Silencing PEX26 as an unconventional mode to kill drug-resistant cancer cells and forestall drug resistance

Promoting the macroautophagy/autophagy-mediated degradation of specific proteins and organelles can potentially be utilized to induce apoptosis in cancer cells or sensitize tumor cells to therapy. To examine this concept, we enriched for autophagosomes from histone deacetylase inhibitor (HDACi)-sensitive U937 lymphoma cells and isogenic HDACi-resistant cells. Mass spectrometry on autophagosome-enriched fractions revealed that HDACi-resistant cells undergo elevated pexophagy, or autophagy of the peroxisome, an organelle that supports tumor growth. To disturb peroxisome homeostasis, we enhanced pexophagy in HDACi-resistant cells via genetic silencing of peroxisome exportomer complex components (PEX1, PEX6, or PEX26). This consequently sensitized resistant cells to HDACi-mediated apoptosis, which was rescued by inhibiting ATM/ataxia-telangiectasia mutated (ATM serine/threonine kinase), a mediator of pexophagy. We subsequently engineered melanoma cells to stably repress PEX26 using CRISPR interference (CRISPRi). Melanoma cells with repressed PEX26 expression showed evidence of both increased pexophagy and peroxisomal matrix protein import defects versus single guide scrambled (sgSCR) controls. In vivo studies showed that sgPEX26 melanoma xenografts recurred less compared to sgSCR xenografts, following the development of resistance to mitogen-activated protein kinase (MAPK)-targeted therapy. Finally, prognostic analysis of publicly available datasets showed that low expression levels of PEX26, PEX6 and MTOR, were significantly associated with prolonged patient survival in lymphoma, lung cancer and melanoma cohorts. Our work highlighted that drugs designed to disrupt peroxisome homeostasis may serve as unconventional therapies to combat therapy resistance in cancer.Abbreviations: ABCD3/PMP70: ATP binding cassette subfamily D member 3; ACOX1: acyl-CoA oxidase 1; AP: autophagosome; COX: cytochrome c oxidase; CQ: chloroquine; CRISPRi: clustered regularly interspaced short palindromic repeats interference; DLBCL: diffuse large B-cell lymphoma; GO: gene ontology; dCas9: Cas9 endonuclease dead, or dead Cas9; HDACi: histone deacetylase inhibitors; IHC: Immunohistochemistry; LAMP2: lysosomal associated membrane protein 2; LCFAs: long-chain fatty acids; LFQ-MS: label-free quantitation mass spectrometry; LPC: lysophoshatidylcholine; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; PBD: peroxisome biogenesis disorders; PTS1: peroxisomal targeting signal 1; ROS: reactive oxygen species; sgRNA: single guide RNA; VLCFAs: very-long chain fatty acids; Vor: vorinostat; WO: wash-off.

Inhibiting the MNK1/2-eIF4E axis impairs melanoma phenotype switching and potentiates antitumor immune responses

Melanomas commonly undergo a phenotype switch, from a proliferative to an invasive state. Such tumor cell plasticity contributes to immunotherapy resistance; however, the mechanisms are not completely understood and thus are therapeutically unexploited. Using melanoma mouse models, we demonstrated that blocking the MNK1/2-eIF4E axis inhibited melanoma phenotype switching and sensitized melanoma to anti-PD-1 immunotherapy. We showed that phospho-eIF4E-deficient murine melanomas expressed high levels of melanocytic antigens, with similar results verified in patient melanomas. Mechanistically, we identified phospho-eIF4E-mediated translational control of NGFR, a critical effector of phenotype switching. Genetic ablation of phospho-eIF4E reprogrammed the immunosuppressive microenvironment, exemplified by lowered production of inflammatory factors, decreased PD-L1 expression on dendritic cells and myeloid-derived suppressor cells, and increased CD8+ T cell infiltrates. Finally, dual blockade of the MNK1/2-eIF4E axis and the PD-1/PD-L1 immune checkpoint demonstrated efficacy in multiple melanoma models regardless of their genomic classification. An increase in the presence of intratumoral stem-like TCF1+PD-1+CD8+ T cells, a characteristic essential for durable antitumor immunity, was detected in mice given a MNK1/2 inhibitor and anti-PD-1 therapy. Using MNK1/2 inhibitors to repress phospho-eIF4E thus offers a strategy to inhibit melanoma plasticity and improve response to anti-PD-1 immunotherapy.

Abstract A53: Phosphorylation of eIF4E promotes phenotype switching and MDSC-mediated immunosuppression in melanoma

Introduction: Melanoma is the deadliest form of skin cancer. Melanoma phenotype switching is characterized by reduced expression of melanocyte lineage transcription factor MITF and its downstream targets, leading to increased invasiveness of melanoma cells and resistance to both targeted therapy and immunotherapy, and worse prognosis. In melanoma, MAPK and PI3K pathways ultimately converge upon eukaryotic translation initiation factor 4E (eIF4E) to induce its phosphorylation (p-eIF4E), which is critical for the oncogenicity of eIF4E. Here, we investigate the role of p-eIF4E in melanoma progression and tumor immunity.

Methods: We crossed p-eIF4E deficient (eIF4EKI) mice with an inducible melanoma mouse model. We monitored the primary tumor outgrowth, metastasis, and survival of the eIF4EKI mice versus eIF4EWT mice. Melanoma samples were isolated for further investigation.

Results: Compared to the eIF4EWT mice, eIF4EKI mice exhibit significantly delayed tumor growth, reduced metastasis, and increased survival. Increased expression of MITF and downstream melanoma antigens were observed in eIF4EKI tumors, suggesting a p-eIF4E-mediated phenotype switching. Cytokine array analysis revealed a novel proinvasive cytokine signature in eIF4EWT melanoma primary culture, further supporting a role of phospho-eIF4E in phenotype switching. The cytokine profiling also revealed a pro-myeloid-derived suppressor cell (MDSC) cytokine signature in the eIF4EWT tumor, indicating a p-eIF4E-linked immunosuppression. In support of the immune suppressive cytokine signature associated with phospho-eIF4E expressing melanomas, immune phenotyping of eIF4EWT melanomas showed a significant increase in MDSCs and less cytotoxic T cells, compared to eIF4EKI melanomas. Finally, pharmacologic inhibition of p-eIF4E in combination with anti-PD-1 immunotherapy results in a synergistic delay in primary tumor outgrowth and reduced metastasis.

Conclusions: Here we showed that phosphorylation of eIF4E promotes melanoma phenotype switching, leading to increased invasiveness and reduced expression of tumor-associated antigens. Further, by increasing the secretion of pro-MDSC cytokines, p-eIF4E permits an immunosuppressive microenvironment. Pharmacologic inhibition of p-eIF4E sensitizes melanoma to anti-PD-1 immunotherapy, potentially by increasing melanoma antigen expression and compromising MDSC-mediated immunosuppression. This study provides a novel therapeutic approach for the treatment of melanoma.

Citation Format: Fan Huang, Christophe Gonçalves, Qianyu Guo, Joelle Rémy-Sarrazin, Audrey Emond, William Yang, Dany Plourde, Margarita Bartish, Jie Su, Yao Zhan, Marina G. Gimeno, Elie Khoury, Alexandre Benoit, David Dankort, Wilson H. Miller, Sonia V. del Rincón. Phosphorylation of eIF4E promotes phenotype switching and MDSC-mediated immunosuppression in melanoma [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A53.