Next-generation sequencing
To detect somatic, mutational events, a molecular screen was set up analyzing 65 candidate genes in unseparated patient leukocytes derived from peripheral blood samples taken soon after 1st diagnosis, at follow-up-1 after ruxolitinib (sample taken 7 months after start of treatment) and follow-up-2 (sample taken 12 months after start of treatment). DNA of unenriched leukocytes from these consecutive samples was analyzed by next generation gene capture based deep sequencing (NGS) using a custom myeloid gene panel (Agilent SureSelect QXT, target enrichment protocol for loci ABL1 (E4–11), ARID1A, ASXL1 (E12), ATRX (E8_10, 17_35), BCOR, BCORL1, BRAF (E15), CALR (E9), CBL (E8,9), CLBB (E9,10), CBLC (E7), CEBPA, CSF3R (E13–17), CSMD1, CSNK1A1 (E3,4), CUX1, DNMT3A, EED, ETNK1, ETV6, EZH2, FLT3 (E14–15,20), GATA1, GATA2, GNAS (E7–9), HRAS, IDH1 (E4), IDH2 (E4), IKZF1, JAK2 (E12–16), JAK3, KIT (E2,8–17), KDM6A (syn. UTX), KMT2A (syn. MLL), KRAS, MPL (E4–12), NPM1 (E12), NRAS, PDGFRA (E12,14,18), PHF6, PIGA, PRPF40B, PTEN (E5,7), PTPN11 (E3,13), RAD21, RUNX1, SETBP1 (E4), SF1, SF3A1, SF3B1 (E13–16), SH2B3 (E2), SMC1A (E2,3,10-12,16–18), SMC3, SRSF2 (E1), STAG1, STAG2, STAT3 (E3,21), SUZ12 (E10–16), TET2, THPO, TP53, U2AF1 (E2,6), U2AF2, WT1 (E7,9), ZRSR2, coding exons +/− 20 bp, „E “denotes exon) on an Illumina MiSeq platform. The sequencing runs yielded 2.4 to 3.5 million reads for the samples with totals of 4.7 to 10.6 gigabases in the untrimmed raw data of the sequencing runs, whereof 91.9, 95.6, and 94.7% had quality scores exceeding Q30, resulting in average coverages of 857, 823, and 1042 reads per base, respectively. The LOD for somatic mutations varies depending on mutation type, percentage of neoplastic cells in the sample and copy number of individual loci. Mostly, mutations with VAF > 4% can be detected with our bioinformatics pipeline: Bioinformatics and evaluation of sequence data after cutadapt Version: 1.9.1, bwa Version: 0.7.5a-r405, SAMtools Version: 1.2 (using htslib 1.2.1). Software: Seqnext (JSI) Version 4.3.1; if required for confirmative Sanger: Seqpilot (JSI) Version 4.4.0 Analyzed NGS data after trimming were 100% above QS-cutoff > 30 (mostly ≥38). The ROI were 100% over minimal sequencing deepness of 100. Mutation nomenclature according to HGVS. Reference sequences of genes in which mutations were detected are given in italics: ASXL1_NM_015338_c.1934dup, p.Gly646Trpfs*12; CSF3R_NM_000760_c.1853C > T p.Thr618Ile plus presumably germline variant CSF3R_ NM_000760_c.1795C > A, p.His599Asn; TET2_NM_001127208_c.3320C > G p.Ser1107Ter; TET2_ NM_001127208_c.4222G > T p.Gly1408Ter; CEBPA_NM_04364_c.1004 T > A p.Leu335Gln; EZH2_NM_004456_c.2069G > A p.Arg690His; NRAS_NM_002524_c.35G > A p.Gly12Asp; STAG2_NM_001042749_c.1178 T > A p.Leu393Ter; U2AF1_NM_006758_c.460 T > A p.Cys154Ser.
Neutrophil isolation and migration assay conditions
For all healthy controls, neutrophils were isolated from 3 ml EDTA-supplemented blood via density centrifugation using Polymorphprep™ (Cat. No.: 1114683, AXIS-SHIELD, Oslo, Norway) as previously described [
13]. In short, Polymorphprep™ was overlaid with blood at a 1:1 ratio and centrifuged at 450 rcf for 30 min without brake. Polymorphonuclear cells (PMN) were collected and washed with sterile PBS (Cat. No.: P04–36500, PAN-Biotech, Aidenbach, Germany). Erythrocytes were lysed for 10 min at room temperature (RT) in lysis buffer, containing 155 mM NH
4Cl, 10 mM KHCO
3, 0.1 mM EDTA in distilled H
2O. After another washing step in sterile PBS, cells were resuspended in sterile hematopoietic progenitor growth medium (HPGM, Cat. No.: PT-3926, Lonza, Basel, Switzerland) and automatically counted using a Cellometer Auto T4 (Nexcelom Bioscience, Lawrence, MA, USA). Since Polymorphprep™ isolation did not reliably separate neutrophils from the aCML patient, isolations of aCML neutrophils after day 14 were carried out using magnetic negative isolation with the MACSxpress® Neutrophil Isolation Kit (Cat. No.: 130–104-434, Miltenyi Biotec, Bergisch Gladbach, Germany) according to manufacturer’s instructions. Residual erythrocytes were also magnetically depleted using MACSxpress® Erythrocyte Depletion Kit (Cat. No.: 130–098-196, Miltenyi Biotec) according to manufacturer’s instructions. Afterwards, purified neutrophils were washed in sterile PBS, resuspended in sterile HPGM and automatically counted. Comparability of the procedures was ensured by side-by-side measurements of the same sample on day 14 (Supplemental Figure
2A) and as previously detailed [
13]. The neutrophil migration assay was performed as previously described [
13]. Briefly, purified neutrophils were seeded in a 96 Well μ-Plate (Cat. No.: 89621, ibidi, Martinsried, Germany) at a density of 8250 cells per well (growth area: 0.56 cm
2) in 198 μl HPGM supplemented with serum replacement 3 (SR3, final concentration: 0.3x, Cat. No.: S2640, Sigma-Aldrich, Munich, Germany). Neutrophils were stimulated with 2 μl fMLP (final concentration: 10 nM; Cat. No.: F3506, Sigma-Aldrich, Munich, Germany), 2 μl human recombinant CXCL1 (final concentration: 100 ng/ml; Cat. No.: 275-GR-010/CF, R&D Systems, Minneapolis, MN, USA), or 2 μl human recombinant CXCL8 (final concentration: 100 ng/ml; Cat. No.: 208-IL-010/CF, R&D Systems). As all stimuli were reconstituted in sterile PBS, the addition of 2 μl PBS alone served as a vehicle control. The plates were centrifuged and incubated at 37 °C, 5% CO
2 for 20 min before microscopy.
Time-lapse microscopy and auto-tracking
All samples were imaged in a Leica DMI6000 B (Leica Microsystems, Wetzlar, Germany) coupled to a workstation running Leica Application Suite X (LASX, Leica Microsystems) with a motorized stage with a HC PL FLUOTAR L 20x/0.40 DRY objective (Cat. No.: 11506243, Leica Microsystems) at an imaging rate of one frame every 8 s for 1 h at 37 °C, without CO2. The generated movies were exported as *.mov files. These files were analyzed with the Automated Cellular Analysis System (ACAS, Metavi-Harmony software, MetaVi Labs, Austin, TX, USA; sales@metavilabs.com). The evaluation interval was set to 30 s, the minimum track duration to 60 s, the movement threshold to 8 μm and the microscopy resolution to 0.458716 pixel/μm.
Flow cytometry
One hundred thousand purified neutrophils were stained with the following antibodies: CD15 VioBlue (dilution: 1:100, clone: VIMC6, Cat. No.: 130–113-488, Miltenyi Biotec), CD16 FITC (dilution: 1:100, clone: REA423, Cat. No.: 130–113-392, Miltenyi Biotec), fMLP receptor Alexa Fluor 647 (final dilution: 1:100, clone: 5F1, Cat. No.: 565623, BD Biosciences, San Jose, CA), CXCR1 PE (dilution: 1:100, clone: 8F1, Cat. No.: 130–105-352, Miltenyi Biotec), and CXCR2 PE-Vio770 (dilution: 1:20, clone: REA208, Cat. No.: 130–100-930, Miltenyi Biotec). After an incubation step of 15 min in the dark at 4 °C, the suspensions were diluted 1:1 with PBS and analyzed on a MACSQuant VYB (Miltenyi Biotec).