Effect of ECP therapy on CAR-T cells at the transcriptional level. (A) PCA of transcriptomes of ECP-treated or untreated CAR-T cells after 16 hour culture, in which Fragments Per Kilobase Million (FPKM) value was used as the input data for each gene in different samples. (B) Volcano map of DEGs between ECP-treated and untreated groups. DEGs were defined as |Log2FC| ≥ 1 and Q value ≤0.05. (C) KEGG pathway analysis of DEGs showing the top 10 enriched pathways. The color indicates the Q value, and the size of nodes was scaled by the gene number. (D) Gene ontology enrichment analysis of DEGs showing the top 10 enriched gene ontology terms in biological process. (E) Classification of enriched KEGG pathways in cellular processes, environmental information processing, genetic information processing, and metabolism. (F) Network analysis of enriched biological process of gene ontology. The size of nodes is scaled by the gene number. (G) Protein-protein interaction network analysis of DEGs by Cytohubba. The top 50 DEGs were colored by yellow and red, whereas the neighbors were colored by purple. (H) Protein-protein interaction network analysis of DEGs by molecular complex detection. (I) Prioritization of DEGs by random forest analysis. The DEGs were ranked by mean decrease in accuracy and mean decrease in Gini. (J) Identification of hub genes by combination of 4 different algorithms. The Venn plot illustrates the number of overlap genes in all different combinations of analyses, including PCA, Cytohubba, molecular complex detection, and random forest analysis. (K) Gene signature sets for immunophenotypes assessed by single sample gene set enrichment analysis. A 2-tailed t test was used for statistical analysis. ∗P < .05. (L) Gene set enrichment analysis of ECP-treated and untreated CAR-T cells. On the x-axis, gene sets are represented by vertical black lines, whereas the enrichment score (ES) is plotted on the y-axis. Points representing genes and their corresponding ES are connected by a green line. The colored band at the bottom indicates the correlation of genes with the ECP treatment, with red indicating a positive correlation and blue indicating a negative correlation. The significance threshold is set at false discovery rate of <0.05. The color code represents the signal to noise. Samples of 3 individual donors were tested.

Effect of ECP therapy on CAR-T cells at the transcriptional level. (A) PCA of transcriptomes of ECP-treated or untreated CAR-T cells after 16 hour culture, in which Fragments Per Kilobase Million (FPKM) value was used as the input data for each gene in different samples. (B) Volcano map of DEGs between ECP-treated and untreated groups. DEGs were defined as |Log2FC| ≥ 1 and Q value ≤0.05. (C) KEGG pathway analysis of DEGs showing the top 10 enriched pathways. The color indicates the Q value, and the size of nodes was scaled by the gene number. (D) Gene ontology enrichment analysis of DEGs showing the top 10 enriched gene ontology terms in biological process. (E) Classification of enriched KEGG pathways in cellular processes, environmental information processing, genetic information processing, and metabolism. (F) Network analysis of enriched biological process of gene ontology. The size of nodes is scaled by the gene number. (G) Protein-protein interaction network analysis of DEGs by Cytohubba. The top 50 DEGs were colored by yellow and red, whereas the neighbors were colored by purple. (H) Protein-protein interaction network analysis of DEGs by molecular complex detection. (I) Prioritization of DEGs by random forest analysis. The DEGs were ranked by mean decrease in accuracy and mean decrease in Gini. (J) Identification of hub genes by combination of 4 different algorithms. The Venn plot illustrates the number of overlap genes in all different combinations of analyses, including PCA, Cytohubba, molecular complex detection, and random forest analysis. (K) Gene signature sets for immunophenotypes assessed by single sample gene set enrichment analysis. A 2-tailed t test was used for statistical analysis. ∗P < .05. (L) Gene set enrichment analysis of ECP-treated and untreated CAR-T cells. On the x-axis, gene sets are represented by vertical black lines, whereas the enrichment score (ES) is plotted on the y-axis. Points representing genes and their corresponding ES are connected by a green line. The colored band at the bottom indicates the correlation of genes with the ECP treatment, with red indicating a positive correlation and blue indicating a negative correlation. The significance threshold is set at false discovery rate of <0.05. The color code represents the signal to noise. Samples of 3 individual donors were tested.

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