Induction Of Synthetic Lethality Research Articles

PARP inhibitors in metastatic prostate cancer.

Poly-ADP ribose polymerase inhibitors (PARPi) are an emerging therapeutic option for the treatment of prostate cancer. Their primary mechanism of action is via induction of synthetic lethality in cells with underlying deficiencies in homologous recombination repair (HRR). In men with metastatic castrate-resistant prostate cancer (mCRPC) and select HRR pathway alterations, PARPi treatment has been shown to induce objective tumor responses as well as improve progression free and overall survival. Presently, there are two PARPi, olaparib and rucaparib, that are FDA approved in the treatment of mCRPC. Ongoing research is focused on identifying which HRR alterations are best suited to predict response to PARPi so that these therapies can be most effectively utilized in the clinic. While resistance to PARPi remains a concern, combination therapies may represent a mechanism to overcome or delay resistance.

Abstract 3494: Characterizing the relationship between genotype and phenotype in DNA damage response-altered pancreatic cancer models

Abstract Alterations in DNA damage response (DDR) proteins are prevalent across cancers and present unique opportunities for the therapeutic induction of synthetic lethality (i.e., two gene deficiencies in the same pathway synergize to kill tumor cells). In pancreatic adenocarcinoma, patients harboring alterations in DDR genes, such as in homology-directed repair (HDR), comprise the 10-20% of patients that may benefit from the recent FDA approval of Olaparib, a poly (ADP-ribose) polymerase inhibitor that disrupts non-homologous end joining (NHEJ). Despite being the best-in-class targeted therapy for DDR-altered pancreatic cancers, a subset of patients fails to respond to Olaparib and those that initially respond eventually go on to develop resistance. The mechanisms underlying resistance are poorly elucidated but suggest that some patients harboring DDR-altered tumors are HDR-proficient or revert to HDR-proficiency during therapy, bypassing the second gene deficiency requisite for synthetic lethal induction with targeted therapy (e.g., Olaparib). Utilizing patient-derived models of cancer, we are actively investigating DDR-altered, pancreatic tumor cell lines and exploring the relationship between DDR-alterations and HDR-deficiency with three goals: [1] To evaluate the prevalence of HDR-proficiency in BRCA-altered tumors, [2] to understand the extent to which patient-derived models of cancer are concordant and predictive of clinical outcomes, and [3] to identify novel therapeutic strategies for resistant patients. So far, we have observed HDR-proficiency by functional assays (e.g., RAD51 foci formation) in DDR-altered patient-derived cell lines that corresponds with poor response to Olaparib in vitro, and resistance to platinum therapy clinically. Whereas DDR-altered HDR-deficient lines had greater sensitivity to Olaparib and platinum therapy. These early data suggest that measures of HDR by functional assay may be more predictive of clinical therapeutic responses than the use of genetic signatures alone. Citation Format: James R. Carroll, Jason M. Link, Jonathan R. Brody. Characterizing the relationship between genotype and phenotype in DNA damage response-altered pancreatic cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3494.

Induction of Synthetic Lethality by Activation of Mitochondrial ClpP and Inhibition of HDAC1/2 in Glioblastoma.

Novel therapeutic targets are critical to unravel for the most common primary brain tumor in adults, glioblastoma (GBM). We have identified a novel synthetic lethal interaction between ClpP activation and HDAC1/2 inhibition that converges on GBM energy metabolism. Transcriptome, metabolite, and U-13C-glucose tracing analyses were utilized in patient-derived xenograft (PDX) models of GBM. Orthotopic GBM models were used for in vivo studies. We showed that activation of the mitochondrial ClpP protease by mutant ClpP (Y118A) or through utilization of second-generation imipridone compounds (ONC206 and ONC212) in combination with genetic interference of HDAC1 and HDAC2 as well as with global (panobinostat) or selective (romidepsin) HDAC inhibitors caused synergistic reduction of viability in GBM model systems, which was mediated by interference with tricarboxylic acid cycle activity and GBM cell respiration. This effect was partially mediated by activation of apoptosis along with activation of caspases regulated chiefly by Bcl-xL and Mcl-1. Knockdown of the ClpP protease or ectopic expression of a ClpP D190A mutant substantially rescued from the inhibition of oxidative energy metabolism as well as from the reduction of cellular viability by ClpP activators and the combination treatment, respectively. Finally, utilizing GBM PDX models, we demonstrated that the combination treatment of HDAC inhibitors and imipridones prolonged host survival more potently than single treatments or vehicle in vivo. Collectively, these observations suggest that the efficacy of HDAC inhibitors might be significantly enhanced through ClpP activators in model systems of human GBM.

Novel IDH1-Targeted Glioma Therapies.

Mutations in the isocitrate dehydrogenase (IDH) 1 gene are commonly found in human glioma, with the majority of low-grade gliomas harboring a recurrent point mutation (IDH1 R132H). Mutant IDH reveals an altered enzymatic activity leading to the synthesis of 2-hydroxyglutarate, which has been implicated in epigenetic mechanisms of oncogenesis. Nevertheless, it is unclear exactly how IDH mutations drive glioma initiation and progression, and it is also not clear why tumors with this mutation generally have a better prognosis than IDH wild-type tumors. Recognition of the high frequency of IDH mutations in glioma [and also in other malignancies, including acute myeloid leukemia (AML) and cholangiocarcinoma] have led to the development of a number of targeted agents that can inhibit these enzymes. Enasidenib and ivosidenib have both gained regulatory approval for IDH mutant AML. Both agents are still in early clinical phases for glioma therapy, as are a number of additional candidates (including AG-881, BAY1436032, and DS1001). A marked clinical problem in the development of these agents is overcoming the blood-brain barrier. An alternative approach to target the IDH1 mutation is by the induction of synthetic lethality with compounds that target poly (ADP-ribose) polymerase (PARP), glutamine metabolism, and the Bcl-2 family of proteins. We conclude that within the last decade, several approaches have been devised to therapeutically target the IDH1 mutation, and that, potentially, both IDH1 inhibitors and synthetic lethal approaches might be relevant for future therapies.

Abstract 1311A: CYP3A5 regulation of androgen receptor signaling: Relevance in African American prostate cancer patients and its development as novel target

Abstract Background: Previously we demonstrated that CYP3A5 positively regulates androgen receptor (AR) signaling and growth of prostate cancer (PC) cells. CYP3A5 inhibition decreases nuclear AR localization and downregulates AR downstream signaling (e.g. PSA and TMPRSS2), resulting in decreased PC cell growth both with and without dihydrotestosterone (DHT) induction. Our current work focusses on the effect of CYP3A5 modulation on AR signaling and therapeutic resistance, mostly in African Americans (AA) widely carrying (73%) wild type CYP3A5 (*1/*1). AAs and have higher incidence of PC and double the mortality rate compared to Non-Hispanic White Americans (NHWA) carrying mutated CY3A5 gene (*3/3, 95%) and expressing truncated non-functional CYP3A5 protein. Methods: Immunoprecipitation was used to identify binding partners of AR. q-RT-PCR based profiler assays was used to detect changes in AR downstream signaling and effect on genes responsible for therapeutic resistance after CYP3A5 inhibition. Effect of CYP3A5 on AR nuclear translocation and induction of synthetic lethality in combination with PARP inhibitors were evaluated using cell fractionation and immunocytochemistry studies. Results: Co-immunoprecipitation of flag-tagged CYP3A5 transfected LNCaP cell extracts showed that CYP3A5 was in a complex with HSP90, AR, HSP70 and HSP40, also confirmed with reverse immunoprecipitation using AR/ HSP90 antibodies and agarose A/G beads. AR regulated genes (SCL45A3, FKBP5, MYC, ELL2, and MT2A) were downregulated with CYP3A5 siRNA treatment in MDA PCa 2b cells (*1/*3, AA origin) in a qPCR-based profiler assay with high fold difference and a P value of ≤0.005. PC patients are often prescribed medications for comorbidities, many of which are CYP3A modulators. Our results indicate that CYP inhibitors (amiodarone, ritonavir, fluoxetine etc.) decrease AR nuclear translocation and inducers (phenytoin, rifampicin, pioglitazone and hyperforin) increase AR nuclear translocation and activation. CYP3A5 siRNA treatment downregulates genes involved in cancer drug therapeutic resistance (TOP2A, BRCA1/2, CCNE1, CDK2/4, DHFR, MVP, MYC, RARB and HPRT1, P ≤ 0.005 ). Loss of TOP2A, BRCA2 and BRCA1is known to impair homologous recombination (HR). In combination with topoisomerase inhibitor etoposide, CYP3A5 siRNA in PC cells increases number of gamma-H2AX foci indicating synthetic lethality. Conclusion: A-Developing CYP3A5-AR-HSP90 interface as a target may provide a novel strategy to block PC growth. B-CYP3A5 modulation of AR signaling can affect the efficacy of androgen deprivation therapy specifically AA patients carrying wild type CYP3A5. C-Since CYP3A5 inhibition, downregulates DNA damage repair genes and impairs HR, CYP3A5 inhibition in combination with PARP inhibitors can be a novel strategy to induce synthetic lethality in PC patients. Citation Format: Priyatham Gorjala, Oscar B. Goodman, Ranjana Mitra. CYP3A5 regulation of androgen receptor signaling: Relevance in African American prostate cancer patients and its development as novel target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1311A.

Polo-like Kinase 1 Inhibition as a Therapeutic Approach to Selectively Target BRCA1-Deficient Cancer Cells by Synthetic Lethality Induction

BRCA1 and BRCA2 deficiencies are widespread drivers of human cancers that await the development of targeted therapies. We aimed to identify novel synthetic lethal relationships with therapeutic potential using BRCA-deficient isogenic backgrounds. We developed a phenotypic screening technology to simultaneously search for synthetic lethal (SL) interactions in BRCA1- and BRCA2-deficient contexts. For validation, we developed chimeric spheroids and a dual-tumor xenograft model that allowed the confirmation of SL induction with the concomitant evaluation of undesired cytotoxicity on BRCA-proficient cells. To extend our results using clinical data, we performed retrospective analysis on The Cancer Genome Atlas (TCGA) breast cancer database. The screening of a kinase inhibitors library revealed that Polo-like kinase 1 (PLK1) inhibition triggers strong SL induction in BRCA1-deficient cells. Mechanistically, we found no connection between the SL induced by PLK1 inhibition and PARP inhibitors. Instead, we uncovered that BRCA1 downregulation and PLK1 inhibition lead to aberrant mitotic phenotypes with altered centrosomal duplication and cytokinesis, which severely reduced the clonogenic potential of these cells. The penetrance of PLK1/BRCA1 SL interaction was validated using several isogenic and nonisogenic cellular models, chimeric spheroids, and mice xenografts. Moreover, bioinformatic analysis revealed high-PLK1 expression in BRCA1-deficient tumors, a phenotype that was consistently recapitulated by inducing BRCA1 deficiency in multiple cell lines as well as in BRCA1-mutant cells. We uncovered an unforeseen addiction of BRCA1-deficient cancer cells to PLK1 expression, which provides a new means to exploit the therapeutic potential of PLK1 inhibitors in clinical trials, by generating stratification schemes that consider this molecular trait in patient cohorts.

AKT inhibition impairs PCNA ubiquitylation and triggers synthetic lethality in homologous recombination-deficient cells submitted to replication stress

Translesion DNA synthesis (TLS) and homologous recombination (HR) cooperate during S-phase to safeguard replication forks integrity. Thus, the inhibition of TLS becomes a promising point of therapeutic intervention in HR-deficient cancers, where TLS impairment might trigger synthetic lethality (SL). The main limitation to test this hypothesis is the current lack of selective pharmacological inhibitors of TLS. Herein, we developed a miniaturized screening assay to identify inhibitors of PCNA ubiquitylation, a key post-translational modification required for efficient TLS activation. After screening a library of 627 kinase inhibitors, we found that targeting the pro-survival kinase AKT leads to strong impairment of PCNA ubiquitylation. Mechanistically, we found that AKT-mediated modulation of Proliferating Cell Nuclear Antigen (PCNA) ubiquitylation after UV requires the upstream activity of DNA PKcs, without affecting PCNA ubiquitylation levels in unperturbed cells. Moreover, we confirmed that persistent AKT inhibition blocks the recruitment of TLS polymerases to sites of DNA damage and impairs DNA replication forks processivity after UV irradiation, leading to increased DNA replication stress and cell death. Remarkably, when we compared the differential survival of HR-proficient vs HR-deficient cells, we found that the combination of UV irradiation and AKT inhibition leads to robust SL induction in HR-deficient cells. We link this phenotype to AKT ability to inhibit PCNA ubiquitylation, since the targeted knockdown of PCNA E3-ligase (RAD18) and a non-ubiquitylable (PCNA K164R) knock-in model recapitulate the observed SL induction. Collectively, this work identifies AKT as a novel regulator of PCNA ubiquitylation and provides the proof-of-concept of inhibiting TLS as a therapeutic approach to selectively kill HR-deficient cells submitted to replication stress.

Nanoencapsulation of Novel Inhibitors of PNKP for Selective Sensitization to Ionizing Radiation and Irinotecan and Induction of Synthetic Lethality

There is increasing interest in developing and applying DNA repair inhibitors in cancer treatment to augment the efficacy of radiation and conventional genotoxic chemotherapy. However, targeting the inhibitor is required to avoid reducing the repair capacity of normal tissue. The aim of this study was to develop nanodelivery systems for the encapsulation of novel imidopiperidine-based inhibitors of the DNA 3'-phosphatase activity of polynucleotide kinase/phosphatase (PNKP), a DNA repair enzyme that plays a critical role in rejoining DNA single- and double-strand breaks. For this purpose, newly identified hit compounds with potent PNKP inhibitory activity, imidopiperidines A12B4C50 and A83B4C63 were encapsulated in polymeric micelles of different poly(ethylene oxide)- b-poly(ε-caprolactone) (PEO- b-PCL)-based structures. Our results showed efficient loading of A12B4C50 and A83B4C63 in PEO- b-PCLs with pendent carboxyl and benzyl carboxylate groups, respectively, and relatively slow release over 24 h. Both free and encapsulated inhibitors were able to sensitize HCT116 cells to radiation and the topoisomerase I poison, irinotecan. In addition, the encapsulated inhibitors were capable of inducing synthetic lethalilty in phosphatase and tensin homologue (PTEN)-deficient cells. We also established the validity of the peptide GE11 as a suitable ligand for active targeted delivery of nanoencapsulated drugs to colorectal cancer cells overexpressing epidermal growth factor receptor (EGFR). Our results show the potential of nanoencapsulated inhibitors of PNKP as either mono or combined therapeutic agents for colorectal cancer.

Induction of synthetic lethality in glioblastoma

Induction of synthetic lethality in glioblastoma

Induction of Synthetic Lethality by Natural Compounds Targeting Cancer Signaling.

Despite the breakthroughs that have been achieved, significant unmet needs relating to the inadequate efficacy and toxicity of currently-available cancer therapies remain. Kinase inhibitors are a class of agents that target signaling factors responsible for the survival of malignant cells, and may address at least some of these issues. The concept of synthetic lethality provides a potential solution to counteract pathway redundancies, and refers to situations in which a mutation in one of two particular genes alone permits cell survival, while simultaneous mutation in both results in cell death. When exploited in the context of cancer therapy, pathways that are uniquely upregulated in cancer cells become selective targets, with reduced off-target toxicity toward their healthy counterparts. Natural compounds represent a large and readily-accessible library of bioactive structures that can be screened for synthetically lethal interactions by testing for the inhibition of kinases relevant to cancer cell survival. In this review, we discuss the concept of synthetic lethality and focus on scenarios in which natural compounds that target kinases may be applied to tip the balance in favor of cancer cell death during therapeutic challenge.

Induction of synthetic lethality in IDH1-mutated gliomas through inhibition of Bcl-xL

Certain gliomas often harbor a mutation in the activity center of IDH1 (R132H), which leads to the production of the oncometabolite 2-R-2-hydroxyglutarate (2-HG). In six model systems, including patient-derived stem cell-like glioblastoma cultures, inhibition of Bcl-xL induces significantly more apoptosis in IDH1-mutated cells than in wild-type IDH1 cells. Anaplastic astrocytoma samples with mutated IDH1 display lower levels of Mcl-1 than IDH1 wild-type tumors and specific knockdown of Mcl-1 broadly sensitizes glioblastoma cells to Bcl-xL inhibition-mediated apoptosis. Addition of 2-HG to glioblastoma cultures recapitulates the effects of the IDH mutation on intrinsic apoptosis, shuts down oxidative phosphorylation and reduces ATP levels in glioblastoma cells. 2-HG-mediated energy depletion activates AMPK (Threonine 172), blunting protein synthesis and mTOR signaling, culminating in a decline of Mcl-1. In an orthotopic glioblastoma xenograft model expressing mutated IDH1, Bcl-xL inhibition leads to long-term survival. These results demonstrate that IDH1-mutated gliomas are particularly vulnerable to Bcl-xL inhibition.

Abstract 3314: Sensitization of human tumor cells to chemotherapy drugs by antisense downregulation of BRCA2 and thymidylate synthase (TS): Induction of synthetic lethality by targeting DNA repair.

Abstract Although genomic instability contributes to tumor progression and development of drug resistance, molecular events underlying instability could also lead to selective sensitivity of tumor cells to certain treatments. Deficiencies in specific mechanisms of DNA repair, with resultant dependence on other repair pathways, have been exploited in therapeutic strategies. For example, BRCA1 and BRCA2, which are involved in homologous recombination repair, have been implicated in hereditary and sporadic carcinomas of the breast, ovary, and other sites. Notably, individuals with BRCA2 mutations respond more favourably to conventional chemotherapy. It is hypothesized that in the absence of functional BRCA2 protein, tumor cells are unable to efficiently repair DNA damage induced by anticancer agents. This "synthetic lethality" can be exploited to selectively kill BRCA1- or BRCA2-deficient tumor cells both in vitro (Nature 434: 913, and 917, 2005) and in patients (NEJM 361: 123, 2009). To advance the utility of this phenomenon to selectively kill cancer cells, it may be possible to use antisense technology to create synthetic lethal situations in tumors. siRNA knockdown of BRCA2 in human A549 non-small cell lung cancer cells inhibited proliferation and induced sensitization to cisplatin (DNA cross-linker), melphalan (alkylating agent), the poly(ADP-ribose) polymerase inhibitor olaparib, and the thymidylate synthase (TS)-targeting agent 5-fluorodeoxyuridine. Three novel oligodeoxynucleotides (ODNs) were synthesized to target the BRCA2 mRNA, 2 against the coding region (ODNs BR1 and BR2) and the other in the 3′-untranslated region (BR3). All three ODNs sensitized A549 cells to cisplatin by up to 80%, and BR1 synergistically inhibited proliferation in combination with an antisense ODN targeting TS, SARI-083. A combination of siRNA treatments that knocked down both BRCA2 and TS sensitized cells to a combination of alkylating agents (cisplatin or melphalan) and a TS-targeting drug (5-FUdR). This combination was more effective at inhibiting proliferation than would be predicted by knockdown of TS and BRCA2 followed by treatment with any single drug (5-FUdR, cisplatin, or melphalan). These data suggest that: (1) targeting BRCA2 is a viable strategy to increase the effectiveness of common chemotherapeutic drugs; and (2) it is possible to use antisense-mediated targeting of both TS and a DNA repair protein to sensitize the same cell to two different drugs, and thus potentiate overall therapeutic effectiveness. This is progressing towards human trials. Supported by a grant from the Canadian Institutes of Health Research (CIHR) to JK and MDV. MR is a scholar of the CIHR Strategic Training Program in Cancer Research and Technology Transfer (CaRTT) and a recipient of the Queen Elizabeth II Scholarship in Science and Technology. Citation Format: Peter J. Ferguson, Mateusz Rytelewski, Mark D. Vincent, René Figueredo, James Koropatnick. Sensitization of human tumor cells to chemotherapy drugs by antisense downregulation of BRCA2 and thymidylate synthase (TS): Induction of synthetic lethality by targeting DNA repair. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3314. doi:10.1158/1538-7445.AM2013-3314

Abstract A106: Induction of synthetic lethality in mutant KRAS cells for lung cancer prevention and therapy

Abstract Lung cancer is the leading cause of cancer death in both men and women in the United States, with a low five-year survival rate despite improved treatment strategies. Mutations and activation of KRAS occur frequently in non-small cell lung cancers (NSCLCs) and are associated with higher risk of drug-resistance, tumor recurrence, and poor prognosis. Currently, there are no effective therapies for targeting mutant KRAS and there is a great need to develop such a strategy. We have previously discovered a synthetic lethal interaction among TNF-related apoptosis-inducing ligand (TRAIL), the second mitochondria-derived activator of caspase Smac/DIABLO (Smac), and mutant KRAS in premalignant lung epithelial cells, which allows for chemoprevention of KRAS-driven lung cancer by the combination of TRAIL and Smac mimic [Cancer Prev Res (Phila). 2011 May;4(5):666–73.]. Here we demonstrated that this synthetic lethal interaction also exists in malignant lung cancer cells. We showed that 3 out of 4 lung cancer cell lines harboring mutant KRAS displayed high sensitivity to the combination of TRAIL and Smac mimic and KRAS wild type lung cancer cell lines were resistant to the treatment. Expression of mutant KRAS in KRAS wild type lung cancer cells sensitized these cells to TRAIL and Smac mimic and knocking down of mutant KRAS in mutant KRAS expressing cells resulted in resistance to the treatment. Furthermore, we showed that TRAIL and Smac mimic treatment inhibited xenograft tumor growth in mutant KRAS dependent manner. Mechanistically, we found that mutant KRAS repressed cellular FADD-like interleukin 1β–converting enzyme (FLICE)-like inhibitory protein (c-FLIP) expression through the activation of Erk/mitogen-activated protein kinase (MAPK)-mediated activation of c-Myc. Mutant KRAS also enhanced the secretion of Prostate Apoptosis Response-4 (Par4) to promote TRAIL-induced apoptosis. Our study provided a potential new approach for lung cancer chemoprevention and therapy based on synthetic lethality that targets mutant KRAS for apoptosis using the combination of and Smac mimic. Citation Information: Cancer Prev Res 2011;4(10 Suppl):A106.