Mapping genetic interactions in cancer: a road to rational combination therapies

Abstract The discovery of synthetic lethal interactions between poly (ADP-ribose) polymerase (PARP) inhibitors and BRCA genes, which are involved in homologous recombination, led to the approval of PARP inhibition as a monotherapy for patients with BRCA1/2-mutated breast or ovarian cancer. Studies following the initial observation of synthetic lethality demonstrated that the reach of PARP inhibitors is well beyond just BRCA1/2 mutants. Insights into the mechanisms of action of anticancer drugs are fundamental for the development of targeted monotherapies or rational combination treatments that will synergize to promote cancer cell death and overcome mechanisms of resistance. The development of targeted therapeutic agents is premised on mapping the physical and functional dependencies of mutated genes in cancer. An important part of this effort is the systematic screening of genetic interactions in a variety of cancer types. Until recently, genetic-interaction screens have relied either on the pairwise perturbations of two genes or on the perturbation of genes of interest combined with inhibition by commonly used anticancer drugs. Here, we summarize recent advances in mapping genetic interactions using targeted, genome-wide, and high-throughput genetic screens, and we discuss the therapeutic insights obtained through such screens. We further focus on factors that should be considered in order to develop a robust analysis pipeline. Finally, we discuss the integration of functional interaction data with orthogonal methods and suggest that such approaches will increase the reach of genetic-interaction screens for the development of rational combination therapies.

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Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies

npj Precision Oncology ◽

10.1038/s41698-021-00232-w ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Marilyne Labrie ◽

Allen Li ◽

Allison Creason ◽

Courtney Betts ◽

Jamie Keck ◽

...

Keyword(s):

Breast Cancer ◽

Parp Inhibitor ◽

Parp Inhibitors ◽

Parp Inhibition ◽

Patient Specific ◽

Combination Therapies ◽

Breast Cancer Patients ◽

Effector Cells ◽

Basal Breast Cancer ◽

Rational Combination

AbstractIn a pilot study, we evaluated the feasibility of real-time deep analysis of serial tumor samples from triple negative breast cancer patients to identify mechanisms of resistance and treatment opportunities as they emerge under therapeutic stress engendered by poly-ADP-ribose polymerase (PARP) inhibitors (PARPi). In a BRCA-mutant basal breast cancer exceptional long-term survivor, a striking tumor destruction was accompanied by a marked infiltration of immune cells containing CD8 effector cells, consistent with pre-clinical evidence for association between STING mediated immune activation and benefit from PARPi and immunotherapy. Tumor cells in the exceptional responder underwent extensive protein network rewiring in response to PARP inhibition. In contrast, there were minimal changes in the ecosystem of a luminal androgen receptor rapid progressor, likely due to indifference to the effects of PARP inhibition. Together, identification of PARPi-induced emergent changes could be used to select patient specific combination therapies, based on tumor and immune state changes.

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PARP Inhibitor Resistance Mechanisms and Implications for Post-Progression Combination Therapies

Cancers ◽

10.3390/cancers12082054 ◽

2020 ◽

Vol 12 (8) ◽

pp. 2054

Author(s):

Elizabeth K. Lee ◽

Ursula A. Matulonis

Keyword(s):

Synthetic Lethality ◽

Parp Inhibitor ◽

Parp Inhibitors ◽

Resistance Mechanisms ◽

Parp Inhibition ◽

Combination Therapies ◽

Mechanisms Of Resistance ◽

Damage Repair ◽

Inhibitor Resistance

The use of PARP inhibitors (PARPi) is growing widely as FDA approvals have shifted its use from the recurrence setting to the frontline setting. In parallel, the population developing PARPi resistance is increasing. Here we review the role of PARP, DNA damage repair, and synthetic lethality. We discuss mechanisms of resistance to PARP inhibition and how this informs on novel combinations to re-sensitize cancer cells to PARPi.

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Poly-ADP-ribose polymerase inhibitor use in ovarian cancer: expanding indications and novel combination strategies

International Journal of Gynecological Cancer ◽

10.1136/ijgc-2019-000499 ◽

2019 ◽

Vol 29 (5) ◽

pp. 956-968 ◽

Cited By ~ 2

Author(s):

Emily Hinchcliff ◽

Shannon Neville Westin ◽

Graziela Dal Molin ◽

Christopher J LaFargue ◽

Robert L. Coleman

Keyword(s):

Ovarian Cancer ◽

Drug Administration ◽

Food And Drug Administration ◽

Parp Inhibitors ◽

Parp Inhibition ◽

Combination Therapies ◽

Combination Strategies ◽

Polymerase Inhibitor

The use of poly(ADP-ribose) polymerase (PARP) inhibition is transforming care for the treatment of ovarian cancer, with three different PARP inhibitors (PARPi) gaining US Food and Drug Administration approval since 2014. Given the rapidly expanding use of PARPi, this review aims to summarize the key evidence for their use and therapeutic indications. Furthermore, we provide an overview of the development of PARPi resistance and the emerging role of PARPi combination therapies, including those with anti-angiogenic and immunotherapeutic agents.

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Frequency and prognostic value of mutations associated with the homologous recombination DNA repair pathway in a large pan cancer cohort

Scientific Reports ◽

10.1038/s41598-020-76975-6 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Daniel R. Principe ◽

Matthew Narbutis ◽

Regina Koch ◽

Ajay Rana

Keyword(s):

Dna Repair ◽

Homologous Recombination ◽

Synthetic Lethality ◽

Parp Inhibitors ◽

The Cancer Genome Atlas ◽

Parp Inhibition ◽

Repair Pathway ◽

Wide Range ◽

Recombination Pathway ◽

Pan Cancer

AbstractPARP inhibitors have shown remarkable efficacy in the clinical management of several BRCA-mutated tumors. This approach is based on the long-standing hypothesis that PARP inhibition will impair the repair of single stranded breaks, causing synthetic lethality in tumors with loss of high-fidelity double-strand break homologous recombination. While this is now well accepted and has been the basis of several successful clinical trials, emerging evidence strongly suggests that mutation to several additional genes involved in homologous recombination may also have predictive value for PARP inhibitors. While this notion is supported by early clinical evidence, the mutation frequencies of these and other functionally related genes are largely unknown, particularly in cancers not classically associated with homologous recombination deficiency. We therefore evaluated the mutation status of 22 genes associated with the homologous recombination DNA repair pathway or PARP inhibitor sensitivity, first in a pan-cancer cohort of 55,586 patients, followed by a more focused analysis in The Cancer Genome Atlas cohort of 12,153 patients. In both groups we observed high rates of mutations in a variety of HR-associated genes largely unexplored in the setting of PARP inhibition, many of which were associated also with poor clinical outcomes. We then extended our study to determine which mutations have a known oncogenic role, as well as similar to known oncogenic mutations that may have a similar phenotype. Finally, we explored the individual cancer histologies in which these genomic alterations are most frequent. We concluded that the rates of deleterious mutations affecting genes associated with the homologous recombination pathway may be underrepresented in a wide range of human cancers, and several of these genes warrant further and more focused investigation, particularly in the setting of PARP inhibition and HR deficiency.

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A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis

10.1101/2021.04.22.440879 ◽

2021 ◽

Author(s):

Umar Khalid ◽

Milena Simovic ◽

Murat Iskar ◽

John KL Wong ◽

Rithu Kumar ◽

...

Keyword(s):

Synthetic Lethality ◽

Parp Inhibitor ◽

Strand Break ◽

Parp Inhibitors ◽

Synergistic Interaction ◽

Parp Inhibition ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Dna Double Strand Break

ABSTRACTChromothripsis is a form of genomic instability characterized by the occurrence of tens to hundreds of clustered DNA double-strand breaks in a one-off catastrophic event. Rearrangements associated with chromothripsis are detectable in numerous tumor entities and linked with poor prognosis in some of these, such as Sonic Hedgehog medulloblastoma, neuroblastoma and osteosarcoma. Hence, there is a need for therapeutic strategies eliminating tumor cells with chromothripsis. Defects in DNA double-strand break repair, and in particular homologous recombination repair, have been linked with chromothripsis. Targeting DNA repair deficiencies by synthetic lethality approaches, we performed a synergy screen using drug libraries (n = 375 compounds, 15 models) combined with either a PARP inhibitor or cisplatin. This revealed a synergistic interaction between the HDAC inhibitor romidepsin and PARP inhibition. Functional assays, transcriptome analyses, and in vivo validation in patient-derived xenograft mouse models confirmed the efficacy of the combinatorial treatment.

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Loss of heterozygosity in multiple myeloma: A role for PARP inhibition?

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.8026 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. 8026-8026 ◽

Cited By ~ 1

Author(s):

Charlotte Pawlyn ◽

Andrea Loehr ◽

Ruslana Tytarenko ◽

Shayu Deshpande ◽

James Sun ◽

...

Keyword(s):

Loss Of Heterozygosity ◽

Poor Prognosis ◽

Synthetic Lethality ◽

Unmet Need ◽

Parp Inhibitors ◽

Disease Stage ◽

Parp Inhibition ◽

Proliferation Index ◽

Clinical Group ◽

Nucleotide Polymorphisms

8026 Background: PARP inhibitors can induce synthetic lethality in tumors characterized by homologous recombination deficiency (HRD). Two PARP inhibitors are approved for the treatment of BRCA mutated ovarian cancer. HRD can be detected by evaluating genome-wide loss of heterozygosity (LOH), which is associated with response to PARP inhibition. Myeloma (MM) is a genetically unstable tumor and we hypothesized that LOH could be detected in patient samples, supporting a potential role for PARP inhibition in MM. Methods: We analyzed 406 cases at all disease stages: MGUS (n = 7), smoldering MM (SMM, n = 30) newly diagnosed MM (NDMM, n = 71), treated MM (TRMM, n = 64) and relapsed MM (RLMM, n = 234). CD138+ plasma cell DNA underwent targeted next generation sequencing (FoundationOne Heme) interrogating 405 cancer related genes and 3543 single nucleotide polymorphisms (SNPs) across the genome. An algorithm using the minor allele frequencies of the examined SNPs and copy number profile across the 22 autosomal chromosomes identified LOH segments. Events unlikely to be caused by HRD, e.g. whole chromosome or chromosome-arm loss, were excluded. The percentage of genomic LOH for each sample was calculated as the sum of the lengths of included LOH segments divided by the length of the interrogated genome. Results: We found evidence of HRD detected by LOH with higher LOH selecting for patients with poor outcome. LOH increases with advancing disease stage from a median of 0.3% in MGUS to 3.1% in RLMM. LOH was highest in the PR and MMSET molecular subgroups and correlated significantly with the gene expression defined risk score GEP70 (R = 0.4, p < 0.001) and proliferation index (R = 0.4, p < 0.001). Outcome of RLMM patients, the biggest clinical group, was analyzed and patients with LOH above the 3rdquartile (≥5%LOH) had significantly worse overall survival than those with lower levels (p < 0.001). LOH correlates and overlaps with other metrics of poor prognosis, suggesting it may be a prognostic marker itself. Conclusions: We demonstrated LOH in MM samples, increasing as disease progresses and associated with poor prognosis. These data support the further evaluation of PARP inhibitors in MM patients, particularly in the relapsed setting with a high unmet need for new treatments.

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Moving beyond PARP Inhibition: Current State and Future Perspectives in Breast Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms22157884 ◽

2021 ◽

Vol 22 (15) ◽

pp. 7884

Author(s):

Michela Palleschi ◽

Gianluca Tedaldi ◽

Marianna Sirico ◽

Alessandra Virga ◽

Paola Ulivi ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Treatment ◽

Synthetic Lethality ◽

Current Knowledge ◽

Parp Inhibitors ◽

Resistance Mechanisms ◽

Breast Cancer Treatment ◽

Parp Inhibition ◽

Combination Strategies ◽

Pubmed Search

Breast cancer is the most frequent and lethal tumor in women and finding the best therapeutic strategy for each patient is an important challenge. PARP inhibitors (PARPis) are the first, clinically approved drugs designed to exploit synthetic lethality in tumors harboring BRCA1/2 mutations. Recent evidence indicates that PARPis have the potential to be used both in monotherapy and combination strategies in breast cancer treatment. In this review, we show the mechanism of action of PARPis and discuss the latest clinical applications in different breast cancer treatment settings, including the use as neoadjuvant and adjuvant approaches. Furthermore, as a class, PARPis show many similarities but also certain critical differences which can have essential clinical implications. Finally, we report the current knowledge about the resistance mechanisms to PARPis. A systematic PubMed search, using the entry terms “PARP inhibitors” and “breast cancer”, was performed to identify all published clinical trials (Phase I-II-III) and ongoing trials (ClinicalTrials.gov), that have been reported and discussed in this review.

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Alternate therapeutic pathways for PARP inhibitors and potential mechanisms of resistance

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00557-3 ◽

2021 ◽

Vol 53 (1) ◽

pp. 42-51

Author(s):

Dae-Seok Kim ◽

Cristel V. Camacho ◽

W. Lee Kraus

Keyword(s):

Clinical Trials ◽

Homologous Recombination ◽

Cancer Cells ◽

Synthetic Lethality ◽

Parp Inhibitor ◽

Cancer Therapeutics ◽

Progression Free Survival ◽

Parp Inhibitors ◽

Parp Inhibition ◽

Combination Strategies

AbstractHomologous recombination (HR) repair deficiency impairs the proper maintenance of genomic stability, thus rendering cancer cells vulnerable to loss or inhibition of DNA repair proteins, such as poly(ADP-ribose) polymerase-1 (PARP-1). Inhibitors of nuclear PARPs are effective therapeutics for a number of different types of cancers. Here we review key concepts and current progress on the therapeutic use of PARP inhibitors (PARPi). PARPi selectively induce synthetic lethality in cancer cells with homologous recombination deficiencies (HRDs), the most notable being cancer cells harboring mutations in the BRCA1 and BRCA2 genes. Recent clinical evidence, however, shows that PARPi can be effective as cancer therapeutics regardless of BRCA1/2 or HRD status, suggesting that a broader population of patients might benefit from PARPi therapy. Currently, four PARPi have been approved by the Food and Drug Administration (FDA) for the treatment of advanced ovarian and breast cancer with deleterious BRCA mutations. Although PARPi have been shown to improve progression-free survival, cancer cells inevitably develop resistance, which poses a significant obstacle to the prolonged use of PARP inhibitors. For example, somatic BRCA1/2 reversion mutations are often identified in patients with BRCA1/2-mutated cancers after treatment with platinum-based therapy, causing restoration of HR capacity and thus conferring PARPi resistance. Accordingly, PARPi have been studied in combination with other targeted therapies to overcome PARPi resistance, enhance PARPi efficacy, and sensitize tumors to PARP inhibition. Moreover, multiple clinical trials are now actively underway to evaluate novel combinations of PARPi with other anticancer therapies for the treatment of PARPi-resistant cancer. In this review, we highlight the mechanisms of action of PARP inhibitors with or without BRCA1/2 defects and provide an overview of the ongoing clinical trials of PARPi. We also review the current progress on PARPi-based combination strategies and PARP inhibitor resistance.

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Shuffle-Seq: En masse combinatorial encoding for n-way genetic interaction screens

10.1101/861443 ◽

2019 ◽

Author(s):

Atray Dixit ◽

Olena Kuksenko ◽

David Feldman ◽

Aviv Regev

Keyword(s):

Large Scale ◽

Genetic Interaction ◽

Synthetic Lethality ◽

Genetic Interactions ◽

Pairwise Interactions ◽

Affect Cell Viability ◽

Melanoma Model ◽

Dividing Cells ◽

Combinatorial Encoding ◽

Massive Number

AbstractGenetic interactions, defined as the non-additive phenotypic impact of combinations of genes, are a hallmark of the mapping from genotype to phenotype. However, genetic interactions remain challenging to systematically test given the massive number of possible combinations. In particular, while large-scale screening efforts in yeast have quantified pairwise interactions that affect cell viability, or synthetic lethality, between all pairs of genes as well as for a limited number of three-way interactions, it has previously been intractable to perform the large screens needed to comprehensively assess interactions in a mammalian genome. Here, we develop Shuffle-Seq, a scalable method to assay genetic interactions. Shuffle-Seq leverages the co-inheritance of genetically encoded barcodes in dividing cells and can scale in proportion to sequencing throughput. We demonstrate the technical validity of Shuffle-Seq and apply it to screening for mechanisms underlying drug resistance in a melanoma model. Shuffle-Seq should allow screens of hundreds of millions of combinatorial perturbations and facilitate the understanding of genetic dependencies and drug sensitivities.

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Combined Strategies with Poly (ADP-Ribose) Polymerase (PARP) Inhibitors for the Treatment of Ovarian Cancer: A Literature Review

Diagnostics ◽

10.3390/diagnostics9030087 ◽

2019 ◽

Vol 9 (3) ◽

pp. 87 ◽

Cited By ~ 24

Author(s):

Stergios Boussios ◽

Peeter Karihtala ◽

Michele Moschetta ◽

Afroditi Karathanasi ◽

Agne Sadauskaite ◽

...

Keyword(s):

Ovarian Cancer ◽

Dna Repair ◽

Synthetic Lethality ◽

Excision Repair ◽

Parp Inhibitor ◽

Advanced Ovarian Cancer ◽

Pegylated Liposomal Doxorubicin ◽

Parp Inhibitors ◽

Parp Inhibition ◽

Biologic Agent

Poly (ADP-ribose) polymerase (PARP) inhibitors are the first clinically approved drugs designed to exploit synthetic lethality, and were first introduced as a cancer-targeting strategy in 2005. They have led to a major change in the treatment of advanced ovarian cancer, and altered the natural history of a disease with extreme genetic complexity and defective DNA repair via homologous recombination (HR) pathway. Furthermore, additional mechanisms apart from breast related cancer antigens 1 and 2 (BRCA1/2) mutations can also result in HR pathway alterations and consequently lead to a clinical benefit from PARP inhibitors. Novel combinations of PARP inhibitors with other anticancer therapies are challenging, and better understanding of PARP biology, DNA repair mechanisms, and PARP inhibitor mechanisms of action is crucial. It seems that PARP inhibitor and biologic agent combinations appear well tolerated and clinically effective in both BRCA-mutated and wild-type cancers. They target differing aberrant and exploitable pathways in ovarian cancer, and may induce greater DNA damage and HR deficiency. The input of immunotherapy in ovarian cancer is based on the observation that immunosuppressive microenvironments can affect tumour growth, metastasis, and even treatment resistance. Several biologic agents have been studied in combination with PARP inhibitors, including inhibitors of vascular endothelial growth factor (VEGF; bevacizumab, cediranib), and PD-1 or PD-L1 (durvalumab, pembrolizumab, nivolumab), anti-CTLA4 monoclonal antibodies (tremelimumab), mTOR-(vistusertib), AKT-(capivasertib), and PI3K inhibitors (buparlisib, alpelisib), as well as MEK 1/2, and WEE1 inhibitors (selumetinib and adavosertib, respectively). Olaparib and veliparib have also been combined with chemotherapy with the rationale of disrupting base excision repair via PARP inhibition. Olaparib has been investigated with carboplatin and paclitaxel, whereas veliparib has been tested additionally in combination with temozolomide vs. pegylated liposomal doxorubicin, as well as with oral cyclophosphamide, and topoisomerase inhibitors. However, overlapping myelosuppression observed with PARP inhibitor and chemotherapy combinations requires further investigation with dose escalation studies. In this review, we discuss multiple clinical trials that are underway examining the antitumor activity of such combination strategies.

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