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16 protocols using c9891

1

Isolation and Culture of Trigeminal Ganglion Cells

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Animals were deeply anesthetized with a mixture of hypnorm (Vm21757/4000; Vetapharma), midazolam (Hameln Pharmaceuticals), and isotonic saline (25%, 25%, 50% v/v. 0.3 ml/100 g) and killed by cervical dislocation. The TG were removed, cut into smaller sections with microscissors, placed in 5 mg/ml collagenase suspension (C9891; Sigma-Aldrich) in Ham’s F12 growth medium (21765-029; Gibco Life Technologies, Invitrogen) supplemented with 1% penicillin/streptomycin (15140; Gibco Life Technologies, Invitrogen) and incubated (37°C) for 15 min. Following incubation, the collagenase solution was centrifuged (280 g) for 5 min. The pellet was re-suspended in 1 ml 0.125% trypsin (15090-046; Gibco Life Technologies, Invitrogen) and placed in the incubator for 5–10 min. prior centrifugation (5 min./280 g). The sectioned and enzymatically digested ganglia were then mechanically dissociated into a homogenous solution by repeated pipetting. The cell solution was added to uncoated culture flasks before being placed in an incubator (37°C – 95% air/ 5% CO2). The growth medium was changed after 3 and 24 hrs, and then continuously every 2–3 days prior to the experimental procedure.
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2

Isolation and Culture of Rat DRG Neurons

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One week after the labeling procedure, the rats were again anesthetized with isoflurane, euthanized by decapitation, and DRGs from Th11-L2 were collected [9 (link), 20 (link)]. Neurons were isolated by mechanical and enzymatic dissociation, as described previously [20 (link)]. The ganglia were incubated with collagenase IA (2 mg/ml C9891, Sigma Aldrich, Munich, Germany in DMEM, PAA Laboratories GmbH, Linz, Austria) for 1 h in 5% CO2 at 37 °C. Enzymatic dissociation was terminated by replacing collagenase-containing DMEM with fresh DMEM + cultural medium (DMEM + , i.e., DMEM plus 10% FCS, 1% penicillin/streptomycin, and 0.1% insulin). Tissue digestion was stopped by FCS. Ganglia were triturated using sterile Pasteur pipettes (Sigmacote®; Sigma-Aldrich, Munich, Germany) to dissociate individual cells. After centrifugation at 100 rcf, cells were resuspended in 10 ml DMEM + and centrifuged once more. The pellet was resuspended in 1.8 ml DMEM+, and cells were plated on glass coverslips coated with poly-L-lysine. The coverslips were cultured in DMEM+ for one day before electrophysiological experiments.
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3

Establishment of Renal Cancer Organoids

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Tumor tissues were obtained by radical nephrectomy or partial nephrectomy. They were cut into 1–2-mm-thick sections before digestion with collagenase type IV (1 mg/mL, C9891, Sigma-Aldrich) and Y-27632 (HY-10071, MCE, 10 μM) for 1 h. The suspension was filtered through a 70-μm mesh. The pellet was resuspended in 200 μL of Basement Membrane Extract (BME, 3533-001-02, R&D) and seeded into prewarmed 12-well plates. After the BME solidified, human renal cancer organoid medium was added for culture.
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4

Bladder Tumor Organoid Culture

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Tumor tissue was obtained by TURBT or radical cystectomy. Then, the tissue samples were cut into small pieces (1-2 mm) and the samples were digested with collagenase type IA (1 mg/ml, C9891, Sigma Aldrich) and Y-27632 (HY-10071, MCE, 10 μM) for 30 min. The cell suspension that was obtained was filtered through a 70-μm mesh and the samples were centrifuged. The pellet was resuspended in 200 μL of Basement Membrane Extract (BME, 3533-001-02, R&D) and seeded into pre-warmed 24-well plates. After BME solidified, a human bladder organoid medium was added for culture.
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5

Immunostaining of Neuromuscular Junctions

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Animals were fixed in 4% paraformaldehyde for 3 h at room temperature. After fixation, the embryos were rinsed several times with PBS and then incubated in PBS containing 1 mg/mL collagenase (20 min, C9891, Sigma-Aldrich, Saint-Quentin Fallavier, France) to remove skin. The collagenase was washed off with PBS Triton X-100 (PBST; 1 h) and heads were cut away. After an incubation of 30 min in blocking solution (1% BSA, 1% triton, PBS, 2% goat serum), the embryos were incubated overnight at 4 °C in synaptic vesicle 2 (sv2, 1:200; Developmental Studies Hybridoma Bank; University of Iowa, Iowa USA) antibody diluted in blocking solution. The embryos were then washed and incubated for 30 min in PBST containing α-bungarotoxin conjugated to Alexa 488 (αBTX, 1:1000; Abcam). The embryos were rinsed several times with PBST and then incubated in freshly prepared block solution containing a secondary antibody (Alexa Fluor 568, 1:1000; Life Technologies, Saint-Aubin, France) for 3h at RT before mounting on glass slide in 50% glycerol. The NMJs were visualized using a Leica SP8 Inverted scanning confocal microscope. All captured images of stained embryos were processed using Imaris Image Analysis software and ImageJ.
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6

Simulating Biomaterial Degradation

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When used clinically, the tested materials undergo natural degradation. To simulate this biodegradation in vitro, collagenase was employed as an enzyme. The collagenase used in this experiment was of bacterial origin, obtained from Clostridium histolyticum. Available as a lyophilized powder (C9891, Sigma Aldrich, St. Louis, USA), it was mixed with either SBF or Klimek (5 unit/ml) before being diluted to 0.5 unit/ml.
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7

Lung Metastasis Immune Cell Analysis

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Vaccinated and control mice with LLC tumors metastasized to lungs were euthanized 35 days after tumor challenge. Lungs were resected and metastasized LLC tumors were dissected and chopped into small pieces before incubation with a mixture of enzymes dissolved in HBSS, including collagenase type IV (400 U/mL; C9891; Sigma-Aldrich; St. Louis, MO, USA), hyaluronidase (0.025 mg/mL; H6254; Sigma-Aldrich) and DNase I (0.01 mg/mL; D5025; Sigma-Aldrich) for 30 minutes at 37 °C with occasional shaking. The resultant cells were washed and passed through a Ficoll gradient (17144002; GE Healthcare; Chicago, IL, USA) to eliminate dead cells. TILs were then analyzed by flow cytometry for the expression of markers for different immune cells. Anti-CD45 antibody was used to selectively exclude CD45 tumor cells from analysis so that only CD45+ immune cells were evaluated. The same number of cells (based on side-scatter and forward-scatter analyses) was acquired in all samples. Respective antibodies specific for the markers were used to quantitate the abundance of different immune cell types. T regulatory cells (Tregs; Foxp3+) were analyzed using the anti-mouse Foxp3 staining kit (00-5523-00; Thermo Fisher).
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8

Muscle Macrophage Isolation from mdx Mice

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Skeletal muscles from male and female, 1-month-old mdx mice were minced in 1.25 mg/ml collagenase types IA and IV (Sigma-Aldrich #C9891, #C5138) in Dulbecco’s Modified Eagle medium (Sigma #D1152) and digested at 37°C for 1 h with gentle trituration each 15 min. The digestate was diluted with DPBS, filtered through 70 μm mesh filters and the liberated cells collected by centrifugation. The cells were resuspended in DPBS, overlaid on Histopaque-1077 (Sigma-Aldrich #1077-1) and centrifuged at 400 x g for 30 min at RT. Macrophages were collected from the DPBS-Histopaque interface and RNA isolated from the cells as described above. QPCR was performed using tpt1 and hprt1 as house-keeping genes. Muscle macrophages were collected from five WT/mdx and three LIF/mdx mice.
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9

Fetal Kidney Cell Isolation and Flow Sorting

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Fetal kidneys were dissociated with collagenase I (2 mg/ml in 1% BSA/PBS; C9891, Sigma) for 20 min at 37 °C. The cell suspension was filtered through a 40 µm pore size filter, washed and then stained using a panel of antibodies for 30 min at 4 °C. Cells were sorted on a SORP LSRII using FACSDiva and analyzed with FlowJo 10.6.1. Antibodies are provided in Supplementary Table 7.
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10

Comprehensive Immune Cell Profiling

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Flow cytometry was used to compare between each genotype and sex (antibodies and gating strategy are detailed in Additional file 1: Supplementary data 3, 4). Whole hearts were removed and washed in PBS. Finely minced tissue was then digested for 30 min at 37 °C [Krebs–Henseleit solution containing collagenase (Clostridium histolyticum Type IA; C9891, Sigma-Aldrich), Type XI collagenase (C7657, Sigma-Aldrich), bovine pancreatic deoxyribonuclease I (D4263, Sigma-Aldrich) and hyaluronidase Type IV from bovine testes (H3884, Sigma-Aldrich)]. Digestates were then passed through a 70-micron cell strainer and reconstituted with PBS prior to density gradient centrifugation (Ficoll-Paque PLUS (17-1440-02, GE Healthcare Life Sciences). Isolated immune cells were washed again with phosphate-buffered saline, incubated with an antibody cocktail comprising CD45-FITC (clone REA737), CD8a-PerCPVio700 (clone 53-6.7), CD4-APC (clone GK1.5), Ly6G-APCVio770 (clone REA526), Ly6C-VioBlue (clone REA796), CD45B220-VioGreen (clone REA755), CD62L-Brilliant Violet 785 (clone MEL-14), F4/80-PE (clone REA126), CD11b-PEVio615 (clone REA592) and CXCR2-PEVio770 (clone REA942). Cells were fixed with 100 μL 2% paraformaldehyde.
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