Landscape of immune-related signatures induced by targeting of different epigenetic regulators in melanoma: implications for immunotherapy

Our plain-English summary of Landscape of immune-related signatures induced by targeting of different epigenetic regulators in melanoma: implications for immunotherapy, by A. Anichini, A. Molla, G. Nicolini, et al (Journal of Experimental & Clinical Cancer Research, 2022).

The study

• Authors: A. Anichini, A. Molla, G. Nicolini, V.E. Perotti, F. Sgambelluri, A. Covre, C. Fazio, M.F. Lofiego, A.M. Di Giacomo, S. Coral, A. Manca, M.C. Sini, M. Pisano, T. Noviello, F. Caruso, S. Brich, G. Pruneri, A. Maurichi, M. Santinami, M. Ceccarelli, G. Palmieri, M. Maio, R. Mortarini, EPigenetic Immune-oncology Consortium AIRC (EPICA) investigators
• Journal: Journal of Experimental & Clinical Cancer Research
• Published: 2022;41(1):325
• Cited by: 20 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Background: Improvement of efficacy of immune checkpoint blockade (ICB) remains a major clinical goal. Association of ICB with immunomodulatory epigenetic drugs is an option. However, epigenetic inhibitors show a heterogeneous landscape of activities. Analysis of transcriptional programs induced in neoplastic cells by distinct classes of epigenetic drugs may foster identification of the most promising agents.

Methods: Melanoma cell lines, characterized for mutational and differentiation profile, were treated with inhibitors of DNA methyltransferases (guadecitabine), histone deacetylases (givinostat), BET proteins (JQ1 and OTX-015), and enhancer of zeste homolog 2 (GSK126). Modulatory effects of epigenetic drugs were evaluated at the gene and protein levels. Master molecules explaining changes in gene expression were identified by Upstream Regulator (UR) analysis. Gene set enrichment and IPA were used respectively to test modulation of guadecitabine-specific gene and UR signatures in baseline and on-treatment tumor biopsies from melanoma patients in the Phase Ib NIBIT-M4 Guadecitabine + Ipilimumab Trial. Prognostic significance of drug-specific immune-related genes was tested with Timer 2.0 in TCGA tumor datasets.

Results: Epigenetic drugs induced different profiles of gene expression in melanoma cell lines. Immune-related genes were frequently upregulated by guadecitabine, irrespective of the mutational and differentiation profiles of the melanoma cell lines, to a lesser extent by givinostat, but mostly downregulated by JQ1 and OTX-015. GSK126 was the least active drug. Quantitative western blot analysis confirmed drug-specific modulatory profiles. Most of the guadecitabine-specific signature genes were upregulated in on-treatment NIBIT-M4 tumor biopsies, but not in on-treatment lesions of patients treated only with ipilimumab. A guadecitabine-specific UR signature, containing activated molecules of the TLR, NF-kB, and IFN innate immunity pathways, was induced in drug-treated melanoma, mesothelioma and hepatocarcinoma cell lines and in a human melanoma xenograft model. Activation of guadecitabine-specific UR signature molecules in on-treatment tumor biopsies discriminated responding from non-responding NIBIT-M4 patients. Sixty-five % of the immune-related genes upregulated by guadecitabine were prognostically significant and conferred a reduced risk in the TCGA cutaneous melanoma dataset.

Conclusions: The DNMT inhibitor guadecitabine emerged as the most promising immunomodulatory agent among those tested, supporting the rationale for usage of this class of epigenetic drugs in combinatorial immunotherapy approaches.

© 2022. The Author(s).

In plain English

This laboratory study did not examine asbestos exposure. Its only link to asbestos-related disease is that three mesothelioma cell lines, from pleural effusions of mesothelioma patients, were among the cells tested. The authors treated human melanoma cell lines with drugs acting on gene regulation (epigenetic drugs: guadecitabine, givinostat, JQ1, OTX-015, GSK126) and with abemaciclib, and measured changes in immune-related genes and proteins. Guadecitabine and givinostat mostly upregulated immune-related genes, while JQ1 mostly downregulated them. In melanoma cell lines, combining two drugs usually did not change immune-related genes more than one drug alone. A computer analysis of gene-expression changes predicted that several immune regulators activated by guadecitabine in melanoma cells were also activated in treated mesothelioma cell lines. In NIBIT-M4 trial tumor samples (guadecitabine plus ipilimumab), almost 92% of guadecitabine-signature genes were upregulated at weeks 4 and 12 versus before treatment. The same analysis, applied to biopsies, predicted progressively greater activation of several guadecitabine-linked regulators in responding than non-responding patients. The authors concluded that the results favor combining checkpoint drugs with DNMT or HDAC inhibitors rather than BET or EZH2 inhibitors.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory (cell line) study of epigenetic drugs, with analysis of an animal xenograft model, published tumor biopsy data from a Phase Ib trial (NIBIT-M4), and the TCGA public tumor database
• Who was studied: Human melanoma cell lines (14 established; ten used for the main drug screening). Also three mesothelioma cell lines (MPP-89, MM98, MES2a) from pleural effusions of mesothelioma patients, human melanoma xenografts in immunodeficient mice, tumor biopsies from melanoma patients in the NIBIT-M4 trial (patient numbers not given in this text), and TCGA tumor datasets.
• Exposure: Epigenetic drugs: guadecitabine and decitabine (DNMT inhibitors), givinostat (HDAC inhibitor), JQ1 and OTX-015 (BET inhibitors), GSK126 (EZH2 inhibitor), plus the CDK4/6 inhibitor abemaciclib. Doses were tailored to each cell line. No asbestos or fiber exposure was studied.
• Main results:
  • In melanoma cell lines, immune-related genes were frequently upregulated by guadecitabine and givinostat but downregulated by JQ1.
  • The guadecitabine-specific signature contained 170 genes, mostly upregulated. The JQ1-specific signature contained 217 genes, mostly downregulated.
  • In melanoma cell lines tested with the NanoString Cancer Immune panel, combining two epigenetic drugs mostly did not increase immune-related gene modulation compared with single drugs.
  • At the protein level, guadecitabine and the BET inhibitors had opposite effects on IFN-pathway proteins (OAS3 and IFITM1), PD-L1/CD274 and CEACAM1 in melanoma cell lines.
  • Across ten guadecitabine-treated melanoma cell lines, upstream regulator analysis identified 51 regulators predicted to be activated (Z score greater than 2) and 9 predicted to be inhibited in at least 6 of 10 lines.
  • Upstream regulator analysis, a computational prediction from gene-expression changes, indicated activation of several of the same immune-related regulators in guadecitabine-treated mesothelioma cell lines as in guadecitabine-treated melanoma cell lines.
  • In NIBIT-M4 trial biopsies, almost 92% of guadecitabine-signature genes were upregulated at week 12 and week 4 compared with week 0.
  • By gene set enrichment analysis, the increase in the signature was significant at week 12 compared with weeks 4 and 0, but not at week 4 compared with week 0.
  • In two published datasets of patients given ipilimumab alone, only 35/166 (21.1%) and 28/166 (16.9%) guadecitabine-signature genes were upregulated on treatment.
  • Upstream regulator analysis of genes differentially expressed between responding and non-responding NIBIT-M4 patients predicted progressive activation of several guadecitabine-specific regulators in on-treatment (week 4 and week 12) biopsies from responders.
  • In TCGA data, 65% of guadecitabine-signature genes were significant in a Cox model, mostly associated with reduced risk. This held mainly in melanoma and not across all tumor types. In the JQ1 signature, 59% of genes were significant.
• The authors' conclusion: The authors concluded that distinct epigenetic drugs elicit specific immune-related programs in melanoma cells. In their view, this provides a preclinical rationale for combining immune checkpoint blockade with DNMT or HDAC inhibitors rather than BET or EZH2 inhibitors.

Topics

Medical terms in this study, explained in our Lexicon: Immunotherapy, Benjamin Foster Company, Ipilimumab (Yervoy), Mesothelioma.

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