Targeting HMGA1-driven leukemic transformation in myeloproliferative neoplasms with pacritinib Free

The transformation of myeloproliferative neoplasms (MPNs) to secondary acute myeloid leukemia (sAML) is a lethal event with a median survival of under six months. A critical unmet need exists for robust early biomarkers to identify high-risk patients and innovative therapies to intercept this progression, particularly given the limited efficacy of first-generation JAK inhibitors. High-mobility group A1 (HMGA1), an architectural chromatin factor, has been implicated in MPN pathogenesis, yet its precise role in leukemic transformation and its clinical utility remain incompletely defined.

We conducted a comprehensive investigation integrating multi-omics profiling (scRNA-seq, CITE-seq, ATAC-seq, CUT&Tag, RNA-seq) with analyzing 240 longitudinal patient biopsies across MPN stages. The clinical utility of HMGA1 was validated in independent cohorts (including OHSU BeatAML). Functional studies utilizing gain and loss-of-function leukemia models and patient-derived xenografts (PDX) elucidated HMGA1-mediated leukemogenic mechanisms and assessed therapeutic vulnerabilities to JAK inhibitors, including the next-generation JAK2/FLT3/IRAK1 inhibitor pacritinib.

We identified HMGA1 as a critical driver and potent predictor of MPN-sAML transformation. HMGA1 protein expression, readily detectable by immunohistochemistry (IHC), demonstrated a stepwise increase from chronic MPN phases to sAML (P<0.0001). HMGA1 IHC exhibited exceptional diagnostic accuracy for sAML (AUC=0.96), outperforming conventional markers (CD34/CD117). Crucially, elevated HMGA1 (>40.78%) in non-blast phase MPN predicted impending leukemic transformation within 12 months (47% conversion rate), offering a median lead time of 6 months before overt blast crisis. Single-cell analyses confirmed that HMGA1 upregulation occurs early and persists across heterogeneous malignant populations, overcoming the limitations of transient stem cell markers.

Clinically, high HMGA1 defined a high-risk transcriptional subtype and served as an independent predictor of poor overall survival in sAML (In-house HR=7.18, P=0.0019; BeatAML HR=3.04, P=0.0096). Furthermore, elevated HMGA1 correlated with resistance to first-generation JAK inhibitors (e.g., ruxolitinib) and lower complete remission rates.

Mechanistically, HMGA1 expression is driven by synergistic cooperation between JAK2V617F and TP53 mutations. Integrative chromatin analysis (CUT&Tag, ATAC-seq) revealed that HMGA1 directly binds and maintains open chromatin at key cell cycle regulatory loci, including E2F targets and G2/M checkpoint genes (e.g., E2F1, CDK2, CCNB1/2). This transcriptional reprogramming promotes proliferation, blocks differentiation, and accelerates leukemic progression in vivo.

We discovered that HMGA1 overexpression confers resistance to ruxolitinib and fedratinib by sustaining E2F/G2-M programs. Notably, pacritinib effectively overcame this resistance, suppressing these oncogenic networks, inducing cell cycle arrest and DNA damage (γ-H2AX) irrespective of HMGA1 status. In HMGA1-overexpressing xenograft models, pacritinib significantly reduced tumor burden (8.0-fold decrease in bioluminescence) and doubled median survival (38 to 79 days, P=0.0006).

Our findings establish HMGA1 as a superior, readily implementable biomarker for early predicting leukemic transformation and risk stratification in MPN. We identify HMGA1 as a central driver of aggressive disease and therapeutic resistance, and validate pacritinib as a rational, clinically available strategy to target HMGA1-driven malignancy. These results strongly advocate for integrating HMGA1 assessment into clinical practice and the prospective evaluation of pacritinib for high-risk MPN-sAML.