{"title":"Electrochemical behavior of Methotrexate upon binding to the DNA of different cell lines","authors":"Douglas Vieira Thomaz, P.H.N. Santos","doi":"10.3390/iecc2021-09215","DOIUrl":"https://doi.org/10.3390/iecc2021-09215","url":null,"abstract":"","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89483837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C. Velázquez, Esin Orhan, I. Tabet, Lise Fenou, Laura Boudarel, C. Theillet
Triple-negative breast cancer (TNBC), representing 15% of breast carcinomas, is an aggressive breast cancer subtype with a high probability of metastasis and limited treatment options. Noticeably, BRCA-deficiency occurs in 25% of the TNBCs and results in deficient homologous recombination (HR) repair. Interestingly, PARP inhibitors (PARPi) have shown synthetic lethality in a BRCA-deficient context, however, their efficacy is frequently hampered by intrinsic or acquired resistance mechanisms involving restoration of the HR. In that regard, the role of some CDKs proven to regulate key HR actors was of interest to us.We aim at understanding the rewiring pathways determining resistance to PARPi in BRCA-deficient cancers and assessing the role of transcriptional regulating CDKs such as CDK7, CDK9 or CDK12 in the transcriptional regulation of key HR genes. Our ultimate goal is to determine whether and which CDK inhibitors could be effective approaches to repress HR gene expression and induce pharmacological HR-deficiency. As such, these CDK-inhibitors could be molecules of choice allowing sensitization of tumors that would otherwise respond poorly to DNA damaging treatment. With this purpose, we use in vitro and in vivo (PDX) models of TNBC and study the attenuation of HR response in tumor cells and PDX models treated with CDK-inhibitors. Our final aim is to determine the most efficient combination CDK-I + PARP-I. Our HR read outs are RAD51 and BRCA1 foci formation upon PARP-I treatment. We also measure the modification of RNA and protein expression levels induced by CDK-I treatment on a series of diagnostic HR genes (BRCA2, PALB2, ATR, FAND2), as a measure of HR repression. We will present data comparing the relative efficiency of 3 CDK-I, dinaciclib, NVP-2 and SR-4835, which have different specificities and inhibit different CDKs with variable efficacy.
{"title":"Exploiting DNA Repair Defect in Triple Negative Brest Cancer Using CDK Inhibition Strategy","authors":"C. Velázquez, Esin Orhan, I. Tabet, Lise Fenou, Laura Boudarel, C. Theillet","doi":"10.3390/iecc2021-09212","DOIUrl":"https://doi.org/10.3390/iecc2021-09212","url":null,"abstract":"Triple-negative breast cancer (TNBC), representing 15% of breast carcinomas, is an aggressive breast cancer subtype with a high probability of metastasis and limited treatment options. Noticeably, BRCA-deficiency occurs in 25% of the TNBCs and results in deficient homologous recombination (HR) repair. Interestingly, PARP inhibitors (PARPi) have shown synthetic lethality in a BRCA-deficient context, however, their efficacy is frequently hampered by intrinsic or acquired resistance mechanisms involving restoration of the HR. In that regard, the role of some CDKs proven to regulate key HR actors was of interest to us.We aim at understanding the rewiring pathways determining resistance to PARPi in BRCA-deficient cancers and assessing the role of transcriptional regulating CDKs such as CDK7, CDK9 or CDK12 in the transcriptional regulation of key HR genes. Our ultimate goal is to determine whether and which CDK inhibitors could be effective approaches to repress HR gene expression and induce pharmacological HR-deficiency. As such, these CDK-inhibitors could be molecules of choice allowing sensitization of tumors that would otherwise respond poorly to DNA damaging treatment. With this purpose, we use in vitro and in vivo (PDX) models of TNBC and study the attenuation of HR response in tumor cells and PDX models treated with CDK-inhibitors. Our final aim is to determine the most efficient combination CDK-I + PARP-I. Our HR read outs are RAD51 and BRCA1 foci formation upon PARP-I treatment. We also measure the modification of RNA and protein expression levels induced by CDK-I treatment on a series of diagnostic HR genes (BRCA2, PALB2, ATR, FAND2), as a measure of HR repression. We will present data comparing the relative efficiency of 3 CDK-I, dinaciclib, NVP-2 and SR-4835, which have different specificities and inhibit different CDKs with variable efficacy.","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81044586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shihori Tanabe, S. Quader, R. Ono, H. Cabral, K. Aoyagi, A. Hirose, H. Yokozaki, H. Sasaki
Molecular network activation states alter dynamically in biology and diseases. In cancer stem cells (CSCs), epithelial-mesenchymal transition (EMT) networks play an important role to acquisition of the drug resistance and cancer malignant feature. To reveal the network pathways in EMT and CSCs, gene expression in diffuse- and intestinal-type gastric cancer (GC) have been analyzed. The several canonical pathways have been found to be altered in diffuse- and intestinal-type GC. Canonical pathway on Cell Cycle: G1/S Checkpoint Regulation was activated in diffuse-type GC, and Cyclins and Cell Cycle Regulation was activated in intestinal-type GC. In Cell Cycle: G1/S Checkpoint Regulation, DNA damage induces p53, which was predicted to be activated in diffuse-type GC. Canonical pathway related to Role of BRCA1 in DNA Damage Response was activated in intestinal-type GC, where BRCA1 which is related to G1/S phase transition was up-regulated. Cell cycle regulation may be altered in EMT condition in diffuse-type GC.
{"title":"The roles of cell cycle and BRCA1 in the DNA damage response","authors":"Shihori Tanabe, S. Quader, R. Ono, H. Cabral, K. Aoyagi, A. Hirose, H. Yokozaki, H. Sasaki","doi":"10.3390/iecc2021-09193","DOIUrl":"https://doi.org/10.3390/iecc2021-09193","url":null,"abstract":"Molecular network activation states alter dynamically in biology and diseases. In cancer stem cells (CSCs), epithelial-mesenchymal transition (EMT) networks play an important role to acquisition of the drug resistance and cancer malignant feature. To reveal the network pathways in EMT and CSCs, gene expression in diffuse- and intestinal-type gastric cancer (GC) have been analyzed. The several canonical pathways have been found to be altered in diffuse- and intestinal-type GC. Canonical pathway on Cell Cycle: G1/S Checkpoint Regulation was activated in diffuse-type GC, and Cyclins and Cell Cycle Regulation was activated in intestinal-type GC. In Cell Cycle: G1/S Checkpoint Regulation, DNA damage induces p53, which was predicted to be activated in diffuse-type GC. Canonical pathway related to Role of BRCA1 in DNA Damage Response was activated in intestinal-type GC, where BRCA1 which is related to G1/S phase transition was up-regulated. Cell cycle regulation may be altered in EMT condition in diffuse-type GC.","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87848464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aleksander Ślusarczyk, H. Bryant, E. Chen, I. Hitchcock, M. Zeidler, A. Chantry, Sally Thomas
Introduction Myeloproliferative neoplasms (MPNs) are a group of haematological malignancies arising from haematopoietic stem cells with acquired driver mutations in JAK2, MPL and CALR. Increased replication stress is seen in the presence of JAK2V617F. Genes involved in the DNA double-strand break (DSB) repair pathways – BRCA-dependent homologous recombination repair (HRR) and DNA-dependent protein kinase-mediated non-homologous end-joining (D-NHEJ) are upregulated in MPN cells expressing mutated JAK2. Aims Using JAK2V617F and CALR (del 52) mutant cell lines: Determine the effect of single-agent DNA damage repair (DDR) inhibitors on cell viability and apoptosis. Evaluate the efficacy of DDR inhibitors in combination with hydroxyurea or ruxolitinib. Materials and Methods Cell lines expressing JAK2 (V617F)- HEL and CALR (del52)- MARIMO were treated with a drug panel comprising hydroxyurea, ruxolitinib, methotrexate, AZD6738 (ATRi), NU7441 (DNA-PKi), Olaparib (PARPi) and VE-821 (ATRi). AlamarBlue assay for cell proliferation and annexin V/ propidium iodide staining for flow cytometry were used to evaluate the toxicity. Results In JAK2 and CALR mutated cell lines, ATR inhibition by AZD6738 or VE-821, DNA-PKs inhibition by NU7441 and hydroxyurea each reduced viability, whereas PARP inhibition by olaparib had a minimal effect. The combination of ATR inhibition and hydroxyurea demonstrated high synergism in both apoptosis induction and proliferation arrest. Ruxolitinib alone had a modest effect in the presence of JAK2V617F and a minimal effect in CALR (del 52) mutated cells. Synergistic toxicity was observed for ruxolitinib and AZD6738/ VE-821 combination in JAK2 mutated cell line. Conclusions DDR inhibition reduces viability in cells expressing the driver mutations seen in MPNs. Most notably, ATR kinase inhibitors have a synergistic effect with the current standard-of-care treatment hydroxyurea. This study provides preliminary evidence that ATR inhibitors combined with standard therapies may be exploited in MPNs harbouring JAK2 and CALR mutations.
{"title":"Pre-clinical investigation of inhibition of the DNA damage response as a targetted therapy in myeloproliferative neoplasms shows synergism of ATR inhibitors with standard-of-care treatment.","authors":"Aleksander Ślusarczyk, H. Bryant, E. Chen, I. Hitchcock, M. Zeidler, A. Chantry, Sally Thomas","doi":"10.3390/iecc2021-09209","DOIUrl":"https://doi.org/10.3390/iecc2021-09209","url":null,"abstract":"Introduction \u0000Myeloproliferative neoplasms (MPNs) are a group of haematological malignancies arising from haematopoietic stem cells with acquired driver mutations in JAK2, MPL and CALR. Increased replication stress is seen in the presence of JAK2V617F. Genes involved in the DNA double-strand break (DSB) repair pathways – BRCA-dependent homologous recombination repair (HRR) and DNA-dependent protein kinase-mediated non-homologous end-joining (D-NHEJ) are upregulated in MPN cells expressing mutated JAK2. \u0000Aims \u0000Using JAK2V617F and CALR (del 52) mutant cell lines: \u0000 \u0000Determine the effect of single-agent DNA damage repair (DDR) inhibitors on cell viability and apoptosis. \u0000Evaluate the efficacy of DDR inhibitors in combination with hydroxyurea or ruxolitinib. \u0000 \u0000Materials and Methods \u0000Cell lines expressing JAK2 (V617F)- HEL and CALR (del52)- MARIMO were treated with a drug panel comprising hydroxyurea, ruxolitinib, methotrexate, AZD6738 (ATRi), NU7441 (DNA-PKi), Olaparib (PARPi) and VE-821 (ATRi). AlamarBlue assay for cell proliferation and annexin V/ propidium iodide staining for flow cytometry were used to evaluate the toxicity. \u0000Results \u0000In JAK2 and CALR mutated cell lines, ATR inhibition by AZD6738 or VE-821, DNA-PKs inhibition by NU7441 and hydroxyurea each reduced viability, whereas PARP inhibition by olaparib had a minimal effect. The combination of ATR inhibition and hydroxyurea demonstrated high synergism in both apoptosis induction and proliferation arrest. Ruxolitinib alone had a modest effect in the presence of JAK2V617F and a minimal effect in CALR (del 52) mutated cells. Synergistic toxicity was observed for ruxolitinib and AZD6738/ VE-821 combination in JAK2 mutated cell line. \u0000Conclusions \u0000DDR inhibition reduces viability in cells expressing the driver mutations seen in MPNs. Most notably, ATR kinase inhibitors have a synergistic effect with the current standard-of-care treatment hydroxyurea. This study provides preliminary evidence that ATR inhibitors combined with standard therapies may be exploited in MPNs harbouring JAK2 and CALR mutations.","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78057014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"G-quadruplexes and DNA damage in colorectal cancer tumorigenesis","authors":"V. Sánchez-Martín","doi":"10.3390/iecc2021-09198","DOIUrl":"https://doi.org/10.3390/iecc2021-09198","url":null,"abstract":"","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88808227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Charlotte Smith, D. Cucchi, Amy Gibson, Kirsten Brooksbank, S. Martin
Despite showing great clinical promise, response rates to immune checkpoint blockade (ICB) vary greatly and biomarkers of response are lacking. A recent Phase II clinical trial in patients with deficiency in the DNA mismatch repair (MMR) pathway indicated that MMR status predicted clinical benefit with the PD-1 inhibitor, pembrolizumab. These findings have led to the first tissue-agnostic approval for anti PD-1 therapy for unresectable or metastatic solid tumours with MMR deficiency. However, it is becoming increasingly clear that many MMR-deficient tumours fail to respond to ICBs with ~50% refractory to treatment. Furthermore, there is a wide diversity of clinical benefit among responders. However why this is the case and how this can be clinically translated remains largely unknown. Our exciting preliminary data suggest that loss of specific MMR genes results in a differential increased expression of the immune checkpoint molecule, PD-L1. Significantly, we observed an upregulation of PD-L1 expression in cells silenced for the MMR genes, MLH1, MSH2, PMS2 and MSH3, as expected. However, we did not observe an increased expression of PD-L1 upon MSH6 loss. This differential expression amongst MMR gene loss was further validated at both RNA and cell surface level. Upon investigation of the molecular mechanism regulating PD-L1 expression after MMR loss, we observed that that phosphorylation of STAT1 positively correlates with PD-L1 expression whilst STAT3 phosphorylation was negatively correlated, such that increased STAT1 phosphorylation was observed upon MLH1 and PMS2 loss and not in MSH6-deficient cells whilst STAT3 phosphorylation was only observed upon MSH6 loss. Significantly, inhibition of STAT3, both pharmacologically and genetically, reinstated PD-L1 expression in MSH6-deficient cells. Therefore, we have evidence that loss of specific MMR genes can trigger differential expression of PD-L1 through a STAT1/STAT3 mediated pathway and we hypothesize that it is this differential expression that may in part determine sensitivity to treatment with ICB.
{"title":"Identification of genetic determinants of DNA mismatch repair loss that predict response to immune checkpoint blockade","authors":"Charlotte Smith, D. Cucchi, Amy Gibson, Kirsten Brooksbank, S. Martin","doi":"10.3390/iecc2021-09195","DOIUrl":"https://doi.org/10.3390/iecc2021-09195","url":null,"abstract":"Despite showing great clinical promise, response rates to immune checkpoint blockade (ICB) vary greatly and biomarkers of response are lacking. A recent Phase II clinical trial in patients with deficiency in the DNA mismatch repair (MMR) pathway indicated that MMR status predicted clinical benefit with the PD-1 inhibitor, pembrolizumab. These findings have led to the first tissue-agnostic approval for anti PD-1 therapy for unresectable or metastatic solid tumours with MMR deficiency. However, it is becoming increasingly clear that many MMR-deficient tumours fail to respond to ICBs with ~50% refractory to treatment. Furthermore, there is a wide diversity of clinical benefit among responders. However why this is the case and how this can be clinically translated remains largely unknown. \u0000Our exciting preliminary data suggest that loss of specific MMR genes results in a differential increased expression of the immune checkpoint molecule, PD-L1. Significantly, we observed an upregulation of PD-L1 expression in cells silenced for the MMR genes, MLH1, MSH2, PMS2 and MSH3, as expected. However, we did not observe an increased expression of PD-L1 upon MSH6 loss. This differential expression amongst MMR gene loss was further validated at both RNA and cell surface level. \u0000Upon investigation of the molecular mechanism regulating PD-L1 expression after MMR loss, we observed that that phosphorylation of STAT1 positively correlates with PD-L1 expression whilst STAT3 phosphorylation was negatively correlated, such that increased STAT1 phosphorylation was observed upon MLH1 and PMS2 loss and not in MSH6-deficient cells whilst STAT3 phosphorylation was only observed upon MSH6 loss. Significantly, inhibition of STAT3, both pharmacologically and genetically, reinstated PD-L1 expression in MSH6-deficient cells. \u0000Therefore, we have evidence that loss of specific MMR genes can trigger differential expression of PD-L1 through a STAT1/STAT3 mediated pathway and we hypothesize that it is this differential expression that may in part determine sensitivity to treatment with ICB.","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82857984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MDM2 is an oncogenic E3 ligase found to be overexpressed in a number of human cancers, leading to poor prognosis. MDM2 overexpression inhibits the function of the tumour suppressor p53, which plays a critical role in safeguarding the integrity of the genome. MDM2 ubiquitinates p53 and tags it for proteasomal degradation. MDM2 also exhibits p53-independent oncogenic activities through targeting other tumour suppressor proteins, such as Foxo3a and Rb. Thus, aberrant regulation of Mdm2 is a key factor in promotion of tumor formation and progression and represents an important cancer therapeutic target. Here, we describe an integrated structure- based approach to develop potential lead compounds for inhibition of MDM2 oncogenic activity. We established a structure-based virtual screening strategy and used the crystal structure of the MDM2:MDMX RING domain heterodimer to predict the potential “druggable” pocket on Mdm2. An in silico screening of a small molecule compound library was employed to identify the candidate compounds that could interact with the MDM2:MDMX heterodimer RING domain. Additionally, using biochemical and cellular assays, the candidate compounds were examined for their ability to inhibit MDM2 E3 ligase activity, to induce apoptosis and to inhibit cell proliferation in cancer cell lines. This study reveals that inhibition of the MDM2:MDMX RING heterodimer could be a plausible approach for the development of MDM2 inhibitors as potential anti-cancer therapeutic agents.
{"title":"An Integrated Structure-based Approach for the Development of MDM2 inhibitors","authors":"Y. Sheng","doi":"10.3390/iecc2021-09208","DOIUrl":"https://doi.org/10.3390/iecc2021-09208","url":null,"abstract":"MDM2 is an oncogenic E3 ligase found to be overexpressed in a number of human cancers, leading to poor prognosis. MDM2 overexpression inhibits the function of the tumour suppressor p53, which plays a critical role in safeguarding the integrity of the genome. MDM2 ubiquitinates p53 and tags it for proteasomal degradation. MDM2 also exhibits p53-independent oncogenic activities through targeting other tumour suppressor proteins, such as Foxo3a and Rb. Thus, aberrant regulation of Mdm2 is a key factor in promotion of tumor formation and progression and represents an important cancer therapeutic target. Here, we describe an integrated structure- based approach to develop potential lead compounds for inhibition of MDM2 oncogenic activity. We established a structure-based virtual screening strategy and used the crystal \u0000structure of the MDM2:MDMX RING domain heterodimer to predict the potential “druggable” \u0000pocket on Mdm2. An in silico screening of a small molecule compound library was employed to identify the candidate compounds that could interact with the MDM2:MDMX heterodimer RING domain. Additionally, using biochemical and cellular assays, the candidate compounds were examined for their ability to inhibit MDM2 E3 ligase activity, to induce apoptosis and to inhibit cell proliferation in cancer cell lines. This study reveals that inhibition of the MDM2:MDMX RING heterodimer could be a plausible approach for the development of MDM2 inhibitors as potential anti-cancer therapeutic agents.","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87946951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hai-xia Yang, Beibei Sun, S. Hall, Ke Xu, Liang Zhao, R. Schmid, R. Peng, F. Yao
(1) Background: Poly (ADP-ribose) polymerases (PARPs) have pleiotropic roles including canonical DNA-damage response (DDR) pathways. PARP inhibition is initially proposed as a synthetic lethal interactor with cancer harboring homologous recombination deficiency (HRD), thus becoming a key therapeutic option for genetically-defined subsets of patients. Recently, there has been increasing evidence supporting the expansion of PARP-targeted therapy beyond HRD. Besides, synthetic lethality pathways for PARP-targeted therapy are being studied extensively due to the rapidly developed resistance to PARP inhibitors (PARPi). (2) Methods: We perform integrative pharmaco-transcriptomic analyses by correlating the drug response profiles of clinically-approved PARPi olaparib with the transcriptomes of solid cancer cell lines (n=659) to establish PARPis responsive gene signatures, which are then evaluated for their reliability using independent drug response datasets, and applied to identify tumor subsets primed for PARPi and potential targets synergistically interacting with PARPi. (3) Results: Based on the pharmaco-transcriptomic correlation analysis, we delineate gene signatures to predict the sensitivity and resistance to olaparib in pan-solid cancer cells, which is confirmed by independent drug response datasets. In further exploring the PARPi sensitivity signature, we identify IDH1/2 (isocitrate dehydrogenase 1/2)-mutated low-grade glioma (LGG) and NEUROD1-driven small cell lung cancer (SCLC) as potential subsets for prioritized PARPi, highlighting relaunching PARPi as a promising and innovative strategy to target these malignancy subtypes. Interestingly, the PARPi responsive signatures display a high degree of heterogeneity in the correlation with the curated HRD signatures across TCGA pan-solid cancer cohort, suggesting that these signatures predictive of PARPi responsiveness are HRD-independent. With the PARPi resistance signature, we identified several potentially synthetic lethal interactors with PARPi, e.g. dasatinib, EGFR, or MEK inhibitors. (4) Conclusions: The established PARPi responsive (sensitive/resistant) signatures in solid tumors exhibit robustness in identifying cancer subtypes that are highly primed for PARP-targeted therapy, and combined targets that synergistically augment the efficacy of PARPi.
{"title":"Responsive signatures established by pharmaco-transcriptomic correlation analysis identifies subsets for PARP-targeted therapy and reveals potential synergistic interactors","authors":"Hai-xia Yang, Beibei Sun, S. Hall, Ke Xu, Liang Zhao, R. Schmid, R. Peng, F. Yao","doi":"10.3390/iecc2021-09207","DOIUrl":"https://doi.org/10.3390/iecc2021-09207","url":null,"abstract":"(1) Background: Poly (ADP-ribose) polymerases (PARPs) have pleiotropic roles including canonical DNA-damage response (DDR) pathways. PARP inhibition is initially proposed as a synthetic lethal interactor with cancer harboring homologous recombination deficiency (HRD), thus becoming a key therapeutic option for genetically-defined subsets of patients. Recently, there has been increasing evidence supporting the expansion of PARP-targeted therapy beyond HRD. Besides, synthetic lethality pathways for PARP-targeted therapy are being studied extensively due to the rapidly developed resistance to PARP inhibitors (PARPi). \u0000(2) Methods: We perform integrative pharmaco-transcriptomic analyses by correlating the drug response profiles of clinically-approved PARPi olaparib with the transcriptomes of solid cancer cell lines (n=659) to establish PARPis responsive gene signatures, which are then evaluated for their reliability using independent drug response datasets, and applied to identify tumor subsets primed for PARPi and potential targets synergistically interacting with PARPi. \u0000(3) Results: Based on the pharmaco-transcriptomic correlation analysis, we delineate gene signatures to predict the sensitivity and resistance to olaparib in pan-solid cancer cells, which is confirmed by independent drug response datasets. In further exploring the PARPi sensitivity signature, we identify IDH1/2 (isocitrate dehydrogenase 1/2)-mutated low-grade glioma (LGG) and NEUROD1-driven small cell lung cancer (SCLC) as potential subsets for prioritized PARPi, highlighting relaunching PARPi as a promising and innovative strategy to target these malignancy subtypes. Interestingly, the PARPi responsive signatures display a high degree of heterogeneity in the correlation with the curated HRD signatures across TCGA pan-solid cancer cohort, suggesting that these signatures predictive of PARPi responsiveness are HRD-independent. With the PARPi resistance signature, we identified several potentially synthetic lethal interactors with PARPi, e.g. dasatinib, EGFR, or MEK inhibitors. \u0000(4) Conclusions: The established PARPi responsive (sensitive/resistant) signatures in solid tumors exhibit robustness in identifying cancer subtypes that are highly primed for PARP-targeted therapy, and combined targets that synergistically augment the efficacy of PARPi.","PeriodicalId":20534,"journal":{"name":"Proceedings of The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86892091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Debanu Das, P. Pellicena, M. Duncton, David Wilson, M. Georgiadis, A. Deacon
Cancer cells respond to increases in DNA damage by upregulating their DNA damage response (DDR). The base excision repair (BER) pathway corrects damage to single DNA bases through the action of multiple enzymes, including the central protagonist, apurinic/apyrimidinic endonuclease 1 (APE1). Numerous studies have shown association between increased APE1 levels and enhanced growth, migration, and drug resistance in human tumor cells, as well as with decreased patient survival. APE1 has been implicated in over 20 human cancers, making this an attractive target for developing anticancer therapies. Despite intensive effort, there are currently no clinical endonuclease inhibitors of APE1. We have used a newly developed high-throughput protein X-ray crystallography-based fragment screen to obtain starting points for the design of molecules to block APE1 function. Starting with a proprietary fragment library, we obtained high quality fragment-bound crystal structures showing diversity of chemical matter and hit location, representing the first experimental 3D structures of APE1 bound to drug-like molecules, thereby resolving a primary bottleneck in the path to inhibitor development. The implementation of this unique lead discovery campaign has facilitated three independent strategies toward the development of APE1 inhibitors, including (i) fragment growing and elaboration of hits bound at the endonuclease site; (ii) linking of fragments bound to distinct but proximally located sites, and (iii) use of fragments for the design of hooks to use in targeted protein degradation (TPD) strategies. We are using a combination of computational and medicinal chemistry, structural biology, and biochemical and biophysical studies and will discuss our progress towards these goals.
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Pub Date : 2018-08-01DOI: 10.1158/1557-3125.ADVBC17-IA15
A. D’Andrea
Large-scale genomic studies have demonstrated that some breast cancers, especially triple-negative breast cancers (TNBCs), harbor genetic and epigenetic alterations in homologous recombination repair (HRR) pathway genes. The most commonly altered HRR genes are BRCA1 and BRCA2, followed by other Fanconi anemia genes including FANCN/PALB2, FANCO/RAD51, FANCJ/BRIP, and FANCA. Loss of HRR causes genomic instability, hyperdependence on alternative DNA repair mechanisms, and enhanced sensitivity to platinum analogues, topoisomerase inhibitors, and PARP inhibitors (PARPi). The synthetic lethal interaction with PARPi is being exploited therapeutically in diverse clinical contexts and most notably in ovarian cancer where the PARPi olaparib is FDA approved for use in patients with germline BRCA1/2 mutations. PARP inhibitor resistance has already emerged as a vexing clinical problem for the treatment of BRCA1/2 deficient tumors. The most prevalent mechanism of PARPi resistance is secondary events that cancel the original HRR alteration and restore HRR proficiency. However, PARPi resistance may still develop without restoration of HRR proficiency via disruption of multiple proteins, such as PTIP or CHD4, that leads to replication fork (RF) stabilization. Importantly, this latter mechanism—namely, the restoration of RF stability—appears to be a highly prevalent mechanism of PARP inhibitor resistance in vitro and in vivo, particularly in tumor cells with an underlying BRCA2 deficiency. Due to their underlying deficiency in BRCA2 and inability to generate RAD51 nucleofilaments, these tumor cells are unable to restore HRR mechanisms. Instead, these cells acquire PARP inhibitor resistance by limiting the nucleolytic degradation of their stalled replication forks. We have recently made the surprising observation that BRCA2-deficient tumors can become resistant to PARPi by downregulating the expression of the polycomb repressive complex PRC2, a methyltransferase complex containing EZH2, SUZ12, EED, and RbAp48. Importantly, downregulation of PRC2 results in the reduced recruitment of the nuclease MUS81 to the RF, thereby providing a novel mechanism of RF protection and PARPi resistance. A molecular understanding of PARP inhibitor resistance mechanisms may allow the generation of a new class of drugs, or a repurposing of existing drugs, which may reverse this resistance and extend the use of PARP inhibitors to more tumor types. Citation Format: Alan D. D’Andrea. PARP inhibitor resistance and acquired vulnerability in breast cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr IA15.
大规模基因组研究表明，一些乳腺癌，特别是三阴性乳腺癌(tnbc)，同源重组修复(HRR)途径基因存在遗传和表观遗传改变。最常见的HRR改变基因是BRCA1和BRCA2，其次是其他范可尼贫血基因，包括FANCN/PALB2、FANCO/RAD51、FANCJ/BRIP和FANCA。HRR的缺失导致基因组不稳定，对替代DNA修复机制的高度依赖，以及对铂类似物、拓扑异构酶抑制剂和PARP抑制剂(PARPi)的敏感性增强。与PARPi的合成致死性相互作用正被用于多种临床环境的治疗，最值得注意的是卵巢癌，PARPi奥拉帕尼已被FDA批准用于生殖系BRCA1/2突变患者。PARP抑制剂耐药性已经成为治疗BRCA1/2缺陷肿瘤的一个令人烦恼的临床问题。PARPi耐药最普遍的机制是次要事件，这些事件取消了原始HRR改变并恢复HRR熟练程度。然而，PARPi耐药性仍然可能通过破坏多种蛋白质(如PTIP或CHD4)而导致复制叉(RF)稳定，而没有恢复HRR的熟练程度。重要的是，后一种机制——即RF稳定性的恢复——似乎是体外和体内PARP抑制剂耐药性的一种高度普遍的机制，特别是在潜在BRCA2缺乏的肿瘤细胞中。由于其潜在的BRCA2缺失和无法产生RAD51核丝，这些肿瘤细胞无法恢复HRR机制。相反，这些细胞通过限制其停滞的复制叉的核分解降解获得PARP抑制剂抗性。我们最近进行了令人惊讶的观察，发现brca2缺陷的肿瘤可以通过下调多梳抑制复合物PRC2(一种含有EZH2、SUZ12、EED和RbAp48的甲基转移酶复合物)的表达而对PARPi产生耐药性。重要的是，PRC2的下调导致核酸酶MUS81向RF的募集减少，从而提供了一种新的RF保护和PARPi抗性机制。对PARP抑制剂耐药机制的分子理解可能会产生一类新的药物，或者对现有药物进行重新利用，这可能会逆转这种耐药性，并将PARP抑制剂的使用范围扩大到更多的肿瘤类型。引用格式:Alan D. D 'Andrea。乳腺癌中PARP抑制剂的耐药与获得性易感性[摘要]。摘自:AACR特别会议论文集:乳腺癌研究进展;2017年10月7-10日;费城(PA): AACR;中华肿瘤杂志，2018;16(8):1 - 5。
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