Fig. 4: Rt3D-palbociclib increases RNA sensor expression and RNA ERV species expression that is dependent on JAK/STAT signalling. ERV peptides are found in the immunoproteome. | Nature Communications

Fig. 4: Rt3D-palbociclib increases RNA sensor expression and RNA ERV species expression that is dependent on JAK/STAT signalling. ERV peptides are found in the immunoproteome.

From: Palbociclib and dsRNA sensor co-operate to enhance anti-cancer effects through ER stress and modulation of immune evasion

Fig. 4: Rt3D-palbociclib increases RNA sensor expression and RNA ERV species expression that is dependent on JAK/STAT signalling. ERV peptides are found in the immunoproteome.

A Volcano plot of RNA sequencing data showing upregulated and downregulated genes for A375 cells treated with Rt3D (MOI 0.1) plus palbociclib (1 μM), compared to Rt3D alone, at 48 h. Data are from n = 3 independent biological replicates. B Proteomic analysis of A375 cells treated with Rt3D (0.1–1) ± palbociclib (1 μM) reveal upregulated (red) and downregulated (blue) histone proteins (48 h, data are from 1 independent experiment). C Proteomic analysis of A375 cells treated with Rt3D (0.1–1) ± palbociclib (1 μM) reveal upregulated (red) and downregulated (blue) categorised under the GO term ‘DNA modification’ (48 h, data are from 1 independent experiment). D RT-qPCR of RIG-I (DDX58), MDA-5 (IFIH1) and TLR3 in A375 cells treated with Rt3D plus palbociclib (1 μM) at 48 h. Data presented are mean values ± SEM, n = 3 biologically independent experiments. P values were determined by one-way ANOVA corrected for multiple comparisons. E siRNA silencing of RNA sensors or scrambled control (SCR) in A375 cells treated with Rt3D (0.1) ∓ palbociclib (1 μM) by sulforhodamine B assay. Data are representative of 3 independent repeats. F RT-qPCR of Rt3D genome in A375-infected cells ± palbociclib (1 μM) at 48 h. Data presented are mean values ± SEM, n = 5 biologically independent experiments. G Replication of Rt3D by one-step virus growth assay for A375 ± palbociclib (1 μM). Data presented are mean values ± SEM, n = 3 biologically independent experiments. H RT-qPCR for the expression of a panel of 26 previously described ERVs in A375, treated with combination therapy, or Rt3D, respectively, from 1 independent biological experiment. I RT-qPCR of the ERVs MER21C, MLTA10, MLT1C627 or MER57B1, in A375 cells treated with Rt3D (MOI 0.1) ± palbociclib at 48 h. Data presented are mean values ± SEM, n = 3 biologically independent experiments. P values were determined by one-way ANOVA corrected for multiple comparisons. J MLT1C49, MER21C, MLTA10, MLT1C627 or MER57B1 expression in A375 cells treated with Rt3D (MOI 0.1) and/or palbociclib (1 μM) ± the JAK/STAT inhibitor, ruxolitinib (RUX, 1 μM) at 48 h. Data presented are mean values ± SEM, n = 3 biologically independent experiments. K Volcano plot of RNA sequencing data showing upregulated and downregulated ERVs in A375 cells treated with Rt3D ∓ palbociclib compared to basal at 48 h (using TETool kit). L Fold change in ERV peptides from captured HLA-I with Rt3D-palbociclib versus basal conditions. ERV Peptides Filtered: 5% Peptide FDR, Confirmed TMT Quant, Single Genomic Loci, Predicted as MHC Binding. P values were derived where p > 0.05 ns, *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. Source data are provided as a Source Data file.

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