Immunohistochemical analysis of SLFN11 expression uncovers potential non-responders to DNA-damaging agents overlooked by tissue RNA-seq

Takashima, Tsuyoshi; Sakamoto, Naoya; Murai, Junko; Taniyama, Daiki; Honma, Reiko; Ukai, Shoichi; Maruyama, Ryoko; Kuraoka, Kazuya; Rajapakse, Vinodh N.; Pommier, ﻿Yves; Yasui, Wataru

doi:10.1007/s00428-020-02840-6

Cited by 31 publications

(35 citation statements)

References 23 publications

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“…SLFN11 is genetically inactivated in ∼50% of all cancer lines and cancer tissues ( 6 , 25 ) and studies are ongoing in various research institutions to establish clinically whether SLFN11 inactivation determines resistance to anticancer treatments as it does in preclinical models ( 20 ). In this study, we demonstrate that inhibition of the ATR pathway in SLFN11-deficient cancer cells overcomes chemoresistance to a broad range of clinical DNA-damaging agents targeting TOP1 (TPT, indotecan [LMP400]), TOP2 (etoposide), PARP (talazoparib), DNA (cisplatin), WEE1 (AZD1775), and Cdc7 (PHA-767491).…”

Section: Discussionmentioning

confidence: 99%

“…SLFN11-expressing cancer cells are consistently hypersensitive to a broad range of chemotherapeutic drugs targeting DNA replication, including topoisomerase inhibitors, alkylating agents, DNA synthesis, and poly(ADP-ribose) polymerase (PARP) inhibitors compared to SLFN11-deficient cancer cells, which are chemoresistant ( 1 , 2 , 4 , 8 – 17 ). Profiling SLFN11 expression is being explored for patients to predict survival and guide therapeutic choice ( 8 , 13 , 18 – 24 ).…”

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confidence: 99%

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SLFN11 promotes CDT1 degradation by CUL4 in response to replicative DNA damage, while its absence leads to synthetic lethality with ATR/CHK1 inhibitors

Murai

Chakka

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Schlafen-11 (SLFN11) inactivation in ∼50% of cancer cells confers broad chemoresistance. To identify therapeutic targets and underlying molecular mechanisms for overcoming chemoresistance, we performed an unbiased genome-wide RNAi screen in SLFN11-WT and -knockout (KO) cells. We found that inactivation of Ataxia Telangiectasia- and Rad3-related (ATR), CHK1, BRCA2, and RPA1 overcome chemoresistance to camptothecin (CPT) in SLFN11-KO cells. Accordingly, we validate that clinical inhibitors of ATR (M4344 and M6620) and CHK1 (SRA737) resensitize SLFN11-KO cells to topotecan, indotecan, etoposide, cisplatin, and talazoparib. We uncover that ATR inhibition significantly increases mitotic defects along with increased CDT1 phosphorylation, which destabilizes kinetochore-microtubule attachments in SLFN11-KO cells. We also reveal a chemoresistance mechanism by which CDT1 degradation is retarded, eventually inducing replication reactivation under DNA damage in SLFN11-KO cells. In contrast, in SLFN11-expressing cells, SLFN11 promotes the degradation of CDT1 in response to CPT by binding to DDB1 of CUL4CDT2 E3 ubiquitin ligase associated with replication forks. We show that the C terminus and ATPase domain of SLFN11 are required for DDB1 binding and CDT1 degradation. Furthermore, we identify a therapy-relevant ATPase mutant (E669K) of the SLFN11 gene in human TCGA and show that the mutant contributes to chemoresistance and retarded CDT1 degradation. Taken together, our study reveals new chemotherapeutic insights on how targeting the ATR pathway overcomes chemoresistance of SLFN11-deficient cancers. It also demonstrates that SLFN11 irreversibly arrests replication by degrading CDT1 through the DDB1–CUL4CDT2 ubiquitin ligase.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

SLFN11 promotes CDT1 degradation by CUL4 in response to replicative DNA damage, while its absence leads to synthetic lethality with ATR/CHK1 inhibitors

Murai

Chakka

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…Of particular interest was downregulated SLFN11. SLFN11 irreversibly blocks DNA replication to kill cells in response to DNA damage and replication stress, and decreased SLFN11 expression is correlated with decreased sensitivity to a variety of DDAs (18)(19)33). SLFN11 deficiency is observed in approximately half of the NCI-60 tumor cell panel (17) and epigenetic mechanisms regulate SLFN11 expression in various tumor cells and tissues (20,34,35).…”

Section: Derepression Of Slfn11 Increases Sensitivity To Pbd Warheadmentioning

confidence: 99%

Resistance to Pyrrolobenzodiazepine Dimers Is Associated with SLFN11 Downregulation and Can Be Reversed through Inhibition of ATR

Mao

Chaerkady

et al. 2021

Molecular Cancer Therapeutics

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Resistance to antibody-drug conjugates (ADCs) has been observed in both preclinical models and clinical studies. However, mechanisms of resistance to pyrrolobenzodiazepine (PBD)conjugated ADCs have not been well characterized and thus, this study was designed to investigate development of resistance to PBD dimer warheads and PBD-conjugated ADCs. We established a PBD-resistant cell line, 361-PBDr, by treating human breast cancer MDA-MB-361 cells with gradually increasing concentrations of SG3199, the PBD dimer released from the PBD drug-linker tesirine. 361-PBDr cells were over 20-fold less sensitive to SG3199 compared with parental cells and were cross-resistant to other PBD warhead and ADCs conjugated with PBDs. Proteomic profiling revealed that downregulation of Schlafen family member 11 (SLFN11), a putative DNA/RNA helicase, sensitizing cancer cells to DNA-damaging agents, was associated with PBD resistance. Confirmatory studies demonstrated that siRNA knockdown of SLFN11 in multiple tumor cell lines conferred reduced sensitivity to SG3199 and PBDconjugated ADCs. Treatment with EPZ011989, an EZH2 inhibitor, derepressed SLFN11 expression in 361-PBDr and other SLFN11deficient tumor cells, and increased sensitivity to PBD and PBDconjugated ADCs, indicating that the suppression of SLFN11 expression is associated with histone methylation as reported. Moreover, we demonstrated that combining an ataxia telangiectasia and Rad3-related protein (ATR) inhibitor, AZD6738, with SG3199 or PBD-based ADCs led to synergistic cytotoxicity in either resistant 361-PBDr cells or cells that SLFN11 was knocked down via siRNA. Collectively, these data provide insights into potential development of resistance to PBDs and PBD-conjugated ADCs, and more importantly, inform strategy development to overcome such resistance.

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“…Additionally the process of ferroptosis might also occur, which reflects a type of programmed cell death dependent on iron and which is also characterized by the accumulation of lipid peroxides [ 78 ]. A further process, especially in cells exposed to antineoplastic drugs, including those causing DNA strand scission [ 79 ], or during suppressing of HIV [ 80 ] is (partially) caused by members of the Schlafen family of proteins [ 81 ]. However, in spite of the fact that the cell motility is also affected, no data have been published that suggest an increase of the cell nucleus during these cell reactions.…”

Section: Discussionmentioning

confidence: 99%

Polyphosphate Reverses the Toxicity of the Quasi-Enzyme Bleomycin on Alveolar Endothelial Lung Cells In Vitro

Müller

Neufurth

Wang

et al. 2021

Cancers

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The anti-cancer antitumor antibiotic bleomycin(s) (BLM) induces athyminic sites in DNA after its activation, a process that results in strand splitting. Here, using A549 human lung cells or BEAS-2B cells lunc cells, we show that the cell toxicity of BLM can be suppressed by addition of inorganic polyphosphate (polyP), a physiological polymer that accumulates and is released from platelets. BLM at a concentration of 20 µg ml−1 causes a decrease in cell viability (by ~70%), accompanied by an increased DNA damage and chromatin expansion (by amazingly 6-fold). Importantly, the BLM-caused effects on cell growth and DNA integrity are substantially suppressed by polyP. In parallel, the enlargement of the nuclei/chromatin in BLM-treated cells (diameter, 20–25 µm) is normalized to ~12 µm after co-incubation of the cells with BLM and polyP. A sequential application of the drugs (BLM for 3 days, followed by an exposure to polyP) does not cause this normalization. During co-incubation of BLM with polyP the gene for the BLM hydrolase is upregulated. It is concluded that by upregulating this enzyme polyP prevents the toxic side effects of BLM. These data might also contribute to an application of BLM in COVID-19 patients, since polyP inhibits binding of SARS-CoV-2 to cellular ACE2.

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Immunohistochemical analysis of SLFN11 expression uncovers potential non-responders to DNA-damaging agents overlooked by tissue RNA-seq

Cited by 31 publications

References 23 publications

SLFN11 promotes CDT1 degradation by CUL4 in response to replicative DNA damage, while its absence leads to synthetic lethality with ATR/CHK1 inhibitors

SLFN11 promotes CDT1 degradation by CUL4 in response to replicative DNA damage, while its absence leads to synthetic lethality with ATR/CHK1 inhibitors

Resistance to Pyrrolobenzodiazepine Dimers Is Associated with SLFN11 Downregulation and Can Be Reversed through Inhibition of ATR

Polyphosphate Reverses the Toxicity of the Quasi-Enzyme Bleomycin on Alveolar Endothelial Lung Cells In Vitro

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