HMGA2 overexpression with specific chromosomal abnormalities predominate in CALR and ASXL1 mutated myelofibrosis

Abstract

Although multiple genetic events are thought to play a role in promoting progression of the myeloproliferative neoplasms (MPN), the individual events that are associated with the development of more aggressive disease phenotypes remain poorly defined. Here, we report that novel genomic deletions at chromosome 12q14.3, as detected by a high-resolution array comparative genomic hybridization plus single nucleotide polymorphisms platform, occur in 11% of MPN patients with myelofibrosis (MF) and MPN-accelerated/blast phase (AP/BP) but was not detected in patients with polycythemia vera or essential thrombocythemia. These 12q14.3 deletions resulted in the loss of most of the non-coding region of exon 5 and MIRLET7 binding sites in the 3'UTR of the high mobility group AT hook 2 (HMGA2), which negatively regulate HMGA2 expression. These acquired 12q14.3 deletions were predominately detected in MF patients with CALR and ASXL1 co-mutations and led to a greater degree of HMGA2 transcript overexpression, independent of the presence of an ASXL1 mutation. Patients with 12q structural abnormalities involving HMGA2 exhibited a more aggressive clinical course, with a higher frequency of MPN-AP/BP evolution. These findings indicate that HMGA2 overexpression associated with genomic deletion of its 3'UTR region is a newly recognized genetic event that contributes to MPN progression.

Fig. 1. HMGA2 but not HMGA1 expression is upregulated in myelofibrosis (MF) patients.

The normalized expression levels of HMGA2 (A) and HMGA1 (B) transcripts in PBMNCs of MF patients (N = 31) relative to those in unaffected, normal donors (ND; N = 10) are shown. Black bars indicate mean values. P values were determined by unpaired t-test. See Supplemental Table 1 for details on the MF PBMNCs used. UMAP plots indicating the 4 NDs and 6 treatment-naive MF samples analyzed from scRNAseq data (GSE144568 [34]) (C) and the classification of hematopoietic stem and progenitor cell populations (D). Violin plots showing the expression of HMGA1 (E) and HMGA2 (F) in individual HSCs. Each dot represents an individual HSC. HSC_ND = 3552 cells, HSC_MF = 4198 cells.

Fig. 2. Deletions in the 3’ UTR of HMGA2 in myelofibrosis (MF) patients.

The image illustrates the location (black bars) and size (numbers in red) of Δ3’HMGA2 common deleted regions in the 14 MF patients identified by CGH + SNP analysis (see Table 1). Twelve patients had a deleted segment between 1.3 and 3.6 kb while two patients had a substantially larger deleted 12q segment. MIRLET7 bindings sites in the 3’UTR of HMGA2 were identified using TargetScan (https://www.targetscan.org/vert_80/).

Fig. 3. Increased expression of HMGA2 transcripts in myelofibrosis (MF) patients with 12q abnormalities involving HMGA2 occurs more frequently in MF patients with CALR mutations but are independent of MPN driver mutation status or co-occurrence of an ASXL1 mutation.

A The normalized levels of HMGA2 transcript expression in PBMNCs of MF patients lacking HMGA2 abnormalities (norm; N = 23) and those with HMGA2 abnormalities (abn, N = 9) as well as in ND (N = 10) are shown. Each dot represents an individual. Color code indicates driver mutation. Black bars indicate mean values. The normalized expression levels of HMGA1 (B) and HMGA2 (C) transcripts in PBMNCs of MF patients in relationship to their JAK2 (N = 13) and CALR (N = 15) or MPL (N = 3) driver mutation are shown to be not statistically different. Distribution of MPN driver mutations in 169 MF patients evaluated by aCGH+SNP (D) and in the 19 MF patients with HMGA2 abnormalities (E). F The normalized levels of HMGA2 transcript expression in PBMNCs of MF patients lacking HMGA2 abnormalities (norm) and those with HMGA2 abnormalities (abn) stratified for wild-type (WT) or mutant (mut) ASXL1 (N_norm+WT = 13, N_norm+mut = 7, and N_abn+mut = 5) are shown. Each dot represents an individual. Color code indicates driver mutation. Black bars indicate mean values. P-values were determined by one-way ANOVA (A, B, C, F). See Supplemental Table 1 for details on the MF PBMNCs used.

Fig. 4. Genomic events involving 12q in 4 unique patients during MPN disease progression.

A Patient ID#4 with prePMF was found to have t(5;12) in 2016 and progressed to symptomatic MF in 2021 and then went on to develop MPN-AP. B Patient ID#8 at diagnosis had gain of 9p and tetrasomy of JAK2. However, he had a decline in JAK2^V617F VAF along with a new acquisition of Δ3’HMGA2 and persistence of the CALR mutation which was associated with evolution to MPN-BP. C Patient ID#15 with PMF and an ASXL1 mutation progressed to MPN-AP while acquiring Δ3’HMGA2 with stable ASXL1 VAF. D Patient ID#1, initially diagnosed with CML, achieved a major molecular response with tyrosine kinase inhibitor therapy, and subsequently developed CALR mutated MF 8 years later. Three years later, the Δ3’HMGA2 was detected along with a t(6;12) chromosomal abnormality.