Loss of Heterozygosity on Chromosome 9p24 Is the Most Frequent Chromosomal Aberration in Polycythemia Vera and Idiopathic Myelofibrosis.

Myeloproliferative disorders (MPD) represent a heterogeneous group of diseases characterized by excessive myeloid cell production and clonal hematopoiesis. The appearance of the MPD stem cell clone is believed to be a consequence of an as yet unknown somatic mutation. The genetic basis for clonal hematopoiesis in MPD has been extensively studied using cytogenetic analysis, but no invariant chromosomal aberration has been found. Recently, we identified loss of heterozygosity of chromosome 9p (9pLOH) as a clonal defect in a small cohort of polycythemia vera (PV) patients. Here we extended this study to a total of 295 patients with MPD; 171 with PV, 91 with essential thrombocythemia (ET), and 33 with idiopathic myelofibrosis (IMF). The 9pLOH was detected in 62/171 patients with PV (36%) and in 10/33 patients with IMF (30%). Thus, 9pLOH is the most frequent chromosomal aberration in PV and IMF described to date. Interestingly, only 2/91 patients with the diagnosis of ET had 9pLOH. The reason for this difference is currently unknown and may be related to the presence of polyclonal hematopoiesis in a proportion of ET. By increasing the microsatellite marker density used for the LOH mapping in all 68 patients with 9pLOH, we identified a 6.2 Mbp minimal common LOH region. Copy number analysis performed by quantitative PCR revealed that all patients with 9pLOH had two copies of the chromosomal region involved in LOH. This finding excludes deletions as the genetic mechanism underlying 9pLOH and indicates that mitotic recombination is involved. This explains why this chromosomal defect remained hidden to cytogenetic analysis, FISH, or comparative genomic hybridization. 9pLOH results in partial uniparental disomy (UDP) of chromosome 9p. The phenotypic consequences of UPD are often associated with genes undergoing genomic imprinting. However, in two of our patients with 9pLOH, we were able to determine the parental origin of the lost chromosome by analyzing their parents. In one patient, the maternal chromosome was lost, whereas in the other patient, the paternal chromosome was missing. This variability of parental origin of UDP makes the involvement of imprinted genes in the expansion of the 9pLOH clone unlikely and favors a tumor suppressor mechanism. CDKN2A and CDKN2B genes (INK4A, INK4B), localized on 9p21, are among the most frequently mutated tumor suppressors in human malignancies. However, the CDKN2A/B locus is not part of the minimal 9pLOH region in MPD. The 6.2 Mbp common 9pLOH region contains 40 genes and ESTs. We determined which of these genes are expressed in hematopoietic cells and are currently sequencing the cDNAs of these genes to search for mutations.