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21 protocols using collagen 1

1

Immunostaining and Imaging of Tumor-Infiltrating T Cells

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Tumor cryo-sections (5 μm) and hydrogels containing T cells were fixed using 4% PFA prior to permeabilization, blocking, and staining with Phalloidin-488 (Life Tech) and anti-myosin light chain kinase (Abcam) for the hydrogels or collagen I (Novus Biologicals) CD8 (Novus Biologicals), and CD3 (Proteintech) for tumors, and DAPI nuclear stain. Secondary anti-Rabbit Alexafluor488 and Alexafluor594 (Thermo Fisher Scientific) as well as ant-rat NL637 (R&D) were used for staining. For immunohistochemical analysis, tissues were dehydrated through graded ethanols followed by antigen retrieval and detection using the ImmPRESS HRP anti-rabbit IgG polymer detection kit (Vector Laboratories). Images were captured using the Zeiss 780 confocal microscope. 3D circularity was calculated using surfaces in Imaris 8.2.1. Second harmonic generation was performed on a Zeiss AxioExaminer microscope equipped with a Coherent Chameleon Visionll multi-photon laser. Number and size of projections were counted in cell tracking videos using FIJI.
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2

Myocardial Collagen I Quantification

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Noninfarcted myocardial tissue (30 mg) was homogenized with 1 mL of modified RIPA buffer in the presence of protease and phosphatase inhibitors. Equal amounts of protein (30 μg) were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and electrophoretically transferred to nitrocellulose membranes (Amersham Biosciences). Western blot analysis was performed as per manufacturer's protocol with collagen- I (Novus Biologicals, Littleton, CO) and pan-actin antibody (NeoMarkers, Fremont, CA) and then visualized by enhanced chemiluminescence (Thermo Scientific, Rockford, IL). Band intensity was analyzed using ImageJ software (U.S. National Institutes of Health, Bethesda, MD). Pan-actin antibody was used to measure endogenous controls proteins.
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3

Immunofluorescence Profiling of TGF-β Pathway

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Immunofluorescence of fixed paraffin-embedded tissue sections, fixed cells and frozen sections of fixed cultures in Matrigel was performed using the following antibodies at the indicated concentrations: phospho-SMAD2 (Cell Signaling #3101, 1:50), phospho-SMAD3 (Cell Signaling #9520, 1:50), TGF-β1 (Santa Cruz Biotechnology #sc146, 1:50), pan-cytokeratin (Sigma-Aldrich #C2562, 1:500), vimentin (Sigma #V5255, 1:200), human specific vimentin [V9] (Abcam #ab8069, 1:100), fibroblast activation protein (FAP) alpha (Abcam #ab53066, 1:200), alpha-smooth muscle actin (α-SMA) Cy3 conjugate (Sigma #C6198, 1:250), collagen I (Novus Biologicals #NB100-92161, 1:100), cleaved caspase-3 (Cell Signaling #9661, 1:200), phospho-histone H3 (Cell Signaling #9701, 1:100), goat anti-mouse IgM μ chain Cy3 conjugate (Jackson ImmunoResearch #115-166-075, 1:200), Alexa 488 anti-mouse, 488 anti-rabbit, 568 anti-rabbit, 647 anti-rabbit secondary antibodies (Molecular Probes A24920, A24922, A21069, A21245, 1:500). Nuclei were stained with DAPI (Vector Laboratories H-1200). Confocal microscopy was performed on a Nikon C1si confocal microscope.
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4

Western Blot Analysis of Osteogenic Markers

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Cells were lysed in a radio-immunoprecipitation assay buffer with protease inhibitors (PIA32963, Thermo Fisher Scientific) and phosphatase inhibitors (2,006,643, Calbiochem, Billerica, MA, USA). After cell lysis, proteins were fractionated by 10%–15% SDS gels and electro-transferred to polyvinylidene difluoride transfer membranes (IPVH00010, Millipore, Billerica, MA, USA). After blocking 1 h with a blocking buffer (1,706,404, Bio-Rad, Hercules, CA, USA), the membrane was incubated overnight with primary antibodies and then with secondary antibodies conjugated with horseradish peroxidase for 45 min (7074 S/7076 S, Cell Signaling, Danvers, MA, USA). We used antibodies against Lrp5, Runx 2, Snail, MSN, Calr, cleaved-caspase 3, caspase 3, CD91, p-CREB, and CREB (Cell Signaling), c-fos, NFATc1, Cathepsin K (Santa Cruz Biotechnology, Dallas, TX, USA), CD47 (Thermo Fisher Scientific), Collagen I (Novus Biologicals, CO, USA), Osteocalcin (abcam, Boston, MA, USA), and β-actin as a control (A5441, Sigma). The protein level was determined using a SuperSignal west femto maximum sensitivity substrate (PI34096, Thermo Fisher Scientific), and a luminescent image analyzer (LAS-3000, Fuji Film, Tokyo, Japan) was used to quantify signal intensities.41 (link) The levels of Calr and MSN in CW008-treated CM were determined using the ELISA kits (MBS263181 and MBS2709503; MyBioSource).
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5

Evaluating ER Stress Markers in TM Cells

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Antibodies were purchased from the following sources: fibronectin (catalog # Ab2413, Abcam, Cambridge, MA, USA), KDEL (catalog # Ab12223, Abcam, Cambridge, MA, USA), collagen I (catalog # NB600-408, Novus Biologicals, Littleton, CO, USA), ATF-4 (catalog # SC-200, Santa Cruz Biotechnology, Dallas, TX, USA)), CHOP (catalog # 13172, Novus Biologicals, Littleton, CO, USA), Alexa Fluor® phalloiden stain (catalog # A12379, Life technologies, Grand Island, NY, USA), GRP78 (catalog # ab21685, Abcam, Cambridge, MA, USA), α-smooth muscle actin (catalog #ab7817, Abcam, Cambridge, MA, USA) and GAPDH (catalog # 3683, Cell signaling technology, Danvers, MA, USA). Both KDEL and GRP78 were used as ER stress markers. Mouse KDEL antibody was primarily used for immunostaining since it works well on fixed cells and formalin fixed human tissues and can be combined with rabbit fibronectin or collagen I antibody. We observed that KDEL primarily recognizes GRP78 and GRP94 in Western blot analysis of human TM cells. Therefore, we used KDEL as an ER stress marker. Rabbit GRP78 antibody was used along with mouse puromycin antibody for immunostaining. For Western blot analysis of ER stress in cells, we primarily utilized the GRP78 antibody.
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6

Histopathological Analysis of Xenografted Myometrial Tissues

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Histological analyses were performed routinely for all human myometrial/fibroid-like tissues generated in the kidneys of the mice. Samples were fixed in 10% buffered formaldehyde for 24h, dehydrated in an ethanol series, cleared in xylene and embedded in paraffin. Sections of 4 µm were obtained from the blocks for staining with haematoxylin and eosin (H&E, Sigma-Aldrich). Prussian blue staining (Sigma-Aldrich) was used to detect labeled iron particles in the cells, in accordance with the manufacturer’s instructions. Immunohistochemistry analyses of these samples were conducted for several antibodies i.e. Ki67 (Santa Cruz, Dallas), human progesterone receptor (Thermo Scientific, Fremont, CA), actin alpha 2 smooth muscle antibody (NovusBio, Littleton, CO) and collagen I (NovusBio, Littleton, CO). Finally, immunolocalization of specific cell populations were analyzed, visualized and photographed using the EVOS® XL Core Cell Imaging System (Life Technologies, NY).
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7

Protein Expression Analysis in Tissues

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The tissue was homogenized in cold lysis buffer (Beyotime Biotechnology Co., Haimen, Jiangsu, China) and centrifuged at 13,200 rpm for 15 min at 4 °C. The supernatant containing total protein was quantified by an Enhanced BCA Protein Assay Kit (Beyotime Biotechnology Co.). The samples were separated on a 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel (loading 30 μg of total protein in each lane) and were transferred to a polyvinylidene fluoride membrane (Millipore, Bedford, MA). The membrane was blocked with 5% skimmed milk overnight at 4 °C and then incubated with primary antibodies recognizing Gapdh (mouse monoclonal, 1:1000; BioTNT), collagen I(rabbit polyclonal, 1:1000; Novus), collagen III (mouse monoclonal, 1:1000; Abcam), MMP1 (rabbit polyclonal, 1:500; Invitrogen), MMP2(mouse monoclonal, 1:1000; Abcam), MMP9(rabbit monoclonal, 1:1000; Abcam), and TIMP1(mouse polyclonal, 1:200; Invitrogen). The primary antibodies were incubated together at 22 °C for 2 h. Then, the membrane was incubated with horseradish peroxidase-conjugated anti-mouse (1:5000; Abcam) or goat anti-rabbit (1:5000; Abcam) secondary antibodies.
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8

Protein Expression Analysis in Atrial Samples

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Total proteins were extracted from atrial samples using radioimmunoprecipitation assay buffer plus phosphoprotease inhibitors (ASPEN Biotechnology, China). The same amount (40 μg) of extracted protein was separated by electrophoresis in SDS-PAGE gels and transferred to polyvinylidene difluoride membranes. Membranes were blocked with 5% blocking buffer for 1 h at room temperature and incubated overnight at 4°C with primary antibodies against CD63 (Biorbyt, England), CD81 (Abcam, USA), TSG101 (Sigma-Aldrich, Germany), Rab27a (Sanying Biotechnology, China), collagen I (Novusbio, USA), collagen III (Abcam, USA), matrix metalloproteinase (MMP)-2 (Bioss, USA), MMP-9 (Bioss, USA), tissue inhibitor of metalloproteinase 3(TIMP3) (Lsbio, USA), and transforming growth factor-β1 (TGF-β1) (Sanying Biotechnology, China). The membranes were washed three times with tris-buffered saline with 0.1% Tween® 20 and then incubated with horseradish peroxidase-conjugated anti-rabbit secondary antibody (ASPEN Biotechnology, China) for 1 h at room temperature. The blots were exposed with an ECL Detection Kit (ASPEN Biotechnology, China). The expression levels of the proteins were determined and normalized to the relative intensity of GAPDH using image analyzer software (AlphaEase FC, USA).
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9

Antibody Sourcing for ER Stress Pathway

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Antibodies were purchased from the following sources; fibronectin (catalog # Ab2413, Abcam), KDEL (catalog # Ab12223, Abcam), collagen I (catalog # NB600-408, Novus Biologicals), ATF4 (catalog # SC-200, Santa Cruz Biotechnology), CHOP (catalog # 13172, Novus Biologicals), GRP78 (catalog # ab21685, Abcam), GRP94 (catalog # 11402, Santa Cruz Biotechnology), Caspase 3 (catalog # 9662, Cell signaling technology), Cleaved PARP (catalog # 9541, Cell signaling technology), puromycin (catalog #A11138, Gibco, Life Technology), RBPMS (catalog # 118619, Gene Tex), cleaved Caspase 3 (catalog # 9661, Cell signaling technology), GAPDH (catalog # 3683, Cell signaling technology), and β-Actin (catalog # 4970, Cell signaling technology, Danvers, MA, USA). For immunoprecipitation studies, a different CHOP (sc-7351, Santa Cruz Biotechnology) was used. All adenoviral vectors used in this study were obtained from ViraQuest Inc. (North Liberty, IA, USA). Lentiviral vectors expressing ATF4 or CHOP were obtained from VectorBuilder Inc.
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10

Reagents for Cell Culture Experiments

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Antibodies and reagents were purchased from the following sources: fibronectin (catalog # Ab2413, Abcam, Cambridge, MA, USA), KDEL (catalog # NBP1–97469, Novus Biologicals, Littleton, CO, USA), collagen I (catalog # NB600–408, Novus Biologicals, Littleton, CO, USA), laminin (catalog # NB300–144, Novus Biologicals, Littleton, CO, USA), CHOP (catalog # 13172, Novus Biologicals, Littleton, CO, USA), and GAPDH (catalog # 3683, Cell signaling technology, Danvers, MA, USA), dexamethasone-21-acetate (Spectrum Chemicals, New Brunswick, NJ, USA), minocycline hydrochloride (Enzo Life Sciences, Inc., New York, NY, USA), and PBA (Scandinavian formulas, PA, USA).
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