Farrugia, David

Abstract Background: Immune checkpoint inhibitors (ICIs) have significantly improved outcomes for patients with metastatic non-small cell lung cancer (NSCLC). However, clinical management is challenging. The PD-L1 biomarker does not optimally guide the choice between ICI monotherapy and combination ICI-chemotherapy, and there are currently no biomarkers to predict immune-related adverse events (irAEs). Here, we describe a versatile platform based on plasma proteomics and machine learning for generating predictive tools to support treatment decisions. Methods: Pre-treatment plasma samples were collected from 616 NSCLC patients receiving ICI-based therapy (NCT04056247). Clinical benefit (CB) data and irAEs were recorded. Proteomic profiling of plasma samples was performed using the SomaScan® assay, covering ~7000 proteins per sample. Proteins associated with Clinical Benefit (progression-free survival at 12 months) were classified as resistance-associated proteins (RAPs). Proteins associated with grade ≥3 irAEs occurring within the first 100 days of treatment were classified as toxicity-associated proteins (TAPs). RAPs and TAPs were integrated into two separate machine learning-based models, yielding CB and irAE probabilities, respectively. The CB model used a CB probability threshold to assign patients a PROphet-positive or PROphet-negative result. Bioinformatic analysis was performed on RAPs and TAPs. Results: CB and irAE models displayed strong predictive performance with a high correlation between predicted probability and observed CB or irAE rate (CB model: R2=0.98; p-value<0.0001; irAE model: R2= 0.92; p-value <0.0001). In the CB model, patients classified as PROphet-positive achieved significantly longer overall survival (OS) than PROphet-negative patients, with a median OS of 25.9 vs. 10.8 months (hazard ratio, HR = 0.51; p-value<0.001). Furthermore, patients with PD-L1 ≥50% tumors and a PROphet-negative result had significantly longer OS with ICI-chemotherapy in comparison to ICI monotherapy (HR=0.23, p-value = 0.0003), suggesting that combination therapy is preferable for such patients despite high PD-L1 levels. Bioinformatic analysis showed that RAPs related to immune regulation, angiogenesis, chemo-resistance, and other potential resistance mechanisms displayed higher expression levels in patients who did not benefit from treatment. Neutrophil- and inflammation-related proteins were significantly enriched in patients who experienced irAEs. Conclusions: We describe two machine-learning based predictive tools that may be used separately or in combination to inform treatment decisions based on the patient’s likelihood to benefit from ICI therapy and to develop serious irAEs. Our findings also provide biological insights related to treatment resistance and immune-related toxicity. Citation Format: Michal Harel, Petros Christopoulos, Igor Puzanov, Jair Bar, Iris Kamer, Niels Reinmuth, Ina Koch, Mor Moskovitz, Adva Levy-Barda, Alona Zer, Michal Lotem, David Farrugia, Rivka Katzenelson, Gillian Price, Abed Agbarya, Helen Cheley, Adam Hassani, Mahmoud Abu-Amna, Tom Geldart, Anirban Chatterjee, Andreas Polychronis, Maya Gottfried, Yanyan Lou, Tatiana Harkovsky, Alison Brewster, Ido Wolf, Ella Tepper, Ben Yellin, Itamar Sela, Coren Lahav, Yehonatan Elon, Raya Leibowitz, Adam P. Dicker, Young Kwang Chae, Ryan J. Sullivan, David Carbone, David Gandara, Jarushka Naidoo. Plasma proteomics-based models for predicting therapeutic benefit and immune-related adverse events in non-small cell lung cancer patients treated with immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1208.

PURPOSE Current guidelines for the management of metastatic non–small cell lung cancer (NSCLC) without driver mutations recommend checkpoint immunotherapy with PD-1/PD-L1 inhibitors, either alone or in combination with chemotherapy. This approach fails to account for individual patient variability and host immune factors and often results in less-than-ideal outcomes. To address the limitations of the current guidelines, we developed and subsequently blindly validated a machine learning algorithm using pretreatment plasma proteomic profiles for personalized treatment decisions. PATIENTS AND METHODS We conducted a multicenter observational trial (ClinicalTrials.gov identifier: NCT04056247 ) of patients undergoing PD-1/PD-L1 inhibitor–based therapy (n = 540) and an additional patient cohort receiving chemotherapy (n = 85) who consented to pretreatment plasma and clinical data collection. Plasma proteome profiling was performed using SomaScan Assay v4.1. RESULTS Our test demonstrates a strong association between model output and clinical benefit (CB) from PD-1/PD-L1 inhibitor–based treatments, evidenced by high concordance between predicted and observed CB ( R 2 = 0.98, P < .001). The test categorizes patients as either PROphet-positive or PROphet-negative and further stratifies patient outcomes beyond PD-L1 expression levels. The test successfully differentiates between PROphet-negative patients exhibiting high tumor PD-L1 levels (≥50%) who have enhanced overall survival when treated with a combination of immunotherapy and chemotherapy compared with immunotherapy alone (hazard ratio [HR], 0.23 [95% CI, 0.1 to 0.51], P = .0003). By contrast, PROphet-positive patients show comparable outcomes when treated with immunotherapy alone or in combination with chemotherapy (HR, 0.78 [95% CI, 0.42 to 1.44], P = .424). CONCLUSION Plasma proteome–based testing of individual patients, in combination with standard PD-L1 testing, distinguishes patient subsets with distinct differences in outcomes from PD-1/PD-L1 inhibitor–based therapies. These data suggest that this approach can improve the precision of first-line treatment for metastatic NSCLC.

9122 Background: Initial treatment selection for advanced NSCLC patients without driver mutations is mainly based on evaluating PD-L1 expression levels in the tumor tissue. However, PD-L1 assays are only moderately predictive. In addition, the guidelines for the PD-L1≥50% subpopulation are not definitive, enabling the usage of immune checkpoint inhibitors (ICI) either as a monotherapy or combined with chemotherapy. Here we aim to provide a decision-making tool for the first-line treatment of advanced NSCLC patients based on plasma derived biomarkers obtained before treatment initiation. Methods: Pre-treatment plasma samples were collected from 545 NSCLC patients receiving ICI-based therapy. Clinical benefit was evaluated based on progression-free survival (PFS) at 12 months as a threshold. Deep plasma proteomic profiling was performed using aptamer technology. Based on the proteomic profiles, a computational model, termed PROphet, was developed and evaluated in a blinded manner on the validation subset (n = 272). The model output, clinical benefit probability, was used to stratify the patients into two groups, PROphet-positive or -negative. Results: The model displayed good performance with a high correlation between the predicted clinical benefit and the observed clinical benefit rate (R2= 0.97), outperforming a PD-L1-based prediction model (R2= 0.35). Patients classified as PROphet-positive achieved significantly longer overall survival (OS) than PROphet-negative patients, with a median OS of 25.9 versus 10.8 months (hazard ratio, HR = 0.51; 95% confidence interval, CI = 0.37-0.70; p-value < 0.001). Next, we examined the clinical utility of combining the PROphet output with PD-L1 levels by comparing different treatment modalities. Focusing on PD-L1≥50%, patients with PROphet-positive results displayed similar OS and PFS when receiving ICI monotherapy or ICI-chemotherapy (OS HR = 0.77; CI = 0.42-1.43; p-value = 0.4096), suggesting that these patients may consider monotherapy, thus avoiding chemotherapy-related toxicity. Conversely, PD-L1≥50% patients with a PROphet-negative result displayed a significantly longer OS and PFS when receiving ICI-chemotherapy in comparison to ICI monotherapy, with a median OS that was not reached versus 11.10 months in the combination therapy and monotherapy groups, respectively (HR = 0.29; CI = 0.14-0.59; p-value < 0.001). These patients should consider combination therapy, avoiding a treatment that is suboptimal for them. Results for PD-L1 1-49% and < 1% provide additional clinical information for each subgroup. Conclusions: Plasma proteomic profiling can provide biomarkers that accurately predict the benefit of ICI-based treatment. The model output complements tissue PD-L1 expression levels as a tool to assist therapeutic decisions.