High-Resolution Chromosomal Microarrays Reveals Exon-Level Deletion in Chromosome 12q14.3 in Patients with Myeloproliferative Neoplasms

High-resolution chromosomal microarrays (CMA) can improve the detection of genomic abnormalities, even in patients (pts) with normal karyotypes, by identifying sub-microscopic copy number alterations (CNA) and regions of copy-neutral loss of heterozygosity (CN-LOH). Increased genomic abnormalities detected by CMAs are associated with disease progression in pts with myeloproliferative neoplasms (MPNs). We and others have observed chromosome 12 abnormalities in about 2% of MPN pts and 3% of myelofibrosis (MF) pts. The most common chromosome 12 aberrations involve the long arms of chromosome 12 at bands 12q13, 12q15, and 12q24, implicating numerous genes in these regions, including NFE2, MDM2, HMGA2, and SH2B3, which potentially contribute to MPN pathogenesis. Utilizing Agilent's aCGH+SNP platform, which allows for the detection of copy number alterations with exon resolution, we retrospectively reviewed the results from conventional cytogenetic (CC) analysis and aCGH+SNP testing of chromosome 12q in 741 MPN pts seen at our institution from 2017-2023 to assess the diagnostic impact of CMA use.

Among 720 MPN pts with an evaluable karyotypic result, 32% had an abnormal karyotype. By adding aCGH+SNP testing (526/720 pts), we detected genomic abnormalities in 50% of pts. To demonstrate the added value of CMA, we focused on MPNs with 12q abnormalities observed in 2% of pts (15/720) by CC analysis alone but detected in 6% (31/526) when CMA was incorporated. Forty-six pts with chromosome 12q abnormalities had the following initial diagnoses: PMF (n=22), ET (n=11), PV (n=10), MPN-U (n=2), and MDS/MPN (n=1). Progression to MF or MPN-AP/BP occurred in 64% of ET and 70% of PV pts, while 23% of PMF progressed to MPN-AP/BP. Integral genomic analysis identified a recurrent genomic abnormality involving the HMGA2 gene at band 12q14.3 in 19 of 46 pts. In 5 of the 19 pts, we identified a balanced translocation involving the HMGA2 gene. These balanced translocations involve HMGA2, with breakpoints near the regulatory sequences of the 3'UTR region involving the binding site for miRNA let-7, a negative regulator of HMGA2, as previously reported (Andrieux et al. 2004). The remaining 14 pts harbored a novel genomic deletion of exon 5 in the 3'UTR of the HMGA2 gene (Δ3'HMGA2), which was detected exclusively using aCGH+SNP. A genomic deletion in the 3'UTR region, including the let-7 binding site, increases HMGA2 expression. Indeed, when we performed qRT-PCR, the relative level of HMGA2 transcripts in these pts with the Δ3'HMGA2was statistically higher than those with any other type of 12q abnormalities (1.9-fold (87.7 vs. 45.4), p=0.03), moreover, it was 5.7 times higher than that in MPN patient MNCs lacking either the Δ3'HMGA2 or other 12q abnormalities (87.7 vs. 15.5; p=0.0002) and 80-fold higher than that observed in normal donor PBMNCs (87.7 vs. 1.1, p=0.000006). Since HMGA1 is closely related to HMGA2 and implicated in the pathogenesis of MPNs, we examined whether genomic abnormalities involving chromosome 6p21.31, where HMGA1 is localized, also occur within the same cohort of pts. We identified chromosomal abnormalities involving 6p in 14 pts (2%). However, unlike HMGA2, none of these 14 pts evaluated by FISH had HMGA1 gene rearrangements, and aCGH+SNP did not detect any genomic abnormalities involving HMGA1 in the remaining 512 patients.

An initial diagnosis of PMF was made in 11 of these 19 pts, with another patient having CML initially, who then became BCR::ABL1 fusion negative and developed PMF 8 years later. The progression from ET/PV to MF in 8 pts occurred after 10-27 years. Notably, HMGA2 abnormalities were exclusively detected at the time of evolution to MF, and 42% of these 19 pts developed >5% PB blasts, with five of these pts progressing to MPN-AP/BP. Four of the 5 pts progressed to MPN-AP/BP within three years of detecting the Δ3'HMGA2. In comparison, 3 of 42 (7%) pts with a normal CMA and a favorable-risk karyotype after 2, 3, and 9 years progressed to MPN-AP/BP. These findings highlight the utility of high-resolution aCGH+SNP platform in identifying clinically significant genomic abnormalities, specifically exon-level deletions. These data provide the impetus for further use of high-resolution aCGH+SNP to detect additional genes that might play a role in MPN disease progression, which could be used as a novel predictive biomarker or a potential therapeutic target.

Schaniel:Cellenkos Inc: Research Funding; Dexoligo Therapeutics by Dexcel Pharma Technologies Ltd.: Research Funding; Sumitomo Pharma: Research Funding. Hoffman:Kymera: Research Funding; Karyopharm therapetics: Research Funding; Protagonist Therapeutics: Consultancy; Cellenkos: Research Funding; Dexcel: Research Funding; Silence Therapeutics: Consultancy.