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122 Quantification of tumor infiltrating lymphocytes (TILs) from pathology slides reflects molecular immune phenotypes
  1. Ciyue Shen1,
  2. Shima Nofallah1,
  3. Jake Conway2,
  4. Chintan Parmar1,
  5. Michael G Drage1,
  6. Fedaa Najdawi1,
  7. Darpan T Sanghavi1,
  8. Limin Yu1,
  9. Raymond Biju1,
  10. Daniel Borders1,
  11. Matthew Bronnimann1,
  12. Laura Chambre1,
  13. Issac Finberg1,
  14. Jonathan Glickman1,
  15. Michael Griffin1,
  16. Sidharth Gupta1,
  17. Natalia Harguindeguy1,
  18. Nhat Le1,
  19. Stephanie Hennek1,
  20. Syed Ashar Javed1,
  21. Christian Kirkup1,
  22. Miles Markey1,
  23. Michael Nercessian1,
  24. Daniel Shenker1,
  25. Sandhya Srinivasan1,
  26. Vignesh Valaboju1,
  27. Samuel AV Mercedes1,
  28. Bahar Rahsepar1,
  29. Ryan Leung1,
  30. Archit Khosla1,
  31. Benjamin Glass1,
  32. Amaro Taylor-Weiner1,
  33. Ylaine Gerardin1 and
  34. John Abel1
  1. 1PathAI, Boston, MA, USA
  2. 2PathAI, Methuen, MA, USA
  • Journal for ImmunoTherapy of Cancer (JITC) preprint. The copyright holder for this preprint are the authors/funders, who have granted JITC permission to display the preprint. All rights reserved. No reuse allowed without permission.


Background Examination of histopathology slides is a crucial step in making cancer diagnoses and treatment decisions. Rapid developments in machine learning models in digital pathology have enabled quantitative high-resolution information to be extracted from whole-slide images. Meanwhile, genomic tests and molecular assays have also become powerful in assisting pathologists and oncologists in decision making, but these tests are not routinely performed to consistently provide molecular information. In this study, we developed tissue and cell classification models using Hematoxylin and Eosin-stained (H&E) slides, extracted human-interpretable features (HIFs) quantifying the tumor microenvironment, and investigated the association between abundance and distribution of tumor infiltrating lymphocytes (TILs) and molecular phenotypes.

Methods We trained convolutional neural network-based tissue and cell classification models using H&E slides with annotations collected from US board-certified pathologists, resulting in PathExplore models specific for eight indications, including breast cancer, colorectal cancer, gastric cancer, melanoma, non-small cell lung cancer, pancreatic cancer, prostate cancer, and renal cell carcinoma. We deployed the models on the corresponding indications in TCGA data and quantified HIFs for over 5,000 slides across 13 cancer types. We then analyzed the TIL-associated HIFs with publicly available gene expression and immune signature data.

Results TIL-associated HIFs, such as the frequency of TILs within cancer tissue (cTIL frequency), were correlated with gene expression of known lymphocyte markers, such as CD8A (median Spearman ρ = 0.539 for individual indications), CD3G (ρ = 0.536), and CD2 (ρ = 0.536). Regularized regression models using a panel of TIL-associated HIFs accurately predicted median-binarized expression of these three genes (median AUROC 0.751–0.755 for individual indications, pan-cancer AUROC 0.775–0.782) with best performance in melanoma (AUROC 0.831–0.850). We found good correlations between cTIL frequency with immune signature scores derived from gene expression, including a published lymphocyte infiltration signature score1 (ρ = 0.504) and T-cell signature score2 (ρ = 0.409). In particular, classification models using TIL-associated HIFs can predict the inflammatory subtype (C3 subtype in,1 median AUROC = 0.691, pan-cancer AUROC = 0.765 ± 0.008, 5-fold cross-validation) and the immune-enriched non-fibrotic subtype (IE subtype in,2 median AUROC = 0.755, pan-cancer AUROC = 0.737 ± 0.017).

Conclusions Histopathology image-based quantification of TILs is consistently associated with immune phenotypes derived from molecular measurements. These results suggest that quantitative HIFs extracted from tissue and cell classification models provide rich information for understanding of inflammation in the tumor microenvironment and potential discovery of immune biomarkers.

Acknowledgements The results shown here are in part based upon data generated by the TCGA Research Network:


  1. Thorsson A, et al. The Immune Landscape of Cancer. Immunity. 2018;48–4:812–830

  2. Bagaev A, et al. Conserved pan-cancer microenvironment subtypes predict response to immunotherapy. Cancer Cell. 2021;39:845–865

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