Journal: medRxiv

Article Title: An integrated single-cell atlas of checkpoint inhibitor-induced liver injury links shared liver-tumour CD8+ T cell clones to cytotoxicity and macrophage crosstalks

doi: 10.64898/2026.04.27.26351449

Figure Lengend Snippet: Representative images demonstrating immunofluorescence staining of selected antigens included in the Phenocycler-Fusion mIF panel across tonsil (left column) and liver (right column) tissues. Antibodies were validated for specificity, signal intensity, and tissue compatibility. Each row shows staining for a given antigen (green), CD3 as the T cell lineage marker (red) and DAPI (blue) as a structural reference. Acquisition details including antibody clone, vendor, barcode, dilution, and exposure time are listed for each antigen. Scale bar = 20 μm.

Article Snippet: Phenocycler-Fusion antibody panel for post-Xenium mIF Supplementary Table 8 can be found as a separate supplementary document.

Techniques: Immunofluorescence, Staining, Marker

Journal: medRxiv

Article Title: An integrated single-cell atlas of checkpoint inhibitor-induced liver injury links shared liver-tumour CD8+ T cell clones to cytotoxicity and macrophage crosstalks

doi: 10.64898/2026.04.27.26351449

Figure Lengend Snippet: (A) Analysis approach to identify T cells of interest with Xenium in situ. Cells with at least one clone transcript were first filtered to remove potential doublets, defined as cells containing transcripts from more than one T cell clone. Next, cells mapped to non–T cell clusters were excluded. The remaining cells were visually validated as T cells using CD3 staining from the Phenocycler-Fusion mIF data. Finally, cells that passed all these criteria were considered a single T cell clone of interest. (B) Visual validation of shared clone transcript assignment. Top: Shared clone transcripts from ChILI_26 liver sample are mapped on Xenium in situ cell type annotation. Bottom: Shared clone transcripts from ChILI_26 liver sample are mapped on PCF mIF staining of the same tissue section. Scale bar = 50 μm. (C) Visual representation of main cell clusters and shared T cell clones within the tumour of ChILI_13. Top: A region in the tumour sample showing interface between tumour and stroma. Red arrow indicates clone 1 which expresses the cytotoxicity markers GZMB , GZMK , NKG7 and PRF1 . Scale bar = 10 µm. Bottom: PCF mIF staining of the same region. Red arrow indicates clone 1. PCF markers were indicated as DAPI, CD8 and S100. CD8 expression of clone 1 is also confirmed at the protein level with PCF. Scale bar = 10 µm.

Article Snippet: Phenocycler-Fusion antibody panel for post-Xenium mIF Supplementary Table 8 can be found as a separate supplementary document.

Techniques: In Situ, Staining, Biomarker Discovery, Clone Assay, Expressing

Journal: medRxiv

Article Title: An integrated single-cell atlas of checkpoint inhibitor-induced liver injury links shared liver-tumour CD8+ T cell clones to cytotoxicity and macrophage crosstalks

doi: 10.64898/2026.04.27.26351449

Figure Lengend Snippet: (A) Workflow of sequential mIF/RISH staining. (B) 38-marker Phenocycler-Fusion staining of ChILI_13 liver biopsy (top). RISH+ cells were identified in different regions of the liver (bottom: Rectangle 1 and 2). White arrows show CASSPLTGELFF+ CD8+ GzmB+ CD45RO+ T cells. Scale bar (merge) = 20 µm, scale bar = 10 µm. (C) 38-marker Phenocycler-Fusion staining of ChILI_13 matched tumour sample. Cells inside the white rectangles are identified as CASSPLTGELFF+ CD8+ GzmB+ CD45RO+ T cells. Scale bar = 10 µm.

Article Snippet: Phenocycler-Fusion antibody panel for post-Xenium mIF Supplementary Table 8 can be found as a separate supplementary document.

Techniques: Staining, Marker