Page 125 - Haematologica-April 2018

Global mRNA changes in stroma-bound lymphoma cells
Table 1. Differential transcript levels in adherent compared to suspension mantle cell lymphoma (MCL) cells in co-culture.
Symbol TPM SEP TPM SUSP TPM ADH FC FDR q Symbol TPM SEP TPM SUSP TPM ADH FC FDR q
Higher transcript levels in adherent Jeko-1 cells:
Lower transcript levels in adherent Jeko-1 cells:
TNF 0.6
EGR1 4.3 FOS 0.8 EGR3 0.2 CCL3 10.2 MIR146A 3.9 EGR2 9.4 CCL4 17.9 MYCN 0.3 NR4A2 1.3 CSF1 3.1 PHLDA1 0.1 LTA 0.3 PLK2 0.4 MAFF 0.1 IL10 0.8 SLAMF1 0.2 RIN2 0.2 CCL4L2 4.4 CD69 17 SEMA7A 6.7 TNFRSF9 0 DUSP2 75.2 GPR3 0.6 STX11 0.1 FOSL1 0.4 HES1 0.6 IL4I1 0.2 ETV5 0.2 NR4A3 11.5 IER3 8 XIRP1 0.1 TNFAIP3 13.3 PPP1R15A 14.8 RGS3 0.8 DUSP4 0 GADD45B 14.6 NFKBIA 97.2 CD83 98.7 ICAM1 16.2 HBEGF 5 KCNK5 0.1 BCL2A1 6.9 NR4A1 27.9 ZC3H12C 2.9 IL21R 0.7 LRRC32 0.6 KLF10 13.1 SPRY2 2.9 GEM 1.7
1.7 39.7 23.35
10.7 178 16.64 1.8 25.5 14.17 5.2 66.4 12.77 36.2 424.2 11.72 5.1 52.9 10.37
14.7 135.3 9.20 70.5 596.9 8.47 0.3 2.5 8.33 3.8 30.1 7.92 5.1 37.9 7.43 1.1 8.1 7.36 0.6 4.3 7.17 0.5 3.5 7.00 0.5 3.4 6.80 2.2 14.9 6.77 0.2 1.3 6.50 0.5 3.1 6.20 14.4 84 5.83 23.3 133.1 5.71 20 110.8 5.54 0.4 2.1 5.25 123.1 637.7 5.18 0.7 3.5 5.00 0.6 2.9 4.83 1.1 5.3 4.82 2.5 11.8 4.72 1.1 5.1 4.64 0.5 2.3 4.60 53.1 241.2 4.54 8.1 36.7 4.53 0.2 0.9 4.50 20.1 90.1 4.48 17.6 75.6 4.30 1.9 7.7 4.05 0.3 1.2 4.00 28.7 114.7 4.00 121 468.2 3.87 292.2 1128.8 3.86 34.1 128.5 3.77 2.9 10.9 3.76 0.6 2.2 3.67 59.5 216.9 3.65 57.9 207.1 3.58 6.4 22.8 3.56 4.3 15.3 3.56 11.7 41 3.50 17 59.5 3.50 8.2 28 3.41 4.6 15.5 3.37
7.6E-46
4.1E-23 7.8E-13 3.6E-20 1.4E-26 9.9E-03 5.0E-13 1.2E-33 1.3E-03 4.5E-16 1.1E-34 1.5E-11 2.9E-09 2.5E-05 1.1E-03 3.8E-11 3.9E-02 1.2E-03 1.7E-08 1.4E-05 2.3E-47 5.8E-05 5.8E-50 5.6E-03 7.8E-06 3.5E-03 2.8E-08 5.9E-09 1.5E-03 8.3E-22 1.7E-13 3.9E-02 2.0E-09 4.0E-06 4.1E-20 1.1E-02 5.8E-32 9.9E-11 2.0E-15 8.2E-36 3.3E-07 1.2E-02 4.1E-17 2.1E-41 1.6E-13 7.9E-14 1.4E-26 1.8E-06 3.6E-11 1.7E-08
RAG1 42.6
GPR56 14.3 SMAD6 4.1 CCDC42B 14.5 NEIL1 6.5 C10orf71 22.8 NYNRIN 5.2
OSR2 10.3
BMP3 33.9 WDR66 9.1 PCDH9 96
PIF1 30.9 CXCR4 901.8 GADD45A 38.9
AICDA 31.3
PSRC1 29.9 FBXO32 3.7 LINC01089 70.2 AOX2P 7.8
KCNA3 24.8 ABCA1 36.9 RASSF6 208.1 TP53INP1 10.8
ASPM 134.5 RNF144B 93.1
SORT1 24 SOX4 68.3 WNT5A 34.8 PROX1 13.3
SMAD1 102.7
ZNF850 4.9 LOC730101 14.9 LOC440173 18.9
FOXN4 15.6 SPPL2B 30.7 TRIM52 23.9 HUNK 8.4 NUAK2 14.2 KIF20A 102.3
MIAT 16.7 MYLIP 23.3 KLHL24 22.3 CDC42BPB 49.8
30.3 5.7 -5.32
6.3 1.7 -3.71 4.1 1.4 -2.93 11.2 4.4 -2.55 7.3 2.9 -2.52 14 5.7 -2.46 3.9 1.6 -2.44 8.8 3.7 -2.38 18.7 8 -2.34 5.7 2.5 -2.28 53.6 24.5 -2.19 28.8 13.2 -2.18 744.3 344.4 -2.16 34.1 16 -2.13 34.6 16.3 -2.12 25 11.9 -2.10 3.1 1.5 -2.07 67.5 33 -2.05 4.5 2.2 -2.05 15.2 7.5 -2.03 33 16.3 -2.02 130.5 65.2 -2.00 6.9 3.5 -1.97 109.9 56.4 -1.95 56.8 29.5 -1.93 17.5 9.2 -1.90 53.8 28.6 -1.88 29.2 15.9 -1.84 13.4 7.3 -1.84 70.2 38.3 -1.83 4.2 2.3 -1.83 9.3 5.1 -1.82 16.2 8.9 -1.82 13 7.2 -1.81 27.5 15.3 -1.80 25.1 14 -1.79 5.9 3.3 -1.79 12.6 7.1 -1.77 96.3 54.4 -1.77 10.6 6 -1.77 28.4 16.1 -1.76 14.1 8 -1.76 35.8 20.4 -1.75
3.5E-74
4.7E-07 2.3E-02 1.4E-02 7.6E-03 1.3E-09 2.9E-03 8.7E-03 1.8E-12 7.3E-03 2.5E-25 4.5E-10 4.9E-72 1.6E-04 4.0E-09 2.6E-05 4.9E-02 1.2E-11 4.0E-02 2.1E-04 1.3E-24 4.1E-41 3.3E-03 1.1E-28 5.3E-10 1.1E-08 1.3E-15 7.3E-11 1.3E-03 2.0E-13 4.2E-02 1.8E-02 3.3E-02 6.1E-03 3.0E-08 2.0E-03 1.5E-02 4.2E-03 1.5E-15 8.1E-06 5.5E-05 3.0E-06 9.1E-12
The most up- and down-regulated genes with an absolute fold change ≥1.75 (max. 50) in the adherent MCL fraction (ADH) as compared to MCL cells in suspension (SUSP) in co-culture with stromal cells.Transcript levels are shown as transcripts per million reads (TPM) for ADH and SUSP as well as for MCL cells grown in mono-culture (SEP),where read counts per gene have been normalized to library size and gene length. Fold change (FC) for comparison of ADH relative to SUSP presented with the associated P-value adjusted for multiple testing by false discovery rate (FDR q-value).
haematologica | 2018; 103(4)
669