NEW YORK – An international team led by investigators in Germany has characterized tumor subclones and potential treatment targets in a difficult-to-treat and prognostically poor form of acute myeloid leukemia (AML) known as "complex karyotype" (CK) AML. This subtype is marked by frequent treatment resistance, poor outcomes, intratumoral heterogeneity (ITH), complicated chromosomal rearrangements, and alterations affecting three or more chromosomal sites.
Researchers from the German Cancer Research Center (DKFZ), the European Molecular Biology Laboratory (EMBL), and other international centers delved into the genetic complexity and structural variant heterogeneity in CK-AML using single-cell multiomic profiling on 10 samples from eight individuals with CK-AML, which typically turns up in 10 to 12 percent of AML cases.
"Despite major clinical need, CK-AML has remained understudied at the genomic, molecular, and cellular levels, largely because of technological limitations in analyzing ITH alongside widespread chromosomal complexity," co-senior and co-corresponding authors Andreas Trumpp, with DKFZ, the Heidelberg Institute for Stem Cell Technology and Experimental Medicine, and the German Cancer Consortium, and Jan Korbel, at EMBL and DKFZ, and their colleagues wrote in a paper published in Nature Genetics on Monday.
Based on scNOVA-CITE data — produced with a Strand-seq-based approach called "single-cell nucleosome occupancy and genetic variation analysis" (scNOVA), together with droplet-based "cellular indexing of transcriptomes and epitopes by sequencing" (CITE-seq) — the team investigated structural variant patterns, tumor transcriptomic ties to protein-level measurements on the cell surface, and broader ITH patterns in CK-AML cells and subclones.
For example, the investigators gained insights into the chromothripsis and linear and circular breakage-fusion-bridge cycles contributing to the structural rearrangements in CK-AML cells. They also highlighted three main types of CK-AML clonal growth and evolution known as monoclonal, linear, and branched polyclonal.
"Although previous studies using bulk whole-genome and single-cell DNA sequencing in AML have identified similar clonal evolution patterns based on single nucleotide variants," the authors noted, "inferring evolutionary history of structural variants is highly challenging in CK-AML as a result of an extensive number of alterations (up to 63 structural variant-altered segments in individual cells) and spontaneous karyotype diversity."
The team went on to explore subclone evolution still further with follow-up functional assays on five patient-derived xenografts, uncovering drug response-related features in leukemic stem cells as well as variability in the evolution of distinct leukemic stem cell subclones.
Using insights from CK-AML subclone-related cell surface phenotypes identified with the new data, meanwhile, the team performed ex vivo drug testing with samples from three CK-AML patients, unearthing possible strategies for targeting leukemic stem cells in at least some of the CK-AML subclones.
Still other treatment response-related features turned up in the researchers' subsequent scNOVA-CITE-based analyses on CK-AML cells found in paired samples collected over time, before and after treatment or relapse.
"Although we were not able to identify inhibitors with strong efficacy toward [leukemic stem cells] in all patients, our platform shows promise for discovering alternative treatments in CK-AML, which may be particularly relevant for personalized cancer therapy," the authors suggested, adding that their work so far "underscores the need for expanded screening to identify patient-specific, [leukemic stem cell]-targeting options through ex vivo drug testing with subclonal readouts."