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1 Supplementary Materials for Neuronal heparan sulfates promote amyloid pathology by modulating brain amyloid- clearance and aggregation in Alzheimer s disease Chia-Chen Liu, Na Zhao, Yu Yamaguchi, John R. Cirrito, Takahisa Kanekiyo, David M. Holtzman, Guojun Bu* The PDF file includes: *Corresponding author. bu.guojun@mayo.edu Published 30 March 2016, Sci. Transl. Med. 8, 332ra44 (2016) DOI: /scitranslmed.aad3650 Materials and Methods Fig. S1. Characterization of neuronal HS-deficient mice. Fig. S2. The mrna expression of HSPG subfamily in APP/PS1 and APP/PS1; next1 CKO mice. Fig. S3. HSPG core proteins codeposit with amyloid plaques in the brain parenchyma and leptomeningeal arteries. Fig. S4. Deficiency of neuronal HS leads to a decrease in amyloid-associated astrogliosis. Fig. S5. Deficiency of neuronal HS increases the clearance of ISF A 42 in the hippocampus of APP/PS1 mice. Fig. S6. A 40 and A 42 deposition is reduced in brain parenchyma, but enhanced along the cerebral vasculature in neuronal HS-deficient mice. Fig. S7. Proposed mechanism by which neuronal HS/HSPGs may regulate brain A clearance and aggregation. Table S1. Demographic characteristics of examined controls and individuals with AD. Table S2. A concentration in the cortex and hippocampus in APP/PS1 and APP/PS1; next1 CKO mice.

2 SUPPLEMENTARY MATERIALS Materials and Methods Animals Ext1 forebrain neuronal knockout mice were generated by breeding the Ext1 flox/flox mice with CaMKII-Cre mice (Jackson Labs) in which the Cre recombinase is expressed broadly in excitatory neurons of the forebrain, including the hippocampus and the cortex (28). Ext1 flox/flox mice were bred to CaMKII-Cre mice to generate HS neuronal deficient (next1 CKO ) mice. To generate APP/PS1 mice with neuronal HS deficiency, APP/PS1; Ext1 flox/flox mice were bred with Ext1 flox/flox, CaMKII-Cre mice. Both male and female APP/PS1; Ext1 flox/flox, CaMKII-Cre (APP/PS1; next1 CKO mice) and littermate control APP/PS1; Ext1 flox/flox (APP/PS1) mice were used for analysis. For tissue preparation, mice were transcardially perfused with PBS. Different regions of brain tissues (cortex, hippocampus and cerebellum) were snap-frozen in liquid nitrogen and stored at -80 C until processing. RNA isolation and real-time PCR analysis Total RNA was isolated by using Trizol (QIAGEN) followed by RNeasy Mini kit (QIAGEN). For real-time PCR analysis, cdna was synthesized from total RNA by SuperScript III reverse transcriptase (Invitrogen). The primer sequences were as follows: IL-1β: 5'- CCTGCAGCTGGAGAGTGTGGAT-3'; 5'-TGTGCTCTGCTTGTGAGGTGCT-3'; TNF-α: 5'- AGCCCACGTCGTAGCAAACCAC-3'; 5'-AGGTACAACCCATCGGCTGGCA-3'; β-actin: 5'- AGTGTGACGTTGACATCCGTA-3'; 5'-GCCAGAGCAGTAATCTCCTTC-3'; IL-6: 5'-CTCT GGGAAATCGTGGAAAT-3'; 5'-CCAGTTTGGTAGCATCCATC-3'; MMP2: 5'-GTCGCCCC TAAAACAGACAA-3'; 5'-GGTCTCGATGGTGTTCTGGT-3'; MMP9: 5'-CGTCGTGATCCC

3 CACTTACT-3'; 5'-AACACACAGGGTTTGCCTTC-3'; IDE: 5'-ACTAACCTGGTGGTGAAG- 3'; 5'-GGTCTGGTATGGGAAATG-3'; NEP: 5'-GCAGCCTCAGCCGAAACTAC-3'; 5'-CACC GTCTCCATGTTGCAGT-3'; Ext1: 5 -GCCCTTTTGTTTTATTTTGG-3 ; 5 -TCTTGCCTTTGT AGATGCTC-3 glypican-1: 5'-GAGCACAGTAGACCAACTTCT-3'; 5'-TGGCTGCACGTTCC TTT-3'; glypican-3: 5'-CTATATTGGCGTTGCTGGGA-3'; 5'-CTACCATCCATGATTCCATC CAG-3'; syndecan-1: 5'-TGTGTTCTCCCCAGATGTTTC-3'; 5'-CATCAAAGAGGTTGTCGA GGA-3'; syndecan-3: 5'-CACTTACTGGCACCTCTGG-3'; 5'-CCAGTCACCACCCAGGA-3'; agrin: 5'-CACAGCTTTCCCATTCTTCAC-3'; 5'-TCGACAACAGCAGACCATTC-3'; perlecan: 5'-TCGATCTGCAGCTGGGT-3'; 5'-CCAGATCCGACTGAGCTTTG-3'. Triplicate reactions were prepared using a 25- l mixture containing universal SYBR Green Supermix (Bio-Rad). Real-time quantification was performed on icycle iq system (Bio-Rad). Immunofluorescence staining Paraffin-embedded sections were blocked with PBS containing 5% of normal serum (goat or rabbit) and 0.3% Triton-X-100 for 30 min at room temperature. When mouse monoclonal antibody was used, brain sections were blocked with M.O.M. IgG blocking reagent (Vector Labs) for 1 hr. For Aβ staining, antigen retrieval was performed by incubating the slides with 88% formic acid for 30 min, followed by 30 min of steam at 95 C in dh2o. Sections were incubated with primary antibody anti-hs (10E4; Seikagaku America, Amsbio), anti-syndecan-3 (R&D), anti-glypican-1 (M95; Santa Cruz), anti-agrin (Santa Cruz) or anti-perlecan (A7L6; Millipore) overnight at 4 C. To verify the specificity of HS antibody, slides were treated with Heparinase III (Sigma) [10 miu/ml in PBS containing sodium and magnesium chloride for 2 hr at 37 C], which eliminated the HS epitope recognized by 10E4 antibody. For frozen

4 cryosections, brain tissue was fixed with acetone and incubated with 5% normal serum from the host species of the secondary antibody, followed by primary antibody. After washing with PBS, brain sections were incubated with Alexa488-conjugated or Alexa568-conjugated IgG secondary antibodies against mouse, rabbit, goat or rat species (1:400; Invitrogen) for 2 hr at room temperature. Alexa488-conjugated goat anti-mouse IgM secondary antibody was used for detecting HS. Sections were mounted with Vector Vectashield fluorescence mounting medium (Vector Labs) containing DAPI for counterstaining of nuclei. To examine the amyloid deposits by Congo red staining, tissue slides were immersed in 0.5% Congo red fluorescent dye (in 50% alcohol) for 20 min, rinsed in distilled water and quickly dipped in alkaline alcohol solution (1% Sodium hydroxide and 50% alcohol). For each HSPG staining, the numbers of amyloid plaques and HSPG-positive plaques from twelve microscopical fields (magnification x100) were manually counted. The percentage of amyloid plaques stained for a specific HSPG was calculated. ELISA quantification Human syndecan-3, syndecan-4 and glypican-3 were measured using a DuoSet ELISA kit (R&D Systems) according to manufacturer s instructions. Human glypican-1 was examined using commercial ELISA (USCN Business Co.) according to manufacturer s instructions. Syndecan-1, perlecan and agrin were analyzed using the Meso Scale Discovery (MSD) SECTOR Imager system. The 96-well plates were coated overnight at 4 C with capture antibody in TBS. After blocking, plates were incubated overnight at 4 C with samples in assay buffer (5 mm NaH2PO4, 20 mm Na2HPO4, 0.1% NaN3, 0.4 M NaCl, 2 mm EDTA, 0.4% Block Ace, 0.5 g/l CHAPS). After washes, plates were incubated for 1 hr at room temperature with detection antibody,

5 followed by SULFO-TAG-labeled anti-mouse, anti-rabbit, or secondary antibodies (Meso Scale Discovery). The signals were measured using the Meso Scale Discovery SECTOR Imager 2400 reader. The amount of syndecan-1 was measured by MSD assay using a polyclonal goat antihuman syndecan-1 as capture antibody (R&D) and biotin-conjugated anti-human syndecan-1 as detection antibody (R&D). The recombinant human syndecan-1 protein (R&D) was used a standard. The amount of perlecan was measured by MSD assay using a mouse monoclonal antihuman perlecan as capture antibody (Thermo Scientific) and a biotin-conjugated anti-human perlecan as detection antibody (R&D). The recombinant human perlecan protein (R&D) was used a standard. The amount of agrin was measured by MSD assay using a rabbit polyclonal anti-agrin (USCN Business Co.) as capture antibody and goat polyclonal anti-agrin (Santa Cruz) as detection antibody. The recombinant human agrin protein (R&D) was used a standard. The quantitation of heparan sulfate was performed as previously described (30). Briefly, tissues were homogenized in buffer (50 mm Tris-HCl, 1 mm CaCl2 and 1% Triton X-100), incubated with pronase (1 mg/ml) at 55 C for 24 hr, and centrifuged. The amount of heparan sulfate in the supernatant was determined by commercial ELISA (Seikagaku America, Amsbio). Western blot analysis Samples were homogenized and incubated in PBS containing 1% Triton X-100, supplemented with protease inhibitor mix and PhosSTOP (Roche). Equal amounts of protein (by Bradford assay) were resolved by SDS/PAGE and transferred to PVDF membranes. After the membranes were blocked, proteins were detected with primary antibody. The membrane was probed with LI- COR IRDye secondary antibodies and detected using the Odyssey infrared imaging system (LI- COR). For Western blot analysis, the following antibodies were used in this study: anti-gfap

6 (Millipore), 6E10 (Covance) for total APP and sapp, anti-human sapp (IBL), anti-app C- terminal antibody (IBL) for APP-CTFs and anti- -actin (Sigma) antibodies.

7 Fig. S1. Characterization of neuronal HS-deficient mice. (A) The mrna expression of Ext1 in the cortex (n=8/group) and cerebellum (n=5/group) of APP/PS1 and APP/PS1; next1 CKO mice examined by real-time PCR. N.S., not significant; **P < (B) The amount of HS in the cortex, hippocampus (Hippo) and cerebellum (Cereb) of APP/PS1 and APP/PS1; next1 CKO mice (n=4/group) evaluated by HS ELISA. Data represent mean ± SEM. N.S., not significant; **P < (C, D) Amyloid deposits and HS in the brain parenchyma (C) and leptomeningeal arteries (D) stained with anti-hs (green) antibody and Congo red for amyloid fibrils, the amyloid core of mature plaques. HS reactivity is abolished by treatment with heparinase III. Scale bar, 50 µm.

8 Fig. S2. The mrna expression of HSPG subfamily in APP/PS1 and APP/PS1; next1 CKO mice. The amounts of glypican-1, glypican-3, syndecan-1, syndecan-3, agrin and perlecan in the cortex of APP/PS1 and APP/PS1; next1 CKO mice (n=6-8/group) evaluated by real-time PCR. Note that neuronal HS deficiency did not significantly affect the expression of HSPG core proteins. Data represent mean ± SEM. N.S., not significant. Statistical analysis was performed using Student s t test.

9 Fig. S3. HSPG core proteins codeposit with amyloid plaques in the brain parenchyma and leptomeningeal arteries. (A) Brain sections from APP/PS1 and APP/PS1; next1 CKO mice at 12 months of age were co-immunostained for syndecan-3 (SDC-3), glypican-1 (GPC-1), agrin or perlecan (red) together with Aβ (green), and counterstained with DAPI (blue) for nuclei. Representative images of co-staining are shown. Scale bar, 50 µm. (B) The numbers of amyloid plaques and HSPG-positive plaques were counted, and the percentages of plaques positive for GPC-1, SDC-3, and agrin are shown. Data represent mean ± SEM. **P < (C) Brain

10 sections from APP/PS1 and APP/PS1; next1 CKO mice at 12 months of age were coimmunostained for SDC-3, agrin or perlecan (red) with Aβ (green), and counterstained with DAPI (blue). Representative images of the leptomeningeal arteries are shown. Scale bar, 50 m.

11 Fig. S4. Deficiency of neuronal HS leads to a decrease in amyloid-associated astrogliosis. (A) Brain sections from APP/PS1 and APP/PS1; next1 CKO mice at 12 months of age were coimmunostained with GFAP (red) and Aβ (green) antibodies. Scale bar, 100 µm. (B) Brain sections from APP/PS1 and APP/PS1; next1 CKO mice at 12 months of age were coimmunostained with Iba1 (red) and Aβ (green) antibodies. Scale bar, 100 µm.

12 Fig. S5. Deficiency of neuronal HS increases the clearance of ISF Aβ42 in the hippocampus of APP/PS1 mice. APP/PS1 and APP/PS1; next1 CKO mice (n= 5-7/group) were analyzed at the age of 3-4 months. (A) To assess Aβ42 half-life, the mice were treated with a -secretase inhibitor, and the hippocampal ISF A 42 amount was monitored. The ISF Aβ concentration during the hours of 9-16 after probe implantation were averaged and served as the basal amount of Aβ (shown as -1~0 hr) prior to -secretase injection. (B) The common logarithm of percentage baseline ISF Aβ42 concentrations versus time is plotted. Data represent mean ± SEM. (C) The slope from the individual linear regressions from log (% ISF Aβ42) versus time for each mouse was used to calculate the mean half-life (t1/2) of elimination for Aβ42 from the ISF. Data represent mean ± SEM. *P < 0.05.

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14 Fig. S6. Aβ40 and Aβ42 deposition is reduced in brain parenchyma, but enhanced along the cerebral vasculature in neuronal HS-deficient mice. (A) Brain sections from APP/PS1 and APP/PS1; next1 CKO mice at 12 months of age were immunostained for Aβ40 (red) antibody and counterstained with DAPI (blue). Representative images of Aβ40 staining in the cortex and hippocampus are shown. Scale bar, 100 m. (B) Brain sections from APP/PS1 and APP/PS1; next1 CKO mice at 12 months of age were immunostained for Aβ42 (red) antibody, and counterstained with DAPI (blue). Representative images of Aβ42 staining in the cortex and hippocampus are shown. Scale bar, 100 m. (C) Representative images of Aβ40 and Aβ42 staining in the leptomeningeal arteries are shown. Scale bar, 50 m.

15 Fig. S7. Proposed mechanism by which neuronal HS/HSPGs may regulate brain A clearance and aggregation. The major A clearance pathways include receptor-mediated lysosomal clearance by cells (neurons and glia) along the ISF drainage pathway or through BBB, and proteolytic degradation by neprilysin (NEP) and insulin degrading enzyme (IDE) (6, 46, 58-60). An impaired clearance of A results in A accumulation in the brain, leading to the formation of toxic A oligomers and amyloid plaques. Binding of A to neuronal HSPGs on the cell surface hinders proteolytic degradation of Aβ, and functions as a catalyst that promotes Aβ oligomerization/aggregation. Thus, in the presence of neuronal HS, Aβ aggregation is accelerated at the neuronal surface or intracellular compartments, leading to eventual formation of extracellular soluble Aβ oligomers. Depletion of neuronal HS leads to more efficient clearance of Aβ through neuronal LRP1, astrocytes/microglia, and extracellular proteolysis, leading to reduced Aβ aggregation in the brain parenchyma and redistribution of Aβ to the cerebrovascular compartments.

16 Table S1. Demographic characteristics of controls and individuals with AD.

17 Table S2. Aβ concentration in the cortex and hippocampus in APP/PS1 and APP/PS1; next1 CKO mice (Data shown in Fig. 1B-E). Aβ40 in cortex Aβ42 in cortex TBS (pg/mg) TBSX (pg/mg) GDN (ng/mg) TBS (pg/mg) TBSX (pg/mg) GDN (ng/mg) Ctrl KO Ctrl KO Ctrl KO Ctrl KO Ctrl KO Ctrl KO Aβ40 in hippocampus Aβ42 in hippocampus TBS (pg/mg) TBSX (pg/mg) GDN (ng/mg) TBS (pg/mg) TBSX (pg/mg) GDN (ng/mg) Ctrl KO Ctrl KO Ctrl KO Ctrl KO Ctrl KO Ctrl KO