ESCAPE™ Single Cell Proteogenomic Analysis:

Application Areas

Tumor Heterogeneity

As cancers evolve and progress, unique subpopulations emerge leading to genetic and transcriptional heterogeneity. Tumor heterogeneity presents problems both for researchers looking for new drugs and clinicians providing therapies.

Proteona ESCAPE™ RNA-Seq single cell proteogenomic analysis provides the most comprehensive view into tumor analysis, with the following key applications.


Liquid tumor heterogeneity and evolution are major drivers of relapse in blood cancers, making it particularly important to identify the different populations of tumor cells.

ESCAPE RNA-Seq analysis helps to understand liquid tumor heterogeneity
  • Take measurements of all of the cells within the environment while retaining the ability to focus in on specific cell types such as malignant cells
  • Monitor tumor burden and identify treatment resistant populations
  • Detailed profiling of immune cell subsets, tracking activation, expansion, and exhaustion

BMMC clustered by RNA expression

Cell clustered by RNA expression

Same cells clustered by protein expression showed improved cluster separation

Cell clustered by protein expression
B cells
Myeloid cells
CD4+ T cells
CD8+ T cells
Plasmacytoid DC
NK cells
Tumor cells

Solid tumors

Solid tumor analysis

In solid tumors, it is especially important to understand the tumor diversity on a single cell level, as well as the environment around the tumor cells including complex populations of support and immune cells.

ESCAPE RNA-Seq analysis helps to understand the whole tumor:
  • Analyse tumor cells, tumor infiltrating lymphocytes, and adjacent normal issues at the same time
  • Deep characterization of tumor heterogeneity and tumor microenvironment
  • Identify populations sensitive or resistant to drug treatment
  • Evaluate immune modulation effect of treatment

Different cell types are identified from a colorectal cancer sample, using their RNA expression.

Cell clustered by RNA expression
T cells
Intestinal stem cells
Dying cells
Tuft cells
Enteroendocrine cells
Globet cells
Paneth cells
Enteroendocrine cells

LGR5+ cells

Cell clustered by protein expression

Immune cells

Gene expression
Protein expression

Cell therapy

Cell therapies are complex treatment that consist of mixed populations of cells. Conventional bulk analysis methods are not ufficient for understanding the patient-to-patient or cell-to-cell variation.

ESCAPE analysis provides the most comprehensive characterization method for cell therapies currently available
  • Deeply characterize cell therapy from both in vitro and in vivo derived samples
  • CAR T panel measures the expression of 42 proteins in addition gene expression analysis
  • Quantification of cell populations and persistence in patient over time
  • Monitor cell state including proliferation and exhaustion
  • Measure immune response and therapy effectiveness
cell therapy characterization

CD3 enriched PBMCs from patient who received CAR T cell theapy were analysed with ESCAPE RNA-Seq. Cells expressing the CAR are shown. Functional CAR T cells expressing both CD8 and CD27 can be observed up to 22 days post treatment.

Post cell therapy follow up of a patient using single cell proteogenomics

Find out more on how you can apply ESCAPE RNA-seq single cell analysis

Contact our team to find out more on how ESCAPE analysis service can help you in your project