Journal: Cell reports. Medicine

Article Title: Receptor transfer between immune cells by autoantibody-enhanced, CD32-driven trogocytosis is hijacked by HIV-1 to infect resting CD4 T cells.

doi: 10.1016/j.xcrm.2024.101483

Figure Lengend Snippet: Figure 2. Characterization of CD32-driven trogocytosis (A) 293T cells transiently expressing C-terminal GFP fusion proteins of FcgRs CD32A, CD32B, or CD32C or, as a control, the nucleocytoplasmic dNTPase SAMHD1 served as donors in co-cultures with CellTrace dye-stained SupT1 T target cells. All culture media contained IgG-depleted FCS. Shown are repre- sentative flow cytometry dot plots and the percentages of CD32+ and GFP+ target T cells. One experiment out of two is shown. (B) Schematic of topology determination of transferred CD32-GFP (top). Bottom: SupT1 T cells were co-cultured as described in (A) and stained with either an anti-GFP mAb or an isotype control antibody, both conjugated to Alexa 647, with or without prior cell permeabilization. One representative experiment is shown (n = 3). The illustration was created with BioRender.com. (C) 293T cells were co-transfected with plasmids encoding C-terminal GFP fusion proteins of CD32A, CD32B, or CD32C or, as a control, histone H2B-GFP, together with a plasmid encoding CCR5. After 2 days, cells were either left untreated or pre-treated with an anti-CD32 Ab or an isotype control Ab prior to co- cultivation with SupT1 T cells. One day later, the expression of GFP and CCR5 on the target T cells was determined by flow cytometry. Mean ± SEM are shown (n = 3). Asterisks indicate statistical significance by two-way ANOVA. p values were corrected for multiple comparison (Tukey). (D) Half-life of CD32 and CCR5 surface expression on SupT1 target cells following co-culture as in (A). Following 1 day of co-culture, SupT1 T cells positive for CD32-GFP were sorted by flow cytometry and kept in culture for an additional 9 days. The expression of CD32 (top) or CCR5 (bottom) on sorted cells was determined for up to 192 h of cultivation. One representative experiment is shown (n = 2). (E) Schematic of CD32B with important amino acids and motifs indicated. (F) Transfer of the indicated CD32B mutants, CD32A WT, CD32C WT, or H2B (GFP fusion proteins), assessed as in (A) (mean ± SEM; n = 4). Asterisks indicate statistical significance by one-way ANOVA. p values were corrected for multiple comparison (Dunnett). (G) Visualization of the material transfer from CD32B-GFP expressing 293T cells to LifeAct-mCherry-expressing SupT1 using live-cell imaging. 293T cells transiently expressing CD32B-GFP (green) were co-cultured with LifeAct-mCherry-expressing SupT1 cells (magenta), cultivated in IgG-depleted FCS and boosted with PGT151 antibody, and imaged using spinning disc microscopy for 4 h. The left panel shows the beginning of co-culture. (a) Labels the area with the first transfer event (middle panel). (b) Labels the area of the second transfer event (right panel). Dashed white box marks the area that is zoomed and depicted with individual time points before and after the transfer event (shown below). The time stamp (upper right corner, relative to the time frame which shows the transfer event (time 00:00) in zoom-ins). Scale bar, 10 mm. *p % 0.05; **p % 0.01; ***p % 0.001.

Article Snippet: Human T cell line SupT1 (DSMZ, ACC 140) was cultivated in RPMI 1640 GlutaMAX (Gibco) supplemented with 10% (v/v) FBS and Penicillin-Streptomycin (100 IU/mL).

Techniques: Expressing, Control, Staining, Cytometry, Cell Culture, Transfection, Plasmid Preparation, Comparison, Co-Culture Assay, Live Cell Imaging, Microscopy

Journal: Cell reports. Medicine

Article Title: Receptor transfer between immune cells by autoantibody-enhanced, CD32-driven trogocytosis is hijacked by HIV-1 to infect resting CD4 T cells.

doi: 10.1016/j.xcrm.2024.101483

Figure Lengend Snippet: Figure 3. CD32-driven trogocytosis is boosted by T cell-autoreactive antibodies associated with chronic HIV-1 infection (A) CD32 expression on CD4 T cells from peripheral blood of healthy donors (HD) (n = 23) and chronic HIV-1 infected patients (CHI) (n = 39). Median with 95% CI are shown. Asterisks indicate statistical significance by Mann-Whitney test. (B) 293T cells transiently co-expressing CD32B-GFP and CCR5 were pre-treated with the indicated patient sera before 1 day of co-culture with SupT1 T cells. Shown are the percentage of CD32B-GFP+ and CCR5+ target cells (median with 95% CI, each dot represents a different patient; see also Figure S7C). CHI, chronic HIV-1 infection; ART, anti-retroviral therapy; AHI, acute HIV-1 infection. Fiebig stages II-III of acute HIV-1 infection42; HIV-2, HIV type 2; HTLV-1, human T cell lymphotropic virus type 1; HCV, hepatitis C virus; DENV, dengue virus; YFV, yellow fever virus-vaccinated; SARS-CoV-2, severe acute respiratory syndrome coronavirus type 2; EC, Echinococcus multilocularis; SCH, Schistosoma spp.; TB, Mycobacterium tuberculosis; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; CG, cryoglobulinemia. Asterisks indicate statistical significance by Mann-Whitney test. (C) Percentage of GFP+ target cells after 1 day of co-culture with 293T cells as in (B). IgG was depleted from the sera of two healthy donor (HD) and two HIV-1 patient (CHI) samples from (B, pink and red) and input (original sera), flowthrough and eluate of the IgG depletion were used for pre-treatment of cells prior to co- culture. Mean of two donors from each category is shown. (D) Correlation of antibody binding to SupT1 T cells and CD32B-GFP trogocytosis as in (B), with sera from HIV-1 patients. P, Pearson correlation coefficient. (E) Binding of sera with high or low trogocytotic activity (pink and red dots in B) to primary CD4 T cells as detected with fluorochrome-coupled anti-human IgG Ab (median with 95% CI, CD4 T cells; n = 3). Kruskal-Wallis test with Dunn’s multiple-testing correction. (F) A panel of bNAbs was analyzed for binding to uninfected resting CD4 T cells (top) or activated CD4 T cells (bottom). Mean ± SEM; n = 3. Asterisks indicate statistical significance by one-way ANOVA (top) or three-way ANOVA (bottom). p values were corrected for multiple comparison (Dunnett). (G) Purified, CMV-encoded, soluble Fc-binding proteins gp34 and gp68, or control proteins gp34 non-binding mutant (mtrp; W65F) and soluble ICOSL (inducible T cell co-stimulator ligand) were added to 293T donor cells as in (A), in the presence of PGT151 Ab, and subsequently co-cultured with SupT1 T cells. CD32 transfer was evaluated as in (B). Asterisks indicate statistical significance by two-way ANOVA. p values were corrected for multiple comparison (Tukey). *p % 0.05, **p % 0.01, ***p % 0.001; n.s., not significant. (H) Schematic of the determinants of antibodies for trogocytosis enhancement.

Article Snippet: Human T cell line SupT1 (DSMZ, ACC 140) was cultivated in RPMI 1640 GlutaMAX (Gibco) supplemented with 10% (v/v) FBS and Penicillin-Streptomycin (100 IU/mL).

Techniques: Infection, Expressing, MANN-WHITNEY, Co-Culture Assay, Retroviral, Virus, Binding Assay, Activity Assay, Comparison, Control, Mutagenesis, Cell Culture

Journal: Nature Communications

Article Title: High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus

doi: 10.1038/s41467-024-50710-5

Figure Lengend Snippet: A Flow chart illustrating the identification of functional candidate SNPs from SLE GWAS data. B SNP-seq: To generate the SNP-seq construct (top), a 31 bp sequence centered on the SNP is positioned between two type IIS restriction enzyme (IIS RE) binding sites. SNPs that fail to bind regulatory proteins such as transcription factors (TF) are negatively selected (bottom), allowing enrichment of protected constructs by PCR. The whole construct can be amplified using primers as per Supplementary Data . Bio biotin. Figure 1B was created with BioRender.com released under a Creative Commons Attribution-NonCommerical-NoDerivs 4.0 International license. C The experimental procedure for SNP-seq; NE nuclear extract, Bio biotin. D Spearman’s correlation with a two-tailed test of SNP-seq allele counts normalized to control between PBMC and BL2 samples (ρ = 0.89, P < 1 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\times$$\end{document} × 10 −15 ). E We selected 248 SNPs that passed next-generation sequencing quality control (NGS-QC) and demonstrated progressive allele-specific protection (Suppl. Fig. 1C). Source data are provided as a Source Data file.

Article Snippet: Human B cell line BL2 was from DSMZ (catalog number ACC 625) and human B cell line Daudi was kindly provided by Dr. Baglaenko Yuriy.

Techniques: Functional Assay, Construct, Sequencing, Binding Assay, Amplification, Two Tailed Test, Control, Next-Generation Sequencing

Journal: Nature Communications

Article Title: High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus

doi: 10.1038/s41467-024-50710-5

Figure Lengend Snippet: A Seven biallelic and two triallelic (rs2297550 and rs936394) SNPs showed consistent allele-imbalanced binding for nuclear by EMSA. Allele-specific gel shift/binding marked with red circles. Experiments were repeated three times using distinct nuclear extracts. Representative blots from PBMCs are shown here; BL2 data and negative SNPs are provided in Supplementary Fig. and Supplementary Data . B Luciferase reporter assay between the reference (red) and alternative (blue) alleles of nine candidate regulatory SNPs from A in Daudi B cells (mean \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\pm$$\end{document} ± s.d, n = 8 biological replicates, Mann–Whitney two-tailed U -test with two-stage step-up correction for multiple hypothesis testing: rs2297550 p = 0.00047, rs906868 p = 0.0013, rs936394 p = 0.00047, rs9907966 p = 0.0071, rs13213604 p = 0.0085). C Diagram displaying the position of 5 SNPs that showed consistent significant differences between alleles through EMSA and luciferase reporter assay; rs2297550 in promoter of IKBKE , rs906868 in intergenic region between YPEL5 and LBH , rs936394 in intron of WBP2 , rs9907966 in intron of IKZF3 , rs13213604 in intron of BLTP3A . The unit of chromosome position is in kilobases (Kb). A diagram of gene features including exon, intron, and UTR was generated using GSDS 2.0 ( http://gsds.gao-lab.org/index.php ). Source data are provided as a Source Data file.

Article Snippet: Human B cell line BL2 was from DSMZ (catalog number ACC 625) and human B cell line Daudi was kindly provided by Dr. Baglaenko Yuriy.

Techniques: Binding Assay, Gel Shift, Luciferase, Reporter Assay, MANN-WHITNEY, Two Tailed Test, Generated