Establishing High Dimensional Immune Signatures from Peripheral Blood via Mass Cytometry in a Discovery Cohort of Stage IV Melanoma Patients

Abstract

The identification of blood-borne biomarkers correlating with melanoma patient survival remains elusive. Novel techniques such as mass cytometry could help to identify melanoma biomarkers, allowing simultaneous detection of up to 100 parameters. However, the evaluation of multiparametric data generated via time-of-flight mass cytometry requires novel analytical techniques because the application of conventional gating strategies currently used in polychromatic flow cytometry is not feasible. In this study, we have employed 38-channel time-of-flight mass cytometry analysis to generate comprehensive immune cell signatures using matrix boolean analysis in a cohort of 28 stage IV melanoma patients and 17 controls. Clusters of parameters were constructed from the abundance of cellular phenotypes significantly different between patients and controls. This approach identified patient-specific combinatorial immune signatures consisting of high-resolution subsets of the T cell, NK cell, B cell, and myeloid compartments. An association with superior survival was characterized by a balanced distribution of myeloid-derived suppressor cell-like and APC-like myeloid phenotypes and differentiated NK cells. The results of this study in a discovery cohort of melanoma patients suggest that multifactorial immune signatures have the potential to allow more accurate prediction of individual patient outcome. Further investigation of the identified immune signatures in a validation cohort is now warranted.

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

“…Some recent reports used single-cell analysis to evaluate the expression of PD-1 and downstream signaling molecules on tumor infiltrating and circulating CD8 + T cells with the aim of identifying such predictive biomarkers 10,11 . However, these approaches are hampered by the limited accessibility of patient material, low dimensionality, overfitting due to the absence of independent validation cohorts, and lack of systematic, unbiased bioinformatics pipelines resulting in a paucity of predictive biomarkers to date 12 . Single-cell analysis of human immune compartments has so far been limited by the parameters that can be visualized by conventional flow cytometry 13 .…”

Determining T-cell specificity to understand and treat disease

“…In particular, it has been used to expose the great extent of functional heterogeneity that T cells possess in both blood and across tissues, and how this relates to the expression of various other cellular markers such as trafficking receptors [102][103][104] . Also in various disease settings including mass cytometry is being used to more broadly profile changes in cellular composition over the course of disease [105][106][107] . Thus, it is clear that T cells are incredibly diverse, especially within tissues, and now the challenge remains to understand how this diversity is related to the antigen-specificities of these cells and how this information can be used to better understand and predict disease outcomes.…”

Cyt‐Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops

“… While mass cytometry has highly contributed to basic scientific discovery, some of the major challenges come when trying to implement this technology in clinical studies. The addition of mass cytometry to the pool of technologies in clinical studies requires better standardization and quality control. Discussion on the validation of mass cytometry assays for clinical use including application validation, reagents and protocols, instrument operation, quality control, and data analysis is needed.…”