Journal: bioRxiv

Article Title: SuperCell2.0 enables semi-supervised construction of multimodal metacell atlases

doi: 10.64898/2026.02.19.706848

Figure Lengend Snippet: A WNN UMAP of monocytes from the CITE-seq PBMC metacells atlas. Metacells are colored by refined blood monocyte subtypes derived from multimodal clustering. B Selected Protein and RNA markers as well as signature scores (based on RNA) in the different monocyte subtypes. C Proportion of monocyte subtypes at the different time points of the HIV vaccine trial for the 8 donors. D Violin plot of LY6E , SIGLEC1 RNA expression and CD169 (encoded by SIGLEC1 ) protein expression in metacells from healthy donors (day 0 of the vaccination trial) in CD14 monocytes compared to interferon-primed CD14 monocyte clusters. (***) indicates an EdgeR FDR < 0.001 and (NS.) indicates a non-significant difference. E Experimental workflow implemented to test LY6E and CD169 as surface markers to study interferon-primed CD14 monocytes. A classical FACS strategy was used to gate CD14 monocytes from four healthy blood donors. Four CD14 subpopulations were defined by CD169 and LY6E surface expression, sorted and subjected to bulk RNA-sequencing. F Monocyte subtype proportions in each donor were measured by FACS. G Upper panel: Heatmap of the protein coding differentially expressed genes between the main CD14+,CD169-,LY6E- monocyte subpopulation and the three other CD14 monocyte subtypes. Lower panel: Selected signature scores differentially expressed between the main CD14+,CD169-,LY6E- monocyte subpopulation and the three other CD14 monocyte subtypes.

Article Snippet: Cells were blocked with human TrueStain FcX (BioLegend, 422302) for 20 minutes and subsequently stained in 50 μL/million cells of Brilliant Stain Buffer (25% v/v in FACS buffer, BD Horizon, 566349) with antibodies against CD169 (PE, BioLegend, 346003, 1:100), CD45 (PE/Cy7, BioLegend, 304015, 1:200), CD14 (FITC, BioLegend, 325604, 1:200), CD11b (BV421, BioLegend, 101236, 1:200), CD15 (BV510, BioLegend, 323028, 1:200), CD16 (BV785, BioLegend, 302045, 1:200), and LY6E (APC, Creative Biolabs, MOB-636, 1:100).

Techniques: Derivative Assay, RNA Expression, Expressing, RNA Sequencing

Journal: Breast Cancer Research : BCR

Article Title: Nuclear PD-L1 drives IFN-γ-promoted lung metastasis of triple-negative breast cancer via POLR2A-mediated transcriptional activation of LY6E

doi: 10.1186/s13058-025-02193-5

Figure Lengend Snippet: LY6E is identified as a key downstream effector of nuclear PD-L1 in metastasis.​​ A ​​ Left: Venn diagram illustrating the strategy for identifying downstream targets of IFN-γ/nuclear PD-L1 from RNA-seq data of PD-L1 WT and KO 4T1 cells treated with or without 50 ng/mL IFN-γ for 24 h. Right: Heatmap of four candidate genes. ​​ B – C ​​ qPCR validation of Cldn1, Ly6e, Anxa8, and Gnb4 mRNA expression in the indicated treatment groups of 4T1 cells ( n = 4). ​​ D ​​ Western blot analysis of Claudin-1 and Ly6E protein expression in PD-L1 WT and KO 4T1 cells treated with or without 50 ng/mL IFN-γ for 24 h. ​​ E – F ​​ qPCR analysis of CLDN1 and LY6E mRNA expression in PD-L1 WT and PD-L1 KO MDA-MB-231 cells treated with or without 50 ng/mL IFN-γ for 48 h. ​​ G – H ​​ Western blot analysis of Claudin-1 and Ly6E protein expression in PD-L1 WT and KO MDA-MB-231 cells treated with or without 50 ng/mL IFN-γ for 48 h. I ​​ Analysis of LY6E and CD274 mRNA expression in TCGA TNBC tumor and adjacent normal tissue samples. ​​ J ​​ Correlation analysis of LY6E and CD274 mRNA expression in TCGA TNBC samples. ​​ K ​​ Representative images of lungs and quantification of metastatic nodules from LY6E overexpression cells. Data are presented as mean ± SD. Student’s t-test was used for two-group data analysis, while One Way ANOVA was used for multiple-group data analysis

Article Snippet: Proteins (20–30 μg) were separated by SDS-PAGE, transferred to nitrocellulose (NC) membranes, and probed with primary antibodies against PD-L1 (CST, #13684; #60475), POLR2A (CST, #2629), LY6E (Proteintech, 22144-1-AP), Claudin-1 (Proteintech, 13050-1-AP), STAT1 and phosphorylated STAT1 (CST, #14994; #9167), and GAPDH (Proteintech, 60004-1-Ig).

Techniques: RNA Sequencing, Biomarker Discovery, Expressing, Western Blot, Over Expression

Journal: Breast Cancer Research : BCR

Article Title: Nuclear PD-L1 drives IFN-γ-promoted lung metastasis of triple-negative breast cancer via POLR2A-mediated transcriptional activation of LY6E

doi: 10.1186/s13058-025-02193-5

Figure Lengend Snippet: Nuclear PD-L1 forms a transcriptional complex with POLR2A to upregulate LY6E.​​ A ​​ Browser view of published ChIP-seq data showing lack of PD-L1 enrichment at the LY6E promoter region (highlighted in yellow) in MDA-MB-231 cells. ​​ B ​​ Transcription factors (TFs) predicted to bind the LY6E promoter in MDA-MB-231 cells, ranked by transcriptional potential score. ​​ C ​​ Venn diagram identifying POLR2A as the only TF overlapping between factors predicted to bind LY6E ( B ) and factors found to interact with PD-L1 by Co-IP/MS in MDA-MB-231 cells. ​​ D ​​ Browser view of ChIP-seq data showing POLR2A enrichment at the LY6E promoter region (highlighted in yellow) in MDA-MB-231 cells. ​​ E ​​ Predicted structural model of the PD-L1/POLR2A interaction generated by ZDOCK. Key interacting residues are labeled: Salt bridge (PD-L1 R140 - POLR2A E517), Electrostatic interactions (PD-L1 K136/K185 - POLR2A D452/D663). ​​ F ​​ Co-immunoprecipitation assay in MDA-MB-231 cells to detect protein interaction between POLR2A and PD-L1

Article Snippet: Proteins (20–30 μg) were separated by SDS-PAGE, transferred to nitrocellulose (NC) membranes, and probed with primary antibodies against PD-L1 (CST, #13684; #60475), POLR2A (CST, #2629), LY6E (Proteintech, 22144-1-AP), Claudin-1 (Proteintech, 13050-1-AP), STAT1 and phosphorylated STAT1 (CST, #14994; #9167), and GAPDH (Proteintech, 60004-1-Ig).

Techniques: ChIP-sequencing, Co-Immunoprecipitation Assay, Generated, Labeling

Journal: Frontiers in Immunology

Article Title: Case Report: Novel IRF2BP2 variant in a Japanese patient with impaired B-cell differentiation, Th1 polarization, and systemic immune dysregulation

doi: 10.3389/fimmu.2025.1662899

Figure Lengend Snippet: Identification of a novel IRF2BP2 mutation. (A) Sanger sequencing chromatograms of the IRF2BP2 gene showing a heterozygous de novo missense mutation (c.1663T>A; p. Cys555Ser) in the patient, which is absent in both parents. (B) Heatmap revealing the relative messenger RNA expression levels of IFI44L , LY6E , and MX1 in PBMCs from the patient and a healthy control, as measured using quantitative polymerase chain reaction. Expression levels are normalized to GAPDH and calculated using the comparative CT method. Red indicates higher expression, and blue indicates lower expression relative to the control. FC, fold change.

Article Snippet: All primers and probes were obtained from Applied Biosystems ( IFI44L [Hs00915292_m1], LY6E [Hs00158942_m1], MX1 [Hs00895608_m1], and GAPDH [Hs02758991_g1]).

Techniques: Mutagenesis, Sequencing, RNA Expression, Control, Real-time Polymerase Chain Reaction, Expressing