Newly-Acquired and Clonally-Increased Mutations in TP53 and RAS Pathways Promote Progressive Disease and Leukemic Transformation in Patients with Myelodysplatic Neoplasms
Authors: Yan Xin , Tian Yulu , Gu Yan , Song Chunhua , Ge Zheng 
Published: December 2024

Background
Myelodysplastic neoplasms (MDS) are heterogeneous clonal hematopoietic neoplasms as progressive disease (PD) and leukemic transformation (LT) are involved with the accumulation of genetic abnormalities (Leukemia,2017,31:1928-1935). However, the relationship between PD/LT and the critical dynamic change in genetic mutations is not yet well defined. This study aimed to explore the key genetic mutations that may promote PD/LT in MDS patients.
Methods
86 paired MDS patients were enrolled in the cohort, including 51 MDS with a low blast (MDS-LB),1 MDS with isolated 5q deletion (MDS-5q-), 6 MDS with low blasts and SF3B1 mutation (MDS-SF3B1),7 MDS with biallelic TP53 inactivation (MDS-biTP53), 2 MDS with fibrosis (MDS-f), 10 MDS with increased blasts type 1(MDS-IB1),8 MDS with increased blasts type 2 (MDS-IB2), from 30 May, 2019 to 16 August, 2023 at our institute. The patients were sequenced two times by our reported targeted exome-seq for 52 human leukemia driver genes (Blood Cancer J. 2022;12:145); The 1st sequencing was at diagnosis and the 2nd sequencing was at PD(20 patients), LT(13 patients), and non-PD/LT(51 patients), respectively.
The mutations were defined into four groups based on the dynamic changes of variant allele frequency (VAF). If a mutation was not detected at 1st sequencing while detected at the 2nd sequencing, it was defined as a newly-acquired mutation. If the VAF of a mutation was increased by ≥10% in the 2nd sequencing versus the 1st sequencing, it was defined as a clonally-increased mutation. If the VAF of a mutation decreased by ≥10% in the 2nd sequencing versus the 1st sequencing, it was defined as a clonally-decreased mutation. If the VAF of a mutation changed ＜10% in the 2nd sequencing versus the 1st sequencing, it was defined as clone-stable mutations.
Results
The median number of genetic mutations in PD/LT cohorts was higher than non-PD/LT cohort (2 vs. 1, P=0.011) at diagnosis. Mutations in TET2 (25.7% vs.5.9%, P=0.012), RUNX1(17.1% vs.2%, P=0.017), and SETBP1(17.1% vs.2%, P=0.017) were more frequent in the PD/LT cohorts compared to the non-PD/LT cohort at diagnosis.
The median number of newly-acquired and clonally-increased mutations in PD/LT cohorts was higher than in the non-PD/LT cohort(2 vs.0, P＜0.001). The newly-acquired and clonally-increased mutations inTP53 (25.7% vs.0%, P＜0.001), RAS pathway (22.9% vs.0%, P＜0.001), TET2(17.1% vs.2%, P=0.017) were more enriched in PD/LT cohorts compared to non-PD/LT cohort during the disease course, which suggested these mutations play a critical role in PD/LT.
Most of the TP53 mutations (9/12,75%) were newly-acquired and clonally-increased mutations in the PD/LT cohorts; On the contrary, all of the TP53 mutations (8/8,100%) were clonally-decreased and clone-stable mutations in non-PD/LT cohorts. Then, we performed the co-mutation analysis with and without TP53 mutations in PD/LT patients, and the results showed that patients with TP53 mutations barely co-mutated with other clonally-decreased and clone-stable mutations. These results suggested that TP53 mutations are the direct factors for PD/LT. For patients without TP53 mutations, the most frequently co-clonally-decreased and co-clone-stable mutations were RAS pathway (6/26,23.1%), TET2 (5/26,19.2%), ASXL1 (4/26,15.4%), DDX41 (3/26,11.5%), and WT1 (3/26,11.5%) mutations.
Similarly, in PD/LT cohorts, most of (8/9,88.8%) the RAS pathway mutations were newly-acquired and clonally-increased mutations, while in non-PD/LT cohorts, all of the RAS pathway mutations were clone-stable mutations.
Conclusion
The study clarified the dynamic changes of genetic mutation of MDS patients during the disease course. The increment of the newly acquired and clonally-increased mutations was associated with the PD/LT of MDS. Newly-acquired and clonally-increased TP53 and RAS pathway mutations may promote PD/LT in MDS patients, which may be potential targets as potential intervention points.