Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation

Abstract

Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or –positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). Tumor cell-intrinsic reprogramming attenuated MAPK-dependency, while enhancing mesenchymal, angiogenic and IFN-inflammatory features and growth/survival dependence on multi-RTKs and PD-L2. In the immune compartment, PD-L2 upregulation in CD11c+ immunocytes drove the loss of T-cell inflammation and promoted BRAFi resistance. Thus, residual melanoma early on MAPKi therapy already displays potentially exploitable adaptive transcriptomic, epigenomic, immune-regulomic alterations.

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

“…However, converging findings from alternative analysis (i.e., GSVA) of the transcriptome data helped to mitigate potential caveats. Finally, in separate work, we found that mutation-targeted therapy (i.e., MAPKi) induces tumor cell-autonomous changes (e.g., mesenchymal transition) (Song et al, 2015) and upregulates anti-PD-1 resistance-associated processes in residual tumors that have regressed in response to MAPKi treatment. Thus, while our findings in this study necessitate confirmation in independent tissue cohorts, the identification of transcriptomic features associated with anti-PD-1 resistance suggests that mitigation of IPRES-related biological processes may enhance response rates to anti-PD-1 (and anti-PD-1 plus MAPKi) therapy.…”

“…Interestingly, this set of 26 IPRES signatures included signatures induced by MAPK inhibitor (MAPKi) treatment of melanoma tumors and cell lines (Table S2C). We have shown recently that MAPKi treatment of melanoma cells induces transcriptome-wide re-programming leading to concurrent phenotype switches (Song et al, 2015). Notably, MAPKi-induced signatures of mesenchymal-invasive transition, angiogenesis, and wound healing signatures were detected in the residual melanoma tumors from patients on MAPKi therapy, suggesting that induction of these signatures may negatively impact responsiveness to combinatorial anti-PD-1/L1 therapy.…”

“…To calculate single-sample gene set enrichment, we used the GSVA program (Hanzelmann et al, 2013) to derive the absolute enrichment scores of previously experimentally validated gene signatures as follow: i) the C2 CGP (chemical and genetic perturbation sets), ii) the C6 and C7 subset of the Molecular Signature Database (Subramanian et al, 2005), iii) self-curated MAPK inhibitor-induced gene signatures using cell lines and patient-derived tumors (Song et al, 2015), iv) post-operation wound signature (Inkeles et al, 2015), and v) melanoma invasive/proliferative signatures (Hoek et al, 2008). To derive the GSVA score of each signature in each tumor sample, we computed from raw RNASeq read counts by HTSEQ COUNT program and then normalized them to log 2 CPM values using EdgeR (McCarthy et al, 2012).…”

“…This resulted in the inclusion of genes for surface receptors PDCD1 (PD-1) , LAG3 , HAVCR2 (Tim-3) , CD160 , and CD244 as well as transcription factors EOMES , PRDM1 (Blimp-1) and TBX21 (T-bet) . We assessed co-enrichment of IPRES content signatures in the i) anti-CTLA-4 pretreatment cohort (Van Allen et al, 2015), ii) MAPKi pretreatment cohort (Hugo et al, 2015; Song et al, 2015), iii) TCGA melanoma (metastatic and primary subsets separately analyzed) (TCGA, 2015), iv) TCGA pancreatic ductal adenocarcinoma (TCGA, provisional, see https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp), v) TCGA lung adenocarcinoma (TCGA, 2014), and vi) TCGA colorectal adenocarcinoma (TCGA, 2012), and vii) TCGA kidney clear cell carcinoma (TCGA, 2013). …”

The Role of Immune Escape and Immune Cell Infiltration in Breast Cancer

“…This might lead to the development and design of therapies in which CPIs will be combined with each other or with targeted therapies, chemotherapy, and/or radiation. Examples are anti-PD-1/anti-PD-L1 or inhibitors of MAP2K and glucocorticoid-induced tumor necrosis factor receptor (GITR) [93,94], which are currently under way and will be covered by a separate article in this issue.…”