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Comprehensive landscape of immune-checkpoints uncovered in clear cell renal cell carcinoma reveals new and emerging therapeutic targets

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Abstract

Clear cell renal cell carcinoma (ccRCC) constitutes the most common renal cell carcinoma subtype and has long been recognized as an immunogenic cancer. As such, significant attention has been directed toward optimizing immune-checkpoints (IC)-based therapies. Despite proven benefits, a substantial number of patients remain unresponsive to treatment, suggesting that yet unreported, immunosuppressive mechanisms coexist within tumors and their microenvironment. Here, we comprehensively analyzed and ranked forty-four immune-checkpoints expressed in ccRCC on the basis of in‐depth analysis of RNAseq data collected from the TCGA database and advanced statistical methods designed to obtain the group of checkpoints that best discriminates tumor from healthy tissues. Immunohistochemistry and flow cytometry confirmed and enlarged the bioinformatics results. In particular, by using the recursive feature elimination method, we show that HLA-G, B7H3, PDL-1 and ILT2 are the most relevant genes that characterize ccRCC. Notably, ILT2 expression was detected for the first time on tumor cells. The levels of other ligand-receptor pairs such as CD70:CD27; 4-1BB:4-1BBL; CD40:CD40L; CD86:CTLA4; MHC-II:Lag3; CD200:CD200R; CD244:CD48 were also found highly expressed in tumors compared to adjacent non-tumor tissues. Collectively, our approach provides a comprehensible classification of forty-four IC expressed in ccRCC, some of which were never reported before to be co-expressed in ccRCC. In addition, the algorithms used allowed identifying the most relevant group that best discriminates tumor from healthy tissues. The data can potentially assist on the choice of valuable immune-therapy targets which hold potential for the development of more effective anti-tumor treatments.

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Abbreviations

ccRCC:

Clear cell renal cell carcinoma

HLA-G:

Human leukocyte antigen-G

IC:

Immune-checkpoints

ILT2:

Immunoglobulin-like transcript 2 (LILRB1)

ILT4:

Immunoglobulin-like transcript 4 (LILRB2)

RFEM:

Recursive feature elimination method

SVM:

Support vector machine

TCGA:

The Cancer Genome Atlas

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Acknowledgements

The authors are particularly grateful to Dr. Nathalie Rouas-Freiss for very instructive discussions and critical reading of the manuscript. We are also thankful to Dr. Marcela Garcia and Santiago Miriuka for their enlightened suggestions on tumor culture procedures. We kindly appreciate the experimental assistance of Alix Jacquier on cytometric assays and Jerome Delmotte on immunochemistry. The results shown are based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcha.

Funding

This work was funded by the Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) and Ecole CentraleSupélec, Université Paris-Saclay.

Author information

Author notes

  1. Mathilde Sautreuil and Mahmoud Bentriou have contributed equally to this work.

Authors and Affiliations

  1. Commissariat à L’Energie Atomique Et Aux Energies Alternatives (CEA), Direction de La Recherche Fondamentale (DRF), Service de Recherche en Hémato-Immunologie (SRHI), Hôpital Saint-Louis, Paris, France

    Diana Tronik-Le Roux, Jérôme Vérine, Marina Daouya, Joel LeMaoult, François Desgrandchamps & Edgardo D. Carosella

  2. Université de paris, U976 HIPI Unit, Institut de Recherche Saint-Louis, 75010, Paris, France

    Diana Tronik-Le Roux, Marina Daouya, Joel LeMaoult & Edgardo D. Carosella

  3. Laboratory of Mathematics and Informatics (MICS), CentraleSupélec, Université Paris-Saclay, 91190, Gif-sur-Yvette, France

    Mathilde Sautreuil, Mahmoud Bentriou, Sarah Lemler & Paul-Henry Cournède

  4. Service D’Anatomo-Pathologie, AP-HP, Hôpital Saint-Louis, Paris, France

    Jérôme Vérine & Fatiha Bouhidel

  5. Cátedra de Citología, Histología Y Embriología A, Facultad de Ciencias Médicas, UNLP, Buenos Aires, Argentina

    Maria Belén Palma

  6. Service D’Urologie, AP-HP, Hôpital Saint-Louis, Paris, France

    François Desgrandchamps

  7. CEA, Direction de La Recherche Fondamentale, Service de Recherche en Hémato-Immunologie, Hôpital Saint-Louis, IUH, 1, avenue Claude Vellefaux, 75010, Paris, France

    Diana Tronik-Le Roux

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  1. Diana Tronik-Le Roux
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  2. Mathilde Sautreuil
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Contributions

DTLR was involved in conceptualization, formal analysis, writing original draft, supervision; MS helped in methodology, software, formal analysis, writing original draft; MB contributed to methodology, software, formal analysis, writing original draft; JV performed experiments, formal analysis and diagnosis; MBP contributed to methodology, performed experiments; MD performed experiments and analysis; FB performed experiments; JLM contributed to methodology, formal analysis, writing original draft; FD provided samples; S.L. contributed to formal analysis, writing original draft; PHC helped in formal analysis, methodological supervision, writing-original draft, funding; EDC was involved in research design, funding.

Corresponding author

Correspondence to Diana Tronik-Le Roux.

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The authors declare no potential conflicts of interest.

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The study was approved by the institutional ethics committee of Saint-Louis Hospital, Paris.

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Patients provided written informed consent before sampling.

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Tronik-Le Roux, D., Sautreuil, M., Bentriou, M. et al. Comprehensive landscape of immune-checkpoints uncovered in clear cell renal cell carcinoma reveals new and emerging therapeutic targets. Cancer Immunol Immunother 69, 1237–1252 (2020). https://doi.org/10.1007/s00262-020-02530-x

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