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Supplemental Methods VEGF-Ablation Therapy Reduces Drug Delivery and Therapeutic Response in ECM-dense tumors Florian Röhrig1,2,3#, Sandra Vorlová2#, Helene Hoffmann1,2,3#, Martin Wartenberg4, Freddy E. Escorcia5, Sabrina Keller1, Michel Tenspolde1, Isabel Weigand1, Sabine Gätzner2, Katia Manova6, Olaf Penack7, David A. Scheinberg5, Andreas Rosenwald4, Süleyman Ergün1, Zvi Granot8 and Erik Henke1,2,3* 1 Institute of Anatomy and Cell Biology, Universität Würzburg, Würzburg, Germany 2 Institute for Clinical Biochemistry and Pathobiochemistry, Universitätsklinikum Würzburg, Würzburg, Germany 3 Graduate School of Life Science, Universität Würzburg, Würzburg, Germany 4 Institute for Pathology, Universität Würzburg, and Comprehensive Cancer Center Mainfranken (CCCMF), Germany 5 Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA 6 Molecular Cytology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA 7 Medizinische Klinik mit Schwerpunkt Hämatologie, Onkologie und Tumorimmunologie Universitätsklinikum Charité, Berlin, Germany 8 Department of Developmental Biology and Cancer Research, Institute for Medical Research IsraelCanada and Hebrew University-Hadassah Medical School, Jerusalem, Israel # These authors contributed equally to this article * To whom correspondence should be addressed: Erik Henke, PhD Institute for Anatomy and Cell Biology, Universität Würzburg. Koellikerstrasse 6 97070 Würzburg, Germany Email: [email protected] Tel: +49-(0)931-3183270, Fax: +49-(0)931-329363 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods IHC and IF staining of tumor sections H&E, picrosirus red, Mason-Goldner trichrome, IHC and IF staining was performed using standard techniques on formalin fixed paraffin embedded sections. For PSR and MGTC staining Kits from Carl Roth (Karlsruhe, Germany) were used according to the supplier’s instructions. Antigen retrieval and staining was performed by an automated tissue stainer (Ventana Medical Systems, Tucson, AZ). Tissues for quantitative evaluation were processed in parallel. For quantification whole tissue sections were imaged on a Zeiss Mirax System (40x objective, Carl Zeiss Microimaging, Germany). The whole virtual slide was used for quantification using the ImageJ software package (rsbweb.nih.gov/ij/). Double immuno fluorescence sections stained for NG2 and PanEC were also imaged on the Zeiss Mirax system. Inspection of acquired images revealed that NG2 staining was observed nearly exclusively (> 95 % of stained area) in perivascular locations. Therefore, the stained area for both channels (NG2/PanEC) was quantified and the ratio was used as a indicator for pericyte affiliation. In addition higher power images of representative fields were taken for illustration. Quantification of PSR staining was performed using ImageJ. RGB images were split in the three color channels. The green channel was used for quantification of the relative area that displayed a signal above a certain, constant threshold. Antibodies used for IHC/IF: PanEC-Antigen (Meca32, Biolegend, 120501), p53 (Vector Labs, VP-P956), NG2 (Millipore AB5320) Cleaved Caspase-3 (Cell Signaling, #9661), Hif1 (Novus NB100), CD31 (BD Biosciences 550274). Hoechst distribution, lectin vessel staining and 3D image evaluation To monitor intra-tumoral distribution of drugs, 50 µL of Hoechst 33342 (Sigma, 20 mg/mL in 0.9% NaCl) and 100 µL of Alexa 488 or Alexa 647-labeled Isolectin GS-B4 (Life Technologies, Darmstadt, Germany. 500 µg/mL in 0.9% NaCl) were injected i.v. into tumor 2 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods bearing mice 20 min before sacrificing the animal. Tumors were removed and flash frozen in OCT (Sakura Finetek Torrance, CA). For Hoechst 33342 tumor distribution 10 µm sections were cut on a cryotome and mounted on glass slides. The whole tissue sections were imaged on a Zeiss Mirax System (40x objective, Carl Zeiss Microimaging, Germany) using the blue fluorescence channel. The whole virtual slide was used for quantification using the ImageJ software package (rsbweb.nih.gov/ij/) by evaluating the area fraction that showed a signal in the blue channel above a certain, constant threshold. For Hoechst 33342 tissue penetration and 3D-vessel evaluation, tissue was cut on a cryotom to 200 µm slices and mounted on glass slides. Z-stacks were acquired by confocal imaging in the blue and near infrared channel (Leica SP4/2, 20x objective). Tissue penetration was measured as the maximal distance from the vessel surface (by Alexa 647 staining) that Hoechst 33342 staining was present using ImageJ. For this purpose the acquired z-stacks were evaluated at the same tissue depth for isolated, longitudinal cut blood vessels. The maximal distance of Hoechst 33342 staining was measured perpendicular to both sides of each blood vessel, the arithmetic mean of the two values was used. Each blood vessel was evaluated at several positions. At least 10 vessels per stack, and four stacks per biological sample were evaluated. 3D vessel-evaluation was done using the ImageJ software package (rsbweb.nih.gov/ij/) or its Fiji distribution (http://fiji.sc/wiki/index.php/Fiji) with additional plugins: Skeletonize 3D (http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:skeletonize3d:start) (1), Tubeness (http://www.longair.net/edinburgh/imagej/tubeness/). For vessel ramification analysis binary stack images were converted with the skeletonize plugin and evaluated for branching points. Vessel surface area was evaluated with the tubeness plugin. 3 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods Biodistribution of doxorubicin For biodistribution studies a bolus of 100 µg doxorubicin or doxil was given on specified days to doxorubicin naïve animals. Mice were sacrificed 2h (doxorubicin) or 24h (Doxil) post injection when doxorubicin could be expected to be cleared from the blood stream (2). Tissue samples were flash frozen and stored at – 80 C until extraction. The method described by Laginha et al. was used with slight modifications (3). In brief: Tissue samples were homogenized by sonification in 9 parts (v/w) water. 200 µL homogenate were combined with 50 µL 10% Triton X-100 (v/v) and 750 µL 0.75 N HCl in 2-propanol. The mixture was vortexed briefly and extracted for 12h at -20 C. Samples were again vortexed at r.t. and cleared by centrifugation (20 min, 4°C, 20,000 x g). Fluorescence was read (Ex.: 470 nm, Em.: 590 nm) in a microplate reader and corrected against extracts from tissue samples of nontreated animals. A standard curve was established by adding defined amounts of doxorubicin/doxil to homogenates of non-treated tissue samples prior to extraction. Biodistribution of 3H-paclitaxel 1 µCi of 3H-paclitaxel (Moravec, Brea, CA) were injected into tumor bearing mice at the specified days. Animals were euthanized 2 h later and major organs were harvested. Specific amounts of the organs (up to 200 mg) were dissolved in 2 mL SoluEne-350 (PerkinElmer, Waltham, MA) at 55 °C. To decolorize 200 µL 30 % H2O2 were added in aliquots and the samples again incubated for 60 min at 55 °C. After addition of 10 mL Hionic-Fluor Cocktail (PerkinElmer) the samples were read on a LS 6000 -scintillation counter (Beckman, Fullerton, CA). Cell toxicity studies Cells were plated (1500 cells in 100 µL DMEM/well) in 96 well MTP and left to adhere overnight. After 24 h 100µL of DMEM containing twice the indicated concentration of cytotoxic chemotherapeutics were added to each well without prior removal of medium. Each 4 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods concentration was tested in a 6-fold replicate. Cells were incubated with the therapeutics for 72 h before media were removed. Relative remaining cell numbers were determined using a fluorescence based cell quantification kit (CyQuant, Life Technologies, Darmstadt, Germany). EC50-values were determined by using a non-linear regression based model using the Prism software (Prism 5, GraphPad, LaJolla, CA) ECM Extraction Extracellular matrix proteins were extracted from tumor tissue using a modified protocol from Kleinman et al. (4). In brief, tumors (size 300 – 500 mm3) were excised, weighted, snap frozen and stored at -80 °C until further work-up. The tumors were homogenized in 2 mL/g WW high salt extraction buffer (HSEB, 3.4 M NaCl, 50 mM Tris HCl, 4 mM EDTA, pH 7.4) on ice with a tissue homogenizer (UltraTurax, IKA, Staufen, Germany). Non-soluble material, including ECM proteins, was pelleted by ultracentrifugation (100.000 x g, 4 °C, 30 min). This HSEB extraction was repeated once, supernatants were collected for western analysis. The pellet was washed with water and PBS, and finally re-suspended in PBS. For urea extraction the HSEB non-soluble pellet was re-suspended in 1.8 mL/g (starting material) of an urea extraction buffer (UEB, 2M urea, 150 mM NaCl, 50 mM Tris HCl, 4 mM EDTA, pH7.4) briefly homogenized and extracted overnight at 4 °C. Still non-soluble material was again pelleted by ultracentrifugation (26.000 x g, 1h 4 °C). The UEB supernatants were dialyzed against a low salt buffer (150 mM NaCl, 50 mM Tris HCl, 4 mM EDTA, pH7.4) for 48 h at 4 °C with two buffer changes. Protein content was determined with the BCA Assay Kit. To all extraction buffers Complete proteinase inhibitor cocktail (Roche Diagnostics, Mannheim, Germany) was added. 5 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods Lysyl oxidase activity assay A modified form of the fluorometric microwell assay described by Fogelgren was used (5). In short: In a black 96-well microtiterplate was added to 120 µL of an freshly prepared assay solution consisting of 75 µL 2x PBS, 15 µL N-Acetyl-Resorufin (100 µM, Ampliflu-Red, Sigma-Aldrich), 15 µL 2,5-diaminopentane (100 mM, cadaverine a substrate of all five lysyl oxidases (5-7)) and 15 µL horseradish-peroxidase (5U/mL, Sigma-Aldrich). For each sample the assay solution was prepared in two triplicate rows. To one triplicate 30 µL water, to the other 30µL APN (3.5 mM in water) was added. Finally 50 µL of cell culture supernatant or protein containing lysate was added and the fluorescence of released resorufin was recorded continuously over 3h in a fluorescence plate reader (PerkinElmer, Wallac II; Ex: 530nm, Em: 570nm). Slope of the fluorescence signal in the linear range was calculated for both APNinhibited and non-inhibited samples; the difference was used as a measure of lysyl oxidase activity. Note: There a conflicting reports whether APN inhibits LOXL2. While some authors demonstrated inhibition of LOXL2 (7-9), at least one group reported that LOXL2 is not inhibited by APN(10). Our own results using recombinant expression of hLOXL2 also indicate that LOXL2 is inhibited by APN. Transwell ECM drug penetration assay The membranes of transwell inserts (24 well MWD format, 33 mm2 membrane area, Costar, Cölbe, Germany) were coated with 3 µg/mm2 of the respective ECM extract or protein by adding the protein suspension in 50 µL of buffer and letting the membranes air dry overnight. ECM was reconstituted by adding 150 µL of PBS to the upper chamber of the transwell and incubation for 1 h. 850 µL of 20 µg/mL doxorubicin in PBS were added to the lower compartment. The plate was read continuously for 6 h in a fluorescence plate reader (PerkinElmer, Wallac II; Ex: 530nm, Em: 570nm). 6 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods For LOX modification assays, 140 µg (10 µg/mm2) of matrigel were mixed with 10 µg purified recombinant hmLOX or hLOXL2 in 50 µL PBS (+/- 500 µM BAPN), the suspension was applied to transwell inserts (96 well MWD format, 14 mm2 membrane area, Costar, Cölbe, Germany) and incubated for 6 h at 37 °C. Afterwards the suspension was dried over night and subjected to the assay described above (100 µL PBS in upper chamber, 300 µL 20 µg/mL doxorubicin in PBS in lower chamber). Recombinant expression and purification of hLOX and hLOXL2 The cDNA encoding both enzymes was amplified from cDNA generated from RNA isolated from HUVEC. To amplify the active, mature hmLOX (AAs 169 to 417, missing the signal and propeptide sequences) the primers 5´- TGCAGGAATTCGCCACCATG GACGACCCTTACAACCCCTAC AAG – 3’ (italics: EcoRI site, underlined: start codon) and 5´-AGCTCTCGAGGCTAGCCTAGTGGTGATGGTGATGATGACCTCCATACGGTG AAATTGTGCAGCCTGAGGCAT-3´ (italics: XhoI site, bold: NheI site, underlined: 6xHistag) were used. The resulting DNA was cloned in the expression vector pGEX-4T1 (GE Healthcare Europe, Freiburg, Germany). The pGEX system was used for heterologous overexpression of hmLOX in E. coli after IPTG induction. The active enzyme was purified by from the media supernatant was purified via a Co2+ affinity column (Thermo Fisher, Rockford, IL) with elution using 250 mM imidazol at pH 7.2. The eluted enzymes were subjected to dialysis versus PBS and used for enzymatic modification of ECM (matrigel). The entire hLOXL2 CDS including the signal peptide was amplified from HUVEC cDNA. In the process a 6xHis-tag was C-terminal fused to the CDS. The amplified DNA was cloned into the lentiviral vector pLVX-puro (Clontech, Mountain View, CA). Lentiviral particles were generated in HEK 293 cells by co-transfection with the pCMV-dR8.9 and pCMV-VSV-G(11) (both plasmids were obtained from Addgene, Cambridge, MA) using a standard CaCl 2-based transfection method. Supernatant was used to transfect HEK 293 cells. Stable cells selected with puromycin (3.5 µg/mL). Active enzyme from the media supernatant was purified via a 7 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods Co2+ affinity column (Thermo Fisher, Rockford, IL) with elution using a stepwise pH gradient (pH 10.5 – pH 6). The eluted enzymes were subjected to dialysis versus PBS and used for enzymatic modification of ECM (Matrigel). Collagen Crosslinking Analysis ECM from APN treated and control tumors was obtained by high salt extraction of cellular components. The insoluble ECM was re-suspended in water and used to coat glass slides (angiogenesis µ-slides, Ibidi, Martinsried, Germany) at µg/well. Interferences reflection Images were acquired as z-stacks (30 slides, z-distance: 1.0 µm) on a Nikon A1 microscope in reflection mode using am 60x oil immersion objective and an 647 nm laser following a published protocol(12). Identifiable collagen fibers in optical fields were manually counted. RNA-isolation RNA was isolated from 2-3 10 µm sections of archival FFPE tumor samples (app. 10 mg tissue per sample) using the Agencourt FormaPure Kit (BeckmanCoulter, Krefeld, Germany) following the manufacturer’s instructions. In a limited number of cases RNA yield was insufficient (below 400 ng) and amplified using the SensationPlus FFPE Amplification kit (Affymetrix) using 50 ng of RNA. RNA was isolated from cells tumors using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacture’s recommendations. RNA was isolated from fresh tumor samples using the Trizol reagent (Life Technologies, Darmstadt, Germany) according to the manufactures recommendation. mRNA-Quantification mRNA-expression levels were quantified using the GeXP-System (BeckmanCoulter, Krefeld, Germany). Protocols for reverse transcription, amplification, labeling, gel electrophoresis and quantification were used as recommended by the manufacturer. RNA-levels were normalized to levels of housekeeping genes -2-microglobulin (B2M) and ribosomal protein S29 8 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods (RPS29)(13) in murine, and -2-microglobulin (B2M) in human samples respectively. Gene specific primer sequences are shown in Table 1. Analysis was done with three technical replicates per biological sample. Mean values of technical replicates was used for statistical analysis. Table 1: Gene specific primer sequences for mRNA quantification using the GeXPsystem. The Sequences contain the necessary tag sequences. Primers were combined to several multiplex sets, that each included the respective primers for B2M and RPS29. Gene Symbol Fragment Size Forward Primer Reverse Primer mFn1 132 AGGTGACACTATAGAATATGTGCACGTGCC TGGGCAAT GTACGACTCACTATAGGGAACGGGAGGACACAGGG CTCC mLama5 135 AGGTGACACTATAGAATAGGTCACACTTAT CAGCCGTGGCA GTACGACTCACTATAGGGAGTCGTCCTGCGTGATG CGCT mCol3a1 126 AGGTGACACTATAGAATAAGAGGCTTTGAT GGACGCAA GTACGACTCACTATAGGGAAGCTCCGTTGTCTCCT GGAA mLamc1 142 AGGTGACACTATAGAATACGCACTGTCCGA CTGGCACT GTACGACTCACTATAGGGACACGGGCGGCACAGTC TCAC mCol2a1 147 AGGTGACACTATAGAATAAGAAGGGTCTGG CTGGCGCT GTACGACTCACTATAGGGAGCTCGCCTCGTTCACC AGCA mCol18a1 151 AGGTGACACTATAGAATACGTGGCGCTGGC CTCTTTGT GTACGACTCACTATAGGGAGACAGTGCACAGGGCT CACCC mFbn1 154 AGGTGACACTATAGAATAAGGCCCCCTGCA GTTACGGT GTACGACTCACTATAGGGACCTCGGCCCATGCCCA TTCC mLama1 188 AGGTGACACTATAGAATATGGCCTCGGTGC TCTGGGTC GTACGACTCACTATAGGGACGGCACGTGCTCCACG AGTTT mCol13a1 146 AGGTGACACTATAGAATAGACGAAGGGAGG CCTGGAGCG GTACGACTCACTATAGGGAGGAACCTCTGCTCCCG GGTCG mFbn2 172 AGGTGACACTATAGAATATCTCTGGATGCC TCTGGGCTGA GTACGACTCACTATAGGGAACTGGTAGTGCTGGAC GTAGCC mCol4a1 175 AGGTGACACTATAGAATAGCATTGGCGGCT CTCCAGGG GTACGACTCACTATAGGGAGGGCCGGGTACACCTT GGTC mLamb1 191 AGGTGACACTATAGAATATGCGCCCCTGTG GATGGAGT GTACGACTCACTATAGGGAGCGTTGCTGTTCCGGC CTTC mCol1a1 196 AGGTGACACTATAGAATATGATGGCAAAAC CGGCCCCC GTACGACTCACTATAGGGATCCGGGAAGGCCTCGC TCTC mCol5a1 201 AGGTGACACTATAGAATATGCCCACCAAGC AGCTGTACC GTACGACTCACTATAGGGAAGAGGAAGACAGGGGA GCGGC mHspg2 217 AGGTGACACTATAGAATAACGGCCTGGCAT CGTGCAAA GTACGACTCACTATAGGGAACCGGCAGGCACTCGG ATCT AGGTGACACTATAGAATAAGTGGCTGCTAC TCGGCGCT GTACGACTCACTATAGGGAGGCGGGTGGAACTGTG TTACG 242 mB2m mLOX1 225 AGGTGACACTATAGAATAGGCCACCCAGCC ACATAGATCG GTACGACTCACTATAGGGAAGTAGGGGTCGGGCAC CAGG mLOXL1 207 AGGTGACACTATAGAATACCGCGTGCTGGA GCCACCT GTACGACTCACTATAGGGAGCCTGCACGTAGTTAG GGTCCG mLOXL2 187 AGGTGACACTATAGAATATTCTTCTGGGCA ACCAGGGCG GTACGACTCACTATAGGGAGCTAGGCTCAGGGAAG GCAGC mLOXL3 178 AGGTGACACTATAGAATATCCAGCCTCTGG AGTTGTGCC GTACGACTCACTATAGGGAACGGAGACCCCACACT GAAGC mLOXL4 127 AGGTGACACTATAGAATAAGGCCCGTTAGC GTACGACTCACTATAGGGATGGGGCCACATCATGG 9 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods mVEGFA mCAIX 226 166 mRPS29 255 hB2M 213 hLOX 195 hLOXL1 177 hLOXL2 146 hLOXL3 167 hLOXL4 135 GCTGCTCTG AGGTGACACTATAGAATAGGCCTCCGAAAC CATGAACT AGGTGACACTATAGAATAGGTGCACCTCAG TACTGCTT AGGTGACACTATAGAATATTCCTTTCTCCT CGTTGGGC TGATTTCAG GTACGACTCACTATAGGGAGTCCACCAGGGTCTCA ATCG GTACGACTCACTATAGGGAATGGGACAGCAACTGT TCGT GTACGACTCACTATAGGGATCCATTCAAGGTCGCT TAGTCC AGGTGACACTATAGAATATCGGGCCGAGAT GTCTCGCT AGGTGACACTATAGAATAGGGCGACGACCC TTACAACCC AGGTGACACTATAGAATACCGCGGTCTCCC TGACTTGG AGGTGACACTATAGAATAACCGGCCGTGGT GAGTTGTG AGGTGACACTATAGAATAGCCCTTAGGGTC CTGCTCGGC AGGTGACACTATAGAATAAACTGGGGGCTC ACCGAAGC GTACGACTCACTATAGGGACAATGTCGGATGGATG AAACCCAGA GTACGACTCACTATAGGGATAGGGGTCGGCCACCA GGTC GTACGACTCACTATAGGGATCGGTGGCCTCAGGGG CATA GTACGACTCACTATAGGGACACCGCCTCTCAGTCG CACC GTACGACTCACTATAGGGACCGTGGAAGGGGACGG AGAC GTACGACTCACTATAGGGATGGCGTCCCCGACCAG AACC Human samples RNA was isolated for expression analysis from fully anonymized archival FFPE tissue. A general approval for use of the samples in the study was given by the Research Ethics Committee of the Universitätsklinikum Würzburg. Statistical Analysis All statistical analysis was done using the Prism5 Software (GraphPad, LaJolla, CA). Differences between two groups were analyzed using an unpaired, two-tailed Student’s T-test. In parallel the samples were tested for significant variation of variance. All statistical tests were performed between sets of individual biological replicates. Appropriate sample and cohort size for animal studies were calculated based on previous results from previous experiments according to standard equations (14). 10 Röhrig, Vorlova, Hoffmann et al. Supplemental Methods References 1. Lee TC, Kashyap RL, Chu CN. Building Skeleton Models Via 3-D Medial Surface Axis Thinning Algorithms. Cvgip-Graph Model Im. 1994;56(6):462-78. 2. 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