Phenochart software version 1

Multiplex immunohistochemistry staining was performed following the protocol of the Opal Polaris 7-Color Manual IHC Kit (Akoya Bioscience, NEL861001KT). The antibody against CD8 (catalog 70306) was purchased from Cell Signaling Technology, and the antibodies against CD20 (catalog ab78237), CD103 (catalog ab224202), Ki67 (catalog ab16667), IgG (catalog ab109489), IgA (catalog ab97215), and CD138 (catalog ab128936) were purchased from Abcam. Slides were imaged and whole slides scanned using a Vectra Polaris Automated Quantitative Pathology Imaging System (Akoya Biosciences), and multispectral images were acquired using Phenochart software, version 1.0.12 (Akoya Biosciences) to unmix and remove autofluorescence. Cell numbers and percentage of GZMK⁺CD103^–CD8⁺ cells were quantified using Halo software (Indica Labs). Focus area in LG biopsies was calculated by Halo software. Focus score was the number of foci per 4 mm² of tissue.

Multiplex immunohistochemical staining was performed following the protocol of the Opal Polaris 7-Color Manual IHC Kit (Akoya Bioscience, NEL861001KT). Antibodies against mouse CD8α (1:800, D4W2Z), F4/80 (1:200, D2S9R) and GFP (1:400, D5.1) were purchased from Cell Signaling Technology. Antibodies against mouse PD-1 (1:100, EPR20665), and CK19 (1:1500, EP1580Y) were purchased from Abcam. Slides were imaged, whole slides were scanned using a Vectra Polaris Automated Quantitative Pathology Imaging System (Akoya Biosciences), and multispectral images were acquired using Phenochart software, version 1.0.12 (Akoya Biosciences), to unmix and remove autofluorescence. The distances between CD8⁺ cells andCK19⁺ cells were calculated by HALO software (Indica Labs).