Immunohistochemical Staining of Cellular Markers

For immunohistochemical analysis, samples were embedded in paraffin and sectioned at 6 μm using a microtome (Leica). Sections were deparaffinized, rehydrated and subjected to high-temperature antigen retrieval at pH 6 for all stains except for pKAP1 at pH 9. Detection of primary antibodies was performed using peroxidase-coupled appropriate secondary antibodies. Sections were counterstained with hematoxylin. Staining was imaged using a Pannoramic DESK scanner and analysed using QuPath^{67 (link)}. Due to the shape of macrophages (Supplementary Fig. 6), proper cell detection was not possible and mean intensity was used for the analysis. For histology, the following antibodies were used: anti-CD3 (Abcam Cat# ab16669, RRID:AB_443425, 1:100), anti-CD4 (Thermo Fisher Scientific Cat# 14-9766-82, RRID:AB_2573008, 1:100), anti-CD8 (Lab Vision Cat# RB-9009-P1, RRID:AB_149750, 1:100), anti-F4/80 (Abcam Cat# ab6640, RRID:AB_1140040, 1:1,000), anti-CD45R/B220 (BD Biosciences Cat# 550286, RRID:AB_393581, 1:50), anti-KAP1 phospho-S824 (Abcam Cat# ab70369, RRID:AB_1209417, 1:500), anti-γ-H2AX (Abcam Cat# ab2893, RRID:AB_303388, 1:1,000).