Exploiting DNA Replicative Stress for Novel Small Cell Lung Cancer Therapies

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

Specific Aim 1A: To evaluate the efficacy of DDR inhibition in combination with DNA-targeted chemotherapy in SCLC and to make such combinations more tolerable: Ataxia-telangiectasia-mutated and rad3-related protein kinase (ATR) is the primary responder to replicative stress and plays a key role in stabilizing the genome when DNA replication is compromised. ATR inhibition enhances replicative stress- by lowering cell cycle checkpoint and DNA repair barriers, causing unchecked proliferation- leading to chromosomal breakage and ultimately cell death. Accordingly, depletion of ATR is synthetically lethal with topoisomerase 1 (TOP1) inhibition-induced replication fork stalling. SCLC have an actionable dependence on ATR-mediated cell cycle checkpoints in preclinical models and ATR inhibition can overcome the rewiring of homologous recombination, which may underlie resistance to DNA targeted agents. Based on these considerations, we initiated a phase I/II clinical trial to test the hypothesis that berzosertib (M6620), a selective inhibitor of ATR and topotecan, a selective inhibitor of TOP1 can be safely combined to heighten replicative stress and to yield durable responses in SCLC. The phase I trial established tolerable doses of the combination and showed enhanced DNA double-stranded breaks supporting synergistic interaction of TOP1 inhibition and ATR inhibition (Thomas A et al. J Clin Oncol 2018). Of 21 patients who enrolled, five had SCLC and all had chemotherapy-refractory disease i.e., disease progression during or within 60-90 days of completing first-line chemotherapy. Three of five patients had a partial response or prolonged stable disease (ongoing at 6 and 7 months and 10 months). Objective response rate among patients with SCLC in the phase II trial was 36% (9/25 patients), achieving the primary efficacy endpoint. Durable tumor regressions were observed in patients with platinum-resistant SCLCs, typically fatal within weeks of recurrence (Thomas A et al. Cancer Cell 2021). We are examining the combination of topotecan and berzosertib in a randomized clinical trial. Specific Aim 1B: To make combinations of DDR inhibition and DNA-targeted chemotherapy more tolerable: Despite promising preclinical data, chemotherapy-DDR inhibitor combinations have proven challenging in clinic. Dose limiting toxicities, specifically myelosuppression has severely limited the ability to dose escalate both PARP inhibitor and chemotherapy in several clinical studies. Kummar et al administered PARP inhibitor veliparib in combination with topotecan and found the combination very myelosuppressive, requiring reduction in doses of both agents. The maximum tolerated dose of veliparib and topotecan represented nearly 3% and 40% of the respective single-agent maximum tolerated doses. Preclinical data show PARP trapping at sites of DNA damage to be an important factor for the synergy of this combination and clinical studies suggest inferior antitumor activity with lower doses of PARP inhibitors. Based on the above considerations, we hypothesized that a dose-escalation strategy that incorporates tumor targeted DNA-damaging chemotherapy delivery and dose scheduling of DDR inhibitors could allow administration of DDR inhibitor-chemotherapy combinations. Based on insights from preclinical studies which provided a better understanding of the mechanisms causing bone marrow toxicity, we designed a clinical trial combining PARP inhibitor olaparib and CRLX101, a nanoparticle formulation of camptothecin, a highly selective inhibitor of TOP1, in patients with advanced solid tumors. The primary endpoint of the phase I trial is to identify the maximum tolerated dose for CRLX101 plus olaparib. This clinical trial is now enrolling patients. The phase II part of the study will test the combination in relapsed SCLC, bladder and prostate cancer patients. Specific Aim 2: To evaluate the efficacy of DDR inhibition in combination with immunotherapy in SCLC: Higher nonsynonymous mutation burden in tumors, molecular smoking signature, and higher neoantigen burden are all associated with improved objective responses and durable clinical benefit to immune checkpoint inhibitors in various cancers. However, the efficacy of immune checkpoint inhibitors in SCLC is far less pronounced than would be expected, despite a high mutational burden. In SCLC cell lines and immune competent murine models, PARP inhibitors enhance the expression of PD-L1. Based on considerations discussed above, we hypothesized that DDR inhibition could render SCLC more susceptible to immune checkpoint blockade, and enrolled a cohort of SCLC patients in the phase II trial of durvalumab plus olaparib to test this hypothesis (Thomas A et al. J Thorac Oncol 2019). The primary objective was to determine anti-tumor efficacy as measured by response rate in relapsed SCLC patients. The study combination did not meet the preset bar for efficacy. We propose that the clinical data indicate a lack of synergistic interaction of PARP inhibition and immune checkpoint blockade (Takahashi et al. Clin Can Res 2020). Specific Aim 3: To identify predictive biomarkers of response to replicative stress-enhancing agents in SCLC: There is a dire need for novel biomarker-directed therapeutics for SCLC. The overall objective of this specific aim is to identify candidate predictive biomarkers of DDR inhibition in SCLC using tissue samples and outcome data from the ongoing prospectively conducted clinical trials. To identify predictors of clinical benefit to immune checkpoint blockade, we performed immunogenomic profiling of tumor samples from patients with relapsed SCLC (Roper et al. Nat Comm 2021). Tumors of patients who derive clinical benefit exhibited cytotoxic T-cell infiltration, high expression of antigen processing and presentation machinery (APM) genes, and low neuroendocrine (NE) differentiation. However, elevated Notch signaling, which positively correlates with low NE differentiation, most significantly predicts clinical benefit to immune checkpoint blockade. Activation of Notch signaling in a NE human SCLC cell line induces a low NE phenotype, marked by increased expression of APM genes, demonstrating a mechanistic link between Notch activation, low NE differentiation and increased intrinsic tumor immunity. Our findings suggest Notch signaling as a determinant of response to ICB in SCLC. To identify predictors of clinical benefit to ATR inhibition, we examined tumor exome and transcriptome of patients who enrolled on the trial of berzosertib and topotecan. Genes upregulated in responding tumors dis-played marked enrichment for multiple pathways associated with cell-cycle progression and DNA repair, including E2F target genes, the G2-M checkpoint, and ATM, ATR, and Fanconi DNA repair pathways, consistent with responding tumors harboring a replication stress phenotype. The enrichment of high NE phenotype with cell proliferation and DNA repair signatures suggest co-regulated tumor phenotypes that together define a distinct SCLC transcriptomic subset.