Journal: bioRxiv

Article Title: Cross-species single-cell atlases chart progression, therapy-driven remodelling and immune evasion in pancreatic cancer

doi: 10.64898/2026.03.19.712924

Figure Lengend Snippet: a) Schematic overview of the experimental design. Mouse PDAC cell lines were clonally barcoded using a lentiviral library (1), expanded and orthotopically transplanted into syngeneic immunocompetent mice (2–3), followed by scRNA-seq profiling of resultant tumours (4). Expressed barcode tracing enabled unambiguous separation of malignant (TAG⁺) from host-derived non-malignant cells (right panel, UMAPs depicting barcoded (TAG + ) (top) and malignant (bottom) cells). b-e) UMAPs of the integrated Mouse PDAC Atlas coloured by dataset (b), sex (c), treatment type (d), and model (orthotopic syngeneic immunocompetent allografts vs. autochthonous GEMMs (e). f) Sample-wise cell-type composition across treatment types, datasets, and models. Autochthonous tumours were dominated by classical epithelial-like malignant states, whereas orthotopic allografts displayed greater heterogeneity with an enrichment of EMT, hypoxic, and mesenchymal programs. g ) Level 3 hierarchical annotation of the Mouse Atlas using the same multi-tiered scheme as the Human Atlas, resolving lymphoid, myeloid, stromal, endocrine, exocrine, endothelial, and malignant compartments. h-j) Substate resolution of major immune and stromal lineages: CD4⁺ T cells (h), CD8⁺ T cells (i), and macrophages (j), showing distinct regulatory, effector, angiogenic, and lipid-processing programs. k) Validation of double-positive (DP) CD4⁺CD8⁺ T cells at the transcriptomics level (transcription density plots, left panel) and at the protein level by flow cytometry (right panel). l) UMAP showing DP T cells coloured by species (left) and Pearson correlation of mouse DP T cell gene expression against the human DP T cell archetype (right).

Article Snippet: For clonal and state-fate analysis by single-cell RNA-seq, primary mouse PDAC cells were clonally tagged with expressed DNA barcodes using the LARRY Barcode Library (Addgene #140024; RRID: Addgene 140024) .

Techniques: Derivative Assay, Biomarker Discovery, Transcriptomics, Flow Cytometry, Gene Expression

Journal: Cell and Tissue Research

Article Title: Histological, ultrastructural, and single-cell profiling reveal immune-mediated remodeling in gallbladder inflammation

doi: 10.1007/s00441-026-04057-6

Figure Lengend Snippet: Transcriptomic and anatomical overview of immune and epithelial alterations in acute cholecystitis and chronic cholelithiasis. Single-cell RNA sequencing (scRNA-seq) of immune cells from one acute cholecystitis and one chronic cholelithiasis sample reveals distinct expression signatures and immune-cell distributions. a Heatmap describing the relative cell expression profiles in acute and chronic conditions based on inflammation- and fibrosis-associated marker genes, illustrating clear transcriptional differences between the two states. b Bar graph summarizing the relative abundance of major immune-cell populations across both conditions. Neutrophils (cluster 0), CD4 + T cells (clusters 1), macrophages/monocytes (clusters 3), cytotoxic lymphocytes (cluster 4), and mast cells (cluster 10) are more abundant in acute cholecystitis, whereas B/plasma cells (cluster 6), CXCL13 + epithelial-interacting macrophages (cluster 7), antigen-presenting macrophages/dendritic cells (cluster 8), fibroblasts/myofibroblasts (cluster 9), and cycling immune cells (cluster 11) predominate in chronic cholelithiasis. c Schematic representation of the analyzed gallbladder regions (body, neck, and peribiliary area) and corresponding epithelial and immune features—acute cholecystitis showing epithelial disruption and infiltration by innate immune cells, and chronic cholelithiasis displaying preserved or hyperplastic epithelium with adaptive-cell predominance, stromal remodeling

Article Snippet: Messenger RNA (mRNA) from each cell was barcoded using GEXSCOPE Single-Cell mRNA Library Kits (Singleron Biotechnologies), ensuring that transcripts from each cell received a unique molecular identifier.

Techniques: Single Cell, RNA Sequencing, Expressing, Marker, Clinical Proteomics, Disruption

Journal: Cell and Tissue Research

Article Title: Histological, ultrastructural, and single-cell profiling reveal immune-mediated remodeling in gallbladder inflammation

doi: 10.1007/s00441-026-04057-6

Figure Lengend Snippet: Targeted validation of immune activation states in acute cholecystitis and chronic cholelithiasis. Targeted gene-expression and immunohistochemical analyses were performed to validate immune signatures identified by single-cell transcriptomic profiling. a Quantitative PCR analysis of inflammatory cytokine expression in independent gallbladder tissue samples demonstrates significantly increased expression of IL1B and IFNG in acute cholecystitis compared with chronic cholelithiasis, whereas IL10 shows a trend toward increased expression in acute inflammation. Data are shown as individual values with median and interquartile range; statistical significance was assessed using the Mann–Whitney U test. b Representative immunohistochemical staining for CD163 in the gallbladder neck and peribiliary regions from acute and chronic conditions. Acute cholecystitis shows increased abundance of CD163 + macrophages within the mucosa and subepithelial compartments compared with chronic cholelithiasis. c Quantification of CD163. + cells in the gallbladder neck and body ( n = 4 per group) demonstrates a significantly higher density in acute inflammation. Scale bars: 200 µm (as indicated). Negative control stainings for CD163 are shown in Supplementary Figs. 1 and

Article Snippet: Messenger RNA (mRNA) from each cell was barcoded using GEXSCOPE Single-Cell mRNA Library Kits (Singleron Biotechnologies), ensuring that transcripts from each cell received a unique molecular identifier.

Techniques: Biomarker Discovery, Activation Assay, Targeted Gene Expression, Immunohistochemical staining, Single Cell, Real-time Polymerase Chain Reaction, Expressing, MANN-WHITNEY, Staining, Negative Control