Table 4.
Differentially expressed genes between homozygous PRDM1 deletion-positive and -negative DLBCL and between BLIMP-1 protein-negative and -positive DLBCL
| Homozygous PRDM1 deletion-positive vs. - negative DLBCL |
Overall BLIMP-1 protein-negative vs. -positive DLBCL |
Wild-type BLIMP-1 protein-negative vs. -positive DLBCL |
|||||
|---|---|---|---|---|---|---|---|
| Overall DLBCL | ABC-DLBCL | Overall DLBCL | ABC-DLBCL | Overall DLBCL | ABC-DLBCL | ||
| Function category | FDR < 0.1 | FDR < 0.3 | FDR < 0.01 | FDR < 0.05 | FDR < 0.01 | FDR < 0.3 | |
| Cytokine, immune/inflammation related | Up | NLRP7, IL10 | NLRP7 | CNR2 | - | - | - |
| Down | - | - | GZMB, SLAMF7, PRF1, IL2RB, GBP1, GZMA, APOBEC3B, GBP5, GBP2, FAM46C, STAT1, FCER1G, C1QC, IRF1, SRGN, C1orf38, RAB27A, IDO1, CST7, CCR5, IL21R, HLA-C, HLA-B, IRF2, NLRC5, B2M, ZBP1, MGC29506, ZC3HAV1, TAP1 | IGJ, APOBEC3B, RAB27A | PRF1, FAM46C, LANCL2, TAP1 | IGJ, APOBEC3B, RAB27A | |
| Differentiation | Up | DPPA4 | - | BCL11A | BCL11A, FOXP1 | BCL11A | FOXP1 |
| Down | - | SLFN5 | BATF | - | BATF | - | |
| B/T antigen/surface receptor and regulation | Up | - | - | MS4A1, CD22, GCNT2, BLK | CD22, CD37 | MS4A1, GCNT2 | CD37 |
| Down | - | - | TARP /// TRGC2 | - | LAX1 | - | |
| Transcription factor; RNA processing; protein synthesis, folding, and transportation; endoplasmic reticulum stress | Up | STAT3, HLF, TCF19, TSHZ1, HMGA2 | HLF, ZNF684, TAF7L, HMGA2 | ELL3 /// SERINC4, PLEKHF2, TEAD2, DNAJC10 | - | ELL3 /// SERINC4, DNAJC10, PLEKHF2, SLC6A16 | GOLGA8B |
| Down | - | - | PRDM1, ELL2, XBP1, HSP90B1, FKBP11, CRTC3, WARS, RUNX3, SUB1, XRN1, SSR4, DNAJC3, CTSB, VAMP5, NEAT1, SAR1B, DNAJB9, LAP3, ARID3A, LITAF, SEC11C, SSR1, SSR3, ARL4C, RALB, RNF149, MANF, HSPA13, C15orf24, SEC24A, RNF213, EDEM2, UFM1, LRPAP1, SELK | PRDM1, UBE2J1, FKBP11, ZBTB38, XBP1, HERPUD1, DNAJC3, SEC24A, HSPA13, ERLEC1, MANF, EIF2AK3, DNAJB9 | PRDM1, ELL2, IRF4, FKBP11, HSP90B1, XBP1, SSR4, DNAJB9, TRAM2, MANF, DNAJC3 | PRDM1, FKBP11, UBE2J1, UBE2J1, XBP1, MANF, ERLEC1, HSPA13, SSR1, HSPA5, DNAJB9, EIF2AK3, CD2BP2 | |
| Cell cycle, DNA replication, chromatin structure, DNA damage response, proliferation, and signaling | Up | NLRP2, CDKN2AIP, EPHA4, SMARCA1, C10orf2, PRM1 | NLRP2, TRIP13, CDKN2AIP, CENPL, EPHA4, RAB3IP, GINS4 | CLLU1, SLC6A16 | CLLU1, GPR39, STX6 | BCL7A | DBF4B |
| Down | - | - | DUSP4, MIR21, VDR, CDKN1B, SERPINA1, SPRY4, PIM2, GIMAP6, TMEM184B, PIK3R5, GRIN3A, CALM1 | DUSP4, VDR, TRIB1 | - | VDR | |
| Cell death, tumor suppression | Up | TNFAIP8 | - | PAWR | - | - | MEG3 |
| Down | - | - | TXNDC5, CFLAR, TMEM49, MLKL, MCL1, GADD45A, GHITM, ARMCX3 | TXNDC5, GHITM | MLKL, TXNDC5, CFLAR | TXNDC5, TMEM59 | |
| Metabolism, autophagy, oxidative stress | Up | CYB5R2, SLC2A13, ELOVL7, MOCOS, LPCAT4 | CYB5R2, LPCAT4, SLC2A13, TGDS | RIMKLB, GYLTL1B, CCBL1, CALCA | ATP8B1, SLC39A9 | - | ACSM1, SLC39A9 |
| Down | - | - | CHST2, WIPI1, TMEM59, SOD2, TXN, GLUL, ACP2, P4HB, SLC39A8, GLA, SAT1, GALM, GSS, APOL6, GLRX, ACSL1 | GSS, TMEM59 | - | - | |
| Adhesion, motility, cytoskeleton, extracellular matrix | Up | NRCAM, C14orf45 | - | PCDHGA4, KANK1, DAAM1, PTK2, MICAL3 | - | PTK2 | MICAL3 |
| Down | - | - | CADM1, MT2A, MT1H, MT1X, MT1G, MT1E, MT1E/H/M, IQGAP2, ITGAL, TMSB10, FNDC3A, C12orf55 | ITGAL, C12orf55 | - | - | |
| Unknown | Up | ZNF385C, PSORS1C2, LOC4orf45, FAM108C1, hCG_17324 | ZNF385C, BTF3L4, MGC87042, FAM108C1, LOC401312 | SYPL1, C8orf37, LOC151162 /// MGAT5 | FAM129C, SNORA74A, TRIM34 /// TRIM6-TRIM34 | SYPL1 | - |
| Down | - | - | LOC541471 /// NCRNA00152, KIAA1618, NKG7, LOC283922, LOC100289053, KLHDC7B | - | C12orf55, C20orf196 | LOC100129637, FAM122C, C16orf70 | |