Abstract 6375: Transcriptomic signatures in melanoma lymph node metastasis that relate to immune oncology treatment
Authors: Bustos Matias A. , Mizuno Shodai , Ryu Suyeon , Hoon Dave S. 
Published: April 2023

Abstract
Background: Frequently, patients with primary cutaneous melanoma develop regional lymph node metastasis (LNM). The outcomes in melanoma patients with LNM can be poor, depending on clinicopathological features including the size and the number of the LNM. Newer immunotherapies including immune checkpoint inhibitors (ICI) have significantly improved outcomes in metastatic melanoma patients, and when tumors respond to ICI the durable responses are noteworthy. The aim of the current study is to identify transcriptomics changes in immune-related genes in LNM that correlate to outcomes in melanoma patients receiving adjuvant ICI therapy.
Methods: The analysis were performed in formalin-fixed paraffin-embedded (FFPE) sections from LNM positive (LNM(+); n=17) and LNM negative (LNM(-); n=8) of patients who received surgery at SJHC. For each tissue, a single section was processed and analyzed for 2,002 genes using the direct (mRNA extraction-free) transcriptomic assay of the HTG EdgeSeq AutoImmune Panel (HTG-AI). The HTG-AI transcriptomic normalized data were compared between both groups. For verification of gene signatures, publicly available RNA-seq datasets were obtained from patients with clinical outcomes receiving anti-PD-1. All biostatistical analysis were performed using HTG Reveal and/or GraphPad Prism software.
Results: Comparisons between melanoma LNM(+) and LNM(-) samples showed 229 DEGs (Log2fold-change ←2; &gt;2 FDR&lt;0.01), with 213 genes upregulated and 16 downregulated. Pathway analyses using Reactome indicated that the DEGs in LNM(+) were associated with cytokine, interferon (IFN), and chemokine signaling, as well as signaling by receptor tyrosine kinases (FDR&lt;0.0001). The chemokines CXCL8, CXCL2, and CXCL10 were significantly upregulated in LNM(+) (p&lt;0.001). LNM(+) showed significantly higher levels of IFN signaling mediators (STAT1, STAT2, IFI6, IFI30, IFI44) compared to LNM(-) specimens (p&lt;0.001). Also, LNM(+) showed a significant increase in CD276 (B7-H3) levels (p&lt;0.001). Then, we correlated the mRNA levels of IFN signaling (STAT1, STAT2, IFI6, IFI30, and IFI44) obtained from samples before anti-PD-1 therapy (Nivolumab or Pembrolizumab) to overall survival (OS). Of clinical importance, patients with elevated levels of the IFN signaling genes showed better OS for patients receiving adjuvant anti-PD-1 (HR=0.6, CI=0.42-0.86, Log-rank test, p=0.0044).
Conclusions: We identified a distinctive transcriptomic profile in LNM(+). Several genes were upregulated and associated with specific pathways. Using publicly available data, we demonstrated that STAT1, STAT2, IFI6, IFI30, and IFI44 gene signature correlated with improved OS for patients receiving adjuvant ICI treatment. The STAT1, STAT2, IFI6, IFI30, and IFI44 genes may represent new biomarkers to assess in biopsies of patients that will receive adjuvant or neoadjuvant ICI therapies.
Citation Format: Matias A. Bustos, Shodai Mizuno, Suyeon Ryu, Dave S. Hoon. Transcriptomic signatures in melanoma lymph node metastasis that relate to immune oncology treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6375.