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bioRxiv · 10.1101/2022.05.15.489654

Pan-cancer scale screening reveals NRF2 associated immunoevasive characteristics in non-small cell lung cancer and squamous malignancies

Harkonen, J.·Polonen, P.·Jawahar-Deen, A.·Selvarajan, I.·Teppo, H.-R.·Dimova, E.·Kietzmann, T.·Ahtiainen, M.·Eklund, T.·Kuopio, T.·Talvitie, E.-M.·Taimen, P.·Kallajoki, M.·Kaikkonen, M. U.·Heinaniemi, M.·Levonen, A.-L.
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Abstract

The NRF2 pathway is frequently activated in various cancer types, yet a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a robust NRF2 activity metric and utilized it to conduct a pan-cancer wide analysis of oncogenic NRF2 signaling. We identified a distinct immunoevasive phenotype where high NRF2 activity is associated with low interferon-gamma (IFN{gamma}), HLA-I expression and T-cell infiltration spanning non-small cell lung cancer (NSCLC) and squamous malignancies of head and neck area, cervix and esophagus. In squamous cell cancers, NRF2 overactive tumors comprise a molecular phenotype with SOX2/TP63 amplification, TP53 mutation and CDKN2A loss. These immune-cold NRF2 hyperactive diseases are associated with upregulation of immunomodulatory NAMPT, WNT5A, SPP1, SLC7A11 and SLC2A1 that represent candidate NRF2 target genes, suggesting direct modulation of the tumor immune milieu. Based on single-cell mRNA data, coupled with a priori information on intercellular ligand-receptor interactions, cancer cells of this subtype exhibit decreased expression of IFN{gamma} responsive ligands, and increased expression of immunosuppressive ligands NAMPT, SPP1 and WNT5A that mediate signaling in intercellular crosstalk. As we observed differential cytokine mRNA expression with IFN{gamma} treatment in NSCLC adenocarcinoma subtype, we explored the cytokine secretome in vitro. We found that secreted neutrophil chemoattractants interleukin-8 (CXCL8) and ENA-78 (CXCL5) are elevated in NRF2 overactive cells, suggesting contribution of immunosuppressive neutrophils in NRF2 driven immune escape. Importantly, as overactive NRF2 is associated with immune-cold characteristics, our results highlight the utility of NRF2 pathway activation as a putative biomarker for stratifying immune-checkpoint blockade responders and non-responders across NSCLC and squamous cancers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/489654v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1f45782org.highwire.dtl.DTLVardef@9d40d0org.highwire.dtl.DTLVardef@a31a5org.highwire.dtl.DTLVardef@1418220_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Harkonen, J., Polonen, P., Jawahar-Deen, A., Selvarajan, I., Teppo, H.-R., Dimova, E., Kietzmann, T., Ahtiainen, M., Eklund, T., Kuopio, T., Talvitie, E.-M., Taimen, P., Kallajoki, M., Kaikkonen, M. U., Heinaniemi, M., Levonen, A.-L.. 2022-05-15. Pan-cancer scale screening reveals NRF2 associated immunoevasive characteristics in non-small cell lung cancer and squamous malignancies. https://doi.org/10.1101/2022.05.15.489654

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