Genomic and Methylation Markers in SCLC and LCNEC for Chemo-Immunotherapy Resistance Prediction (STRATUS)

The STRATUS Trial (Study of Tumor Characteristics and Molecular Signatures in Neuroendocrine Tumors and SCLC) is an ambitious, prospective observational study designed to explore the molecular and genomic mechanisms underlying resistance to chemo-immunotherapy in patients diagnosed with extensive-stage small cell lung cancer (ES-SCLC) and metastatic large cell neuroendocrine carcinoma (LCNEC). These two aggressive forms of cancer represent a significant unmet clinical need, with high relapse rates and limited therapeutic options available following the development of treatment resistance. The study seeks to uncover actionable biomarkers, characterize resistance mechanisms, and improve our understanding of tumor evolution under selective pressures from standard therapies. By leveraging cutting-edge molecular techniques, such as next-generation sequencing (NGS), DNA methylation profiling, and liquid biopsies, STRATUS aims to set the foundation for personalized cancer treatment approaches in these difficult-to-treat malignancies. Background and Rationale The Challenge of Resistance in ES-SCLC and LCNEC Small cell lung cancer (SCLC) and large cell neuroendocrine carcinoma (LCNEC) are both high-grade neuroendocrine tumors characterized by rapid growth, early dissemination, and a poor prognosis. Approximately two-thirds of SCLC cases are diagnosed as extensive-stage disease (ES-SCLC), where the tumor has spread beyond the hemithorax and regional lymph nodes. Similarly, LCNEC, though rare, is frequently diagnosed at metastatic stages, with limited systemic treatment options available. Standard treatment for ES-SCLC includes platinum-based chemotherapy combined with immune checkpoint inhibitors (ICIs), such as atezolizumab or durvalumab. While initial response rates exceed 70%, resistance develops rapidly in most patients, leading to disease progression within months. For LCNEC, the therapeutic landscape is even more limited, with a lack of targeted therapies or predictive biomarkers guiding treatment. Need for Molecular Insights Resistance mechanisms in these cancers are thought to involve tumor heterogeneity, clonal evolution, epigenetic modifications, and immune evasion. However, the exact processes that drive resistance remain poorly characterized. Molecular profiling offers an opportunity to identify genomic and epigenetic alterations that correlate with treatment failure, allowing for the development of predictive biomarkers and targeted therapeutic strategies. Role of Liquid Biopsies Liquid biopsies, including the analysis of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), have emerged as powerful tools for non-invasive tumor monitoring. These biomarkers provide real-time insights into tumor dynamics, enabling the detection of resistance mechanisms, clonal evolution, and molecular relapse. Study Objectives Primary Objective To identify and characterize genomic, epigenetic, and methylation signatures associated with resistance to chemo-immunotherapy in ES-SCLC and LCNEC patients. Secondary Objectives To evaluate the relationship between circulating biomarkers (CTCs, ctDNA) and clinical outcomes, including progression-free survival (PFS) and overall survival (OS). To compare molecular profiles between long-term responders and patients who develop early resistance. To assess tumor-immune interactions and their role in resistance mechanisms, focusing on PD-L1 expression, T-cell exhaustion, and cytokine signaling pathways. Exploratory Objectives To investigate clonal evolution and emergent subpopulations associated with resistance using phylogenetic analyses. To explore spatial transcriptomic patterns within the tumor microenvironment. To evaluate the potential of novel biomarkers for guiding treatment decisions and monitoring disease progression. Study Design The STRATUS Trial is a multicenter, prospective observational study involving patients treated at the 3rd Department of Medicine, National and Kapodistrian University of Athens, Sotiria Hospital, and other participating centers. The study includes detailed clinical, molecular, and imaging assessments over a three-year follow-up period. Inclusion Criteria Adults aged 18-85 years diagnosed with ES-SCLC or LCNEC. ECOG performance status of 0-2. Histological confirmation of diagnosis with available tumor tissue for molecular analysis. At least one measurable or evaluable lesion according to RECIST 1.1 criteria. Willingness to provide blood samples and participate in follow-up visits. Exclusion Criteria Inability to tolerate chemo-immunotherapy. Presence of another active malignancy or significant comorbidity. Patients with no measurable disease or inadequate follow-up potential. Data Collection and Sample Handling Baseline Assessments Before starting treatment, participants will undergo: Comprehensive clinical evaluations, including medical history, ECOG performance status, and comorbid conditions. Imaging studies (e.g., CT, PET) to assess tumor burden and metastatic sites. Blood sample collection for baseline ctDNA and CTC analysis. Tumor biopsies for genomic, transcriptomic, and methylation profiling. On-Treatment Monitoring Participants will attend follow-up visits every 9 weeks, during which: Blood samples will be collected to monitor ctDNA and CTC levels. Imaging studies will evaluate tumor response according to RECIST 1.1 criteria. Adverse events, clinical progression, and treatment modifications will be documented. Disease Progression Assessments For patients with progressive disease: Repeat biopsies of newly emerging lesions will be performed to identify resistance-associated changes. Blood samples will capture dynamic shifts in ctDNA and CTC profiles, enabling comparisons with baseline and on-treatment data. Laboratory Methods NGS-Based Genomic Analysis: Comprehensive sequencing will identify mutations, copy number alterations, and structural rearrangements. Epigenetic Profiling: DNA methylation arrays will uncover resistance-related epigenetic changes. Spatial Transcriptomics: High-resolution analysis of tumor microenvironment architecture and gene expression patterns. Statistical Analysis Sample Size A total of 111 patients will be enrolled, providing sufficient power to detect significant differences in molecular markers across subgroups. Primary Analysis Regression models will evaluate associations between molecular markers and treatment resistance. Descriptive statistics will summarize biomarker distributions and clinical outcomes. Secondary Analysis Kaplan-Meier survival curves will estimate PFS and OS. Cox proportional hazards models will assess the prognostic significance of identified biomarkers. Exploratory Analysis Machine learning models will predict resistance based on integrated multi-omic data. Clonal evolution will be modeled using phylogenetic techniques to trace tumor adaptation under therapeutic pressure. Ethical Considerations The study will comply with the Declaration of Helsinki and GDPR guidelines for data protection. Participants will provide written informed consent, and all data will be de-identified to ensure confidentiality. Significance and Anticipated Impact The STRATUS Trial is expected to: Identify actionable biomarkers for predicting and overcoming resistance. Advance the understanding of tumor evolution and immune evasion in SCLC and LCNEC. Guide the development of personalized treatment strategies, ultimately improving patient outcomes. Conclusion The STRATUS Trial represents a landmark effort to address the challenges of resistance in SCLC and LCNEC. By combining advanced molecular analyses with robust clinical monitoring, this study has the potential to transform the management of these aggressive cancers and pave the way for a new era of precision oncology.