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16 protocols using gm6001

1

Chemotaxis of Mouse Monocytes toward Islet Supernatants

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The chemotaxis of mouse monocytes toward rat islet supernatants was evaluated using a 5-µm pore Transwell membrane (Corning Inc., Corning, NY, USA), as described previously.22 (link) The rat islet culture supernatants used in this assay were the same as those used to determine cytokine concentrations. MACS-enriched monocytes (1.0 × 105) were seeded in the upper chamber in 100 µL of serum-free medium, and 600 µL of islet supernatant or RPMI was placed in the lower chamber. Chemotactic activity is expressed as the mean number of migrated monocytes in 10 high-power microscope fields. Monocyte migration toward RPMI served as the negative control.
To validate the effects of MCP-3 on chemotaxis, anti-MCP-3 monoclonal antibody (mAb; 2 µg/mL; Abcam, Cambridge, UK) was added to the islet supernatant to neutralize MCP-3. Isotype-matched mouse immunoglobulin G (2 µg/mL; Santa Cruz Biotechnology Inc., Santa Cruz, CA, USA) served as the control. To inhibit chemotaxis induced by MMPs, the MMP inhibitor GM6001 (10 μmol/L; Santa Cruz Biotechnology, Inc.) was used, as described previously.23 (link) GM6001 inhibits MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-12, MT-MMP1, and MMP-26.
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2

Chemical Treatments in Zebrafish Injury Study

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The chemical treatments used in this study are taxol (Acros), GM6001
(Santa Cruz Biotechnology), and SU6656 (Santa Cruz Biotechnology). Stock
solutions of these reagents were stored at −20°C. The taxol
stock solution was stored at 2.2 mM, the GM6001 stock solution was stored at
1.0 mM, and the SU6656 stock was stored at 375mM - all in DMSO. Treated
animals were exposed to the chemical directly following injury (expect in
Figure 2F where animals were
exposed at varying time-points after injury) at concentrations of 22 mM for
taxol, 1 μM for GM6001, and 3μM diluted in egg water (Nichols and Smith, 2019 (link)). DMSO-treated
animals were exposed to 1% DMSO in egg water.
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3

Transwell Migration Assay for HUVEC

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HUVECs from pooled donors were purchased from VEC Technologies and grown in complete EGM-2 medium (Lonza) at 37°C and 5% CO2 on tissue culture dishes coated with 0.2% gelatin. Transwell migration assays were performed as described previously (Mitchell et al., 2009 (link)). In brief, transwell tissue culture inserts with 8-µm pores (Costar) were coated with 0.2% gelatin overnight. HUVECs were serum starved for 24 h, trypsinized, and seeded onto top surfaces of transwells at 5 × 104 cells per insert. Lower chambers contained serum-free EBM-2 medium (Lonza) that had been conditioned by the indicated MK cell variants in a 7:3 ratio with complete EGM-2 medium (Mitchell et al., 2009 (link)) with or without the MMP inhibitor GM 6001 (Santa Cruz Biotechnology, Inc.), as indicated. After 4 h at 37°C, migrated cells were fixed, permeabilized, and stained with DAPI (Thermo Fisher Scientific). Migrated HUVECs were visualized in room temperature PBS using an inverted microscope (IX70; Olympus; 4× objective), and images were collected using a digital camera (SensiCam; Cooke). The total stained area was quantified using ImageJ software (National Institutes of Health).
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4

Protease Inhibitor Cocktail Preparation

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α1-antitrypsin, trypsin inhibitor from Glycine max (soybean), leupeptin, aprotinin were from Sigma-Aldrich, and dissolved in F12K medium without serum. GM6001 and E64 were from Santa Cruz Biotechnology, and dissolved in DMSO. Protease inhibitor cocktail solution in DMSO was from Sigma. It contained AEBSF (104 mM), aprotinin (80 μM), bestatin (4 mM), E64 (1.4 mM), leupeptin (2 mM) and pepstatin (1.5 mM). BMS200261 was from KeraFast (Boston, USA), and dissolved in water. N-acetylcysteine was from Sigma, and dissolved in cell culture medium without serum and pH adjusted to 7.0 with sodium hydroxide. Dimethylthiourea was from Acros, and dissolved in cell culture medium without serum. 1-(2-Cyano-3,12,28-trioxooleana-1,9(11)-dien-28-yl)-1H-imidazole (CDDOIm) was from the National Cancer Institute or Tocris, and dissolved in DMSO.
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5

Analyzing Arthropod-Mediated Inflammatory Pathways

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GCE was purchased from the Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine (Seoul, Korea). Small interfering RNAs (siRNAs) against AP1, NF-κB, SP1, ETS1, and MMP1 were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Anti-TLR2 antibody and anti-phosphorylated and control p44/42 antibodies were purchased from R&D Systems (Minneapolis, MN, USA) and Cell Signaling Technology (Denvers, MA, USA), respectively. The broad-spectrum MMP inhibitor GM6001 and the MAPK/ERK inhibitor PD98059 were purchased from Santa Cruz Biotechnology and Cell Signaling Technology, respectively.
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6

Inhibition of FAK and MMP Invasion

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Spheroids formed from H1299 shLKB1 or pLKO.1 control cells were generated as described earlier. During embedding of spheroids in the 3D collagen matrix, the FAK inhibitor PF-573228 (Sigma-Aldrich) was added at 1 μM or GM-6001 (Santa Cruz Biotechnology) was added at 20 μM to both the collagen and complete RPMI medium on top of the collagen matrix. DMSO was used as the vehicle control. Spheroids were incubated at 37°C and 5% CO2 for 16–20 h to allow for invasion.
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7

Visualizing Adhesion Dynamics in Live Cells

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For confocal microscopy live cell imaging, we used the same microscopic setting as for FRAP. Cells were imaged for the indicated time with 20 s or 30 s intervals with 1–3% laser power depending on the fluorophores. To block MMP activities, cells were plated for 5 h with or without 50 µM GM6001 (no sc-203979, Santa Cruz) before live cell imaging. For data illustration, fluorescent images were background-subtracted and passed through low-pass filters followed by Unsharp Mask in ImageJ.
For the tracking of sliding adhesions, a time lapse of 20 min with 2 min intervals was extracted from the full Supplementary Videos. Raw images were background-subtracted. Single adhesions were identified by thresholding and tracked with the TrackMate plugin in ImageJ. Structures with sizes below 3 pixels (0.04 µm per pixel) were excluded. Adhesion sites with lifetimes above 6 min were tracked to measure their sliding velocities. Average adhesion sliding velocities were calculated on the basis of all analysed adhesions for each cell. For the determination of sliding velocities of central adhesions, vinculin-mCherry-positive adhesions were analysed within 20 µm distance from nuclei in the first frame. For the FAs in the cell protrusions, vinculin-mCherry-positive adhesions were analysed within 10 µm behind the protruding leading edge in the first frame.
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8

Metalloprotease and Rho Signaling Assay

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The assay is described elsewhere (Makowiecka et al., 2016 (link)). In some experiments 25 μM of a non-selective inhibitor of metalloproteases (GM6001, Santa Cruz Biotechnology Inc.), 10 μM Rac1 inhibitor (NSC 23766, Santa Cruz Biotechnology Inc.) or 10 μM ROCK1 inhibitor (Y-27632, Santa Cruz Biotechnology Inc.) were added to the medium, in which cells were seeded.
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9

Cell Lines Culture and Transfection

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MCF10A epithelial cell line and breast cancer cell lines were purchased from American Type Culture Collection (Manassas, VA). All cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) or RPMI-1640 Medium (Gibco) supplement with 10% FBS, 2-mM L-glutamine, 0.1-mM non-essential amino acids and 1% penicillin/streptomycin in a 5% CO2 atmosphere at 37 °C. GM 6001 and ARP100 purchased from Santa Cruz Biotechnology (Dallas, TX, USA) were dissolved in dimethyl sulfoxide (DMSO). The GPNMB and pCMV6 expression constructs were purchased from OriGene (Rockville, MD, USA). For transfection, cells were seeded into 6-cm dish for 24 h and transfected using Lipofectamine 3000 (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.
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10

Ammonium Chloride Exposure and MMP Inhibition in Zebrafish

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NH4Cl (Sigma 254134) was performed as previously described [80 (link)]. Embryos were exposed to 100nM of NH4Cl in EM for 24 hours from 3 dpf to 4 dpf. After rinsing in EM, embryos were prepared for western blot or staining.
To determine if MMP inhibitors would cause kif5Blof-like phentoypes, we exposed Wt (sox10:GFP) embryos to either the broad-spectrum metalloproteinase inhibitor EDTA (0.5mM and 1mM) or the MMP inhibitor GM6001 (200μ; Santa Cruz, sc-203979) from 48 hpf to 4 dpf with daily changes of the medium and drug daily. Sibling embryos were exposed to DMSO 1% as a control.
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