Page 127 - Haematologica-April 2018

Global mRNA changes in stroma-bound lymphoma cells
Table 2. Functional clusters of genes distinguishing stromal-cell attached MCL cells from mantle cell lymphoma (MCL) suspension cells in co- culture.
C Description Functional categories Genes
Functional clusters for which gene transcripts are more abundant in adherent MCL cells compared to suspension MCL cells in the same co-culture
c1 CD40 and NF-κB signaling
c2Toll-likereceptorand MAP kinase signaling
c3 Respiration
c4 Lymphocyte activation
c5 BCL2 family andanti-apoptosis
c6 Extracellular
I kappaB kinase kappaB cascade, Positive regulation of I KappaB kinase NF kappaB cascade, positive
regulation of signal transduction, Protein kinase cascade, regulation of I kappaB kinase NF kappaB cascade
BST2, BUD31, CARD9, CASP1, CD40,
CDKN1C, FAF1, HMOX1, IKBKE, LGALS1,
LGALS9, LITAF, MAP3K6, MIER1, MKNK1, MKNK2, MUL1, NDFIP2, NEK6, NMI, NR4A3,
OTUD7B, PLCE1, PRDX4, REL, RHOC, RIPK2, SIK1, SLC20A1, SLC35B2, SQSTM1, STK17B, STK38L, TAB2, TBK1, TICAM1, TLR6,
TMEM9B, TRAF2, TRIP6, VAPA APP,ATF1,CD180,CNPY3,DUSP3,DUSP7,IRAK4,
ReactomeactivatedTLR4signaling,Reactomeinnateimmunesystem,
Reactome map kinase activation in TLR cascade, Reactome MAPK targets
nuclear events mediated by map kinases, Reactome MYD88 mal cascade
initiated on plasma membrane, Reactome NFκB and MAP kinases activation TLR10, TLR2, TLR4, TLR7 mediated by TLR4 signaling repertoire, Reactome nuclear events kinase
and transcription factor activation, Reactome toll receptor cascades, Reactome TRAF6 mediated induction of NFκB and MAP kinases upon TLR7 8 or 9 activation, Reactome TRIF mediated TLR3 signaling
Reactome respiratory electron transport ATP synthesis
by chemiosmotic coupling and heat production by uncoupling proteins, Reactome TCA cycle and respiratory
electron transport
KEGG allograft rejection, KEGG autoimmune thyroid disease,
KEGG cell adhesion molecules cams, KEGG graft versus host disease, KEGG type I diabetes mellitus, KEGG viral myocarditis,
PID IL12 STAT4 pathway
KEGG viral myocarditis signal, PID IL12 STAT4 pathway
Anti apoptosis, Apoptosis GO, Negative regulation of apoptosis, Negativeregulationofdevelopmentalprocess,Negativeregulation of programmed cell death, Programmed cell death
KEGG cytokine cytokine receptor interaction,
ATP5B, ATP5C1, ATP5D, ATP5F1, ATP5G1, ATP5J, BSG, COX4I1, COX5A, COX5B, COX6B1, COX6C, COX7A2L, COX7B, COX7C, COX8A, CYC1, CYCS,
DLD, ETFA, ETFB, ETFDH, FH, IDH3A, IDH3B, IDH3G, L2HGDH, LDHA, LDHB, MDH2, NDUFA1, NDUFA12, NDUFA2, NDUFA3, NDUFA5, NDUFA8, NDUFA9, NDUFAB1, NDUFB10, NDUFB2, NDUFB3, NDUFB5, NDUFB7, NDUFB9, NDUFS3, NDUFS4, NDUFS5, NDUFS6, NDUFS8, NDUFV2, OGDH, PDHA1, PDHX, PDK1, PDP1, PDP2, SDHB, SDHD, SLC16A1, SLC16A3, SUCLA2, SUCLG1, UQCR11, UQCRB, UQCRC2, UQCRFS1, UQCRH, UQCRQ
CAV1, CD28, CD80, CD86, HLA-DOB, HLA-DQA2, HLA-DRA, HLA-DRB1, HLA-E, MYH15, PRF1
AATF, ACVR1, AMIGO2, ANXA5, BAG1, BCL2A1,
BCL2L1,BCL3,BIK,BNIP1,BRE,CASP7,CD70,
CD74, CDK5R1, CDKN2D, COL4A2, DAD1, DDAH2,
DUSP22, FAIM3, GADD45B, GPX1, IER3, IL24,
MCL1, MRPS30, NOL3, NOTCH4, PEA15, PIM1,
PLAGL1, PMAIP1, PPP1R13B, PPP1R15A, PSEN2, RUNX3, SERPINB9, SIRT2, STK17A, TNFAIP8,
TNFSF9, TRIAP1, TSPO, UTP11L, XIAP ADAM8, ANGPTL6, ANXA6, CCL4L2, CLEC17A,
COL9A2, CRELD2, CRIM1, CSF1, CST7, CSTB, CTSH, CTSZ, EDA, EMILIN2, HBEGF, HYAL2, IGFBP4, INHBE, KAZALD1, P4HA1, PDGFA, PLOD3, PLXNA1, S100A11, S100A4, S100A6, SDC3, SDC4, SEMA7A, SERPINE2, SRGN, THPO, VEGFA, VWA5A, WNT10A, ZP3
AIMP1, CD164, CD22, CD79A, CD83, CD97, DYRK3, ELF4, FTH1, GEM, GPR65, HDAC9, HELLS, ICOSLG, IL32, IL4R, LAT2, LAX1, LRMP, LY86, MS4A1, NFIL3, NLRC3, PDCD1, PRELID1, PREX1, PTGER4, SIT1, SP2, TAPBP, TGFB1, TNFRSF14, XBP1
matrix - Matrisome NABA matrisome associated, NABA matrisome, NABA secreted factors
c7 B-cell receptor/ cytokine signaling
Cell activation, Immune response, Immune system process, Leukocyte activation, Lymphocyte activation, Positive regulation of immune system process, Positive regulation of multicellular organismal process, Regulation of immune system process, Regulation of lymphocyte activation, Regulation of multicellular organismal process, T-cell activation
JUN, MAP2K3, MAP2K4, MAP2K6, MAPK10, MAPK11, MAPK7, MAPKAPK2, MEF2C, PELI1, TLR1,
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