Supplementary Table S1

Patient ID Age/Sex Rai stage Previously treated CD38 FISH IGHV ZAP70 CLL-01 72 M I N NEG 17p- Mutated NEG CLL-02 56 F II N POS Normal NA POS CLL-03 72 F 0 N NEG +12 Mutated NA CLL-04 61 F I Y NEG 11q NA NA CLL-05 47 M 0 N NEG Normal Mutated NA CLL-06 89 F I N NEG Normal NA NA CLL-07 59 M II N NEG 13q- Mutated NA CLL-08 79F 0 N NEG 13q- Unmutated NA CLL-09 54 M II N NEG 13q- Unmutated NA CLL-10 92M IV N POS 13q- NA NA CLL-11 72M II N NEG 17p- NA NEG CLL-12 58M I N NEG NA Mutated NA CLL-13 67M 0 N NEG 11q Unmutated NEG CLL-14 61F 0 Y NA NA Mutated NA CLL-15 55M II N NEG 13q- Mutated NEG CLL-16 58F II N NEG 11q Mutated NEG CLL-17 72F IV Y POS 17p- Unmutated POS CLL-18 77M NA Y NEG 17p- Mutated NEG CLL-19 72M IV Y NEG NA NEG CLL-20 75M IV Y POS 13q- Unmutated POS CLL-21 75F I N NEG 13q- Mutated NEG CLL-22 69M NA Y POS 17p- Mutated POS CLL-23 41M II N POS 17p- Unmutated POS CLL-24 70M I N NEG 13q- Mutated NEG CLL-25 49M III N NA 17p- Unmutated NA CLL-26 47M I N NEG NA Mutated NEG CLL-27 64M I N NEG 13q- Mutated NEG CLL-28 50M I N NA 11q Unmutated NA CLL-29 46M III N POS NA NA POS CLL-30 61M IV N POS Normal Unmutated POS CLL-31 49F I N NEG 13q- Mutated NEG CLL-32 61F II N NEG 17p- Unmutated NEG CLL-33 67F 0 N NEG 13q- Unmutated NEG CLL-34 47M III N NEG 17p- Mutated NEG CLL-35 67F I N NEG 13q- NA NEG CLL-36 58F IV N POS 13q- Unmutated POS CLL-37 66F I N POS 17p- Unmutated POS CLL-38 57M NA N POS 11q Mutated NA CLL-39 55F NA N NEG 13q- Unmutated NEG CLL-40 63M I N NEG 17p- Mutated NEG CLL-41 39M NA N POS +12 Unmutated POS CLL-42 48M NA N NA Normal Mutated NA Supplementary Table S2

Patient ID Age/Sex Rai stage Previously treated CD38 FISH IGHV ZAP70 IB response Time on treatment 12 MO ALC Resistance Mutation IB-1 69M IV N POS +12 Mutated NEG PR 36 MO 48.98 NA IB-2 71F II N NEG 13q-- Mutated POS PR 24 MO 9.93 NA IB-3 51F II N POS 17p- Mutated NEG PRL 36 MO 65.6 NA IB-4 48M I N NEG 17p- Unmutated NA CR 36 MO 11.57 NA IB-5 63M IV N POS 17p- Unmutated POS PR 36 MO 62.4 NA IB-6 39M IV N NEG 17p- Unmutated NEG PR 36 MO 29.32 NA IB-7 70M I N POS 17p- Unmutated POS PR 36 MO 19.39 NA IB-8 59M IV N NEG 17p- Mutated NA PR 24 MO 63.08 NA IB-9 71M IV N NEG 17p- Mutated NEG PR 24 MO 15.05 NA IB-10 69F III N NEG 17p- Unmutated NEG PR 24 MO 20.63 NA PD-1 79M IV Y POS 17p- Unmutated NA PD 38 MO 2.43 BTK PD-2 62F III Y NEG 17p- Unmutated POS PD 38 MO 3.63 none PD-3 73M IV Y NEG 17p- Unmutated NA PD 38 MO 3.4 BTK, PLCγ2 PD-4 56M IV N NEG 17p- Unmutated NA PD 15 MO 1.52 PLCγ2 PD-5 60F II N POS 17p- Unmutated NEG PD 23MO 2.24 PLCγ2 PD-6 77M IV Y NEG +12 Unmutated NA PD 28 MO 27.97 BTK, PLCγ2 PD-7 56M IV Y NEG 17p- Mutated NEG PD 33 MO 6.61 BTK, PLCγ2 PD-8 66F IV Y POS 17p- Unmutated POS PD 36 MO 1.49 BTK, PLCγ2 PD-9 64F I N NEG 17p- Mutated NEG PD 42 MO 4.58 none PD-10 65M IV Y POS 17p- Unmutated NEG PD 47 MO 52.3 BTK Supplementary Table S3

Gene mutation PCR primers Probes BTK: tGc>tCc Fw: GCGCATCTCCCTCAG Wt: CCAATGGCTGCCTCC C481S Re: CATCTTCATCATCACTGAGTA Mt: CCAATGGCAGCCTCC PLCG2: Cgg>Tgg Fw: GAGGCAGAGGACATGC Wt: CCCGGGGAATCCTCA R665W Re: TCTCGCTTCCGGATCA Mt: TCCCGGGAAATCCTCA PLCG2: ttA>ttT Fw: TGTCTTGTTTCTTCACAGAT Wt: CCGTCCCGGGGAAT L845F Re: GTATTGAGGTCCAATATTCCT Mt: CCCGTCCCAGGGAAT Custom forward (Fw) and reverse (Re) primers and probes complementary to wildtype (Wt, HEX label) and mutant (Mt, FAM label) sequences were ordered from BioRad. Supplementary Table S4

Down-regulated genes (N=312) Up-regulated genes (N=126) AC015969.3 AC012314.8A65B3B4:BB4:B129 ARHGEF40 KCNN2 LRP1 AC005523.3 RNASE4 RP11-82K18.2 C10orf82 C21ORF51 CPNE5 CTD-2140G10.2 ADAMTSL4-AS1 LIN7A DMRTC1B RPL23AP60 CD1C ABCA8 CCDC54 ATP1A2 LINC00330 DCN AP001056.1 GABARAPL1 LEPREL4 HIST1H2AC LLNLR-470E3.1 RP11-254F7.3 AC069363.1 RP11-354K4.1 IGF1 HIST2H2BE HELZ2 RP11-10K17.3 TAS2R3 AGPAT9 IFIT3 TMEM178B OASL HSPA5 BSPRY RP11-110I1.13 CHRNA9 RBAKDN MYLIP RP11-164P12.3 ABCD1 HIST1H2AM RP13-452N2.1 ADH1B KIF7 HLA-P CCDC114 CXorf31 RP5-1112D6.7 RP11-428P16.2 TRERF1 TXNRD1 ASAP3 RP11-707G18.1 EID3 HIST2H3D RP11-20G13.5 TXN RP11-288L9.1 LHFPL4 RP11-597G23.1 MGC32805 SCD GCLM ASPA RP11-512F24.1 RPS20P24 RP11-671E7.1 AF131216.5 HIST1H4I HNRNPA1P57 PRMT5-AS1 MGAM RP11-307L14.1 ZPBP2 STON1-GTF2A1L TYMS TRAV1-2 GPR25 RP11-229P13.2 LST1 SCARNA2 SDHAP2 AC009502.4 RP11-178L8.7 HNRNPH1P2 ST3GAL6 RP11-571M6.15 AC004448.5 AKR1D1 ESPNL SPARCL1 FXYD2 RNU12 EPB41L1 HMGA1P1 GALNT8 RP11-49K24.5 MX2 RP11-603K19.1 TNFRSF9 RP11-119B16.2 BRSK1 RP11-634H22.1 ZNF385C RP11-462L8.2 MPEG1 MANF CCDC150P1 RP13-638C3.2 SH3PXD2B RP11-584P21.2 RP11-697E2.9 LINC00571 CMPK2 RP11-769N19.2 FAM225A MANSC4 CTB-133G6.2 TALDO1 CTC-508F8.1 MIR22HG RP11-274B18.2 SORBS1 CSPG4 AC008592.8 IFI6 KRT42P SLC12A3 AC016629.7 IFIT1 CATSPER3 OXCT1-AS1 AC092155.1 LIMA1 ANKUB1 HNF1B RP4-778K6.1 RGS16 EIF4A2P2 SIRPB2 RP11-763B22.4 HID1 ALG3P1 RP11-672A2.6 UBA52P6 RP11-875O11.3 RP3-414A15.11 ADAP2 RP4-597N16.4 C2CD4D SRCRB4D RP3-399L15.3 CALR NPW AP000525.9 FA2H RP11-46I1.1 LYPD8 HIST1H1E RP11-617F23.2 RP11-392A14.9 FCGR1A RP11-394B2.6 MYADM RP4-669P10.16 RP11-320P7.1 XBP1 LILRB4 RP11-530C5.4 RP11-647K16.1 RP11-113C12.4 ERP27 SNORA73A BAHCC1 RP11-840I19.3 DCHS2 CH17-262O2.1 PRR29 CTD-2525I3.2 RP11-215G15.5 NOP56P3 GS1-166A23.2 FTH1P8 LHX3 TBX15 RSAD2 RPL29P14 AP001046.5 RP11-301O19.1 TRIB1 RP11-667M19.2 TNS4 RP11-796G6.2 IL2RB LINC01393 EGR3 KLHL31 RP11-514P8.7 RP5-1024G6.8 CACNA1A AC068286.1 SEMA7A NADK2-AS1 AC011933.2 RP11-561O23.5 CTD-2252P21.1 SLC25A36P1 RP11-456O19.4 RP11-367G18.2 RP11-468E2.6 RP11-572B2.1 CASQ1 ARL13A ID2 AC096558.1 ICAM2 DPF1 RN7SKP150 FDPSP7 TNFSF10 RP11-362K14.6 RP11-667F9.1 ANKRD20A3 SYNGR3 RPS4XP21 AUNIP CTD-2562G15.3 LMTK3 SRXN1 CXCL10 RASAL2 RP13-131K19.1 RP11-15J22.8 ANO7P1 SV2C RP11-425A6.5 RP3-400N23.6 CCR2 ZNF705E RP11-30L15.4 IGHV2-26 ZNF385A RPSAP52 SORT1 XXbac-BPG299F13.14 EGR1 LAG3 ISG15 SIGLEC14 GALNT6 RP11-649G15.2 RP11-165F24.5 UBXN10-AS1 WNT10A CD38 CDRT15P1 BEND3 C4A LINC00102 CCL20 SBK1 PDCD1LG2 ADAM8 AHNAK2 KLHDC8A RP11-495P10.5 ITGB2 GNAT2 LDB2 PLXNB2 TLR4 HRG RPS3AP30 CGN DYRK3 RAB26 HCAR1 RP11-220I1.2 FSCN2 RP11-89K21.1 RPL19P12 RPL7P4 CHCHD4P3 RP4-734P14.4 CDKL5 PPT2 TMEM229B CSMD3 FMO1 DTX4 RPL29P23 GPR3 RP11-1016B18.1 RP11-282O18.3 PLEKHA5 RP11-542M13.2 ST5 CTB-55O6.4 FKBP10 DNMT3B AC097523.1 RP11-196B3.3 ENPP2 OLFML2A RP11-309G3.3 TMEM74B SMIM6 ABCA17P GH1 CRIP2 LYZL4 SUCLG2-AS1 PRELP DGCR10 RP11-259N19.1 MGC27382 RNF219-AS1 MAG RP11-177C12.4 RP11-345J18.2 RP5-991G20.1 IQSEC1 RP11-511B23.2 WBSCR27 BZRAP1-AS1 CTD-2396E7.11 USP18 HLX-AS1 P2RX5 CTD-2007H13.3 FAM53B-AS1 RP11-360O19.5 NHSL2 SFTPB C3orf52 SIGLEC5 MRAS PAX5 CCND2 CD1D AC011294.3 C17orf96 CTD-2050N2.1 DDC8 HPDL GLDN AOC1 RP11-1096G20.5 RP11-867G23.8 HIPK4 RP11-712B9.4 PPP1R14A RP11-800A3.3 CTD-2410N18.3 TRIP10 SOX9-AS1 IFITM2 ITM2C TMEM163 TFAP2E RP4-593H12.1 RPS4XP17 RP11-329N22.1 RP11-714L20.1 TNS1 CTD-3214H19.6 FHL3 PLSCR1 AC002306.1 AC004381.6 DLGAP3 OAS3 ASTL PDE6H RP11-91K8.4 YBX2P1 GLDC GLYATL2 DUSP2 MYO1C OSM SAMHD1 GSG2 PTGS1 RP11-58E21.1 PDGFA RP11-430H10.1 DOK3 HIVEP3 TSPAN1 RP11-770J1.3 ACTBP8 APLN CNIH2 LINC01260 LINC00276 RAB44 C1orf200 AC012065.5 ATP6V0CP3 PDCD1 CPNE6 PTPN6 KIT DYSF OLFM1 RP11-521B24.3 SPIB MINOS1-NBL1 MST1R SLC12A8 TLCD1 BCL6B ITGB3 RP11-331F9.4 SCARF2 SOBP FMN1 RP11-214K3.20 BCL2L14 COLCA2 MRVI1 NHSL1 RPL23P2 IFITM3 SHE RP11-527L4.5 RP11-566K19.6 RP11-676J12.4 RP11-439L18.2 SH2B2 Supplementary Table S5

Gene sets down-regulated by MI-2 Category Number of enriched NES FDR, q value gene sets Signaling/Interaction with the ME 22 INF pathway 2 -2.14 0.000 JAK-STAT pathway 3 -2 0.000 NF-κB pathway* 4 -1.86 0.000 Ras pathway 6 -1.78 0.010 Ag presentation 1 -1.73 0.000 Wnt pathway 3 -1.69 0.010 BCR pathway^ 2 -1.62 0.012 EGFR pathway 1 -1.59 0.020

Proliferation/Malignancy 10 Inflammation 1 -1.89 0.000 Cell cycle/Proliferation 3 -1.76 0.010 Homeobox 1 -1.72 0.017 Stemness 1 -1.71 0.014 Invasion/Metastasis 1 -1.61 0.020 Cyclin D1 regulated genes 1 -1.55 0.035 DNA dammage 2 -1.52 0.046

Total 32