Exploiting DNA Replicative Stress for Novel Small Cell Lung Cancer Therapies

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

1. Targeting replication stress in cancer: Stalled replication forks activate ataxia telangiectasia and Rad3-related kinase (ATR), which subsequently phosphorylate downstream kinases including CHK1. The replication stress-response cascade controls the stalling of replication forks, the initiation of DNA replication, ensures sufficient supply of nucleotides, and limits mitotic entry of cells that have not yet completed DNA replication. Failure to resolve replication stress leads to collapse of replication forks, DNA double-strand breaks (DSBs), and genome instability. Our studies validated ATR as a therapeutic target in high replication stress tumors. a. In a phase I trial, we combined the first-in-class ATR inhibitor berzosertib (M6620) and standard of care SCLC therapeutic topotecan which produces replication stress by trapping TOP1 cleavage complexes in patients whose tumors had relapsed after chemotherapy (Sci Trans Med 2016; J Clin Oncol 2018). Pharmacodynamic studies showed evidence of ATR inhibition and enhanced DSBs in response to the combination. Peak plasma concentrations of berzosertib exceeded doses required for pharmacodynamic modulation of ATR activity in vivo, with no evidence of drug-drug interactions. Notably, we did not observe additive normal tissue toxicities, likely due to the differentiating features of rapidly dividing cancer cells, including higher replication stress. b. In a phase II trial, the combination yielded confirmed partial responses in 36% of 25 patients with relapsed SCLC, meeting the primary objective (Cancer Cell 2021). Efficacy of the combination exceeded those of currently available therapies, especially in platinum-resistant SCLC, i.e., relapse within 3 months of completing initial therapy, typically fatal within weeks. The median duration of response was 6.4 months and four of six responders with platinum-resistant SCLC had responses lasting more than 6 months. Building on these findings, we have launched two independent trials combining topotecan and berzosertib. c. Ongoing studies are targeting replication stress in extra-pulmonary small cell cancers that share aggressive clinical course and molecular phenotypes with SCLC, testing approaches to improve the therapeutic index of DNA repair-targeted combinations, profiling replication stress in patient tumors to enable better patient selection (Cancer Res Comm 2022), and understanding how replication stress and its consequences including abnormal chromosome segregation and immune activation shape SCLC phenotypes and its therapeutic vulnerabilities. 2. Leveraging SCLC genomic instability to drive anti-tumor immune responses: Despite a highly mutated genome, only 12-18% of SCLC patients treated with chemo-immunotherapy at diagnosis remain progression free after a year. Our studies defined the relevance of immunophenotypes for SCLC responses and seek to understand and overcome the unique SCLC immunosuppressive mechanisms. a. We hypothesized that PARP inhibition could render SCLC more susceptible to immune checkpoint blockade and enrolled relapsed SCLC patients on a phase II trial of Programmed Death-Ligand 1 (PD-L1) inhibitor durvalumab and olaparib (J Thorac Oncol 2018). The study did not meet the preset bar for efficacy. However, pre- and during-treatment biopsies showed for the first time that tumor immune phenotypes are important determinants of SCLC immunotherapy responses. Notably, over two thirds of the SCLCs exhibited an immune-excluded phenotype with T cells restricted around the outer edge of the tumor. b. We have also studied immunotherapy resistance in mismatch repair-deficient tumors despite exceptionally high frameshift insertions and deletions and treatment-induced intra-tumoral T-cell infiltrates, finding tumor immunoediting driven by defective JAK1 signaling as the potential basis of resistance (Cold Spring Harb Mol Case Stud. 2020). 3. SCLC subtypes and subtype-specific vulnerabilities: Molecular characterization of SCLC has lagged other cancer types. Thus, despite its exceptionally high mortality, SCLC is treated as a single disease with the same treatments for all patients. Our studies identified vulnerabilities of SCLC subtypes and defined new subtypes, together paving the way for molecular profile-based therapies for SCLC patients. a. We profiled pre-treatment tumors of patients treated with replication-stress targeted therapies to find significant enrichment of essential components of the checkpoint response, including, including E2F target genes, the G2-M checkpoint, and NE differentiation in responding tumors (Cancer Cell 2021). In ongoing studies, we are investigating the mechanistic basis of high replication stress in NE SCLCs. b. Using a similar approach, immunogenomic profiling of pre-treatment tumors revealed cytotoxic T-cell infiltration, elevated Notch signaling, and non-NE differentiation in tumors responding to immunotherapy (Nat Comm 2021). Activation of Notch signaling in a NE human SCLC cell line induced a non-NE phenotype, marked by increased expression of antigen processing and presenting machinery (APM) genes, demonstrating a mechanistic link between Notch activation, non-NE differentiation, and increased intrinsic tumor immunity. c. We also identified a new NE-v2-like subtype, frequently identified in liver biopsies, characterized by enrichment of xenobiotic and drug transporter pathways, marked chemo-resistance, and exceptionally poor survival (Nat Comm 2022). d. We identified inherited mutations in cancer predisposing genes in approximately 10% of SCLC patients (Sci Trans Med 2021). SCLC patients with these mutations respond better to standard chemotherapy and experience longer periods of remission after treatment than patients without these mutations. These studies lay the groundwork for screening and targeted therapies for a small but important group of SCLC patients based on their germline genotype. 4. Roots of SCLC heterogeneity their non-invasive detection in plasma: Most patients with SCLC are diagnosed with and succumb to metastatic disease, yet the current knowledge of SCLC heterogeneity is almost entirely derived from model systems. a. We integrated histology, transcriptome, exome, and treatment outcomes of relapsed SCLC from a range of metastatic sites, revealing complex intra- and intertumoral heterogeneity of NE differentiation (Nat Comm 2021). Importantly, the transcriptional diversity of patient tumors is not fully recapitulated in the corresponding patient-derived model systems, with transcriptional phenotypes strongly skewing towards the NE state in patient-derived model systems. b. In ongoing studies, we are studying the concordance of somatic genome and inferred gene expression between circulating tumor DNA and matched metastatic tumor. Extending these studies, we are also examining whether histone modifications of plasma cell free nucleosomes recover the unique epigenetic states of SCLC tissue and cell of origin, and importantly tumoral expression of SCLC lineage-defining transcription factors (biorxiv 2022). Together, our research to date has defined unique vulnerabilities of SCLC subtypes, advanced a novel therapeutic combination to late-phase clinical trials, identified new subtypes defined by germline genotype and high chemoresistance, provided insights into the heterogeneity of transcriptomic features within and between patient tumors and the extent to which they are depicted in patient derived models.