Abstract PR018: Plasma proteomic biomarkers reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade
Authors: Wright Samuel J. , Zamora Izabella , Parikh Milan , Yeramosu Deepika , Bi Lynn , Kang Sarah , Rucevic Marijana , Sade-Feldman Moshe , Liu Baolin , Nguyen Ngan , Guess Jamey , Schneider Alexis , Lieb David , Woods Elliot , Michaud William , Lawless Aleigha R. , Sharova Tatyana , Kasumova Gyulnara , Kim Michelle S. , Park Ryan J. , Jenkins Russell W. , Klempner Samuel J. , Sullivan Ryan J. , Flaherty Keith T. , Hacohen Nir , Boland Genevieve M. , Mehta Arnav 
Published: November 2024

Abstract
Most patients treated with immune checkpoint blockade (ICB) do not have durable treatment responses, stressing a critical need to identify early non-invasive biomarkers of response. Circulating biomarkers provide easy access for serial monitoring and can provide insight on the mechanisms of response to ICB. We performed plasma proteomics (2943 proteins) on 250 metastatic melanoma patients before and on ICB treatment and performed analysis to identify response- and time point-associated peripheral protein biomarkers. We next generated patient- matched peripheral blood lymphocyte (PBL) surface proteomic data to measure the proportions of immune cell subsets in circulation. We further obtained 13 tumor samples that were processed for single-cell RNA-sequencing (scRNA-seq). We fit linear mixed effects (LME) models to predict plasma protein abundances, using the sample time point, response status and interaction term between time point and response as covariates. We identified 397 proteins with a significant time point, response, or interaction effect. For proteins upregulated post-ICB, gene ontology analysis suggested these proteins were associated with inflammatory pathways involving the activation of effector immune functions. LME models fitted on the circulating immune cell proportions and parallel analysis of immune-related plasma proteins supported that post-ICB samples may be defined by increased immune activity, including T cell infiltration. Moreover, expression of genes corresponding to these post-ICB proteins in the tumor scRNA-seq data tended to be favored by immune subsets, namely those involved in immune cell recruitment and tumor reactivity, such as CXCL10+ macrophages and CXCL13+ T cells, respectively. On the other hand, expression of genes corresponding to plasma proteins upregulated in non-responders in the TME tended to be favored by suppressive myeloid subsets such as SPP1+ macrophages as well as malignant cells, suggesting the potential of immunosuppressive and pro-tumor biological processes to be involved in ICB resistance. Inference of cell-cell interactions in the TME further showed the involvement of these non-responder genes in potentially immunosuppressive and pro-tumor processes, including the PTPRC-MRC1 axis, involved in myeloid cell plasticity, the IGF1/2-IGF1R axis, involved in growth and survival of normal and neoplastic cells, and the GAS6-TYRO3 axis, associated with carcinogenetic mechanisms in multiple malignancies. We further identified a correlation between IL13 protein abundance in circulation and GAS6 expression in the tumor, suggesting that IL13 may reach the tumor from circulation to turn on the STAT6 pathway in receiving cells and upregulate GAS6 in turn to participate in this interaction with TYRO3. Together, these data represent one of the deepest peripheral biomarker studies using paired samples in melanoma patients treated with anti-PD1 therapy, and begin to elucidate the complex interplay between tumors and the systemic immune response within the host.
Citation Format: Samuel J. Wright, Izabella Zamora, Milan Parikh, Deepika Yeramosu, Lynn Bi, Sarah Kang, Marijana Rucevic, Moshe Sade-Feldman, Baolin Liu, Ngan Nguyen, Jamey Guess, Alexis Schneider, David Lieb, Elliot Woods, William Michaud, Aleigha R. Lawless, Tatyana Sharova, Gyulnara Kasumova, Michelle S. Kim, Ryan J. Park, Russell W. Jenkins, Samuel J. Klempner, Ryan J. Sullivan, Keith T. Flaherty, Nir Hacohen, Genevieve M. Boland, Arnav Mehta. Plasma proteomic biomarkers reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR018.