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11 protocols using h3667

1

SARS-CoV-2 Antiviral Efficacy of FB2001

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FB2001 (batch #: D20071301) was provided by Frontier Biotechnologies Inc. (Nanjing, Jiangsu, China). To test the antiviral effect of FB2001 on SARS-CoV-2 in the presence of different concentrations of human serum, Vero E6 cells were inoculated with SARS-CoV-2 (2019-nCoV-WIV04) at MOI of 0.01 in a BSL-3 laboratory. The medium was removed at 1 h after incubation. Cells were washed with PBS, followed by additional 24-h incubation with different concentrations of FB2001 (16.60, 5.55, 1.85, 0.62, and 0.21 μM) diluted in DMEM (200 μL/well) containing different concentrations of human serum (10%, 20%, 30%, 40% and 50%; H3667; Sigma-Aldrich, St. Louis, MO, USA) at 37 °C. DMSO was used as a negative control. The cell supernatant was collected at 24h after incubation. The viral RNA in the supernatant was extracted using a MiniBEST viral RNA/DNA extraction kit (#9766; Takara, Japan).
The content of DMSO in the final testing concentration did not exceed 0.2%. This concentration of DMSO had no effect on the replication of SARS-CoV-2.
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2

Antigen-specific PBMC Expansion Assay

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PBMCs were isolated from EDTA collection tubes and processed using a Ficoll gradient. Antigen-specific PBMC expansion was adapted from previously described protocols61 ,62 . Fresh or cryopreserved PBMCs were stimulated with 130 pooled alpha-myosin peptides at a final concentration of 400ng/mL of each peptide or a pool of control CMV, EBV, and flu (CEF) peptides (AnaSpec, AS-61036-003). PBMCs were cultured in CTS OpTmizer medium (CTS OpTmizer T Cell Expansion SFM with CTS supplement A1048501, substituted with 2mM L-glutamine, and 2% human serum, Sigma-Aldrich, H3667) with cytokine supplementation (25ng/mL each of rhIL-2, rhIL-7 and rhIL-15, Peprotech). For myocarditis patients 1,2, and 3, expansion cultures were also supplemented with autologous LCLs to serve as antigen presenting cells at a ratio of 1 APC per 10 PBMC. For healthy donors, expansion was done directly from fresh, not cryopreserved, blood. Peptides were only added on the first day of culture. On day 3, additional media with cytokines was added. On day 7, cells were transferred to a new culture dish with fresh media with cytokines. Cells were analyzed or cryopreserved on day 14.
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3

Culturing Human Primary Fibroblasts

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All cells were grown in animal component-free conditions. Cells were cultured in DMEM 1 g/l glucose + phenol red (31885023, Gibco™), 10% human serum (H3667, Sigma Aldrich) and 1% 10,000 U/ml penicillin—10,000 µg/ml streptomycin (15140122, Gibco™). We used TryPLE™ Express (12604013, Gibco™) to detach cells. A Hirschmann haemocytometer was used to perform cell counts, which together with the cPDL numbers given by Promocell and the Coriell Institute, enabled assessment of cPDL at the time of seeding for experiments. Cells were transferred to antibiotic-free media for 48 to 72 h before seeding. Cells were seeded at approximately 30,000 cells/well in 12-well plates for staining experiments. For harvesting RNA for RT-qPCR analysis, cells were seeded at approximately 50,000 cells/well in 6-well plates. Dosing for trametinib studies was taken from our previous work, where a 10 µM dose suspended in 10% DMSO (HY-10999, MedchemExpress; J66650.AD, Thermo Scientific Alfa Aesar) resulted in attenuation of splicing factor expression and rescue of aspects of the senescent cell phenotype in wild-type human primary dermal fibroblasts [28 (link)].
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4

Immunocytochemical Staining of Cells

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Cells were grown on 13 mm coverslips in 12-well plates, washed in DPBS (14190136, Gibco™) before fixation with 4% paraformaldehyde and storage in DPBS. Before immunocytochemical staining, cells were washed in DPBS, and blocked using ADST [antibody diluent solution—triton: DPBS, 0.1 M L-Lysine (303341000, Thermo Scientific™), 1% w/v Human Serum Albumin Fraction V (12668-10GM, Sigma-Aldrich), Triton X-100 (A16046.AP, Thermo Scientific Alfa Aesar)] and 5% human serum (H3667, Sigma Aldrich) for 30 min. Cells were washed and primary antibodies at 2.5 µg/ml (suspended in ADST with 2% human serum) were applied overnight. After washing, secondary antibodies at 5 µg/ml and 4′,6-diamidino-2-phenylindole (DAPI, D1306, Invitrogen™) at 1 µg/ml (suspended in ADST with 2% human serum) were applied for 1 h, before mounting coverslips using Dako mounting medium (S302380-2, Agilent). Antibodies were sourced from Abcam: Rb anti-Ki67 (ab15580, ab16667), Ms anti-γH2AX (ab26350), Alexa Fluor ® 555 Goat pAb to Rb (ab150078, ab150086) and Alexa Fluor ® 488 Goat pAb to Ms (ab150117). Images were captured using the Leica DM4 B Upright Microsope at 10 × magnification and were counted manually using Leica Application Suite X 2019 3.7.1.21655v software (Leica Microsystems, Wetzlar, Germany).
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5

MART-1 TCR CD8 T Cell Generation

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MART-1 TCR CD8 T cells were generated as previously described.21 (link) In short, primary CD8 T cells were isolated from healthy male or female donor buffy coats (Sanquin, Amsterdam, the Netherlands), activated with plate-coated CD3 and CD28 antibodies (both 5 μg/ 2x106 cells/ 24-well, 16-0037-85 and 16-0289-85, Thermo Fisher Scientific) for 48 h in primary human CD8 T cell medium (RPMI Medium (GIBCO) containing 10% human serum (H3667, Sigma-Aldrich), 100 U/ml of Penicillin-Streptomycin (GIBCO), 100 U/ml IL-2 (Proleukin, Novartis), 10 ng/ml IL-7 (11340077, ImmunoTools) and 10 ng/ml IL-15 (11340157, ImmunoTools)). Right after 48 h activation, T cells were removed from activation plates and spinfected with MART-1 TCR retrovirus on Retronectin-coated (25 μg/ 24-well, TB T100B, Takara) non-tissue culture-treated plates. Cells were harvested and maintained in primary human CD8 T cell medium 24 h after transduction. 1 week after transduction, MART-1 TCR expression was checked by flow cytometry (α-mouse TCR β chain, 553172, BD Pharmingen) and cells were cultured in human CD8 T cell medium (RPMI containing 10% fetal bovine serum (Sigma), 100 U/ml of Penicillin-Streptomycin (GIBCO) and 100 U/ ml IL-2 (Proleukin, Novartis)).
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6

Ethical Approval for SCC Tumor and Serum Studies

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Investigation has been conducted in accordance with the ethical standards and according to the Declaration of Helsinki and according to national and international guidelines and has been approved by the authors' institutional review board. Human SCC tumors (n = 21) were obtained from SA Pathology under oversight of the Royal Adelaide Hospital Research Ethics Committee (approval number 120113). Human SCC serum (n = 3) samples were kindly donated by A/Prof Ian Darby, RMIT University, Victoria, Australia under oversight of the St Vincent's Hospital Research Ethics Committee (approval number HREC-A 129/09). The clinical investigations were conducted according to the Declaration of Helsinki principles and written informed consent was obtained. The control group for immunohistochemistry experiments consisted of human skin samples collected during cosmetic surgical procedures (ethics approval number 11-CHREC-F007) from four patients with no known dermatological conditions. Normal human serum (H3667) obtained from Sigma-Aldrich (Castle Hill, NSW, Australia) was used as a control for western blotting experiments using SCC patient serum.
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7

Establishment of Neuroblastoma Primary Cultures

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30 samples derived from 24 patients with neuroblastoma were included in this study. All tumor samples were collected from patients at the Great Ormond Street Hospital following written informed consent. In the case of minors, consent was obtained from adults with parental responsibility, with written assent from the child being optional for older participants. Ethical approval for the study was obtained through the national United Kingdom research ethics application system of the UK Health Research Authority; reference 14/WM/1253 “Establishing primary cultures and cell lines from pediatric cancers”. Tumor tissue was disaggregated manually into 1–2 mm fragments in X-VIVO 15 media (BE02-060F, Lonza) supplemented with 5% heat-inactivated human AB serum (H3667, Sigma-Aldrich), 100IU/mL penicillin (P4333, Sigma-Aldrich) and 100 μg/mL streptomycin (P4333, Sigma-Aldrich).
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8

Culturing Primary Human Cells

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HAoEC were cultured in Promocell Endothelial MV2 medium (C-22221, Promocell) supplemented with 2% foetal bovine serum (FBS) (16140071, Gibco™). All human primary dermal fibroblasts were grown in animal component-free conditions in Dulbecco's modified eagle medium (DMEM) 1 g/l glucose + phenol red (31885023, Gibco™), 10% human serum (H3667, Sigma Aldrich), and 1% 10,000 units/ml penicillin-10,000 µg/ml streptomycin (15140122, Gibco™). HCH were cultured in DMEM F12 (21331020, Gibco™), 1% nonessential amino acids (NEAA) (11140035, Gibco™), 10% FBS (10270106, Gibco™), and 1% penicillinstreptomycin (15, (link)140, 122, Gibco™) . Cells were grown on 13-mm coverslips in 12-well plates at approximately 30,000 cells per well.
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9

Plasma Stability Assay for Test Compounds

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To 100 uL of human plasma (H3667, Sigma-Aldrich) was added 1μL of 10 mM test compound (6, 9, and 10). The mixtures were incubated at 37 °C for 0, 60, 120 min. The reactions were stopped at each time point by adding 200 μL ice-cold methanol containing 50 μM internal standard. For the T0 min samples, 200 μL ice-cold methanol containing internal standard was added to human plasma prior to addition of test compound. Precipitated proteins were pelleted by centrifuging at 13500 rpm for 20 min at 4 °C. The supernatants were collected and analyzed on an Acquity UPLC / MS sysem, coupled with a PDA detector. Column chromatography was carried out on a C18 Column, 130Å, 1.7 μm, 2.1 mm × 100 mm. The percentage of compounds remaining at each time points relative to starting concentration were calculated using integrated UV peak areas normalized to the internal control. Procaine was included as the positive control compound in each experiment.
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10

Troponin I Assay Development and Evaluation

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For the Troponin I tests, we utilized commercialized kits (Humasis, Republic of Korea). CNTI recombinant antigen (GRNCTNIN101, Fappon) was employed as a control material and serially diluted using human serum (H3667, Sigma Aldrich). We prepared samples covering a broad concentration range, ranging from 0.5 ng/ml to 20 ng/ml (clinically relevant range: >0.4 ng/ml). Negative data were exclusively derived using the running buffer from each kit. Both positive and negative datasets were systematically captured as time-series at 10-s intervals.
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