Spatially mapping the immune landscape of melanoma using imaging mass cytometry

Abstract

Melanoma is an immunogenic cancer with a high response rate to immune checkpoint inhibitors (ICIs). It harbors a high mutation burden compared with other cancers and, as a result, has abundant tumor-infiltrating lymphocytes (TILs) within its microenvironment. However, understanding the complex interplay between the stroma, tumor cells, and distinct TIL subsets remains a substantial challenge in immune oncology. To properly study this interplay, quantifying spatial relationships of multiple cell types within the tumor microenvironment is crucial. To address this, we used cytometry time-of-flight (CyTOF) imaging mass cytometry (IMC) to simultaneously quantify the expression of 35 protein markers, characterizing the microenvironment of 5 benign nevi and 67 melanomas. We profiled more than 220,000 individual cells to identify melanoma, lymphocyte subsets, macrophage/monocyte, and stromal cell populations, allowing for in-depth spatial quantification of the melanoma microenvironment. We found that within pretreatment melanomas, the abundance of proliferating antigen-experienced cytotoxic T cells (CD8 + CD45RO + Ki67 + ) and the proximity of antigen-experienced cytotoxic T cells to melanoma cells were associated with positive response to ICIs. Our study highlights the potential of multiplexed single-cell technology to quantify spatial cell-cell interactions within the tumor microenvironment to understand immune therapy responses.

Detailed spatial immunophenotyping of primary melanomas reveals immune cell subpopulations associated with patient outcome

“…One notable omission from our TME analysis was the characterization of myeloid cells such as macrophages. Similar studies in primary and metastatic melanoma characterizing macrophages solely on the basis of CD68 positivity have produced conflicting findings, with one study associating macrophages – particularly HLA-DR- macrophages – with a poor prognosis ( 22 ), while others found macrophages in primary melanomas were associated with improved survival ( 23 , 47 ). Although CD68 has been commonly used as a pan-macrophage marker ( 48 , 49 ), it is now accepted that macrophages – especially tumor-associated macrophages (TAM) – exist on a vast phenotypic and functional gradient, from anti-tumor-polarized M1 to pro-tumor M2 macrophages ( 50 – 52 ).…”

“…CD69, when expressed independently from CD103, is also a marker of intermediate tumor residency ( 13 , 16 ). Recent efforts to assess immune infiltrates in primary melanomas in a broader context have focused on gene expression profiling and imaging mass cytometry ( 19 – 23 ). Increasingly, spatial analysis has provided further insights into tumor and immune cell interactions in the TME ( 24 – 26 ).…”

Pan-cancer whole genome comparison of primary and metastatic solid tumors

“…Finally, genomic changes cannot entirely explain how tumor cells are able to colonize other organs while avoiding the strong bottlenecks imposed by the immune system 69 or by aggressive treatment regimes. Therefore, additional information from complementary tumor omics studies 70,71 and from the tumor microenvironment 72,73 will be needed to further dissect and better understand tumor evolution and resistance to cancer therapy and eventually contribute to improved management of this deadly disease.…”

IMC-Denoise: a content aware denoising pipeline to enhance Imaging Mass Cytometry

“…This novel imaging technology allows for the detection of more than 40 antigens simultaneously. It enables single-cell, spatially resolved, highly multiplexed analysis of solid tissues and provides essential information on the distribution of transcripts, proteins, and protein modifications within single cells, microenvironments, and entire tissues [8][9][10][11][12][13][14][15][16][17]. The pixel data is processed into an image, thereby allowing the visualization of phenotypes and incorporation of spatial information in subsequent analyses.…”