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5 protocols using rituximab

1

Peptide Synthesis and Characterization

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The following peptides were used in the study:
VYPNGA-NH2, VYPDGA-NH2, VYPL-isoDGA-NH2 (L-isoD is l-isoaspartic
acid), PGPQGFQ-NH2, PGPEGFQ-NH2, and PGPL-isoEGFQ-NH2 (L-isoE is l-isoglutamic acid). These peptides were custom-synthesized
by Biomatik Corp. (Kitchener, ON, Canada). Additionally, delta-sleep-inducing
peptide (DSIP, WAGGDASGE), l-isoAsp5-delta-sleep-inducing
peptide (L-isoD-DSIP, WAGGL-isoDASGE), and d-isoAsp5-delta-sleep-inducing peptide
(D-isoD-DSIP, WAGGD-isoDASGE)
were obtained from Bachem America (Torrance, CA). Chicken egg lysozyme,
rituximab, pyridine, acetic anhydride, deuterium oxide (99.9 atom
% D), and hydrazine (35 wt % in H2O) were purchased from
Sigma-Aldrich (St. Louis, MO). All other chemicals were either of
reagent grade or the highest commercially available quality.
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2

Establishing Preclinical CLL Models

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PDX models were established in 6-12 week old, male and female, NOD/Shi-SCID/IL-2Rγctm1sug/Jic (NOG), Mus musculus Linnaeus, 1758 (mouse) strain animals (in-house) as previously described [43 (link), 44 (link)].
Ibrutinib (Seleckchem; S2680) was resuspended in 1% methylcellulose and 0.4% Cremephor EL (Sigma; M0262 and C5135), and administered daily for 9 days by oral gavage at 12.5mg/kg, a dose which is sufficient to ensure 90% occupancy of Bruton tyrosine kinase (BTK) [45 (link)]. Rituximab (40mg/kg; Roche; 2530376), or saline control was given intravenously 3 times per week.[46 (link)] Fludarabine (0.625mg/kg, TEVA; 231-10-04151) and cyclophosphamide (6.25mg/kg, Baxter; 1001995501) or saline (control) were injected intraperitoneally 3 times per week, for two weeks, [47 (link)] whereas chlorambucil (5mg/kg; Sigma; CO253) or 3% dimethyl sulfoxide (DMSO, Sigma; D2650) vehicle control was administered daily for 5 days intraperitonally [48 (link)].
At specific time points (one week following treatment with chlorambucil, Fludarabine/cyclophosphamide or Rituximab and the next day following treatment with Ibrutinib) animals were sacrificed and single cell solutions produced from their homogenized spleens. CLL cells were sorted by flow-cytometry as demonstrated in the Supplementary Figure 1.
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3

Characterization of Small Molecules and Proteins

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Type 1 water was provided by a Milli‐Q purification system from Millipore (Burlington, MA, USA). The mobile phase components, namely formic acid (FA), trifluoroacetic acid (TFA), methanol (MeOH) and ACN were obtained from Sigma Aldrich (Steinheim, Germany). The small molecules analyzed in this work: atenolol, caffeine, nadolol, propranolol, ibuprofen, methylparaben, ethylparaben, propylparaben, and butylparaben were also obtained from Sigma‐Aldrich. The six proteins digested to obtain the tryptic digest analyzed in this work, namely human serum albumin (HSA), BSA, β‐casein, myoglobin, lysozyme, and cytochrome C were all obtained from Sigma‐Aldrich. The intact proteins, namely insulin, α‐lactalbumin, and HSA were obtained from Sigma‐Aldrich, while rituximab was obtained as European Union pharmaceutical‐grade drug products from its respective manufacturer (Roche, Basel, Switzerland). Finally, some reagents such as DL‐1,4‐dithiothreitol and iodoacetamide were obtained from Acros Organics (Geel, Belgium), while trypsin was obtained from Sigma‐Aldrich.
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4

Peptide Microarray: Screening and Binding

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Peptide microarrays: A peptide library of 160,000, peptides as well other peptide microarrays for the substitutions and the KD analysis, were fabricated via the ultra-high-density peptide microarray technology of AXXELERA (Karlsruhe, Germany) [49 ]. The AXXELERA technology allows for the 30 µm-sized square peptide spots with a pitch of 60 µm that corresponds to ca. 28,000 spots/cm2.
Immunostaining: Peptide microarrays were incubated with the monoclonal anti-CD20 antibody rituximab (Sigma-Aldrich, Steinheim, Germany) with concentrations depending on the type of experiment, diluted in PBS-T (Phosphate Buffered Saline with Tween) overnight at 4 °C. A rituximab concentration of 30 µg/mL was used for the first screen of the entire resemblance-ranking peptide library. Then, the peptide chips were stained with the fluorescently labeled secondary anti-human-IgG antibodies (Jackson ImmunoResearch, Philadelphia, PA, USA). The signals from the spots were read out with the confocal scanner Innoscan 1100 AL. The scans were performed in the red channel (635 nm), with a resolution of 2 µm/pixel, a speed of 35 µm/s, and a PMT gain of 9.
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5

Lung Cancer Cell Isolation Protocol

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All chemicals, solvents, enzymes and monoclonal antibody (mab) Rituximab were purchased from Sigma. Lung cancer cells (HTB-171) were used from previous study 22 and lung cancer tissue was obtained through bronchoscopy following the protocol approved by the regional Ethics Committee of University Hospital in Brno.
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