Human brain samples
This study was approved by the ethics committee of Universidad Miguel Hernández de Elche, Spain, and it was carried out in accordance with the WMA Declaration of Helsinki. Brain samples (frontal cortex) were obtained from the Brain Bank of the Institute of Neuropathology, Bellvitge University Hospital. Late-onset AD cases (12 females/18 males; average age 75±1 years) were categorized according to the Braak stage of neurofibrillary tangle (NFT) pathology ([18]; Braak stage I-II n= 10; Braak stage III-IV, n= 10; Braak stage V-VI, n= 10). Special care was taken not to include cases with combined pathologies to avoid bias in the pathological series. Samples from non-demented (ND) controls (2 females/6 males; average age 52±7 years) corresponded to individuals with no clinical dementia and no evidence of brain pathology. The mean post-mortem interval of the tissue was ~8 h in all cases, with no significant difference between the groups.
Brain membrane-enriched fractions
Brain cortex samples were homogenized using a polytron Heidolph RZR-1 at 600-800 rpm, in a glass potter applying 10-15 pulses in buffer at 10% (w/v) (Hepes 1mM, sucrose 0,32 M, Cl2Mg mM, EDTA 1mM, NaHCO3 1mM, PMSF, protease inhibitors (Cocktail Complete EDTA free, Roche), antiphosphatase inhibitor (PhosSTOP, Sigma). The homogenized was centrifuged at 1000 x g during 20 minutes at 4ºC. The supernatant (post-nuclear fraction) was centrifuged at 13000 x g during 15 minutes at 4ºC. The supernatant (cytosolic fraction) was aliquoted and the resulting pellet (membrane-enriched fraction) was resuspended in buffer (Hepes 1mM, Cl2Mg mM, EDTA 1mM, NaHCO3 1mM, PMSF, protease inhibitor cocktail, antiphosphatase inhibitor).
Cell cultures
SH-SY5Y cells, a human neuroblastoma cell line, were seeded at a density of 1×105 cells/well in 6-well plates and cultured in Dulbecco's Modified Eagle medium (DMEM) supplemented with Glutamax (GIBCO Thermo Fisher Scientific, Rockford, USA), 1% heat-inactivated fetal bovine serum (FBS), penicillin (100 U/mL) and streptomycin (100 μg/mL) in a 5% CO2 incubator. To neurodifferentiate the cells, 10 μM all-trans-retinoic acid (RA, Sigma-Aldrich Co, MO, USA) in DMEM with 3% FBS was added every 2 days. After 6 days, cells were treated with recombinant reelin, 12 µg/ml for 24 hours. Other cells were treated with suspensions of β-amyloid 1-42 (Aβ42) or scrambled control peptide (Aβsc; AIAEGDSHVLKEGAYMEIFDVQGHVFGGKIFRVVDLGSHNVA) (both from Anaspec Peptide, Eurogentec) in DMEM with 1% FBS, for two consecutive days without changing the media, at a final concentration of 5 µM.
Non differentiated SH-SY5Y cells were transfected with Lipofectamine 3000 (ThermoFisher) following manufacturer’s instructions, with cDNA for the full-ApoER2 receptor, ApoER2-ICD and GFP/cDNA3.1 as mock-transfection as in [14] for 48 h. After 24 hours, some cells were treated with recombinant reelin (12 ug/ml) for another 24 hours.
CHO cells stably over-expressing wild-type human APP (CHO-PS70, [19]) were grown in DMEM® containing 10% FBS, 0.1% Puromicin (Sigma-Aldrich) and 0.2% G418 disulfate salt (Sigma-Aldrich). CHO-PS70 cells were transfected with full-length LRP3 cDNA (a kind gift from Christine Lavoie, [20]) for 48 h.
Microarray analysis
Gene expression was analysed 48 h after transfection with human full-length ApoER2, using microarrays SurePrint G3 Human Microarrays (ID 039494, Agilent Technologies, Spain) and performed by Bioarray SL (http://www.bioarray.es). The concentration and the purity of the total RNA extracted were measured by a NanoDrop spectrophotometer, and RNA quality was determined with the kit R6K Screen Tape (Agilent Technologies, Spain). The estimated RNA integrity number ranged between 9.5 and 9.7. Each sample (four samples and four controls) was labeled with Cy3 using the One-Color Microarray-Based Gene Expression Microarrays Analysis v.6.6 (Agilent Technologies, Spain). Data were imported to the linear models for microarray data Bioconductor software (Limma, Marray, affy, pcaMethods and EMA). Raw data were first subjected to background subtraction, then to within-array loess normalization. Finally, across-array normalization was performed. Normalized data were fitted to a linear model. The significance of the gene expression changes was analysed according to the adjusted p value (adj. p ˂ 0.05).
qRT-PCR analysis
RNA was extracted from human brains, SH-SY5Y cells or CHO-PS70 cells using the TRIzol® Reagent in the PureLinkÔ Micro-to-Midi Total RNA Purification System (Life Technologies, Carlsbad, CA, USA) following the manufacturer’s instructions. SuperScriptÔ III Reverse Transcriptase (Life Technologies, Carlsbad, CA, USA) was used to synthesize cDNAs from this total RNA (2 µg) using random primers according to the manufacturer’s instructions. Quantitative PCR amplification was performed on a StepOneÔ Real-Time PCR System (Applied Biosystems, Thermo Fisher Scientific, Rockford, USA) with TaqMan probes specific for human LRP3 (assay ID: HS01041220_m1), LDLR (assay ID: HS00181192_m1), (Applied Biosystems, Thermo Fisher Scientific, Rockford, USA), and human 18S as a housekeeping gene (Applied Biosystems, Thermo Fisher Scientific, Rockford, USA) for human brain and SH-SYSH cells samples. In CHO-PS70, mRNA expression was measured with primers for human APP (forward: AACCAGTGACCATCCAGAAC; reverse: ACTTGTCAGGAACGAGAAGG), and for glyceraldehyde 3-phosphate dehydrogenase (GAPDH, forward: AGAAGGTGGTGAAGCAGGCAT; reverse: AGGTCCACCACTCTGTTGCTGT) to normalize the expression levels of the target gene by the ΔCt method curves.
Recombinant reelin
HEK-293T cells stably transfected with reelin cDNA and GFP (mock) were grown in 175 cm2 flasks at a density of 10×106 cells / flask. After 3 days in culture with Optimem, the supernatants were filtered through 0.2 µm pores and then concentrated by an Amicon Ultra size 100 kDa-filter of molecular exclusion (Millipore). For quantification, a coomasie gel was loaded with different volumes of the concentrated supernatants as well as with different bovine serum albumin solutions to perform an extrapolation.
Western blotting
Brain membrane-enriched fractions, SH-SY5Y extracts or CHO-PS70 extracts (30 µg) were run on SDS-PAGE (7.5%, 12%, precast 4-15% gradient, or Tris-tricine 16%) after boiling at 98ºC for 5 min in 6× Laemmli sample buffer. Proteins were transferred by electrophoresis to nitrocellulose membranes and detected with antibodies against the C-terminal of LRP3 (mouse, 1:200, Sigma-Aldrich, St. Louis, MO, USA), N-terminal of LRP3 (rabbit, 1:100, Sigma-Aldrich, St. Louis, MO, USA), Flag (mouse, 1:1000, Sigma-Aldrich); C-terminal of LDLR (rabbit, 1:200, Sigma-Aldrich), C-terminal of ApoER2 (rabbit, 1: 2000, Abcam, Cambridge, UK), C-terminal of APP (rabbit, 1: 2000, Sigma-Aldrich), N-terminal of APP (rabbit, 1: 2000, Sigma-Aldrich) or α-tubulin (1:4000, Sigma-Aldrich) as a loading control. Primary antibody binding was visualized with fluorescently (IRDye) labeled secondary antibodies (1: 10000) and images were acquired using an Odyssey CLx Infrared Imaging system (LI-COR Biosciences GmbH).
Immunoprecipitation
Brain extracts (200 µL) or CHO-PS170 extracts (50 µL) were incubated on a roller for 2.5 h at room temperature with 100 µL of magnetic beads (Dynabeads, Merk Millipore) coupled to either the N-terminal LRP3 (Sigma-Aldrich), reelin (Millipore), C-terminal APP (Sigma-Aldrich) or apoE (Sigma-Aldrich). The input, bound and unbound fractions were analyzed by western blotting.
Immunofluorescence
CHO-PS70 cells overexpressing LRP3-flag were washed with cold Hank-buffered salt solution and fixed with 4% paraformaldehyde and 0.1 M EGTA for 10 minutes. Nonspecific sites were blocked with 10% (w/v) bovine serum albumin for 30 minutes. Cells were incubated with anti-LRP3 Ct (mouse; Sigma-Aldrich) for 1 hour followed by the secondary anti-body (Cy5 anti-rabbit; GE-Healthcare) for 1 hour. After 2 washes with PBS, cells were incubated briefly with Hoechst dye to label nuclei (Invitrogen). Pictures were acquired in a Leica SPEII upright TCL-SL confocal microscope using an oil-immersion 40x objective.
Statistical analysis
The distribution of data was tested for normality using a D’Agostino-Pearson test. The data were analyzed using unpaired Student´s t test (a Welch´s correction was employed in data with different standard deviations) or Mann-Whitney test. The results are presented as the means± SE and all the analyses were performed using GraphPad Prism (Version 7; GraphPad Software, Inc). p value < 0.05 was considered significant.