Comparative Genomic and Expression Analysis of Chronic and Blast-Phase Cells in Patients with Myeloproliferative Neoplasms

Background. Progression to acute myeloid leukemia (sAML) occurs in 20% of myelofibrosis (MF) and 10% of polycythemia vera (PV) or essential thrombocythemia (ET). sAML has dismal outcome with median survival of <6 months. We recently reported that a restricted set of mutations predict for leukemic transformation in MPN (Vannucchi AM, Leukemia 2013; Tefferi A, Blood Adv. 2016). However, the molecular mechanisms underlying transformation to sAML are poorly characterized, in particular the relationships between the clones establishing the chronic phase and the one dominating the leukemic phase.

Aim. To study clonal heterogeneity and clonal progression in the leukemic transformation of MPN we performed whole exome (WES) and trascriptome (RNAseq) sequencing of paired samples (chronic (CP)/blast phase(BP).

Patients and Methods. WES and RNAseq was done on CD34+ or blast cells of 12 paired samples from 5 PMF, 3 PET-MF, 1 PPV-MF, 3 ET pts who transformed to sAML. In addition, a myeloid neoplasm-relevant 34-gene panel was used for target NGS sequencing of paired samples plus an additional 23 samples collected from MPN pts at leukemic phase (15 PMF, 3 PET-MF, 3 ET, 2 PV).

Results. In the entire series, 20 pts (57%) were JAK2 V617F mutated at CP, 8 CALR (23%; 6 type-1 and 2 type-2) and 7 (8.6%) MPL mut, while 4 (11.4%) were triple-negative. JAK2 variant allele frequency (VAF) declined by ≥50% (n=3; 15%) or became undetectable (n=4; 20%) whereas 3 heterozygous pts (15%) became homozygous at the time of BP. One of the 8 CALR mut cases halved its VAF, whereas no meaningful VAF changes were observed in MPL mut pts. The most frequent mutated genes detected by NGS at BP, other than driver mutations, were ASXL1 (51.4%), RUNX1 (37.1%), TET2 (17%), SRSF2 (16%), IDH1 (14%), TP53 (14%), NRAS (14%), FLT3 (14%), U2AF1 (11%) and KRAS (11%); three (8%) cases were mutated for EZH2DNMT3A, CBL and PTPN11, 2 cases for IDH2, SH2B3, SF3B1 IKZF1, SETBP1 and ZRSR2, and 1 case for ABL1, ATV6, BRAF and ARID1A. There were also 5 CEBPA-mutated pts, 3 of which, unlike none of 27 CEBPA-mutated de novo AML, showed an in-frame 6-bp duplication polymorphism (p. P196_197insHP) reported in 20-40% of all de novo AML and <1% of healthy population (rs762459325). Compared to the CP of the 12 paired samples, 10 pts (83%) acquired novel mutations, 3 of which acquired ≥3 variants. RUNX1 and ASXL1 were those with the highest number of acquisition (n=7 and 5, respectively). Conversely, loss of variants was observed only in ASXL1 (n=3).

By WES analysis, on average 60.000 variants per paired sample unique to the BP compared with CP were identified. However, no recurrent abnormalities were found in the 12 paired samples outside the above listed mutations found by target sequencing. For RNAseq analysis, transcripts were annotated according to UCSC hg19 for a total of 25,369 genes. We found large transcriptional differences between CP and BP with 129 transcripts differentially expressed (23 up- and 106 down-regulated) and 4,155 isoforms (2,120 up- and 2,035 down-regulated). Among the most abnormally expressed transcripts we selected 8 genes (5 down-regulated: LCN2, PDGFB, PRTG, CRISP3, PF4; 3 up-regulated CDKN2, SH2D1A and LIN28) for validation by QRT-PCR based on the extent of differential expression. PF4 and CDKN2 were confirmed to be down-regulated and over-expressed in BP, respectively (P<0.0001). Analysis of RNA-seq data for fusion genes revealed 10 fusion genes acquired during BP; however, only 3 of them were confirmed by Sanger sequencing (2 cases of BCR-ABL, 1 case of KMT2A- MLLT3 and 1 case of CBFB-MYH11). Pathway analysis included Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis. Six pathways were significantly deregulated in BP compared with CP: Mitotic Spindle (P<0.0001); Androgen response (P=0.004); TGF-beta signaling (P=0.04); Apoptosis (P=0.03); PI3K-AKT-MTOR signaling (P=0.04); Reactive Oxygen Species- Pathway (P=0.03).

Conclusions. Comprehensive comparative analysis of genomic and RNA abnormalities acquired in the transition from CP to BP in MPN has not been previously reported. Our data indicate that BP is associated with significant changes in mutation complexity and RNA expression, overall affecting different intracellular pathways whose further characterization might help to identifying potential targets for therapy.