Journal: bioRxiv
Article Title: RareFold: Structure prediction and design of proteins with noncanonical amino acids
doi: 10.1101/2025.05.19.654846
Figure Lengend Snippet: PBMCs and tonsil organoids from independent donors were stimulated with WT, C14, or L17 peptides (0.25, 2.5, or 25 µM) for up to seven days. Each concentration was tested in duplicate wells. Positive controls were cells stimulated with the TLR7/8 agonist R848 and anti-CD3/CD28 antibodies. In all panels, the first column represents unstimulated cells. a) Cytokine concentrations (IL-6, TNF-α, IL-1β, IFN-γ, IL-12) in supernatants at days 2, 5, and 7, measured by ELISA (mean ± SD, pg/mL). C14 and L17 did not induce cytokine production above WT baseline or control with no stimulation. R848 or anti-CD3/CD28 strongly induced IL-6, TNF-α, IL-1β, and IFN-γ, whereas IL-12 was undetectable under all conditions. b) Antibody responses assessed by ELISA. The first three panels show total peptide-specific antibody levels (IgG/IgM/IgA) in supernatants from PBMC and tonsil organoid cultures at day 7 (0.25–25 µM peptides), with unstimulated cultures as the control. The fourth panel shows pooled sera from three healthy donors tested across serial dilutions (1:20–1:640), with non-coated wells as the control. In all cases, OD450 values for peptide-coated wells (WT, C14, L17) did not exceed controls, indicating no peptide-specific antibodies. Neither R848 nor anti-CD3/CD28 induced antibody responses. c) Immune cell subsets analyzed on day 7 by flow cytometry. Upper panels show PBMC cultures and lower panels show tonsil organoid cultures. Left: CD4⁺ and CD8⁺ T cells as a proportion of CD3⁺γδ⁻ T cells. Middle: naïve (CD19⁺CD27⁻) and switched memory (CD19⁺CD27⁺IgD⁻) B cells as a percentage of CD19⁺CD20⁺ cells. Right: monocytes (CD14⁺, CD16⁺) as a frequency of total monocytes. No differences were observed between cell cultures stimulated with modified peptides and those stimulated with the WT peptide, whereas R848 and anti-CD3/CD28 induced alterations in T-cell distributions and monocyte frequencies.
Article Snippet: Positive controls included cells stimulation with the TLR7/TLR8 agonist R848 (5 μg/mL, InvivoGen) or wells pre-coated with anti-CD3 and anti-CD28 antibodies (1 μg/mL each, Invitrogen) plus 5 ng/mL IL-2 for PBMCs.
Techniques: Concentration Assay, Enzyme-linked Immunosorbent Assay, Control, Flow Cytometry, Modification