Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing

Abstract

In melanoma, the lymphocytic infiltrate is a prognostic parameter classified morphologically into 'brisk', 'non-brisk' and 'absent' entailing a functional association that has never been proved. Recently, it has been shown that lymphocytic populations can be very heterogeneous, and that anti-PD-1 immunotherapy supports activated T cells. Here, we characterize the immune landscape in primary melanoma by high-dimensional single cell multiplex analysis in tissue sections (MILAN technique) followed by image analysis, RT-PCR and shotgun proteomics. We observed that the brisk and non-brisk patterns are heterogeneous functional categories that can be further sub-classified into active, transitional or exhausted. The classification of primary melanomas based on the functional paradigm also shows correlation with spontaneous regression, and an improved prognostic value when compared to that of the brisk classification. Finally, the main inflammatory cell subpopulations that are present in the microenvironment associated with activation and exhaustion and their spatial relationships are described using neighbourhood analysis.

Data availability

All data generated or analysed during this study are included in the submission as source data files. We also included the codes to ease the review in process.

The following previously published data sets were used

Article and author information

Author details

  1. Francesca Maria Bosisio

    Laboratory of Translational Cell and Tissue Research and Pathology Department, KU Leuven and UZ Leuven, Leuven, Belgium
    For correspondence
    f.bosisio1@gmail.com
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8874-2003
  2. Asier Antoranz

    National Technical University of Athens, ProtATonce Ltd, Athens, Greece
    For correspondence
    asierantoranz91@gmail.com
    Competing interests
    Asier Antoranz, Asier Antoranz is affiliated with ProtATonce Ltd. The author has no other competing interests to declare.
  3. Yannick van Herck

    Laboratory of Experimental Oncology, KU Leuven and UZ Leuven, Leuven, Belgium
    Competing interests
    No competing interests declared.
  4. Maddalena Maria Bolognesi

    Department of Medicine and Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
    Competing interests
    Maddalena Maria Bolognesi, Maddalena Maria Bolognesi has received funding from GlaxoSmithKline . The author has no other competing interests to declare.
  5. Lukas Marcelis

    Laboratory of Translational Cell and Tissue Research and Pathology Department, KU Leuven, Leuven, Belgium
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5446-1801
  6. Clizia Chinello

    Department of Medicine and Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
    Competing interests
    No competing interests declared.
  7. Jasper Wouters

    Laboratory of Translational Cell and Tissue Research and Pathology Department, KU Leuven and UZ Leuven, Leuven, Belgium
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7129-2990
  8. Fulvio Magni

    Department of Medicine and Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
    Competing interests
    No competing interests declared.
  9. Leonidas Alexopoulos

    National Technical University of Athens, ProtATonce Ltd, Athens, Greece
    Competing interests
    No competing interests declared.
  10. Marguerite Stas

    Department of Surgical Oncology, KU Leuven and UZ Leuven, Leuven, Belgium
    Competing interests
    No competing interests declared.
  11. Veerle Boecxstaens

    Department of Surgical Oncology, KU Leuven and UZ Leuven, Leuven, Belgium
    Competing interests
    No competing interests declared.
  12. Oliver Bechter

    Laboratory of Experimental Oncology, KU Leuven and UZ Leuven, Leuven, Belgium
    Competing interests
    No competing interests declared.
  13. Giorgio Cattoretti

    Department of Medicine and Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3799-3221
  14. Joost van den Oord

    Laboratory of Translational Cell and Tissue Research and Pathology Department, KU Leuven and UZ Leuven, Leuven, Belgium
    Competing interests
    No competing interests declared.

Funding

Horizon 2020 Framework Programme (642295)

  • Francesca Maria Bosisio

Horizon 2020 Framework Programme (675585)

  • Asier Antoranz

BEL114054 (HGS1006-C1121)

  • Maddalena Maria Bolognesi

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: Ethical approval was obtained from the Ethical Committee/IRB OG032 of the University Hospital of Leuven. After the approval, the study was identified with the number S57266. According to the Clinical Trial regalement no informed consent was needed due to the use of post-diagnostic left-over material.

Reviewing Editor

  1. C Daniela Robles-Espinoza, International Laboratory for Human Genome Research, Mexico

Version history

  1. Received: October 23, 2019
  2. Accepted: February 14, 2020
  3. Accepted Manuscript published: February 14, 2020 (version 1)
  4. Version of Record published: February 25, 2020 (version 2)

Copyright

© 2020, Bosisio et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,373
    Page views
  • 347
    Downloads
  • 31
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Francesca Maria Bosisio
  2. Asier Antoranz
  3. Yannick van Herck
  4. Maddalena Maria Bolognesi
  5. Lukas Marcelis
  6. Clizia Chinello
  7. Jasper Wouters
  8. Fulvio Magni
  9. Leonidas Alexopoulos
  10. Marguerite Stas
  11. Veerle Boecxstaens
  12. Oliver Bechter
  13. Giorgio Cattoretti
  14. Joost van den Oord
(2020)
Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing
eLife 9:e53008.
https://doi.org/10.7554/eLife.53008

Further reading

    1. Cancer Biology
    Gehad Youssef, Luke Gammon ... Adrian Biddle
    Research Article

    Cancer stem cells (CSCs) undergo epithelial-mesenchymal transition (EMT) to drive metastatic dissemination in experimental cancer models. However, tumour cells undergoing EMT have not been observed disseminating into the tissue surrounding human tumour specimens, leaving the relevance to human cancer uncertain. We have previously identified both EpCAM and CD24 as CSC markers that, alongside the mesenchymal marker Vimentin, identify EMT CSCs in human oral cancer cell lines. This afforded the opportunity to investigate whether the combination of these three markers can identify disseminating EMT CSCs in actual human tumours. Examining disseminating tumour cells in over 12,000 imaging fields from 74 human oral tumours, we see a significant enrichment of EpCAM, CD24 and Vimentin co-stained cells disseminating beyond the tumour body in metastatic specimens. Through training an artificial neural network, these predict metastasis with high accuracy (cross-validated accuracy of 87-89%). In this study, we have observed single disseminating EMT CSCs in human oral cancer specimens, and these are highly predictive of metastatic disease.

    1. Cancer Biology
    2. Medicine
    Dingyu Rao, Hua Lu ... Defa Huang
    Research Article

    Esophageal cancer (EC) is a fatal digestive disease with a poor prognosis and frequent lymphatic metastases. Nevertheless, reliable biomarkers for EC diagnosis are currently unavailable. Accordingly, we have performed a comparative proteomics analysis on cancer and paracancer tissue-derived exosomes from eight pairs of EC patients using label-free quantification proteomics profiling and have analyzed the differentially expressed proteins through bioinformatics. Furthermore, nano-flow cytometry (NanoFCM) was used to validate the candidate proteins from plasma-derived exosomes in 122 EC patients. Of the 803 differentially expressed proteins discovered in cancer and paracancer tissue-derived exosomes, 686 were up-regulated and 117 were down-regulated. Intercellular adhesion molecule-1 (CD54) was identified as an up-regulated candidate for further investigation, and its high expression in cancer tissues of EC patients was validated using immunohistochemistry, real-time quantitative PCR (RT-qPCR), and western blot analyses. In addition, plasma-derived exosome NanoFCM data from 122 EC patients concurred with our proteomic analysis. The receiver operating characteristic (ROC) analysis demonstrated that the AUC, sensitivity, and specificity values for CD54 were 0.702, 66.13%, and 71.31%, respectively, for EC diagnosis. Small interference (si)RNA was employed to silence the CD54 gene in EC cells. A series of assays, including cell counting kit-8, adhesion, wound healing, and Matrigel invasion, were performed to investigate EC viability, adhesive, migratory, and invasive abilities, respectively. The results showed that CD54 promoted EC proliferation, migration, and invasion. Collectively, tissue-derived exosomal proteomics strongly demonstrates that CD54 is a promising biomarker for EC diagnosis and a key molecule for EC development.