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

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 (TP53^mut). 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 TP53^mut 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 TP53^mut (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 TP53^mut, we further investigated each abn separately. Patients with Chr5 abn/TP53^mut, Chr5 abn/TP53^wt and Chr5 normal/TP53^mut had similar OS (2-yr OS of 9%, 14%, and 6%, respectively). In contrast, patients with Chr5 normal/TP53^wt 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 TP53^mut, the 2-yr OS was similar regardless of the presence of Chr7 abns (6% vs 12%, respectively P=ns). For patients with Chr5 normal/TP53^wt, 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/TP53^mut, which likely contribute to chromoanagenesis genetic instability. This cohort exhibited a significantly worse outcome, compared to patients with CK and Chr5 normal/TP53^wt. Based on this data, the worse outcomes traditionally associated with CK should be considered in the presence of with Chr5 abn or TP53^mut.