Molecular profiling has transformed risk stratification in myelodysplastic neoplasms (MDS). However, the independent prognostic value of specific genomic alterations beyond comprehensive molecular scoring remains unclear. We investigated whether CUX1 copy-number loss (haploinsufficiency) adds prognostic value and its association with other mutations. Given its correlation with chromosome 7 abnormality, we examined its independent significance within the current MDS molecular framework. A cohort of 501 MDS patients with available CUX1 copy-number data (CNACS gene-level calls) and complete clinical follow-up was analyzed from cBioPortal. We assessed associations with clinical characteristics, co-occurring alterations, and survival. Cox proportional hazards models evaluated independence adjusting for IPSS-R and IPSS-M. CUX1 loss occurred in 129/501 patients (26%), nearly always with − 7/del(7q) (98%). Patients with CUX1 loss had higher marrow blasts (median 7% vs. 4%, P < 0.001), IPSS-R scores (6.9 vs. 4.6), and IPSS-M scores (2.33 vs. 0.79). CUX1 loss strongly associated with EZH2 alterations (OR 223.8) and complex karyotype (60%). In univariable analysis, CUX1 loss predicted inferior overall survival (OS; median 11.8 vs. 27.1 months; HR 2.39, 95%CI 1.85–3.08, P < 0.001) and leukemia-free survival (LFS; HR 2.30, 95%CI 1.78–2.98, P < 0.001). After IPSS-M adjustment, associations were non-significant (OS HR 1.27, P = 0.11; LFS HR 1.23, P = 0.15) with negligible incremental discrimination. Within the − 7/del(7q) subgroup, no survival difference was detected (OS P = 0.41; LFS P = 0.31). CUX1 loss identifies high-risk MDS with − 7/del(7q) and EZH2 co-alterations but provides no independent prognostic information beyond IPSS-M. Isolated CUX1 deletions are rare. CUX1 loss reflects − 7/del(7q) biology rather than independent prognostic significance.
Khamis et al. (2026) studied this question.