Probe setGene Symbol Gene Title RefSeq Transcript ID p-value

Fold-Change

226218_at IL7R interleukin 7 receptor NM_002185 0.015968 6.98753

206545_at CD28 CD28 moleculeNM_001243077 /// NM_001243078 /// NM_006139 0.0165945 6.92511

210512_s_at VEGFA vascular endothelial growth factor A

NM_001025366 /// NM_001025367 /// NM_001025368 /// NM_001025369 /// NM_001025370 0.0300845 5.98444

210690_at KLRC4killer cell lectin-like receptor subfamily C, member 4 NM_013431 0.0435395 5.81104

201694_s_at EGR1 early growth response 1 NM_001964 0.00617136 5.16785

204798_at MYBv-myb myeloblastosis viral oncogene homolog (avian)

NM_001130172 /// NM_001130173 /// NM_001161656 /// NM_001161657 /// NM_001161658 0.00063586 4.94855

206546_at SYCP2 synaptonemal complex protein 2 NM_014258 0.0320383 3.95423208078_s_at SIK1 salt-inducible kinase 1 NM_173354 0.0315449 3.74018

218829_s_at CHD7chromodomain helicase DNA binding protein 7 NM_017780 0.00124722 3.41881

230170_at OSM oncostatin M NM_020530 0.038183 2.97723

212803_at NAB2NGFI-A binding protein 2 (EGR1 binding protein 2) NM_005967 0.032675 2.79983

202431_s_at MYCv-myc myelocytomatosis viral oncogene homolog (avian) NM_002467 0.00948668 2.7585

1555167_s_at NAMPTnicotinamide phosphoribosyltransferase NM_005746 /// NM_182790 0.00978463 2.6474

205479_s_at PLAU plasminogen activator, urokinase NM_001145031 /// NM_002658 0.00224563 2.63127

204562_at IRF4 interferon regulatory factor 4NM_001195286 /// NM_002460 /// NR_036585 /// NR_046000 0.0359947 2.43914

229464_at MYEF2 myelin expression factor 2 NM_016132 0.0185376 2.43343

1569149_at PDLIM7 PDZ and LIM domain 7 (enigma)NM_005451 /// NM_203352 /// NM_203353 /// NM_213636 0.0127095 2.29946

210229_s_at CSF2colony stimulating factor 2 (granulocyte-macrophage) NM_000758 0.0438107 2.29885

209921_at SLC7A11

solute carrier family 7 (anionic amino acid transporter light chain, xc- system) NM_014331 0.0272886 2.29328

1560274_at WTAP Wilms tumor 1 associated protein NM_004906 /// NM_152857 /// NM_152858 0.00507062 2.26454

203372_s_at SOCS2 suppressor of cytokine signaling 2

NM_001270467 /// NM_001270468 /// NM_001270469 /// NM_001270470 /// NM_001270471 0.0358922 2.21727

218918_at MAN1C1mannosidase, alpha, class 1C, member 1 NM_020379 0.0392292 2.1999

217594_at ZCCHC11zinc finger, CCHC domain containing 11

NM_001009881 /// NM_001009882 /// NM_015269 0.0137747 2.18895

219355_at CXorf57 chromosome X open reading frame 57 NM_001184782 /// NM_018015 0.0401662 2.17188

220358_at BATF3basic leucine zipper transcription factor, ATF-like 3 NM_018664 0.0110211 2.15717

232879_at CRTC3CREB regulated transcription coactivator 3 NM_001042574 /// NM_022769 0.00867865 2.13572

203140_at BCL6 B-cell CLL/lymphoma 6NM_001130845 /// NM_001134738 /// NM_001706 /// NM_138931 0.00128291 2.1305

213596_at CASP4caspase 4, apoptosis-related cysteine peptidase NM_001225 /// NM_033306 /// NM_033307 0.0188063 2.12182

211139_s_at NAB1NGFI-A binding protein 1 (EGR1 binding protein 1) NM_005966 0.0295677 2.10901

239648_at DCUN1D3DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae) NM_173475 0.0201687 2.09991

232487_at SFT2D1 SFT2 domain containing 1 NM_145169 0.0489379 2.09813220843_s_at DCAF13 DDB1 and CUL4 associated factor 13 NM_015420 0.0317607 2.0711

242260_at MATR3 Matrin 3

NM_001194954 /// NM_001194955 /// NM_001194956 /// NM_018834 /// NM_199189 /// N 0.0127817 2.06872

221569_at AHI1 Abelson helper integration site 1NM_001134830 /// NM_001134831 /// NM_001134832 /// NM_017651 0.0424571 2.01295

205891_at

ADORA2B /// LOC100652851 /// LOC100653318

adenosine A2b receptor /// uncharacterized LOC100652851 /// uncharacterized LOC1

NM_000676 /// XM_003403468 /// XM_003403684 0.0434844 -2.00623

209201_x_at CXCR4 chemokine (C-X-C motif) receptor 4 NM_001008540 /// NM_003467 0.0307514 -2.01292

Supplementary Table 1: Differentially expressed genes between persisting and non-persisting clones (page1)

Probe setGene Symbol Gene Title RefSeq Transcript ID p-value

Fold-Change

217542_at MDM2Mdm2, p53 E3 ubiquitin protein ligase homolog (mouse)

NM_001145336 /// NM_001145337 /// NM_001145339 /// NM_001145340 /// NM_002392 // 0.02245 -2.03109

225974_at TMEM64 transmembrane protein 64 NM_001008495 /// NM_001146273 0.013722 -2.0312

239118_at KCNA2potassium voltage-gated channel, shaker-related subfamily, member 2 NM_001204269 /// NM_004974 0.0382185 -2.05798

219439_at C1GALT1

core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase NM_020156 0.0280939 -2.06772

209784_s_at JAG2 jagged 2 NM_002226 /// NM_145159 0.00311047 -2.08176205174_s_at QPCT glutaminyl-peptide cyclotransferase NM_012413 0.00719158 -2.08608235318_at FBN1 fibrillin 1 NM_000138 0.0400623 -2.10427239208_s_at YBEY YbeY metallopeptidase (putative) NM_001006114 /// NM_058181 0.0101511 -2.11358238935_at RPS27L ribosomal protein S27-like NM_015920 0.0146375 -2.11699

229242_at TNFSF15tumor necrosis factor (ligand) superfamily, member 15 NM_001204344 /// NM_005118 0.00274354 -2.12396

204149_s_at GSTM4 glutathione S-transferase mu 4NM_000850 /// NM_147148 /// NM_147149 /// NR_024538 0.00208468 -2.14684

227030_at IKZF3 IKAROS family zinc finger 3 (Aiolos)

NM_001257408 /// NM_001257409 /// NM_001257410 /// NM_001257411 /// NM_001257412 0.0115875 -2.15546

219305_x_at FBXO2 F-box protein 2 NM_012168 0.0410813 -2.16626

223207_x_at PHPT1 phosphohistidine phosphatase 1NM_001135860 /// NM_001135861 /// NM_014172 0.00035939 -2.18144

230224_at ZCCHC18zinc finger, CCHC domain containing 18 NM_001143978 /// NR_026694 0.0382822 -2.18652

202887_s_at DDIT4 DNA-damage-inducible transcript 4 NM_019058 0.0227037 -2.18986

227193_at SLC30A4solute carrier family 30 (zinc transporter), member 4 NM_013309 0.00401091 -2.2385

205692_s_at CD38 CD38 molecule NM_001775 0.0204432 -2.24379

209295_atTNFRSF10B

tumor necrosis factor receptor superfamily, member 10b NM_003842 /// NM_147187 /// NR_027140 0.00054101 -2.24849

211833_s_at BAX BCL2-associated X protein

NM_004324 /// NM_138761 /// NM_138762 /// NM_138763 /// NM_138764 /// NR_027882 0.00021409 -2.27993

1556308_at PRRT3 proline-rich transmembrane protein 3 NM_207351 0.0124444 -2.29529218560_s_at JMJD4 jumonji domain containing 4 NM_001161465 /// NM_023007 0.00652396 -2.35608

204613_at PLCG2phospholipase C, gamma 2 (phosphatidylinositol-specific) NM_002661 0.0109426 -2.36139

209644_x_at CDKN2A cyclin-dependent kinase inhibitor 2ANM_000077 /// NM_001195132 /// NM_058195 /// NM_058196 /// NM_058197 0.00840063 -2.3787

1553311_at C20orf197chromosome 20 open reading frame 197 NM_173644 0.0407092 -2.38472

207813_s_at FDXR ferredoxin reductase

NM_001258012 /// NM_001258013 /// NM_001258014 /// NM_001258015 /// NM_001258016 0.00294989 -2.39201

207167_at CD101 CD101 moleculeNM_001256106 /// NM_001256109 /// NM_001256111 /// NM_004258 0.0179875 -2.39784

218634_at PHLDA3pleckstrin homology-like domain, family A, member 3 NM_012396 0.00075392 -2.40344

242961_x_at DDX58DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 NM_014314 0.0251973 -2.42169

202672_s_at ATF3 activating transcription factor 3

NM_001030287 /// NM_001040619 /// NM_001206484 /// NM_001206485 /// NM_001206486 2.46E-02 -2.42884

209366_x_at CYB5A cytochrome b5 type A (microsomal)NM_001190807 /// NM_001914 /// NM_148923 0.044212 -2.43949

244413_at CLECL1 C-type lectin-like 1NM_001253750 /// NM_001267701 /// NM_172004 0.0449327 -2.44188

225912_at TP53INP1tumor protein p53 inducible nuclear protein 1 NM_001135733 /// NM_033285 0.0102333 -2.46809

227522_at CMBLcarboxymethylenebutenolidase homolog (Pseudomonas) NM_138809 0.00698173 -2.48743

200644_atMARCKSL1 MARCKS-like 1 NM_023009 /// NR_052852 0.0378812 -2.5054

204584_at L1CAM L1 cell adhesion moleculeNM_000425 /// NM_001143963 /// NM_024003 0.0431925 -2.51809

224937_at PTGFRNprostaglandin F2 receptor negative regulator NM_020440 0.0246948 -2.59062

Supplementary Table 1: Differentially expressed genes between persisting and non-persisting clones (page2)

Probe setGene Symbol Gene Title RefSeq Transcript ID p-value

Fold-Change

231732_at SMPD3

sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II NM_018667 0.00018914 -2.6679

206090_s_at

DISC1 /// TSNAX-DISC1

disrupted in schizophrenia 1 /// TSNAX-DISC1 readthrough

NM_001012957 /// NM_001012958 /// NM_001012959 /// NM_001039383 /// NM_001164537 0.0430998 -2.70058

203725_at GADD45Agrowth arrest and DNA-damage-inducible, alpha

NM_001199741 /// NM_001199742 /// NM_001924 0.00080435 -2.70983

204114_at NID2 nidogen 2 (osteonidogen) NM_007361 0.0238238 -2.72711

210762_s_at DLC1 deleted in liver cancer 1NM_001164271 /// NM_006094 /// NM_024767 /// NM_182643 0.00167513 -2.77946

202644_s_at TNFAIP3tumor necrosis factor, alpha-induced protein 3 NM_006290 0.0371965 -2.86641

226137_at ZFHX3 zinc finger homeobox 3 NM_001164766 /// NM_006885 0.0182354 -2.8687206307_s_at FOXD1 forkhead box D1 NM_004472 0.0261468 -2.87306

204748_at PTGS2

prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxyge NM_000963 0.0306956 -2.93479

229254_at MFSD4major facilitator superfamily domain containing 4 NM_181644 0.00137903 -2.94215

210609_s_at TP53I3 tumor protein p53 inducible protein 3NM_001206802 /// NM_004881 /// NM_147184 0.0255089 -2.95456

209016_s_at KRT7 keratin 7 NM_005556 0.0396377 -3.07262221538_s_at PLXNA1 plexin A1 NM_032242 0.016441 -3.07289

226668_at WDSUB1WD repeat, sterile alpha motif and U-box domain containing 1

NM_001128212 /// NM_001128213 /// NM_152528 0.0459202 -3.13932

227221_at ZMAT3 zinc finger, matrin-type 3 NM_022470 /// NM_152240 0.00030794 -3.14659208923_at CYFIP1 cytoplasmic FMR1 interacting protein 1 NM_001033028 /// NM_014608 0.00526256 -3.215

225606_at BCL2L11 BCL2-like 11 (apoptosis facilitator)

NM_001204106 /// NM_001204107 /// NM_001204108 /// NM_001204109 /// NM_001204110 0.0333319 -3.25634

229971_at GPR114 G protein-coupled receptor 114 NM_153837 0.0153434 -3.2795

206907_at TNFSF9tumor necrosis factor (ligand) superfamily, member 9 NM_003811 0.00179722 -3.2986

206508_at CD70 CD70 molecule NM_001252 0.00246867 -3.33596226225_at MCC mutated in colorectal cancers NM_001085377 /// NM_002387 0.0209347 -3.38257

207426_s_at TNFSF4tumor necrosis factor (ligand) superfamily, member 4 NM_003326 0.00050034 -3.83688

229797_at MCOLN3 mucolipin 3 NM_001253693 /// NM_018298 0.0404844 -3.8634

228937_at LACC1laccase (multicopper oxidoreductase) domain containing 1 NM_001128303 /// NM_153218 0.00276434 -3.96617

206873_at CA6 carbonic anhydrase VI NM_001215 0.00508658 -4.07431208890_s_at PLXNB2 plexin B2 NM_012401 0.0103517 -4.4534

208131_s_at PTGISprostaglandin I2 (prostacyclin) synthase NM_000961 0.0449316 -4.49543

205569_at LAMP3lysosomal-associated membrane protein 3 NM_014398 0.00381878 -4.6834

204777_s_at MAL mal, T-cell differentiation proteinNM_002371 /// NM_022438 /// NM_022439 /// NM_022440 0.0236599 -4.79926

211144_x_atTARP /// TRGC2

TCR gamma alternate reading frame protein /// T cell receptor gamma constant 2 NM_001003799 /// NM_001003806 0.0497887 -5.9034

201417_at SOX4 SRY (sex determining region Y)-box 4 NM_003107 0.00129016 -6.44274

213135_at TIAM1T-cell lymphoma invasion and metastasis 1 NM_003253 0.0222017 -6.71067

236313_at CDKN2Bcyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) NM_004936 /// NM_078487 0.00837304 -7.81711

Supplementary Table 1: Differentially expressed genes between persisting and non-persisting clones (page3)

Supplementary Figure 1

% IL-7R expressing cells in the infusion bag correlates with persistence of CD8+ effector clones.

Correlation between pre-infusion % of IL-7R expressing cells in the infusion bag of CD8+ T effector clones (n=9) and peripheral blood persistence (% CD8+Tet+) at day 30 after adoptive transfer. 

0 5 10 150

2

4

6

8

10

% IL-7R cells

Clo

nal

per

sist

ence

(% C

D8+

Tet

+) R2= 0.71

P = 0.004

Supplementary Figure 2

CD45RO

CD62L

CD27

IL-2Ra

IL-15R

4-1BB

OX-40

PD-1

TIM3

CTLA4

Clone M4

100100

155

5344

5164

6465

2217

32

4141

1224

4747

Patient M4 PBL

IL-7R+ cells

IL-7R- cells

5956

9040

9760

2720

6160

2914

42

2529

<2<2

4948

-103 0 103 104 105

  Representative phenotypic profiling of IL7R+ and IL7R- subsets found within infused effector clones

Pre-infusion phenotype of IL7R+ and IL-7R- subsets identified in infused M4 clone by flow cytometry. For reference, phenotyping of IL7R+ and IL-7R- subsets within open repertoire autologous PBL (CD3+CD8+ gated) is shown. Gray shaded histogram represents isotype staining. Staining of IL-7R+ cells are shown in red outline and IL-7R- cells are shown in blue outline. Numbers in plots are similarly color coded to denote % shift from isotype.

Supplementary Figure 3

0 400 800 12000

500

1000

1500

2000

Clone IL-7R (MFI)

R2 = 0.78P = 0.018

c-m

yc

/b-a

ctin

(x

10

5 ) m

RN

A

IL-7R expression correlates with c-myc mRNA expression in CD8+ effector clones.

Correlation between IL-7R cell surface expression (MFI) and c-myc mRNA (per 105 b-actin copies) expression in infused CD8+ effector clones (n=6). 

Supplementary Figure 4

0 400 800 12000

25

50

75%

pS

TAT

5

Clone IL-7R (MFI)

IL-7 StimR2 = 0.86

P = 0.0025

 IL-7R expression correlates with induced pSTAT5 expression in CD8+ effector clones.

Correlation between IL-7R cell surface expression (MFI) and IL-7-induced pSTAT5 expression in infused CD8+ effector clones (n=7).