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12 protocols using b cll cell isolation kit

1

Characterization of NOTCH1 Mutated CLL

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Seven NOTCH1-mutated and eight NOTCH1-wt CLL peripheral blood samples were collected from the patients who were admitted to our department. Detailed characteristics of patients were shown in Supplementary Table 1. The diagnosis was based on the International Workshop on CLL-National Cancer Institute criteria. Ficoll-Hypaque solution (Tbdscience, Tianjin, China) and B-CLL cell isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) were applied to obtain purified B cells (>95%). NOTCH1 mutation was detected by Sanger sequencing or next-generation sequencing. Moreover, this study was approved by the hospital ethics committee (No. 2019–SR-307) and the informed consent of all patients was provided in line with the Helsinki Declaration of 1975.
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2

Isolation and Culture of B-Cells for CLL Studies

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Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll density gradient centrifugation. CD19+ CD5+ B-cells were isolated from PBMCs using magnetic-bead-activated cell sorting, using a B-CLL cell isolation kit (Miltenyi Biotec). To evaluate the effect of AA on normal lymphocytes, naïve B-cells were isolated from donor lymphocyte infusions using a Naïve B-cell Isolation kit (Miltenyi Biotech). The purity assessed by CD19 expression on flow cytometry was around 98%. OSU-CLL cells were a gift from E. Hertlein and colleagues [28 (link)]. JVM3 cells were purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). Freshly isolated B-cells and CLL cell lines were cultured in RPMI 1640 medium (PAN Biotech, #P04–16500) with 10% fetal bovine serum (FBS) (PAN Biotech, #P30–3306) and L-glutamine, penicillin and streptomycin (1%) (Eurobio Scientific). When indicated, CLL B-cells were cultured in Iscove’s modified Dulbecco’s Medium (IMDM) (Merck, #FG0465) and alpha-MEM medium (Sigma Aldrich, #M4526) (n = 7). Cells were cultured at a density of 4 × 105/ml in 48-well plates and were treated with either vehicle or AA or drugs for 24 h. To simulate hypoxia condition, cells were cultured in presence of 100 μM Cobalt(II) chloride hexahydrate (CoCl2.6H2O, Sigma Aldrich) for 24 h. Cells were then washed and incubated with AA for 24 h.
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3

Quantifying IL-2 Production in CLL-SKW3 Co-culture

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SKW3-T18 cells were cultured in complete RPMI-1640. Cell line identity was confirmed using short tandem repeat analysis (Powerplex 16 System, Promega, Southampton, UK) and absence of mycoplasma was confirmed using Mycoplasma PCR detection kit (Applied Biological Materials, Richmond, Canada). CLL cells were purified from PBMCs using a B-CLL cell isolation kit (Miltenyi Biotec) and incubated with soluble antibody or antibody-coated beads (2:1 bead:cell ratio) for 15 or 60 min, respectively. CLL cells were then co-cultured with SKW3-T18 cells at a final density of 100,000 SKW3-T18 and 400,000 CLL cells in a total volume of 0.2 mL. Supernatants were collected after 24 h and IL-2 quantified using an enzyme-linked immunosorbent assay (ELISA; R&D Systems) according to the manufacturer’s instructions. All assays were performed in duplicate.
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4

Isolation of T cells, B cells, and CD34+ cells

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Peripheral blood mononuclear cells were isolated from whole blood by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Chicago, IL, USA). CD4+, CD8+, or CD3+ T cells were isolated from PBMCs using the CD4+ T Cell, CD8+ T Cell, or Pan T Cell isolation kits (Miltenyi Biotec, Bergisch Gladbach, Germany). CLL cells were obtained from PBMCs, using the B-CLL Cell Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany), or from whole blood, using the RosetteSep Human B Cell Enrichment Cocktail (Stemcell Technologies, Vancouver, Canada). CD34+ cells were enriched from umbilical cord blood using the CD34 Microbead Kit (Miltenyi Biotec, Bergisch Gladbach, Germany).
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5

Isolation and Characterization of CLL Cells

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PBMCs from CLL patients were obtained by ficoll gradient centrifugation and CLL cells were isolated with a MACS-based B-CLL Cell Isolation Kit (Miltenyi, 130103466). Purity above 90% was confirmed by flow cytometry staining for CD19 (HIB19, eBioscience, 1:100). Physiological B cells from voluntary blood donors were isolated using the same procedure and were used as controls. Paraffin-embedded lymph node biopsies from patients with and without Richter’s transformation were used for RNA isolation and qRT-PCR. All experiments were approved by the Ethics Committee of the University of Tübingen and written informed consent was obtained from all patients who contributed samples to this study.
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6

Chemo-naïve CLL patient protocol

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Peripheral blood from chemo-naïve CLL patients participating in a previously reported clinical trial (AGMT-REVLIRIT trial, ClinicalTrials.gov Identifier: NCT00738829 and NCT01703364) [18 (link)] with first line treatment with lenalidomide in combination with fludarabine and rituximab was collected upon informed consent and ethical approval by the Ethics Committee of the Province of Salzburg (415-E/1287/4–2011, 415-E/1287/8–2011). Sampling was performed prior treatment start and CLL cells were obtained by density gradient centrifugation and B-CLL Cell Isolation kit (Miltenyi Biotec). Cell purity was >90% in all samples. The determination of prognostic markers was performed routinely at our department as described previously [19 (link)]. DNA and RNA was purified using DNeasy Blood and Tissue kit or RNeasy Mini kit (both Qiagen), respectively. Patient details and type of analysis are given in supporting Table 1. Primers are listed in supporting Table S2. RNA/DNA sequencing data from AGMT-REVLIRIT patients and MEC1 cells are available under BioProject PRJNA540189 at https://www.ncbi.nlm.nih.gov/sra. In addition, RNA sequencing and clinical data from CLL samples and normal B cells were downloaded from the European Genome-phenome Archive (EGAS00001000374) [20 (link)].
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7

Chemo-naïve CLL Patient Blood Samples

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Peripheral blood from 44 chemo-naïve CLL patients participating in a previously reported clinical trial (AGMT-REVLIRIT trial, ClinicalTrials.gov Identifier: NCT00738829 and NCT01703364) [23 (link)] receiving first line treatment with lenalidomide in combination with fludarabine and rituximab was collected upon informed consent and ethical approval by the Ethics Committee of the Province of Salzburg (415-E/1287/4–2011, 415-E/1287/8–2011). Sampling was performed prior to treatment starting, and CLL cells were obtained by density gradient centrifugation and a B-CLL Cell Isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany). The cell purity was >90% in all samples. The determination of prognostic markers was performed routinely in our department as described previously [23 (link)].
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8

Isolation and Characterization of CLL Cells

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Samples were obtained from 128 CLL patients. Peripheral blood mononuclear cells (PBMCs) were sorted for CLL cells using a B-CLL cell isolation kit (Miltenyi Biotec; 130-093-661). Purity of sorted cells was assessed by flow cytometry and subsequent FISH analyses were corrected for the proportion of CLL cells in each sample by subtracting from the percentage of cells identified without cytogenetic aberrations.
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9

Quantifying IL-2 Production in CLL-SKW3 Co-culture

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SKW3-T18 cells were cultured in complete RPMI-1640. Cell line identity was confirmed using short tandem repeat analysis (Powerplex 16 System, Promega, Southampton, UK) and absence of mycoplasma was confirmed using Mycoplasma PCR detection kit (Applied Biological Materials, Richmond, Canada). CLL cells were purified from PBMCs using a B-CLL cell isolation kit (Miltenyi Biotec) and incubated with soluble antibody or antibody-coated beads (2:1 bead:cell ratio) for 15 or 60 min, respectively. CLL cells were then co-cultured with SKW3-T18 cells at a final density of 100,000 SKW3-T18 and 400,000 CLL cells in a total volume of 0.2 mL. Supernatants were collected after 24 h and IL-2 quantified using an enzyme-linked immunosorbent assay (ELISA; R&D Systems) according to the manufacturer’s instructions. All assays were performed in duplicate.
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10

Isolation of Primary CLL Cells

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Primary CLL cells were obtained from patients at the outpatient clinic of the university hospital Ulm after written informed consent (Ulm Ethics Committee, Votum 96/08) in accordance with the Declaration of Helsinki. CLL B-cells were isolated from heparinized blood of CLL patients using the B-CLL cell isolation kit (Miltenyi Biotech, Bergisch Gladbach, Germany) according to the manufacturer's instructions, and viably preserved in liquid nitrogen. Patient characteristics are shown in supplementary Table 1.
Information about additional methods can be found in the supplementary information file.
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