CTLA4 methylation predicts response to anti–PD-1 and anti–CTLA-4 immunotherapy in melanoma patients

Abstract

Recent years have witnessed the groundbreaking success of immune checkpoint blockage (ICB) in metastasized malignant melanoma. However, biomarkers predicting the response to ICB are still urgently needed. In the present study, we investigated CTLA4 promoter methylation (mCTLA4) in 470 malignant melanoma patients from The Cancer Genome Atlas (non-ICB cohort) and in 50 individuals with metastasized malignant melanomas under PD-1/CTLA-4-targeted immunotherapy (ICB cohort). mCTLA4 levels were quantified using the Infinium HumanMethylation450 BeadChip (non-ICB cohort) and methylation-specific quantitative real-time PCR in DNA formalin-fixed and paraffin-embedded tissues (ICB cohort). Methylation levels were associated with molecular and clinicopathological variables and analyzed with respect to response (irRECIST) and overall survival. CTLA-4 mRNA and mCTLA4 showed a significant inverse correlation (non-ICB cohort: Spearman's ρ = -0.416, P < 0.001). In ICB-treated melanoma patients, low mCTLA4 was further strongly correlated with response to therapy (P = 0.009, ANOVA) and overall survival (hazard ratio = 2.06 [95% CI: 1.29-3.29], P = 0.003). Our data strongly support the assumption that mCTLA4 predicts response to both anti-PD-1 and anti-CTLA-4 targeted ICB in melanoma and provides paramount information for the selection of patients likely to respond to ICB.

Immune checkpoint inhibitors: The linchpins of modern immunotherapy

“…127 CTLA-4 methylation has been shown to inversely correlated with CTLA4 mRNA, with lowmethylated CTLA-4 correlating with response to both anti-PD-1 and anti-CTLA4. 15 High baseline serum biomarkers of excessive extracellular matrix remodeling and collagen breakdown products correlated with worse response to anti-CTLA-4 blockade with ipilimumab and shorter OS, perhaps reflecting worsened T-cell recruitment/infiltration and association with TGF-β activity. 94 Over the ensuing years, it has become increasingly clear that a single biomarker will not be sufficient to identify responding pa- Exploration of biomarkers correlating with response to immune checkpoint blockade in sarcomas are very limited due to the few prospective studies that have been performed with a limited number of patients.…”

“…Additionally, CTLA‐4 leads to downstream inhibition of PI3K/Akt pathways, cyclin D3, CDK4/CDK6, and NF‐κB, altering T‐cell differentiation . CTLA‐4 can also be expressed on tumor cells and is associated with decreased survival in nasopharyngeal carcinoma and improved outcomes in non‐small‐cell lung cancer (NSCLC) and melanoma treated with checkpoint inhibitors …”

“…Immune profiling by mass cytometry of peripheral blood melanoma patients demonstrated that non‐responders to anti‐PD‐1 had lower CD69 and MIP‐1β‐expressing NK cells, whereas CTLA‐4 responders had lower frequencies of CD45RA + cells in both CD4 + and CD8 + T cells, which did not correlate with PD‐1 inhibitor responses . CTLA‐4 methylation has been shown to inversely correlated with CTLA4 mRNA, with low‐methylated CTLA‐4 correlating with response to both anti‐PD‐1 and anti‐CTLA4 . High baseline serum biomarkers of excessive extracellular matrix remodeling and collagen breakdown products correlated with worse response to anti‐CTLA‐4 blockade with ipilimumab and shorter OS, perhaps reflecting worsened T‐cell recruitment/infiltration and association with TGF‐β activity …”

LAG3(LAG-3,CD223) DNA methylation correlates with LAG3 expression by tumor and immune cells, immune cell infiltration, and overall survival in clear cell renal cell carcinoma

“…Shown is chromosome 12, position 6 771 404-6 779 853, including the LAG3 gene, its transcripts and regulatory elements (promoter, promoter flank, and CCCTCbinding factor (CTCF) binding site), and the investigated loci. The LAG3 methylation target sites of the HumanMethylation450 BeadChip beads (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16) and qMSP assays (4 and 8) are based on Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13). The illustration (modified) was exported from www.ensemble.org (release 98).…”

“…The illustration (modified) was exported from www.ensemble.org (release 98). 50 Beads are numbered as follows: cg26956535 (1), cg22777668 (2), cg16352928 (3), cg02695343 (4), cg10500147 (5), cg17213699 (6), cg19872463 (7), cg04671742 (8), cg01820374 (9), cg19421125 (10), cg10191002 (11), cg20652042 (12), cg06157570 (13), cg14292870 (14), cg11429292 (15), and cg15828668 (16). LAG3, lymphocyte activating 3; qMSP, quantitative methylation-specific PCR.…”