Single-Cell Analysis Technologies for Immuno-Oncology Research: From Mechanistic Delineation to Biomarker Discovery

Abstract

The successes with immune checkpoint blockade (ICB) and chimeric antigen receptor (CAR)-T-cell therapy in treating multiple cancer types have established immunotherapy as a powerful curative option for patients with advanced cancers. Unfortunately, many patients do not derive benefit or long-term responses, highlighting a pressing need to perform complete investigation of the underlying mechanisms and the immunotherapy-induced tumor regression or rejection. In recent years, a large number of single-cell technologies have leveraged advances in characterizing immune system, profiling tumor microenvironment, and identifying cellular heterogeneity, which establish the foundations for lifting the veil on the comprehensive crosstalk between cancer and immune system during immunotherapies. In this review, we introduce the applications of the most widely used single-cell technologies in furthering our understanding of immunotherapies in terms of underlying mechanisms and their association with therapeutic outcomes. We also discuss how single-cell analyses help to deliver new insights into biomarker discovery to predict patient response rate, monitor acquired resistance, and support prophylactic strategy development for toxicity management. Finally, we provide an overview of applying cutting-edge single-cell spatial-omics to point out the heterogeneity of tumor–immune interactions at higher level that can ultimately guide to the rational design of next-generation immunotherapies.

Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL

“…We find that CD19-positive relapsed patients ( n = 5) have a deficit of CAR T cells capable of inducing a T helper type 2 (T H 2) functional response and of maintaining stem cell–like memory and central memory states compared with very durable responders ( n = 5), whereas the expression levels of activation- or coinhibitory-related proteomic markers are comparable between two groups. We have performed an independent functional validation of these findings in two cohorts comprising 49 patients by means of flow cytometry and a multiplexed secretomic assay ( 30 ). In addition, we have incorporated the identified biomarkers into a predictive index using a binomial logistic regression.…”

Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy

“…Cell therapy, represented by CAR-T cells, has made rapid developments in recent years, but there is still a lack of effective methods to analyze CAR-T cells after they enter the tumor microenvironment. Single-cell proteomics analysis cannot only obtain the activation status of CAR-T cells, but also determine the trend of CAR-T proteome changes at different time points, which can assist drug development scientists in the design and optimization of chimeric antigen receptors (CARs) ( Bai et al, 2021 ). Xue et al (2017) performed SCS of CD19 CAR-T pre-infusion products prepared from four healthy donors to assess the functional characteristics of CD19 CAR-T cells after antigen-specific stimulation.…”

Microenvironmental reorganization in brain tumors following radiotherapy and recurrence revealed by hyperplexed immunofluorescence imaging

“…For this reason, high-dimensional imaging techniques have become increasingly vital to the study of the TME. Imaging mass cytometry (IMC) 17 , tissue cyclic immunofluorescence (t-CycIF) 18 , Multiplexed Ion Beam Imaging by Time of Flight (MIBI-TOF) 19 , MALDI mass spectrometry imaging (MALDI-IMS) 20 , and oligo-conjugated antibody cyclic immunofluorescence (Ab-oligo cyCIF) 21 are among the current approaches 22 , 23 for highly multiplexed tissue imaging capable of assessing 20–100 markers on a single tissue section.…”