Real-time RT-PCR : Real-time reverse-phase polymerase chain reaction

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Real-time RT-PCR : Real-time reverse-phase polymerase chain reaction Supplemental Table 1. Details of handling and experimental usage of CLL lymphocytes obtained from patients # of samples Assays and experimental details Before oral duvelisib intake (C1D1) After 7 days of oral duvelisib intake (C1D8) After 28 days of oral duvelisib intake (C2D1) Sample condition Assays done 42 Frozen Blood RNAseq Nanostring 16 Fresh Blood Microfluidic chip real-time RT-PCR Real-time RT-PCR RPPA Immunoblots Microfluidic qRT-PCR (Applied Biosystems): included 93 apoptotic genes; 384 well plate Real-time RT-PCR : Real-time reverse-phase polymerase chain reaction RPPA: Reverse Phase Protein Array

Supplemental Table 2. Cytogenetics and prognostic markers of patient samples used for RPPA, immunoblot analyses. Pt No C1D1- WBC C2D1- WBC Rai Stage Age FISH IGHV ZAP70 CD38 Prior therapy #702 24.7 150.3 4 58 13q M pos neg 1 #877 5.8 17.6 72 11q no PCR #406 5.2 19.8 53 17p UM 5 #738 18.1 116.4 78 NA #733 35.9 15.2 3 61 NA #125 10.3 27.3 75 8 #005 25.9 69 2 #862 6.2 88.9 68 #431 73.3 82.6 71 T12 #087 60.9 76.9 56 7 #228 115.5 27.6 74 #345 13 16.9 #317 77.1 38 #524 55.3 120.4 80 #290 39 70.4 60 #310 54.3 118.4 82 NA: Information not available; PR: Partial response; SD: Stable disease; PROG: Progressive disease; M: Mutated; UM: Unmutated

Ligands, reagents, antibodies Source; Catalogue No Supplemental Table 3. List of ligands, reagents and antibodies along with their sources Ligands, reagents, antibodies Source; Catalogue No Navitoclax (ABT-737) Provided by Abbott, Abbott Park, IL Actin antibody (mouse) Santa Cruz Biotechnology, Dallas, TX; sc-47778 Actin antibody (rabbit) Cell Signaling Technology, Danvers, MA; 8457 Anti-IgM MP Biomedicals, Santa Ana, CA; 55055 Bax antibody Santa Cruz Biotechnology, Dallas, TX; sc-20067 Bax (Activated) antibody Enzo Life Sciences, Farmingdale, NY; ALX-804-224-C100 Bcl-2 antibody (mouse) Dako, Carpinteria, CA; M0887 Bcl-2 antibody (rabbit) Santa Cruz Biotechnology, Dallas, TX; sc-783 Bcl-xl antibody Santa Cruz Biotechnology, Dallas, TX; ac-634 Bim antibody Abcam, Cambridge, MA; ab32158 Dimethyl sulfoxide (DMSO) Sigma Aldrich, St. Louis, MO Duvelisib (IPI-145) Infinity Pharmaceuticals, Inc. Cambridge, MA Ibrutinib Selleckchem, Houston, TX; S2680 Idelalisib Gilead Sciences, Foster City, CA Mcl-1 antibody Life Technologies, Carlsbad, CA; AHO0102 Noxa antibody Abcam, Cambridge, MA; ab13654 PARP antibody BD Biosciences, San Jose, CA; 556362 Puma antibody Sigma Aldrich, St. Louis, MO; P4743 Recombinant Human IL-10 PeproTech, Rocky Hill, NJ; 200-10 Recombinant Human IL-2 PeproTech, Rocky Hill, NJ; 200-02 Recombinant Human sCD40-Ligand PeproTech, Rocky Hill, NJ; 310-02 Vinculin antibody Cell Signaling Technology, Danvers, MA; 13901 Venetoclax (ABT-199) Xcessbio, San Diego, CA; M60075

Supplemental Table 4. Transcript and protein expressions of Bcl-2 family members measured through different techniques. Bcl2 family Gene Name Protein Name Mircofluidic chip qRTPCR (Fold change) RNA Seq Nanostring RPPA Median *P value n Anti-apoptotic BCL2 Bcl-2 2.81 0.002 5 1.40 < 0.0001 31 1.38 0.0001 30 1.26 0.0012 16 BCL2A1 (BFL-1) Bfl-1 0.92 0.527 1.25 0.0016 NA - 0.95 0.0112 9 BCL2L1 (BCL-XL) Bcl-xL 0.60 0.683 0.55 0.0059 0.57 0.0004 0.97 0.5403 MCL1 Mcl-1 0.91 0.321 1.01 0.4059 0.93 0.0460 BCL2L2 (BCL-W) Bcl-w 1.22 0.118 1.36 0.0008 BCL2L10 (BCL_B) Bcl-b 0.69 0.602 ND -- 0.98 0.9291 Pro-apoptotic multi-domain BAK1 Bak 1.05 0.329 1.02 0.675 0.1581 BAX Bax 1.20 0.308 0.4425 0.6952 0.89 0.0022 BOK Bok 0.62 0.780 1.10 0.5379 Pro-apoptotic BH3 only BAD Bad 2.34 0.005 0.0227 1.08 0.5344 BBC3 (PUMA) Puma 2.76 0.071 2.14 0.1203 1.24 0.0017 HRK Hrk 20.08 0.012 3.11 <0.0001 2.56 PMAIP1 (NOXA) Noxa 1.85 0.067 2.18 1.45 BCL2L11 (BIM) Bim 1.31 0.459 1.37 1.34 0.00002 BID Bid 0.51 0.274 1.11 0.7408 1 0.6706 BIK Bik 0.56 0.014 0.63 0.0104 0.38 BCL2L13 (BCL-RAMBO) Bcl-rambo 1.58 0.029 1.13 0.0328 0.7918 BCL2L14 (BCL-G) Bcl-g 1.07 0.863 BMF Bmf 1.50 *Unpaired student t-test; ND, below limit of detection; NA, not applicable (not in the assay)

Patient Sample Duvelisib, nM + ABT-199, nM % Apoptosis Expected Supplemental Table 5. Combination of duvelisib and venetoclax: Expected % apoptosis vs Observed % apoptosis . Red: Expected % apoptosis < Observed % apoptosis indicates either additive or synergistic combination. Green: Expected % apoptosis > Observed % apoptosis indicates either non-additive, non-synergistic or antagonistic combination. Method of calculating Expected % apoptosis: 1) Raw viability was normalized to "% viability”. 2) Expected % viability was calculated using following formula: “ % viability of drug A * % viability of drug B / 100” . 3) Expected % apoptosis was calculated as "100-(Expected % apoptosis)" Patient Sample Duvelisib, nM + ABT-199, nM % Apoptosis Expected Observed Culture condition Suspension IgM Cytokine #300 100 + 0.5 14.1 14.7 7.7 6.0 11.6 12.3 #576 5.9 6.5 7.5 8.5 2.0 2.4 100 + 1 21.3 26.8 14.9 13.1 15.5 6.1 12.7 9.4 14.3 2.2 #708 100 + 5 52.2 65.4 57.3 63.6 46.6 58.6 #215 20.7 23.6 6.4 14.4 10.3 18.9 #638 21.6 34.2 51.9 37.8 71.9 49.9 100 + 10 65.5 75.7 66.3 78.1 67.2 77.0 24.9 29.4 25.6 23.7 30.2 49.7 35.4 54.7 55.0 74.9 62.6