Integrated cytogenetic and genomic profiling of the MDS-L cell line

Among the human leukemia cell lines described in the literature, only the MDS-L cell line has been definitively established from a patient during the myelodysplastic syndrome (MDS) phase of the disease. However, the limited studies on its genomic complexity have restricted its applicability as an in vitro model for MDS. Here, we aimed to better characterize the chromosomal and genetic alterations of MDS-L. A comprehensive approach was employed combining conventional G banding, multicolor FISH (M-FISH), SNP arrays with the novel Optical Genome Mapping (OGM) technology. In addition, the mutational landscape was defined using targeted next-generation sequencing (NGS). G-banding revealed two karyotypically distinct cell populations, both exhibiting complex karyotypes. Using G-banding and OGM, we identified previously undescribed structural alterations, including der(1)t(1;7)(q11;q11.2), del(1)(q11), der(4)t(4;5)(p16;q11.2), i(5)(p10), der(6)t(6;15)(p21.3;q15), i(8)(q10), der(9)t(9;10)(q34;p11.21), der(19)t(6;19)(p13;p22) and i(22)(q10). Both OGM and SNP microarray analyses detected multiple copy number variants and regions of homozygosity. Chromosome breakpoints were precisely defined by OGM, allowing the identification of gene disruption events. Moreover, M-FISH technique validated the origins of additional chromosomal material observed in the karyotype, identified cryptic rearrangements, and distinguished the two clonal populations within the cell line. Finally, NGS revealed mutations in CEBPA, NRAS, TET2 and TP53 genes associated with MDS pathology. This multi-technique approach has enabled a precise characterization of the MDS-L cell line's genomic complexity, highlighting the unique contributions of each technique in uncovering various genetic alterations and establishing a valuable resource for mechanistic studies and pre-clinical drug development.