Loss of Heterozygosity of Chromosome 9p and Progression in MPNs
Authors: Coltoff Alexander , Green Kimberly Michelle , Baratam Praneeth 
Published: December 2023

Introduction
Copy-neutral loss of heterozygosity (LOH) of chromosome 9p, concomitant with mutated JAK2, can occur in myeloproliferative neoplasms (MPNs), and may be the most common chromosomal aberration in patients with polycythemia vera (PV). The prevalence of LOH of 9p varies amongst the different MPNs and is highest in PV where it has been reported to be between 30-70%. The reported prevalence of LOH of 9p is 20-50% and 10-20% in patients with myelofibrosis (MF) and essential thrombocythemia (ET), respectively. A hallmark feature of MPNs is the tendency to progress to more aggressive disease phenotypes (i.e., PV/ET to MF to accelerated- or blast-phase MPN) through the acquisition or loss of cytogenetic and molecular clonal markers. Although loss of LOH of 9p likely contributes to progression in MPNs, its pathologic role is still incompletely defined.
Methods
We conducted a retrospective review of patients at a single-center, tertiary-care institution who were diagnosed with an MPN, either chronic, accelerated or blast-phase (MPN-AP/BP), from January 1 st, 2017 until July 1 st, 2023. All patients underwent a microarray-based chromosome analysis using the I Scan System with the Global Diversity Array-8 (GDA) v1.0 Array BeadChip. Mutational profiling was done using the NextGENe software (SoftGenetics LLC) and MiSeq Reporter, and variant annotation and filtration was performed using VarSeq (Golden Helix).
Results
Fifty-two patients with MF were identified. Twenty-eight patients (53.8%) were found to have LOH of 9p, 15 of whom had secondary MF (7 with preceding ET and 8 with preceding PV). Eight of 9 patients (88.9%) with PV-MF harbored LOH of 9p, vs. 6 of 13 (46.2%) with ET-MF. The median cell fraction affected was 70% (range, 5-95%) and the median JAK2 variant allele frequency (VAF) was 75% (range, 16-97%). Eleven of the 24 patients without LOH of 9p harbored JAK2 mutations, at a median VAF of 40%. Nine patients (32.2%) with LOH of 9p had abnormal cytogenetics by conventional karyotyping, compared to 8 (33.3%) without LOH of 9p. Eleven patients (39.3%) with LOH of 9p were MIPSS-70 v2 high or very high risk, compared to 10 (41.7%) patients without LOH of 9p. Nine patients (32.1%) with LOH of 9p were DIPSS-plus intermediate-2 or high-risk, compared with 9 (37.5%) patients without LOH of 9p.
Twenty patients with MPN-AP/BP were identified, of whom 11 had MPN-AP and 9 had MPN-BP. Four patients (20%), all with MPN-BP, had LOH of 9p. Median JAK2 VAF in these patients was 50% (range, 38-80%), vs. 4% (range, 3-48%) in the 6 patients with JAK2 without LOH of 9p.
Two of 19 patients (10.5%) with ET were found to have LOH of 9p, with a corresponding JAK2 VAF of 70% and 20%. Twelve of the 17 patients (70.6%) who did not have LOH of 9p had a JAK2 mutation, at a median VAF of 27% (range, 4-44%). One patient with LOH of 9p had a thrombotic event, vs. 4 of 17 patients (23.5%) without LOH of 9p. Three of 9 patients (33%) with PV were found to have a LOH of 9p, with a median corresponding JAK2 VAF of 61% (range, 55-81%). Median JAK2 VAF for the other 6 patients (all with a JAK2 mutation) was 34% (range, 26-46%). One patient with LOH of 9p had a thrombotic event vs. 3 of 6 patients (50%) without LOH of 9p.
Discussion
The highest prevalence of LOH of 9p in patients with an MPN was seen in those with MF (&gt;50%), followed by PV, MPN-AP/BP and ET. These results are generally in line with those previously reported, though the prevalence in PV was lower than other studies (likely due to small sample size). The prevalence of LOH of 9p in ET-MF was more than four times higher than in ET, suggesting that LOH of 9p may be an acquired cytogenetic aberration involved in ET progression. LOH of 9p was seen in almost 90% of PV-MF vs. 33% of PV patients, further supporting that LOH of 9p may be implicated in MPN progression.
Notably, LOH-9p was seen in far fewer patients with accelerated- or blast-phase disease. It is likely that clonal evolution of MPNs to MPN-AP/BP is driven more so by the acquisition of high-risk mutations (e.g., TP53, ASXL1, U2AF1) and less by changes such as LOH of 9p and increased JAK2 VAF. In summary, our data largely confirms previous reports regarding the prevalence of LOH of 9p in MPNs while suggesting a role for the gain or loss of LOH of 9p in the progression of these hematologic cancers.