Fig. 1

High SMG1 expression correlates with worse survival and lower immune infiltration in some tumors. (A) Patients with different tumors from TCGA cohorts were classified in two categories according to their SMG1 expression levels: ‘low’ or ‘high’ and significance of long-term survival was determined using long-rank test. Statistical significance was set in p ≤ 0.01 (dot line). n ≥ 100 patients per cohort. (B) Kaplan-Meyer curves of statistically significant tumors from (A): PAAD, LUAD and BRCA. (C) Heatmap illustrating correlations between the expression of genes for NMD factors and immune response-related markers in BRCA patients. scRNAseq expression data reanalyzed [21]. Heatmap shows Pearson’s r coefficient. (D) Uniform Manifold Approximation and Projection (UMAP) map of breast cancer patient [21] classified depending on their SMG1 expression as ‘high’ or ‘low’ based on the SMG1 expression on tumor cells from pretreatment samples (n= 31). Each cell type is determined by color code. (E) Bar plot showing absolute cell numbers of each population shown in (D). (F) Differentiated T-cell subpopulations in BRCA patients with low and high SMG1 expression levels as in (D). UMAP clusters of 14 different cell types depicted by color code T cells were classified as naive (CD4+ TN and CD8+ TN), regulatory T cells (CD4+ TREG), effector/memory T cells (CD4+ TEM and CD8+ TEM), recently activated effector/memory T cells (CD8+TEMRA), tissue-resident memory T cells (CD8+ TRM), exhausted T cells (CD4+ and CD8+ TEX) and proliferating T cells, resting NK cells (NKres) and cytotoxic NK cells (NKcyto), gamma-delta T cells with semi-invariant T-cell repertoires (Vγ9/Vδ2 Tγδ) and with memory features (Tγδ). (G) Bar plot showing absolute cell numbers of each population shown in (F). (H) Heatmap showing the abundance exhaustion markers on T cells in samples with different SMG1 expression as in (D), but SMG1 expression was divided in 4 quartiles from low to high: Q1, Q2, Q3 and Q4. Percentage of positive cells for each of the main exhaustion markers is shown (LAG3, PDCD1, CTLA4, TOX and HAVCR2)