DNA Repair, Cell Cycle Checkpoints and Apoptosis as Targets for Anticancer Drugs

DNA 修复、细胞周期检查点和细胞凋亡作为抗癌药物的靶点

• 批准号: 10925958
• 负责人: YVES POMMIER
• 金额: $ 231.16万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10925958
• 关键词: APEXL2 Gene; Acyclovir; Advanced Malignant Neoplasm; Antineoplastic Agents; Antineoplastic Combined Chemotherapy Protocols; Apoptosis; Ataxia Telangiectasia; Binding; Biochemical; Biological Assay; Biology; CCR; CDT1 Gene; CHEK1 gene; Cancer cell line; Cell Cycle Checkpoint; Cell Death; Cell Line; Cells; Chromatin; Clinic; Clinical; Clinical Pharmacology; Clinical Trials; Collaborations; Communities; Complex; Crystallography; Cytarabine; DNA; DNA Damage; DNA Repair; DNA Synthesis Inhibitors; DNA replication fork; DNA-protein crosslink; Databases; Digestion; Drug Combinations; ERCC1 gene; Enzymes; Excision; FDA approved; Genes; Genomics; Glycoside Hydrolases; Histone Deacetylase Inhibitor; Hydrolysis; Immune checkpoint inhibitor; Induction of Apoptosis; Knock-out; Licensing Factor; Malignant neoplasm of ovary; Manuscripts; Mediating; Methylation; Molecular; Molecular Mechanisms of Action; Mutation; National Center for Advancing Translational Sciences; Online Systems; Organoids; Pathway interactions; Patient Selection; Patients; Peptide Hydrolases; Pharmaceutical Preparations; Pharmacogenomics; Pharmacology; Phosphodiesterase Inhibitors; Platinum; Poly(ADP-ribose) Polymerase Inhibitor; Post-Translational Protein Processing; Proteolysis; Publishing; RNA; Rationalization; Recombinants; Regulation; Replication Licensing; Research; Resistance; Resources; Site; Stress; Structure; Sumoylation Pathway; TOP1 gene; TOP2A gene; Testing; Time; Tissues; Topoisomerase; Topoisomerase Inhibitors; Tubulin; Tumor Suppressor Proteins; Tyrosine; Ubiquitination; Virus Replication; Work; Zidovudine; adduct; anticancer research; arginine methyltransferase; base; biomarker signature; cancer therapy; clinical development; clinically relevant; drug candidate; drug response prediction; drug testing; endonuclease; genomic data; genomic predictors; genomic signature; homologous recombination; improved; inhibitor; kinase inhibitor; malignant breast neoplasm; mitochondrial genome; molecular modeling; multicatalytic endopeptidase complex; novel; nuclease; patient biomarkers; patient response; precision medicine; predicting response; predictive marker; prevent; protein kinase inhibitor; proteostasis; proteotoxicity; public database; recruit; repaired; replication stress; response; response biomarker; small cell lung carcinoma; targeted agent; temozolomide; therapeutic target; tool; tumor; tyrosyl-DNA phosphodiesterase; ubiquitin ligase; web app; web site

We are pursuing complementary projects to elucidate the molecular pharmacology of clinically relevant inhibitors of topoisomerases, DNA repair and cell cycle checkpoints. Project #1. Repair of topoisomerase cleavage complexes (TOPccs) by tyrosyl-DNA-phosphodiesterases (TDPs), endonucleases and SUMOylation/ubiquitylation/PARylation Aim 1:Post-translational modifications of TOPccs: TOPccs are excised from DNA by two main mechanisms: 1/ hydrolysis of the covalent linkage between the catalytic tyrosine of topoisomerases and the DNA broken end by tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2); 2/ endonuclease cleavage of the DNA fragment adjacent to the TOPcc by nucleases (Mre11, XPF-ERCC1, XPG, FEN1, APE2...). Because the covalent topoisomerase-tyrosyl-DNA bonds to be cleaved by TDP1 and TDP2 are deep within the TOPccs, TOPccs need to be proteolyzed and/or denatured to provide access to the TDPs (TDP1 and TDP2). We are studying the proteolytic pathways for TOPccs. Our results demonstrate the rapid engagement of the SUMOylation and ubiquitylation pathways, which, in turn drive proteasome-mediated topoisomerase degradation. We have also discovered that, unique to TOP1, TOP1ccs are rapidly PARylated by PARP1 and de-PARylated by PARG (PolyADPribose Glycohydrolase). Thus, PARylation regulates the proteolytic digestion of TOP1ccs by preventing their excessive proteasomal degradation while recruiting TDP1. Aim 2: Biology of TDPs: TDP1 and TDP2 preferentially repair TOP1cc and TOP2cc, respectively. In addition to TOP1cc, TDP1 removes damaged and non-canonical bases and adducts from 3'-DNA ends. This explains why lack of TDP1 sensitizes cells not only to TOP1 inhibitors but also to temozolomide, cytarabine, zidovudine (AZT) and acyclovir. We demonstrated that TDP2 removes TOP2cc in the mitochondrial genome and showed for the first time that the arginine methyltransferase (PRMT5) activates TDP1 by directly binding and methylating TDP1. Our recent studies show that TDP2 also excises TOP3Bccs both from DNA and RNA, and that TDP2 excises TOP3Accs after their proteolysis by the replication-associated protease Spartan (SPRTN). Aim 3: Pharmacology and targeting of TDPs: The rationale for targeting TDPs is rooted in the emerging importance of TDPs for DNA repair and viral replication, and the potential of TDP inhibitors for anticancer drug combinations. We are using biochemical assays with recombinant TDP enzymes. We are also taking advantage of TDP1 and TDP2 knockout cell lines, crystallographic determinations, and molecular modeling to study the molecular pharmacology of the drug candidates. We published the first crystal structures of TDP1 inhibitors in complex with their target enzyme. Project #2. PARP trapping by PARP inhibitors: molecular mechanisms and translational implications PARP inhibitors represent the most advanced cancer therapeutics targeting the DNA damage response. PARP inhibitors (olaparib, rucaparib, niraparib and talazoparib) are FDA-approved. PARP inhibitors are the first drugs to exploit the concept of synthetic lethality for homologous recombination deficiency (HRD) in the clinic. Our studies revealed 'PARP trapping' as a key mechanism explaining the molecular mechanism of action of PARP inhibitors as anticancer agents. This discovery and our work with talazoparib contributed to the approval of talazoparib for breast and ovarian cancer in 2018. Our studies focus on 1/ the most synergistic combinations with temozolomide and with TOP1 inhibitors, including our non-camptothecin indenoisoquinoline TOP1 inhibitors; 2/ the repair mechanisms and determinants of response to PARP inhibitors beyond homologous recombination (HR; BRCAness). We recently showed that the DNA-protein crosslink protease (Spartan: SPTN), TDPs and ubiquitination are involved for the removal of trapped PARP1 and that ubiquitylation of PARP1 by the SUMO-dependent ubiquitin ligase RNF4 precedes the eviction of PARP1 from chromatin. Project #3. Patient-derived cancer cell lines and organoids to discover and validate novel genomic predictive biomarkers for patient selection and rational drug combinations with TOP1, PARP and DNA damage response (DDR) and cell cycle checkpoint (ATR) inhibitors as part of CellMiner The current lack of predictive biomarkers for widely used DNA-targeted anticancer therapies and the lack of direct correlation between their primary targets and cellular response warrant the need to identify DDR determinants for predicting drug responses and rationalizing drug combinations. Taking advantage of the extensive NCI-60 drug database ( 40,000 drugs including FDA approved and investigational clinical drugs), whole genomic data and our CellMiner facility, we discovered several novel predictive biomarkers for DNA-targeted agents: SLX4 (FANCP) mutations, ATAD5 (ELG1) mutations, and SLFN11 (Schlafen 11) expression. We have extended these analyses to tissue-specific cancer cell line databases (NCI Small Cell Lung Cancers), and larger databases (CCLE: MIT-Broad Institute and CGP: MGH-Sanger), and to CCR clinical trials to test predictive biomarker signatures. Those cancer cell line databases have been made widely and freely available to the research community via CellMiner web-based application (http://discover.nci.nih.gov/cellminercdb). We have generated a novel database and web-based pharmacogenomic tool for patient-derived small cell lung cancers (SCLC): SCLC-CellMiner in collaboration with the NCI-DTP (Beverly Teicher Molecular Pharmacology group) and John Minna (UTSW). The manuscript and resource have been published at Cell Press. We have also integrated in the CellMinerCDB database the response of 183 cancer cell lines to 2,650 drugs tested at the National Center for Advancing Translational Sciences (NCATS. These publicly available database and website have been published in Cancer Research and highlighted by the CCR Press Office. Project #4. Schlafen 11 (SLFN11) a predictive biomarkers of response to DNA damaging drugs: We discovered SLFN11 as dominant predictor of response to DNA and replication damaging drugs. SLFN11 determines response to TOP1, TOP2, PARP inhibitors, DNA synthesis inhibitors and platinum derivatives but not to tubulin or protein kinase inhibitors or apoptosis-inducing drugs. SLFN11 is inactivated in approximately 50% of cancer cells lines, making them resistant to DNA damaging agents. Our aims are to elucidate the molecular mechanism of SLFN11 action and regulation, and relevance for patient responses and rationale drug combinations. We discovered that SLFN11 is recruited to DNA damage sites and to stressed replication forks by binding to RPA and the replicative CMG complex, opening chromatin, inducing the immediate early response (EIR) stress genes, and promoting the degradation of the replication licensing factor CDT1. This year, we showed that SLFN11 regulating protein homeostasis and proteotoxic stress. We propose that SLFN11 acts as a "Restriction Factor" for cells with replicative stress and as "potential tumor suppressor". We have also demonstrated that SLFN11 inactivation in approximately 50% of all cancer cell lines and patient tumors can be reversed by treatment with histone deacetylase (HDAC) inhibitors to overcome resistance to DNA-targeted anticancer drugs.

项目成果

Deazaflavin Inhibitors of Tyrosyl-DNA Phosphodiesterase 2 (TDP2) Specific for the Human Enzyme and Active against Cellular TDP2.

酪酶-DNA磷酸二酯酶2（TDP2）的Deazaflavin抑制剂特异于人酶，并对细胞TDP2进行活性。

• DOI: 10.1021/acschembio.5b01047
• 发表时间: 2016-07-15
• 期刊: ACS chemical biology
• 影响因子: 4
• 作者: Marchand C;Abdelmalak M;Kankanala J;Huang SY;Kiselev E;Fesen K;Kurahashi K;Sasanuma H;Takeda S;Aihara H;Wang Z;Pommier Y
• 通讯作者: Pommier Y

Zalypsis (PM00104) is a potent inducer of gamma-H2AX foci and reveals the importance of the C ring of trabectedin for transcription-coupled repair inhibition.

• DOI: 10.1158/1535-7163.mct-09-0336
• 发表时间: 2009-07
• 期刊: Molecular cancer therapeutics
• 影响因子: 5.7
• 作者: Guirouilh-Barbat J;Antony S;Pommier Y
• 通讯作者: Pommier Y

Report on the first SLFN11 monothematic workshop: from function to role as a biomarker in cancer.

• DOI: 10.1186/s12967-017-1296-3
• 发表时间: 2017-10-02
• 期刊: Journal of translational medicine
• 影响因子: 7.4
• 作者: Ballestrero A;Bedognetti D;Ferraioli D;Franceschelli P;Labidi-Galy SI;Leo E;Murai J;Pommier Y;Tsantoulis P;Vellone VG;Zoppoli G
• 通讯作者: Zoppoli G

RNAi screening identifies TAK1 as a potential target for the enhanced efficacy of topoisomerase inhibitors.

• DOI: 10.2174/156800911797264734
• 发表时间: 2011-10
• 期刊: Current cancer drug targets
• 影响因子: 3
• 作者: Martin SE;Wu ZH;Gehlhaus K;Jones TL;Zhang YW;Guha R;Miyamoto S;Pommier Y;Caplen NJ
• 通讯作者: Caplen NJ

Dual targeting of EWS-FLI1 activity and the associated DNA damage response with trabectedin and SN38 synergistically inhibits Ewing sarcoma cell growth.

• DOI: 10.1158/1078-0432.ccr-13-0901
• 发表时间: 2014-03-01
• 期刊: Clinical cancer research : an official journal of the American Association for Cancer Research
• 作者: Grohar PJ;Segars LE;Yeung C;Pommier Y;D'Incalci M;Mendoza A;Helman LJ
• 通讯作者: Helman LJ