Establishment and characterization of a novel cell line ICH-BCPALL-3 from B cell precursor acute lymphoblastic leukemia with TCF3::HLF

Abstract

In vitro models of acute leukemia are crucial for understanding its biology and developing effective treatments. The authors have established and characterized a novel cell line, ICH-BCPALL-3, which expresses the TCF3::HLF fusion from B cell precursor acute lymphoblastic leukemia (BCP-ALL). The karyotype of the cultured cells is 46,XY, der(1)(1qter- > 1q11::1p32- > 1q11::4q21- > 4qter), der(4)t(1;4)(q11;p32), add(8)(q24), del(17)(q24). Analysis of the diagnostic sample revealed deletions in RB1, VPREB1, and NR3C1. The cell line showed additional deletions of VPREB1, NR3C1, and CDKN2A/2B, as well as a gain of AKT1. The loci for PAX5 and BTG1 were retained. Exome and Sanger sequencing identified nucleotide variants of ARID5B and NCOR1 in the diagnostic sample, as well as a KRAS variant (p.Lys117Asn) in the first recurrent sample and another KRAS variant (p.Asp119Gly) in the second recurrent sample and the cell line. Transcriptome analysis and RT-PCR confirmed that all examined samples contained a TCF3::HLF chimeric transcript. However, molecular cytogenetics did not verify the juxtaposition of TCF3 and HLF loci. Further long-range PCR analyses confirmed that genomic material containing HLF exon 4 was inserted into TCF3 intron 16. Using dimensional reduction techniques, we found that the current cell line shares an expression pattern with other TCF3::HLF-positive BCP-ALL cell lines. The cytotoxicity assay indicated that the cell line is sensitive to Aurora Kinase B inhibitor, but not to BCL2 inhibitor. This cell line is the first TCF3::HLF-positive BCP-ALL model without the t(17;19) translocation, facilitating research into leukemogenesis and the development of novel treatments for patients with poor prognosis associated with TCF3::HLF-positive BCP-ALL.

Keywords: TCF3::HLF; B cell precursor acute lymphoblastic leukemia; Cell line; Cytotoxicity assay; Oligoclonality; Transcriptome.