For quantitative RT-PCR, SYBR® GREEN PCR Master Mix (Applied Biosystems, Foster City, CA) was used for all amplifications, which were performed in a 7500 Real-Time PCR thermal cycler (Applied Biosystems) using the following parameters: 95° for 15 seconds, then 60° for 60 seconds for 40 cycles. GAPDH was used as the endogenous reference while Priess messenger RNA (mRNA) was used as the calibrator. Quantification of gene expression was determined using the relative standard curve
method developed by Applied Biosystems. Briefly, a standard curve is generated with gene-specific oligonucleotide primers and cellular mRNA from the calibrator sample (Priess), and this curve is used to determine the quantity of specific mRNA in the unknown samples. All samples are Hydroxychloroquine in vitro normalized to the endogenous reference mRNA (GAPDH) and are then
divided by the normalized calibrator value. The normalized calibrator therefore has a value of 1, and the normalized unknown samples are expressed as an n-fold difference relative to the calibrator. Wild-type NVP-BKM120 cost or LAMP-2-deficient B-LCL were incubated with the rat 3.5.9-13F10 antibody or the mouse L243 mAb for 60 min on ice to detect surface HLA-DR4β or HLA-DR dimers, respectively. After washing with phosphate-buffered saline (PBS) + 1% bovine serum albumin (BSA) + 0·1% NaN3, cells were incubated with the FITC-conjugated F(ab′)2 fragment of goat anti-mouse IgG or the Cy2-conjugated F(ab′)2 fragment of donkey anti-rat IgG secondary antibody for 30 min on ice. Cells were washed again and fixed in 1% paraformaldehyde. Additionally, wild-type or LAMP-2-deficient B-LCL were fixed with 1% paraformaldehyde, permeabilized with 0·1% saponin, blocked with goat serum in PBS + 1% BSA + 0·1% NaN3, and incubated for 60 min on ice with the MTMR9 mouse mAb W6/32 or L243 to detect intracellular MHC class I molecules and HLA-DR dimers, respectively or
with the mouse mAb MaP.DM1 or a mouse mAb for HLA-DO to detect intracellular HLA-DM or HLA-DO, respectively. After washing with PBS + 1% BSA + 0·1% NaN3, cells were incubated with the PE-conjugated F(ab′)2 fragment of rabbit anti-mouse immunoglobulin for 30 min on ice. Cells were washed again before analysis. Flow cytometry was performed on a FACScan™, and the data were analysed with cellquest™ software (BD Biosciences). Wild-type 7C3.DR4 and LAMP-2-deficient DB.DR4 B-LCL were washed with cold Hanks’ balanced salt solution (HBSS) + 3% BSA and incubated with 5 mg/ml FITC-albumin (Sigma-Aldrich) for 0 and 120 min at 37°. At each time-point, cells were again washed with cold HBSS + 3% BSA and fixed with 1% paraformaldehyde. Uptake of FITC-albumin was determined using flow cytometry performed on a FACScan™, and the data were analysed with cellquest™ software (BD Biosciences). Wild-type Frev or LAMP-2-deficient DB.DR4 B-LCL were incubated with 200 nm LysoTracker Red (Invitrogen, Carlsbad, CA) for 18 hr at 37°.