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12 protocols using a1153

1

Mouse Brain Protein Fractionation

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Mouse brain tissues were homogenized in 0.2 ml of ice-cold buffer (0.1 M 3-[N-morpholino]propanesulfonic acid, pH 7.0, 1 mM ethylenediaminetetraacetic acid, 0.5 mM MgSO4, 1 M sucrose [Panreac AppliChem, A2211]) containing 1 mM NaF, 1 mM Na3VO4, 1 mM phenylmethylsulfonyl fluoride and 10 μg/ml each of aprotinin (Sigma-Aldrich, A1153) and 1 μg/ml leupeptin (Sigma-Aldrich, L8511). The homogenates were cleared by centrifugation at 50,000 × g for 20 min at 4°C, and the supernatants were collected as soluble fractions. To prepare the sarkosyl-insoluble fraction, the pellets were resuspended in lysis buffer (0.1 M 3-[N-morpholino]propanesulfonic acid, pH 7.0, 10% sucrose, 2 mM ethylene glycol tetraacetic acid [Sigma-Aldrich, E3889], 0.5 mM MgSO4, 500 mM NaCl, 1 mM MgCl2, 10 mM NaH2PO4, 20 mM NaF) containing 1% N-lauroylsarcosine (sarkosyl; Sigma-Aldrich, L9150) with protease inhibitors (Sigma-Aldrich, L8511, A1153 and P7626), vortexed for 1 min at room temperature, incubated at 4°C for 16 h, and then centrifuged at 200,000 × g for 30 min at room temperature. The supernatant fractions were collected as sarkosyl-soluble fractions, and the pellets, sarkosyl-insoluble fractions, were resuspended in sodium dodecyl sulfate protein loading buffer and incubated at 95°C for 5 min.
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2

Fabrication of HUVEC-Coated Fibrin Beads

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HUVECs were mixed with Cytodex 3 microcarriers (Amersham 17-0485-01) at a concentration of 400 HUVECs per bead in 1 mL of growth media. Beads with cells were shaken gently every 20 minutes for 4 hours at 37°C and 5% CO2. After incubating, beads with cells were transferred to a 25-cm2 tissue culture flask and left overnight in 5 mL of media supplemented with rIGFBP-1 (500 ng/mL) at 37°C and 5% CO2. The following day, beads with cells were washed 3 times with 1 mL of media and resuspended at a concentration of 200 cell-coated beads/mL in 2 mg/mL of fibrinogen (Sigma-Aldrich F-8630) with 0.15 units/mL of aprotinin (Sigma-Aldrich A-1153), 5 ng/mL VEGF, and 5 ng/mL FGF. A total of 500 µL of fibrinogen/bead solution was added to 0.625 units of thrombin (Sigma-Aldrich T-3399) in 1 well of a 24-well tissue culture plate. Fibrinogen/bead solution was allowed to clot for 5 minutes at room temperature and then at 37°C and 5% CO2 for 20 minutes. One milliliter of media supplemented with rIGFBP-1 (500 ng/mL) was then added and incubation continued at 37°C and 5% CO2. Beads were imaged 24 hours later [40 ].
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3

Engineered Heart Tissue Generation

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The EHTs were made as previously described by Ribeiro et al35 using the commercially available EHT platform provided by River Biomedics.18 Shortly, three tissues per well (12‐well plate format) were made using hiPSC‐CMs and hESC‐CMs, with a 3% HCF. First, the cells were thawed and resuspended in MM with 4.5 mM glucose and 5 mM sodium dl‐lactate. Then, 3% of HCF were mixed to a fixed amount of CMs (8 × 105 cells for one well of the 12‐well plate) and each condition was resuspended to a final concentration of 16.8 × 106 cells/mL. After that, cells were mixed with an extracellular matrix (ECM) mixture consisting of 2× MM medium, fibrinogen (final concentration 2 mg/mL, Sigma‐Aldrich F8630), Matrigel (final concentration 1 mg/mL), and aprotinin (final concentration 2.5 μg/mL, Sigma‐Aldrich, A1153). Finally, 0.6 U/mL of thrombin (Sigma, T7513) was added to the mix and 15 μL were used to make each one of the three tissues per well.35 The first refreshment was done after 24 h and after that every 2 or 3 days.
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4

Isolation and Stimulation of Mouse Hepatocytes

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Isolation of mouse hepatocytes was based on a previously published protocol (36 ). Male mice (8-10 weeks of age) were used in this study. After overnight incubation, isolated hepatocytes were incubated in Krebs-Henseleit bicarbonate (KRB) buffer (pH 7.4, 1 × KRB buffer, HEPES (15630-056, Gibco), NaOH (25080-060, Gibco), 2mM glucose) (control) and stimulated with either BHB (either 1 or 10 mM) (A1153, Sigma Aldrich), trichostatin A (TSA) (10nM or 100nM) (Sigma Aldrich, Cat. no. 58880-19-6), TMP269 (0.1uM, 1uM or 10uM) (Selleckchem Cat. no. S7324) or AR319277 (AR277) (10nM, 100nM or 1uM) (Arena Pharmaceuticals, CA, USA) in duplicates, triplicates, or quadruplicates for 4 hours at 37 °C with 5% CO2. After stimulation, media was removed and cells were lysed in RLT buffer:beta mercaptoethanol (100:1) (74034, Qiagen, Germany). All lysates were kept at −80 °C until analysis. Mice were normalized independently and collected in the same analysis; n is the number of biologically independent samples for which data were averaged from duplicate, triplicate, or quadruplicate measurements.
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5

Generation of Fibrin-based Engineered Heart Tissues

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Fibrin-based EHTs were generated as described previously.33 (link) Each EHT
contained 1.5–2.0 × 106 hiPSC-derived cardiomyocytes, differentiated
for 16 days. Briefly, casting molds were generated with Teflon spacers (EHT
technologies #C0002) placed in 2% liquid agarose molds (Millipore #121853) in
24-well plates. Agarose was allowed to solidify for 15 min and silicone racks
containing two posts per well (EHT Technologies; C0001) were positioned in the
casting molds. The cell-hydrogel suspension consisting of cardiomyocytes,
fibrinogen, thrombin and Matrigel was then poured around the posts and incubated
at 37°C/5% CO2 for 1.5–2 h to allow polymerization. EHTs adhered to
the silicon racks and were transferred to culture medium containing DMEM/F12 low
glucose (Sigma Aldrich D5546), 5% heat inactivated horse serum (ThermoFisher
#26050088); 1% penicillin/streptomycin (ThermoFisher #15070-063); 0.1% (w/v)
Aprotinin (Sigma Aldrich A1153) and 0.1% Insulin (Sigma Aldrich I9278). Medium
was replenished thrice a week. EHTs demonstrated regular contractions 5–7 days
after fabrication.
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6

Engineered Vascularized Intestinal Organoids

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Before cell culture, the fully assembled device was first sterilized by exposing it to ultraviolet light (Electro-lite ELC-500) for at least 30 min. To engineer vascularized organoids in OCTOPUS-EVO, we prepared 20 μl of cell suspension solution containing fibrinogen (5 mg ml−1; F8630, Sigma), thrombin (1 U ml−1; T7513, Sigma), aprotinin (0.15 U ml−1; A1153, Sigma), human intestinal stem cells, primary human umbilical vein endothelial cells (HUVECs) (5 × 106 cells per ml) and primary normal human lung fibroblasts (1 × 106 cells per ml), and injected it into the open cell culture chamber through its inlet access port. The device was then left in a cell culture incubator at 37 °C and 5% CO2 for 30 min. Upon gelation, IntestiCult media mixed with EGM-2 endothelial media were added to the medium reservoirs and the side microchannels.
Following the formation of a cell-laden hydrogel construct, the side microchannels were incubated with an FN solution (25 μg ml−1 in PBS; 356008, Corning) for 2 h at 37 °C to create an ECM coating on the channel surface. Then, the channels were washed once with IntestiCult/EGM-2, and 10 μl of HUVEC suspension (1 × 107 cells per ml) was introduced into both channels. The seeded cells were allowed to attach to the channel surface over a period of 1 h. Upon 1 h of incubation, pre-warmed medium was added to each medium reservoir.
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7

Generation of Fibrin-based Human EHTs

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Fibrin-based human EHTs were generated in agarose casting molds with transparent silicone posts as previously described.50 (link),51 (link) In brief, casting molds were generated in a 24-well plate using 2% agarose in PBS and spacers. Transparent silicone posts were placed into the casting molds and the master mix (1 million hiPSC cardiomyocytes, 5.6 µL 2× DMEM, 0.1% 10 mM Y-27632); before use, 2.5 µL/EHT fibrinogen (200 mg/mL in NaCl 0.9%; F4753 [Sigma]) and NKM added up to 97 µL/EHT (DMEM [F0415; Biochrom], 1% Pen/Strep, 10% horse serum [26050; Gibco], 1% of 200 mM glutamine [Gibco]) was prepared. For each EHT, 97 µL master mix was first pipetted into 3 µL of 3 U/mL thrombin (BP11101104; Biopur) and then into the agarose molds around the posts. The plate was then incubated at 37°C, 7% CO2, 40% O2, and 98% relative humidity for 1.5 to 2 hours until the fibrin was polymerized and EHTs were transferred into a new 24-well plate containing prewarmed culture medium (DMEM [Sigma], 1% Pen/Strep, 10% horse serum, 10 μg/mL insulin, 33 μg/mL aprotinin [A1153; Sigma]). The culture medium was changed 3 times each week and supplemented with 200 µM tranexamic acid (857653-50G; Sigma) for matrix stabilization. After 7 to 10 days, a beating pattern could be observed macroscopically, allowing video-optical contraction analysis.
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8

Protein Expression Analysis by Western Blot

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Western blot analyses were performed as previously described (35). Briefly, cells were washed 3 times with PBS and lysed at 4°C in RIPA buffer (P0013C, Beyotime Biotechnology) containing phenylmethylsulfonyl fluoride (0.5 mM, ST506, Beyotime Biotechnology), aprotinin (5 μg/mL, A1153, Sigma-Aldrich), and leupeptin (5 μg/mL, L2884, Sigma-Aldrich). Approximately 50 μg of protein was separated by 8% SDS-PAGE and blotted onto a nitrocellulose membrane. The membrane was blocked with 5% skim milk in Tris-buffered saline with 0.05% Tween 20 for 1 h at room temperature and then incubated overnight at 4°C with primary antibodies at the following dilutions: p65 (1:1000 dilution; 6956), p38 (1:1000 dilution; 14,451), JNK (1:1000 dilution; 9252), p-p38 (1:1000 dilution; 9215s), p-JNK (1:1000 dilution; 9251), p-ERK1/2 (1:1000 dilution; 4370T) and β-actin (1:1000 dilution; 4970, Cell Signaling Technology). The blots were then incubated for 1 h at room temperature with the appropriate secondary antibodies conjugated to horseradish peroxidase (1:2000 dilution; ZSGB-Bio). Proteins were visualized using an enhanced chemiluminescent detection reagent (6683, Signaling Technology). Densitometric analysis was performed with Image-J software, and target protein expression was normalized to β-actin expression.
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9

HUVEC Sprouting Angiogenesis Assay

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According to the manufacturer's protocol, bead solution (Sigma-Aldrich, C3275-10G), fibrinogen (Sigma-Aldrich, F8630-1G), aprotinin (Sigma-Aldrich, A1153), and thrombin stock solutions (Sigma-Aldrich, T4648-1KU) were prepared separately. HUVECs were trypsinized and mixed with bead solution by inverting the tube every 20 min for 4 h and cultured overnight. On day 2, beads coated with HUVECs were transferred to a conical tube, washed and dispersed in a fibrinogen/aprotinin mixture, and added to a pre-coated 24-well plate with thrombin solution. We randomly captured six fields per sample on day 7 and calculated the average bead sprouting length per sample using the Sprout Morphology plugin in Fiji (ImageJ).
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10

In vitro angiogenesis assay using fibrin gel beads

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In vitro fibrin gel beads assay was carried out as previously described [57 ]. In brief, HUVECs transfected with either control siRNA or DIXDC1 siRNA were trypsinized and 1 × 106 HUVECs were coated on approximately 2500 Cytodex-3 beads (Amersham Biosciences, Catalog 17-0485-01) overnight at 37 °C. On the following day, the coated beads were washed 3 times with EGM-2 (Lonza, Catalog CC-3162) and 2.0 mg/ml fibrinogen type I (Sigma-Aldrich, Catalog F-8630) solution containing 0.15 U/ml aprotinin (Sigma-Aldrich, Catalog A-1153) at concentration of 500 beads/ml was added. Next, 0.625 U/ml Thrombin (Sigma-Aldrich, Catalog T-3399) was added to a 24-well plate and fibrinogen solution with beads was added to each well by pipetting 4–5 times. After clot formation, 20,000 fibroblasts in EGM-2 were added to each well. Pictures were taken every day for a week with a light microscope at a magnification of × 200. The number and lengths of the sprouts were analyzed using ImageJ.
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