REH

Genomic, Transcriptomic, and Epigenomic Sequencing Data of REH Cell Lines

This data paper aims to describe a collection of 33 genomic, transcriptomic, and epigenomic sequencing datasets of the B-cell ALL cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features.

The cell line’s authenticity was confirmed by karyotyping and STR analysis. The datasets are divided into nine library types. Of the seven library types using DNA as input, five are whole genome sequencing (WGS) methods producing genomic data, one is a method producing chromatin accessibility data (single-cell ATAC-seq), and one is a whole genome methylome sequencing method producing epigenomic data (EM-seq). The WGS methods include Illumina TruSeq DNA PCR-Free, PacBio SMRT, Oxford Nanopore (ONT), MGISEQ stLFR, and linked-read WGS (10 × Genomics), while RNA was used as input to two RNA-seq methods, Illumina TruSeq Stranded Total RNA and PacBio IsoSeq. The datasets include raw sequencing reads in FASTA and FASTQ formats, reference-mapped BAM files, and de-novo assemblies (Table 1).

Table. 1 Overview of the data file. (Lysenkova Wiklander M, et al., 2023)

Cathepsin B Is Not Intrinsic to Reh Cell Line Asparaginase Resistance

L-asparaginase (ASNase) is a biopharmaceutical used as an essential drug in the treatment of ALL. The REH ALL cell line, used as a model for studying the most common subtype of ALL, is considered resistant to treatment with ASNase. Cathepsin B (CTSB) is one of the proteases involved in the regulation of in vivo ASNase serum half-life and it has also been associated with the progression and resistance to treatment of several solid tumors.

CTSB REH (Fig. 1) and CTSB KO cells were generated utilizing the clustered regularly interspaced repeats with associated protein 9 (CRISPR/Cas9) system. REHcas9 cells were monitored for 27 days via quantification of GFP levels across all conditions (Fig. 2A). The GFP levels of REH cells bearing CTSB sgRNAs, and those from the non-targeting control Rosa 26 condition remained steady through the analysis. These results were supported by the GFP level monitoring analysis of FACS-isolated CTSB KO cells and Rosa26-targeted cells, which remained unchanged over time (Fig. 2B). These results support that REH ALL cells do not depend on the expression of CTSB for overall survival and proliferation.

REHcas9 and REHcas9 + sgRNA-1 cells were treated with different concentrations of ASNases for 72 h, and then cell viability was determined. In all the conditions tested, the cell viability profile was the same between REHcas9 and REHcas9 + sgRNA1 cells (Fig. 3). Thus, deletion of CTSB in REH ALL cells did not confer ASNase treatment sensitivity, thus suggesting that intrinsic expression of CTSB is not a mechanism that drives the resistant nature of these ALL cells to enzymes used as the first-line treatment against leukemia.

Fig. 1 Representative image of REHcas9 infection. (Costa IM, et al., 2023)

Fig. 2 Monitoring of REHcas9-sgRNA cell proliferation by flow cytometry. (Costa IM, et al., 2023)

Fig. 3 In vitro cytotoxicity assay of CTSB KO cells in the presence of ASNase. (Costa IM, et al., 2023)