Supplementary Figure Legends

Supplementary Figure S1. (a) Unsupervised two-way cluster analysis of microarray data. Data was first filtered to remove raw data with intensity less than 50 in all samples resulting in 12537 genes. (b) Cluster analysis of genes differentially expressed in PPBL samples (P<0.05) by at least 2-fold. Analysis was carried out in Agilent Genespring GX software (Agilent Technologies, Palo Alto, CA).

Supplementary Figure S2. Two-way cluster analysis of (a) top 30 up- and down-regulated genes (Supplementary Table S2 and S3) and (b) four-gene signature (ID2, ANX1, P2RY14, SCN3A) of PPBL, control and CLL samples (GEO dataset: GSE9250). Analysis was carried out in Agilent Genespring GX software (Agilent Technologies, Palo Alto, CA).

Supplementary Figure S3. Ingenuity (Ingenuity Systems, Redwood City, CA) pathway mapping of genes differentially expressed in PPBL.

Supplementary Figure S1.

Supplementary Figure S2

Supplementary Figure S3.

Supplementary Table S1. PPBL patient details.

ID / Sex / Age / i(3q) / PCC / Lymphocyte
1 / F / 52 / - / - / 6.5
2 / F / 59 / + / + / 7.2
3 / F / 38 / + / - / 4.8
4 / M / 46 / - / - / 3.7
5 / F / 36 / - / + / 3.9
6 / F / 57 / - / + / 5.1
7 / M / 47 / + / - / 6.6
8 / F / 5- / + / + / 4.6
9 / F / 65 / + / + / 4.9
1- / F / 48 / + / - / 5.1
11 / F / 31 / + / + / 6.8
12 / M / 54 / + / - / 8.5
13 / M / 46 / - / + / 5.2
14 / F / 37 / - / + / 9.-

*Presence of i(3q) or PCC (premature chromosome condensation) were preformed by conventional cytogenetic or FISH techniques as previously described (Mossafa H, Tapia S, Flandrin G, Troussard X. Chromosomal instability and ATR amplification gene in patients with persistent and polyclonal B-cell lymphocytosis (PPBL). Leuk Lymphoma 2004; 45: 1401-1406).

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Supplementary Table S2. Top 30 up- regulated genes

Log ratio / P value / Name / Map / Ingenuity Canonical Pathway / Description
4.105395 / 1.95E-07 / FOS / 14q24.3 / TGFβ signalling* / Fos-oncogene: member of AP-1 complex
3.98002 / 1.88E-05 / ANXA1 / 9q12-q21 / Glucocortidoid receptor signalling / Annexin A1: up-regulated in cholangiocarcinoma
3.941276 / 6.68E-08 / ID2 / 2p25 / - / Inhibitor of DNA binding 2: induces MCF7 proliferation and up-regulated in peripheral T cell lymphoma
3.719909 / 5.62E-07 / RGS1 / 1q31 / - / Regulator of G-protein signalling 1: involved in B cell development
3.30234 / 6.00E-06 / KLF4 / 9q31 / VDR/RXR Activation / Kruppel-like factor 4: reduced expression in B memory cells
3.211432 / 9.30E-07 / NR4A2 / 2q22-q23 / - / Nuclear receptor subfamily 4, group A, member 2: up-regulated in plasma cells; anti-apoptotic
3.199721 / 1.92E-07 / SOCS3 / 17q25.3 / IL-10 signalling; JAK/STAT signalling / Suppressor of cytokine signalling 3: constitutively expressed in CD30+ cutaneous T cell lymphoma
3.194817 / 1.54E-05 / S100A12 / 1q21 / - / S100 calcium binding protein A12: expressed in granulocytes
3.136162 / 1.24E-05 / EGR1 / 5q31.1 / B cell receptor signalling / early growth response 1: expressed in B cells
3.114253 / 8.72E-04 / CCL3 / 17q11-q21 / Glucocortidoid receptor signalling / chemokine (C-C motif) ligand 3: up-regulated in CLL
3.071924 / 5.07E-07 / MALAT1 / 11q13.1 / - / metastasis associated lung adenocarcinoma transcript 1
3.043453 / 1.28E-05 / CSTA / 3q21 / - / cystatin A: up-regulated by Fos and Jun
2.999886 / 4.35E-13 / CDC27 / 17q12-17q23.2 / - / cell division cycle 27 homolog: down-regulated in Waldenstrom’s macroglobulinemia
2.997524 / 4.19E-07 / BCL11B / 14q32.2 / - / B-cell CLL/lymphoma 11B: fusion partner in T-ALL
2.997147 / 1.34E-07 / JUN / 1p32 / TGFβ signalling* / Jun-oncogene: Member of AP-1 complex
2.971355 / 2.48E-06 / CST3 / 20p11.21 / - / cystatin C: up-regulated in plasma cells
2.944717 / 2.93E-04 / VIM / 10p13 / - / Vimentin: up-regulated by Jun
2.930708 / 2.43E-04 / CD14 / 5q22-q32 / VDR/RXR Activation* / Activates NFkB and induces growth and differentiation of B cells
2.907055 / 4.93E-05 / CD69 / 12p13-p12 / - / Induces TGFβ and expressed in memory B cells
2.905361 / 2.16E-05 / FCN1 / 9q34 / - / Ficolin: expressed in monocytes
2.894042 / 6.25E-05 / FOSB / 19q13 / - / Member of AP-1 complex
2.877707 / 1.33E-09 / RORA / 15q21-q22 / - / RAR-related orphan receptor A
2.874693 / 9.67E-07 / IL7R / 5p13 / - / interleukin 7 receptor (CD127): anti-apoptotic in lymphocytes
2.866006 / 5.29E-06 / GABARAPL1 / 12p13.2 / - / GABA(A) receptor-associated protein like 1: autophagy in prostate cancer
2.860691 / 4.17E-05 / MAFF / 22q13.1 / NRF2-mediated Oxidative Stress Response / v-maf musculoaponeurotic fibrosarcoma oncogene homolog F
2.850363 / 7.31E-06 / MAFB / 20q11.2 / - / v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian)
2.825442 / 3.53E-07 / TIAM1 / 21q22.1 / Actin Cytoskeleton Signaling; Tight Junction Signaling / T-cell lymphoma invasion and metastasis 1
2.819869 / 2.79E-05 / CLEC7A / 12p13.2 / - / C-type lectin domain family 7, member A: expressed in non-small-cell lung carcinoma
2.809130 / 1.82E-08 / JUNB / 19p13.2 / NRF2-mediated Oxidative Stress Response / Member of AP-1 complex
2.791479 / 1.10E-05 / PRKCA / 17q22 / Apoptosis signalling* / protein kinase C, alpha subunit: up-regulated in Burkitt’s lymphoma

*More than one Ingenuity canonical pathway listed.

Supplementary Table S3. Top 30 down- regulated genes

Log ratio / P value / Name / Map / Ingenuity Canonical Pathway / Description
-4.52804 / 1.12E-13 / P2RY14 / 3q21-q25 / - / purinergic receptor P2Y, G-protein coupled, 14: chemotaxis of hematopoietic cells
-4.44936 / 1.93E-19 / SCN3A / 2q24 / - / sodium channel, voltage-gated, type III, alpha subunit: expressed in small cell lung carcinoma
-4.33617 / 3.22E-09 / TCL1A / 14q32.1 / - / T-cell leukemia/lymphoma 1A: pro-apoptotic; decreases growth of lymphocytes
-4.27420 / 8.48E-16 / COCH / 14q12-q13 / - / coagulation factor C homolog
-3.81805 / 4.30E-15 / PCDH9 / 13q14.3 / - / protocadherin 9: not expressed in memory B cells
-3.51938 / 2.80E-10 / CD200 / 3q12-q13 / - / Up-regulated by apoptosis; expressed angioimmunoblastic T cell lymphoma
-3.50831 / 4.07E-09 / LYPLAL1 / 1q41 / - / lysophospholipase-like 1
-3.39337 / 1.94E-06 / TNFRSF17 / 16p13.1 / NFkB signalling / Decreases B lymphocyte proliferation and binding of BAFF
-3.36635 / 5.17E-07 / PPAPDC1B / 8p12 / - / phosphatidic acid phosphatase type 2 domain containing 1B
-3.35277 / 3.07E-11 / SSPN / 12p11.2 / - / sarcospan (Kras oncogene-associated gene)
-3.32942 / 1.67E-08 / IGHA1 / 14q32.33 / - / immunoglobulin heavy constant alpha 1
-3.30326 / 5.25E-14 / TRIM13 / 13q14 / - / tripartite motif-containing 13: expressed in B cells; part of CDR (13q14) of CLL
-3.13633 / 1.27E-09 / STK17A / 7p12 / - / serine/threonine kinase 17a (DRAK1) Down-regulated in non-hodgkin’s lymphoma
-3.03985 / 3.48E-13 / GRAMD1C / 3q13.31 / - / GRAM domain containing 1C
-3.01187 / 5.28E-09 / SLC15A2 / 3q13.33 / - / solute carrier family 15 (H+/peptide transporter), member 2:
-3.00625 / 5.44E-17 / KCNH8 / 3p24.3 / - / potassium voltage-gated channel, subfamily H (eag-related), member 8
-2.98377 / 4.54E-09 / SMAD4 / 18q21 / TGFβ signalling; cell cycle* / Decreases cell growth
-2.96533 / 9.26E-10 / PLEKHF2 / 8q22.1 / - / pleckstrin homology domain containing, family F (with FYVE domain) member 2
-2.88613 / 1.91E-09 / FLJ10159 / 6q21 / - / sine oculis binding protein homolog (Drosophila) (SOBP): expressed in prostate cancer
-2.88049 / 1.15E-10 / CNTNAP2 / 7q35-q36 / - / contactin associated protein-like 2: expressed in colon cancer
-2.85433 / 2.38E-09 / BACH2 / 6q15 / - / BTB and CNC homology 1, basic leucine zipper transcription factor 2: pro-apoptotic in lymphoma cell lines, decreases colony formation and growth; B cell specific TF, decreased expression with B cell maturation.
-2.84765 / 1.16E-13 / RNGTT / 6q16 / - / RNA guanylyltransferase and 5'-phosphatase: expressed in cervical cancer
-2.84908 / 3.17E-04 / DSP / 6p24 / - / Desmoplakin: pro-apoptotic in cardio myocytes
-2.83588 / 2.33E-10 / TLOC1 / 3q26.2 / - / translocation protein 1: regulated by p53
-2.81399 / 4.85E-11 / CCR6 / 6q27 / - / chemokine (C-C motif) receptor 6: increased T cell numbers in knock-out mice; B cell development; expression restricted to marginal and mantle zone B cells
-2.76867 / 1.36E-09 / PTPRO / 12p13.3 / - / protein tyrosine phosphatase, receptor type, O: pro-apoptotic
-2.6739 / 1.43E-06 / CLLU1 / 12q22 / - / chronic lymphocytic leukemia up-regulated 1
-2.69665 / 1.03E-10 / NT5E / 6q14-q21 / Purine metabolism* / 5'-nucleotidase, ecto (CD73): antibody treatment increases T cell growth
-2.65621 / 1.43E-08 / TLR7 / Xp22.3 / NFkB signalling / toll-like receptor 7: B cell differentiation

*More than one Ingenuity canonical pathway listed.

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Supplementary Table S4. PPBL sample microarray expression levels of genes identified as being differentially expressed in ALCL and HL compared to other hematological samples.2

Gene / Fold Change / P value / Up/Down in ALCL/HL
TIMP1 / 3.254 / 1.98E-08 / Up
NK4 / 2.978 / 4.20E-09 / Up
FER1L3 / 2.269 / 1.17E-05 / Up
IL1R2 / 2.195 / 5.11E-04 / Up
CCL4 / 1.932 / 2.15E-02 / Down
IL1R1 / 1.294 / 2.12E-02 / Up
NFIL3 / 1.272 / 2.34E-01* / Up
MTUS1 / 1.19 / 4.22E-02 / Up
SDC4 / 1.17 / 1.38E-01* / Up
MGST3 / 1.139 / 4.75E-02 / Up
CD79A / 1.11 / 3.83E-01* / Down
TNFRSF8 / 1.058 / 5.78E-01* / Up
E2F2 / 1.043 / 4.37E-02 / Down
ATM / 1.036 / 6.73E-01* / Down
RASGRP3 / -1.0235 / 8.42E-01* / Down
POLD4 / -1.1876 / 2.61E-01* / Down
CD79B / -1.2626 / 2.12E-01* / Down
POU2F2 / -1.3405 / 5.23E-06 / Down
SCRN1 / -1.3717 / 4.70E-02 / Down
APS / -1.3889 / 4.31E-02 / Down
LY86 / -1.3889 / 8.77E-02* / Down
P2RX5 / -1.3928 / 7.71E-02* / Down
CNR2 / -1.4 / 4.11E-02 / Down
SYK / -1.4498 / 4.03E-02 / Down
CD22 / -1.5192 / 3.32E-02 / Down
TOSO / -1.8416 / 9.38E-07 / Down
NCF1 / -1.9288 / 1.36E-02 / Down
CD19 / -1.9401 / 7.95E-03 / Down
IGKC / -2.1053 / 9.29E-03 / Down
MS4A1/CD20 / -2.2017 / 4.47E-03 / Down
PNOC / -2.2072 / 5.66E-03 / Down
LY64 / -2.5218 / 3.06E-03 / Down
BTK / -2.6183 / 3.00E-03 / Down
P2Y10 / -2.8478 / 1.90E-03 / Down
BLNK / -2.9504 / 2.57E-03 / Down
KIAA0922 / -3.2437 / 1.18E-03 / Down
CHI3L2 / -3.4891 / 8.75E-04 / Down
IGHD / -3.6101 / 5.00E-04 / Down
IGJ / -3.6228 / 1.21E-03 / Down
STX7 / -4.2222 / 9.46E-04 / Down
IGHM / -7.5891 / 2.72E-04 / Down
TNFRSF17 / -11.38 / 1.67E-04 / Down

*Not significantly different (P > 0.05).

Supplementary Table S5. Death receptor pathway genes.

Name / Description / ID / Log Ratio / p-value
Bcl-2 / B-cell CLL/lymphoma 2 / 232210_at / -1.846788486 / 1.58E-03
Caspase 2 / apoptosis-related cysteine peptidase / 226032_at / -1.247116259 / 2.01E-06
TANK / TRAF family member-associated NFKB activator / 209451_at / -1.179769567 / 6.13E-04
HtrA2 / HtrA serine peptidase 2 / 203089_s_at / -1.089871308 / 3.06E-05
FLIP / CASP8 and FADD-like apoptosis regulator / 239629_at / -1.044851404 / 2.56E-03
Caspase 3 / apoptosis-related cysteine peptidase / 202763_at / -0.917385893 / 2.36E-04
FADD / Fas (TNFRSF6)-associated via death domain / 202535_at / -0.833600039 / 9.01E-04
APO2L / tumor necrosis factor (ligand) superfamily, member 10 / 214329_x_at / -0.776326841 / 1.14E-01*
Caspase 7 / caspase 7, apoptosis-related cysteine peptidase / 207181_s_at / -0.688694889 / 1.88E-02
TRADD / TNFRSF1A-associated via death domain / 1729_at / -0.503428522 / 3.29E-02
Apaf1 / apoptotic peptidase activating factor 1 / 204859_s_at / -0.486109143 / 1.56E-01*
Caspase 9 / caspase 9, apoptosis-related cysteine peptidase / 210775_x_at / -0.457998242 / 6.03E-03
Diablo / diablo homolog (Drosophila) / 219350_s_at / -0.453343766 / 4.64E-03
Fas / Fas (TNF receptor superfamily, member 6) / 215719_x_at / -0.427987314 / 4.51E-02
ASK1 / mitogen-activated protein kinase kinase kinase 5 / 203836_s_at / -0.413999618 / 3.34E-02
TBK1 / TANK-binding kinase 1 / 218520_at / -0.368517458 / 4.33E-02
Caspase 6 / caspase 6, apoptosis-related cysteine peptidase / 242323_at / -0.360795573 / 3.50E-01*
TRAF2 / TNF receptor-associated factor 2 / 204413_at / -0.279124405 / 3.80E-02
TL1 / tumor necrosis factor (ligand) superfamily, member 15 / 221085_at / -0.060302575 / 3.36E-01*
FasL / Fas ligand (TNF superfamily, member 6) / 211333_s_at / 0.05503489 / 4.92E-01*
Daxx / death-associated protein 6 / 216038_x_at / 0.140552541 / 3.29E-01*
RAIDD / CASP2 and RIPK1 domain containing adaptor with death domain / 242638_at / 0.19828504 / 1.36E-02
APO3L / tumor necrosis factor (ligand) superfamily, member 12 / 205611_at / 0.20142613 / 2.32E-01*
JNK1 / mitogen-activated protein kinase 8 / 210477_x_at / 0.301190266 / 7.40E-02*
RIP / receptor (TNFRSF)-interacting serine-threonine kinase 1 / 209941_at / 0.306239632 / 9.46E-02*
DR6 / tumor necrosis factor receptor superfamily, member 21 / 218856_at / 0.817288803 / 3.89E-04
tBid / BH3 interacting domain death agonist / 211725_s_at / 0.956469258 / 3.46E-04
TNF-R2 / tumor necrosis factor receptor superfamily, member 1B / 203508_at / 0.978746069 / 2.86E-03
Cyto C / cytochrome c, somatic / 244546_at / 0.979435326 / 1.58E-02
TNF-alpha; / tumor necrosis factor (TNF superfamily, member 2) / 207113_s_at / 1.097913792 / 3.67E-02
TNF-R1 / tumor necrosis factor receptor superfamily, member 1A / 207643_s_at / 1.295758451 / 2.83E-06
DR3 / tumor necrosis factor receptor superfamily, member 25 / 219423_x_at / 1.862582583 / 5.08E-07

*Not significantly different (P > 0.05).

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