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The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma
Orsi Giricz, Yongkai Mo, Kimberly B. Dahlman, Xiomaris M. Cotto-Rios, Chiara Vardabasso, Hoa Nguyen, Bernice Matusow, Matthias Bartenstein, Veronika Polishchuk, Douglas B. Johnson, Tushar D. Bhagat, Rafe Shellooe, Elizabeth Burton, James Tsai, Chao Zhang, Gaston Habets, John M. Greally, Yiting Yu, Paraic A. Kenny, Gregg B. Fields, Kith Pradhan, E. Richard Stanley, Emily Bernstein, Gideon Bollag, Evripidis Gavathiotis, Brian L. West, Jeffrey A. Sosman, Amit K. Verma
Orsi Giricz, Yongkai Mo, Kimberly B. Dahlman, Xiomaris M. Cotto-Rios, Chiara Vardabasso, Hoa Nguyen, Bernice Matusow, Matthias Bartenstein, Veronika Polishchuk, Douglas B. Johnson, Tushar D. Bhagat, Rafe Shellooe, Elizabeth Burton, James Tsai, Chao Zhang, Gaston Habets, John M. Greally, Yiting Yu, Paraic A. Kenny, Gregg B. Fields, Kith Pradhan, E. Richard Stanley, Emily Bernstein, Gideon Bollag, Evripidis Gavathiotis, Brian L. West, Jeffrey A. Sosman, Amit K. Verma
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Research Article Oncology

The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma

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Abstract

Resistance to current therapies still impacts a significant number of melanoma patients and can be regulated by epigenetic alterations. Analysis of global cytosine methylation in a cohort of primary melanomas revealed a pattern of early demethylation associated with overexpression of oncogenic transcripts. Loss of methylation and associated overexpression of the CSF 1 receptor (CSF1R) was seen in a majority of tumors and was driven by an alternative, endogenous viral promoter in a subset of samples. CSF1R was particularly elevated in melanomas with BRAF and other MAPK activating mutations. Furthermore, rebound ERK activation after BRAF inhibition was associated with RUNX1-mediated further upregulation of CSF-1R and its ligand IL-34. Importantly, increased CSF-1R and IL-34 overexpression were detected in an independent cohort of resistant melanomas. Inhibition of CSF-1R kinase or decreased CSF-1R expression by RNAi reduced 3-D growth and invasiveness of melanoma cells. Coinhibition of CSF-1R and BRAF resulted in synergistic efficacy in vivo. To our knowledge, our data unveil a previously unknown role for the autocrine-regulated CSF-1R in BRAF V600E resistance and provide a preclinical rationale for targeting this pathway in melanoma.

Authors

Orsi Giricz, Yongkai Mo, Kimberly B. Dahlman, Xiomaris M. Cotto-Rios, Chiara Vardabasso, Hoa Nguyen, Bernice Matusow, Matthias Bartenstein, Veronika Polishchuk, Douglas B. Johnson, Tushar D. Bhagat, Rafe Shellooe, Elizabeth Burton, James Tsai, Chao Zhang, Gaston Habets, John M. Greally, Yiting Yu, Paraic A. Kenny, Gregg B. Fields, Kith Pradhan, E. Richard Stanley, Emily Bernstein, Gideon Bollag, Evripidis Gavathiotis, Brian L. West, Jeffrey A. Sosman, Amit K. Verma

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Figure 5

ERK-pathway rebound following 96-hour BRAF V600E inhibitor treatment is associated with increased expression of RUNX1, CSF1R, and IL-34.

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ERK-pathway rebound following 96-hour BRAF V600E inhibitor treatment is ...
(A) CSF1R probe methylation shows negative correlation with CSF1R gene expression across all 471 TCGA melanoma samples (Spearman’s correlation, r = –0.3995, P < 0.0001, orange line denotes linear regression). (B and C) CSF1R expression shows positive correlation with that of RUNX1 (r = 0.464, P < 0.0001) (B) or with the expression of IL34 (r = 0.533, P < 0.0001) (C). (D and E) CSF1R probe methylation (D) and gene expression (E) of TCGA melanomas with MAPK-activating mutation (act-MAPK) and without (triple WT, TWT) (unpaired t test, 2-tailed). (F–M) A2058 (F, H, J, L) or WM-266-4 (G, I, K, M) cells were treated with 3 μM PLX4720 and/or serum-free medium for a total of 96 hours. (F and G) Cell lysates assayed for gene expression and protein expression; supernatants assayed for secreted proteins. Detailed schematic of the experiment is provided in Supplemental Figure 7A. Melanoma cell numbers were counted for every time-point condition. Immunoblotting of total protein extracts from all time points was performed to detect protein levels of phospho-ERK, total ERK, and actin, as well as to evaluate both the levels and posttranslational maturation of CSF-1R protein. Surface expression of CSF-1R protein was followed by flow cytometry (small inserts). (H and I) qPCR analysis (mean ± SEM) for relative expression of RUNX1 and for both transcripts of CSF1R. (J and K) qPCR of IL-34 expression and ELISA analysis of IL-34–secreted protein expression (mean ± SEM for both). (L and M) Luciferase activity in melanoma cells stably harboring a plasmid construct of the canonical promoter of CSF1R or the CSF1R MaLR LTR linked to Firefly luciferase show increased activity at both regulatory regions (mean ± SEM). Representative images from 3 independent experiments.

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