Abstract 4755: Role of PAK4 in cancer immune cell exclusion
Authors: Abril-Rodriguez Gabriel , Grasso Catherine S. , Zaretsky Jesse M. , Berent-Maoz Beata , Hu-Lieskovan Siwen , Ribas Antoni 
Published: August 2018

Lack of T-cell infiltration is the main mechanism of primary resistance to checkpoint blockade therapies. Here, we performed a transcriptomic analysis of metastatic melanoma biopsies taken from patients treated with anti-PD1 (n=23) with biopsies pre- (n=17) and during treatment (n=22), and investigated cancer cell intrinsic mechanisms of immune evasion. We classified our samples based on their T-cell infiltration status using a validated set of immune genes for T-cell infiltration (Spranger et al., 2015), normalized within gene and scored the samples from 0 (least infiltrated) to 1 (most infiltrated). In order to identify genes that anti-correlate with infiltration, we performed differential gene expression analysis between non-infiltrated (n= 18) and infiltrated tumors (n=21) regardless clinical response and condition. The analysis resulted in total of 1904 genes enriched in the non-infiltrated group (log2foldchange &gt; 1, q-value &lt; 0.05 and infiltration threshold = 0.5). Since Wnt signaling pathway has been previously suggested as a potential mechanism of immune exclusion, we aimed to select targetable proteins implicated in β-catenin signaling. Interestingly, p21 (RAC1) Activated Kinase 4 (PAK4) was significantly over-expressed in the non-infiltrated group (log2folchange = 1.04, q-value = 1.08e-05). PAK4 is a kinase involved in cell migration, proliferation and apoptosis and it is known that it can directly phosphorylate β-catenin to promote Wnt signaling. In addition, PAK4 was found to be also significantly enriched in on-treatment samples of non-responders (n=7) compared to responders (n=7) (mean of non-responder = 3.68, mean of responders = 2.69, p-value = 0.007). We next aimed to determine genes negatively associated with infiltration using Pearson correlation coefficient. PAK4 was on the top 5 of genes negatively associated with CD8A (pcc = -0.56, p-value 1.8e-04), HLA-DMB (pcc = -0.64, p-value 8.4e-06), TNF (pcc = -0.66, p-value 4.8e-06) among other immune genes. Altogether, this data suggests that PAK4 have an active role in T-cell exclusion. In order to validate our finding, we analyzed 472 melanoma samples from the TCGA. We first performed RNA-seq deconvolution to estimate the infiltration status of each sample and then determined genes that anti-correlated with the different immune cell subtypes. In line with the hypothesis that PAK4 was causatively excluding T-cell from tumors, we found that PAK4 performed the strongest anti-correlation with dendritic cells (pcc= -0.45, p-value = 2.2e-16) and CD8+ T-cells (pcc = -0.22, p-value = 1.12e-06). PAK4 expression was enriched in TCGA non-infiltrated samples (p-value = 4.92e-09, infiltration threshold = 0.5). In summary, this data suggests that PAK4 might be driving T-cell exclusion and that inhibition of PAK4 kinase activity with small molecules could facilitate T-cell infiltration and synergize with current checkpoint blockade therapies.

Citation Format: Gabriel Abril-Rodriguez, Catherine S. Grasso, Jesse M. Zaretsky, Beata Berent-Maoz, Siwen Hu-Lieskovan, Antoni Ribas. Role of PAK4 in cancer immune cell exclusion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4755.