

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Fig. 5 | Deletion of PMAIP1 in AML cell lines abrogates venetoclax and 5-Aza activity.

A. Western blot analysis of BCL-2 family expression in OCI-AML5, Kasumi-1, and MV4-11 cell

lines deficient in PMAIP1 compared to the respective parental cell line. Approximate protein

molecular size calculated using protein size standards. B. Cell viability following 24 hours of

treatment with either 5-Aza or venetoclax was compared for the parental and PMAIP1 knockout

cell lines (n=3, *p < 0.05). C. Cells with active caspase-3/-7 (aCasp-3/-7+) over time following

venetoclax or 5-Aza treatment of the parental and PMAIP1-/- cell lines OCI-AML5, Kasumi-1, and

MV4-11 (n=3).

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Fig. 6 | PMAIP1 deletion in AML cell lines abrogates combinatorial activity of venetoclax

and 5-Aza.

A. Dose-response curves for venetoclax and 5-Aza combination in the OCI-AML5 parental and

PMAIP1-/-cell lines (n>3). B. EC50 for the 5-Aza and venetoclax combinations in the parental and

PMAIP1-/- OCI-AML5, Kasumi-1, and MV4-11 cell lines (n>3, *p < 0.05). C. Synergy between

venetoclax and 5-Aza drug combination as measured by the Bliss independence model for the

parental and PMAIP1-/- cell lines (n>3, *p < 0.05).