Supplemental Table S1. Clinical variables associated with response to therapy.

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Ethelbert Atkinson
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1 Supplemental data: Supplemental Table S1. Clinical variables associated with response to therapy. Supplemental Table S2. Treatment-related AEs. CTC version 3. Supplemental Table S3. Top 50 genes differentially regulated in CD138 negative cells in the bone marrow following Pom. Supplemental Table S4. Gene Ontology (GO) Analysis of top differentially regulated genes in the tumor bed following Pom therapy. Supplemental Table S5. Comparison of baseline tumor IHC scores for cereblon, Ikaros, or Aiolos with clinical response to Pom/dex therapy. Supplemental Table S6. Univariate analysis of baseline tumor IHC scores for cereblon, Ikaros, or Aiolos and overall survival following Pom/dex therapy. Supplemental Table S7. Correlation between CRBN, IKZF1 and IKZF3 RNA versus IHC score (protein). Supplemental Table S8. Correlation between RNA levels of CRBN, IKZF1 and IKZF3 and best response to Pom/dex therapy. Supplemental Table S9. Correlation between RNA levels of CRBN, IKZF1 and IKZF3 and overall survival following Pom/dex therapy. Supplemental Table S10. Correlation between baseline tumor IHC scores for CRBN, IKZF1 and IKZF3 and percent reduction in measurable disease following cycle 1 of therapy. Supplemental Table S11. Correlation between RNA levels for CRBN, IKZF1 and IKZF3 and percent reduction in measurable disease following cycle 1 of therapy. Supplemental Figure Legends: Figure S1. Patient flow Figure S2. Characterization of changes in peripheral blood T and. Peripheral blood obtained pre therapy (Pre-POM) as well as day 7 post therapy with Pomalidomide (Post-POM) was examined for the presence of T cells (, ),, B cells and monocytes. NK markers including CD56, CD16 as well as activation marker NKG2D.

2 We also studied T and NK cell cytokine profile, expression of cytolytic molecules Granzyme and Perforin as well as surface expression of co-inhibitory receptors including BTLA, PD-1 and TIM- 3. Figures 2a-I show flow cytometry data from representative patients (total patient cohort n=39) S2a. Gating strategy used as well changes in peripheral blood T cells,, B cells and monocytes Pre therapy (top panel) and 7 days after starting Pomalidomide therapy (bottom panel). S2b. Changes in the CD56+ CD16+ in patients receiving Pomalidomide therapy (Post- POM) compared to that prior to staring therapy (Pre-POM). S2c. Representative bar graphs for changes in T cells and through cycle 1 (POM alone) and cycle 2 (with dexamethasone) in patients treated with continuous dose (Cohort 1) and intermittent dose (Cohort 2) Pomalidomide therapy. Figure shows absolute T and NK cell numbers pre Pomalidomide therapy (Pre) at day 7 of cycle one (C1D7) and day 1 and day 7 of cycle 2 (C2D1 and C2D7 respectively). S2d-e. PBMCs obtained pre therapy as well as post therapy were thawed together. After overnight rest, the cells were either cultured alone (unstim) or stimulated with PMA/ionomycin for 5 hours stained and examined for the secretion of cytokines. Figure shows gating strategy used as well as cytokine secretion by, and. S2f. PBMCs obtained pre therapy as well as post therapy were thawed and examined for expression of cytolytic molecules. Figure shows granzyme and perforin levels in and NK cells, pre and post POM therapy. S2g-h. PBMCs were thawed, stimulated and stained as in S2d above. Figure shows polyfunctional T and pre and post POM therapy. S2i. Freshly thawed PBMCs from blood drawn prior to starting therapy and at day 7 of therapy with POM were stained for surface expression of co-inhibitory receptors BTLA, PD-1 and TIM-3 as shown in the figure. Figure S3. Characterization of changes in bone marrow T and. Bone marrow mononuclear cells were obtained prior to and approximately 2 months after starting therapy with Pomalidomide. The samples obtained before and after starting therapy with POM were thawed together and examined for expression of granzyme and perforin as well as for expression of immune checkpoint regulators. Some cells were rested overnight and the next day either left unstimulated or stimulated with PMA/ionomycin for 5 hrs, stained and examined for cytokine secretion using flow cytometry (n=3). 3a. Figure shows representative data for cytokine secretion by bone marrow, and NK cells.

3 3b. Figure shows changes in polyfunctional bone marrow T cells and before and after starting POM therapy. 3c. Expression of Granzyme and Perforin in T cells and before and after POM therapy. 3d. Surface expression of co-inhibitory receptors BTLA, PD-1 and TIM-3 as shown in the figure.

4 Supplementary Table S1. Univariate analysis of clinical variables versus objective response (> PR) Variable Responders (n=13) Non-responders (n=26) P value Mean Age (yrs) Male 9 (69%) 13 (50%) 0.31 IgG isotype 5 (38%) 15 (58%) 0.56 IgL kappa 11 (86%) 17 (65%) 0.27 Mean lines of prior therapy Mean serum B2M (mg/l) Mean serum albumin (g/dl) Len as immediate prior therapy 5 (38%) 10 (38%) 0.99 Deletion chromosome 13 5 (41%) 8 (32%) 0.56 Deletion chromosome 17p 2 (22%) 5 (29%) 0.99 Double Len+Bortezomib refractory disease 10 (77%) 21 (84%) 0.67

5 Supplementary Table S2. Treatment-related CTC grade 3-4 adverse events No. of patients, n (%) Adverse events (AEs) Cohort 1, 2mg 28/28 (N= 19) # Cohort 2, 4 mg 21/28 (N= 20) # P value Total (N= 39) SAEs Study drug-related SAEs 7 (37) 5 (26) 11 (55) 8 (40) (46) 13 (33) Any grade 3/ 4 AEs Study drug related grade 3/ 4AEs 13 (68) 11 (58) 18 (90) 18 (90) (79) 29 (74) Study drug-related CTC grade 3 / 4 AEs: Blood and lymphatic system disorders Anemia Neutropenia Thrombocytopenia Febrile neutropenia 9 (47) 2 (11) 8 (42) 4 (21) 3 (16) 10 (50) 2 (10) 9 (45) 1 (5) 1 (5) 19 (49) 4 (10) 17 (44) 5 (13) 4 (10) General / Constitutional Fatigue 3 (16) 3 (16) 3 (15) 2 (10) 6 (15) 5 (13) Infections Pneumonia 2 (11) 2 (11) 3 (15) 2 (10) 5 (13) 4 (10) Respiratory disorders Dyspnea 1 (5) 1 (5) 3 (15) 2 (10) 4 (10) 3 (8) Nervous system disorders Syncope 1 (5) 1 (5) 1 (5) 1 (5) 2 (5) 2 (5) CTC- National Cancer Institute Common Toxicity Criteria, v3.0 # numbers in parentheses represent percentage of the cohort.

6 Supplementary Table S3. Top differentially expressed (fold change > 2) genes (n=50) in CD138 negative purified cells from tumor bed following Pomalidomide therapy. Probe ID p Regulation FC Symbol Entrez Definition Gene_ID up IL1R Homo sapiens interleukin 1 receptor, type II (IL1R2), transcript variant 2, mrna up OLFM Homo sapiens olfactomedin 4 (OLFM4), mrna up CD Homo sapiens CD163 molecule (CD163), transcript variant 2, mrna up FKBP Homo sapiens FK506 binding protein 5 (FKBP5), mrna up IL18RAP 8807 Homo sapiens interleukin 18 receptor accessory protein (IL18RAP), mrna up MT2A 4502 Homo sapiens metallothionein 2A (MT2A), mrna up P2RY Homo sapiens purinergic receptor P2Y, G-protein coupled, 13 (P2RY13), transcript variant 1, mrna up MT1A 4489 Homo sapiens metallothionein 1A (MT1A), mrna up LOC PREDICTED: Homo sapiens similar to cytokine, transcript variant 3 (LOC728835), mrna up MT1E 4493 Homo sapiens metallothionein 1E (MT1E), mrna up DHRS Homo sapiens dehydrogenase/reductase (SDR family) member 9 (DHRS9), transcript variant 1, mrna up ZBTB Homo sapiens zinc finger and BTB domain containing 16 (ZBTB16), transcript variant 1, mrna up KLF9 687 Homo sapiens Kruppel-like factor 9 (KLF9), mrna E- up CEBPD 1052 Homo sapiens CCAAT/enhancer binding protein (C/EBP), 04 delta (CEBPD), mrna up SLA 6503 Homo sapiens Src-like-adaptor (SLA), mrna up IL7R 3575 PREDICTED: Homo sapiens interleukin 7 receptor (IL7R), mrna up HDC 3067 Homo sapiens histidine decarboxylase (HDC), mrna.

7 up SMAP Homo sapiens small ArfGAP2 (SMAP2), mrna up GFOD Homo sapiens glucose-fructose oxidoreductase domain containing 1 (GFOD1), mrna up LILRA Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3 (LILRA3), mrna up TXNIP Homo sapiens thioredoxin interacting protein (TXNIP), mrna up ADORA3 140 Homo sapiens adenosine A3 receptor (ADORA3), transcript variant 3, mrna up ARG1 383 Homo sapiens arginase, liver (ARG1), mrna up FGR 2268 Homo sapiens Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR), transcript variant 1, mrna up AKR1C Homo sapiens aldo-keto reductase family 1, member C3 (3- alpha hydroxysteroid dehydrogenase, type II) (AKR1C3), mrna up FPR Homo sapiens formyl peptide receptor 1 (FPR1), mrna up C19orf Homo sapiens chromosome 19 open reading frame 59 (C19orf59), mrna up SORL Homo sapiens sortilin-related receptor, L(DLR class) A repeats-containing (SORL1), mrna down CD Homo sapiens CD19 molecule (CD19), mrna down IFNAR Homo sapiens interferon (alpha, beta and omega) receptor 2 (IFNAR2), transcript variant 3, mrna down UBE2J Homo sapiens ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast) (UBE2J1), mrna down PPAPDC1B Homo sapiens phosphatidic acid phosphatase type 2 domain containing 1B (PPAPDC1B), mrna down POU2AF Homo sapiens POU class 2 associating factor 1 (POU2AF1), mrna down SDC Homo sapiens syndecan 1 (SDC1), transcript variant 1, mrna down LAMA Homo sapiens laminin, alpha 5 (LAMA5), mrna down CD79B 974 Homo sapiens CD79B antigen (immunoglobulin-associated beta) (CD79B), transcript variant 1, mrna.

8 down MARCKS 4082 Homo sapiens myristoylated alanine-rich protein kinase C substrate (MARCKS), mrna down PIM Homo sapiens pim-2 oncogene (PIM2), mrna down Homo sapiens 3 molecule (3), transcript variant 1, mrna down LOC PREDICTED: Homo sapiens similar to Ig gamma-2 chain C region (LOC649923), mrna down FKBP Homo sapiens FK506 binding protein 11, 19 kda (FKBP11), mrna down CAV1 857 Homo sapiens caveolin 1, caveolae protein, 22kDa (CAV1), mrna down CD79B 974 Homo sapiens CD79B antigen (immunoglobulin-associated beta) (CD79B), transcript variant 2, mrna down FCRLA Homo sapiens Fc receptor-like A (FCRLA), mrna down CD79B 974 Homo sapiens CD79b molecule, immunoglobulin-associated beta (CD79B), transcript variant 3, mrna down Homo sapiens 3 molecule (3), transcript variant 2, mrna down DNTT 1791 Homo sapiens deoxynucleotidyltransferase, terminal (DNTT), transcript variant 2, mrna E- 04 down LOC Homo sapiens hypothetical protein LOC90925 (LOC90925), mrna down VPREB Homo sapiens pre-b lymphocyte gene 3 (VPREB3), mrna down VPREB Homo sapiens pre-b lymphocyte 1 (VPREB1), mrna down DUSP Homo sapiens dual specificity phosphatase 5 (DUSP5), mrna.

9 Supplementary Table S4. Analysis of GO terms based on genes differentially expressed (> 2 fold) in the tumor bed following Pomalidomide therapy. GO Accesssion GO Term P value count in selection total GO: immune response 1.09E GO: immune system process 3.74E GO: antigen binding 3.95E

10 Supplementary Table S5. Correlation of baseline tumor IHC scores for cereblon, ikaros and aiolos with clinical response following pomalidomide therapy Variable Responders (n=10)^ Nonresponders (n=23)^ P value# Nuclear cereblon 188 (20, 273) 123 (40, 250) 0.06 Cytoplasmic cereblon 242 (37, 273) 143 (23, 267) 0.07 Total (nuclear + cytoplasmic) cereblon 430 (57, 547) 250 (67, 517) 0.06 Nuclear Aiolos 217 (150, 270) 233 (147, 273) 0.58 Nuclear Ikaros 153 (37, 207) 130 (70, 207) 0.42 # Wilcoxon rank sum test ^ median (range)

11 Supplementary Table S6. Correlation of baseline tumor immunohistochemical (IHC) scores for cereblon, ikaros and aiolos with overall survival following pomalidomide therapy. Variable P Value # Hazard Ratio Cereblon (cytoplasmic) IHC score Cereblon (nuclear) IHC score Cereblon (total nuclear + cytoplasmic) IHC score Ikaros (nuclear) IHC score Aiolos (nuclear) IHC score # Wald test

12 Supplemental Table S7. Correlation of RNA versus protein for Cereblon, Ikaros and Aiolos Gene Correlation coefficient # P value Cereblon Ikaros Aiolos # Pearson

13 Supplemental Table S8. Correlation of baseline tumor RNA expression for cereblon, ikaros and aiolos with objective clinical response following pomalidomide therapy Variable Responders (n=6)^ Nonresponders (n=17)^ P value# Cereblon 211 (149, 446) 185 (136, 250) 0.22 Ikaros 203 (143, 220) 184 (137, 530) 0.46 Aiolos 188 (136, 315) 220 (114, 276) 0.97 # Wilcoxon rank sum test ^ median (range)

14 Supplementary Table S9. Correlation of baseline tumor RNA expression for cereblon, ikaros and aiolos with overall survival following pomalidomide therapy. Variable P Value # Hazard Ratio Cereblon Ikaros Aiolos # Wald test

15 Supplemental Table S10. Correlation between baseline tumor IHC scores for CRBN, IKZF1 and IKZF3 and percent reduction in measurable disease following cycle 1 of therapy. Gene Correlation coefficient # P value Cereblon-cytoplasmic Cereblon - nuclear Cereblon- total Ikaros Aiolos # Pearson

16 Supplemental Table S11. Correlation between baseline tumor RNA levels for CRBN, IKZF1 and IKZF3 and percent reduction in measurable disease following cycle 1 of therapy. Gene Correlation coefficient # P value Cereblon Ikaros Aiolos # Pearson

17 Supplemental figure S1

18 Supplemental figure S2 S2a T cells B cells 4 Monocytes Pre-POM 8 10 SSC 47 4 Post-POM FSC SSC CD56 SSC SSC CD19 CD14 S2b Pre-POM Post-POM CD56 NKG2D CD16 CD56 S2c 50 T cells % of PBMCs % of PBMCs Pre C1D7 C2D1 C2D7 Pre C1D7 C2D1 C2D7 0 Pre C1D7 C2D1 C2D7 Pre C1D7 C2D1 C2D7 Cohort 1 Cohort 2 Cohort 1 Cohort 2

19 S2d Living Event Count: Specimen_001_P018-C1-Uns Event Count: Event C SSC FSC SSC Dead cell exclusion dye CD56 T cells IFN-γ TNF-α IL-2 IL-4 IL Specimen_001_P018-C1-Pre Event Count: Event C cimen_001_p018-c1-pre.fcs -Pre.fcs Count: Unstim cimen_001_p018-c1-pre.fcs -Pre.fcs nt unt: Count: Event Count: Specimen_001_P018-C1-Un Event Count: Event Count: ecimen_001_p018-c1-pre.fcs 1-Pre.fcs en_001_p018-c1-pre.fcs Event Event Count: Count: Event Event Count: Count: Event Count: Specimen_001_P018-C1-U Count: Event ent Count: Event Count: Count: Event Specimen_001_P018-C1-Pos Event Count: Count: Event Event Count: Count: Event Event Count: Count: Event Count: Event Co Specimen_001_P018-C1-Un Event Count: Specimen_001_P018-C1 Event Count: Event Count: Event Event Count: Count: Event Count: Event Count: Event Count: Pre-POM cimen_001_p018-c1-post.fcs -Post.fcs t Count: Post.fcs imen_001_p018-c1-post.fcs Event Count: Event Count: unt: t Count: Event Count: Event Count: Specimen_001_P018-C1-Pr Event Count: Event Count: Event Count: cimen_001_p018-c1-post.fcs en_001_p018-c1-post.fcs Event Count: Count: nt 1-Post.fcs Event Count: Event Count: Count: Specimen_001_P018-C1-P Event Post-POM Event Count: Event Count: Count: Event Event Count: Count: Event Specimen_001_P018-C1-Pre Event Count: Count: Event Count: Event Count: Event Count: Event Specimen_001_P018-C1 Count: Event Count: Event Count: Event Count: Cytokine S2e Event Count: Event Count: Event Count: Event Count: 82899Event Count: Event Count: Specimen_001_P018-C1-Po Event Event Count: Count: Event C Event Event Count: Count: Event Event Count: Count: Event Event Count: Count: Event Count: 82899Event Count: Event Count: Specimen_001_P018-C1-P Specimen_001_P018-C1-Pos Event Event Count: 82899Event Count: Event Count: Event Event Count: Count: Unstim Pre-POM Post-POM Specimen_001_P018-C1- Count: Event C Event Count: IFN-γ _001_P018-C1-Unstim.fcs nt: Event Event Event Count: Count: Count: Event Event Event Count: Count: Count: Event Event Event Count: Count: Count: n_001_p018-c1-unstim.fcs ount: 01_P018-C1-Unstim.fcs Event Event Count: Count: Event Event Count: Count: Event Count: 6591 Event Count: 4000 Event Event Event Count: Count: Count: SSC TNF-α 001_P018-C1-Pre.fcs Cytokine nt: Event Event Event Count: Count: Count: Event Event Event Count: Count: Count: Event Event Event Count: Count: n_001_p018-c1-pre.fcs S2f 01_P018-C1-Pre.fcs : unt: Event Count: Granzyme 6591 Event Count: 4000 Event Count: 4000 Event Event Count: Count: Perforin Event Event Count: Count: Event Count: 4000 Event Count: 7850 NK NK Pre-POM 001_P018-C1-Post.fcs t: _001_P018-C1-Post.fcs Event Event Event Count: Count: Count: Event Event Event Count: Count: Event Event Count: Count: unt: 1_P018-C1-Post.fcs Event Count: 6591 Event Count: 4000 Event Count: Event Event Count: Count: Event Event Count: Count: Event Event Count: Count: Post-POM Granzyme Perforin

20 IFN-γ IFN-γ IL-4 IL-13 S2g T cells Unstim vent Count: Pre-POM _P018-C1-Unstim.fcs t: Post-POM Event Event Count: Count: Event Event Event Count: Count: Event Event Count: Count: TNF-α IL-2 IL-2 S2h 001_P018-C1-Pre.fcs cells t: Event Event Count: Count: Event Event Count: Count: Event Event Count: Count: Unstim Pre-POM Post-POM BTLA BTLA BTLA TIM3 01_P018-C1-Post.fcs TNF-α 4 T CELLS T CELLS T t: CELLS T CELLS T CELLS T NK NK CELLS CELLS T CELLS T NK T NK T CELLS T T CELLS T CELLS T NK NK CELLS T CELLS T T C Event Event Count: Count: Event Event Count: Count: Event Event Count: Count: BTLA BTLA BTLA TIM3 4 T CELLS T CELLS S2i T CELLS T CELLS T CELLS T NK NK CELLS CELLS T CELLS T NK T NK T CELLS T T CELLS T CELLS T NK NK CELLS T CELLS T T C BTLA BTLA BTLA BTLA TIM3 BTLA PD-1 TIM-3 T CELLS ISOTYPE 4 T CELLS T CELLS T CELLS T CELLS T CELLS NK CELLS NK CELLS T CELLS T CELLS NK T NK T T CELLS CELLS T T T CELLS CELLS T CELLS T CELLS NK NK NK CELLS CELLS T CELLS T CELLS NK CEL T C ISOTYPE NK NK cells NK NK cells NK Isotype ISOTYPE NK cells NK cells NK cells NK cells PRE PRE NK NK cells cells NK cells NK cells PRE PRE Pre-POM NK NK cells NK cells NK cells PRE PRE Post-POM POST NK cells 67 NK cells NK cells NK cells NK cells 15 NK cells NK cells NK cells POST BTLA NK cells PD1 NK TIM3 cells NK cells POST POST NK cells NK cells NK cells NK cells NK cells NK NK cells cells NK cells NK cells

21 IFN-γ Supplemental figure S3 3a T cells IFN-γ TNF-α IL-2 IFN-γ TNF-α Unstim Pre-POM Post-POM Cytokine Cytokine 3b NK Unstim Pre-POM Post-POM TNF-α 3c Granzyme Perforin NK NK Pre-POM Post-POM Granzyme Perforin

22 3d BTLA PD-1 TIM-3 Isotype Pre-POM Post-POM BTLA PD-1 TIM-3

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