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10 protocols using dmem with high glucose

1

Co-Immunoprecipitation and VIP Assay in HEK293T Cells

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HEK293T cells (kindly provided by Hiroyuki Takatsu, Kyoto University) were plated on 6-cm dishes and cultured in DMEM with high glucose (Nacalai Tesque) supplemented with 10% fetal bovine serum (FBS). The cells were transfected with expression vectors for an EGFP fusion construct and a hemagglutinin (HA) fusion construct using Polyethylenimine Max and cultured for 24 h. The cells were then lysed in lysis buffer (50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid [HEPES]-KOH, pH 7.4, 100 mM KCl, 5 mM NaCl, 3 mM MgCl2, 0.5% Triton X-100, 10% glycerol, and 1 mM dithiothreitol [DTT]) containing a protease inhibitor cocktail (Nacalai Tesque). The cell lysates were immunoprecipitated with GST–anti-GFP Nb prebound to glutathione–Sepharose 4B beads, and bound proteins were subjected to SDS–PAGE and immunoblotting analysis using anti-HA, anti-mRFP, anti-tRFP, or anti-GFP antibodies as described previously (Katoh et al., 2015 (link), 2016 (link); Nozaki et al., 2017 (link)).
The VIP assay was performed as described previously (Katoh et al., 2015 (link), 2016 (link)) with a slight modification; in this study, cells expressing EGFP-tagged and mChe-tagged proteins were lysed in the HMDEKN cell lysis buffer (10 mM HEPES, pH 7.4, 5 mM MgSO4, 1 mM DTT, 0.5 mM EDTA, 25 mM KCl, 0.05% NP-40; Cole et al., 1998 (link)).
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2

Fluorescent Protein Binding Assay

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The VIP assay was performed as described previously (Katoh et al., 2015 (link), 2016 (link)). Briefly, HEK293T cells grown to ∼1.6 × 106 cells on a six-well plate in DMEM with high glucose (Nacalai Tesque) supplemented with 5% fetal bovine serum (FBS) were transfected with expression vectors for EGFP and mChe/tRFP fusions (2 µg each) using Polyethylenimine Max (20 µg). After 24 h, the cells were lysed in 250 µl of lysis buffer (20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid–KOH, pH 7.4, 150 mM NaCl, 0.1% Triton X-100, and 10% glycerol) containing a protease inhibitor cocktail (EDTA-free; Nacalai Tesque). The lysates were mixed with 5 µl of GST–anti-GFP Nb beads at 4°C for 1 h. After washing three times with lysis buffer, the precipitated beads bearing fluorescent proteins were observed using an all-in-one-type fluorescence microscope (Biozero BZ-8000, Keyence) with a 20×/0.75 objective lens under constant conditions (sensitivity ISO 400, exposure 1/30 s for green; and sensitivity ISO 800, exposure 1/10 s for red) unless otherwise noted.
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3

Chondrogenic Differentiation of hACs in Micromass Culture

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hACs were cultured as a micromass (1 × 105 cells in 10 μL) on 12 well plates to evaluate ECM synthesis ability as described previously (Tateiwa et al., 2022 (link)). After a 3 h incubation, the chondrogenic basal media and each of the EV, BG sample or vehicle control (PBS) were added. Chondrogenic basal media consisted of DMEM with high glucose (Nacalai), 50 μg/mL L‐ascorbic acid, 40 μg/mL L‐proline (Wako), 1% ITS+ Premix (Corning, New York, NY, United States) and 1% AA, and each sample of sEVs, BG or vehicle control was added at a concentration of 5 × 109 particles/mL for each of the EV group elements or at an equivalent volume for each of the BG or control groups. After 2 days of incubation, cell masses were collected by QIAzol (Qiagen, Hilden, Germany). RNA was isolated by Direct‐zol RNA Microprep kit (Zymo Research, Irvine, CA, United States) and cDNA was synthesized by using ReverTra Ace qPCR RT Master Mix with gDNA Remover (Toyobo) as described previously (Hanai et al., 2020 (link)). Gene expression (COL1A1 and COL2A1) was assessed by real‐time PCR on a Step One Plus system (Applied Biosystems, Carlsbad, CA, USA). Beta‐actin (ACTB) was used as an internal control gene for normalization and relative gene expression was calculated with the 2−ΔΔ CT method. Primer sequences are listed in Table S1.
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4

Establishment of IFT27 and CEP19 Knockout Cell Lines

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Antibodies, chemicals, and plasmids used in this study are listed in Supplemental Table S1. HEK293T cells (RBC2202; RIKEN BioResource Research Center) were cultured in DMEM with high glucose (Nacalai Tesque) supplemented with 5% fetal bovine serum (FBS). hTERT-RPE1 cells (CRL-4000; American Type Culture Collection) were grown in DMEM/Ham’s F-12 medium (Nacalai Tesque) supplemented with 10% FBS and 0.348% sodium bicarbonate at 37°C in 5% CO2. IFT27-KO cells (cell line #IFT27-2-2) and CEP19-KO cells (cell lines #CEP19-1-2 and #CEP19-1-12) were established from hTERT-RPE1 cells, as described previously (Nishijima et al., 2017 (link); Zhou et al., 2022 (link)).
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5

Cell culture conditions for various cell lines

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HEK293 cells (ATCC CRL-1573), HT-29 cells (ATCC HTB-38), U-251 MG cells (CVCL_0021), SH-SY5Y cells (ATCC CRL-2266), HeLa cells (ATCC CCL-2), and their KO derivatives were cultured in Dulbecco's Modified Eagle Medium (DMEM) with high glucose (Nacalai Tesque). Raji cells (ATCC CCL-86), THP-1 cells (ATCC TIB-202), K-562 cells (ATCC CCL-243), and their derivatives were cultured in RPMI medium 1640 (Nacalai Tesque). HAP1 cells (kindly provided by Thijn Brummelkamp, The Netherlands Cancer Institute, Amsterdam, The Netherlands) and their KO derivatives were cultured in Iscove's Modified Dulbecco's Medium (Nacalai Tesque). CHO (Chinese Hamster Ovary) K1 cells (ATCC CCL-61) and their derivatives were maintained in DMEM/F-12 (Nacalai Tesque). All cell culture medium contained 10% heat-inactivated fetal bovine serum (FBS) (172012-500ML, Sigma). All cells were maintained in an incubator at 37 °C and 5% CO2.
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6

Culturing HEK293, HeLa, and CHO K1 Cells

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HEK293 cells (ATCC CRL-1573) or HeLa cells (ATCC CCl-2) and their derivatives were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose (Nacalai Tesque, Japan) containing 10% heat-inactivated Fetal Bovine Serum (FBS, Sigma). CHO K1 cells (ATCC CCL-61) and their derivatives were maintained in DMEM/F-12 (Nacalai Tesque) supplemented with 10% heat-inactivated FBS. All cells were maintained at 37 °C and in 5% CO2.
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7

Characterization of human IFT54/TRAF3IP1 isoforms

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IFT54 constructs used in this study are listed in Table S1. In the current and previous studies (Hiyamizu et al., 2023 (link); Katoh et al., 2016 (link)), we used a cDNA encoding human IFT54/TRAF3IP1 isoform 2 (625-amino acids; NP_001132962) instead of isoform 1 (691-amino acids; NP_056465), because the IFT54 proteins from most other vertebrate species correspond to isoform 2. The other constructs were described previously (Hiyamizu et al., 2023 (link)). Antibodies used in this study are listed in Table S2. Glutathione S-transferase (GST)-tagged anti-mCherry Nb (LaM-2 version) prebound to glutathione–Sepharose 4B beads were prepared as described previously (Ishida et al., 2021 (link); Katoh et al., 2015 (link)). SAG was purchased from Enzo Life Sciences. hTERT-RPE1 cells (American Type Culture Collection, CRL-4000) were grown in DMEM/Ham's F-12 medium (Nacalai Tesque) supplemented with 10% fetal bovine serum (FBS) and 0.348% sodium bicarbonate at 37°C in 5% CO2. HEK293T cells (RIKEN BioResource Research Center, RBC2202) were cultured in DMEM with high glucose (Nacalai Tesque) supplemented with 5% FBS.
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8

Culturing KSHV-infected Lymphoma Cells

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A KSHV-infected (KSHV +) primary effusion (body cavity-based) lymphoma cell line, BC3, was grown in RPMI 1640 medium (Nacalai Tesque, Japan) containing 10% heat inactivated fetal bovine serum (FBS; Equitech-Bio, United States). The stable control (BC3-ScrambledKO) and PML-knockout BC3 cells (BC3-PMLKO) were also grown in the same medium supplemented with puromycin (5 μg/mL). BC3 cells stably overexpressing PML (BC3PML) were established by transduction with the retrovirus expressing the longest PML (see below) and maintained in the same medium supplemented with hygromycin B (500 μg/mL). The Lenti-X 293T and GP2 cell lines (originated from HEK293) were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose (4.5 g/L; Nacalai Tesque, Japan), supplemented with 10% Tet system approved FBS (Clontech, United States) and heat inactivated 10% FBS (Equitech-Bio, United States), respectively. All the media contained 100 μ/mL penicillin G, 100 μg/mL streptomycin, and 0.25 μg/mL amphotericin B (Nakalai Tesque, Japan), and the cells were cultured at 37°C in a 5% CO2 atmosphere.
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9

Differentiation of Hu5/E18 cells into myocytes

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The Hu5/E18 cell line was purchased from RIKEN BioResource Center. Hu5/E18 cells were maintained and differentiated as previously reported.44 (link) Cells were maintained in DMEM with high glucose (Nacalai Tesque) containing 20% fetal bovine serum (Gibco). Cells were differentiated into human myocytes in DMEM containing 5 μg/mL holo-transferrin bovine (Sigma-Aldrich), 10 μg/mL insulin (bovine, Sigma-Aldrich), 10 nM sodium selenite (Sigma-Aldrich), and 2% horse serum (Gibco) 7 days before SeV-L-N-I transduction into iPSCs. The iPSCs were transduced with SeV-L-N-I on day 0, dissociated with Accumax plus 10 μM Y-27632, and then transferred onto Hu5/E18-cultured plates on day 7. The medium was changed to MN medium. Cells were fixed with 4% paraformaldehyde (pH 7.4) for 30 min on day 14 and assessed by immunocytochemistry.
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10

Culture of 293FT cells in DMEM

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293FT cells (Thermo Fisher Scientific) were cultured at 37 °C in 5% CO2 in DMEM with high glucose (Nacalai Tesque) containing 10% fetal bovine serum (Japan Bio Serum), 0.1 mM nonessential amino acids (Thermo Fisher Scientific), and 1 mM sodium pyruvate (Sigma-Aldrich).
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