Figure 2S

4 7 A - C 080125 CSCs 080418 CSCs - + IFN-a 48 h + IFN-a 48 h + IFN-a 72 h 6 + IFN-a 72 h

3 5 MRFI

4

2

3

2 1

1

0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4

7 B 13 080125 FBS - D 080418 FBS - + IFN-a 48 h 12 + IFN-a 48 h + IFN-a 72 h + IFN-a 72 h 6 080125 FBS 11 10 5 9

8 4 7

6 3 MRFI 5

4 2 3

2 1

1

0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4

Molecule Molecule

FIGURE 4S FIGURE 5S

Panel A Panel B FIGURE 6S A B

C D

Supplemental Results

Table 1S. Modulation by IFN-α of APM in GBM CSC and FBS tumor cell lines.

Molecule *

Cell line IFN-α‡ HLA β2-m# HLA LMP TAP1 TAP2

class II

A A HC§ 2 7 10

080125 CSCs - 1∞ (1) 3 (65) 2 (91) 1 (2) 6 (47) 2 (61) 1 (3) 1 (2) 1 (3)

+ 2 (81) 11 (80) 13 (99) 1 (3) 8 (88) 4 (91) 1 (2) 1 (3) 2 (68)

080125 FBS - 2 (81) 4 (63) 4 (83) 1 (3) 6 (80) 3 (67) 2 (86) 1 (3) 2 (75)

+ 2 (99) 14 (90) 7 (97) 5 (75) 7 (100) 6 (98) 2 (90) 1 (4) 3 (87)

080418 CSCs - 2 (51) 1 (1) 1 (3) 2 (47) 2 (83) 2 (54) 1 (4) 1 (2) 1 (3)

+ 2 (81) 3 (76) 5 (75) 2 (50) 2 (83) 3 (71) 1 (3) 2 (87) 1 (2)

080418 FBS - 1 (3) 3 (70) 2 (88) 1 (4) 3 (87) 2 (76) 1 (3) 1 (3) 1 (2)

+ 2 (78) 7 (98) 5 (99) 2 (94) 5 (100) 3 (100) 1 (4) 2 (100) 1 (2)

070104 CSCs - 1 (2) 1 (3) 1 (3) 2 (78) 1 (3) 1 (2) 1 (3) 1 (3) 1 (2)

+ 2 (98) 8 (100) 10 (88) 4 (89) 3 (98) 3 (94) 1 (4) 2 (86) 2 (79)

* expression of APM molecules was evaluated by intracellular staining and cytofluorimetric analysis; ‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α;

# β-2 microglobulin;

§ β-2 microglobulin-free HLA-A heavy chain;

∞ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 0.8

≤ 4.

Table 2S . Expression of proteasome and APM-associated chaperon molecules in GBM CSC and FBS tumor cell lines.

Cell line Molecule *

Delta MB1 Z Calreticulin ERp57 Tapasin

0627 CSCs 7 ‡ (100) 1 (3) 1 (5) 20 (100) 2 (92) 2 (67) 2 (86)

0627 FBS 1 (1) 1 (2) 1 (3) 3 (99) 1 (3) 1 (2) 1 (2)

080125 CSCs 16 (85) 1 (2) 1 (2) 49 (99) 2 (85) 1 (3) 2 (99)

080125 FBS 1 (5) 1 (4) 1 (5) 28 (100) 3 (95) 1 (2) 1 (3)

080418 CSCs 8 (100) 1 (5) 1 (4) 13 (100) 2 (99) 1 (5) 1 (4)

080418 FBS 7 (89) 1 (5) 1 (4) 16 (98) 3 (98) 1 (3) 1 (5)

080201 CSCs 36 (99) 3 (98) 3 (98) 55 (100) 10 (98) 3 (98) 7 (97)

080201 FBS 16 (98) 3 (98) 6 (98) 80 (100) 9 (98) 2 (97) 5 (98)

071011 CSCs 17 (98) 3 (87) 3 (75) 100 (100) 15 (98) 3 (87) 7 (76)

071011 FBS 16 (100) 1 (4) 2 (87) 20 (100) 4 (87) 1 (3) 2 (98)

080325 CSCs 10 (98) 3 (98) 4 (98) 200 (100) 5 (99) 2 (95) 5 (98)

070104 CSCs 1 (3) 2 (93) 1 (4) 52 (100) 2 (88) 1 (4) 1 (3)

1869 EBV-B 2 (99) 3 (89) 2 (82) 100 (91) 2 (94) 2 (81) 2 (70)

* expression of APM molecules was evaluated by immunofluorescence on permeabilized cells and cytofluorimetric analysis;

‡ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 1.2

≤ 4.

Table 3S . Modulation by IFN-α of the expression of proteasome and APM-associated chaperon molecules in GBM CSC and FBS tumor cell lines.

Molecule *

Cell line IFN-α ‡ Delta MB1 Z Calnexin Calreticulin ERp57 Tapasin

080125 CSCs - 16# (85) 1 (2) 1 (5) 49 (100) 2 (95) 1 (2) 2 (3)

+ 22 (100) 1 (3) 1 (4) 73 (100) 2 (100) 1 (2) 2 (2)

080125 FBS - 1 (5) 1 (4) 1 (5) 28 (100) 3 (95) 1 (2) 1 (3)

+ 10 (99) 1 (2) 2 (99) 30 (100) 3 (98) 2 (89) 1 (2)

080418 CSCs - 8 (100) 1 (5) 1 (4) 13 (100) 2 (99) 1 (5) 1 (4)

+ 8 (100) 1 (4) 1 (3) 13 (100) 3 (100) 8 (99) 1 (3)

080418 FBS - 7 (89) 1 (5) 1 (4) 16 (98) 3 (98) 1 (3) 1 (5)

+ 9 (100) 1 (3) 1 (3) 26 (100) 3 (99) 1 (2) 1 (3)

070104 CSCs - 1 (3) 2 (93) 1 (4) 52 (100) 2 (88) 1 (4) 1 (3)

+ 13 (99) 1 (3) 1 (4) 27 (100) 3 (98) 1 (3) 1 (3)

* expression of APM molecules was evaluated by immunofluorescence on permeabilized cells and cytofluorimetric analysis;

‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α;

# values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 1 ≤ 4. Table 4S. Modulation of MHC and APM molecules by 5-Aza CdR treatment of GBM and FBS tumor cell lines

Cell line 5-Aza-CdR * Molecule ‡

MHC II MICA MB1 LMP10 TAP1

080125 CSCs - 1# (2) 1 (4) 1 (2) 1 (3) 1 (2) + 1 (2) 1 (3) 2 (98) 1 (3) 1 (3) 080125 FBS - 1 (2) 3 (95) 1 (3) 1 (4) 1 (2) + 1 (3) 3 (98) 3 (90) 2 (80) 2 (88)

080418 CSCs - 1 (2) 1 (2) 1 (5) 1 (4) 1 (3) + 1 (3) 1 (3) 1 (3) 1 (3) 1 (2) 080418 FBS - 1 (3) 3 (95) 3 (98) 4 (97) 1 (3) + 1 (3) 4 (99) 6 (100) 6 (100) 6 (99)

070104 - 2 (18) 1 (3) 2 (93) 1 (3) 1 (3) + 5 (87) 1 (4) 2 (97) 1 (2) 1 (3)

1869 EBV-B - 12 (96) 1 (3) 3 (89) 3 (91) 4 (95) + 20 (100) 1 (3) 5 (100) 4 (100) 8 (100)

* 5-Aza-2'-deoxycytidine (5μM) was added to culture medium for 4 days; ‡ molecule expression was assessed by surface (MHC II and MICA) or intracellular staining (MIB, LMP10 and TAP1) of cells with specific (see Material and Methods) and cytofluorimetric analysis.

# values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times; SD for each value ≥ 1 ≤

4. Table 5S. Expression of immune response inhibitory molecules by GBM CSC or FBS tumor cell lines

Cell line Molecule* CTLA-4 PD-1 PD-L1 PD-L2

070104 CSC 2‡ (69) 5 (95) 12 (98) 1 (4)

080125 CSCs 2 (81) 2 (94) 10 (99) 1 (3) 080125 FBS 2 (65) 3 (96) 19 (99) 2 (70)

080418 CSCs 2 (55) 2 (85) 7 (99) 1 (2) 080418 FBS 1 (5) 1 (2) 9 (98) 1 (3)

080201 CSCs 2 (77) 3 (95) 11 (99) 1 (3) 080201 FBS 2 (95) 2 (97) 31 (98) 2 (93)

071011 CSCs 2 (42) 2 (59) 4 (97) 1 (2) 071011 FBS 1 (5) 1 (4) 2 (50) 1 (3)

080325 CSCs 2 (62) 2 (56) 4 (94) 1 (3)

SW480 col 2 (59) 2 (80) 6 (98) 1 (1)

1061 mel 2 (54) 1 (1) 6 (99) 1 (2)

1869 EBV-B 1 (1) 2 (83) 5 (97) 1 (2)

* expression of the indicated molecules was evaluated by immunofluorescence and cytofluorimetric analysis; ‡ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control (MRFI); bold values indicate significant MRFI (≥ 2). The numbers in parenthesis represent the percentage of positive cells. The experiment has been repeated three times with SD for each value ≥ 0.6 ≤ 4.

SW480 col and 1061 mel, that are a colorectal and a melanoma cell lines, respectively, were used in the experiment as not GBM tumor cells. Table 6S. differentially expressed between CSC and FBS, p<0.005. Genes are ranked according to fold change.

Fold- Paramet Permutati change symbol Description UG cluster ric p- on p-value (CSC/FB value S) oligodendrocyte transcription OLIG1 factor 1 (OLIG1), mRNA. Hs.56663 7.53E-05 1.00E-04 2192 ubiquitin specific peptidase 30 USP30 (USP30), mRNA. Hs.486434 45281 906 2077 calsequestrin 2 () CASQ2 (CASQ2), mRNA. Hs.57975 4.00E-07 134 1593 SPARC-like 1 (hevin) (SPARCL1), transcript variant 2, SPARCL1 mRNA. Hs.62886 46627 114 996 carbonic anhydrase X (CA10), CA10 transcript variant 3, mRNA. Hs.463466 18432 84 828 ADAM metallopeptidase domain 19 (meltrin beta) (ADAM19), ADAM19 transcript variant 2, mRNA. Hs.483944 26136 64 750 3-hydroxy-3-methylglutaryl- Coenzyme A synthase 1 (soluble) (HMGCS1), transcript variant 2, HMGCS1 mRNA. Hs.397729 2109 25 691 SRY (sex determining region Y)- SOX8 box 8 (SOX8), mRNA. Hs.243678 16431 53 684 ribosomal S6 kinase, 90kDa, polypeptide 2 (RPS6KA2), transcript variant 2, RPS6KA2 mRNA. Hs.719131 1855 11 655 dipeptidyl-peptidase 4 (DPP4), DPP4 mRNA. Hs.368912 25174 8 583 periostin, osteoblast specific factor (POSTN), transcript variant POSTN 2, mRNA. Hs.136348 27286 779 569

KIAA1549 KIAA1549 (KIAA1549), mRNA. Hs.605380 1857 57 553 CDNA FLJ32758 fis, clone hCG_1999814 TESTI2001792 Hs.666511 22226 2 544 collagen, type VIII, alpha 2 COL8A2 (COL8A2), mRNA. Hs.353001 43215 2117 538 epithelial 2 EMP2 (EMP2), mRNA. Hs.531561 2084 1.00E-04 506 guanine nucleotide binding protein (G protein), gamma 7 GNG7 (GNG7), mRNA. Hs.515544 1.94E-05 1.00E-04 505 PREDICTED: misc_RNA LOC346329 (LOC346329), miscRNA. 2.57E-05 5.00E-04 484 arylsulfatase D (ARSD), transcript ARSD variant 1, mRNA. Hs.528631 29984 823 473 shroom family member 2 SHROOM2 (SHROOM2), mRNA. Hs.567236 507 3.00E-04 416 olfactory , family 51, subfamily B, member 2 OR51B2 (OR51B2), mRNA. Hs.680163 44691 1307 410 ST3 beta-galactoside alpha-2,3- sialyltransferase 6 (ST3GAL6), ST3GAL6 mRNA. Hs.148716 7475 9.00E-04 410 signal-induced proliferation- associated 1 like 2 (SIPA1L2), SIPA1L2 mRNA. Hs.715656 1074 38 381 CD164 molecule, sialomucin (CD164), transcript variant 5, CD164 mRNA. Hs.520313 1.10E-06 1.00E-04 381 calumenin (CALU), transcript CALU variant 1, mRNA. Hs.718425 7871 799 377 paroxysmal nonkinesigenic dyskinesia (PNKD), transcript PNKD variant 2, mRNA. Hs.98475 5.75E-05 5.00E-04 375 kelch domain containing 8A KLHDC8A (KLHDC8A), mRNA. Hs.10414 15658 54 369 RAB11 family interacting protein RAB11FIP4 4 (class II) (RAB11FIP4), mRNA. Hs.406788 43079 169 352 11 open reading C11orf66 frame 66 (C11orf66), mRNA. Hs.502726 2682 25 348 trinucleotide repeat containing 6B (TNRC6B), transcript variant 2, TNRC6B mRNA. Hs.372082 25239 409 338 WAS/WASL interacting protein family, member 1 (WIPF1), WIPF1 transcript variant 1, mRNA. Hs.128067 2101 1.00E-04 334 growth differentiation factor 1 GDF1 (GDF1), mRNA. Hs.412355 2916 1.00E-04 328

CPNE2 copine II (CPNE2), mRNA. Hs.339809 8009 9.00E-04 316 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 (AGAP1), transcript variant 2, AGAP1 mRNA. Hs.435039 7203 18 315 chemokine (C-C motif) receptor 8 CCR8 (CCR8), mRNA. Hs.113222 1548 729 291 protein 555 (ZNF555), ZNF555 mRNA. Hs.47712 28039 398 288 ring finger protein 144B RNF144B (RNF144B), mRNA. Hs.148741 4786 7.00E-04 287 sprouty homolog 2 (Drosophila) SPRY2 (SPRY2), mRNA. Hs.18676 17819 27 286 sprouty homolog 4 (Drosophila) (SPRY4), transcript variant 2, SPRY4 mRNA. Hs.323308 45094 9 283 tetratricopeptide repeat domain 3 (TTC3), transcript variant 2, TTC3 mRNA. Hs.368214 24706 46 282 prostaglandin D2 receptor (DP) PTGDR (PTGDR), mRNA. Hs.306831 19878 84 281 CDNA FLJ31574 fis, clone NT2RI2001782 Hs.680579 31374 39 275 kin of IRRE like (Drosophila) KIRREL (KIRREL), mRNA. Hs.657006 43367 1287 272 open 175 (C1orf175), transcript C1orf175 variant 1, mRNA. Hs.412482 9362 48 268 myristoylated alanine-rich protein kinase C substrate (MARCKS), MARCKS mRNA. Hs.519909 35251 4 266 diazepam binding inhibitor (GABA receptor modulator, acyl- Coenzyme A binding protein) (DBI), transcript variant 3, DBI mRNA. Hs.78888 5.10E-06 1.00E-04 265 small nuclear ribonucleoprotein polypeptide N (SNRPN), SNRPN transcript variant 1, mRNA. Hs.564847 1176 1.00E-04 258 3-hydroxy-3-methylglutaryl- Coenzyme A reductase (HMGCR), transcript variant 2, HMGCR mRNA. Hs.713530 5564 23 257 tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1 (TANC1), transcript variant 2, TANC1 mRNA. Hs.61590 42403 68 256 CDNA FLJ38039 fis, clone CTONG2013934 Hs.46506 5242 25 249 sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C (SEMA4C), SEMA4C mRNA. Hs.516220 1.34E-05 1.00E-04 245 PREDICTED: misc_RNA LOC729732 (LOC729732), miscRNA. 38897 119 242 LSM10, U7 small nuclear RNA LSM10 associated (LSM10), mRNA. Hs.654622 15469 413 237 RNA binding motif protein 26 RBM26 (RBM26), mRNA. Hs.558528 20766 56 236 protein-L-isoaspartate (D- aspartate) O-methyltransferase domain containing 2 (PCMTD2), PCMTD2 transcript variant 2, mRNA. Hs.473317 2294 64 235 2-aminoethanethiol (cysteamine) ADO dioxygenase (ADO), mRNA. Hs.99821 26491 73 234 sterol regulatory element binding 2 (SREBF2), SREBF2 mRNA. Hs.443258 4628 6.00E-04 234 sorting nexin 18 (SNX18), SNX18 transcript variant 1, mRNA. Hs.432755 10643 32 234 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1 ST8SIA1 (ST8SIA1), mRNA. Hs.408614 48715 64 233 collagen, type VIII, alpha 1 (COL8A1), transcript variant 1, COL8A1 mRNA. Hs.654548 9864 18 228 raftlin family member 2 (RFTN2), RFTN2 mRNA. Hs.591615 8719 13 228 musculin (activated B-cell factor- MSC 1) (MSC), mRNA. Hs.442619 7.50E-06 1.00E-04 227 CDNA FLJ36111 fis, clone LOC283480 TESTI2021999 Hs.662212 2657 74 226 LanC lantibiotic synthetase component C-like 1 (bacterial) (LANCL1), transcript variant 3, LANCL1 mRNA. Hs.13351 6949 5.00E-04 224 kelch domain containing 5 KLHDC5 (KLHDC5), mRNA. Hs.505104 19665 26 223 chromosome 13 open reading C13orf18 frame 18 (C13orf18), mRNA. Hs.98117 5105 32 223

protein phosphatase, non- receptor type 6 (PTPN6), PTPN6 transcript variant 2, mRNA. Hs.63489 27445 91 222 metallothionein 2A (MT2A), MT2A mRNA. Hs.647371 42815 275 222 lamin B receptor (LBR), transcript LBR variant 2, mRNA. Hs.435166 43319 69 219 FK506 binding protein 10, 65 kDa FKBP10 (FKBP10), mRNA. Hs.463035 46909 135 218

YWHAZ 14-3-3 protein Hs.492407 25398 25 217 cyclin-dependent kinase 2 associated protein 1 (CDK2AP1), CDK2AP1 mRNA. Hs.719107 21395 24 216 CDNA FLJ37981 fis, clone CTONG2010566 Hs.655537 23039 39 216 RAB10, member RAS oncogene RAB10 family (RAB10), mRNA. Hs.467960 10138 13 214 coiled-coil domain containing 25 CCDC25 (CCDC25), mRNA. Hs.445512 6631 14 212 hypothetical protein DKFZp686O24166 DKFZp686O241 (DKFZp686O24166), non-coding 66 RNA. 34052 53 210 Control stringency: 70% identity to oligo Alien1 158 1.00E-04 209

ETV5 (ETV5), mRNA. Hs.43697 3528 13 208 zinc finger protein 501 (ZNF501), ZNF501 mRNA. Hs.401045 20082 26 206 Ig rearranged lambda-chain mRNA V-Jl2 region, polyreactive Hs.659929 11949 48 206 myotubularin related protein 9 MTMR9 (MTMR9), mRNA. Hs.591395 46537 94 203 adenylate cyclase 6 (ADCY6), ADCY6 transcript variant 2, mRNA. Hs.525401 25215 45 202 cytochrome P450, family 4, subfamily Z, polypeptide 1 CYP4Z1 (CYP4Z1), mRNA. Hs.176588 37353 33 202 lysine-rich coiled-coil 1 KRCC1 (KRCC1), mRNA. Hs.469254 28239 45 202 mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), transcript variant 1, MAP4K4 mRNA. Hs.719073 2577 8.00E-04 202 cytoplasmic linker associated CLASP2 protein 2 (CLASP2), mRNA. Hs.108614 29368 104 200 DIP2 disco-interacting protein 2 homolog B (Drosophila) (DIP2B), DIP2B mRNA. Hs.505516 15671 137 200 SAM and SH3 domain containing SASH1 1 (SASH1), mRNA. Hs.193133 46288 63 200 vascular endothelial zinc finger 1 VEZF1 (VEZF1), mRNA. Hs.463569 8.85E-05 1.00E-04 199 suppressor of defective silencing 3 homolog (S. cerevisiae) (SUDS3), SUDS3 mRNA. Hs.416630 4.63E-05 1.00E-04 198 paraoxonase 2 (PON2), transcript PON2 variant 2, mRNA. Hs.719159 31362 48 198 chromobox homolog 5 (HP1 alpha homolog, Drosophila) (CBX5), CBX5 transcript variant 2, mRNA. Hs.349283 19039 3 197 perforin 1 (pore forming protein) (PRF1), transcript variant 1, PRF1 mRNA. Hs.2200 7.79E-05 1.00E-04 196 barrier to autointegration factor 1 (BANF1), transcript variant 1, BANF1 mRNA. Hs.433759 10956 8.00E-04 195 toll-like receptor adaptor molecule TICAM1 1 (TICAM1), mRNA. Hs.29344 11889 54 193 , down-regulated in LDOC1 cancer 1 (LDOC1), mRNA. Hs.45231 26441 62 193 pecanex-like 2 (Drosophila) (PCNXL2), transcript variant 1, PCNXL2 mRNA. Hs.370605 5115 12 193 male-specific lethal 1 homolog MSL1 (Drosophila) (MSL1), mRNA. Hs.532786 8601 18 192 glycosyltransferase 25 domain GLT25D1 containing 1 (GLT25D1), mRNA. Hs.418795 23359 4 190 centrosomal protein 68kDa CEP68 (CEP68), mRNA. Hs.709257 14027 21 189 alanine-glyoxylate aminotransferase 2 (AGXT2), nuclear gene encoding AGXT2 mitochondrial protein, mRNA. Hs.34494 21004 2 188 cyclin D binding -like transcription factor 1 (DMTF1), DMTF1 transcript variant 3, mRNA. Hs.196129 41064 109 188 TMEM44 Unknown 2753 6 188 SH3-domain kinase binding protein 1 (SH3KBP1), transcript SH3KBP1 variant 2, mRNA. Hs.719268 49779 57 188 protein disulfide isomerase family PDIA6 A, member 6 (PDIA6), mRNA. Hs.212102 11739 42 186 dysferlin, limb girdle 2B (autosomal recessive) (DYSF), transcript DYSF variant 3, mRNA. Hs.252180 2763 2 186 Unknown 10537 54 185 nexilin (F binding protein) NEXN (NEXN), mRNA. Hs.612385 21214 58 183 ADP-ribosylation factor-like 2 binding protein (ARL2BP), ARL2BP mRNA. Hs.645184 8039 5.00E-04 179 kelch domain containing 7A KLHDC7A (KLHDC7A), mRNA. Hs.406913 33105 34 178 zinc finger protein 541 (ZNF541), ZNF541 mRNA. Hs.14161 6834 11 177 natriuretic peptide precursor A NPPA (NPPA), mRNA. Hs.75640 4671 1.00E-04 176 zinc finger, SWIM-type ZSWIM4 containing 4 (ZSWIM4), mRNA. Hs.466015 1377 1.00E-04 176 CDNA FLJ30988 fis, clone HLUNG1000030 Hs.555065 4574 8 175 multiple EGF-like-domains 9 MEGF9 (MEGF9), mRNA. Hs.715550 20938 21 175 chromosome 9 open reading frame 127 (C9orf127), transcript C9orf127 variant 2, mRNA. Hs.493808 38912 117 174 ORAI calcium release-activated calcium modulator 1 (ORAI1), ORAI1 mRNA. Hs.55148 3376 65 174 H1 histone family, member 0 H1F0 (H1F0), mRNA. Hs.715673 3263 11 172 GRB2-associated binding protein 2 (GAB2), transcript variant 1, GAB2 mRNA. Hs.429434 43801 67 171 seven in absentia homolog 1 (Drosophila) (SIAH1), transcript SIAH1 variant 1, mRNA. Hs.295923 20567 31 171 ring finger protein 144A RNF144A (RNF144A), mRNA. Hs.22146 37357 66 170 NODAL modulator 1 (NOMO1), NOMO1 mRNA. Hs.719082 13275 19 169 vestigial like 1 (Drosophila) VGLL1 (VGLL1), mRNA. Hs.496843 37828 55 169 phosphatidylinositol-5-phosphate 4-kinase, type II, alpha PIP4K2A (PIP4K2A), mRNA. Hs.57079 29024 1.00E-04 167 potassium channel tetramerisation domain containing 13 (KCTD13), KCTD13 mRNA. Hs.534590 2148 1.00E-04 167 antigen identified by monoclonal Ki-67 (MKI67), MKI67 transcript variant 2, mRNA. Hs.80976 13229 6.00E-04 167 ring finger protein 103 (RNF103), RNF103 mRNA. Hs.469199 30168 57 166 low density lipoprotein receptor- related protein 5-like (LRP5L), LRP5L transcript variant 2, mRNA. Hs.634058 25966 4 166 T-cell lymphoma invasion and TIAM1 metastasis 1 (TIAM1), mRNA. Hs.517228 2298 11 164 phospholipase B domain PLBD1 containing 1 (PLBD1), mRNA. Hs.131933 5524 13 163 muscle RAS oncogene homolog (MRAS), transcript variant 2, MRAS mRNA. Hs.527021 25141 2 163 vacuolar protein sorting 54 homolog (S. cerevisiae) (VPS54), VPS54 transcript variant 2, mRNA. Hs.48499 3031 1.00E-04 162 CDNA FLJ33235 fis, clone KIRREL ASTRO2002202 Hs.609291 38298 3 160 ankyrin repeat domain 36B ANKRD36B (ANKRD36B), mRNA. Hs.532921 22295 3 158 bone morphogenetic protein 8a BMP8A (BMP8A), mRNA. Hs.472497 6885 6.00E-04 158

Transcribed Hs.515586 44068 72 158 Bardet-Biedl syndrome 2 (BBS2), BBS2 mRNA. Hs.333738 21078 12 158 CDNA FLJ33454 fis, clone BRAMY2000231 Hs.659371 44445 81 158

KIAA1751 KIAA1751 (KIAA1751), mRNA. Hs.232092 40238 44 157 nudE nuclear distribution gene E homolog 1 (A. nidulans) (NDE1), NDE1 transcript variant 2, mRNA. Hs.655378 6619 1.00E-04 156 MCM3AP antisense RNA (non- protein coding) (MCM3APAS), MCM3APAS non-coding RNA. 7.00E-04 21 154 ring finger protein 212 (RNF212), RNF212 transcript variant 2, mRNA. Hs.248290 43508 24 154 zinc finger protein 444 (ZNF444), ZNF444 mRNA. Hs.24545 21432 44 154 transcription factor 6 (E2F6), E2F6 mRNA. Hs.603093 46725 68 152 glucosidase, alpha; neutral AB (GANAB), transcript variant 3, GANAB mRNA. Hs.595071 44344 106 151 ubiquitin specific peptidase 9, Y- USP9Y linked (USP9Y), mRNA. Hs.598540 18234 29 151 WD repeat domain 36 (WDR36), WDR36 mRNA. Hs.533237 47743 5 150 solute carrier family 39 (zinc transporter), member 13 (SLC39A13), transcript variant 1, SLC39A13 mRNA. Hs.523664 25987 4 -150 RAD51-like 1 (S. cerevisiae) (RAD51L1), transcript variant 3, RAD51L1 mRNA. Hs.172587 16585 12 -150 CUB domain containing protein 2 CDCP2 (CDCP2), mRNA Hs.568555 24484 28 -151

LOC200261 PP4277 Hs.352228 4963 53 -151 HLA-B associated transcript 1 (BAT1), transcript variant 2, BAT1 mRNA. Hs.254042 15585 1.00E-04 -152 ligase III, DNA, ATP-dependent (LIG3), nuclear gene encoding mitochondrial protein, transcript LIG3 variant beta, mRNA. Hs.100299 20034 25 -152

OK/SW-CL.87 Hs.576954 19386 23 -153 PREDICTED: misc_RNA LOC389322 (LOC389322), miscRNA. 23754 24 -153 SPRY domain containing 4 SPRYD4 (SPRYD4), mRNA. Hs.128676 198 1.00E-04 -153 EF-hand domain family, member EFHB B (EFHB), mRNA. Hs.670883 7232 5.00E-04 -154 phosphoenolpyruvate carboxykinase 2 (mitochondrial) (PCK2), nuclear gene encoding mitochondrial protein, transcript PCK2 variant 1, mRNA. Hs.75812 37 6 -155 acyl-CoA thioesterase 8 (ACOT8), transcript variant 3, ACOT8 mRNA. Hs.444776 37653 25 -155 nucleolar complex associated 4 homolog (S. cerevisiae) NOC4L (NOC4L), mRNA. Hs.558536 16106 32 -155 Unknown 17195 15 -155 Unknown 7.54E-05 1.00E-04 -155 polyglutamine binding protein 1 (PQBP1), transcript variant 5, PQBP1 mRNA. Hs.534384 3181 22 -155 PREDICTED: hypothetical protein LOC152742 LOC152742 (LOC152742), mRNA. Hs.135435 767 1.00E-04 -155 keratin associated protein 9-3 KRTAP9-3 (KRTAP9-3), mRNA. Hs.307012 3074 1.00E-04 -155 PREDICTED: similar to C-type lectin domain family 4, member g LOC729645 (LOC729645), mRNA. 46268 56 -156 methylmalonic aciduria (cobalamin deficiency) cblA type (MMAA), nuclear gene encoding MMAA mitochondrial protein, mRNA. Hs.452864 3886 86 -156 CDNA PSEC0061 fis, clone NT2RP2000720, highly similar to Asparagine-linked glycosylation 1 homolog (yeast, beta-1,4- ALG1 mannosyltransferase) Hs.592086 3749 6.00E-04 -156 Unknown 37775 26 -157 mitochondrial S11 (MRPS11), nuclear gene encoding mitochondrial protein, MRPS11 transcript variant 2, mRNA. Hs.111286 33847 6 -157 dynein, axonemal, heavy chain 11 DNAH11 (DNAH11), mRNA. Hs.655326 29522 27 -157 MUS81 endonuclease homolog MUS81 (S. cerevisiae) (MUS81), mRNA. Hs.288798 28589 3 -158 PREDICTED: hypothetical protein LOC100134618 LOC100134618 (LOC100134618), mRNA. 36612 58 -159 abhydrolase domain containing 8 ABHD8 (ABHD8), mRNA. Hs.515664 37233 57 -160 Control: Negative- Randomly generated oligo 17439 1.00E-04 -160 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa (NDUFB11), NDUFB11 transcript variant 2, mRNA. Hs.521969 41151 14 -160

ZNF33A KIAA0065 Hs.435774 21056 12 -161 tryptophanyl-tRNA synthetase (WARS), transcript variant 3, WARS mRNA. Hs.497599 41307 62 -161 RNA terminal phosphate cyclase domain 1 (RTCD1), transcript RTCD1 variant 2, mRNA. Hs.484222 46811 81 -162 hypothetical protein FLJ37078 FLJ37078 (FLJ37078), mRNA. Hs.511025 5579 1.00E-04 -162 SIVA1, apoptosis-inducing factor (SIVA1), transcript variant 1, SIVA1 mRNA. Hs.112058 18693 22 -163 STEAP family member 3 (STEAP3), transcript variant 3, STEAP3 mRNA. Hs.647822 25709 49 -163 SRY (sex determining region Y)- SOX18 box 18 (SOX18), mRNA. Hs.8619 12567 12 -163 SH3 domain containing 20 SH3D20 (SH3D20), mRNA. Hs.205326 10797 6.00E-04 -163 ferritin, heavy polypeptide 1 FTH1 (FTH1), mRNA. Hs.524910 28372 5 -164 inturned planar cell polarity effector homolog (Drosophila) INTU (INTU), mRNA. Hs.391481 46788 71 -164 spinster homolog 3 (Drosophila) SPNS3 (SPNS3), mRNA. Hs.657543 24763 35 -165 open reading C11orf46 frame 46 (C11orf46), mRNA. Hs.502208 10161 21 -165 Unknown 37461 51 -165 G protein-coupled receptor kinase interacting ArfGAP 1 (GIT1), GIT1 transcript variant 2, mRNA. Hs.514051 38134 52 -166 rhomboid domain containing 3 RHBDD3 (RHBDD3), mRNA. Hs.106730 19999 25 -166 Control stringency: 80% identity to oligo H200007830 31634 41 -167

MFAP3L CDNA clone IMAGE:4828817 Hs.593942 25107 53 -167 zinc finger protein 593 (ZNF593), ZNF593 mRNA. Hs.477273 3551 12 -167 calponin 2 (CNN2), transcript CNN2 variant 2, mRNA. Hs.651923 15049 55 -167 DPH1 homolog (S. cerevisiae) DPH1 (DPH1), mRNA. Hs.513856 21356 32 -167 Chromosome 6 open reading C6orf223 frame 223 (C6orf223), mRNA Hs.531926 22807 15 -168

HOXB5 B5 (HOXB5), mRNA. Hs.654456 42518 16 -168 SSU72 RNA polymerase II CTD phosphatase homolog (S. SSU72 cerevisiae) (SSU72), mRNA. Hs.657061 14573 31 -168 integrator complex subunit 1 INTS1 (INTS1), mRNA. Hs.532188 42117 45 -169 transmembrane protein 223 TMEM223 (TMEM223), mRNA. Hs.530463 16149 19 -169 serine peptidase inhibitor, Kunitz SPINT2 type, 2 (SPINT2), mRNA. Hs.31439 4497 41 -169 ubiquinol-cytochrome c reductase complex (7.2 kD) (UCRC), UCRC transcript variant 1, mRNA. Hs.284292 49527 61 -169 zinc finger CCCH-type containing ZC3H3 3 (ZC3H3), mRNA. Hs.521915 9.95E-05 1.00E-04 -169 similar to RIKEN cDNA C030006K11 gene (MGC70857), MGC70857 mRNA. Hs.105685 14849 8.00E-04 -169 paired-like homeodomain 1 PITX1 (PITX1), mRNA. Hs.84136 14601 2 -169 CDNA FLJ34606 fis, clone C19orf60 KIDNE2013731 Hs.655317 2136 8.00E-04 -170 Unknown 12934 53 -171 NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa (NDUFV2), nuclear gene encoding mitochondrial protein, NDUFV2 mRNA. Hs.464572 22451 25 -172 solute carrier family 43, member 2 SLC43A2 (SLC43A2), mRNA. Hs.160550 3547 1.00E-04 -172 guanine nucleotide binding protein (G protein), beta 5 (GNB5), transcript variant 1, GNB5 mRNA. Hs.155090 39013 8 -172 Tu , mitochondrial (TUFM), nuclear gene encoding mitochondrial TUFM protein, mRNA. Hs.12084 1087 6.00E-04 -172 ribosomal protein S13 (RPS13), RPS13 mRNA. Hs.446588 32101 54 -172 pseudouridylate synthase-like 1 PUSL1 (PUSL1), mRNA. Hs.400659 40363 62 -172 protoporphyrinogen oxidase (PPOX), nuclear gene encoding mitochondrial protein, transcript PPOX variant 1, mRNA. Hs.517373 7172 1.00E-04 -173 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, NDUFB10 10, 22kDa (NDUFB10), mRNA. Hs.513266 30186 25 -173 protein arginine methyltransferase PRMT7 7 (PRMT7), mRNA. Hs.712584 30813 46 -173 ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 UQCRFS1 (UQCRFS1), mRNA. Hs.170107 12587 25 -173 kinase, 70kDa, polypeptide 2 RPS6KB2 (RPS6KB2), mRNA. Hs.534345 239 1.00E-04 -174 Unknown 38582 1.00E-04 -174 high-mobility group nucleosomal binding domain 2 (HMGN2), HMGN2 mRNA. Hs.181163 1059 14 -174

interferon gamma receptor 1 IFNGR1 (IFNGR1), mRNA. Hs.520414 25984 54 -174 follicle stimulating hormone, beta polypeptide (FSHB), transcript FSHB variant 2, mRNA. Hs.36975 43306 145 -175 prolyl 4-hydroxylase, alpha P4HA3 polypeptide III (P4HA3), mRNA. Hs.660541 6576 36 -175 zinc finger protein 44 (ZNF44), ZNF44 mRNA. Hs.296731 45593 43 -175 family with sequence similarity 119, member A (FAM119A), FAM119A transcript variant 1, mRNA. Hs.664764 4775 15 -175 mediator complex subunit 19 MED19 (MED19), mRNA. Hs.43619 30782 23 -176 PREDICTED: similar to high mobility group nucleosomal binding domain 2, transcript LOC649445 variant 2 (LOC649445), mRNA. 4549 36 -176

TNF receptor-associated factor 2 TRAF2 (TRAF2), mRNA. Hs.522506 38892 55 -176 mature T-cell proliferation 1 neighbor (MTCP1NB), nuclear gene encoding mitochondrial MTCP1NB protein, mRNA. Hs.6917 39522 101 -176 dual-specificity tyrosine-(Y)- phosphorylation regulated kinase 1A (DYRK1A), transcript variant DYRK1A 1, mRNA. Hs.719269 26943 18 -178 Unknown 4251 32 -178 proteasome (prosome, macropain) activator subunit 1 (PA28 alpha) (PSME1), transcript variant 1, PSME1 mRNA. Hs.75348 28685 69 -179 RD RNA binding protein RDBP (RDBP), mRNA. Hs.423935 3578 1 -179 MRNA; cDNA DKFZp547P1417 (from clone DKFZp547P1417) Hs.684033 30971 44 -179 adaptor-related protein complex 2, mu 1 subunit (AP2M1), transcript AP2M1 variant 2, mRNA. Hs.518460 3181 6.00E-04 -180 chromosome 1 open reading C1orf212 frame 212 (C1orf212), mRNA. Hs.27160 44979 102 -181 ribosomal protein S14 (RPS14), RPS14 transcript variant 3, mRNA. Hs.719080 3451 1 -182 family with sequence similarity 128, member B (FAM128B), FAM128B mRNA. Hs.469925 15604 26 -182 IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae) (IMMP2L), nuclear gene encoding mitochondrial IMMP2L protein, mRNA. Hs.655722 5.06E-05 1.00E-04 -182 adrenocortical dysplasia homolog (mouse) (ACD), transcript variant ACD 2, mRNA. Hs.78019 46578 103 -182 aurora kinase A interacting protein 1 (AURKAIP1), transcript AURKAIP1 variant 2, mRNA. Hs.632515 5809 6.00E-04 -182 DiGeorge syndrome critical region gene 6-like (DGCR6L), DGCR6L mRNA. Hs.410965 18052 25 -182 ribosomal protein, large, P2 RPLP2 (RPLP2), mRNA. Hs.437594 34615 72 -183 chromosome 21 open reading frame 34 (C21orf34), transcript C21orf34 variant 3, mRNA. Hs.719301 29824 41 -183 Putative ankyrin-repeat containing protein. [Source:Uniprot/SPTREMBL;Acc TANC2 :Q9NXY9] 21426 36 -183 tumor protein binding protein 1 (TP53BP1), transcript variant 2, TP53BP1 mRNA. Hs.440968 35463 62 -184 TBC1 domain family, member 29 TBC1D29 (TBC1D29), mRNA. Hs.241421 45489 279 -184 chromosome 9 open reading C9orf103 frame 103 (C9orf103), mRNA. Hs.530261 37491 167 -184 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa (NDUFB11), NDUFB11 transcript variant 2, mRNA. Hs.521969 2775 1 -185 glycolipid transfer protein domain GLTPD1 containing 1 (GLTPD1), mRNA. Hs.515689 6495 23 -186 mitochondrial ribosomal protein L35 (MRPL35), nuclear gene encoding mitochondrial protein, MRPL35 transcript variant 1, mRNA. Hs.433439 3763 1.00E-04 -186 prostaglandin E receptor 1 (subtype EP1), 42kDa (PTGER1), PTGER1 mRNA. Hs.159360 5742 21 -186 Ras association (RalGDS/AF-6) domain family member 1 (RASSF1), transcript variant B, RASSF1 mRNA. Hs.476270 1088 19 -186 ribosomal protein S28 (RPS28), RPS28 mRNA. Hs.719103 16895 42 -186 surfeit 1 (SURF1), nuclear gene encoding mitochondrial protein, SURF1 mRNA. Hs.512464 5479 2 -187 DEAD (Asp-Glu-Ala-Asp) box DDX21 polypeptide 21 (DDX21), mRNA. Hs.223141 24962 74 -188 death-associated protein kinase 2 DAPK2 (DAPK2), mRNA. Hs.237886 44257 118 -188 heterogeneous nuclear ribonucleoprotein H1 (H) HNRNPH1 (HNRNPH1), mRNA. Hs.604001 3439 58 -189 peroxiredoxin 6 (PRDX6), PRDX6 mRNA. Hs.120 6.69E-05 1.00E-04 -189 coiled-coil domain containing 12 CCDC12 (CCDC12), mRNA. Hs.631918 3091 23 -189 chromosome 1 open reading C1orf227 frame 227 (C1orf227), mRNA. Hs.153274 37117 78 -189 zinc finger, DHHC-type containing 23 (ZDHHC23), ZDHHC23 mRNA. Hs.21902 37596 43 -190 chromosome 8 open reading C8orf84 frame 84 (C8orf84), mRNA. Hs.439040 33378 39 -190 B-cell novel protein 1 [Source:RefSeq_peptide;Acc:NP_ NP_775815.2 775815] 5696 3 -190 chromosome 1 open reading C1orf53 frame 53 (C1orf53), mRNA. Hs.61329 33663 39 -191 pallidin homolog (mouse) PLDN (PLDN), mRNA. Hs.719102 26699 37 -191 armadillo repeat containing 9 ARMC9 (ARMC9), mRNA. Hs.471610 8402 33 -191 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (FAU), FAU mRNA. Hs.387208 19753 16 -192 v- musculoaponeurotic fibrosarcoma oncogene homolog MAFB B (avian) (MAFB), mRNA. Hs.169487 36518 75 -192 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa (NDUFB7), nuclear gene encoding mitochondrial NDUFB7 protein, mRNA. Hs.532853 9008 14 -193

KIAA1853 KIAA1853 (KIAA1853), mRNA. Hs.112577 21167 36 -193 3, subunit K (EIF3K), EIF3K mRNA. Hs.314359 17018 36 -193 reactive oxygen species modulator 1 (ROMO1), nuclear gene encoding mitochondrial protein, ROMO1 mRNA. Hs.472564 3538 1.00E-04 -193 open reading C7orf29 frame 29 (C7orf29), mRNA. Hs.655915 2899 34 -194 hypothetical LOC93429 (DKFZp434J0226), non-coding DKFZp434J0226 RNA. 24282 35 -195 opioid growth factor receptor-like OGFRL1 1 (OGFRL1), mRNA. Hs.656091 1374 47 -195 cytochrome c oxidase subunit Va (COX5A), nuclear gene encoding COX5A mitochondrial protein, mRNA. Hs.401903 6025 1 -195 zinc finger protein 425 (ZNF425), ZNF425 mRNA. Hs.31743 1727 44 -196 glutathione peroxidase 4 (phospholipid hydroperoxidase) (GPX4), transcript variant 1, GPX4 mRNA. Hs.433951 39175 69 -196 2 (ER beta) (ESR2), transcript variant a, ESR2 mRNA. Hs.660607 48803 86 -196 alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) (ATRX), transcript variant 2, ATRX mRNA. Hs.533526 3.45E-05 1.00E-04 -197 methylmalonyl Coenzyme A mutase (MUT), nuclear gene encoding mitochondrial protein, MUT mRNA. Hs.485527 1678 2 -198 ubiquinol-cytochrome c reductase hinge protein-like (UQCRHL), UQCRHL mRNA. Hs.568229 2165 43 -198 PREDICTED: similar to insulinoma protein (rig) LOC440733 (LOC440733), mRNA. 24685 53 -198 Transcribed locus, strongly similar to NP_001080124.1 ribosomal protein S9 [Xenopus laevis] Hs.467284 10603 65 -198

KIAA1654 KIAA1654 protein Hs.658191 4288 9.00E-04 -199 Transcribed locus, weakly similar to XP_786200.2 PREDICTED: similar to Beta heavy chain of outer-arm axonemal dynein ATPase [Strongylocentrotus purpuratus] Hs.713485 37374 357 -199 Unknown 49759 57 -200 (YBX1), YBX1 mRNA. Hs.473583 46827 83 -200 GLIS family zinc finger 3 (GLIS3), transcript variant 2, GLIS3 mRNA. Hs.162125 38644 239 -201 MAP kinase interacting serine/threonine kinase 2 (MKNK2), transcript variant 1, MKNK2 mRNA. Hs.515032 12996 23 -201 TRM5 tRNA methyltransferase 5 homolog (S. cerevisiae) TRMT5 (TRMT5), mRNA. Hs.380159 47113 65 -201 TCF3 (E2A) fusion partner (in childhood Leukemia) (TFPT), TFPT mRNA. Hs.590939 7.55E-05 1.00E-04 -202 Unknown 26395 37 -202 hypothetical LOC84771 (MGC13005), transcript variant 1, MGC13005 non-coding RNA. 6152 27 -202 Unknown 39068 98 -203 PREDICTED: hypothetical LOC283412 (LOC283412), LOC283412 mRNA. 8066 52 -203 eukaryotic translation initiation factor 5A (EIF5A), transcript EIF5A variant A, mRNA. Hs.534314 34095 88 -203 Unknown 13041 33 -203 Parkinson disease (autosomal recessive, early onset) 7 (PARK7), transcript variant 2, PARK7 mRNA. Hs.419640 44954 102 -204 3-hydroxymethyl-3- methylglutaryl-Coenzyme A lyase HMGCL (HMGCL), mRNA. Hs.533444 9335 1.00E-04 -204 testis expressed 10 (TEX10), TEX10 mRNA. Hs.494648 2144 63 -205 chromosome 1 open reading frame 122 (C1orf122), transcript C1orf122 variant 2, mRNA. Hs.532749 37433 72 -206 CDNA FLJ31972 fis, clone LOC145757 NT2RP7008142 Hs.612155 9458 24 -206 stromal cell derived factor 4 (SDF4), transcript variant 2, SDF4 mRNA. Hs.42806 25241 61 -207 G patch domain and KOW motifs GPKOW (GPKOW), mRNA. Hs.503666 3.48E-05 1.00E-04 -209

PIM1 pim-1 oncogene (PIM1), mRNA. Hs.81170 7.20E-06 18 -209 ribosomal protein L10 (RPL10), RPL10 transcript variant 1, mRNA. Hs.534404 6939 1.00E-04 -209 kinesin family member 20A KIF20A (KIF20A), mRNA. Hs.718626 5079 21 -209 polymerase (RNA) I polypeptide D, 16kDa (POLR1D), transcript POLR1D variant 1, mRNA. Hs.507584 1856 1.00E-04 -210 glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast) (GPAA1), GPAA1 mRNA. Hs.627962 4481 1.00E-04 -211 tuberous sclerosis 1 (TSC1), TSC1 transcript variant 1, mRNA. Hs.370854 32261 164 -211 Unknown 816 47 -211 family with sequence similarity 50, member A (FAM50A), FAM50A mRNA. Hs.54277 1354 7.00E-04 -212 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle (ATP5A1), nuclear gene encoding mitochondrial protein, transcript ATP5A1 variant 2, mRNA. Hs.298280 8866 15 -212 Nucleoporin 50kDa (NUP50), NUP50 transcript variant 3, mRNA Hs.715672 3996 155 -212 enhancer of yellow 2 homolog ENY2 (Drosophila) (ENY2), mRNA. Hs.492555 11543 1.00E-04 -213 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5 (LILRB5), transcript variant 3, LILRB5 mRNA. Hs.655338 1.94E-05 1.00E-04 -215

ARD1 homolog A, N- acetyltransferase (S. cerevisiae) ARD1A (ARD1A), mRNA. Hs.433291 4546 25 -215

LOC440792 KIAA1653 protein Hs.613849 24228 258 -216 mitochondrial ribosomal protein S11 (MRPS11), nuclear gene encoding mitochondrial protein, MRPS11 transcript variant 1, mRNA. Hs.111286 1.88E-05 1.00E-04 -216 LIM and calponin homology domains 1 (LIMCH1), transcript LIMCH1 variant 5, mRNA. Hs.335163 40908 52 -217 transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B) (TCEB2), transcript TCEB2 variant 1, mRNA. Hs.172772 7194 13 -217 transforming growth factor beta 1 induced transcript 1 (TGFB1I1), TGFB1I1 transcript variant 1, mRNA. Hs.513530 2073 75 -218 Transcribed locus, strongly similar to NP_058848.1 ribosomal protein S17 [Rattus norvegicus] Hs.512525 23642 35 -218 homer homolog 2 (Drosophila) (HOMER2), transcript variant 3, HOMER2 mRNA. Hs.578443 35984 93 -218 actin related protein 2/3 complex, subunit 4, 20kDa (ARPC4), ARPC4 transcript variant 3, mRNA. Hs.323342 28664 1.00E-04 -218 hypothetical LOC114130 MGC16384 (MGC16384), non-coding RNA. 2.37E-05 1.00E-04 -219 coiled-coil alpha-helical rod protein 1 (CCHCR1), transcript CCHCR1 variant 3, mRNA. Hs.485075 1923 6.00E-04 -220 trafficking protein particle complex 2-like (TRAPPC2L), TRAPPC2L mRNA. Hs.461722 12556 65 -220 , heavy chain 3, , embryonic (MYH3), MYH3 mRNA. Hs.440895 40124 906 -220 secretory leukocyte peptidase SLPI inhibitor (SLPI), mRNA. Hs.517070 26933 51 -220

PLEK pleckstrin (PLEK), mRNA. Hs.468840 43497 103 -221 ribosomal protein S17 (RPS17), RPS17 mRNA. Hs.433427 39672 81 -221 fucosidase, alpha-L- 1, tissue FUCA1 (FUCA1), mRNA. Hs.370858 31449 6 -222 collagen, type V, alpha 3 COL5A3 (COL5A3), mRNA. Hs.235368 18637 39 -223

Transcribed locus Hs.476965 8285 26 -223

ezrin (EZR), transcript variant 2, EZR mRNA. Hs.487027 1038 24 -224 glutathione S-transferase pi 1 GSTP1 (GSTP1), mRNA. Hs.523836 11133 15 -226 UDP-Gal:betaGlcNAc beta 1,3- galactosyltransferase, polypeptide B3GALT2 2 (B3GALT2), mRNA. Hs.518834 3493 9.00E-04 -228 PREDICTED: similar to ribosomal protein L10 LOC100129975 (LOC100129975), mRNA. 49978 94 -229 ribosomal protein L17 (RPL17), RPL17 transcript variant 2, mRNA. Hs.293653 4693 106 -231 Q9NSI1_HUMA N Unknown 1326 1.00E-04 -231 glutathione S-transferase omega 2 GSTO2 (GSTO2), mRNA. Hs.203634 5609 33 -231 Huntingtin interacting protein K HYPK (HYPK), mRNA. Hs.631692 25485 28 -231 open reading C10orf82 frame 82 (C10orf82), mRNA. Hs.121347 2394 18 -233 Unknown 1523 18 -234 Control: Negative- Randomly generated oligo 37855 39 -234 proteasome maturation protein POMP (POMP), mRNA. Hs.268742 1.94E-05 1 -235 chromosome 1 open reading frame 43 (C1orf43), transcript C1orf43 variant 2, mRNA. Hs.287471 2077 11 -236 methenyltetrahydrofolate synthetase domain containing (MTHFSD), transcript variant 5, MTHFSD mRNA. 48476 56 -237 Unknown 41886 8 -237 HUS1 checkpoint homolog b (S. HUS1B pombe) (HUS1B), mRNA. Hs.669039 5303 26 -238 PREDICTED: similar to 60S acidic ribosomal protein P1 LOC100129028 (LOC100129028), mRNA. 717 23 -240 dickkopf homolog 3 (Xenopus laevis) (DKK3), transcript variant DKK3 3, mRNA. Hs.292156 2402 1.00E-04 -241 PDLIM1 interacting kinase 1 like (PDIK1L), transcript variant 1, PDIK1L mRNA. Hs.468801 1607 6.00E-04 -241 small nucleolar RNA host gene 12 (non-protein coding) (SNHG12), SNHG12 non-coding RNA. 19259 79 -241 family with sequence similarity 110, member B (FAM110B), FAM110B mRNA. Hs.154652 3241 1.00E-04 -242 sphingosine kinase 1 (SPHK1), SPHK1 transcript variant 3, mRNA. Hs.68061 2303 42 -242 HCLS1 associated protein X-1 (HAX1), transcript variant 2, HAX1 mRNA. Hs.199625 1638 5 -245 Rab interacting lysosomal protein RILP (RILP), mRNA. Hs.534497 1919 7.00E-04 -246

AMBRA1 CDNA FLJ60985 complete cds Hs.654644 44727 8 -247 ribosomal protein L5 (RPL5), RPL5 mRNA. Hs.532359 40347 83 -247 CDNA FLJ33293 fis, clone LOC149773 BNGH42000675 Hs.473192 14813 264 -248 ER degradation enhancer, mannosidase alpha-like 2 (EDEM2), transcript variant 2, EDEM2 mRNA Hs.356273 6764 24 -248 ribosomal protein S5 (RPS5), RPS5 mRNA. Hs.378103 21824 46 -248 PDZ and LIM domain 1 PDLIM1 (PDLIM1), mRNA. Hs.368525 10944 47 -248 Unknown 3229 12 -249

Transcribed locus Hs.638581 6428 21 -249

AXIN2 axin 2 (AXIN2), mRNA. Hs.156527 2297 45 -249 methyl-CpG-binding domain protein 3-like 5-like (MBD3L5), MBD3L5 mRNA. Hs.717312 91 18 -249 ribosomal protein L21 (RPL21), RPL21 mRNA. Hs.381123 2684 1.00E-04 -249 TRIO and F-actin binding protein (TRIOBP), transcript variant 1, TRIOBP mRNA. Hs.533030 2874 5 -250 RAD54-like (S. cerevisiae) (RAD54L), transcript variant 2, RAD54L mRNA. Hs.642042 48783 179 -250

IL8 interleukin 8 (IL8), mRNA. Hs.624 20533 37 -251 ribosomal protein L7 (RPL7), RPL7 mRNA. Hs.571841 20802 51 -252 inositol(myo)-1(or 4)- monophosphatase 1 (IMPA1), IMPA1 transcript variant 3, mRNA. Hs.656694 34225 864 -252 solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 (SLC3A2), SLC3A2 transcript variant 6, mRNA. Hs.502769 11841 26 -253 ribosomal protein L8 (RPL8), RPL8 transcript variant 1, mRNA. Hs.178551 38847 99 -253 Unknown 6.00E-07 1.00E-04 -253 olfactory receptor, family 51, subfamily E, member 1 OR51E1 (OR51E1), mRNA. Hs.470038 7237 34 -255 PREDICTED: hypothetical LOC440589 (LOC440589), LOC440589 mRNA. 3334 45 -258 RAS, dexamethasone-induced 1 RASD1 (RASD1), mRNA. Hs.25829 3.09E-05 1.00E-04 -258 kelch-like 17 (Drosophila) KLHL17 (KLHL17), mRNA. Hs.109212 3.36E-05 22 -258 MAP kinase interacting serine/threonine kinase 2 (MKNK2), transcript variant 1, MKNK2 mRNA. Hs.515032 7186 32 -259 CDNA FLJ37666 fis, clone BRHIP2011576 Hs.667944 1795 13 -259 leucine rich repeat (in FLII) interacting protein 2 (LRRFIP2), LRRFIP2 transcript variant 2, mRNA. Hs.719246 8.26E-05 1.00E-04 -260 potassium inwardly-rectifying channel, subfamily J, member 8 KCNJ8 (KCNJ8), mRNA. Hs.102308 74 51 -262 ATPase, Na+/K+ transporting, beta 1 polypeptide (ATP1B1), ATP1B1 transcript variant 1, mRNA. Hs.291196 17683 55 -266 fibrillarin-like 1 (FBLL1), non- FBLL1 coding RNA. 5042 42 -266 chromodomain helicase DNA binding protein 9 (CHD9), CHD9 mRNA. Hs.59159 23158 411 -267 BCL2-associated athanogene BAG1 (BAG1), mRNA. Hs.377484 21607 47 -269 PREDICTED: hypothetical LOC388621 (LOC388621), LOC388621 mRNA. 1764 1.00E-04 -270 retinol binding protein 1, cellular (RBP1), transcript variant 1, RBP1 mRNA. Hs.529571 34525 122 -270 chemokine (C-X-C motif) ligand CXCL14 14 (CXCL14), mRNA. Hs.483444 13099 76 -271 chromosome 11 open reading C11orf30 frame 30 (C11orf30), mRNA. Hs.352588 4.51E-05 55 -271 interferon regulatory factor 2 binding protein 2 (IRF2BP2), IRF2BP2 transcript variant 2, mRNA. Hs.693837 744 26 -272 D-dopachrome tautomerase (DDT), transcript variant 2, DDT mRNA. Hs.656723 4.42E-05 1.00E-04 -272 hydroxypyruvate isomerase HYI homolog (E. coli) (HYI), mRNA. Hs.709864 18091 4 -274 Ras association (RalGDS/AF-6) domain family (N-terminal) member 7 (RASSF7), transcript RASSF7 variant 3, mRNA. Hs.72925 18673 44 -274 translocase of inner mitochondrial membrane 44 homolog (yeast) (TIMM44), nuclear gene encoding TIMM44 mitochondrial protein, mRNA. Hs.465784 27904 5 -277 TBC1 domain family, member 20 TBC1D20 (TBC1D20), mRNA. Hs.590876 21964 129 -281 eukaryotic translation initiation factor 2B, subunit 3 gamma, EIF2B3 58kDa (EIF2B3), mRNA. Hs.533549 34242 73 -282

KIAA1522 KIAA1522 (KIAA1522), mRNA. Hs.591502 49561 122 -282 ring finger protein 113A RNF113A (RNF113A), mRNA. Hs.458365 11804 16 -284 alkB, alkylation repair homolog 5 ALKBH5 (E. coli) (ALKBH5), mRNA. Hs.462392 44841 1283 -285 C10orf130 protein. Q6DHV5_HUM [Source:Uniprot/SPTREMBL;Acc AN :Q6DHV5] 8.70E-05 1.00E-04 -294 ribosomal protein L21 (RPL21), RPL21 mRNA. Hs.381123 1703 1.00E-04 -295 caveolin 1, caveolae protein, CAV1 22kDa (CAV1), mRNA. Hs.74034 3006 74 -295 insulin-like growth factor binding IGFBP7 protein 7 (IGFBP7), mRNA. Hs.479808 30712 67 -298 PREDICTED: similar to ribosomal protein L37 LOC648217 (LOC648217), mRNA. Hs.447582 24873 92 -299 uridine phosphorylase 1 (UPP1), UPP1 transcript variant 1, mRNA. Hs.488240 40081 92 -300 mito_tRNA-Tyr 1646 13 -301 CDNA FLJ51855 complete cds, highly similar to Homo sapiens reticulon 3 (RTN3), transcript RTN3 variant 3, mRNA Hs.719090 1.85E-05 1.00E-04 -303 mito_tRNA-Cys 21694 61 -309 D-dopachrome tautomerase (DDT), transcript variant 2, DDT mRNA. Hs.656723 3.35E-05 1.00E-04 -310 ribosomal protein, large, P1 (RPLP1), transcript variant 2, RPLP1 mRNA. Hs.356502 9.18E-05 7.00E-04 -310 succinate dehydrogenase complex, subunit B, iron sulfur (Ip) (SDHB), nuclear gene encoding mitochondrial protein, SDHB mRNA. Hs.465924 17016 65 -320 Unknown 1828 1.00E-04 -323 S100 calcium binding protein A13 (S100A13), transcript variant 5, S100A13 mRNA. Hs.516505 196 7.00E-04 -327 thymosin beta 4, X-linked TMSB4X (TMSB4X), mRNA. Hs.522584 26628 59 -328 Tax1 (human T-cell leukemia virus type I) binding protein 3 TAX1BP3 (TAX1BP3), mRNA. Hs.12956 16722 5.00E-04 -329

VASN vasorin (VASN), mRNA. Hs.372579 2.43E-05 1.00E-04 -330 ribosomal protein, large, P1 (RPLP1), transcript variant 2, RPLP1 mRNA. Hs.356502 3.20E-06 1.00E-04 -331 Chromosome 6 open reading C6orf141 frame 141 (C6orf141), mRNA Hs.485528 35884 96 -339 Unknown 8373 55 -342 chromosome 1 open reading C1orf151 frame 151 (C1orf151), mRNA. Hs.466662 8.25E-05 1.00E-04 -346 Unknown 1893 9.00E-04 -350 transgelin (TAGLN), transcript TAGLN variant 2, mRNA. Hs.410977 29669 73 -356 2 (beta) (TPM2), TPM2 transcript variant 3, mRNA. Hs.300772 43188 144 -364 ST6 (alpha-N-acetyl-neuraminyl- 2,3-beta-galactosyl-1, 3)-N- acetylgalactosaminide alpha-2,6- sialyltransferase 2 ST6GALNAC2 (ST6GALNAC2), mRNA. Hs.592105 25831 69 -365 Ferritin heavy chain, 5'UTR FTH1 region Hs.524910 7258 18 -366 nudix (nucleoside diphosphate linked moiety X)-type motif 14 NUDT14 (NUDT14), mRNA. Hs.526432 11819 28 -371 ferritin, heavy polypeptide 1 FTH1 (FTH1), mRNA. Hs.524910 2272 1.00E-04 -376 ST6 (alpha-N-acetyl-neuraminyl- 2,3-beta-galactosyl-1, 3)-N- acetylgalactosaminide alpha-2,6- sialyltransferase 2 ST6GALNAC2 (ST6GALNAC2), mRNA. Hs.592105 4049 17 -380 gamma-aminobutyric acid (GABA) A receptor, alpha 3 GABRA3 (GABRA3), mRNA. Hs.123024 1317 19 -380 arylsulfatase A (ARSA), transcript ARSA variant 5, mRNA. Hs.88251 47476 59 -389 Unknown 12543 114 -395

peroxisome proliferator-activated receptor gamma (PPARG), PPARG transcript variant 4, mRNA. Hs.162646 24849 885 -400 kelch-like 4 (Drosophila) (KLHL4), transcript variant 1, KLHL4 mRNA. Hs.49075 2568 854 -402 CDNA FLJ20843 fis, clone ADKA01954 Hs.675435 48993 208 -404 superoxide dismutase 2, mitochondrial (SOD2), nuclear gene encoding mitochondrial protein, transcript variant 3, SOD2 mRNA. Hs.487046 12299 42 -409 plasminogen activator, urokinase (PLAU), transcript variant 1, PLAU mRNA. Hs.77274 3227 198 -412 Chromosome 7 open reading C7orf11 frame 11 (C7orf11), mRNA Hs.654989 8766 3 -415 Ferritin heavy chain, 5'UTR FTH1 region Hs.524910 2945 7.00E-04 -434 Transmembrane protein 192, mRNA (cDNA clone MGC:24936 TMEM192 IMAGE:4778254) Hs.708090 4191 14 -436 Unknown 4628 871 -444 glutamine-fructose-6-phosphate GFPT2 transaminase 2 (GFPT2), mRNA. Hs.696497 27128 51 -446 angiomotin like 2 (AMOTL2), AMOTL2 mRNA. Hs.426312 35971 94 -460 RNA, 7SK small nuclear RN7SK (RN7SK), non-coding RNA. 37804 774 -504 chromosome 16 open reading C16orf55 frame 55 (C16orf55), mRNA. Hs.655171 2.69E-05 1.00E-04 -522 inhibitor of DNA binding 3, dominant negative helix-loop- ID3 helix protein (ID3), mRNA. Hs.76884 2403 8.00E-04 -522 caveolin 2 (CAV2), transcript CAV2 variant 2, mRNA. Hs.212332 31135 113 -530 Chromosome 9 open reading frame 86, mRNA (cDNA clone C9orf86 IMAGE:5728463) Hs.370555 28189 2118 -541 retinol binding protein 1, cellular (RBP1), transcript variant 1, RBP1 mRNA. Hs.529571 29645 78 -563 dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis) (DACT1), transcript variant 2, DACT1 mRNA. Hs.48950 126 1.00E-04 -575 catechol-O-methyltransferase domain containing 1 (COMTD1), COMTD1 mRNA. Hs.355333 3.02E-05 1.00E-04 -576 CDNA fis, A-COL04217, highly similar to Homo sapiens , NADH dehydrogenase subunit 2 Hs.631494 1466 25 -615 S100 calcium binding protein A2 S100A2 (S100A2), mRNA. Hs.516484 1483 1.00E-04 -627 growth arrest-specific 6 (GAS6), GAS6 transcript variant 2, mRNA. Hs.646346 3742 1.00E-04 -637 tripartite motif-containing 45 (TRIM45), transcript variant 2, TRIM45 mRNA. Hs.301526 45929 1222 -761 fibulin 1 (FBLN1), transcript FBLN1 variant D, mRNA. Hs.24601 2301 6.00E-04 -919

Transcribed locus Hs.481491 9183 2 -1167 IKAROS family zinc finger 2 (Helios) (IKZF2), transcript IKZF2 variant 1, mRNA. Hs.604950 1508 1309 -1393 solute carrier family 17 (sodium phosphate), member 3 (SLC17A3), transcript variant 1, SLC17A3 mRNA. Hs.327179 1731 2069 -1403 SMEK homolog 1, suppressor of mek1 (Dictyostelium) (SMEK1), SMEK1 mRNA. Hs.533887 7159 2014 -1457 HERV-K_12q14.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (EnvK1 protein) [Contains: Surface protein (SU); Transmembrane protein (TM)]. [Source:Uniprot/SWISSPROT;Ac ENK1_HUMAN c:P61565] 2765 906 -1842 WD repeat domain 25 (WDR25), WDR25 mRNA. Hs.497600 1445 127 -1903 RNA, 5S ribosomal 1 (RN5S1), RN5S1 non-coding RNA. 2058 1235 -3546

Figure 1S. Characterization of GBM CSCs

GBM CSC lines (# 07104, 080125, 080418 and 080325) were endowed with self- renewal ability as shown by population analysis (panel A). As exemplified here by the

070104 line, the three major neural lineage markers were detected in all GBM CSC lines, by immunofluorescence for neuronal (Tuj1, red), glial (GFAP, green) and oligo- dendroglial (GalC, red) markers, thus demonstrating the multipotency of CSC lines

(panel B and C; magnification: 400X). The tumorigenic potential of GBM CSCs was assessed by intracranial transplantation (panel D). GFP-transduced 070104 CSCs gave rise to tumors that infiltrated the normal brain, even extending into the contralateral emisphere (GFP, green).

Figure 2S. Expression of MHC and MHC-related molecules by GBM CSC and FBS tumor cell lines.

The expression of MHC class I and II molecules and of NKG2DLs (MICA/MICB;

ULBP-1-4) was evaluated by immunofluorescence and flow cytometry using the specific mAbs indicated in Material and Methods. The Figure represents data of CSC

(panels A and C) and FBS tumor cell (panels B and D) line pairs isolated from two

GBM patients (080125, panels A and B and 080418, panels C and D, respectively) and treated or not (clear grey bar) with 1000 IU of IFN-α for 48 (black bar) or 72

(dark grey bar) hours. Data are indicated as MRFI that represents the ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control. Results represent averages of data obtained from three separate experiments with SD ≤ 8 %.

Figure 3S. In vivo expression of MHC and APM molecules by tumor tissue of GBM patients.

The IHC analysis of the expression of MHC and APM molecules has been performed on paraffin-preserved neoplastic tissues isolated from 4 GBM patients (070104, panels A, E and I; 080125, panels B, F and L; 080418, panels C, G and M; 080325 panels D, H and N; see Material and Methods). Data represent the staining for SOX 2, as positive control, (panels A-D), I-HC (panels E-H) and HLA-DR (panels I-N).

Original magnification 200X.

Figure 4S. CSC-specific Granzyme B release by T lymphocytes stimulated in vitro with autologous CSCs.

Independent T cell lines with specific recognition of autologous CSCs were in vitro isolated (# 2, 3 and 10) as described in the legend of Figure 1. The reactivity against autologous or allogeneic GBM CSCs was assessed by Granzyme B release (ELISPOT assay). T cells were stimulated with autologous CSCs (black bar), autologous CSCs pre-treated with anti-MHC class I (W6/32) or anti-MHC class II (L243) mAbs (clear grey and dark grey bars, respectively), autologous CSC in vitro cultured for few weeks in the presence of FBS (grey dotted bar), autologous FBS cultured CSCs pre- treated with anti-MHC class I (W6/32) or anti-MHC class II (L243) mAbs (clear grey dotted and small grid bars, respectively), allogeneic HLA-mismatched CSCs (0627 and 070112, dark grey shingle bars, respectively) and, as positive control with OKT3 mAb (black dotted bar). Data are expressed as N spot/4 x 104 cells. Results represent averages of triplicates with SD≤ 10 %; statistical analysis of differences between means of Granzyme B released by T cells was performed by two-tailed t-test

Figure 5S. Gene profile analysis of GBM CSCs vs FBS tumor cells. a) Whole transcriptome analysis of CSCs compared to FBS tumor cells. Hierarchical clustering diagrams are shown representing 469= unique genes; fold change >1.5, p<0.005, permutation p<0.017. b) Canonical pathways involvement by differentially expressed genes; gene names and statistical analysis are given in Table 6S.

Figure 6S. Secretion of soluble factors by CSC and FBS tumor cell lines isolated from

GBM patients.

Evaluation of soluble TGFβ-1 and TGFβ-2 (panels A and B) in cell culture supernatants of GBM CSCs or FBS was performed by ELISA; while IL-6 and IL-8

(panels C and D) released by the same cell lines were measured by SearchLight Array

Technology (see Material and Methods). The same array included the assessment of

IL-10, IL-13 and TNF-α release, though none of these factors was detected. Data in the figure are expressed as pg/ml. 501 Mel and 1869 EBV-B cells represented control cell lines for the assessment of soluble factor release. Results represent averages of duplicates with SD≤ 10 %.

Figure 7S. Expression of COA-1 and Survivin by GBM CSCs. The expression of COA-1 and survivin was detected by intracellular staining with the specific Abs (see Material and Methods) and confocal microscopy analysis. CSCs isolated from GBM of patients 080125 (panels A and B), 071210 (panel C) and

080418 (panel D) were examined. FITC-conjugated goat anti-rabbit (green) or PE- conjugated goat anti-mouse (red) secondary antibodies were used for COA-1 or survivin staining, respectively; 40x magnifications have been shown in the figure.