True-T - improving T-cell response quantification with holistic artificial intelligence based prediction in immunohistochemistry images

Yasmine Makhlouf*, Vivek Kumar Singh, Stephanie Craig, Aoife McArdle, Dominique French, Maurice B. Loughrey, Nicola Oliver, Juvenal Baena Acevedo, Paul O'Reilly, Jacqueline A. James, Perry Maxwell, Manuel Salto-Tellez*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)
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The immune response associated with oncogenesis and potential oncological therapeutic interventions has dominated the field of cancer research over the last decade. T-cell lymphocytes in the tumor microenvironment are a crucial aspect of cancer’s adaptive immunity, and the quantification of T-cells in specific cancer types has been suggested as a potential diagnostic aid. However, this is currently not part of routine diagnostics. To address this challenge, we present a new method called True-T, which employs artificial intelligence-based techniques to quantify T-cells in colorectal cancer (CRC) using immunohistochemistry (IHC) images. True-T analyses the chromogenic tissue hybridization signal of three widely recognized T-cell markers (CD3, CD4, and CD8). Our method employs a pipeline consisting of three stages: T-cell segmentation, density estimation from the segmented mask, and prediction of individual five-year survival rates. In the first stage, we utilize the U-Net method, where a pre-trained ResNet-34 is employed as an encoder to extract clinically relevant T-cell features. The segmentation model is trained and evaluated individually, demonstrating its generalization in detecting the CD3, CD4, and CD8 biomarkers in IHC images. In the second stage, the density of T-cells is estimated using the predicted mask, which serves as a crucial indicator for patient survival statistics in the third stage. This approach was developed and tested in 1041 patients from four reference diagnostic institutions, ensuring broad applicability. The clinical effectiveness of True-T is demonstrated in stages II-IV CRC by offering valuable prognostic information that surpasses previous quantitative gold standards, opening possibilities for potential clinical applications. Finally, to evaluate the robustness and broader applicability of our approach without additional training, we assessed the universal accuracy of the CD3 component of the True-T algorithm across 13 distinct solid tumors.

Original languageEnglish
Pages (from-to)174-185
Number of pages12
JournalComputational and Structural Biotechnology Journal
Publication statusAccepted - 24 Nov 2023


  • Artificial intelligence
  • Computational biotechnology
  • Digital pathology
  • Immune
  • Response

ASJC Scopus subject areas

  • Biotechnology
  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Computer Science Applications


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