Biology subjects

Gezelius, H.

Publications and source records attributed to Gezelius, H..

3 recordsLinked to original sources

bioRxiv2024

Mapping the Spatial Proteome of Leukemia Cells Undergoing Fludarabine Treatment

Recent advancements in spatial biology have revolutionized our understanding of the organization and functional dynamics of cells and tissues. In this study, we applied Molecular Pixelation (MPX), a single-cell spatial proteomics assay, to investigate the modulation of the cell surface proteome in an in vitro drug screening model using the ETV6::RUNX1 acute lymphoblastic leukemia (ALL) cell line, Reh. Specifically, we focused on the in vitro response to fludarabine, a chemotherapeutic agent used prior to allogenic stem cell transplantation and chimeric antigen receptor (CAR)-T cell therapy in high-risk, refractory, or relapsed ALL patients. Using MPX, we quantified changes in protein abundance, spatial distribution, and colocalization of 76 targeted cell surface proteins in Reh cells before and after fludarabine treatment. Our analysis revealed 25 proteins with altered abundance, 24 proteins with increased polarity, and 138 protein pairs with modified colocalization following treatment. Notably, the tetraspanins CD82 and CD53, which are known for their roles in chemotherapy resistance, exhibited increased abundance, polarization, and colocalization post-treatment, suggesting their potential as a therapeutic scaffold. These findings underscore the unique ability of spatially resolved single-cell proteomics to uncover nuanced cellular responses that would otherwise remain undetected.

cancer biology↗

bioRxiv2023

COMPARISON OF HIGH-THROUGHPUT SINGLE-CELL RNA-SEQ METHODS FOR EX VIVO DRUG SCREENING

Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27,327 cells are freely available to extend to future scRNA-seq methodological comparisons.

genomics↗

bioRxiv2023

A complete digital karyotype of the B-cell leukemia REH cell line resolved by long-read sequencing

The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6-RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-year-old at relapse, the cell line offers a practical model for the study of high-risk pediatric B-ALL patients. In recent years, short-read DNA and RNA sequencing have emerged as a complement to analog karyotyping techniques in the resolution of structural variants in an oncological context. However, it is challenging to create a comprehensive digital karyotype of a genome with these techniques alone. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole genome sequencing (WGS), IsoSeq RNA-sequencing, and short-read sequencing to create a detailed digital karyotype of the REH cell line. WGS refined the breakpoints of known aberrations and clarified the molecular traits of disrupted ALL-associated genes BTG1 and TBL1XR1, as well as the glucocorticoid receptor NR3C1. Several previously underreported structural variants were also uncovered, including deletions affecting the ALL-associated genes VPREB1 and NFATC1. Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community. KEY POINTSO_LIA complete digital karyotype of the REH cell line was produced with short- and long-read DNA and RNA sequencing technologies. C_LIO_LIThe study enabled precise identification of structural variants, and the fusion genes expressed as the result of these variants. C_LI

cancer biology↗