Complex cytogenetics in myeloid malignancies: A deconstruction analysis redefining complex karyotypes

Abstract

Abstract Background: In myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), a complex karyotype (CK) is defined as ³3 unrelated chromosome (Chr) abnormalities (abns) according to most prognostic classifications. In AML, a CK must also lack class-defining recurring genetic abnormalities. CK is associated with poor outcomes and TP53mutations (TP53mut). However, this definition fails to reflect the underlying biological mechanisms driving CK. Herein we analyzed a large cohort of patients with MDS and AML with CK, deconstructing their karyotypes to better understand and redefine this entity. Methods: This is a retrospective, single-center study including patients with newly diagnosed MDS and AML with CK diagnosed from 2014 to 2022. Karyotyping was done by conventional G-banded chromosomal analysis, and mutations were detected with a targeted NGS panel. CK was defined as described above, with the additional criteria of at least one structural abnormality and presence in >1 metaphase. We developed a cytogenetic extractor function tool to deconstruct CK for detailed analysis. Results: Among 3819 patients with MDS and AML, 939 patients (25%, MDS=429, AML=510) had CK. The median age was 68 (20-94) years, and 57% were male. Therapy-related MDS was more frequent than therapy-related AML (54% vs 28%, P <0.001). All AML patients were adverse risk by ELN 2022 classification. In MDS patients, 19% and 71% were high and very high risk by IPSS-R, and 17% and 75% by IPSS-M, respectively. The most frequent mutations were TP53(MDS=79%, AML=70%), DNMT3A (MDS=13%, AML=12%) and TET2 (MDS=9%, AML=12%). Chromosomal abnormalities in CK were not random. The most frequently affected chr were Chr5 (77%), Chr7 (58%) and Chr17 (46%). Chr10, Chr2, or sex chromosomes were the less frequently affected in CK (<15% for each). Among Chr5 abns, 5q abns were the most frequent (59% of all CK). For Chr7 abns, Chr7 monosomy (29% of all CK) and 7q abns (28% of all CK) were the most frequent. Within Chr17 abns, the most frequent were 17p abns (21% of all CK) and Chr17 monosomy (17% of all CK). Notably, monosomies of Chr 18 (23% of all CK), Chr 16 (15%, 9% of all MDS with CK and 19% of all AML with CK, P=0.002) and Chr 20 (15% of all CK) were also frequent in CK. Correlation analysis between Chr abns and mutations revealed that TP53mut were significantly positively associated with the presence of 5q and monosomy of Chr5, Chr12, Chr17, Chr18 (P<0.001), Chr16 and Chr20 (P<0.05). Conversely, there was a significant negative correlation between 5q abn and ASXL1 or NPM1 mutations (P<0.05). We used hierarchical clustering using deconstructed cytogenetic and genetic data to identify subgroups among patients with CK. A major cluster (Cluster 1, n=787) segregated patients with chr5 anbs and TP53mut (88% and 86% of patients in cluster 1, respectively). In this cluster, abns in Chr7q and Chr17p and monosomies (specially chr 7 and 18) were also frequent. A smaller cluster (Cluster 2, n=152) segregated patients with Chr7 abns (41%), Chr8 trisomy (40%) and mutations in DNMT3A (22%), ASXL1 (21%) and TET2 (20%). Patients in cluster 1 had a worse OS than patients in cluster 2 (2-yr OS 9% vs 29%, P<0.001). This difference was more pronounced in MDS patients with CK (2-yr OS 13% vs 55%, P<0.001). Given that cluster 1 segregated most of the CK patients with either Chr5 abn or TP53mut, we further investigated each abn separately. Patients with Chr5 abn/TP53mut, Chr5 abn/TP53wt and Chr5 normal/TP53mut had similar OS (2-yr OS of 9%, 14%, and 6%, respectively). In contrast, patients with Chr5 normal/TP53wt had better outcomes than the previous groups (2-yr OS 36%, P<0.001). Notably, Chr7 abnormalities did not impact in outcomes of CK. Among patients with Chr5 abn or TP53mut, the 2-yr OS was similar regardless of the presence of Chr7 abns (6% vs 12%, respectively P=ns). For patients with Chr5 normal/TP53wt, the presence or absence of chr7 abns did not impacted OS (2-yr OS was 40% and 34, P=ns). Conclusion: CK abnormalities are not random. Clustering analysis identified a major group of patients with Chr5 abns/TP53mut, which likely contribute to chromoanagenesis genetic instability. This cohort exhibited a significantly worse outcome, compared to patients with CK and Chr5 normal/TP53wt. Based on this data, the worse outcomes traditionally associated with CK should be considered in the presence of with Chr5 abn or TP53mut.