Longitudinal genomic shifts associated with disease transformation in patients with polycythemia vera (PV) enrolled in REVEAL

Abstract Background: Molecular markers associated with PV progression to myelofibrosis (MF) or acute myeloid leukemia (AML) remain limited. The Prospective Observational Study of Patients (Pts) With Polycythemia Vera in US Clinical Practices Trial (REVEAL; NCT02252159) enrolled pts between 2014 and 2019 for a median follow-up of 4 years. Optional blood and saliva biospecimens were collected at usual care visits. Of 2510 pts enrolled in REVEAL, 114 had MF transformation (Oh S. Blood 2024). The aim of this study was to utilize deep genomic sequencing to investigate changes in mutational profiles associated with PV transformation to MF/AML. Methods Transformation to MF was determined using modified WHO criteria (Grunwald MR. Blood 2023). Whole exome sequencing was performed on samples from pts who transformed to MF during the study with enrollment biospecimens and additional samples collected close to or after transformation (longitudinal samples). This analysis included pts with both an enrollment sample and ≥1 longitudinal sample. Biospecimens were sequenced using the Illumina (paired-end) platform at an average depth of 300× coverage and processed using Genome Analysis Toolkit best practices followed by variant calling via Mutect2 (Broad Institute, Cambridge, MA, USA). Enrollment samples were collected on average 699 days before transformation (range 56, 1535). Longitudinal samples were collected on average 71 days after transformation (range –82, 546). Where multiple longitudinal samples were available, the sample collected nearest to the transformation event was analyzed. Results A total of 41 pts with transformed MF were available for analysis;all 41 were JAK2V617F positive at enrollment (median JAK2V617F VAF 0.768 [range 0.056, 0.958]). Copy neutral loss of heterozygosity (CN-LOH) at chr9p encompassing JAK2 locus was detected in 35/41 pts (85%) at enrollment, which correlated with higher JAK2 VAF. Overall, JAK2V617F VAF was not significantly different in longitudinal samples (median 0.796 [range 0.009, 0.963]) compared with enrollment (P=0.708). However, several patterns were observed. Of 6 pts without CN-LOH at chr9p at enrollment, 5 acquired CN-LOH at chr9p at transformation, accompanied by an increase in JAK2V617F VAF. The remaining pt had a low, constant JAK2V617F VAF between enrollment and transformation, but increased TET2 and RUNX1 VAF (0.157 to 0.293 and not detected to 0.106, respectively). Change in LOH level measured by allelic imbalance correlated with changes in JAK2V617F VAF (Spearman Rho=0.96, P<2.2×10-16). The loci affected by CN-LOH at chr9p was consistent between the 2 timepoints. JAK2V617F VAF increased >5% in 17, remained consistent in 13, and decreased >5% in 11 pts between enrollment and transformation. Additional variants in genes associated with myeloid malignancies were identified in 18/41 pts. 12/17 pts who increased JAK2V617F >5% carried CN-LOH at chr9p at enrollment; the remaining 5 pts acquired a CN-LOH at 9p at transformation. Of 13 pts with consistent JAK2V617F VAF, 5 either acquired or expanded an additional variant(s) in genes such as CBL, RUNX1, DNMT3A, or GNAS; 1 had a consistent TP53 variant (VAF 0.289 to 0.302). Of 11 pts with >5% decrease in JAK2V617F, 3 had acquired/expanded variants in genes such as KRAS and STAG2; 2 had consistent IDH2 and TET2 variants. Loss of CN-LOH at 9p was observed in 2 pts; 1 had a consistent IDH2 variant (VAF 0.350 to 0.388) and the other had an increased allelic burden in KRAS (VAF 0.066 to 0.228). Overall, CN-LOH at 9p was observed in 38/41 pts at transformation. Conclusions Monitoring genomic shifts over time has the potential to impact understanding of, and treatment for, myeloproliferative neoplasms. Together, our analyses show heterogeneous and distinct molecular patterns are associated with disease transformation. The presence of CN-LOH at chr9p was frequent at enrollment but not a common driver for disease transformation. Clonal complexity was evident in pts with co-occurring mutations as shifts in VAFs were different compared with JAK2V617F. Transformation was also seen in pts without co-occurring variants in myeloid genes and in the presence of a decreasing JAK2V617F VAF, suggesting that unknown molecular abnormalities and/or independent clones could drive disease transformation in these pts. These findings warrant further comprehensive genomic analyses to facilitate the monitoring and treatment of pts with PV at high risk of transformation.