Understanding and Therapeutic Targeting of Extramedullary Acute Leukemia

/ABSTRACT Myeloid sarcoma (MS) is a subtype of acute myeloid leukemia (AML) found in ~5-10% of patients. In MS, myeloid blasts form solid tumor-like, invasive masses in multiple extramedullary sites, including the skin, the lymph nodes, and the gastrointestinal tract. MS is a heterogeneous disease that is clinically unified by its poor survival outcomes, with almost inevitable relapse if treated with standard cytotoxic chemotherapy. Survival rates for MS patients are dismal, with a 5-year overall survival rate below 20%. Such patients are excluded from AML clinical trials, making the introduction of novel therapies in MS a clinical emergency. In the last several years, we have initiated an extensive transcriptomic (bulk and single cell RNA sequencing), genomic (whole genome and mutant panel sequencing) and spatial mapping of human MS. Our analysis included samples at diagnosis, matched bone marrow (BM) and extramedullary site collections, and, in some cases MS samples from a number of extra- medullar sites from the body of the same patient. Our data reveal: a) site-specific extramedullary clonal tumor evolution, including the presence of site-specific, “solid tumor-like” mutations (APC, MITF, MTOR), b) the over- representation of RAS pathway mutations (NRAS, KRAS, PTPN11, CBL), c) RAS/ERK pathway activation (by phospho-ERK1/2 activation in AML blasts), and, d) changes in the cellular and transcriptional landscape suggestive of a gradual transition to a solid tumor environment (by upregulation of EMT-like, adhesion, apical junction genes), and, e) genetic and pharmacological targeting of the RAS/ERK pathway leads to a significant reduction in tumor burden. These findings introduce the hypothesis that myeloid sarcoma is characterized by unique mutational signatures, aberrant gene expression, and immunological adaptations leading to immune escape and the eventual emergence of a “solid-tumor”-like myeloid blast that has the ability to expand outside of the bone marrow (BM). To address this hypothesis, we will initially focus on mapping myeloid sarcoma ultra- structure and understanding the molecular mechanisms of the adaptation to a solid microenvironment. Also, we focus on the RAS/MEK/ERK pathway that is activated in the majority of MS patients and test whether its inhibition constitutes an “Achilles heel” of this treatment-refractory AML subtype, with a future goal to provide data-driven support for the design of the first frontline trial for MS patients. This is the first large-scale study in myeloid sarcoma, combining genomic, transcriptomic, and spatial mapping of the extramedullary disease. It is also the first study that proposes spatial imaging, generation of novel MS animal models, establishment of PDX models, and pre-clinical testing of new therapy protocols in this devastating disease. Project Number: 1R01CA305969-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Iannis Aifantis (+1 co-PI) | Institution: NEW YORK UNIVERSITY SCHOOL OF MEDICINE, NEW YORK, NY | Award Amount: $716,681 | Activity Code: R01 | Study Section: Molecular Cancer Diagnosis and Classification Study Section[MCDC] View on NIH RePORTER: https://reporter.nih.gov/project-details/11391429