A unique gene expression signature is significantly differentially expressed in tumor-positive or tumor-negative sentinel lymph nodes in patients with melanoma

Abstract

Purpose Molecular characterization through gene expression profiling of node positive and node negative sentinel lymph nodes (SLNs) in patients with clinical stage I–II melanoma may improve the understanding of mechanisms of metastasis and identify gene signatures for SLN+/SLN− that correlate with diagnosis or clinical outcome. Methods Gene expression profiling was performed on SLN biopsies of 48 (24 SLN+, 24 SLN−) patients (T3a/b, T4a/b) who underwent SLN for staging using transcriptome profiling analysis on 5μ sections of fresh SLN. U133A 2.0 Affymetrix gene chips were used. Significance Analysis of Microarrays (SAM) was used to test the association between gene expression level and SLN status. Genes with fold change>1.5 and q value <0.05 were considered differentially expressed. Pathway analysis was performed using Ingenuity Pathway Analysis. Benjamini and Hochberg method was used to adjust for multiple testing in pathway analysis. Results We identified 89 probe sets significantly differentially expressed (1.5–27 fold; q value <0.05). Upon pathway analysis, 25 genes were common among the most significant and biologically relevant canonical pathways. The molecules and pathways that achieved differential expression of highest statistical significance were notably related to melanoma and its microenvironment and signaling pathways implicated in immunosuppression and development of cancer. Conclusions A 25 gene signature is significantly differentially expressed between SLN+ and SLN− and is related to melanoma oncogenesis and immunosuppression. The identified expression profile provides a signature of melanoma nodal involvement. These findings warrant further investigation in relation to the mechanisms of metastasis, melanoma metastasis diagnosis and prediction of outcome.

An Interferon-Driven Oxysterol-Based Defense against Tumor-Derived Extracellular Vesicles

“…The MP1 cohort consisted of 40 patients with melanoma (stage I, II, III or IV). The MP2 cohort was described in details elsewhere (Tarhini et al, 2017)). These patients had a sentinel lymph node involved (SLN + , n=20) or not (SLN -, n=20) by melanoma metastasis as assessed by H&E and immunohistochemistry.…”

Sentinel Lymph Node Gene Expression Signature Predicts Recurrence-Free Survival in Cutaneous Melanoma

“…The SLN sections were immediately placed in 700 μL of RNA lysis buffer (Qiagen RNeasy kit) and frozen at −80 °C for future mRNA extraction for gene expression profiling. SLN tissue procurement procedure and mRNA expression assays were described previously [ 17 ]. Primary melanoma characteristics including location, histology, Breslow thickness, presence/absence of ulceration, number of mitoses, and the degree of tumor-infiltrating lymphocytes (TIL) was retrieved from pathology reports.…”

ASO Author Reflections: Gene Expression-Profiling and Implications for Adjuvant Therapy in Melanoma

“…1 Although gene expression in the primary tumor currently is being investigated, the SLN plays an important role in tumor control, and SLN gene expression has been shown to differ between patients with and without nodal metastases. 2 This study characterized expression of 730 immune-related genes in the SLNs of 60 patients in a retrospective melanoma cohort and created a multivariate prediction model for RFS that incorporated expression of 12 differentially expressed genes. 3 Although these results have not been validated to date and are limited by the small, retrospective nature of the study, they provide preliminary evidence that immunologic gene expression in SLNs correlate with clinical outcomes.…”