Journal: bioRxiv

Article Title: LSD1 inhibitors induce neuronal differentiation of Merkel cell carcinoma by disrupting the LSD1-CoREST complex and activating TGFβ signaling

doi: 10.1101/2020.04.14.041657

Figure Lengend Snippet: a , Bulk mouse skin labeled with IgM-PE mouse isotype control. b , Bulk mouse skin labeled with NCAM-PE. DAPI - cells were sorted. c , Merkel cells labeled with IgM-PE mouse isotype control. d , Merkel cells labeled with NCAM-PE. DAPI - /NCAM + cells were sorted. Each plot shows the subpopulation gated for in the preceding plot to the left.

Article Snippet: Merkel cells were stained with anti-PSA-NCAM-PE antibody (Miltenyi Biotec, Cat. 130-117-394) or with mouse IgM-PE isotype control (Miltenyi Biotec, Cat. 130-120-070) according to manufacturer’s instructions, for 10 min at 4°C.

Techniques: Labeling, Control

Journal: Nanoscale

Article Title: Bioconjugates of photon-upconversion nanoparticles with antibodies for the detection of prostate-specific antigen and p53 in heterogeneous and homogeneous immunoassays.

doi: 10.1039/d5nr00176e

Figure Lengend Snippet: Fig. 1 (A) Schematic representation of bioconjugation of UCNPs with biomolecules: (1) ligand exchange reaction, replacing oleic acid residues with hydrophilic Cl−or BF4 −anions, (2) binding of the Ner-PEG-alkyne linker via the bisphosphonic group of neridronate, (3) copper(I)-catalyzed azide– alkyne cycloaddition (CuAAC) between the alkyne group on the UCNP surface and (3a) the azide-modified antibody or (3b) azide-modified streptavi- din. (B) The scheme of ULISA: (1) immobilization of the capture antibody onto the MTP surface, (2) binding of the analyte (antigen) to the capture antibody, and either (3a) binding of the UCNP–detection antibody conjugate or (3b) binding of the biotinylated detection antibody followed by (4) the UCNP–SA conjugate.

Article Snippet: Polyclonal anti-PSA antibody (AF1344), biotinylated polyclonal anti-PSA antibody (BAF1344), monoclonal anti-PSA antibody (MAB1344), polyclonal anti-p53 antibody (AF1355), biotinylated polyclonal anti-p53 antibody (BAF1355), monoclonal anti-p53 antibody (MAB1355), and p53 protein standard (SP450) were obtained from R&D Systems (USA).

Techniques: Binding Assay

Journal: Nanoscale

Article Title: Bioconjugates of photon-upconversion nanoparticles with antibodies for the detection of prostate-specific antigen and p53 in heterogeneous and homogeneous immunoassays.

doi: 10.1039/d5nr00176e

Figure Lengend Snippet: Fig. 3 Calibration curves obtained using Er-doped UCNPs conjugated with polyclonal antibodies in ULISA for (A) PSA and (B) p53. Error bars rep- resent the standard deviations of 3 independent wells. The dotted lines represent 3 times the standard deviation of the blank above the baseline of the regression curve, and their intersections with the respective fits correspond to the LODs.

Article Snippet: Polyclonal anti-PSA antibody (AF1344), biotinylated polyclonal anti-PSA antibody (BAF1344), monoclonal anti-PSA antibody (MAB1344), polyclonal anti-p53 antibody (AF1355), biotinylated polyclonal anti-p53 antibody (BAF1355), monoclonal anti-p53 antibody (MAB1355), and p53 protein standard (SP450) were obtained from R&D Systems (USA).

Techniques: Standard Deviation

Journal: bioRxiv

Article Title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

doi: 10.1101/2025.02.16.638489

Figure Lengend Snippet: (A) Schematic representation of the pro-phagocytic module screening strategy. (B) Correlation between log2 fold change and −log10 rho scores for pro-phagocytic CAR variant screens. Data represent 18 biological replicates across six NaSDC lentivirus batches. (C) FACS-based quantification of PC3-PSMA tumor cell phagocytosis by CAR-Ms (n = 4 biological replicates). (D) Schematic representation of the pro-inflammatory module screening strategy. (E) Correlation between log2 fold change and −log10 rho scores for pro-inflammatory CAR variant screens. Data represent 15 biological replicates across five NaSDC lentivirus batches. (F) Relative mRNA expression of TNF , IL6 and IL1B in CAR-Ms cocultured with PSMA positive target tumor cells (n = 4 biological replicates). (G) Schematic representation of the pro-infiltrating module screening strategy. (H) Correlation between log2 fold change and −log10 rho scores for pro-infiltrating CAR variant screens. Data represent 9 biological replicates across three NaSDC lentivirus batches. (I) Relative mRNA expression of MMP family genes in CAR-Ms cocultured with PSMA positive target tumor cells (n = 4 biological replicates). Dashed lines in ( C , F , I ) indicate −log10(0.05) (horizontal) and log2 fold change of truncated CARs (CARΔ) (vertical). Data in (C) are presented as mean ± s.e.m. and analyzed using one-way ANOVA followed by Dunnett’s multiple-comparison test.

Article Snippet: Biotinylated human PSMA proteins (ACROBiosystems) were added to the beads at a concentration sufficient to occupy 25% of the binding sites.

Techniques: Variant Assay, Expressing, Comparison

Journal: bioRxiv

Article Title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

doi: 10.1101/2025.02.16.638489

Figure Lengend Snippet: (A) Description of CAR variants used for individual characterization. (B) FACS-based quantification of PC3-PSMA tumor cell phagocytosis by UTD and CAR-Ms (n = 4 biological replicates). (C) Flow cytometric histograms showing surface expression of CD80 and CD86 in UTD and CAR-Ms cocultured with PSMA positive tumor cells. (D) Flow cytometric histograms of reactive oxygen species (ROS) levels in UTD and CAR-Ms cocultured with PSMA positive tumor cells. DCF, 2’-7’dichlorofluorescein. (E) Relative mRNA expression of TNF and IL6 in UTD and CAR-Ms cocultured with PSMA positive tumor cells (n = 4 biological replicates). (F) Relative mRNA expression of MMP11 and MMP13 in UTD and CAR-Ms cocultured with PSMA positive tumor cells (n = 4 biological replicates). Data in ( B) are presented as mean ± s.e.m. and analyzed using one-way ANOVA followed by Dunnett’s multiple-comparison. Data in ( C , D) are representative of three independent experiments. Dashed lines ( C , D ) represent the mean fluorescence intensity (MFI) for UTD macrophages.

Article Snippet: Biotinylated human PSMA proteins (ACROBiosystems) were added to the beads at a concentration sufficient to occupy 25% of the binding sites.

Techniques: Expressing, Comparison, Fluorescence

Journal: bioRxiv

Article Title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

doi: 10.1101/2025.02.16.638489

Figure Lengend Snippet: (A) Schematic illustration of the humanized immune system TME model. PC3-PSMA tumors were established bilaterally, followed by PBMC engraftment on day 7. On day 14, 5 × 10 6 UTD or CAR-Ms were injected IT. Tumors were harvested on day 18 for scRNA-seq. SC, subcutaneously. IV, intravenously. IT, intratumorally. (B) Proportions of cell types from scRNA-seq (left) and tSNE-based clustering of all sequenced cells (right). B, B cell. T, T cell. Mac, macrophage. (C) Dimensionality reduction (tSNE) and clustering for macrophages. Data are colored by treatment conditions. (D) Density plots within tSNE maps depicting the distribution of CAR-expressing cells. (E) AUC scores of M1 and M2 gene sets in the indicated macrophage clusters. (F) Feature plots showing expression levels of selected genes. (G) MFI of HLA-ABC and HLA-DR in UTD and CAR-Ms after 24 h coculture with PSMA positive tumor cells (n = 3 biological replicates). (H) AUC scores of T cell cytotoxicity and exhaustion gene sets in the indicated T cell clusters. Unless specified otherwise, data are presented as mean ± s.e.m. and analyzed using the two-tailed Student’s t-test.

Article Snippet: Biotinylated human PSMA proteins (ACROBiosystems) were added to the beads at a concentration sufficient to occupy 25% of the binding sites.

Techniques: Injection, Expressing, Two Tailed Test

Journal: bioRxiv

Article Title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

doi: 10.1101/2025.02.16.638489

Figure Lengend Snippet: (A) Specific killing of PC3-PSMA cells by UTD and COMB7 CAR-Ms at varying E/T ratios. Data represent two independent experiments from two human donors. (B) Specific killing of PC3-PSMA cells by UTD, CD247 CAR-Ms or COMB7 CAR-Ms at an E/T ratio of 3/1. Data collected from two human donors. (C-D) Specific killing of HER2 + SKOV3 or GPC3 + HepG2 cells by UTD or COMB7 CAR-Ms at an E/T ratio of 3/1 (n = 6 biological replicates). (E) NCG mice were IP injected with 1 × 10 6 PC3-PSMA cells, followed by treatment with PBS, 5 × 10 6 UTD, or 5 × 10 6 COMB7 CAR-Ms one day later. (F) Overall survival for mice in each treatment group (n = 6 for PBS, n = 5 for UTD and COMB7). (G) Tumor burden measured by bioluminescence (total flux). Data shown are individual values (n = 6 for PBS, n = 5 for UTD and COMB7). Unless specified otherwise, data are presented as mean ± s.e.m. and analyzed using the two-tailed Student’s t-test.

Article Snippet: Biotinylated human PSMA proteins (ACROBiosystems) were added to the beads at a concentration sufficient to occupy 25% of the binding sites.

Techniques: Injection, Two Tailed Test