Table 3. The top 5 canonical biology pathways and related differentially expressed genes (DEGs) in responder groups (RM1 and RD2) and non-responder groups (NM1 and ND2).
| Canonical pathways | Downregulated DEGs | Upregulated DEGs | |
|---|---|---|---|
| RM1 | Granulocyte Adhesion and Diapedesis | 14/162 (9%): CSF3R, ICAM1, PPBP, ITGA5, CXCL5, SDC4, CCL3, ITGB3, GNAI2, CLDN5, CCL3L3, IL1B, CXCL1, CXCL2 | 1/162 (1%): ITGB1 |
| Integrin Signaling | 15/212 (7%): ITGA2B, MAP3K11, ITGA5, MYLK, ITGB3, MYL9, PARVB, AKT1, RHOB, CAPN1, ACTN4, CTTN, ARPC4, ACTN1, ITGB5 | 2/212 (1%):ITGB1, PPP1R12A | |
| TREM1 Signaling | 7/70 (10%): ICAM1, AKT1, NLRP12, ITGA5, IL1B, CD83, CCL3 | 2/70 (3%): ITGB1, NLRC3 | |
| Agranulocyte Adhesion and Diapedesis | 13/172 (8%): ICAM1, PPBP, ITGA5, CXCL5, SDC4, CCL3, GNAI2, MYL9, CLDN5, CCL3L3, IL1B, CXCL1, CXCL2 | 1/172 (1%):ITGB1 | |
| Sertoli Cell-Sertoli Cell Junction Signaling | 13/175 (7%): TUBB1, MAP3K11, TUBA4A, ITGA5, MAPK14, AKT1, PRKAR2B, CLDN5, TUBA8, SPTB, PRKACA, ACTN4, ACTN1 | 1/175 (1%): ITGB1 | |
| RD2 | Opioid Signaling Pathway | 15/239 (6%): AP2M1, AP2A1, CAMK1, AP1B1, GNAI2, CALM1 (includes others), PRKAR2B, GNG11, AKT1, CACNA1B, PRKACA, PNOC, RGS14, RPS6KA4, FGR | 3/239 (1%): RGS1, ATF2, CTNNB1 |
| Transcriptional Regulatory Network | 6/53 (11%): HIST1H4F, HIST2H4B, HIST1H4I, OTX1, HNF4A, HIST1H4H | 2/53 (4%): RIF1, SMARCAD1 | |
| Lipid Antigen Presentation by CD1 | 5/19 (26%): AP2A1, AP2M1, PSAP, CANX, AP1B1 | 0/19 (0%) | |
| Amyloid Processing | 6/50 (12%): PRKAR2B, AKT1, CAPN1, PRKACA, APP, PSEN1 | 1/50 (2%): CSNK1D | |
| DNA Methylation and Transcriptional Repression | 4/33 (12%): HIST1H4F, HIST2H4B, HIST1H4I, HIST1H4H | 1/33 (3%): MECP2 | |
| NM1 | Polyamine Regulation | 2/21 (10%): SAT1, CTNNB1 | 0/21 (0%) |
| PRPP Biosynthesis I | 1/3 (33%): PRPS1 | 0/3 (0%) | |
| Spermine and Spermidine Degradation I | 1/4 (25%): SAT1 | 0/4 (0%) | |
| Unfolded protein response | 1/55 (2%): PPP1R15A | 1/55 (2%): BCL2 | |
| Sirtuin Signaling | 4/277 (1%): PFKFB3, MT-CYB, GABARAPL1, ATG16L2 | 0/277 (0%) | |
| ND2 | Eicosanoid Signaling | 3/62 (5%): PLA2G16, PLB1, PTGDS | 0/62 (0%) |
| Phospholipases | 2/56 (4%): PLA2G16, PLB1 | 0/56 (0%) | |
| Role of Macrophages | 4/306 (1%): IRAK3, CEBPB, TCF7L2, FCGR3A/FCGR3B | 0/306 (0%) | |
| Glycoaminoglycan-protein Linkage Region Biosynthesis | 1/7 (14%): B3GAT1 | 0/7 (0%) | |
| Regulation of the Epithelial-Mesenchymal Transition Pathway | 2/189 (1%): ZEB2, TCF7L2 | 1/189 (1%): TWIST1 |
Abbreviations: DEGs: differentially expressed genes; ECP: extracorporeal photopheresis; BL: baseline; ND2: samples collected after treatment at Day 2 from patients resistant to ECP; NM1: samples collected after treatment at 1 month post-ECP from patients resistant to ECP; RD2: samples collected after treatment at Day 2 from patients responsive to ECP; RM1: samples collected after treatment at 1 month post-ECP from patients responsive to ECP.