Characterization of transcriptional changes within the gene expression profile during serial transplantation in PDX models of adult acute lymphoblastic leukemia using single cell sequencing

Preclinical models in oncology usually comprise in vitro cell culture systems and cell line-based xenograft models. However, the vast majority of clinically evaluated substances does not achieve clinical approval, suggesting reduced meaningfulness of those model systems. Patient-derived xenograft (PDX) models are better in recapitulating the clinical situation. By using primary cells, the polyclonality of the material remains intact. Further, orthotopic transplantation sites guarantee a microenvironment comparable with the human tumor. To generate sufficient material for successive experiments, tumor cells are amplified for several passages. Comparative analyses of our own and other published samples indicate that xenograft-derived cells mainly resemble the primary cells’ therapeutic response and molecular signatures. Acute lymphoblastic leukemia (ALL) is a rare and heterogeneous disease with devastating prognoses especially for adult patients. Due to several distinct molecular subtypes and resulting varying pathogenetic mechanisms and disease properties it is important to consider this heterogeneity in preclinical testing. PDX models play an increasing role also in ALL research. Still, it remains unclear if and how serial transplantation for several passages influences the clonal architecture and evolution of leukemic blasts. Our own ALL biobank currently comprises 44 adult ALL samples of which 18 have been amplified and molecularly characterized in PDX models for consecutive passages. Conventional next generation bulk sequencing methods have been applied to generate allele frequency and gene expression data of variants and genes, but no statement regarding the simultaneous prevalence of two or more changes in a cell is possible using these applications. Performing single cell sequencing (scSeq) generates data sets of distinct cells, offering valuable information regarding the molecular sub-structure of tumor clones as well as clonal evolution during therapy progression or serial transplantation. Using scSeq as well as a selected primary sample and thereof derived PDX models of three passages, this research project aims to investigate if changes in the total number of tumor clones occur during passaging, if the gene expression of leukemic drivers is altered and how two samples of the same passage differ from each other. This project will therefore generate data that will contribute to the enhanced understanding of the molecular processes during serial transplantation and thus elucidate the potentials and limitations of PDX models in preclinical ALL research.