University of Groningen Kinome directed target discovery and validation in unique ovarian clear cell carcinoma models Caumanns, Joost

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University of Groningen

Kinome directed target discovery and validation in unique ovarian clear cell carcinoma models

Caumanns, Joost

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Publication date: 2019

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Caumanns, J. (2019). Kinome directed target discovery and validation in unique ovarian clear cell carcinoma models. University of Groningen.

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526956-L-sub01-bw-Caumanns 526956-L-sub01-bw-Caumanns 526956-L-sub01-bw-Caumanns 526956-L-sub01-bw-Caumanns Processed on: 7-12-2018 Processed on: 7-12-2018 Processed on: 7-12-2018

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CHAPTER 2

ARID1A mutant ovarian clear cell

carcinoma: A clear target for synthetic

lethal strategies

Joseph J. Caumanns

1

_{, G. Bea A. Wisman}

1

_{, Katrien Berns}

3

_{Ate G.J.}

van der Zee

1

_{and Steven de Jong}

2

1_{Department of Gynecologic Oncology and}2_{Department of Medical Oncology,}

Cancer Research Centre Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands.

3_{Division of Molecular Carcinogenesis, the Netherlands Cancer Institute,}

Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Biochim Biophys Acta. 2018;1870:176-184

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CHAPTER 2

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INTRODUCTION

ATP dependent chromatin remodeling is an epigenetic process regulating gene transcription in which chromatin structure can be coordinated through mobilization of nucleosomes. The evolutionary conserved ATP dependent chromatin remodelers consist of four subclasses. These are Imitation SWI (ISWI), INO80, nucleosome remodeling and histone GHDFHW\ODVH0L&+'185'0L&+' DQGVZLWFKVXFURVHQRQIHUPHQWLQJ6:, SNF) and are involved in diverse cellular SURFHVVHVVXFKDVWLVVXHGLႇHUHQWLDWLRQ proliferation and DNA repair (1). While all chromatin remodelers contain ATPase GRPDLQV DGGLWLRQDO VXEXQLWV GLႇHU SHU subclass and are important for modulation of ATPase activity and chromatin FRPSOH[UHFUXLWPHQWRQWRWLVVXHVSHFL¿F JHQRPLF ORFL 6:,61) FKURPDWLQ remodeling complexes are implicated in many stages of pluripotency and WLVVXH GLႇHUHQWLDWLRQ DORQJ PDPPDOLDQ GHYHORSPHQW &RPSDUHG WR WKH 6:,

SNF subclass, the role of ISWI, INO80 DQG 0L&+' FKURPDWLQ UHPRGHOLQJ complexes in these processes is limited EXW VXSSOHPHQWDU\ WR 6:,61) IRU D review see Hota et al %$) 6:, SNF chromatin remodeling complexes contain multiple subunits with mutual exclusive characteristics, which include the DNA targeting subunits ARID1A and ARID1B, and the ATPase subunits SMARCA2 and SMARCA4 (Fig. 1). These mutual exclusive members GLVFULPLQDWH %$) 6:,61) FRPSOH[HV IURP FRXQWHUSDUW 3%$) 6:,61) complexes that contain SMARCA4 but not the other three proteins. BAF and 3%$)6:,61)FRPSOH[HVKDYHGLVWLQFW regulatory roles in lineage development. )RU LQVWDQFH %$) VSHFL¿F 60$5&$ plays a key role in smooth muscle IRUPDWLRQ ZKLOH WKH 3%$) VSHFL¿F subunit ARID2 is important for coronary

PRUSKRJHQHVLV 0RUH 6:,61)

subunits have been shown to coordinate

VSHFL¿F GHYHORSPHQWDO SURFHVVHV

(2). Therefore, it is conceivable that

ARID1A

mutant ovarian clear cell carcinoma: A clear target

for synthetic lethal strategies

Joseph J. Caumanns, G. Bea A. Wisman, Katrien Berns, Ate G.J. van der Zee and Steven de Jong

SWI/SNF chromatin remodeling complexes play an important role in the epigenetic regulation of chromatin structure and gene transcription. Mutual exclusive subunits in the SWI/SNF complex include the DNA targeting members ARID1A and ARID1B as well as the ATPases SMARCA2 and SMARCA4. SWI/SNF complexes are mutated across many cancer types. The highest mutation incidence is found in ARID1A, primarily consisting of deleterious mutations. Current advances have reported synthetic lethal interactions with the loss of ARID1A in several cancer types. In this review, we discuss targets that are only important for tumor growth in an ARID1A mutant context. We focus on synthetic lethal strategies with ARID1A loss in ovarian clear cell carcinoma, a cancer with the highest ARID1A mutation incidence (46-57%). ARID1A directed lethal strategies that can be exploited clinically include targeting of the DNA repair proteins PARP and ATR, and the epigenetic factors EZH2, HDAC2, HDAC6 and BRD2.

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SYNTHETIC LETHAL STRATEGIES FOR ARID1A MUTANT OCCC

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describes a relation between two genes in which cells remain viable after loss of either gene alone but loss of both genes will result in a lethal phenotype (16). Synthetic lethal targets, including proteins involved in DNA repair and epigenetic regulation are reviewed, IRFXVLQJRQWDUJHWVUHFHQWO\LGHQWL¿HGLQ ARID1A mutant OCCC.

2. Role of ARID1A in ovarian clear cell carcinoma

Mutations in ARID1A are often heterozygous nonsense or frameshifts that are not enriched in hotspot sites (9, 10). ARID1A mutations, homo- or heterozygous, coincides with loss of ARID1A protein expression in OCCC. 7KLV VXJJHVWV KDSORLQVXႈFLHQF\ RU WKH occurrence of other mechanisms that are responsible for complete loss of protein expression, such as epigenetic silencing, mutations in non-coding regions or post transcriptional mechanisms (9, 17-20). Additionally, two studies described loss of ARID1A protein expression in precursor lesions of OCCC, i.e. ovarian endometriosis, indicating that ARID1A loss is an early event in progression to OCCC (21, 22). Two studies described D VSHFL¿F VXEXQLW PXWDWLRQ FDXVHV

FKDQJHVLQ6:,61)FKURPDWLQELQGLQJ at typical transcriptional enhancer sites, which ultimately results in loss of GLႇHUHQWLDWLRQ SRWHQWLDO DQG GULYHV FHOOV into a proliferative state (3). Over 20% of cancers contain a mutation in at least one of the members of the 15-subunit %$) 6:,61) FRPSOH[ KHUHLQDIWHU UHIHUUHG WR DV 6:,61) (VSHFLDOO\ ARID1A and ARID1B and SMARCA2 and SMARCA4 have high mutation frequencies and are suggested to be driver mutations in multiple cancers 7KH PXWDWLRQ LQFLGHQFH LQ 6:, SNF subunits varies per tumor type, LQGLFDWLYH IRU GLVWLQFW UROHV RI 6:, SNF complexes in human tissues. For LQVWDQFH $5,'$ GH¿FLHQW PLFH DUH resistant to hepatocellular carcinoma initiating agents while mice with established hepatocellular carcinoma showed enhanced metastasis upon ARID1A loss (7). Conversely, ARID1A mutations promote colorectal tumor

formation, indicating the context

GHSHQGHQW HႇHFW RI $5,'$ ORVV ARID1A is the most frequently mutated 6:,61)FRPSOH[PHPEHU7KHKLJKHVW alteration incidence, 46-57%, is found in ovarian clear cell carcinoma (OCCC) (9-11). Other tumor types harboring ARID1A mutations comprise uterine

endometrioid carcinoma (47-60%),

ovarian endometrioid carcinoma (30%), gastric cancer (29%), colorectal cancer (5-10%) and pancreatic cancer (3-5%) (6, 12-14). Tumors with mutations in ARID1B include OCCC (18%), colorectal cancer and gastric cancer (5-10%) (Fig. 2). Mutations in SMARCA2 are found in colorectal cancer, lung cancer (3-5%) and OCCC (2%). Mutations in SMARCA4 are found in melanoma, lung cancer (5-10%) and OCCC (5%) (6, 15) (Fig. 3).

In this review, we discuss recent developments in strategies that take advantage of cellular dependencies VSHFL¿F IRU ARID1A mutant cancers. This concept, named synthetic lethality,

Figure 1 | SWI/SNF complex members. ARID1A

and ARID1B are mutual exclusive core compo-QHQWV LQ WKH PDPPDOLDQ %$) 6:,61) FKURPD-tin remodeling complex. Other core members are shown in turquoise and exchangeable components in yellow. SMARCD1/2/3 SMARCD1/2/3 ACTL6 ACTL6 SMARCE1 SMARCMARCE1 DPF2DPF2 BRD9 BRD9 SS18SS18 SMARCA2/4 SMARCA2/MARCA2/4 SMARCC1

S ARCCMAR 1 SMARCC2SMARCCMAR 2

SMARCB1 SMARCB1C BCL11A/BC / BCL11A/B ARID1A/BRID1A/B/ A

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CHAPTER 2

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SURPRWHG HSLWKHOLDO GLႇHUHQWLDWLRQ DQG metastasis (30). Moreover, Chandler et al. demonstrated that ovarian tumor formation only occurred in mice with concurrent homozygous knockout of ARID1A and PIK3CAH1047R_missense mutation. These tumors manifested an OCCC like histopathology and gene expression signature. Furthermore, a PHFKDQLVWLFOLQNZDVLGHQWL¿HGEHWZHHQ ARID1A loss and PIK3CA activation with the induction of cytokine expression, LQFOXGLQJ,/YLD1)ڡ%VLJQDOLQJ In vitro and in vivo suppression of IL-6 reduced the tumor cell proliferation, presenting IL-6 blocking as potential synthetic lethal strategy in an ARID1A and PIK3CA mutant OCCC background (32).

3. Mutual exclusive roles for ARID1A and ARID1B

7KH 6:,61) VXEXQLW HQFRGLQJ JHQHV ARID1A and ARID1B share 60% sequence identity but are thought to have disparate roles in cell cycle regulation (33). ARID1B mutations are less prevalent in cancer with fewer a worse progression-free survival in

$5,'$ GH¿FLHQW 2&&& SDWLHQWV However, literature consistently showed that overall survival in OCCC is not predicted by ARID1A status (11, 23-25).

ARID1A_{or ARID1A}_knockout causes lethality in early embryonic mouse development (26). In contrast,

depletion of ARID1A expression

induced proliferation in ovarian surface epithelium cells. Another study showed that knockdown of ARID1A provided

phenotypic changes associated

with neoplastic transformation in an immortalized endometriosis cell line (27). Upon ARID1A knockdown the expression of 99 genes was up or downregulated. Many of these genes are also dysregulated in OCCC tumors (28). 6WLOO$5,'$ ORVV LWVHOI LV QRW VXႈFLHQW to induce tumorigenesis in the ovaries of conditional Cre-Lox mouse models. Only mice with combined ARID1A and PTEN loss developed ovarian hyperplasia, which progressed to tumors in 59% (29). Another study showed that additional ARID1A_{or ARID1A}_{knockout in} APC and PTEN null mice actually delayed ovarian tumor formation but

ARID1A

Lymphoid Diffuse Large B-cell LymphomaRecurrent and Metastatic H&N Cancer Metastatic esophagogastric cancer TCGA data for Esophagus-Stomach CancersPancreatic Cancer Cancer Cell Line EncyclopediaCholangiocarcinoma Uterine CarcinosarcomaNCI-60 Cell Lines Bladder Cancer, Plasmacytoid VariantAdenoid Cystic Carcinoma Stomach AdenocarcinomaBladder Cancer Bladder Urothelial Carcinoma Bladder Urothelial CarcinomaStomach Adenocarcinoma Uterine Corpus Endometrial Carcinoma Uterine Corpus Endometrial Carcinoma

0 10 20 30 40 Multiple alterations Mutation Deletion Amplification Alteration frequency (%) ARID1B

Adenoid Cystic Carcinoma Neuroendocrine Prostate CancerCholangiocarcinoma Stomach Adenocarcinoma The Metastatic Breast Cancer ProjectBreast cancer patient xenografts

0 10 20 30

Mutation Deletion Amplification

Alteration frequency (%) 40

Figure 2 | ARID1A and

ARID1B alterations in

can-cer. Alteration frequencies of

ARID1A and ARID1B in

pub-lished and provisional data-sets incorporated in cBioPor-tal are depicted with a 10% FXWRႇ KWWSFELRSRUWDORUJ downloaded 3-10-2017). Of note, ARID1A and ARID1B mutations are commonly found in several cancer types, but not always displayed due WRWKHFXWRႇ

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cell lines (36). Subsequently, Helming et al. demonstrated a reduced proliferation in two ARID1A mutant OCCC cell lines after shRNA induced ARID1B loss. They found a destabilization of full size 6:,61) FRPSOH[HV DIWHU ORVV RI ERWK proteins, suggesting that depletion of LQWDFW6:,61)FRPSOH[HVLVUHVSRQVLEOH for the observed synthetic lethality. Co-mutations in ARID1A and ARID1B do occur but never biallelic in both genes, indicating some ARID1 function is essential for cell survival of both cancer and normal cells (36).

4. ARID1A-directed synthetic lethality Several studies have shown that ARID1A directed synthetic lethality can be attained through diverse molecular mechanisms. These synthetic lethal interactions with ARID1A mutations go beyond direct targeting of ARID1B. 4.1 Lethal relationship between ARID1A loss and inhibition of the DNA damage response

Besides ARID1A’s regulatory role in deleterious mutations as compared to

ARID1A (Fig. 2). In 2007, Nagl et al. reported opposing roles for ARID1A and ARID1B in regulating proliferation in osteoblasts. They found that ARID1B had a more proliferation inducing role via MYC and Cyclin E activation as compared ZLWK$5,'$$5,'$ORVVPRGL¿HV chromatin accessibility in colorectal cancer cells and this accessibility is IXUWKHUPRGL¿HGE\ORVVRI$5,'%,QWKH presence of wild-type ARID1A, ARID1B ORVVGLGQRWKDYHDQHႇHFWRQFKURPDWLQ DFFHVVLELOLW\LQGLFDWLQJDGRPLQDQWHႇHFW of ARID1A. It was reported that ARID1B in the absence of ARID1A facilitates expression of proliferative genes involved LQ3,.$.7P725DQG(5%%UHFHSWRU tyrosine kinase signaling in colorectal carcinoma and OCCC cells (35). These ¿QGLQJV K\SRWKHVL]H WKDW UHGXQGDQW LQFRUSRUDWLRQRI$5,'%LQUHVLGXDO6:, 61) FRPSOH[HV LQ $5,'$ GH¿FLHQW cells could stimulate proliferation. The consecutive discovery that ARID1A PXWDQWWXPRUVDUHVSHFL¿FDOO\YXOQHUDEOH to ARID1B loss was based on the Achilles project, a loss of function genetic screen database, which include over 200 cancer

SMARCA2

SMARCA4

Bladder Urothelial Carcinoma Breast cancer patient xenograftsNon-Small Cell lung Cancer Ovarian Serous CystadenocarcinomaBladder Urothelial Carcinoma Lung Adenocarcinoma Uterine Corpus Endometrial CarcinomaCancer Cell Line Encyclopedia Ovarian Serous CystadenocarcinomaNCI-60 Cell Lines Uterine Corpus Endometrial CarcinomaPre-treatment metastatic melanoma Uterine Carcinosarcoma Neuroendocrine Prostate Cancer

0 10 20 30 Multiple alterations Mutation Deletion Amplification Alteration frequency (%) 40

TCGA data for Esophagus-Stomach CancersStomach Adenocarcinoma Stomach Adenocarcinoma Adenoid Cystic Carcinoma Bladder Urothelial Carcinoma Bladder Urothelial Carcinoma Cancer Cell Line Encyclopedia Paired-exome sequencing of acral melanomaBreast cancer patient xenografts NCI-60 Cell Lines Neuroendocrine Prostate Cancer Malignant Peripheral Nerve Sheath Tumor

0 10 20 30 Alteration frequency (%) Multiple alterations Mutation Deletion Amplification 40

Figure 3 | SMARCA2 and

SMARCA4 alterations in cancer. Alteration

fre-quencies of SMARCA2 and

SMARCA4 in published

and provisional datasets incorporated in cBioPortal are depicted with a 10% FXWRႇ KWWSFELRSRUWDORUJ downloaded 3-10-2017). Of note, SMARCA2 and

SMARCA4 mutations are

commonly found in several cancer types, but not al-ways displayed due to the FXWRႇ

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CHAPTER 2

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cells to DSB inducing treatments such as oxaliplatin and cisplatin (38, 40). Two studies have investigated synthetic lethality approaches based on targeting of DDR proteins in ARID1A mutant cancers. Shen et alLGHQWL¿HGDUROHIRU ARID1A in DSB repair as binding partner of ATR, a DDR central regulator involved in DSB and single strand DNA breaks (39). With chromatin immunoprecipitation assays they found ARID1A to be enriched at chromatin regions close to DSBs, a recruitment that was lost upon ATR inhibition. Phenotypically, ARID1A stopcodon introduction in HCT116 colorectal carcinoma cells resulted in LPSDLUHG *0 FKHFNSRLQW FRQWURO XSRQ irradiation-induced DSBs. Cells lacking ARID1A more frequently re-entered the cell cycle after irradiation as compared with control cells. The phosphorylation of ATR and CHK1, another DDR protein 6:,61) FRPSOH[ ELQGLQJ WR '1$ LW

is also involved in DNA double-strand EUHDN '6% UHSDLU ,QLWLDOO\ WKH 6:, SNF ATPase subunits SMARCA2 and SMARCA4 were described to interact ZLWK WKH '6% ORFDOL]LQJ SURWHLQ Ȗ+$; upon DSB formation, suggesting a role for 6:,61)LQWKH'1$GDPDJHUHVSRQVH (DDR) (37). Recently, ARID1A and ARID1B were found to localize to DSBs and facilitate non-homologous end joining (NHEJ) and ARID1A was assigned a role in homologous recombination (HR) (38, 39). NHEJ is the more error prone DSBs repair mechanism compared to HR. ARID1A and ARID1B recruit the NHEJ proteins KU70 and KU80 to the site of DNA damage and are thus involved in this type of DSB repair at an early stage. Downregulation of ARID1A or ARID1B sensitized osteosarcoma cells and immortalized pancreatic ductal epithelial

SWI/SNF ARID1A ATR Inhibition of PI3K/AKT pathway DNA damage repair ROS reduction TOP2A Chromatin localization PIK3IP1 PI3K ANXA1 AKT ROS HDAC6 Apoptosis regulation P53 P53 Ac AKT P

Figure 4 | ARID1A implicated mechanisms with synthetic lethal opportunities after ARID1A loss.

$5,'$LWVHOIRULQFRUSRUDWHGLQWKH6:,61)FKURPDWLQUHPRGHOLQJFRPSOH[LVLQYROYHGLQPXOWLSOHRQ-cogenic suppressive processes. Therapeutic targeting of these indicated mechanisms were found to be lethal in an ARID1A mutant background.

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of ARID1APXWDQW729*2&&&FHOOV In this study, it was also demonstrated that ARID1A loss in HCT116 cells resulted in accumulation of cells in *0 ,Q OLQH ZLWK WKLV UHVXOW ARID1A mutant HCT116 xenografts showed reduced tumor growth. In the presence of ATR inhibitors, they found reduced accumulation of ARID1A mutant HCT116 FHOOVLQ*0DQGPXOWLSOHLQGLFDWLRQVRI chromosomal instability and apoptosis induction in these cells (41).

Previously, it was reported that SMARCA4 deprived mouse embryonic stem cells have decreased DNA localization of DNA topoisomerase 2-alpha (TOP2A), an enzyme important in DNA transcription and translation (42). Elaborating on this study, Williamson et al. found ARID1A mutant HCT116 cells to have decreased TOP2A DNA localization as well, indicating that 6:,61) FRPSOH[HV DUH LPSRUWDQW IRU stable function of TOP2A (41). Since ARID1A status did not determine 723$ H[SUHVVLRQ PRUH OLNHO\ 6:, SNF complexes directly bind to TOP2A via ARID1A, which is important for the localization of TOP2A to at least 12.000 genomic loci, as demonstrated earlier (Fig. 4) (42).

4.2 Epigenetic targeting and ARID1A synthetic lethality

Synthetic lethality between ARID1A loss and inhibition of multiple distinct epigenetic proteins was recently found in OCCC. The lethal interaction between ARID1A mutation and inhibition of polycomb repressive complex 2 (PRC2) catalytic subunit EZH2 resulted in the ¿UVW WKHUDSHXWLFDOO\ GUXJJDEOH WDUJHW IRU ARID1A mutant cancers (43). In contrast WR6:,61)FRPSOH[HVWKDWJHQHUDWHD more open chromatin structure, PRC2 closes chromatin by methylation of histone 3 lysine 27 (H3K27me3), which is associated with gene repression (44). Disruption of epigenetic chromatin LPSRUWDQW LQ *0 FKHFNSRLQW FRQWURO

was reduced in ARID1A mutant cells, indicating that ARID1A is involved LQ *0 SURJUHVVLRQ )XUWKHUPRUH ARID1A loss reduced localization of WKH ''5 DGDSWRU SURWHLQV Ȗ+$; DQG 53BP1 at the site of DSBs. Collectively, they reveal an important role for ARID1A to conduct ATR-mediated DDR signaling required for HR (Fig. 4). It is unclear if ARID1A alone or in complex with other 6:,61) PHPEHUV ORFDOL]HV WR '6%V and activates ATR and subsequent DDR. The involvement of ARID1A in DSB repair led Shen et al. to test for synthetic lethality of PARP inhibitors in ARID1A mutant cells as these inhibitors are known to be lethal in cells with DSB UHSDLU GH¿FLHQFLHV VXFK DV BRCA1/2 mutations. Multiple inhibitors of PARP provided toxicity in (BRCA wild-type) isogenic pairs of ARID1A-depleted non-transformed breast epithelial, breast epithelial carcinoma and colorectal carcinoma cells and a panel of ovarian carcinoma cell lines, showing more than three-fold reduced colony formation in ARID1A-depleted cell lines. Additionally, 3$53 WUHDWPHQW HႈFDF\ ZDV GHWHFWHG in (BRCA wild-type) ARID1A-depleted xenograft models of breast and colorectal cancer (39).

In another study by Williamson et al 51$L VFUHHQLQJ OLEUDULHV LGHQWL¿HG ARID1A loss as a genetic determinant of sensitivity to ATR inhibition in the triple negative (ER, PR and ERBB2 negative) breast cancer cell line HCC1143 and immortalized normal mammary epithelial cell line MCF12A (41). ARID1A loss in FRPELQDWLRQ ZLWK$75 LQKLELWLRQ E\ 9; ZDV FRQ¿UPHG WR EH RYHU WKUHH IROG PRUH HႇHFWLYH LQ PXOWLSOH FDQFHU lineages, including several OCCC cell OLQHV DQG DQ LVRJHQLF$5,'$GH¿FLHQW pair of the colorectal cancer cell line HCT116. Sensitivity to ATR inhibition was observed in xenograft models of the isogenic HCT116 cancer cell line pair and to a lesser extent in the xenograft model

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caused re-expression of PIK3IP1 in ARID1A mutant OCCC cells, which resulted in reduced proliferation and

LQFUHDVHGDSRSWRVLV9RULQRVWDW,&₅₀was

10-fold lower in ARID1A mutant (n=4) versus ARID1A wild-type (n=4) ovarian cancer cell lines. Similar results were observed with two primary cultures.

For clinical applicability it will be important to know if the synthetic lethal interaction between ARID1A loss and HDAC2 or EZH2 inhibition holds true in a larger set of OCCC models and in other tumor lineages.

To this end, EZH2 inhibition was found to be lethal in lung, adrenal gland and renal carcinoma cell lines with mutations LQ WKH 6:,61) FRPSRQHQWV ARID1A, PBRM1 and SMARCA4 (47). Kim et al. SURSRVH WKDW 6:,61) PXWDQW WXPRUV could generally depend on EZH2 activity. Their data suggests that EZH2 inhibition is only lethal when the EZH2-PRC2 complex interaction is destabilized, an HႇHFW ZKLFK *6. GLG QRW DFKLHYH in all cell lines. Based on the Achilles project they additionally showed RAS mutations to predict resistance to EZH2 LQKLELWLRQLQ6:,61)PXWDQWFDQFHUFHOO lines. Future inhibitors of EZH2 with the ability to disrupt EZH2-PRC2 complex interaction can presumably be applied in ARID1A, PBRM1 and SMARCA4 mutant cancers with wild-type RAS.

In other work by Bitler et al. shRNA interference of 11 histone deacetylases (HDACs) in ARID1A mutant OCCC led to the discovery of a lethal relationship between ARID1A loss and inhibition of HDAC6, an epigenetic protein known to deacetylate numerous substrates (48). Chemical inhibition of HDAC6 ZLWK$&< ZDV RQO\ HႇHFWLYH LQ DQ ARID1A mutant background in a panel of four ARID1A mutant versus four ARID1A wild-type OCCC cell lines (10-fold lower

IC₅₀) and in orthotopically transplanted

ARID1A mutant xenografts. They further LGHQWL¿HG$5,'$DVGLUHFWWUDQVFULSWLRQDO repressor of HDAC6. ARID1A loss remodeling is suggested to drive

oncogenesis in tumors that lack genomic instability (1). Therefore, Bitler et al. presumed ARID1A mutant OCCC depend on epigenetic mechanisms since genomic instability is lower compared with ARID1A wild-type OCCC. A panel of HDAC and EZH2 inhibitors was tested on RMG1 OCCC cells with ARID1A knockdown in 3D matrigel cultures. The highest tumor sphere reduction was achieved by GSK126, an inhibitor of EZH2 H3K27Me3 methyltransferase activity. Treated tumor spheres showed loss of the proliferation marker Ki67 and increased apoptosis. Similar results were found in xenografts. Approximately two-fold increase in GSK126 sensitivity was observed in ARID1A mutant (n=4) versus ARID1A wild-type (n=3) OCCC 3D cell line models. Gene expression SUR¿OLQJRIARID1A mutant cells treated ZLWK *6. LGHQWL¿HG PIK3IP1, a QHJDWLYH UHJXODWRU RI 3,.$.7P725 signaling, as a mechanistic link for the synthetic lethality between ARID1A loss and EZH2 inhibition (45). PIK3IP1 was found to be downregulated upon ARID1A loss. After ARID1A loss EZH2 methyltransferase induced H3K27Me3 methylation of the PIK3IP1 gene thus preventing expression of PIK3IP1, which LVWKHQIROORZHGE\LQGXFWLRQRI3,.$.7 mTOR signaling and proliferation (Fig. 4). GSK126-induced loss of the PIK3IP1 promoter H3K27Me3 mark resulted in PIK3IP1 expression and lethality, demonstrating the addiction of ARID1A mutant ovarian cancer cells to low PIK3IP1 levels (43). Consecutive work indicated that ARID1A mutant OCCC is selectively susceptible to inhibition of HDAC2, a known binding partner of the EZH2-containing PRC2 complex (46). As it turns out, HDAC2 only interacts with this complex in the absence of ARID1A. In line with the observations on EZH2 inhibition, knockdown of HDAC2 or chemical inhibition of HDAC2, using the QRQVSHFL¿F +'$& LQKLELWRU YRULQRVWDW

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previously described mutual exclusive relation between ARID1A and ARID1B can at least partially explain the lethal interaction between BET inhibitor mediated BRD2 inhibition and ARID1A loss (36). In addition to ARID1B UHGXFWLRQ PRUH 6:,61) PHPEHUV were downregulated at the mRNA level, potentially augmenting to the lethal SKHQRW\SHE\IXUWKHUUHGXFLQJWKH6:, 61)IXQFWLRQ7KLVVWXG\SURYLGHVD¿UVW opportunity to chemically inhibit ARID1B expression and utilize the ARID1A and ARID1B mutual exclusive properties in ARID1A mutant OCCC.

4.3 Synthetic lethality of ROS induction with ARID1A

Previous observations indicated that 6:,61) IXQFWLRQ LV UHTXLUHG IRU oxidative stress resistance in the model organisms Saccharomyces cerevisiae and Caenorhabditis elegans (52, 53). A comparison of about 140 drug sensitivities in ARID1A mutant versus wild-type human cancer cell lines in the “genomics of drug sensitivity in cancer” database (cancerrxgene.org), encompassing over 700 cancer cell lines, revealed the HSP90 inhibitor and reactive oxygen species (ROS) inducing DJHQWHOHVFORPRODVWKHPRVWGLႇHUHQWLDO sensitive drug (54). Only cell lines with ARID1A frameshift or nonsense mutations were retained in the analysis, potentially generating a bias considering the proportion of cancer patients with this type of ARID1A mutations (9). Subsequently, Kwan et al. proved elesclomol sensitivity to be higher in ARID1A mutants in a panel of 11 ovarian cancer cell lines, including four OCCC cell lines, and three endometrial cancer FHOO OLQHV (OHVFORPRO ZDV ¿YH WR VL[IROGPRUHHႇHFWLYHLQARID1A mutant cells compared with ARID1A wild-type cells and increased ROS levels and apoptosis. Re-expression of ARID1A induced resistance to elesclomol. led to re-expression of HDAC6, which

VSHFL¿FDOO\GHDFHW\ODWHSO\VLQHD residue known to regulate p53-mediated apoptosis (Fig. 4). Knockdown of TP53 reverted ACY1215 mediated apoptosis induction and proliferation inhibition in ARID1A mutant cells, illustrating that ARID1APXWDQW2&&&VSHFL¿F$&< sensitivity is p53 dependent. Additional data demonstrated that acetylated p53-lysine120 localizes to mitochondria and destabilizes mitochondrial membrane potential, presenting a mechanism for the lethal relationship between ARID1A loss and HDAC6 inhibition.

Recently, a fourth epigenetic

determinant of ARID1A mutation

dependent synthetic lethality was LGHQWL¿HGE\VK51$PHGLDWHGVFUHHQLQJ against all human kinases. In a panel of nine ARID1A PXWDQW YHUVXV ¿YH ARID1A wild-type OCCC cell lines, knockdown of the BET bromodomain member BRD2 HVWDEOLVKHG VSHFL¿F lethality in ARID1A mutant lines (49). BET bromodomains bind acetylated lysine histone tails and are involved in transcriptional regulation, but have also been reported to act as kinases (50, 51). As a result of high homology between WKH%(7PHPEHUV%5'DQG%5'7 only inhibitors that target all four proteins are available to date. The BET inhibitors -4DQGL%(7GHPRQVWUDWHGVSHFL¿F sensitivity in ARID1A mutant OCCC FHOOVZKLFKZDVYHUL¿HGLQWZRARID1A GH¿FLHQW LVRJHQLF 2&&& FHOO OLQH SDLUV in ARID1A mutant OCCC xenografts and patient-derived xenograft models. Explicitly, ARID1A mutant cells had over two-fold stronger growth reduction DIWHU-4WUHDWPHQWDVREVHUYHGLQWKH panel of nine ARID1APXWDQWYHUVXV¿YH ARID1AZLOGW\SH2&&&FHOOOLQHV-4 or shRNA mediated inhibition of BRD2 reduced the expression of ARID1B. Chromatin immunoprecipitation assays indicated direct transcriptional regulation of ARID1B expression by BRD2 at the ARID1B promoter. Therefore, the

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as determinants of dasatinib sensitivity. Dasatinib treatment was previously shown to induce p21 expression (56). ARID1A mutant xenograft growth of 729* ZDV UHGXFHG DIWHU GDVDWLQLE treatment, demonstrating therapeutic HႈFDF\ LQ YLYR 5HVXOWV IURP WKLV VWXG\ are consistent with previous research describing p21 to be regulated via ARID1A (57). However, Miller et al. did not indicate a mechanism through which dasatinib could result in p21 and RB1 induction. Regulation of these two proteins could be mediated by YES1 or other dasatinib targets.

4.5 Targeting of PI3K/AKT signaling in ARID1A mutant cancers

Results from the Achilles project demonstrated PIK3CA to be the second best hit for synthetic lethality with ARID1A loss (36). Accordingly, another analysis from the drug sensitivity in cancer database from Kwan et al. showed $=' DQ P725& LQKLELWRU WKDW WDUJHWV3,.$.7VLJQDOLQJGRZQVWUHDP as second best hit in ARID1A mutant cells in their screen (54). Both studies suggest a link between ARID1A loss DQG 3,.$.7P725 DFWLYDWLRQ 7KH co-existence of ARID1A mutations and DFWLYDWLRQ RI 3,.$.7P725 VLJQDOLQJ has been described in multiple cancer W\SHV6LJQL¿FDQWHQULFKPHQWRIPIK3CA activating mutations and PTEN loss were detected in ARID1A mutant endometrial

cancer. Moreover, knockdown of

ARID1A induced phosphorylation of the PI3K downstream target AKT (58). 3,.$.7 SDWKZD\ DFWLYDWLRQ RFFXUUHG after ARID1A depletion in MCF7 breast cancer cells. These cells gained AKT phosphorylation, and enhanced sensitivity to AKT and PI3K inhibitors upon ARID1A knockdown (59). In OCCC, concurrent PIK3CA activating mutations DQG 37(1 ORVV ZHUH VLJQL¿FDQWO\ associated with ARID1A mutations, but ARID1A knockdown did not induce ,PSRUWDQWO\NQRFNGRZQRIWKH6:,61)

subunits SMARCA4 and SNF5 induced elesclomol sensitivity in ARID1A wild-type OCCC cells, suggesting that loss of RWKHU6:,61)FRPSRQHQWVFDQSUHGLFW elesclomol sensitivity as well. ARID1A knockdown induced intracellular ROS levels in two ovarian cancer cell lines. A similar observation was made in OCCC tumor samples where low ARID1A expression was associated with high expression of 8-hydroxyguanosine, as a marker of oxidative stress (54). The V\QWKHWLF OHWKDO ¿QGLQJ E\ .ZDQ et al. is not supported by in vivo data and the mechanisms underlying ROS induction after ARID1A loss are inconclusive (Fig. 4).

4.4 ARID1A synthetic lethality approaches using dasatinib

In another drug screening study, 68 clinically approved or late-stage clinically developed inhibitors were screened on three ARID1A wild-type and eight ARID1A mutant OCCC cell lines (55). The SRC, ABL and C-KIT LQKLELWRUGDVDWLQLEJDYHWKHPRVWVSHFL¿F LQKLELWRU\HႇHFWLQARID1A mutant OCCC cells, demonstrating a more than two-fold increased sensitivity compared to ARID1A wild-type OCCC cells. Dasatinib synthetic lethality was consistently found after ARID1A knockdown in two OCCC cell lines, one breast cancer cell line and ARID1A knockout in the cell line HCT116. Using mass spectrometry analysis of DFWLYH NLQDVHV ¿YH WDUJHWV RI GDVDWLQLE were shown to be upregulated in ARID1A mutant OCCC cells. The dasatinib target and SRC family protein YES1 was most VHOHFWLYH IRU $5,'$ GH¿FLHQW 2&&& cell lines. Dasatinib treatment increased G1 cell cycle arrest and caspase activity in ARID1A mutant lines, indicating a FHOOF\FOH DUUHVWDSRSWRWLF SKHQRW\SH Using siRNA screening, Miller et al. LGHQWL¿HG H[SUHVVLRQ RI S &,3 WAF1) and its downstream target RB1

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AKT phosphorylation in OCCC cell lines (60, 61). One study described ARID1A

mutant OCCC lines to have lower IC₅₀

for AKT inhibitors. However, no induction RI3,.$.7SDWKZD\DFWLYLW\ZDVIRXQG in these cells after ARID1A knockdown (59). Moreover, ARID1A status could

not discriminate between IC₅₀ for PI3K

and mTOR inhibitors in a large panel of OCCC cell lines and PDX models (11).

Some mechanistic links between $5,'$ ORVV DQG 3,.$.7 SDWKZD\ activation have been established. As stated earlier, ARID1A was found to LQKLELW 3,.$.7 DFWLYLW\ E\ UHJXODWLQJ expression of the PI3K suppressor PIK3IP1 in ovarian cancer (43). In EUHDVW FDQFHU $5,'$ ZDV LGHQWL¿HG as negative transcriptional regulator of ANXA1, a membrane bound protein and activator of AKT (Fig 4.) (62). These two studies suggest that ARID1A loss may indirectly activate PI3K in some cancer types. Given that PI3K and mTOR inhibitor sensitivity is not only dependent on ARID1A mutational status in OCCC,

WDUJHWLQJWKH3,.$.7SDWKZD\VKRXOG not be regarded as a synthetic lethal strategy for ARID1A mutant OCCC. 5. Clinical development of agents with $5,'$VSHFL¿FOHWKDOLW\

Multiple agents showing synthetic lethality in an ARID1A mutant context are in clinical development (Table 1). From the epigenetic targets with ARID1A PXWDWLRQ VSHFL¿F OHWKDOLW\ LQ 2&&& WKH ¿UVW JHQHUDWLRQ (=+ LQKLELWRUV (DZNep) gave toxicity in vivo. Two novel EZH2 inhibitors are now in clinical trials (63). An alternative for EZH2 targeting agents is HDAC2 inhibition using the clinically applicable broad HDAC inhibitor vorinostat. The HDAC6 inhibitor ACY1215 proved to be well tolerated in myeloma patients, supporting clinical applicability of HDAC6 inhibition for WUHDWLQJ$5,'$GH¿FLHQW2&&&SDWLHQWV in the future (64). BET bromodomain inhibition has attracted great interest for the treatment of cancer. Many BET

Table 1 | Clinical development of agents with ARID1APXWDWLRQVSHFL¿FOHWKDOLW\DQGWKHLULQGXVWU\

QDPHVIURP&OLQLFDO7ULDOVJRYKWWSFOLQLFDOWULDOVJRY

Molecular target

Most advanced clinicalphase

Compounds in clinical development, most advanced are depicted in bold

EZH2 Phase II EPZ-6438, CPI-1205

HDAC6 Phase II ACY-125, KA2507

BRD2 Phase II I-BET-762, GSK2820151, RO6870810, CPI-0610,

(BET) *6,1&%,1&%$%99 BMS-986158, FT-1101, PLX-51107, SF1126, CC90010, ZEN003694, BI894999, N-methyl pyrrolidone, ODM-207

YES1 3KDVH,9 BMS-354825, AZD0530, SKI-606

ATR Phase II VX-970, BAY1895344, AZD6738

PARP1/2 3KDVH,9 AZD2281, ABT-888, BMN673, AG-014699, MK-4827,

SHR3162, SC10914, SOMCL-9112, BGB-290

HSP90 Phase II AT13387, TAS-116, SNX-2112, XL888, PEN-866 3,.Įȕį Phase III BKM120, RP6530, BYL719, PKI-587, AZD8186, BAY80-6946, TGR-1202, GSK2636771, SF1126,

KA2237, GDC0032, INK1197, GDC-0077, GDZ173,

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inhibitors are under clinical investigation, and several BET inhibitors, such as iBET-762, are currently evaluated in phase II trials. ARID1A status might be a biomarker to enrich for sensitivity in OCCC and possible other cancer types as well. Dasatinib is approved for the treatment of leukemia’s and is under investigation in multiple solid WXPRUV 'DVDWLQLE HႈFDF\ LQ UHFXUUHQW ovarian cancer patients was limited (65). However, no selection based on ARID1A status was made. PI3K, PARP and ATR inhibitors are being tested in clinical trials for diverse genetic backgrounds LQFDQFHUXWPRVWLQSKDVH,,,,9DQG,, respectively. Considering the advanced clinical development of PI3K and PARP targeting compounds, including trials in ovarian cancer patients, these agents may provide direct therapeutic opportunities for ARID1A mutant cancer patients including ARID1A mutant 2&&&7KRXJKHႈFDF\DJDLQVWARID1A wild-type OCCC should not be excluded. 6. SMARCA2 and SMARCA4-directed synthetic lethal strategies

Aside from synthetic lethal targeting strategies in the context of ARID1A PXWDWLRQV WKH 6:,61) FRPSOH[ members SMARCA2 and SMARCA4 have been exploited for this purpose as well. Having SMARCA2 and SMARCA4 mutations in approximately 2% and 5% RIWKHWXPRUV2&&&FRXOGEHQH¿WIURP such strategies (15). In 2013, Oike et al. described susceptibility for SMARCA2 LQKLELWLRQ LQ 60$5&$ GH¿FLHQW QRQ small cell lung cancer. Treatment with SMARCA2 siRNA induced markers of senescence in SMARCA4 mutant cell lines (66). An epigenome directed shRNA screen further supported the ¿QGLQJWKDW60$5&$GH¿FLHQWFDQFHUV GHSHQG RQ 60$5&$ 60$5&$ SMARCA4 synthetic lethality was later demonstrated in multiple other cancer types (67). SMARCA4 loss resulted

in enhanced integration of SMARCA2 LQ WKH UHVLGXDO 6:,61) FRPSOH[HV which in turn may drive oncogenesis

(68). SMARCA2 and SMARCA4

alterations have a similar incidence in cancer, with the exception of small cell carcinoma of the ovary hypercalcaemic type (SCCOHT) in which SMARCA4 mutations are present in 90% of the tumors (Fig. 3). A recent study reported the absence of SMARCA2 expression in 60$5&$GH¿FLHQW6&&2+7LQGLFDWLQJ

WKDW 60$5&$60$5&$ PXWXDO

exclusivity is not synthetic lethal in all cancer types. Somehow these cancers have overcome dependency on either RQHRIWKH6:,61)$73DVH0RUHRYHU restoration of SMARCA2 or SMARCA4 inhibited proliferation (69). These results VXJJHVW WKDW GHSHQGHQF\ RQ 6:, SNF ATPases is lost in SCCOHT. In line with these observations, another VWXG\ LGHQWL¿HG VHYHUDO SMARCA4 mutant cancers cell lines with absent or low expression of SMARCA2. Inhibition of the PRC2 subunit EZH2 re-expressed SMARCA2 only in the EZH2 sensitive SMARCA4 mutant subset of FHOO OLQHV (=+ LQKLELWLRQ VSHFL¿FDOO\ induced apoptosis in one (the ovarian HQGRPHWULRLGFDQFHUFHOOOLQH729' of the four EZH2 sensitive SMARCA4 mutant lines (70). It is unknown whether WKH 6:,61) IXQFWLRQ LV UHWDLQHG DIWHU loss of SMARCA2 and SMARCA4 or that these tumors are more dependent on other chromatin remodelers. Chemical inhibitors of SMARCA2 and SMARCA4 are currently under development. The

¿UVW 60$5&$60$5&$ VSHFL¿F

inhibitor PFI-3 did not show anti-SUROLIHUDWLYHHႇHFWVLQOXQJFDQFHUFHOOV SRVVLEO\EHFDXVHRILQVXႈFLHQWLQKLELWLRQ of SMARCA2 binding to DNA (71). 7R XWLOL]H WKH 60$5&$60$5&$ dependency in a clinical setting, development of inhibitors that target either SMARCA2 or SMARCA4 might EHEHQH¿FLDOWRDFKLHYHWXPRUVHOHFWLYH lethality.

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7. Conclusion and future considerations The abundance of ARID1A loss of function mutations across cancer types designates mutant ARID1A as an attractive target for synthetic lethal approaches. Mechanistic insight into inhibitor induced synthetic lethality with ARID1A loss is at least partially revealed (Fig. 4). EZH2, HDAC2, HDAC6, BRD2 and YES1 inhibition were found to be VSHFL¿FDOO\ OHWKDO LQ ARID1A mutant OCCC. Additional lethal targets that KDYH EHHQ YHUL¿HG DFURVV PXOWLSOH other ARID1A mutant cancer lineages, included PARP, ATR and HSP90 (Fig. 5).

Inhibition of the synthetic lethal targets HDAC2 and HDAC6 demonstrated a ODUJH GLႇHUHQFH LQ VHQVLWLYLW\ EHWZHHQ ARID1A mutant and wild-type OCCC cell lines. Since both targets were tested in a limited number of cell lines evaluation in a larger cell line panel would be required to verify the robustness of HDAC2 and HDAC6 inhibition. Synthetic lethality of drugs targeting EZH2 and BRD2 in ARID1A mutant OCCC was less pronounced. Though, the advantage of these last two studies was the use of 3D in vitro models for the assessment of sensitivity to EZH2 inhibition and the use of patient-derived xenotransplants in addition to a large panel of OCCC cell lines to determine sensitivity to BRD2 LQKLELWLRQ 7KH GLVWLQFW IXQFWLRQ RI 6:, SNF complexes among tissues indicates that molecular dependencies in ARID1A PXWDQW FDQFHUV DUH OLQHDJH VSHFL¿F thus requiring testing of ATR and HSP90 inhibitors in the context of OCCC. For example, PARP inhibitor potency has been evaluated in OCCC cell lines but did not seem to provide selective sensitivity in ARID1A mutant OCCC cells (11, 72). We found no enrichment for alterations in DNA repair genes in ARID1A mutant versus wild-type OCCC tumors and cell lines, which may provide an explanation for this observation (11). However, genetic evidence using isogenic OCCC

models still needs to be provided. Besides, ARID1A was recently assigned an important role in mismatch repair as it recruits the mismatch repair gene MSH2 to chromatin during DNA replication. ARID1A loss correlated ZLWK PLVPDWFK UHSDLU GH¿FLHQF\ KLJK mutational load and increased numbers

RI WXPRULQ¿OWUDWLQJ O\PSKRF\WHV

across many human cancer types (73). These data propose that ARID1A loss induces microsatellite instability, which subsequently provides a vulnerability to immunotherapy. In ARID1A mutant syngeneic mouse ovarian and colorectal cancer models high susceptibility to immune checkpoint blockade of PD-L1 compared to isogenic ARID1A wild-type models was already shown (73). A small study in OCCC patients found high PD-/H[SUHVVLRQDQGPRUHWXPRULQ¿OWUDWLQJ lymphocytes in microsatellite instable cancers, but the ARID1A mutation status was not determined (74). However, the frequency of microsatellite instability in OCCC is relatively low (10-14%), implying that the percentage of OCCC

Figure 5 | Synthetic lethal therapies identi-¿HGLQARID1A mutant OCCC and other tumor types. Inhibition of EZH2, HDAC2, HDAC6, BRD2

and YES1 were found to be synthetic lethal in ARI-'$GH¿FLHQW2&&&ARID1A mutation dependent (driven) synthetic lethality was observed in other tumor types with ROS induction (via HSP90 inhibi-tion) and inhibition of ATR, PARP, PI3K and PD-L1. Whether these synthetic lethal therapies can be applied to OCCC remains to be proven.

OCCC Applicable to OCCC? $75 3$53 526 3,. 3'/ ,QKLELWRU ,QKLELWRU ,QGXFHU ,QKLELWRU ,QKLELWRU (=+ +'$& +'$& %5' <(6 ,QKLELWRU ,QKLELWRU ,QKLELWRU ,QKLELWRU ,QKLELWRU SWI/SNF ARID1A

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tumors with microsatellite instable and ARID1A loss will be even lower (74, 75). Taken together, these results support exploring immunotherapeutic approaches in the context of ARID1A mutant OCCC and could be relevant for a small subset of OCCC patients (Fig. 5).

The question remains whether direct targeting of ARID1B in an ARID1A mutant context in OCCC is feasible. It will be challenging to chemically inhibit ARID1B, since both ARID1A and ARID1B lack actionable ATPase or catalytic domains. Moreover, in several OCCC tumors mutations in both ARID1A and ARID1B were observed, suggesting that in these cells some expression of ARID1A or ARID1B was retained, the 6:,61)FRPSOH[LVQRORQJHUDFWLYHRU compensatory proteins have taken over the DNA binding function of ARID1A and $5,'% ZLWKLQ WKH 6:,61) FRPSOH[

(15). Synthetic lethality in SMARCA2 or SMARCA4 mutant OCCC may be an alternative strategy. However, limited results indicate context dependency of loss of SMARCA2 and SMARCA4 as well, but this has not been investigated in the context of OCCC. Important questions are whether inhibitors selective for either SMARCA2 or SMARCA4 can be developed and which other targets can be used for synthetic lethality approaches in the context of SMARCA2 or SMARCA4 loss in OCCC.

ARID1A mutation directed lethal strategies using agents in clinical development are becoming feasible in ARID1A mutant OCCC. Ultimately, simultaneous inhibition of multiple synthetic lethal targets in ARID1A mutant OCCC should be assessed to overcome the onset of resistance toward single target synthetic lethality.

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