Journal: Nature Communications

Article Title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer

doi: 10.1038/s41467-025-66800-x

Figure Lengend Snippet: a Schematic of B2M KO generation in murine SCLC primary cell line. Created in BioRender. Meder, L. (2025) https://BioRender.com/4u5k5v3 . b , c Relative MHC-I or PD-L1 expression of WT and MHC-I KO cells analyzed by flow cytometry, determined by mean fluorescence intensity (MFI) normalized to IgG control. Histograms of one representative experiment are shown ( n = 3 biological replicates). d Schematic of experimental setup showing intravenous injection of MHC-I KO and WT cells into immunocompetent C57BL/6/immunodeficient NSG mice, tissue harvest and subsequent IHC and FACS analyses. Created in BioRender. Meder, L. (2025) https://BioRender.com/w6kb2vb . e Representative images of H&E-stained livers and intestinal lymph node tissues from iv. WT and MHC-I KO injected immunocompetent mice. Scale bars, liver 2.5 mm, for lymph nodes 1 mm. Additional FACS based quantification of liver tumor cell infiltration ( n = 4 mice per group). f Representative images of CD45 and CD3 IHC staining in liver tissue from WT and MHC-I KO-injected mice. Quantification was performed using QuPath analysis with 5 regions of interest (ROIs) analyzed per individual ( n = 2 per group). g Representative histograms showing CD107a expression measured by flow cytometry and corresponding quantification (WT n = 4 mice, MHC-I KO n = 5 mice). h Representative images of H&E- and NCAM1-stained liver tissue of MHC-I KO and WT injected immunodeficient NSG mice (MHC-I KO n = 3, WT n = 4) and quantification of tumor cell infiltration in 5 representative ROIs by QuPath analysis. Scale bars, H&E 2.5 mm, NCAM1 100 μm. Statistical analysis was performed using a two-sided, unpaired Student’s t -test. Data in this figure are shown as mean ± SEM. ns not significant, * p < 0.05, ** p < 0.01, *** p < 0.001. Source data are provided as a Source Data file.

Article Snippet: The following antibodies and isotype controls were used for staining: CD3 (Alexa-Fluor-700, clone 17A2, Biolegend, Cat. #100216), CD4 (PE-Dazzle 594, clone GK1.5, Biolegend, Cat. # 100456), CD45 (APC-Cy7, clone 30-F11, Biolegend, Cat. # 103116), CTLA-4 (PE, UC10-4B9 Thermo Fisher, Cat. #14-1522-82), CD56 (APC, R&D Systems, clone 809220, Cat. # FAB7820A), CD8a (FITC, clone 53-6.7, Biolegend, Cat. # 100705; Pacific blue, clone 53-6.7, Biolegend, Cat. # 100728), H2Kb (Pacific Blue, clone AF6-88.5, Biolegend, Cat. # 116517), PD-1 (APC, clone 29 F.1A12, Biolegend, Cat. # 135210), PD-L1 (PE-Cy7, clone 10 F.9G2, Biolegend, Cat. # 124313), TIM-3 (PerCP-Cy5.5, clone B8.2C12, Biolegend, Cat. # 134011), Rat IgG2aΚ (Biolegend FITC, Cat. # 400505, PE, Cat. # 400507, PerCP-Cy5.5, Cat. # 400531, APC, Cat. # 400511, Alexa Fluor 700, Cat. # 400528), PE-Dazzle594 Armenian Hamster IgG (PE-Dazzle594, clone HTK888, Biolegend, Cat. # 400951), Rat IgG2bΚ (PE-Cy7, clone RTK4530, Biolegend, Cat. # 400617) and mouse BALB/c IgG2aΚ (Pacific Blue, clone G155-178, BD Biosciences, Cat. # 558118).

Techniques: Expressing, Flow Cytometry, Fluorescence, Control, Injection, Staining, Immunohistochemistry

Journal: bioRxiv

Article Title: Genotype-phenotype correlations in Wilms tumor initiation

doi: 10.1101/2025.11.19.689177

Figure Lengend Snippet: (A) Fraction of NCAM1+/ALDERED double positive cells in developing embryonic kidneys comparing control versus Wt1 mutants from the three lineage-specific Cre-drivers at E12.5 and E18.5. No significant differences observed between groups, using a non-parametric Mann-Whitney U test between groups. P-values indicated. (B) Raw data files from the Six2 GCiP driven control versus mutant kidneys, using DEAB for setting the cutoff for the ALDH activity measured through ALDERED expression. (C) Raw data files from the Foxd1 GC driven control versus mutant kidneys, using DEAB for setting the cutoff for the ALDH activity measured through ALDERED expression. (D) Raw data files from the Wt1 CE driven control versus mutant kidneys, using DEAB for setting the cutoff for the ALDH activity measured through ALDERED expression.

Article Snippet: The rest of the single cells were stained for Ncam1 (1:125; NCAM-1/CD56 Antibody, R&D systems, AF2408) with a Donkey-anti-Goat Alexa Fluor 405 (1:1500; Abcam, ab175665), followed by the ALDERED assay kit (EMD Millipore, SCR150) according to the manufacturer’s protocol.

Techniques: Control, MANN-WHITNEY, Mutagenesis, Activity Assay, Expressing

Journal: bioRxiv

Article Title: Genotype-phenotype correlations in Wilms tumor initiation

doi: 10.1101/2025.11.19.689177

Figure Lengend Snippet: (A) ALDH paralogue enrichment in Wilms tumor Xenograft derived CSCs. A comparison between unsorted and sorted fractions, for NCAM1+/ALDEFLUOR- and NCAM1+/ALDEFLUOR+. (B) ALDH paralogue protein staining in ex vivo kidney cultures, cultured for 24, 48 and 72 hours. Scale bar: 50µm. (C) FOXD1 and ALDH1A2 protein expression in ex vivo kidney cultures cultured for 96 hours. Scale bar: 50µm.

Article Snippet: The rest of the single cells were stained for Ncam1 (1:125; NCAM-1/CD56 Antibody, R&D systems, AF2408) with a Donkey-anti-Goat Alexa Fluor 405 (1:1500; Abcam, ab175665), followed by the ALDERED assay kit (EMD Millipore, SCR150) according to the manufacturer’s protocol.

Techniques: Wilms Tumor Assay, Derivative Assay, Comparison, Staining, Ex Vivo, Cell Culture, Expressing

Journal: bioRxiv

Article Title: Genotype-phenotype correlations in Wilms tumor initiation

doi: 10.1101/2025.11.19.689177

Figure Lengend Snippet: (A) Staining for CSC markers NCAM1, ALDH1A2, SIX2 and CITED1 in the normal developing embryonic kidney at E12.5 and E18.5. White arrows indicate triple-marker expressing cells. Scale 100µm. (B) CSC marker expression in Six2 GCiP driven Wt1 mutant kidneys at E12.5 and E18.5. Scale 100µm. (C) CSC marker expression in Foxd1 GC driven Wt1 mutant kidneys at E12.5 and E18.5. White arrows indicate triple-marker expressing cells. Scale 100µm. (D) CSC marker expression in Wt1 CE driven Wt1 mutant kidneys at E12.5 and E18.5. White arrows indicate triple-marker expressing cells. Scale 100µm.

Article Snippet: The rest of the single cells were stained for Ncam1 (1:125; NCAM-1/CD56 Antibody, R&D systems, AF2408) with a Donkey-anti-Goat Alexa Fluor 405 (1:1500; Abcam, ab175665), followed by the ALDERED assay kit (EMD Millipore, SCR150) according to the manufacturer’s protocol.

Techniques: Staining, Marker, Expressing, Mutagenesis

Journal: bioRxiv

Article Title: Genotype-phenotype correlations in Wilms tumor initiation

doi: 10.1101/2025.11.19.689177

Figure Lengend Snippet: (A) Fraction of NCAM1+/ALDERED double positive cells in developing embryonic kidneys comparing control versus LIN28B mutants at E12.5 and E18.5. No significant differences observed between groups, using a non-parametric Mann-Whitney U test between groups. (B) Raw data files from the control versus mutant kidneys at E12.5, using DEAB for setting the cutoff for the ALDH activity measured through ALDERED expression. (C) Raw data files from the control versus mutant kidneys at E18.5, using DEAB for setting the cutoff for the ALDH activity measured through ALDERED expression.

Article Snippet: The rest of the single cells were stained for Ncam1 (1:125; NCAM-1/CD56 Antibody, R&D systems, AF2408) with a Donkey-anti-Goat Alexa Fluor 405 (1:1500; Abcam, ab175665), followed by the ALDERED assay kit (EMD Millipore, SCR150) according to the manufacturer’s protocol.

Techniques: Control, MANN-WHITNEY, Mutagenesis, Activity Assay, Expressing

Journal: bioRxiv

Article Title: Co-Stimulatory Blockade Prevents Intragraft Accrual of Class-Switched, Activated B Cells Despite Failing to Prevent T-Cell Mediated Rejection

doi: 10.1101/2025.10.24.683156

Figure Lengend Snippet: A) UMAP demonstrating distribution of cells previously annotated as γ/δ T cells. B) FeaturePlots demonstrating distribution of indicated genes and lack of segregation of T, NK, and γ/δ T cells, where T cell genes are in blue and NK cell genes are in red. C) Representative immunofluorescent image demonstrating presence of T (CD3ε + ), NK (CD3ε - , CD56 + ), and γδ T cells (CD3ε + , TCRδ + ) cells in TAC_1. D) UMAPs demonstrating successful integration (top) of the Peters and Depasquale dataset, and distribution of those reference markers in the integrated dataset (bottom). E) UMAP demonstrating segregation of annotated γ/δ T cell and NK cell types F) Violin plot showing expression of marker genes G) Bar plot demonstrating distribution of cell type by mIS.

Article Snippet: Next, the primary antibodies incubated overnight at 4°C with rabbit anti-human CD3ε (dilution 1:50, 85061, Cell Signaling Technology), goat anti-human CD56 (dilution 1:50, AF2408, R&D Systems), mouse anti-human TCR δ (dilution 1:50, sc-100289, Santa Cruz), and rat anti-human CD16 (dilution 1:100, ab308607, Abcam), all were diluted in the blocking solution used previously.

Techniques: Expressing, Marker

Journal: Scientific Reports

Article Title: Investigating the role of molecular coating in human corneal endothelial cell primary culture using artificial intelligence-driven image analysis

doi: 10.1038/s41598-025-14367-4

Figure Lengend Snippet: Validation of the AI-based method for quantifying the various hCECs morphological parameters. ( A ) Endothelial cell cultures of highly variable quality used for AI algorithm validation. Cell lateral membranes were labeled with anti-NCAM (in green) and the nuclei were counterstained using DAPI (in blue). The images were taken in the center of each well at x10 magnification with a zoom x6 in the center of the image. Image scale bar = 300 μm, zoom scale bar = 50 μm. ( B ) Evaluation of 6 parameters across 4 different culture qualities. Graph illustrating 6 objective evaluation parameters across 4 culture qualities: (1) EndoMT cells at passage 7; (2) Mixed population quality at passage 5; (3) High quality – young donor (below 30 yo) at passage 4; (4) High quality – aged donor (over 30 yo), at passage 11. ns = non-significant = p-value > 0.05, *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001.

Article Snippet: The hCECs were incubated with the primary antibody for 1 h at 37 ̊C: NCAM (1:400, MAB24081, R&D Systems, Minneapolis, MN, USA).

Techniques: Biomarker Discovery, Labeling

Journal: Scientific Reports

Article Title: Investigating the role of molecular coating in human corneal endothelial cell primary culture using artificial intelligence-driven image analysis

doi: 10.1038/s41598-025-14367-4

Figure Lengend Snippet: Representative example of the effects of coating molecules on hCECs cultured in vitro. Molecular names were expressed on the top left of each image. Images were taken in the center of each well at x40 magnification. The control represented a well without coating. Cell lateral membranes were stained with anti-NCAM (green) and the nuclei were counterstained using DAPI (blue). The donor used for this example was “c” in Table . Scale bars are placed in the bottom-right images of columns IV and CTRL (100 μm).

Article Snippet: The hCECs were incubated with the primary antibody for 1 h at 37 ̊C: NCAM (1:400, MAB24081, R&D Systems, Minneapolis, MN, USA).

Techniques: Cell Culture, In Vitro, Control, Staining