P004 | Genomic and functional characterization of the murine acute myeloid leukemia cell line c1498 as a preclinical model of venetoclax/azacitidine resistance

Abstract

Introduction: The murine leukemia cell line C1498, derived from a C57BL/6J mouse, induces a lethal acute myeloid leukemia (AML)-like disease in immunocompetent hosts. Given its widespread use in preclinical studies of AML pathogenesis, tumor-host interactions and therapeutic responses, a comprehensive molecular characterization is crucial to fully define its translational relevance.
Methods: We performed an integrated genomic and molecular cytogenetic characterization of C1498 cells through whole-genome sequencing (WGS; median coverage 70×) and multicolor fluorescence in situ hybridization (M-FISH). Variants were annotated by mouse and human ortholog databases as OncoKB, and filtered against population references (Mouse Genomes Project, Ensembl). Drug sensitivity to the venetoclax/azacitidine (ven/aza) combination was assessed by in vitro dose–response assay.
Results: WGS (Figure A) identified 2,075 variants in the coding genome, absent from population databases. Among 1,800 mutated genes, 1,632 had human orthologs, with 155 variants in 133 cancer-related genes, including 17 mutations in 14 AML-associated genes (Asxl2, Bcor, Crebbp, Flt3, Gnas, Idh1, Kit, Kmt2d, Nf1, Notch1/2, Setbp1, Tet2, Trp53). High-impact lesions included stopgain mutations in Bcor and Tet2, nonsynonymous alterations in the NADP-dependent domain of Idh1, the RAS-GAP domain of Nf1, and the DNA-binding site of Trp53. Pathway analysis showed enrichment of mutated genes in transcriptional regulation, signaling and epigenetics.
M-FISH and WGS revealed a highly rearranged karyotype (37–42 chromosomes, Fig.B) with complex translocations, deletions, and amplifications. Copy number variant analysis identified 81 high-confidence calls, with amplifications involving Stk32b and Bub1 kinases. Notably, deletion events involved Trp53, Brca1, Stag1/2, Pds5b, and Rad50, while Myc was tandemly duplicated. Among structural variants, 239 overlapped with cytogenetic rearrangements and 27 translocations involved at least one cancer-related gene, including the previously described E2f3::Cdkal1 fusion. Data integration revealed double-hit events including mutations co-occurring with deletions of tumor suppressor genes (Trp53, Nf1, Recql4) and amplifications of oncogenes (Idh1, Ccnd3, Ret, Gnas, Ntrk3). Drug testing showed that C1498 cells were resistant to ven/aza (Fig.C), with IC₅₀ values of 9.85 µM ven/98.5 µM aza at 48h and 3.16 µM ven/31.6 µM aza at 72h, in line with the presence of Trp53 mutation and recent prognostic AML signatures.
Conclusions: C1498 cells display a complex genomic landscape characterized by Trp53 and Tet2 mutations, Myc amplification, and cohesin gene deletions. Its limited sensitivity to ven/aza mirrors the TP53-mutated AML resistance phenotype. This integrated molecular profile provides a robust framework for the rational use of C1498 as a preclinical model to study AML biology and evaluate novel therapeutic and immunologic strategies.
Acknowledgements: AIRC MFAG 2023 (29381).