IRCCS Humanitas Research Hospital & Humanitas University
Published October 16, 2025 | Version v1
Dataset Open

Tissue-specific anti-tumor NK cell subsets identified in colorectal cancer liver metastases express candidate therapeutic targets

Authors/Creators

  • 1. ROR icon IRCCS Humanitas Research Hospital
  • 2. ROR icon University of Milan

Contributors

  • 1. ROR icon IRCCS Humanitas Research Hospital
  • 2. ROR icon University of Milan
  • 3. ROR icon University of Milano-Bicocca
  • 4. University Medical Center Hamburg-Eppendorf
  • 5. ROR icon Medizinische Hochschule Hannover
  • 6. Humanitas Clinical and Research Center - IRCCS – Rozzano (Mi) Italy
  • 7. University of Rijeka
  • 8. ROR icon Human Technopole
  • 9. ROR icon National Research Council
  • 10. Humanitas Clinical and Research Center
  • 11. ROR icon Humanitas University
  • 12. ROR icon National Heart Lung and Blood Institute

Description

This record contains processed data related to article Tissue-specific anti-tumor NK cell subsets identified in colorectal cancer liver metastases express candidate therapeutic targets

Abstract

Liver metastases are relatively resistant to checkpoint blockade immunotherapy. The hepatic tissue has distinctive features including high numbers of NK cells. It was therefore important to conduct in depth single-cell analysis of NK cells in colorectal cancer liver metastases (CRLMs) with the effort to dissect their diversity and to identify candidate therapeutic targets. 
By combining unbiased single-cell transcriptomic with multiparametric flow cytometry analysis, we identified an abundant family of intrahepatic CD56Bright NK cells in CRLMs endowed with anti-tumor functions resulting from specific transcriptional liver programs. Intrahepatic CD56Bright and CD56Dim NK lymphocytes expressed unique transcription factors (IRF8, TOX2), high level of chemokines, and targetable immune checkpoints (ICs), including CXCR4 and the IL-1 receptor family member IL-1R8. CXCR4 pharmacological blocking and an anti-IL-1R8 mAb enhanced the effector function of CRLM NK cells. Targeting the diversity of liver NK cells and their distinct immune-checkpoint repertoires is key to optimize the current immune-therapy protocols in CRLM.

 

Experimental design

Single-cell RNA sequencing (scRNA-seq) was performed on samples collected from three  colorectal-liver metastasis patients. For each patient, matched samples were obtained from invasive margin (IM, n = 3) and core-tumor adjacent tissue regions (peri-tumor, n = 3) of the liver tumor, as well as from peripheral blood (n = 3).
scRNA-seq was performed on flow cytometry-sorted NK cells (Lin-CD56+, excluding CD3+ lymphocytes, myeloid and B cells), as well as on matched flow cytometry-sorted NK cells from PBMCs

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