1.08 ARNT-related gene overexpression correlates with low immune signature and worse survival in melanoma

K. M. Leick1,2, J. M. Obeid2, S. Bekiranov2, C. L. Slingluff2  1University Of Iowa,Iowa City, IA, USA 2University Of Virginia,Charlottesville, VA, USA

Introduction:  We have identified a set of 8 genes expressed in human melanomas and associated with lack of T cell infiltrate and shortened overall survival. These include filaggrin (FLG) and 7 proteins that mediate mechanical barrier function in normal skin through cell-cell adhesions. These barrier molecule genes (BMGs) are concordantly expressed with genes of the epidermal differentiation complex (EDC), which is responsible for terminal differentiation of keratinocytes and is regulated by aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT). Thus, we hypothesized that AHR/ARNT genes would be expressed concordantly with BMG and EDC genes and would also be negatively associated with immune signatures in melanoma.

Methods:  RNA-seq data from 471 patients with cutaneous melanoma were available from the Cancer Genome Atlas (TCGA). Our gene search included the EDC pathway, BMGs, and immune genes. Overexpression of selected genes was identified at z = 1.5, and heatmaps were generated using nonsupervised clustering. Associations of clusters with overall patient survival were assessed using Kaplan Meier curves and log-rank tests.

Results: Gene expression profiles divided tumors into 4 categories: (1) ImmuneHI, (2) BMG/EDCHI, (3) ARNTHI, and (4) Mixed (Figure 1A). ARNT-related genes clustered separately from BMG and EDC genes, which were concordantly expressed. ARNTHI demonstrated upregulation of ARNT-related genes with low immune signature and low BMG/EDC expression. BMG/EDCHI had low ARNT-related and immune gene expression in the presence of upregulated BMGs. Both the ARNTHI and BMG/EDCHI tumors had significantly shorter survival than tumors with high immune signatures (p=0.0003, Figure 1B).

Conclusion: Among patients lacking immune signatures, we have identified 3 different patient subsets: (a) ARNTHI, (b) BMG/EDCHI, and (c) mixed gene expression profiles. Overexpression of BMG/EDC genes are associated with worst survival overall. Despite the fact that AHR and ARNT induce BMG/EDG gene expression in keratinocytes, discordant expression of ARNT genes and BMG/EDC genes in melanomas suggests that BMG/EDC gene expression is controlled in an ARNT-independent manner in melanoma. ARNT HI tumors represent another subset of tumors, in addition to BMG/EDCHI tumors, where immune barriers exist. These findings raise the possibility that barriers to immune infiltrates may differ between EDC/BMG HI and ARNT HI groups. Future studies will define the regulation of EDC and BMG expression and how they may interfere with immune cell infiltration and survival of patients with melanoma and other cancers.