Transcriptional correlates of <i>ARNT</i> expression and its impact on survival outcomes in clear-cell renal cell carcinoma (ccRCC).

Abstract

e16554 Background: Encoded by ARNT , hypoxia-inducible factor-1β (HIF1β) is an obligate heterodimer for HIF1α and HIF2α, enabling their transcriptional activation of HIF-target pathways, such as angiogenesis. Here, we examine the relation of ARNT expression with hypoxia and immune programs, and its impact on survival outcomes in ccRCC. Methods: We included patients (pts) with RNA-seq data from TCGA-KIRC (stages I-IV; n = 529), and 2 first-line clinical trials in metastatic ccRCC involving VEGF-pathway inhibitor alone vs combined with immunotherapy: Javelin Renal-101 (JR: n = 741) and CheckMate-9ER (CM: n = 403). Transcripts per million (TPM) were log2-transformed and scaled per 1 SD change. Buffa Hypoxia Score (BHS) was computed per prior reports (Bhandari et al., 2020): expression for each of BHS’ 50 genes per patient was assigned +1, if ≥ median for this gene, or -1 if &lt; median, then summed. The immune signatures, IMmotion150 Angio, T eff and Myeloid, JAVELIN and Tumor Inflammatory Score (TIS) were calculated as means of their genes’ log2-transformed TPMs. Spearman correlation associated ARNT expression with each signature, and HIF1A and HIF2A expressions. Multivariable (MV) Cox models assessed the association of ARNT expression with progression-free (PFS) and overall (OS) survival per each full cohort, adjusted for age, sex, stage and sarcomatoid features in KIRC, and for age, sex, IMDC risk, treatment arm and sarcomatoid features in the trials. Likelihood ratio test (LRT) assessed interaction between ARNT and treatment arm in predicting survival. Results: Across three cohorts, higher ARNT expression correlated with higher BHS (ρ = 0.23-0.49), Angio signature (ρ = 0.14-0.57) and TIS (ρ = 0.14-0.21) (p &lt; 0.05). Higher ARNT correlated with higher T eff and JAVELIN signatures in KIRC (T eff : ρ = 0.19, p = 8.3×10⁻⁶; JAVELIN: ρ = 0.16, p = 1.8×10⁻⁴) and JR (T eff : ρ = 0.16, p = 1.2×10⁻ 5 ; JAVELIN: ρ = 0.17, p = 1.8×10⁻⁶) but not CM9 (ρ = 0.09 for both, p &gt; 0.05). A positive correlation was identified between Myeloid signature and higher ARNT expression in JR (ρ = 0.17, p = 2.3×10⁻⁶) and CM9 (ρ = 0.12, p = 0.02), but not KIRC (ρ = 0.05, p = 0.24). A consistent correlation was observed between ARNT and HIF1A (ρ = 0.30-0.51) and HIF2A expressions (ρ = 0.19-0.61), across all cohorts (p &lt; 0.05). MV Cox models revealed no significant association between ARNT expression and PFS and OS (Table), independent of treatment arm per trial (LRT p &gt; 0.05). Conclusions: ARNT expression tracks with hypoxia, angiogenic and immune transcriptional states in ccRCC but is not independently prognostic, suggesting biologic relevance without clear predictive value in current VEGF- and immunotherapy-based regimens. MV Cox for PFS and OS. Cohort PFS HR adj , 95% CI PFS p-value OS HR adj , 95% CI OS p-value KIRC 0.94, 0.79-1.10 0.42 0.9, 0.78-1.05 0.18 JR 1.03, 0.94-1.14 0.48 1.02, 0.88-1.18 0.78 CM9 1.01, 0.90-1.14 0.86 0.98, 0.84-1.13 0.75