Analysis Of Molecular Responses and Chromosomal Aberrations In Patients With Polycythemia Vera Treated With Peg-Proline-Interferon Alpha-2b (AOP2014/P1101) In The Peginvera Study

Polycythemia vera (PV) is one of the most common type of BCR-ABL negative myeloproliferative neoplasms. It is characterized by elevated erythrocyte mass, variable presence of thrombocytosis and leukocytosis, predisposition to secondary myelofibrosis, thrombosis, bleeding and leukemic transformation. Most patients carry the JAK2-V617F mutation (up to 95%) or the less common JAK2 exon 12 mutations (around 3%). The current treatments include phlebotomy, low-dose aspirin, hydroxyurea, interferon alpha (IFNa) and bone marrow transplantation. However, PV is still lacking a curative treatment, with the exception of cases with successful bone marrow transplantation (in the spent phase) and few reports of complete clinical and molecular remission using IFNa. Measuring mutant JAK2 burden offers an opportunity to evaluate efficacy of therapy on the molecular level. We have previously reported sound clinical and molecular responses of PV patients treated with a new, once every 14 days formulation of peg-proline-IFNa-2b (AOP2014/P1101) in the Phase I/II clinical study PEGINVERA. The rational of the cytogenetic evaluation in this study is to investigate if chromosomal aberrations have an influence on the clinical course of PV patients, treated with AOP2014/P1101. It might be that cytogenetically complex patients have lower response rates to IFNa therapy. Furthermore, cytogenetic lesions may serve as additional markers to evaluate the response in parallel to JAK2 mutational burden analysis.

Results of JAK2 mutational burden as well as high-resolution SNP array-based cytogenetic analysis, in 45 patients, treated with AOP2014/P1101, are presented here. Genome-wide human SNP 6.0 Affymetrix arrays were performed for the baseline sample (at the start of IFNa treatment) and latest follow-up sample. Mutant JAK2-V617F burden was determined by allele specific-PCR and quantitative PCR. For JAK2 exon 12 mutations a fragment analysis-based assay was used. Molecular response, defined by at least 10% decrease in mutant JAK2 burden, was observed in 73% of patients. The median follow-up time of patients was 500 days. The median follow-up time of molecular responding patients was 633 days, for partial responders 959 days and for non-responding patients 168 days.

At least one chromosomal aberration was present in 69% of patients, of which chromosome 9p uniparental disomies (9pUPDs) were the most prevalent ones. Molecular non-responding patients did not have recurrent specific cytogenetic lesions or more chromosomal aberrations than responding patients. Molecular responses analyzed by JAK2 mutational burden correlated well with cytogenetic changes. A complete cytogenetic remission with around 3% residual JAK2-V617F burden could be achieved in 3 patients, all showing chromosome 9p UPDs at baseline. Interestingly, one patient had in addition to the 9p UPD a chromosome 14q UPD and another one trisomies of chromosome 8 and 9. This indicates that IFNa therapy is not restricted to mutant JAK2 clones but is also able to target other aberrant clones with common genetic changes found in MPN.

Cytogenetic lesions found in follow-up samples that were not detected at baseline may indicate clonal evolution during IFNa therapy. These emerging clones might be responsible for acquisition of IFNa resistance and/or acceleration of disease progression. We found 3 such patients in our study, 1 with molecular response that acquired a small clone with a deletion of chromosome Y, 1 with partial molecular response where a single gene deletion on chromosome 10p (USP6NL) was detected and 1 that had no molecular response which showed a single gene gain on chromosome 3q (FXR1) as well as a single gene deletion on chromosome 7p (NXPH1). Additional follow-up samples will be necessary to assess the impact of the clonal evolution in these patients. Not only acquired somatic changes (including large chromosomal aberrations and point mutations) but also germline variants might influence IFNa response or resistance. Since we did not observe any difference in cytogentic lesions between molecular responding and non-responding patients, we suspect that in some cases germline variants are likely to influence the outcome of IFNa therapy. Further characterization of AOP2014/P1101 treated patients and later follow-up samples will help to better understand the clonal evolution and molecular responses during long-term IFNa treatment.