Table 2.
Molecular changes after neoadjuvant chemotherapy.
| Pathway | Gene count | Gene | |
|---|---|---|---|
| Upregulated | Lymphocyte infiltrate | 10 | CCL21, CCL2, CXCR4, PTPRC, IL-10RA, FYB, CD52, SRGN, TYROBP, TNFAIP8 |
| Tumor marker | 4 | EGR3, MMP2, PTGS2, ZEB1 | |
| Cytokine signaling | 4 | IL-6, IL-4, CSF1R, CSF2RB | |
| Checkpoint pathway | 4 | CD69, PDCD1LG2, CD28, ENTPD1 | |
| TCR coexpression | 3 | ITK, CD3E, IL-7R | |
| Adhesion_migration | 3 | NCAM1, ITGA1, ADGRE5 | |
| Innate_immune_response | 2 | LYZ, AXL | |
| Antigen_presentation | 2 | CD1C, CD83 | |
| Type_II_interferon_signaling | 1 | CX3CL1 | |
| T_cell_regulation | 1 | KLF2 | |
| T_cell_differentiation | 1 | EGR2 | |
| PD_1_signaling | 1 | FOXO1 | |
| NK_cell_marker | 1 | NCR3 | |
| NK_activation | 1 | KLRG1 | |
| Myeloid_marker | 1 | MPO | |
| Lymphocyte_development | 1 | IKZF1 | |
| Lymphocyte_activation | 1 | SH2D1A | |
| Leukocyte_migration | 1 | VCAM1 | |
| Dendritic_cell | 1 | NRP1 | |
|
| |||
| Downregulated | Proliferation | 5 | CCNB2, TOP2A, MAD2L1, KIAA0101, MELK |
| Neutrophil | 2 | KREMEN1, DGAT2 | |
| Checkpoint_pathway | 1 | TNF | |
| Antigen_processing | 1 | HLA-C | |
| Tumor_antigen | 1 | BAGE | |