Subpopulation heterogeneity and microenvironmental engagement as predictors for treatment resistance in lymphoma

Most personalized treatment approaches do not account for intra-tumour heterogeneity (ITH).

New single-cell omics assays provide us, for the first time, with the opportunity to molecularly detect and characterise both types of ITH: genetic and non-genetic.We will use viably frozen single cell solutions isolated from lymph node biopsies to characterize lymphoma subpopulations and their cellular microenvironment thoroughly.

We will characterizes the transcriptome and surface proteome of single cells by CITE-Seq, revealing ITH at high resolution.

Transcriptionally distinct lymphoma subpopulations will be isolated flow cytometry followed by genome sequencing, in depth proteomics and ex-vivo drug sensitivity profiling.

This multi-omics data on fresh frozen samples is used to determine the minimal number of features needed to characterize ITH; which will be used to trace ITH in formalin fixed paraffin embedded (FFPE) tissue by multiplexed immunofluorescence, to investigate ITH in clinical routine samples. In FFPE samples the tumour cell populations are evaluated by digital spatial profiling (DSP).

In addition, the lymphoma specimens undergo laser microcapture microscopy followed by sequencing or proteome analysis.

Using this data, we will develop an automated image analysis pipeline for risk assesment and patient stratification, in routine clinical. We will bridge from state-of-the-art single cell techniques to routine diagnostic FFPE material.