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16 protocols using ab765p

1

Immunostaining and Microscopy Analysis of Bone Sections

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Immunostaining was conducted on 6 or 10 μm frozen cryostat sections of the undecalcified head, according to the method of Kawamoto (Leica, CM3050S)28 (link). Sections were blocked with 1% BSA/PBS and then incubated with goat anti-mouse MMP-9 polyclonal antibody (AF909, R&D) or rabbit anti-mouse collagen type I polyclonal antibody (AB765P, Merck Millipore) overnight at 4 °C, followed by donkey anti-goat Alexa Fluor 647 or donkey anti-rabbit Alexa Fluor 488 secondary antibodies (Thermo Fisher Scientific), respectively. Osteocalcin was detected on demineralized paraffin sections that had been deparaffinized, treated with 1% H2O2 in methanol, blocked with 1% BSA/PBS, and incubated with rabbit anti-osteocalcin polyclonal antibody (ALX-210-333, Enzo). Corresponding nonimmune rabbit IgG served as a control. Horse anti-rabbit IgG-HRP secondary antibody (MP-7401, VECTOR) was detected with a diaminobenzidine (DAB) HRP substrate (VECTOR). Sections were observed under a confocal laser microscope (LSM-710, Zeiss; FV3000, Olympus) or a light microscope (BX53, Olympus).
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2

Collagen Type I Detection in Liver Tissue

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Frozen liver tissue was homogenized in 50 mM HEPES, 150 mM NaCl, 10% Glycerol, 0.1% Tween 20, 7.5 mM EDTA, and 7.5 mM MgCl2*6H2O. Protein content was determined using a DC Protein Assay kit (Bio-Rad Laboratories, Inc., Hercules, CA), and homogenates were diluted to 5 mg/ml. To reduce nonspecific binding of the anti-collagen type I antibody, liver homogenates were digested with pepsin prior to electrophoresis. To accomplish this, pepsin (Powder 1:3000; VWR, Radnor, PA) was diluted to 2 mg/ml in 2 N HCl, and 10 μl of this pepsin preparation was added to 100 μl of liver homogenate (500 μg protein). This sample was incubated for 2 hours at 20°C and then neutralized with 10 μl of 2 N NaOH and resuspended in SDS loading buffer (100 mM Tris-Cl pH 6.8, 4% SDS, 0.2% bromophenol blue and 20% glycerol) containing 400 mM β-mercaptoethanol. pepsin-digested samples (6 μl/lane) were resolved on an 8% SDS-polyacrylamide gel, transferred to nitrocellulose, and incubated with an anti-collagen type I antibody (#AB765P, EMD Millipore, Hayward, CA). Undigested liver homogenates (25 μg protein/lane) were probed with an anti-actin antibody (Santa Cruz Biotech, Dallas, TX) and served as a quasi-loading control. Blots were subsequently incubated with species-specific, HRP-conjugated secondary antibodies, and bands were visualized with Pierce ECL Western Blotting Substrate (Thermo Scientific).
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3

Aortic Extracellular Matrix Immunohistochemistry

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Ten-micrometer cross sections of the murine aorta prepared in Tissue Tek® O.C.T frozen blocks were fixed with 4% paraformaldehyde (PFA) for 10 min at room temperature (RT). Sections were incubated with blocking buffer containing 5% normal goat serum in PBS and permeabilized with 0.1% Triton-X for 30 min at RT. Primary antibodies used were: anti-mouse collagen type I antibody (1:100; AB765P, Merck Millipore), rabbit anti-mouse versican (GAG beta domain) polyclonal antibody (1:200; AB1033, Chemicon international), rabbit anti-aggrecan polyclonal antibody (1:200; AB1031, Chemicon international). All antibodies were diluted in 5% BSA with 0.1% Triton-X in PBS and incubated overnight at 4°C. Secondary antibodies (Alexa 546 mouse or rabbit) were incubated for 1 hr at RT. Vectashield with DAPI (Vector Laboratories) was used to mount the slides and samples were analyzed with a laser scanning microscope LSM 710 (Zeiss GmbH). At least three mice per genotype were used for analysis.
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4

Histological Evaluation of Excisional Wound Healing

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6 mm excisional wounds were generated as previously described (73 (link)). After 10 days, wounds were prepared for histological evaluation using the following procedure. Excised wounds were fixed by placing them in 4% paraformaldehyde for 24 hours, following fixation the wound was placed in a cassette that allowed for the dehydration of the tissue, followed by clearing of the tissue using xylene (Fisher brand), and finally imbedding the tissue in paraffin wax. Sections (5 μm) of the paraffin block were placed on clear glass slides for further treatment and staining. Staining and probing for Masson’s trichrome, Picrosirius red, Hsp47 (rabbit polyclonal anti-Hsp47 (Abcam ab109117); 1:4000), rabbit polyclonal anti-Fibroblast activating protein (Abcam ab53066); 1:200), and mouse polyclonal anti-type I collagen (Millipore AB765P); 1:1000) were performed by Histo-Scientific Research Laboratories Inc.
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5

Immunofluorescent Analysis of Bone Collagens

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Long bones were fixed in freshly made 4% paraformaldehyde/PBS (pH 7.2) at 4 °C overnight and changed to 14% EDTA for 2–7 days at 4 °C. Decalcified bones were immersed in 30% sucrose/PBS for 1 h before embedded in OCT compound. Then, 8–12 µm sections were prepared using CryoStar NX70 Cryostat. Hyaluronidase treatment (2 mg/ml in PBS [pH 5.0]) was used for antigen retrieval, 20’ for embryonic or 30’ for postnatal tissue at 37 °C. Primary antibodies used were anti-mouse collagen type I (Millipore AB765P, 1:50) and anti-Collagen X antibody (ab58632, 1:200). Secondary antibodies were Alexa fluor 488 goat anti-rabbit IgG and Alexa fluor 488 goat anti-mouse IgG (Molecular probes). IF sections were mounted with Prolong Gold antifade reagent with DAPI (Invitrogen P36931).
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6

Investigating TGF-β Signaling Pathways

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Recombinant mouse TGF-β protein (7666-MB) was purchased from R&D Systems (Minneapolis, MN). Angiotensin II (AngII) (CSN10313) was purchased from CSNpharm (Chicago, IL). Antibodies against α-smooth muscle actin (α-SMA) (ab5694, for immunoblot analysis), phospho-SMAD3 (SMAD family member 3) (ab52093), and KDM5B (ab181089, for immunofluorescence analysis) were obtained from Abcam (Cambridge, UK). Antibodies against collagen type I (AB765p) were obtained from Millipore (Billerica, MA). Antibodies against α-SMA (5228, for immunofluorescence and immunohistochemistry) were obtained from Sigma‒Aldrich (Darmstadt, Germany). Antibodies against collagen type III (NB600-594) were obtained from Novus Biologicals (Littleton, CO). Antibodies against phospho-SMAD2 (SMAD family member 2) (3108), SMAD2 (5339), SMAD3 (9523), phospho-ERK (extracellular signal-regulated MAP kinase) (9106), ERK (4696), phospho-JNK (c-Jun N-terminal kinase) (4668), JNK (9252), phospho-p38 (4511), p38 (9212), phospho-p65 (3033 S), p65 (8242), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (5174) and ATF3 (18665) were obtained from Cell Signaling Technology (Danvers, MA). Antibodies against KDM5B (A301-813A, for immunoblot analysis) were obtained from Bethyl Laboratories (Montgomery, TX).
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7

Immunohistochemistry and Immunofluorescence for Bone Tissue

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Bones fixed in 4% paraformaldehyde in PBS (pH 7.4) overnight were decalcified and embedded for CryoJane frozen sections as previously described [39] (link). Sections were treated with hyaluronidase (Sigma, H4272, 2 mg/ml in PBS [pH 5.0]) at 37°C for 20 minutes for embryonic samples or 30 minutes for postnatal samples and incubated with anti-EGFP (Invitrogen A11122) at room temperature for 1 hour or with anti-mouse collagen type I (Millipore AB765P) at 4°C overnight. For IHC, the sections were then incubated with HRP polymer conjugates (Invitrogen 87-9263) and developed with a Vectastain ABC kit (Vector PK-4000). For IF, the sections were then incubated with anti-rabbit Alexa Fluor 555 (Invitrogen A21428). For anti-EGFP and anti-col1a1 double IF, after incubation with anti-EGFP and anti-rabbit Alexa Fluor 555, the sections were incubated with Alexa Fluor 488-labeled (Invitrogen A10468) anti-mouse collagen type I at 4°C overnight. For anti-EGFP and anti-Ocn double IF, after incubation with anti-EGFP (abcam ab13970) and anti-Ocn (A93876), the sections were incubated with anti-chicken Alexa 488 (abcam) and anti-rabbit Alexa Fluor 555 (Invitrogen A21428). All IF sections were mounted with Prolong Gold antifade reagent with DAPI (Invitrogen P36931).
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8

Tumor Extracellular Protein Enrichment

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Samples described above were mechanically disrupted using a Bullet Blender (Next Advance). Tumor lysates were then subjected to incubation in a series of buffer (CNCS Compartmental Protein Extraction Kit, Millipore) resulting in the extraction of soluble and mostly intracellular components and the enrichment for insoluble extracellular proteins (for more details, see 63 (link),64 (link)). The decellularization efficiency was monitored by western blot analysis monitoring the depletion of collagen I (Millipore, AB765P), actin (rabbit polyclonal antibody 14–4 generated in the Hynes lab at MIT), and histone H4 (Abcam, ab52178) across the 4 sequential extraction steps (see Supplementary Figure 2B, lanes 2 to 5).
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9

Tumor Extracellular Protein Enrichment

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Samples described above were mechanically disrupted using a Bullet Blender (Next Advance). Tumor lysates were then subjected to incubation in a series of buffer (CNCS Compartmental Protein Extraction Kit, Millipore) resulting in the extraction of soluble and mostly intracellular components and the enrichment for insoluble extracellular proteins (for more details, see 63 (link),64 (link)). The decellularization efficiency was monitored by western blot analysis monitoring the depletion of collagen I (Millipore, AB765P), actin (rabbit polyclonal antibody 14–4 generated in the Hynes lab at MIT), and histone H4 (Abcam, ab52178) across the 4 sequential extraction steps (see Supplementary Figure 2B, lanes 2 to 5).
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10

Quantifying Collagen Deposition in Mouse Liver

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After euthanasia, mouse livers were fixed in 10% buffered formalin for 24 hours at room temperature, transferred to Ethanol 70°, and then embedded in paraffin. Tissues were sectioned at 5-μm thickness and subjected to collagen immunostaining (primary antibody: anti-mouse collagen type I, AB765P; Millipore; secondary antibody: anti-rabbit IgG cy5) with DNA staining using Hoechst. Observations were performed with a Zeiss LSM 700 confocal microscope (Zeiss Microscopy, Peabody, MA) with Zen 2011 software version 7.1. This software was used to determine the percentage of veins presenting with collagen accumulation, determined through the examination of 10 veins per slide. Fibrosis also was evaluated using Masson trichrome (kit ab150686; Abcam, Cambridge, MA) and Sirius red (kit ab15068; Abcam) staining, performed on 5-μm thickness paraffin liver sections and following the manufacturer's instructions. Photoshop CS6 edition was used to quantify the red staining specifically, using the same settings and threshold for all of the slides.
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