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Original research
The tumour microenvironment shapes innate lymphoid cells in patients with hepatocellular carcinoma
  1. Bernd Heinrich1,
  2. E Michael Gertz2,
  3. Alejandro A Schäffer2,
  4. Amanda Craig3,
  5. Benjamin Ruf1,
  6. Varun Subramanyam1,
  7. John C McVey1,
  8. Laurence P Diggs1,
  9. Sophia Heinrich3,
  10. Umberto Rosato1,
  11. Chi Ma1,
  12. Chunhua Yan4,
  13. Ying Hu4,
  14. Yongmei Zhao5,
  15. Tsai-Wei Shen5,
  16. Veena Kapoor6,
  17. William Telford6,
  18. David E Kleiner7,
  19. Merril K Stovroff8,
  20. Harmeet S Dhani8,
  21. Jiman Kang8,
  22. Thomas Fishbein8,
  23. Xin Wei Wang3,9,
  24. E Ruppin2,
  25. Alexander Kroemer8,
  26. Tim F Greten1,9,
  27. Firouzeh Korangy1
  1. 1Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
  2. 2Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
  3. 3Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
  4. 4The Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
  5. 5CCR-SF Bioinformatics Group, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
  6. 6Experimental Transplantation and Immunotherapy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
  7. 7Laboratory of Pathology, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
  8. 8MedStar Georgetown Transplant Institute, MedStar Georgetown University Hospital and the Center for Translational Transplant Medicine, Georgetown University Medical Center, Washington, District of Columbia, USA
  9. 9NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, Maryland, USA
  1. Correspondence to Dr Firouzeh Korangy, National Institutes of Health, Bethesda, MD 20892, USA; firouzeh.korangy{at}nih.gov

Abstract

Objective Hepatocellular carcinoma (HCC) represents a typical inflammation-associated cancer. Tissue resident innate lymphoid cells (ILCs) have been suggested to control tumour surveillance. Here, we studied how the local cytokine milieu controls ILCs in HCC.

Design We performed bulk RNA sequencing of HCC tissue as well as flow cytometry and single-cell RNA sequencing of enriched ILCs from non-tumour liver, margin and tumour core derived from 48 patients with HCC. Simultaneous measurement of protein and RNA expression at the single-cell level (AbSeq) identified precise signatures of ILC subgroups. In vitro culturing of ILCs was used to validate findings from in silico analysis. Analysis of RNA-sequencing data from large HCC cohorts allowed stratification and survival analysis based on transcriptomic signatures.

Results RNA sequencing of tumour, non-tumour and margin identified tumour-dependent gradients, which were associated with poor survival and control of ILC plasticity. Single-cell RNA sequencing and flow cytometry of ILCs from HCC livers identified natural killer (NK)-like cells in the non-tumour tissue, losing their cytotoxic profile as they transitioned into tumour ILC1 and NK-like-ILC3 cells. Tumour ILC composition was mediated by cytokine gradients that directed ILC plasticity towards activated tumour ILC2s. This was liver-specific and not seen in ILCs from peripheral blood mononuclear cells. Patients with high ILC2/ILC1 ratio expressed interleukin-33 in the tumour that promoted ILC2 generation, which was associated with better survival.

Conclusion Our results suggest that the tumour cytokine milieu controls ILC composition and HCC outcome. Specific changes of cytokines modify ILC composition in the tumour by inducing plasticity and alter ILC function.

  • hepatocellular carcinoma
  • immune response
  • immunoregulation
  • immunology
  • liver immunology

Data availability statement

Data are available in a public, open access repository. Data are available on reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information. Data for single-cell RNA sequencing data reported in this publication can be accessed under the Gene Expression Omnibus (GEO; GSE179795). Bulk RNA-sequencing can be accessed from GEO (GSE179746). The LCI and TIGER cohorts are previously published, and data can be accessed from GEO (GSE76297 [4] and GSE14520 [5]). Data for all tumour types in The Cancer Genome Atlas (TCGA) cohort had been retrieved previously as described for melanoma [6]. These data include gene expression and survival. Here, we analysed 371 cases of hepatocellular carcinoma (TGCA tumour type LIHC). Gene expression values were log-transformed before analysis.

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Data availability statement

Data are available in a public, open access repository. Data are available on reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information. Data for single-cell RNA sequencing data reported in this publication can be accessed under the Gene Expression Omnibus (GEO; GSE179795). Bulk RNA-sequencing can be accessed from GEO (GSE179746). The LCI and TIGER cohorts are previously published, and data can be accessed from GEO (GSE76297 [4] and GSE14520 [5]). Data for all tumour types in The Cancer Genome Atlas (TCGA) cohort had been retrieved previously as described for melanoma [6]. These data include gene expression and survival. Here, we analysed 371 cases of hepatocellular carcinoma (TGCA tumour type LIHC). Gene expression values were log-transformed before analysis.

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Footnotes

  • Twitter @BenniRuf, @JackMcVey14

  • Contributors BH, TFG, FK: conceptualisation, formal analysis, investigation and data acquisition, methodology, project administration, visualisation, writing. BR, VS, MKS, HSD, JK, TMF, AK: investigation and data acquisition. MEG, AAS, AJC, BR, VS, JCM, LPD, SH, UR, CM, CY, YH, YZ, TWS, VK, WT, DK, XWW, ER, AK: formal analysis. All authors reviewed and edited the article.

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.

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