MATERIALS AND METHODS Animals and surgery All animal procedures were conducted according to the ‘‘Guide for the Care and Use of Laboratory Animals’’ (NIH Notice Number: NOT-OD-12-020) and were approved by the Institutional Animal Care and Use Committee at the University of Mississippi Medical Center. Male and female 3- to 7-month-old C57BL6/J wild type (WT) and MMP-9 null mice were used in this study. Both WT and MMP-9 null colonies were bred in-house as homozygous colonies and were maintained in the same room since birth. The MMP-9 null mice were generated in Zena Werb’s laboratory and backcrossed by Lynn Matrisian’s laboratory and are on the C57BL/6J background (1,2). Animals were housed at constant temperature (22±2°C) on a 12 h light/dark cycle, fed standard laboratory mice chow ad libitum, and had free access to tap water. For the C-1158/59 fragment and MMP-9 time-courses, 5 time points were studied for each genotype: control (no MI = day 0) and 1, 3, 5, and 7 post-MI. MI was induced by permanent ligation of the left anterior descending coronary artery, as described previously (3). For the in vivo treatment studies only WT mice were used. Animals were randomly divided into 2 groups by an investigator blinded to treatment: MI with vehicle control (saline), and MI with p1158/59 treatment. At 3 h post-MI, infarction was confirmed by electrocardiography and echocardiography and osmotic pumps with p1158/59 (Aztec 1007D, 950 μg/day/kg body weight) or saline were inserted subcutaneously and animals sacrificed 7 days post-MI. A minimal of 6 surviving animals were used per group and time point for all in vivo studies. 1 Echocardiography and necropsy evaluations Echocardiograms were acquired under spontaneous respiration with 1–2% isoflurane in an oxygen mix. Images were acquired with the use of a Vevo 2100™ High-Resolution In Vivo Imaging System (Visual Sonics, Toronto, Canada), at heart rates >400 bpm. Electrocardiogram and heart rate were monitored throughout the imaging procedure. Echocardiographic measurements were taken from the two-dimensional parasternal long-axis and short-axis (mmode) recordings of the LV. For each parameter, 3 images from consecutive cardiac cycles were measured and averaged. The spherical index was calculated as the end-diastolic volume divided by the volume of a sphere with a diameter equal to the left ventricle (LV) end-diastolic dimension. One reader analyzed all of the echocardiograms in a blinded manner. Values ±2 standard deviations of mean were considered outliers and all echocardiography parameters measured post-MI were normalized to LV mass index (4,5). At necropsy, mice were anesthetized with 1.5-2.5% isoflurane in an oxygen mix. Heparin (4 U heparin/g body weight) was injected intraperitoneally, and after 5 min blood was collected from the carotid artery. The plasma was isolated by centrifugation and stored with 1x protease inhibitors (Roche Diagnostics, Indianapolis, IN) at -80°C. After blood collection, the heart was excised and flushed with cardioplegic solution (6). The LV and right ventricle were separated and weighed individually. The LV was sectioned into 3 transverse sections and stained with 1% 2, 3, 5-triphenyltetrazolium chloride (Sigma, St Louis, MO) for infarct area determination. The infarcted LV (LVI) and remote (LVC) regions of the apex and base segments were separated under a microscope, individually snap frozen, and stored at −80°C for biochemical analysis. The LV middle-section was fixed in 10% zinc formalin, processed in paraffin, and sectioned at 5 µm for immunohistochemistry studies. 2 Identification of the novel collagen/MMP-9 cleavage site A human recombinant collagen Iα1 (60220CL, R&D) that contains the collagen Iα1 Nterminal, 60 G-X-Y repeats without the common MMP-9 cleavage site, and the C-terminal (overall residues Gln23-Lys277 + Gly1094-Leu1464) was incubated with MMP-9 catalytic domain (PF040, Calbiochem) in a 1:5 enzyme/substrate ratio. The reaction was performed at 37°C overnight with 1x zymogram buffer (BioRad). Cleavage was inactivated by adding ethylenediaminetetraacetic acid (EDTA, 25 mM final concentration) for 10 min at room temperature. Cleavage products were separated by 1-D SDS-PAGE electrophoresis in a 4-12% Bis-Tris gel and stained with EZBlue™ gel staining reagent (Sigma Aldrich), which is a Coomassie brilliant blue-based dye compatible with MS analysis. New cleavage products were excised from the gel, de-stained and dehydrated, and the proteins digested in situ with trypsin (Promega). The digests were analyzed by capillary HPLC-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) on a Thermo Fisher LTQ Orbitrap Velos mass spectrometer fitted with a New Objective Digital PicoView 550 NanoESI source. On-line HPLC separation of the digests was accomplished with an Eksigent/AB Sciex NanoLC-Ultra 2-D HPLC system: column, PicoFrit™ (New Objective; 75 μm i.d.) packed to 15 cm with C18 adsorbent (Vydac; 218MS 5 μm, 300 Å). Precursor ions were acquired in the Orbitrap in profile mode at 60,000 resolution (m/z 400); data-dependent collision-induced dissociation (CID) spectra of the 6 most intense ions in the precursor scan above a set threshold were acquired sequentially in the linear trap at the same time as the precursor ion scan. Mascot (version 2.3.02; Matrix Science) was used to search the uninterpreted CID spectra against a combination of the mouse subset of the NCBInr database [Mus. (145,083 sequences)] and a database of common contaminants (179 sequences). Methionine oxidation was considered 3 as a variable modification; semitrypsin was specified as the proteolytic enzyme, with 1 missed cleavage allowed. The Mascot data files were combined in Scaffold (Proteome Software; version 3) for a subset search of the CID spectra using X! Tandem, cross correlation of the X! Tandem, Mascot results, determination of protein, and peptide identity probabilities. The thresholds for acceptance of peptide and protein assignments in Scaffold were 95% and 99%, respectively, and minimum of 2 unique peptides. Peptides and antibody design and synthesis We designed a “spanning peptide” (peptide sequence Ac-CGPPGPRGRTGDSGP-NH2) that contains the identified MMP-9/collagen cleavage site (site 1158/59) in the middle of the sequence. This peptide was used to check for MMP cleavage, identify the cleavage site, and for generation of a cleavage-site specific antibody (spanning peptide and antibody synthesized by New England Peptides Inc., Gardner, MA). The antibody was designed against the amino acids downstream of the 1158/59 site and binds to the unique sequence RTGDSPAGC that does not repeat throughout the remaining molecule. An “activity peptide” was designed and synthesized containing the 15 amino acids most downstream of the cleavage site (p1158/59, sequence AcRTGDSGPAGPPGPPG-NH2, CPC Scientific Inc.). Peptide p1158/59 was used for all the in vitro and in vivo activity studies. Tissue, protein, and peptide cleavage assays Protein extracts (5 µg) from the LVI or remote LVC regions from MMP-9 null mice at day 7 post-MI were incubated with MMP-9 as described above. Cleavage assays were previously optimized by testing different enzyme concentrations and several incubation times (enzyme:protein ratios tested 1:2, 1:5, 1:10, and 1:20, from 3 h up to 72 h). Recombinant 4 collagen Iα1 (R&D, 1 µg) was incubated with MMP-2, -8, -11 (all R&D) or MMP-9 (Calbiochem) and cleavage assays were performed for 24 and 48 h. The spanning peptide was dissolved with distilled water to a stock solution concentration of 1 mg/mL. Pro-form MMP-2 and -8 were activated with 1 mM p-aminophenylmercuric acetate (APMA). One microgram of the stock solution peptide was mixed with 1 µL of 10X zymogen buffer and 0.5 µL of active MMP-2, -8, -9, or -11 recombinant protein (100 ng/µL) and made up to 10 µL with distilled water in order to obtain a final 1:20 enzyme:peptide ratio. Negative control had all but no enzyme and blank had all but no protein. Reactions were mixed and incubated at 37°C for 24 h. After incubation, C18 ziptip was used for peptide desalting and 12 ng of the cleaned peptide was analyzed by LC-MS. MS/MS spectra were searched with SEQUEST using Proteome Discoverer (version 1.3; Thermo Fisher) against the mouse RefSeq database (Date 11/03/2013) containing 27186 sequences. For this database search, the precursor mass tolerance and fragment mass tolerance were set at 10 ppm and 0.02 Da, respectively. No protease was specified. A decoy version of the RefSeq mouse database was used to estimate peptide and protein false discovery rate. Analyses were performed on Q Exactive (Thermo Fisher, Waltham, MA) coupled with a 15 cm x 75 µm C18 column (5 µm particles with 100 angstrom pore size). A nano UPLC at 300 nL/min with a 20 min linear acetonitrile gradient (from 5-45% B over 20 min; A = 2% acetonitrile and 0.2% formic acid in water, B = 0.2% formic acid in 90% acetonitrile) was used. A top 2 data dependent MS/MS with exclusion for 25 sec was set. The samples were run with higher-energy C-trap dissociation (HCD) fragmentation at normalized collision energy of 30 and an isolation width of 2 m/z. A lock mass of the polysiloxane peak at 371.1012 was used to 5 correct the mass in MS and MS/MS. Target values in MS were 1e6 ions at a resolution setting of 70,000 and in MS2 1e5 ions at a resolution setting of 17,500. Cardiac fibroblast isolation We used C57BL/6 WT mice 3-6 months old, both male and female (n=10/sex). The hearts were washed in phosphate saline buffer (PBS) and the LV separated from the right ventricle. The LV was minced and digested in a collagenase solution (collagenase type 2 600U/mL and DNase I 60U/mL in HBSS) for 45 min at 37ºC. Cell aggregates were mechanically dissociated by pipetting in between incubation. Cell lysate was centrifuged at 250 xg for 5 min and cells resuspended in fibroblast medium (DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic solution). Cardiac fibroblasts were cultured at 37ºC with 5% CO2 and used up to passage 3. Cytotoxicity, proliferation, and migration assays Cellular cytotoxicity was assessed at passage 2 using the Quanti-Chrom™ LDH cytotoxicity assay kit (Bioassay Systems). In summary, cells were plated in a 24-well plate at a concentration of 1x105 cells/mL until semi-confluence (80% confluence), cells were then starved for 16 h, and stimulated in serum free + p1158/59 (1 nM, 10 nM, 100 nM, and 1 µM) or spanning peptide for 24 h. Cytotoxicity levels were measured according to the manufacturers’ instructions. Cell proliferation was assessed in a similar fashion by use of a colorimetric immunoassay, based on the measurement of bromodeoxyuridine (BrdU) incorporation during DNA synthesis (Roche Ltd.), according to the manufacturer’s instructions. Cells grown in 10% FBS medium were used as a positive control. 6 Wound healing was analyzed using Electric Cell-substrate Impedance Sensing (ECIS, Applied Biophysics). Cells at passage 3 were plated in an ECIS-wound 96-well plate (4.0x104 cells/mL, quadruplicates/condition). Cells were allowed to proliferate until stable impedance values were observed (~48 h). The fibroblast media was removed and replaced with the following conditions: 1) negative control, serum free media; 2) positive control, fibroblast medium; 3) serum free media + 100 nM p1158/59; 4) serum free media + 1 µM p1158/59; and 5) serum free media + 1 µM spanning peptide. Cells were wounded for 10 sec at 1200 uA, 40,000 Htz. After wounding, impedance values were recorded for 48 h and normalized to respective value pre-wound to account for cell number differences. Fibroblast stimulation assays Cardiac fibroblasts were stimulated using the conditions described above for the wound healing assay. Cells were plated in 6-well plates (passage 2, 40,000 cells/mL, duplicates/condition) and allowed to reach semi-confluence. Cells were starved in serum free media for 16 h, after which media was replaced by appropriate stimulus condition for 24 h. Conditioned media and cells were collected separately and frozen at -80°C. HUVEC tube formation assay Human umbilical vein endothelial cells (HUVEC) were purchased from American Type Culture Collection (ATCC, PCS-100-010™) and cultured until passage 3. The angiogenic properties of p1158/59 were tested using the Cultrex In Vitro Angiogenesis Assay kit Tube Formation (R&D). Cells (2 x 104 cells/ well) were incubated with 1 μM p1158/59, spanning peptid, or saline in vascular basal media (ATCC, PCS-100-030™) for 6 h, per manufacturers’ instructions. Tube formation was visualized using an inverted light microscope and 7 representative images were acquired at 10X. All images were identically processed using the photocopy tool. Protein extraction For the in vitro assays, the conditioned media was concentrated for 4 h in a speed vacuum (Savant SPD121P), and all samples were adjusted to a final volume of 200 µL using serum free fibroblast media. For the in vivo studies, the tissue wet weight was recorded and samples homogenized in Protein Extraction Reagent Type 4 (Sigma) and 1x proteinase inhibitors cocktail (PI, Roche) as described previously (7). Protein quantification was performed using a Coomassie Brilliant Blue G-250-based assay (Quick Start™ Bradford Protein Assay, Bio-Rad). All samples were stored at -80°C until use. Immunoblots An aliquot of each sample (10 µg protein) was loaded onto a 4-12% Bis-Tris gel and separated by 1-D SDS-PAGE electrophoresis. Proteins were transferred to a nitrocellulose membrane, which was treated with the MemCode™ Reversible Protein Stain Kit (Pierce, Thermo Scientific), to check for efficiency of protein transfer and for use as a loading control. De-stained membranes were blocked for 1 h at room temperature with 5% non-fat milk (BioRad) and hybridized overnight at 4°C with primary antibodies against the following: collagen I primary antibody (Cedarlane, #CL50141AP-1, 1:2000), MMP-9 primary antibody (Chemicon, #AB804, 1:1000 ), C-1158/59 primary antibody (New England Peptides, 1:500), and biotinylated Griffonia simplicifolia lectin 1 (Vector Laboratories, #B-1105, 1:50). After 1 h incubation with a secondary antibody, positive signaling was detected by chemiluminescent using an ECL substrate (GE Healthcare). Immunoblots were densitometrically analyzed using GE Image Quant 8 LAS4000 luminescent image analyzer (GE Healthcare). The signal intensity of each sample was normalized to the total protein in its respective lane. Gene expression assays RNA extraction from cells and tissue was performed using TRIzol® Reagent and Purelink® RNA (Invitrogen) according to the manufacturer’s instructions. RNA levels were quantified using the NanoDrop ND-1000 Spectrophotometer (Thermo Scientific). Reverse transcription of equal RNA content (500 ng) was performed using the RT² First Strand Kit (Qiagen). Real-Time RT2-PCR gene array for extracellular matrix and adhesion molecules (Qiagen PAMM-013A) was performed to quantify mRNA levels. Forkhead box O3 (Foxo3) and tissue inhibitor of matrix metalloproteinase-4 (Timp4) gene expression were quantified using Taqman primers (Life Technologies, Mm01185722_m1 and Mm01184417_m1). Gene assays were performed and analyzed according to the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. While we measured 5 housekeeping genes (glucuronidase beta, Gusb; hypoxanthine guanine phosphoribosyl transferase 1 (Hprt1); heat shock protein 90 alpha (cytosolic), class B member 1, Hsp90ab1; glyceraldehyde-3-phosphate dehydrogenase, Gapdh; and beta actin, Actb) all data was normalized only to the 1 reference gene Hprt1 since the expression of the other 4 genes changed in the post-MI LV (Table S1). Genes that showed no statistical difference between groups are displayed in Table S2. 9 Table S1. Hprt1 was the only housekeeping gene not altered post-MI. Ct values for all 5 housekeeping genes analyzed. At the top are the Day 0 no MI controls (normal heart, no injury) and at the bottom are infarcted hearts at Day 7 post-MI [n=6 mice, mean and standard deviation (SD)]. Day 0 #10806 #10807 #10809 #10810 #10811 #10812 Mean SD 25.3 24.6 25.1 25.1 24.9 25.2 Gusb 25.0 0.26 22.8 22.5 22.9 22.6 22.8 22.8 Hprt1 22.7 0.18 19.5 18.9 18.9 18.9 18.8 19.0 Hsp90ab1 19.0 0.26 18.7 17.9 18.3 18.1 17.9 18.3 Gapdh 18.2 0.30 20.3 19.5 20.2 19.2 19.9 19.9 Actb 19.8 0.42 Day 7 #10911 #10888 #10735 #10889 #11025 #11165 Mean SD 23.3 22.6 22.3 23.9 23.6 22.2 Gusb 23.0 0.70 22.7 22.4 21.6 23.8 23.3 22.7 Hprt1 22.8 0.74 20.3 19.6 19.1 20.4 19.7 19.6 Hsp90ab1 19.8 0.47 20.9 20.4 18.4 22.1 20.9 21.0 Gapdh 20.6 1.21 18.1 17.2 16.8 19.9 19.8 18.3 Actb 18.3 1.29 T.TEST 0.0001 0.9750 0.0046 0.0009 0.0226 Histology and immunohistochemistry Collagen deposition was evaluated by picrosirius red staining as described previously (8). Staining for Griffonia simplicifolia lectin 1 (GSL-1, Vector Laboratories, #B-1105, 1:50) were performed in serial sections of zinc-formalin fixed LV. Tissue sections were deparaffinized, dehydrated, and heat-incubated with antigen retrieval solution (Dako) for approximately 15 min. Tissue was blocked with horse serum (Vector) and incubated with primary antibody in blocking serum at room temperature for 1 h. The avidin-biotinylated enzyme complex was added, followed by DAB chromogen. Representative images for all staining methods were acquired using an Olympus BX43 microscope. A minimum of 5 random fields at 40x magnification from each section were scanned and quantified. Positive staining was quantified by using Image-Pro software (Media Cybernetics) to calculate the percentage of positive stained area (red staining for collagen and brown DAB staining for GSL-1) per total section area. The data are presented as the area of 10 positive staining per total area. All histology mages were displayed using the same saturation, tone, and contrast intensities. Representative images for collagen deposition were acquired under polarized light. Quantification of C-1158/59 in human plasma Written informed consent was collected from all patients under protocols approved by the ethics committee of the University of Mississippi Medical Center (IRB protocol #2013-0164). Plasma was obtained by centrifugation of blood samples collected 24-48 h post-MI diagnostic (n= 8 control patients, no-MI, median age 56 years old; n=20 MI patients, median age 59 years old). Patient characteristics are listed on supplemental Table S3. Equal volume loading was used to separate proteins by SDS-PAGE electrophoresis. Immunoblot was performed as described above using the C-1158/59 primary antibody (New England Peptides, 1:100 dilution). Statistical analysis Data are reported as mean±SEM. Multiple group comparisons were analyzed by one-way ANOVA, followed by the Student Newman-Keuls when the Bartlett’s variation test passed, or by the Kruskall-Wallis non-parametric test when the Bartlett’s variation test did not pass, with the Dunn’s multiple comparison post-test used when differences were observed. Comparisons between the saline and p1158/59 groups were performed by unpaired Student t-test. A p<0.05 was considered significant. Literature Cited in Supplemental Methods 1. 2. Lindsey ML, Escobar GP, Dobrucki LW et al. Matrix metalloproteinase-9 gene deletion facilitates angiogenesis after myocardial infarction. Am J Physiol Heart Circ Physiol 2006;290:H232-9. Vu TH, Shipley JM, Bergers G et al. MMP-9/gelatinase B is a key regulator of growth plate angiogenesis and apoptosis of hypertrophic chondrocytes. Cell 1998;93:411-22. 11 3. 4. 5. 6. 7. 8. Ma Y, Halade GV, Zhang J et al. Matrix metalloproteinase-28 deletion exacerbates cardiac dysfunction and rupture after myocardial infarction in mice by inhibiting M2 macrophage activation. Circ Res 2013;112:675-88. Armstrong AC, Gidding S, Gjesdal O, Wu C, Bluemke DA, Lima JA. LV mass assessed by echocardiography and CMR, cardiovascular outcomes, and medical practice. JACC Cardiovascular imaging 2012;5:837-48. Reffelmann T, Kloner RA. Transthoracic echocardiography in rats. Evalution of commonly used indices of left ventricular dimensions, contractile performance, and hypertrophy in a genetic model of hypertrophic heart failure (SHHF-Mcc-facp-Rats) in comparison with Wistar rats during aging. Basic Res Cardiol 2003;98:275-84. Michael LH, Ballantyne CM, Zachariah JP et al. Myocardial infarction and remodeling in mice: effect of reperfusion. Am J Physiol 1999;277:H660-8. de Castro Brás LE, Ramirez TA, DeLeon-Pennell KY et al. Texas 3-step decellularization protocol: looking at the cardiac extracellular matrix. J Proteomics 2013;86:43-52. Chiao YA, Ramirez TA, Zamilpa R et al. Matrix metalloproteinase-9 deletion attenuates myocardial fibrosis and diastolic dysfunction in ageing mice. Cardiovasc Res 2012;96:444-55. 12 Table S2. List of extracellular matrix and associated adhesion molecules that did not show gene expression differences between p1158/59 treated mice and the saline group, at day 7 post-MI (n=6/group). Gene name Protein encoded p value Adamts1 A disintegrin-like and metallopeptidase with thrombospondin type 1 motif, 1 0.441 Adamts5 Adamts type 1 motif, 5 (aggrecanase-2) 0.096 Adamts8 Adamts type 1 motif, 8 0.204 Cdh1 Cadherin 1 0.467 Cdh2 Cadherin 2 0.399 Cdh3 Cadherin 3 0.057 Cdh4 Cadherin 4 0.979 SCntn1 Contactin 1 0.146 Col1a1 Collagen type I, alpha 1 0.112 Col2a1 Collagen type II, alpha 1 0.097 Col4a3 Collagen type IV, alpha 3 0.566 Col6a1 Collagen type VI, alpha 1 0.135 Ctnna1 Catenin (cadherin associated protein), alpha 1 0.065 Ctnna2 Catenin (cadherin associated protein), alpha 2 0.091 Fbln1 Fibulin 1 0.590 Foxo3 Forkhead box O3 0.168 Hapln1 Hyaluronan and proteoglycan link protein 1 0.819 Hc Hemolytic complement 0.555 Itga2 Integrin, alpha 2 0.121 Itgae Integrin, alpha e 0.562 Itgal Integrin, alpha l 0.142 Itgav Integrin, alpha v 0.085 Itgax Integrin, alpha x 0.439 Itgb4 Integrin, beta 4 0.126 Lama2 Laminin, alpha 2 0.120 Lama3 Laminin, alpha 3 0.432 Lamb2 Laminin, beta 2 0.265 Lamb3 Laminin, beta 3 0.251 Mmp1a Matrix metallopeptidase 1 0.181 Mmp2 Matrix metallopeptidase 2 0.109 Mmp3 Matrix metallopeptidase 3 0.189 Mmp7 Matrix metallopeptidase 7 0.224 Mmp9 Matrix metallopeptidase 9 0.121 Mmp10 Matrix metallopeptidase 10 0.361 Mmp12 Matrix metallopeptidase 12 0.099 Mmp13 Matrix metallopeptidase 13 0.522 Mmp15 Matrix metallopeptidase 15 0.610 Ncam1 Neural cell adhesion molecule 1 0.054 Ncam2 Neural cell adhesion molecule 2 0.259 Pecam1 Platelet/endothelial cell adhesion molecule 1 0.088 Postn Periostin 0.085 Sell Selectin, lymphocyte 0.254 Spock1 Sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1 0.166 Syt1 Synaptotagmin I 0.118 Thbs1 Thrombospondin 1 0.307 Thbs2 Thrombospondin 2 0.050 Timp1 Tissue inhibitor of metalloproteinase 1 0.068 Timp2 Tissue inhibitor of metalloproteinase 2 0.992 Timp3 Tissue inhibitor of metalloproteinase 3 0.134 Timp4 Tissue inhibitor of metalloproteinase 4 0.186 Vtn Vitronectin 0.258 Table S3. Patient characteristics. Values are mean±standard deviation. Controls n=8 MI patients n=20 Age, years 55±14 61±12 Sex, female/male 5/3 6/14 Race, African American/Caucasian 3/5 8/12 Previous myocardial infarction, MI NA 4/20 Hypertension NA 13/20 Diabetes mellitus NA 8/20 Body mass index NA 30±9 Systolic blood pressure NA 125±27 Diastolic blood pressure NA 75±16 Glucose NA 158±110 Hemoglobin NA 34±90 White blood cells count NA 11±4 Red cell distribution width NA 14±1 Peak troponin NA 3±5 Beta blocker NA 6/20 ACEI or ARB NA 6/20 Aspirin NA 6/20 Statin NA 5/20 ACEI= angiotensin-converting enzyme inhibitor, ARB= angiotensin II receptor antagonist, NA- not applicable or available.