Supplementary Figures 1-22 from Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer

Katey S.S Enfield,Emma Colliver,Claudia Lee,Alastair Magness,David A Moore,Monica Sivakumar,Kristiana Grigoriadis,Oriol Pich,Takahiro Karasaki,Philip S Hobson,Dina Levi,Selvaraju Veeriah,Clare Puttick,Emma L Nye,Mary Green,Krijn K Dijkstra,Masako Shimato,Ayse U Akarca,Teresa Marafioti,Roberto Salgado,Allan Hackshaw,Mariam Jamal-Hanjani,Febe Van Maldegem,Nicholas Mcgranahan,Benjamin Glass,Hanna Pulaski,Eric Walk,James L Reading,Sergio A Quezada,Crispin T Hiley,Julian Downward,Erik Sahai,Charles Swanton,Mihaela Angelova

doi:10.1158/2159-8290.25956810.v1

Abstract

<p>Supplementary Figures 1-22 with the corresponding figure legends inline. Supplementary Figure S1. TRACERx 100 imaging mass cytometry cohort. Supplementary Figure S2. Analysis of imaging mass cytometry data. Supplementary Figure S3. Characterisation of cell subtypes and spatial cellular communities in non-small cell lung cancer. Supplementary Figure S4. Clinicogenomic correlations with cell subtypes and communities. Supplementary Figure S5. TME class associations with cell types and clinical variables. Supplementary Figure S6. Cancer cell-intrinsic and -extrinsic features associated with immune cell infiltration. Supplementary Figure S7. Spatial, histological and metabolic features of the Tumour/Stroma:Neutrophil High TME class. Supplementary Figure S8. Transcriptomic features of TS:Neutrophil High TME class and Tumour-Associated Neutrophil scoring. Supplementary Figure S9. Somatic mutations in PIK3CA were associated with neutrophil recruitment through CXCL8 upregulation. Supplementary Figure S10. TAN score association with disease-free survival. Supplementary Figure S11. Validation of the prognostic association from the TAN scoring approach with an automated, deep learning approach in The Cancer Genome Atlas. Supplementary Figure S12. Imaging mass cytometry panel development. Supplementary Figure S13. Spillover matrices for imaging mass cytometry data. Supplementary Figure S14. Multiplexed Consensus Cell Segmentation. Supplementary Figure S15. Investigation of batch effects. Supplementary Figure S16. Raw pixel intensities. Supplementary Figure S17. Pathologist-guided labels. Supplementary Figure S18. Communities methodology and histology associations. Supplementary Figure S19. Multiplexed immunohistochemistry validation of checkpoint molecule expression. Supplementary Figure S20. Cell-cell relationships differ by TME class. Supplementary Figure S21. Cell-cell relationships differ by tumour genomics. Supplementary Figure S22. Cell-cell relationships based on tumour cell phenotypes.</p>

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