Single-Cell Studies of Antigen-Specific T Cells using dCODE^®

Area

Featured Publication

Summary

Species

Sample Type

dCODE® reagents used in study

Immunotherapy

Kim et al., Cell https://doi.org/10.1016/j.cell.2025.03.047  (2025)

Are mis-splicing-derived neoantigens the Achilles heel of AML?

Mutations in RNA splice factor genes are prevalent in MDS and AML giving rise to large numbers of mis-splicing derived and cancer specific neoantigens. This study identified a large set of mis-splicing derived neoantigens that are shared across myeloid cancer patients.

Neoantigen-reactive T cells were sorted from AML patient blood samples by multiplexing with 50 different barcoded MHC I dCODE Dextramer® and characterized by single cell analysis. The results confirm the presence of clonally expanded T cells specific for mis-splicing derived neoantigens in peripheral blood of AML patients. However, their transcriptional activity suggests impaired cytotoxicity potentially explaining why these cells are unable to mount an effective immune response.

The results demonstrate that large numbers of public mis-splicing derived neoantigens in MDS and AML could be exploited for the development of effective cancer vaccines and T cell receptor-based autologous cell therapy. The article also showcases that multiplexing with dCODE Dextramer® can be used effectively for parallel TCR discovery and phenotyical characterization of T cells specific for large numbers of cancer neoantigens.

CMV-specific CD8+ T cells

Characterizing human CMV-specific CD8+ T cells using multi-layer single-cell omics

Ioanna Gemünd et al. Cell Reports Methods https://doi.org/10.1016/j.crmeth.2025.101085 (2025)

The first five-layer multi-omics dataset using dCODE Dextramer® and the BD Rhapsody™ Single Cell Analysis System for the characterization of human antigen-specific T cells, capturing:

• Whole transcriptome
• TCR sequences
• T cell antigen specificity
• Surface marker proteins
• Sample multiplexing combining two distinct hashing approaches

One key question was whether dCODE Dextramer® could detect antigen-specific T cells at low frequencies. The results of spike-in experiments confirmed that dCODE Dextramer® were indeed capable of this, even when spike-in frequencies were below 1%. For instance, one clone had a frequency as low as 0.4%, yet Dextramer-positive cells from this clone were still detectable.

dCODE Dextramer® (RiO)

ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs

Siwei Luo et al. Nature communications doi: https://doi.org/10.1038/s41467-024-54675-3 (2025)

Human

PBMCs

dCODE Dextramer® (10x) - MART-1 and CMV specificities.

SARS-CoV-2

Human SARS-CoV-2 challenge uncovers local and systemic response dynamics

Rik G. H. Lindeboom et al. Nature doi: https://doi.org/10.1038/s41586-024-07575-x (2024)

This study is part of the world’s first COVID-19 human challenge study. The team used a multi-allele panel of 44 SARS-CoV-2 antigen-specific dCODE Dextramer® (10x) reagents to study antigen-specific T cell dynamics by single-cell multi-omics.

This study set out to capture immune responses right from exposure, in an immunologically naïve cohort (16 individuals) for the first time.

This is the most comprehensive timeline to date of the body’s immune response to SARS-CoV-2 exposure.

Human

PBMCs

dCODE Dextramer® (10x) -

44 SARS-CoV-2 antigen-specific reagents

Cancer immunotherapy (Melanoma)

LAG-3 and PD-1 synergize on CD8+ T cells to drive T cell exhaustion and hinder autocrine IFN-γ-dependent anti-tumor immunity

Lawrence P. Andrews et al.  Cell doi: https://doi.org/10.1016/j.cell.2024.07.016 (2024)

This study shows that CD8+ T cells deficient in both PD-1 and LAG-3 mediate enhanced tumor clearance and long-term survival in mouse models of melanoma!

Immune-mediated resistance to PD-1 blockade is a challenge to overcome. This study sheds light on how PD-1 and LAG-3 synergize to hinder anti-tumor immunity.

The study reveals that the absence of both PD-1 and LAG-3 results in reshaped exhaustion patterns and heightened anti-tumor immune responses, potentially mediated by an autocrine IFN-γ-dependent mechanism.

These findings could pave the way for novel therapeutic strategies in the fight against cancer.

Human

PBMCs from melanoma patients

dCODE Dextramer® (10x):

HLA-A*0201/ELAGIGILTV (WB02162DXG); HLA-A*0201/SLLMWITQC (WB02696DXG); HLA-A*0201/IMDQVPFSV (WB02158DXG); HLA-A*0201/YMDGTMSQV (WB03245DXG)

Cancer immunotherapy

Immunotherapy targeting different immune compartments in combination with radiation therapy induces regression of resistant tumors

Nils-Petter Rudqvist et al. Nature communications doi: https://doi.org/10.1038/s41467-023-40844-3 (2023)

Immunotherapy targeting different immune compartments in combination with radiation therapy induces regression of resistant tumors.

Radiation therapy and cytotoxic T-lymphocyte-associated protein 4 inhibition (CTLA4i) interact to generate effective T-cell responses.

This study characterized the CD4+ and CD8+ T cell differentiation states induced by the combination of therapies.

The T-cell differentiation clusters identified in mice were also associated with survival in patients.

dCODE Dextramer® was used to sort AH1 antigen-specific T cells as part of the single-cell RNA sequencing workflow using the 10x Chromium Single-Cell Analysis System.

Mouse

Tumor-infiltrating single-cell suspensions from mouse 4T1 tumors

dCODE Dextramer® (10x) H2-Ld/SPSYVYHQF (AH1) (JG03294DXG)

CMV-, EBV-, influenza-, and SARS-CoV-2-specific CD8⁺ T cells

In-depth analysis of human virus-specific CD8+ T cells delineates unique phenotypic signatures for T cell specificity prediction

Florian Schmidt, et al. Cell Reports doi: https://doi.org/10.1016/j.celrep.2023.113250 (2023)

Schmidt and colleagues from ImmunoScape conducted the most comprehensive in-depth characterization of T cells specific for CMV, EBV and flu antigens to date. 

The study demonstrates that machine learning can be used to provide unique phenotypic signatures of antigen-specific T cells and can accurately predict virus specificity for bulk T cells.

Human

PBMCs

dCODE Klickmer® (10x) – Panel/PE

dCODE Klickmer® (10x) - Panel/APC (Custom)

SARS-CoV-2

Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection

Bingjie Zhang, et al. Nature Immunology doi: https://doi.org/10.1038/s41590-023-01608-9 (2023)

Zhang and colleagues from the New York Genome Center performed a longitudinal analysis of circulating human leukocytes collected before and after immunization against COVID-19, using a selection of 16 dCODE Dextramer® for single-cell multi-omics analysis.

This study published in Nature Immunology highlights the importance of evaluating the antigen-specific immune response, in combination with other surface and gene expression markers.

The frequency and differentiation outcomes of a vaccine-induced population of antigen-specific T cells were predictive of subsequent clinical outcomes in COVID-19 patients.

Human

PBMCs

dCODE Dextramer® (10x) – 16 specificities designed to bind SARS-CoV-2 spike

protein MHC class I epitopes across 7 HLA haplotypes (RX19)

dCODE Dextramer® reagents can be used to investigate T cell cross-reactivity.

In this study, Minervina et al. found that four of the investigated COVID-19 epitopes were highly similar to common cold coronavirus orthologs. As UMI counts of the COVID-19 and common cold specific dCODE® reagents correlated, researchers found that the same T cells could bind both versions of the epitope.

Human

PBMCs

dCODE Klickmer® (10x)