PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways

Anuli C Uzozie,Janice Tsui,Theodore G Smith,Christopher A Maxwell,Philipp F Lange,Gregor S D Reid,Enes K Ergin,C James Lim,Samuel S H Weng,Amanda Lorentzian,Lorenz Nierves,Nina Rolf

doi:10.1186/s13046-021-01835-8

Abstract

BackgroundMurine xenografts of pediatric leukemia accurately recapitulate genomic aberrations. How this translates to the functional capacity of cells remains unclear. Here, we studied global protein abundance, phosphorylation, and protein maturation by proteolytic processing in 11 pediatric B- and T- cell ALL patients and 19 corresponding xenografts.MethodsXenograft models were generated for each pediatric patient leukemia. Mass spectrometry-based methods were used to investigate global protein abundance, protein phosphorylation, and limited proteolysis in paired patient and xenografted pediatric acute B- and T- cell lymphocytic leukemia, as well as in pediatric leukemia cell lines. Targeted next-generation sequencing was utilized to examine genetic abnormalities in patients and in corresponding xenografts. Bioinformatic and statistical analysis were performed to identify functional mechanisms associated with proteins and protein post-translational modifications.ResultsOverall, we found xenograft proteomes to be most equivalent with their patient of origin. Protein level differences that stratified disease subtypes at diagnostic and relapse stages were largely recapitulated in xenografts. As expected, PDXs lacked multiple human leukocyte antigens and complement proteins. We found increased expression of cell cycle proteins indicating a high proliferative capacity of xenografted cells. Structural genomic changes and mutations were reflected at the protein level in patients. In contrast, the post-translational modification landscape was shaped by leukemia type and host and only to a limited degree by the patient of origin. Of 201 known pediatric oncogenic drivers and drug-targetable proteins, the KMT2 protein family showed consistently high variability between patient and corresponding xenografts. Comprehensive N terminomics revealed deregulated proteolytic processing in leukemic cells, in particular from caspase-driven cleavages found in patient cells.ConclusionGenomic and host factors shape protein and post-translational modification landscapes differently. This study highlights select areas of diverging biology while confirming murine patient-derived xenografts as a generally accurate model system.

Highlights

Murine xenografts of pediatric leukemia accurately recapitulate genomic aberrations
Clusters depict protein-level similarities and differences between model organisms (13 patients, 19 Patientderived Xenograft (PDX), 4 cell lines), disease subtypes (8 B-acute lymphoblastic leukemia (ALL), 3 T-cell leukemia), and disease stages (7 diagnosis, 6 relapse). e Each box plot shows the percentage of proteins with equivalent protein abundance for each combination of sample pairs compared within a sample group (See Methods for details of TOSTone test)
The box plots show the percentage number of equivalent proteins from TOSTone tests performed between each ALL patient and the non-leukemic samples, leukemic patients and pediatric ALL cell lines, PDXs and pediatric ALL cell lines, all leukemic patients irrespective of disease subtype, non-matched patients and PDXs, patients with the same ALL subtype, matched patient and PDX pairs, and between multiple PDXs generated from a similar patient material

Summary

Introduction

Murine xenografts of pediatric leukemia accurately recapitulate genomic aberrations How this translates to the functional capacity of cells remains unclear. Established clinical phenotypes and genomic alterations characterize pediatric acute lymphoblastic leukemia (ALL), the most common hematologic malignancy in early childhood [1,2,3]. These core genetic alterations, combined with other cooperating oncogenic drivers contribute to leukemogenesis. The degree to which protein functional molecules and associated mechanisms broadly impact leukemic subtypes is yet to be understood Such knowledge is crucial to determine if disease stratification based on proteome features can be attained, how well this complements known genomic subtypes, and what biological mechanisms provide stable molecules for precise therapeutic targeting. Functional and drug sensitivity studies in PDX models of leukemia can only be extrapolated to patients if the relevant pathways, protein networks and modifications are conserved between patient and murine model [16]

Methods

Results

Discussion

Conclusion