CDKN2A/P16 Deletion in Head and Neck Cancer Cells Is Associated with Cdk2 Activation, Replication Stress, and Vulnerability to Chk1 Inhibition

Author Manuscript Published OnlineFirst on December 11, 2017; DOI: 10.1158/0008-5472.CAN-17-2802 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

CDKN2A/p16 deletion in head and neck cancer cells is associated with Cdk2 activation, replication stress, and vulnerability to Chk1 inhibition

Mayur A. Gadhikar1, Jiexin Zhang2, Li Shen2, Xiayu Rao2, Jing Wang2, Mei Zhao1, Nene N. Kalu3, Faye M. Johnson3, Lauren A. Byers3, John Heymach3, Walter N. Hittelman6, Durga Udayakumar4,5, Raj K. Pandita4, Tej K. Pandita4, Curtis R. Pickering1, Abena B. Redwood7, Helen Piwnica-Worms7, Katharina Schlacher8 , Mitchell J. Frederick9*, Jeffrey N. Myers1*.

1, Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA 2 Department of Biostatistics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA 3 Thoracic Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA 4 Department of Radiation Oncology, Institute for Academic Medicine, Houston Methodist 6 Department of Experimental Therapeutics, University of Texas, MD Anderson Cancer Center, University of Texas MD Anderson Cancer Center, Houston, TX , USA 7 Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA 8 Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA 9 Department of Otolaryngology - Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA Present address: 5Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, USA

Running Title: p16 deletion associates with Chk1i sensitivity in HNSCC Keywords: CDKN2A/p16 deletions, prexasertib, replication stress, HNSCC Grant support: This work was supported by NIH/NIDCR grants P50 CA97007, R01 DE024601, and R01 DE014613 to J.N. Myers (PI) and 1U01DE025181 to J. N. Myers (PI) and M.J. Frederick (PI). T.K.Pandita was supported by NIH grants CA129537 and GM109768. * Corresponding Authors:

Dr. Jeffrey N. Myers, MD, PhD, FACS, Professor and Director of Research, Department of Head and Neck Surgery, MD Anderson Cancer Center, PO Box 301402, Unit 1445, Houston, TX 77230-1402, USA. Phone: (713) 745-2667; Fax: (713) 794-4662; E-mail: [email protected]

Dr. Mitchell J Frederick, PhD, Associate Professor, Department of Otolaryngology - Head and Neck Surgery, Baylor College of Medicine, 6501 Fannin Street, Room NA514, Houston, TX 77030, USA. Phone: (713) 7798-1263; E-mail: [email protected]

Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2017 American Association for Cancer Research. Author Manuscript Published OnlineFirst on December 11, 2017; DOI: 10.1158/0008-5472.CAN-17-2802 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

Abstract

Checkpoint kinase inhibitors (CHKi) exhibit striking single agent activity in certain tumors, but the mechanisms accounting for hypersensitivity are poorly understood. We screened a panel of 49 established human head and neck squamous cell carcinoma (HNSCC) cell lines and report that nearly 20% are hypersensitive to CHKi monotherapy. Hypersensitive cells underwent early S- phase arrest at drug doses sufficient to inhibit greater than 90% of Chk1 activity. Reduced rate of DNA replication fork progression and chromosomal shattering were also observed, suggesting replication stress as a root causative factor in CHKi hypersensitivity. To explore genomic underpinnings of CHKi hypersensitivity, comparative genomic analysis was performed between hypersensitive cells and cells categorized as least sensitive because they showed drug IC50 value greater than the cell panel median and lacked early S phase arrest. Novel association between CDKN2A/p16 copy number loss, Cdk2 activation, replication stress and hypersensitivity of HNSCC cells to CHKi monotherapy was found. Restoring p16 in cell lines harboring CDKN2A/p16 genomic deletions alleviated Cdk2 activation and replication stress, attenuating CHKi hypersensitivity. Taken together, our results suggest a biomarker-driven strategy for selecting HNSCC patients who may benefit the most from CHKi therapy.

Introduction

Therapeutic advances in head and neck squamous cell carcinoma (HNSCC) have been stymied by resistance to conventional therapies and lack of molecular targets. Inhibition of critical components in the DNA Damage response (DDR) pathway, such as cell cycle checkpoint kinases (Chk1/2), potentiates genotoxic therapies in cancer cell lacking wild type p53 function [1-5]. While early stage clinical trials are currently exploring the utility of combining Chk inhibitors with chemotherapy in various cancers, single agent sensitivity to chk1 inhibition has been sporadically reported for a limited number of tumor cell lines derived from various cancers [4, 6-9]. Whether susceptibility to Chk1 inhibition monotherapy is confined to a few cancer types or could represent a broader phenomenon remains unclear. Importantly, the genomic or molecular factor(s) influencing susceptibility to Chk1 inhibition monotherapy in any given tumor type has remained elusive. In melanoma cells, high basal levels of DNA damage were associated with vulnerability to Chk1 inhibition [8]; whereas in ovarian tumors, subtypes bearing high endogenous Chk1 activity exhibited greatest sensitivity to Chk1 inhibition [9]. Elevated levels of endogenous DNA damage resulting from transgenic overexpression of c-myc in murine lymphoma models has also been associated with Chk1 inhibition sensitivity [7]. More recently, sensitivity to Chk1 inhibition in tumor cells has been ascribed to Cdk2 activation in S phase and associated with an elevation of DNA damage[10].

In all of these studies, compared to checkpoint kinase 1 inhibitor (Chk1i) resistant cancers, much higher levels of DNA damage arose in susceptible tumors post Chk1 inhibition, which was sometimes associated with an abnormally long S-phase [4, 7-9]. These findings suggest that Chk1 inhibition sensitivity could be related to the induction of replication stress. In support of this idea, Chk1 plays a vital role during S-phase in the suppression of abnormal replication origin firings and in the maintenance of fork stability to aid proper completion of DNA replication [11, 12]. Tumor cell resistance to Chk1 inhibition can be overcome by artificial induction of replication stress which triggers replication checkpoint and promotes cell reliance on Chk1 function [13]. Even so, it has not been firmly established why certain tumor cells are innately sensitive to Chk1 inhibition and others are not. Moreover, direct experimental demonstration of replication stress in tumor cells acutely sensitive to Chk1 inhibition has been lacking. Instead, most studies have relied on

surrogate markers linked to replication stress or focused more on downstream events preceding cell death, such as replication catastrophe, caspase activation, apoptosis, and abnormal mitosis [4, 7-9].

In HNSCC, the efficacy of Chk inhibition monotherapy was reported in a Phase I dose escalation study (Cancer Res 2013; 73(8 Suppl): Abstract nr LB-200). We screened 49 HNSCC cell lines for their sensitivity to a Chk inhibitor, prexasertib (LY2606368 mesylate monohydrate) and found that 9 out of 49 cell lines (18%) were hypersensitive and exhibited an early S-phase cell cycle arrest at or below drug doses that inhibited greater than 90% of Chk1 activity. Knockdown studies with siRNA revealed that Chk1, not Chk2, mediates survival in hypersensitive cells. Chk1 inhibition also led to reduction in the replication fork progression rate, DNA breaks, and chromosomal shattering, directly demonstrating replication stress as the underlying upstream cause of acute hypersensitivity to Chk1 inhibition in a subset of HNSCC. Importantly, through comprehensive integrated genomic analysis, we identify high level copy number losses, low RNA and protein expression of CDKN2A/p16 in hypersensitive cells and propose it as a major deterministic factor associated with Cdk2 activation, replication stress and hypersensitivity to Chk1 inhibition in HNSCC. Further validation of these findings could enable the possibility of treatment selection of patients with CDKN2A/p16 deletion for treatment with Chk1 inhibition.

Materials and Methods

Please refer to the supplemental data for detailed experimental procedures on immunoblotting, DNA fiber assay, and exome-sequencing and mutational calling.

Cell Culture and Reagents: HNSCC cell lines for this study were obtained from an established cell repository in the laboratory of Dr. Jeffrey N. Myers (University of Texas MD Anderson Cancer Center, Houston, TX) under approved institutional protocols. HNSCC cells were authenticated against the parental cell lines using short-tandem repeat analysis within six months of use for the current study [14]. Culture media was supplemented with fetal bovine serum, glutamine, sodium pyruvate, penicillin/streptomycin, nonessential amino acids, and vitamins. Cell line specific additives were added as recommended in [14] and all cell lines were cultured in 370C with 5% CO2, and periodically tested to ensure mycoplasma-free culture environment. All experiments

were performed using cells from early passages (5

MTT Assay: Roughly, 1000-3000 cells per well were seeded in 96-well plates. A baseline MTT optical density (OD) reading was obtained the next day (day zero). Plates were then exposed to various drug treatments as indicated and at day 5, OD values were obtained again. The cell proliferation curves were plotted using the net OD values (differences between day 5 and day zero readings) on GraphPad prism.

Clonogenic assay: Clonogenic assays were performed in 6-well plates. Roughly, 500-to-600 cells per well were seeded in 6-well-plates and allowed to attach overnight. Treatment wells were exposed to drug concentrations for indicated time periods, following which the drug containing media was aspirated. All wells were washed three times with PBS and fresh media was supplied. Colonies were allowed to form 12-14 days, after which media was aspirated and colonies were fixed in methanol and stained with crystal violet (1.5 %). Colony images were scanned and colony counts per well were obtained using ImageJ software (NIH, Bethesda, MD).

Cell Cycle: Roughly, 150-200k cells were plated in 60-mm dish and exposed to various treatments as indicated. At indicated time points, cell media per condition was collected and set aside to retain any floating cells. Cells were then trypsinized, and the collected media was used to neutralize the trypsin. Media was removed after spinning down the cells and cell pellet was washed with cold PBS. After washing with PBS, cells were re-suspended and fixed overnight at 40C in 70% ethanol. On the analysis day, cells were stained with RNase containing propidium iodide solution and subjected to flow cytometry analysis.

SiRNA-mediated knockdown. 1.5μg of siRNAs against Chk1, Chk2, Cdk1 (Qiagen #SI00299859; #SI02224271; #SI00299712, respectively), and Cdk2 (ThermoScientific #M-003236-04-0005) and non-silencing siRNA (Ambion #4390846) were used for electroporation of HNSCC cells on nucleofector II apparatus (Amaxa). Electroporation conditions were optimized using manufacture supplied pmaxGFP vector, Nucleofector® buffer and program such that greater than

80% transfection efficiency was achieved for each cell line. After electroporation, cells were counted and immediately seeded for various biological assays.

BrdU incorporation: At given time points, HNSCC cells were pulse labelled with BrdU (10 μM) for 40 min, after which the cells were harvested, fixed overnight at 40C and permeabilized using manufacturer supplied buffers for 30 min on ice (#559619, BD-Biosciences). Cells were then treated with DNase for 1hr at 370C and post washing stained with anti-BrdU antibodies for 90 minutes. Samples were processed on FACS Fortessa cytometer and data was analyzed on FlowJo (TreeStar).

Metaphase Spreads: HNSCC cells were exposed to colcemid (0.04 µg/ml) for 25 min at 37°C and to hypotonic treatment (0.075 M KCl) for 20 min at RT. Cells were fixed in methanol: acetic acid (3:1) for 15 min. The slides were then air-dried, stained in 4% Giemsa and coded for blind analysis. A total of 35 metaphases were analyzed from each sample to detect presence of chromosome aberrations (as evidenced by both chromosome- and chromatid-type breaks), fragments, tetraploidy and fusions. Each experiment was conducted at least three times. Images were captured using a Nikon 80i microscope equipped with karyotyping software from Applied Spectral Imaging (ASI) Inc., Vista, CA.

Inducible expression system: A tetracycline-inducible expression system was purchased from Clontech (# 631349). UMSCC22A cells were first transfected with pLVX-Tet3G Vector (regulatory vector), and stable clones were selected by G418 (600 µg/ml). pLVX-TRE3G-mCherry (inducible vector) was modified to include PACI restriction site such that the endogenous IRES ATG site became the start site of translation for a cloned insert. Modified pLVX-TRE3G-mCherry was linearized using PacI and NdeI restriction enzyme and the human p16 cDNA (RC220937, OriGene) was subcloned into the modified vector using In-Fusion cloning strategy. UMSCC22A cells stably expressing pLVX-Tet3G were transfected with modified vector containing p16 cDNA insert, and the stable clones (UMSCC22A-p16) were selected by puromycin treatment (2 µg/ml). UMSCC22A-p16 cells treated with doxycycline (16 hrs) were subjected to flow sorting to enrich for cells expressing similar expression levels of mCherry, and the enriched cells were then expanded in culture and used for experiments.

Confocal Microscopy: UMSCC1-mVenus and HN31-mVenus cells were seeded at 30-40k cells/well in 2 well chamber slides (Thermofisher), and allowed to attach overnight. The next day, cells were exposed to DMSO or prexasertib for 6hrs and pulsed with EdU for 1hr prior to the collection point. Cells were then fixed in 4% paraformaldehyde in PBS, and processed as per manufacturer’s instruction (Click-iT® Plus EdU Alexa Fluor® 594 Imaging Kit, # C10639, ThermoFisher). Nuclear content was stained with ToPro3 (30 µM) overnight at 40C. Slides were then mounted in Dabco glycerol medium containing ToPro3 (5 µM) and imaged. Staining patterns (Nucleus only, Cytoplasm only, Nucleus and Cytoplasm) of EdU positive cells were quantified manually (more than 200 cells per condition).

High Throughput Microscopy: HN31-Venus and UM1-mVenus cells were seeded at 8-10,000 cells/well density in 12-well chamber slides (Ibidi). Cells were allowed to attach overnight. The following day, half the number of wells within the chamber slide were treated with DMSO and the remaining wells received prexasertib (3 nmol/L) in 150 µl of media. At 6 hrs, cells were rinsed in PBS and fixed in 4% paraformaldehyde for 20 min at RT. Cells were then permeabilized with Triton-X 100 (0.1 % in PBS) for 10-15 min at RT, washed in PBS and stained with 10 µM DAPI for 2 hr at RT. Chamber-wells were them removed and slides were mounted in fluorescence mounting media. Data capture: The chamber slides were first scanned at 4X magnification with Perkin Elmer Vectra 3. Subsequently, each well was stamped at 25-50% coverage for capturing multispectral data at 20X magnification. Single color controls were used to identify spectral signals for each fluorophore used (unstained = auto-fluorescence, DAPI only = Blue, and Alexa 488 only (DHB-mVenus) = Green). These spectral curves were then used to unmix the images into their respective channels. Cells were segmented into nuclear and cytoplasmic regions using Perkin Elmer’s InForm software. There was a 1 pixel gap between the nucleus and the cytoplasmic space to ensure signal spatial purity. The DAPI signal was used to obtain the nuclear mask and the cytoplasmic mask was determined from the Alexa 488 and auto-fluorescent signals. Integrated intensity values of DAPI in the nuclear space was used to plot DNA content. Similarly, integrated intensity values of Alexa 488 in the nuclear (N) and cytoplasmic (C) spaces were obtained and C/N ratio was determined.

Genome wide copy number analysis: Genomic DNA isolated from 38 cell lines was hybridized to Affymetrix SNP6.0 or CytoscanHD arrays (Affymetrix) according to manufacturer’s instructions. Segmentation using Partek software (v6.6, Partek, Inc.), sample adjustment for purity and ploidy with ASCAT software, and fine adjustment so that the majority of copy number values were close to integers, were all performed as previously described [15]. Lastly, adjusted copy number values were further scaled to a ploidy of 2 so that comparisons of copy number values between cell lines with different average ploidy values would accurately reflect relative genomic content. Essentially, for each cell line all adjusted copy number values were divided by the average ploidy value for the particular cell line and multiplied by a ploidy of 2. Consequently, a final copy number of 1 and 3 corresponded to a loss and gain of half genomic content, irrespective of original ploidy values, and values outside this range were considered high level deletions or gains. Copy number changes in cell lines were also determined for chromosomal regions, identified previously as having significant recurrent focal amplifications or deletions in primary head and neck cancer tumors, based on Gistic2 analysis of TCGA data available online (https://gdac.broadinstitute.org/). Boundaries for 28 focally amplified and 48 focally deleted regions were taken from the Gistic2 TCGA outputs and copy number changes for the regions in cell lines were defined by the gene with the highest copy number change within the region boundaries. Non-parametric Mann-Whitney U tests were used to assess whether copy number values in regions were different between hypersensitive and least sensitive cell lines, following FDR adjustment for multiple testing.

RNA and protein expression: Whole transcriptome RNA expression was determined by RNASeq. Briefly, cell line RNA was isolated with an RNeasy Plus kit (Qiagen) and Illumina compatible libraries made with a TrueSeq Stranded Total RNA Sample Prep Kit (Illumina, Inc.). Libraries were sequenced with an Illumina HiSeq3000 instrument using the 75-bp paired-end format. Post sequencing, BCL files were converted to “FastQ.gz” format and individual sample libraries de- multiplexed using CASAVA 1.8.2 software (Illumina) with no mismatches. FASTQ files were checked for read quality using FastQC, aligned to hg19 using TopHat [16], and alignment quality was checked with RSeQC [17]. BAM files with mapped reads were sorted and outputted with SAMtools [18], and reads mapping to genes were counted with HTSeq-count [19]. Reads were

then normalized using the trimmed mean of M (TMM) method implemented in the R Bioconductor package edgeR to generate expression values for each gene [20]. Protein expression for p16 was determined following Reverse Phase Protein Array analysis of cell lysates as previously described [21], using anti-CDKN2A/p16INK4a antibody (catalogue # ab81278) from Abcam.

Results:

A significant subset of HNSCC cell lines is acutely sensitive to Chk1 inhibition

To comprehensively investigate the molecular determinants for therapeutic efficacy of single agent Chk inhibition in HNSCC, we screened a panel of 49 established HNSCC cell lines [14] with a checkpoint kinase inhibitor, prexasertib in a MTT cell proliferation assay. HNSCC cells demonstrated a wide spectrum of sensitivity to prexasertib with the IC50 ranging from 1 nmol/L to >40 nmol/L (Fig. 1A). To validate the MTT results and to examine if survival differences accounted for the differential sensitivity to Chk inhibition in HNSCC cells, we performed clonogenic assays in a subset of HNSCC cell lines representing opposite ends of the sensitivity spectrum. Cells that were “more sensitive” to prexasertib in the MTT assay (183, UMSCC1, UMSCC4 and MDA1386LN) also had lower IC50 values for the drug (ranging from 1.62 to 3.47 nmol/L) in the clonogenic assays and cells that were “less sensitive” to prexasertib in the MTT assay (HN31, FADU and Cal27) revealed relatively higher clonogenic IC50 values of the drug (ranging from 13.1 to 33.51 nmol/L) (Fig. 1B). These results indicated that prexasertib IC50 differences in HNSCC cells reflected a disparity in cell survival upon prexasertib treatment. To investigate the possibility that prexasertib was simply less efficient at inhibiting its presumed target in less sensitive cells, the relative impact of prexasertib on Chk1 activity was compared between more sensitive (183, UMSCC1) and less sensitive (HN31, FADU) cells. Cells in both groups were exposed to UV irradiation (70 mJ/m2), a known activator of ATR-Chk1 pathway, and the prexasertib dose required to abolish Chk1 activity was determined. Levels of Chk1 autophosphorylation (S296), which is a commonly employed readout of Chk1 activity, were basally undetectable in both more sensitive and less sensitive cells. While UV treatment led to robust increases in Chk1 (S296) levels in both group of cells, co-treatment with prexasertib at 3

nmol/L abolished Chk1 activity (i.e., suppressed induction of Chk1 S296) in both treated groups (Fig. 1C). Because prexasertib concentrations close to the IC50 values of more sensitive cells was similarly efficient at inhibiting Chk1 activity in less sensitive cells, it suggested that reduced sensitivity to prexasertib in less sensitive cells was unlikely due to residual Chk1 activity. The colony survival differences between the two groups of cells was readily apparent even at a prexasertib concentration of 5 nmol/L, which was more than sufficient to inhibit 90% of the presumed drug target (Supplementary Fig. S1A). Given the role of Chk1 kinase in regulating the process of DNA replication [11, 12], we compared the effect of prexasertib on cell cycle progression in more sensitive and less sensitive cells. After treatment with 3 nmol/L prexasertib, which ablates detectable Chk1 activity in both the cell groups, a prominent increase in the S- phase fraction was observed at both 24 and 48 h, in UMSCC1 and 183 (sensitive) cells but not in the HN31 and HN4 (less sensitive) cells (Fig. 1D; Supplementary Fig. S1B). Of note, treatment of HN31 and FADU cells with a much higher dose of prexasertib (close to their IC50 value) resulted in G2/M rather than early S phase arrest (Supplementary Fig. S1C). These data suggested that phenotypic outcomes in less sensitive cells at high prexasertib concentrations may have been triggered due to biological pathways distinct from the sensitive cells.

The foregoing results demonstrated that there is a unique subset of HNSCC cell lines that have IC50 values less than or close to drug concentrations that inhibits greater than 90% of Chk1 activity, and also show qualitative differences in the cell cycle response (i.e., S phase arrest). These cell lines were deemed as “acutely sensitive or hypersensitive” cells (Table 1), after confirming S-phase arrest following prexasertib treatment. For further analysis and mechanistic studies, we defined cell lines with IC50 values greater than the median for prexasertib (i.e., 9.973 nmol/L) as “least sensitive cells” (Table 1), and all other remaining cell lines were categorized as “moderately sensitive”. Of note, because the IC50 value of human normal oral keratinocyte cells was substantially higher than hypersensitive cells, it suggested that enhanced sensitivity in a subset of HNSCC cells was acquired during tumorigenesis (Supplementary Fig. S1D).

To determine whether sensitivity distinction within cell lines was due to an off-target effect, we performed siRNA-mediated loss of function studies in the hypersensitive and the least sensitive

cells. A knockdown of Chk1, but not Chk2, in UMSCC1 and 183 (hypersensitive) cells resulted in significant reduction in cell proliferation compared to the controls (Fig. 1E-F, p<0.0001). In stark contrast, no significant change in the cell proliferation was evident after Chk1 or Chk2 knockdown in HN31 and FADU (least sensitive) cells, which suggested that Chk1 pathway was dispensable for viability in these cells.

Chk1 inhibition evokes perturbation in the S phase progression of hypersensitive cells, but not in the least sensitive cells

To further investigate cell cycle alterations in UMSCC1 cells after Chk1 inhibition, we pulsed the cells with BrdU for 1hr w/o prexasertib at the indicated time points and processed cells for cell cycle analysis. A significant increase in the percentage of BrdU positive cells in the gated early S phase region (S1) was detected at the indicated time points (Supplementary Fig. S2). While there was an increase in the BrdU positive cells in the early S-phase region with prexasertib, the mean intensity of early S-phase BrdU positive cells dropped at later time points suggesting hindrance to S-phase progression. These data along with earlier cell cycle results (Figure 1D; Supplementary Fig. S1B) raised the possibility that DNA replication dynamics may have been differentially affected by prexasertib in hypersensitive and least sensitive cells.

To investigate the changes in the DNA replication dynamics, we compared the replication fork progression rate in UMSCC1 (hypersensitive) and FADU (least sensitive) cells in the presence and absence of prexasertib using a DNA fiber assay [22]. Consistent with our notion, prexasertib treatment resulted in a significantly decreased median replication fork velocity in UMSCC1 cells (DMSO vs prexasertib; 0.338 Vs 0.111 microns/min, p<0.0001) not observed in FADU cells (DMSO vs prexasertib; 0.165 Vs 0.183 microns/min, n.s) (Fig. 2A-C).

Collectively, these results suggested that prexasertib treatment selectively perturbed the S-phase dynamics of hypersensitive cells which was manifested by reduced replication fork velocity and an impedance to S-phase progression. Furthermore, it appeared that sensitivity phenotypes seen upon Chk1 inhibition could be connected to these S-phase alterations.

DNA damage and replication stress markers are selectively induced at higher levels in the hypersensitive cells upon Chk1 inhibition

To investigate molecular signaling changes in response to Chk1 inhibition between hypersensitive and least sensitive cells, we examined the drug-induced changes in several protein markers in the DNA damage response pathway (DDR) wherein Chk1 plays a vital role. Compared to the least sensitive cells, the hypersensitive cells displayed slightly higher basal levels of pChk1 (S345), however, prexasertib treatment induced robust increases in pChk1 (S345) in both hypersensitive and least sensitive cells (Fig. 3A). Interestingly, decreases in total Chk1 levels was noted in two least sensitive (HN31 and HN4) and one hypersensitive (UMSCC1) cell line following prexasertib treatment. Proteolytic turnover of total Chk1 following its robust activation is a known homeostatic event that promotes checkpoint resetting within cells [4, 9]. Assessment of γH2AX, a commonly employed marker of DNA damage, revealed non-uniform basal level differences between the two cell panels, however, prominent increases in the γH2AX levels were noted following prexasertib treatment in the hypersensitive but not in the least sensitive cells. Given that biological pathways besides DNA damage can trigger γH2AX induction [23-25]; we performed metaphase spread analysis to visualize the impact of prexasertib on chromatin organization and quantitated proportion of cells exhibiting structural chromosomal aberrations following prexasertib treatment. Under basal conditions, the fraction of cells exhibiting structural aberrations was comparable between the two panels; however, prexasertib treatment resulted in significant increases in the proportion of hypersensitive cells with structural aberrations (p=0.0040), which were not observed in the least sensitive cells (Fig. 3B). Additionally, pATM (S1981), a marker commonly associated with double stranded DNA breaks, revealed non-uniform differences at basal levels between the two panels; however, prexasertib treatment led to marked increases in pATM (S1981) levels exclusively in the hypersensitive cells (Fig. 3A). Collectively, these results suggested that induction of severe DNA damage likely involving DNA double strand breaks after Chk1 inhibition may have contributed to the loss of viability in hypersensitive cells. Hyperphosphorylated RPA32 combined with γH2AX induction are commonly employed markers for replication stress [26]. The hyperphosphorylated form of RPA32 which migrates at higher molecular weight and associated with prolonged ssDNA generation, was

selectively induced in hypersensitive cells post prexasertib treatment (Fig. 3A). Replication stress is also reported to trigger activation of the p38 stress signaling pathway [27-29]. Levels of pHSP27 (S82), a downstream mediator of this pathway [27, 28], were also examined following Chk1 inhibition. A massive elevation in the pHSP27 (S82) levels following Chk1 inhibition was detected in the hypersensitive cells (Fig. 3A), however, no such increases were observed in the least sensitive cells. Taken together, the cell cycle and western blot findings indicate that Chk1 inhibition-induced replication stress was a distinguishing feature of hypersensitive cells.

Hypersensitivity to Chk1 inhibition correlates with genomic loss of p16 and p15, but not somatic mutation.

A qualitative difference in the way hypersensitive cell lines responded to low concentrations of drugs targeting Chk1 (i.e., S-phase arrest, cell death) suggested the possibility of synthetic lethality with some other genomic event. To look for possible association with somatic mutations as an explanation for hypersensitivity, we focused on the 50 recurrent mutations common to HNSCC that have been previously identified as significantly mutated in this disease based upon Mutsig2CV analysis of the head and neck cancer TCGA cohort (https://gdac.broadinstitute.org/). This list of genes includes top candidate drivers such as TP53, NOTCH1, FAT1, PIK3CA, etc. Mutation status for all 50 significantly mutated genes was obtained for cell lines through whole exome sequencing (See methods). Comparisons were made between the two groups of cell lines that exhibited the most extreme responses to Chk1 inhibition. A total of 9 cell lines derived from 7 unique patient tumors were classified as hypersensitive, and 23 cell lines derived from 21 unique patient tumors were classified as least sensitive, using previously described criteria (Table 1). Fisher’s exact tests failed to identify an association between any of the 50 commonly mutated genes in Head and Neck cancer and Chk1 inhibitor sensitivity, when isogenic cell lines from the same patient were represented just once (Supplementary Table 1). Under recently described Evolutionary Action (EA) classification system, p53 mutations in HNSCC have been accorded prognostic significance based on their EA score [30]. While there was no significant association (p= 0.13) between p53 EA classification and Chk1 inhibitor sensitivity, at least 3/5 (60%)

hypersensitive lines (from unique patients) were found to harbor high risk p53 mutations (Table 1).

Recurrent gene copy number alterations frequently occur in HNSCC [15, 31]. Therefore, we examined whether hypersensitive HNSCC cell lines had significant differences in copy number gains or deletions compared to least sensitive cell lines, for focal regions previously identified as recurrent in the HNSCC TCGA cohort by Gistic2 analysis (https://gdac.broadinstitute.org/). Diploid scaled copy number values (see methods) from the 28 chromosomal regions of gain and 48 regions of deletion previously defined by GISTIC2 were compared between hypersensitive and least sensitive cells by non-parametric analysis, with isogenic cell lines represented only once. After correction for multiple testing, none of the regions of gain showed any difference between the two groups of cells (Supplementary Table 2). Nevertheless, two chromosomal regions of deletion, 9p21 and 7q31.3, showed significant differences that withstood multiple test correction (i.e., Adj. P =0.0396, Supplementary Table 3). The region within 7q31.1 harbors just two genes, only one of which, IMMP2L was expressed in the cell lines from RNAseq data (See methods). However, IMMP2L was excluded from importance because no significant accompanying differences in mRNA expression were observed between the hypersensitive and least sensitive group (Supplementary Fig. S3A). Using Gistic boundaries (Supplementary Table 3), the 9p21 region of deletion contains the well-known tumor suppressor genes CDKN2A (p16) and CDKN2B (p15), in addition to 37 other genes. The average diploid adjusted copy number values for all 39 genes in the region for hypersensitive and least sensitive cells was compared and ranked according to absolute difference (Supplementary Table 4). The three largest differences were found for p16, p15, and C9orf53 which encodes an antisense RNA to p16, with average copy numbers for all 3 genes <1 for the hypersensitive group compared to values closer to 2 for the least sensitive cells. Based upon diploid scaling, values <1 are indicative of losing more than half the genomic content suggesting that high level deletions in the regions harboring p16 and p15 were more frequent among the hypersensitive group. The p16 and p15 genes are also the only protein-coding genes from the 9p21 deleted region that fall precisely within the actual Gistic peak boundaries [31], suggesting they are important drivers of HNSCC progression. Gene copy number values were significantly lower in hypersensitive versus least sensitive cells (Fig. 4A) for both p16

(P= 0.0043) and p15 (P=0.0085). This also translated into significantly lowered RNA expression values for p16 and p15, with means of 4.4 ± 4.4 and 3.2 ± 4.0 in hypersensitive cells compared to 8.4 ± 3.8 and 8.3 ± 3.5 in least sensitive cells, respectively. Protein expression data from RPPA (available only for p16), strongly supported the copy number and RNA findings, as levels of p16 protein were significantly lower in the hypersensitive group (P= 0.029, Fig. 4B).

The results of genomic analysis led us to hypothesize that high-level deletions in CDKN2A/p16 associated with diminished p16 protein expression may be a contributing factor to Chk1i hypersensitivity in HNSCC cells. To test this hypothesis, we functionally investigated whether restoration of p16 expression in hypersensitive cells could alter cellular responses to Chk1 inhibition. We established a doxycycline-inducible p16 expression system (see methods) in UMSCC22A cells (hereafter UMSCC22A-p16), which had low p16 copy number, mRNA and protein expression values reflective of the hypersensitive cells and displays minimal leakiness with the inducible promoter system (unpublished data) The doxycycline dose-response relationship with p16 induction was examined by western blot (Fig. 4C). Doxycycline doses less than 250 ng/ml caused a slight reduction in the cellular proliferation of UMSCC22A-p16 cells as assessed by MTT assay, however a strong inhibition in cellular growth/proliferation was noted at doxycycline doses that were 2 to 4 fold higher than 250 ng/ml (Supplementary Fig. S3B). To assay the impact of p16 expression on the cell cycle following Chk1 inhibition, we exposed UMSCC22A- p16 cells to indicated doses of doxycycline for 24hrs and then with the combination of doxycycline and DMSO or prexasertib (3 nmol/L) for another 24hrs. As a negative control, UMSCC22A-p16 cells not exposed to doxycycline were similarly subjected to DMSO or prexasertib treatment for 24hrs. As expected, doxycycline untreated UMSCC22A-p16 cells (in absence of p16 induction) revealed a strong S phase accumulation following prexasertib treatment (Fig. 4D). Doxycycline-induced p16 expression resulted in a dose dependent but marginal reduction in the S phase proportion of UMSCC22A-p16 cells under DMSO treatment (Fig. 4D; Supplementary Fig. S3B). Importantly, we found that p16 induction diminished prexasertib induced S phase accumulation in UMSCC22A-p16 in a dose dependent manner.

We next investigated the effect of p16 induction on replication dynamics of UMSCC22A-p16 cells. In the absence of p16 induction, prexasertib led to a significant decrease in the mean replication fork velocity of UMSCC22A-p16 cells (-doxy DMSO vs -doxy prexasertib, 0.149+0.06 vs 0.0496+0.032 microns/min, p<0.0001) compared to DMSO treatment (Fig. 4E). Induction of p16 alone in the absence of prexasertib (i.e., DMSO) had no significant effect on the mean replication fork velocity (-doxy DMSO vs +doxy DMSO, 0.158+0.058 vs 0.149+0.06 microns/min, p=0.5560); however, p16 induction counteracted the decrease in mean replication fork velocity following Chk1 inhibition in UMSCC22A-p16 cells (-Doxy prexasertib vs +Doxy prexasertib, 0.0917+0.04 Vs 0.0496+0.032 microns/min, p<0.0001).

Finally, we assessed the effect of p16 induction on the growth of UMSCC22A-p16 cells under Chk1 inhibition. In absence of p16 induction, prexasertib treatment significantly inhibited cell proliferation of UMSCC22A-p16 cells (p< 0.0001) (Fig. 4F). Induction of p16 led to a marginal decrease in the cell proliferation of UMSCC22A-p16 cells upon DMSO treatment that was not significant. More importantly, prexasertib treatment resulted in no significant drop in the cell proliferation of UMSCC22A-p16 cells when p16 was induced (p=0.0868, n.s). These findings suggested that enhanced sensitivity to prexasertib in hypersensitive cells could be an outcome of severely reduced p16 expression and function, stemming from high-level copy number losses in the genomic loci harboring this gene.

An early S phase increase in Cdk2 activity associated with Chk1 inhibition underlies emergence of the hypersensitivity phenotype

Because p16 has been previously reported to exert its effect through modulation of Cdk2 kinase activity [32-34], we investigated whether the hypersensitivity phenotype following Chk1 inhibition arises as a result of increased Cdk2 activity. As phosphor-Cdk2 antibodies cannot discern between cdk1 and Cdk2 [35], we generated hypersensitive and least sensitive cell lines (UMSCC1-mVenus and HN31-mVenus) stably expressing a fluorescent and highly-specific Cdk2 activity sensor, DHB-mVenus [36]. The intracellular localization of DHB-mVenus hinges on the level of Cdk2 activity, making it a suitable surrogate for measuring Cdk2 activity [36]. Under ordinary conditions, DHB-mVenus is localized inside the nucleus when Cdk2 activity is low (i.e.,

G1 phase), exhibits both cytoplasmic and nuclear localization when Cdk2 activity is intermediate (i.e., S phase) and is localized entirely in the cytoplasm when the Cdk2 activity is maximum (i.e., G2/M phase). Therefore, in assessing the association between Chk1 inhibition and changes in Cdk2 activity, it is vital to control for phase of the cell cycle. Based on our data demonstrating replication stress and perturbations in the S-phase for hypersensitive cells treated with Chk1 inhibitor, we investigated whether hypersensitive cells would show more profound changes in Cdk2 activity during S phase following Chk1 inhibition. Cells under treatment were pulsed with EdU for 1hr prior to fixation to enable the detection of replicating cells and then imaged with confocal microscopy. In the absence of prexasertib treatment, the majority of EdU-positive HN31-mVenus and UMSCC1-mVenus cells exhibited a cytoplasmic and nuclear localization pattern, consistent with intermediate Cdk2 activity during S-phase (Supplementary Fig. S4). Prexasertib treatment in HN31-mVenus cells resulted in no discernible change in this localization pattern. In contrast, a significant increase in the percentage of cells showing predominantly cytoplasmic staining (i.e., increased Cdk2 activity) accompanied by a significant decrease in cells with cytoplasmic and nuclear localization of DHB-mVenus was observed following prexasertib treatment of EdU-positive hypersensitive UMSCC1-mVenus cells (Supplementary Fig. S4). As hypersensitive cells had exhibited early S-phase accumulation following Chk1 inhibition (Fig. 1D, Supplementary Fig. S1B and S2), we further evaluated DHB-mVenus localization specifically within the early S phase population by scoring cells based on the diffuse pattern of EdU staining, which is discernibly stronger and more punctuate in later S-phase [37]. In UMSCC1-mVenus, the early S-phase cells showed a significant increase in the percentage with cytoplasmic only DHB- mVenus localization following prexasertib treatment; however no such increases were evident in the early S-phase HN31-mVenus cells (Fig. 5A). These results suggested that Cdk2 activity increases during early S phase following Chk1 inhibition uniquely in the hypersensitive cells following prexasertib treatment.

To more quantitatively assess differences in Cdk2 activity of individual S phase cells in the presence or absence of prexasertib treatment, we used image analysis to directly measure the nuclear and cytoplasmic signal from DHB-mVenus. A histogram plot of integrated DAPI intensities following image analysis of the same experiment allowed identification of UMSCC1-mVenus and

HN31-mVenus cells within early S phase [38] (Fig. 5B). The Cdk2 activity of individual early S phase cells (in the presence or absence of Chk1 inhibition) was computed using their Cytoplasmic to Nuclear ratios of integrated DHB-mVenus intensities (C/N) and is plotted in (Fig. 5B). While no significant quantitative alteration (p = 0.4834) in the DHB-mVenus C/N ratios was observed for early S phase HN31-mVenus cells following prexasertib treatment, a significant increase (P < 0.0001) in DHB-mVenus C/N ratio was found for early S phase UMSCC1-mVenus cells following treatment with the Chk1 inhibitor. These data provided further evidence that Cdk2 activity was substantially elevated only in the hypersensitive UMSCC1-mVenus cells following Chk1 inhibition.

To further explore the possibility that increased Cdk2 activity was responsible for generation of the hypersensitive phenotype, we used roscovitine, a pan cyclin dependent kinase (Cdk) inhibitor, to block Cdk2 activity in hypersensitive cells and assessed their clonogenic survival after prexasertib treatment. Hypersensitive cells seeded for a clonogenic assay were pre-treated with 5 μmol/L roscovitine for 2 h before exposure to prexasertib (3 nmol/L or 6 nmol/L) for an additional 48 h. prexasertib treatment alone at 3 nmol/L and 6 nmol/L doses led to a significant reduction in the colony survival of hypersensitive cells (p<0.0001) (Fig. 6A). Roscovitine treatment alone had no significant effect on clonogenic survival of hypersensitive cells. While prexasertib treatment resulted in roughly 70% loss of clonogenic survival of hypersensitive cells, only 20% reduction in colony survival was noted after roscovitine co-treatment (p<0.0001). To further corroborate the role of Cdk2 for the generation of hypersensitivity phenotype post Chk1 inhibition, we performed siRNA knockdown of cdk1 and/or Cdk2 in hypersensitive cells, and then exposed the cells to prexasertib. While control scrambled siRNA or cdk1 knockdown failed to rescue hypersensitive cells from the lethal effects of Chk1 inhibition, a strong protection was observed upon Cdk2 knockdown or with the double knockdown of cdk1 and Cdk2 (Fig. 6B). These results suggested that protection from Chk1 inhibition induced lethality by roscovitine was mediated mainly through negative regulation of Cdk2.

Next we examined whether roscovitine co-treatment could mitigate prexasertib-induced cell cycle perturbations and molecular changes associated with the hypersensitive phenotype. Co- treatment of prexasertib with roscovitine prevented the early S phase accumulation induced by

prexasertib in hypersensitive cells (Fig. 6C; Supplementary Fig. S5A). We also observed an increase in the G2/M fraction of hypersensitive cells with roscovitine treatment alone. This increase in the G2/M fraction after roscovitine treatment could be due to inhibition of G2-M transition regulator, cdk1, which is also a target of roscovitine [11, 39]. Importantly, roscovitine itself did not appear to provide its protective effects by inhibiting entry of cells into S-phase, as there was no accumulation of cells in G1. Further corroborating the role of Cdk2 activity in mediating replication stress induced by Chk1 inhibition, roscovitine prevented the slowdown in replication fork velocity following prexasertib treatment (Fig. 6D) and also prevented induction of γH2AX and hyperphosphorylated RPA32 in UMSCC1 cells (Fig. 6E).

Discussion

Chk kinase inhibitors have been shown to augment tumoricidal effects of genotoxic therapies in a variety of cancers and several human clinical trials are currently underway to evaluate the clinical potency of this therapeutic strategy. Intriguingly, Chk1 inhibition alone has demonstrated variable therapeutic activity across several cancer types, driving mechanistic investigations into the molecular or genetic basis for single agent activity. In this study, we conducted a comprehensive drug sensitivity screen in a panel of 49 HNSCC cell lines using the Chk1 inhibitor prexasertib and found that nearly 20% of HNSCC cells lines are acutely sensitive to single agent Chk1 inhibition. Moreover, siRNA knockdown experiments revealed that Chk1, but not Chk2, is uniquely essential for cell survival and proliferation in the hypersensitive cells, arguing that Chk1 is the critical target of prexasertib.

The prexasertib-induced survival differences appeared not to be due to unequal degrees of target inhibition between hypersensitive and the least sensitive cells as equimolar prexasertib doses completely abolished Chk1 activity in more sensitive and less sensitive cells. These results suggested that acute sensitivity to Chk1 inhibition was likely an outcome of inherent biological properties shared by hypersensitive cells and is substantiated by the observation that viabilities of the least sensitive cells were unaffected by the loss of Chk1. Studies in other tumor types have reported that basal expression levels of pChk1 (S296) correlate with sensitivity to Chk1 inhibition [9]; however this does not seem to be the case for hematopoietic cancer cell lines [4]. Our data

suggest that basal pChk1 (S296) levels may not be a useful biomarker to predict sensitivity to Chk1 inhibition in HNSCC cells, as basal phosphorylation of Chk1 at serine 296 was low and not consistently detected by western blotting in hypersensitive and least sensitive cells alike.

Chk1 inhibition in hypersensitive cells led to a characteristic early S-phase arrest which was absent in the least sensitive cells, suggesting that Chk1 was uniquely necessary to ensure unimpeded progression of S phase in the hypersensitive cells. Cell synchronization experiments showed that the subG1 fraction following Chk1 inhibition in the hypersensitive UMSCC1 cells (Supplementary Fig. S1E) arose likely from the S-phase cells, probably due to replication catastrophe [40, 41]. This is further supported by the high degree of chromosomal shattering apparent in the fraction of prometaphase cells, and the increases in γH2AX and hyperphosphorylated RPA32 markers following Chk1 inhibition. A previous study investigating the mechanism of cell death under replication stress, induced by excess thymidine, demonstrated that TP53-null Chk1-depleted cancer cells underwent premature “S phase” mitosis leading to loss of viability [42]. Future studies are needed to determine whether similar S-to-M phase slippage also occurs in a fraction of HNSCC cells that are hypersensitive to Chk1 inhibition; however, it might explain why we observed chromosomal shattering in metaphase cells treated with prexasertib.

Agents causing DNA lesions and disruption in nucleotide supply are known to shift tumor dependency on Chk1 to counteract replication stress inside tumor cells [43-45]. Chk1 depletion under these conditions exacerbates replication stress leading to increased RPA hyperphosphorylation and renders normally resistant tumor cells susceptible to Chk1 inhibition. Provocatively, we found that Chk1 inhibition alone led to RPA hyperphosphorylation in the hypersensitive HNSCC cells which suggests that these cells may be chronically under replication stress that is effectively masked by Chk1 function.

A comprehensive genomic profiling of all 49 HNSCC cell lines using three orthogonal platforms — DNA copy number alterations, RNA sequencing, and RPPA analysis—revealed that Chk1 inhibition hypersensitivity was associated with, reduced p16 RNA and protein expression resulting from a high level deletion of the gene. Induced expression of p16 in hypersensitive cells mitigated the

phenotypes associated with hypersensitivity to Chk1 inhibition. The S-phase accumulation, loss of viability, and reduction in fork progression rate following Chk1 inhibition was considerably alleviated when p16 was induced. Because p16 expression was induced at a level that was permissive for S phase entry, it is unlikely that protection against Chk1 inhibition was due to S phase entry block imposed by p16. Nonetheless, a modest drop in the proportion of cells entering S phase was noted at these p16 expression levels. These results imply that p16 may be influencing drug sensitivity partly by slowing or preventing premature entry into the S-phase.

While the precise mechanism underlying the p16-mediated protection from Chk1 inhibition remains unknown, we postulate that p16-dependent molecular pathways participating in the regulation of Cdk2 activity could be at play. Forced expression of p16 in tumor cells has been shown to downregulate Cdk2 activity by triggering re-assortment of Cyclin-Cdk-Inhibitor complexes [32, 33]. It is thus conceivable that genomic losses in p16 in the hypersensitive cells could have led to disruption in the p16-dependent pathways regulating Cdk2 activity. Using a highly specific Cdk2 activity sensor, we compared the effect of Chk1 inhibition on Cdk2 activity in hypersensitive and the least sensitive cells and found that Cdk2 activity following Chk1 inhibition rose significantly in the hypersensitive, but not in the least resistant cells. These results suggest that high-level losses in p16 may have increased cellular dependency on Chk1 to suppress Cdk2 activity. Therapeutic targeting of Chk1 resulted in lethal consequences, highlighting synthetic lethal relationship between high-level CDKN2A losses and Chk1 inhibition monotherapy as depicted in the graphical model (Supplementary Fig. S5B). Cdk2 knockdown or roscovitine co- treatment protected hypersensitive cells from Chk1 inhibition-induced lethality and also reversed all other phenotypic responses seen after Chk1 inhibition in hypersensitive cells. These results indicate that cellular outcomes upon Chk1 inhibition were mediated by Cdk2. p16 losses have been shown to correlate with poor prognosis in SCCs [46]. A recent study evaluating survival of HNSCC patients with stratified p53 mutations (based on the EAp53 classification system), revealed that p16 deletions co-occurring with high-risk p53 mutations were associated with worsened outcomes in HNSCC [47]. Because a small subset of hypersensitive cells were found to harbor high-risk p53 mutations, a corollary follows that these

difficult-to-treat HNSCC patients bearing p16 deletions and high-risk p53 mutations might benefit from Chk1 inhibition therapy, either as single agent or in combination.

In summary, we have identified a genomic alteration that predisposes a nearly 20% of HNSCC tumors to Chk1 inhibition monotherapy through replication stress. Our findings suggest that high-level deletions in CDKN2A/ p16 could serve as a potential genomic biomarker for a priori identification of patient tumors that will most likely respond to single agent chk1 inhibitor. This would find potential utility for selection of patient subset for Phase II human clinical trials with Chk1 inhibitor monotherapy. Furthermore, we also propose that RPA32 hyperphosphorylation, γH2AX, pATM, pHSP27 are candidate pharmacodynamic markers of chk1 inhibitor efficacy in HNSCCs that merit further investigations in follow-up preclinical studies or human clinical trials.

Acknowledgements

The authors thank Dr. Tobias Meyers lab for providing DHB-mVenus lentiviral construct, thank Eli Lilly for providing prexasertib (Material Transfer Agreement # 10024), Dr. Asha Multani and Dr. Sen Pathak for their help with metaphase spread experiments, and our various donors for all their generous contributions.

References

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Table 1 Sensitivity of HNSCC cell lines to prexasertib The prexasertib IC50 for each HNSCC cell line is shown in columns along with corresponding drug sensitivity classification (see result section for details on sensitivity classification). TP53 mutations were classified according to the EA score of the most impactful mutation present as either High risk (EA>75), Low risk (EA<75), or N/A (not applicable, wt p53 or splice mutation).

IC50 EA p53 Drug Sensitivity Cell lines prexasertib mutation Classification (nmol/L) Classification MDA1386LN 1.441 Hypersensitive Low risk MDA1386TU 1.984 Hypersensitive Low risk UMSCC22B 2.205 Hypersensitive Low risk UMSCC22A 2.306 Hypersensitive Low risk UMSCC4 2.552 Hypersensitive High risk 1483 2.763 Hypersensitive High risk UMSCC1 2.869 Hypersensitive others 183 3.046 Hypersensitive others HN5 3.224 Hypersensitive High risk MDA1586 5.122 Moderately sensitive High risk JHU022 5.171 Moderately sensitive High risk PJ34 5.802 Moderately sensitive Low risk Ca922 6.272 Moderately sensitive High risk MDA686TU 6.707 Moderately sensitive Low risk 584A2 6.768 Moderately sensitive others MDA686LN 6.791 Moderately sensitive Low risk UMSCC85 7.236 Moderately sensitive N/A (wt p53) JHU029 7.863 Moderately sensitive High risk HMS001 7.925 Moderately sensitive N/A (wt p53) JHU011 8.926 Moderately sensitive others HOSC1 9.973 Moderately sensitive others PCI15A 9.406 Moderately sensitive High risk MDA1986LN 10.19 Moderately sensitive others TR146 10.16 Moderately sensitive High risk UMSCC14B 12.13 Least Sensitive High risk PCI15B 11.5 Least Sensitive High risk MSK922 11.44 Least Sensitive High risk HN4 12.54 Least Sensitive others UMSCC25 13.79 Least Sensitive others DETROIT562 14.12 Least Sensitive High risk UMSCC17B 14.93 Least Sensitive High risk HN30 14.91 Least Sensitive N/A (wt p53) UMSCC17A 15.95 Least Sensitive N/A (wt p53) UMSCC6 15.88 Least Sensitive High risk PCI24 16.48 Least Sensitive High risk UMSCC47 16.68 Least Sensitive N/A (wt p53) UMSCC14A 15.93 Least Sensitive High risk HN31 15.89 Least Sensitive High risk UMSCC3 19.99 Least Sensitive High risk FADU 22.44 Least Sensitive High risk OSC19 22.76 Least Sensitive others SCC61 24.22 Least Sensitive Low risk UMSCC33 25.66 Least Sensitive High risk Cal27 >40 Least Sensitive High risk UMSCC19 >40 Least Sensitive others SQCCY1 >40 Least Sensitive High risk MDA1686 >40 Least Sensitive High risk Median 9.973

Figure Legends

Figure 1. A significant subset of HNSCC cell lines is acutely sensitive to Chk1 inhibition. A) HNSCC cells seeded in 96-well plates were treated with prexasertib at various concentrations (diluted in 0.1% DMSO) in quadruplicate for 2 days. At the end of drug treatment, cells were supplied with fresh media and MTT optical density values were obtained at day 5. Cell line IC50 value for prexasertib was determined by plotting the absorbance/cell proliferation vs concentration graph.

B) Cells representing left end of the sensitivity spectrum in Figure 1A were termed “more sensitive” while those representing right end of the spectrum were termed “less sensitive” cells. More sensitive (UMSCC1, 183, UMSCC4, and MDA1386LN) and less sensitive (HN31, FADU, and Cal27) cells seeded for clonogenic assays were exposed to different concentrations of prexasertib for 2 days. At the end of drug treatment, colonies were allowed to form for 12-14 days, after which they were stained, and counted. Surviving colonies under the treatments were normalized to control and IC50 values were determined by plotting surviving fraction versus log prexasertib concentration from three independent experiments.

C) Equimolar doses of prexasertib inhibits Chk1 activity in both more sensitive as well as less sensitive cells. UMSCC1, 183 (more sensitive) and HN31, FADU (less sensitive) cells were pretreated with DMSO (0.1%) or prexasertib at 3 nmol/L, 6 nmol/L or 15 nmol/L for 2 hrs. At 2 hrs, a batch of DMSO or prexasertib pretreated cells were then exposed to UV irradiation (75 mJ/m2) and immediately supplied with media containing DMSO or prexasertib. After 1.5 hrs post UV exposure, cell lysates under each treatment condition were collected and western blot was performed to probe for pChk1 (S296) levels. The experiment was repeated at least twice. β-actin was used as loading control.

D) UMSCC1, 183 (more sensitive) and HN4, HN31 (less sensitive) cells were treated with DMSO (0.1 %) or prexasertib (3 nmol/L) for 24hr and 48hrs. Cells were harvested at these time points, fixed in 70% ethanol overnight, stained with propidium iodide and processed for flow cytometry analysis. The mean fraction of cells in each cell cycle phase was calculated from three independent experiments and plotted.

E) Western blot was performed to confirm siRNA knockdown of Chk1 and Chk2 in all four cell lines using their cell lysates collected at 30 hrs post electroporation. β-actin was used as loading control.

F) Please refer to the result section for definition of hypersensitive and least sensitive cells. UMSCC1, 183 (Hypersensitive) and FADU, HN31 (least sensitive) cells were electroporated with control scrambled siRNA or siRNA targeting Chk1 or Chk2 and immediately seeded (at equal density) for MTT assay. At 5 days post electroporation, MTT optical density (OD) readings were determined and the Net OD or the difference between the day five and day zero OD readings was plotted. Experiments were repeated at least twice. *, Significantly lower than scramble siRNA, using two tailed Student t test. n.s, differences not statistically significant (p>0.05).

Figure 2. Chk1 inhibition decreased replication fork velocity selectively in hypersensitive cells

A) Experimental schema for DNA fiber assay is shown. UMSCC1 (hypersensitive) and FADU (least sensitive) cells were pre-incubated with the indicated treatments for 90 min and sequentially labelled with IdU and CldU for 25 min each in presence of DMSO or prexasertib (3nmol/L). Labelled DNA fibers detected with fluorescent antibodies and imaged.

B) Representative DNA fiber image for UMSCC1 and FADU cells under each treatment condition is depicted. The distribution plot of fork progression rates for both cell lines under each treatment condition is shown. Greater than 150 fibers were counted under each treatment and replication fork progression rate was calculated by dividing replication track length by the pulse time.

C) The tabulated results show median fork progression rate for both cells under each treatment condition. For both cell lines, the median fork progression rate across treatment conditions was compared using Mann-Whitney test and p values were derived.

Figure 3. DNA damage and replication stress markers are selectively induced at higher levels in the hypersensitive cells upon Chk1 inhibition.

A) HN31 and HN4 (least sensitive cells) and UMSCC1 and 183 (hypersensitive cells) were treated with DMSO or prexasertib (3 nmol/L) and cell lysates were collected at 24hrs. Western blotting

was performed using these cell lysates and the levels of cell signaling molecules in the DNA damage response pathway under each condition was assessed. Experiment was repeated at least two times. β-actin was used as loading control. Fold expression changes for Gamma H2AX and pATM (S1981) markers under treatment conditions are shown underneath the blots.

B) UMSCC1 (hypersensitive) and HN31 (least sensitive) cells were treated with DMSO or prexasertib 3 nmol/L for 24hrs. Metaphase spreads were prepared and analyzed for chromosomal aberrations that included chromosome and chromatid type breaks and fusions. A total of 35 metaphases were analyzed from each sample and the experiment was repeated three times. Percentage of cells containing chromosomal aberrations including breaks and fusions under each condition are plotted on the right. Experiment was repeated three times. Representative images of metaphase spread for UMSCC1 and HN31 cells under DMSO or prexasertib treatment condition are shown. Black arrow indicate chromosomal breaks. *, significantly higher percentage than untreated cells using Chi-squared test; n.s, differences not statistically significant.

Figure 4. Hypersensitivity to Chk1 inhibition correlates with high level deletions in p16

A) Diploid adjusted copy number and RNA expression values for p16 and p15 were compared among hypersensitive, moderately sensitive, and least sensitive HNSCC cell lines derived from unique patients. Statistical differences were determined with either a Dunn’s non-parametric multiple comparison test (copy number) or a parametric Holm-Sidak multiple comparison (mRNA).

B) Protein expression for p16 measured by RPPA was compared among hypersensitive, moderately sensitive, and least sensitive HNSCC cell lines. Statistical differences were determined with a Holm-Sidak multiple comparison test.

C) UMSCC22A cells transfected with doxycycline-inducible p16 expression plasmid (UMSCC22A- p16) were exposed to the indicated doses of doxycycline and cell lysates were collected at 48hrs to assess p16 protein expression levels by western blot.

D) UMSCC22A-p16 cells treated with doxycycline for 24hrs were subsequently treated with the combination of doxycycline and DMSO or prexasertib for another 24 hrs. Cells were then

harvested and processed for flow cytometry analysis. The S phase fraction of cells under indicated treatments is shown.

E) UMSCC22A-p16 cells were treated w/o doxycycline (125 ng/ml) for 24hrs and subsequently exposed to doxycycline + DMSO or prexasertib (3 nmol/L) for 90 min and then sequentially labelled with IdU and CldU for 25 min each while still under treatment. DNA fibers were spread on slides, fixed, incubated with fluorescent antibodies to IdU and CldU and imaged. Representative DNA fiber image for UMSCC22A-p16 under each treatment condition is shown. A minimum of 140 fibers were counted under each treatment and replication fork progression rate was calculated by dividing replication track length by the pulse time. The distribution plot of fork progression rates under each treatment condition is presented as mean + SD. Experiment was repeated at least twice. p values were obtained by two way ANOVA and Bonferroni’s multiple comparison test.

F) UMSCC22A-p16 cells were seeded at equal density in quadruplicates in 96 well-plates. The next day, a MTT based colorimetric assay was performed to obtain baseline OD readings. Cells were exposed to doxycycline for 24hrs and subsequently treated with the combination of doxycycline and DMSO or prexasertib (3 nmol/L) for 48hrs. Cells were fed with fresh media after drug treatments. Three days later, OD readings were determined again. The Net OD or the difference between the last day and day zero reading under each condition was plotted as shown. Experiment was repeated at least twice. *, significantly lower than DMSO (-Doxy) using Two way ANOVA and Bonferroni’s multiple comparison’s test.

Figure 5. Chk1 inhibition selectively boosts Cdk2 activity in hypersensitive cells.

A) Cells in early S phase were identified based on the pattern of DNA replication (diffuse pattern of EdU incorporation), and their corresponding percentages with different DHB-mVenus staining patterns (nucleus only (N), cytoplasm only (C), nucleus and cytoplasm (C&N)) were plotted. Blue arrows inside Edu compartment point to early S phase cells with cytoplasmic and nuclear (C&N) staining pattern of DHB-mVenus, Filled-in orange arrows point to early S phase cell with Cytoplasmic only (C) staining pattern, hollow orange arrows point to late S phase cells with Cytoplasmic only (C) staining pattern. A minimum of 120 cells were assessed under each group

and group comparisons were made using Chi-Squared test. *, significantly lower than DMSO treated cells; **, significantly greater than DMSO treated cells; n.s, differences not statistically significant.

B) UMSCC1-mVenus and HN31-mVenus cells were exposed to DMSO or prexasertib (3 nmol/L) for 6hrs. Cells were fixed in 4% paraformaldehyde, permeabilized, and stained with DAPI (10 μM). Cells under each treatment condition were imaged in an automated high throughput manner. For data processing, nuclear and cytoplasmic regions were segmented using Perkin Elmer’s InForm software. A nuclear mask was obtained from the DAPI signal in the nuclear space and cytoplasmic mask was obtained from the Alexa-488 (DHB-mVenus) signal in the cytoplasmic space. The DNA content plots under each treatment were generated from the integrated nuclear DAPI intensity values and overlaid. The early S phase region was gated (marked in red) and the integrated intensity values of Alexa-488 (DHB-mVenus) from the cytoplasmic and nuclear compartments for the corresponding cells were used to plot the C/N ratio. *, significantly greater than DMSO treated cells using two tailed student’s t test; n.s, differences not statistically significant.

Figure 6. Roscovitine cotreatment mitigates the hypersensitivity phenotypes associated with Chk1 inhibition and rescues the hypersensitive cells from Chk1 inhibition-induced lethality

A) UMSCC1 and 183 (hypersensitive) cells were seeded for clonogenic assay were pretreated with DMSO or roscovitine 5 μmol/L for 2hrs. Pretreated cells were then exposed to roscovitine alone or roscovitine plus prexasertib (3nmol/L or 6 nmol/L) combination treatment for 48hrs. Cells were then washed, fed with fresh media and allowed to form colonies for 10-12 days. Colonies were stained with crystal violet, counted and normalized to control treatment and plotted in the graph. The experiment was repeated at least three times. Representative images of colonies under each treatment condition for 183 cells are shown. *, significantly greater than prexasertib treated cells at 3nmol/L and 6 nmol/L dose, respectively by one way ANOVA and bonferroni’s multiple comparison test.

B) UMSCC1 (hypersensitive) cells were electroporated with scrambled, siRNA targeting Cdk1, Cdk2 or their combination and immediately seeded at equal density for clonogenic assay. 27 hrs post

electroporation, cells were exposed to DMSO or prexasertib (3nmol/L) for 48hr. After treatment, cells were allowed to form colonies for 10 -12 days and stained with crystal violet. Colonies were then counted, normalized to scrambled, untreated cells and plotted on the graph as shown. Experiment was repeated at least three times. *, **, significantly lower than scrambled or non-targeting siRNA cells; ***, significantly lower than cells with cdk1 knockdown alone; n.s, differences not statistically significant, all using one way ANOVA and Bonferroni’s multiple comparison test;. UMSCC1 cells were electroporated with scrambled, siRNA targeting Cdk1, Cdk2 or their combination and seeded for western blot and cell lysates were harvested 27hrs later. Western blot was performed to confirm knockdown of cdk1 and cdk2 in UMSCC1 cells. Experiment was repeated at least two times.

C) UMSCC1 and 183 cells were pretreated with DMSO or roscovitine 10 μmol/L for 2hrs and then were exposed to roscovitine alone or roscovitine plus prexasertib (3nmol/L) for 24 hrs after which they were fixed overnight in 70% ethanol, stained with propidium iodide and processed for cell cycle analysis. The experiment was repeated three times. Representative images of cell cycle profile under each treatment are shown and fraction of cells in each cell cycle phase were quantified and plotted.

D) Experimental schema for the DNA fiber assay is shown. UMSCC1 cells were pre-incubated with DMSO or roscovitine (5 μmol/L) for 2 hrs and subsequently exposed to prexasertib (3 nmol/L) for 90 min and then sequentially labelled with IdU and CldU for 25 min each while still under treatment. DNA fibers were fixed, incubated with fluorescent antibodies and imaged. Representative DNA fiber image for UMSCC1 under each treatment condition is shown. A minimum of 180 fibers were counted under each treatment and replication fork progression rate was calculated by dividing replication track length by the pulse time. The distribution plot of fork progression rates under each treatment condition is shown. The tabulated results show mean fork progression rate + SD under each treatment condition. Experiment was repeated at least twice. p values were obtained by one way ANOVA and Bonferroni’s multiple comparison test.

E) UMSCC1 (hypersensitive) cells were pretreated with DMSO or roscovitine (5 μmol/L) for 2hrs. After 2hrs, roscovitine pretreated cells were exposed to DMSO or roscovitine plus prexasertib (3nmol/L) for 24hrs. At the same time, DMSO pretreated cells were left untreated or exposed to prexasertib (3nmol/L) alone. Cell lysates were collected at 24hrs, and western blot was performed to probe for

the levels of pChk1 (S345), Chk1, H2AX (S139), and RPA32. Asterisk indicate RPA32 hyperphosphorylated band. β- actin was used as loading control. Experiment was repeated at least twice.

CDKN2A/p16 deletion in head and neck cancer cells is associated with Cdk2 activation, replication stress, and vulnerability to Chk1 inhibition

Mayur A Gadhikar, Jiexin Zhang, Li Shen, et al.

Cancer Res Published OnlineFirst December 11, 2017.

Updated version Access the most recent version of this article at: doi:10.1158/0008-5472.CAN-17-2802

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