Rare RUNX1 Gene Amplification Marks a Aggressive, Treatment-Resistant Case of Leukemia in a Young Man

Doctors in Riyadh have described an exceptionally rare genetic fingerprint in a 27-year-old man with acute myeloid leukemia (AML) that refused to respond to standard treatment. His leukemia carried more than ten copies of the RUNX1 gene in every analyzed cell, a phenomenon known as high-level RUNX1/21q22 amplification or iAMP21, alongside a deletion on chromosome 7q, an extra chromosome 8, loss of one CBFB signal, and a pathogenic TP53 mutation. AML is a genetically heterogeneous cancer of the blood and bone marrow, and modern classification systems, including the World Health Organization (WHO), the International Consensus Classification (ICC), and the European LeukemiaNet (ELN), rely heavily on cytogenetic and molecular findings to define disease entities, assign risk, and guide therapy.

Recurrent fusion genes such as PML::RARA, CBFB::MYH11, and RUNX1::RUNX1T1 define distinct AML subtypes, while abnormalities like deletion of chromosome 7q mark AML with myelodysplasia-related changes. TP53 mutations, long recognized as harbingers of chemoresistance and poor survival, are treated as a separate entity, AML with mutated TP53, in the ICC when the variant allele fraction reaches at least 10 percent, and as adverse risk in the ELN framework. High-level amplification of RUNX1 at chromosome band 21q22 is best known in B-lymphoblastic leukemia, where it defines a poor-prognosis subgroup that benefits from intensified therapy.

In AML, however, the lesion is far less common and has been reported mostly in older patients, in therapy-related disease, or in AML with myelodysplasia-related changes accompanied by complex karyotypes. The patient in this report had no significant medical history when he first presented with weight loss, night sweats, oral ulceration, and an axillary lesion suspicious for abscess. His initial blood counts revealed pancytopenia: a white blood cell count of 1.85 × 10³/µL against a reference range of 4.0 to 11.0, hemoglobin of 7.5 g/dL, and platelets of just 22 × 10³/µL.

A peripheral blood film showed 16 percent circulating blasts, and bone marrow examination at presentation revealed approximately 42 percent blasts, medium to large cells with high nuclear-to-cytoplasmic ratios, immature chromatin, prominent nucleoli, and scant-to-moderate basophilic cytoplasm. No definite Auer rods were identified. The diagnostic work-up combined morphology, multiparameter flow cytometry, interphase and metaphase fluorescence in situ hybridization (FISH), quantitative PCR, and a next-generation sequencing (NGS) myeloid tumor panel.

Flow cytometry identified an abnormal population comprising about 75 percent of nucleated cells, with a myeloblast gate showing CD34, CD117, CD13, CD33, and CD38 positivity, TdT expression, and partial HLA-DR and myeloperoxidase, alongside a monocytic population expressing CD13, CD33, CD38, CD11c, CD11b, CD4, CD64, and CD14. No B- or T-lineage markers were detected, confirming a myeloid immunophenotype. The FISH results were striking.

Using a RUNX1T1/RUNX1 probe set, the team found more than ten RUNX1 signals per nucleus in all 100 cells analyzed, with no evidence of RUNX1::RUNX1T1, BCR::ABL1, PML::RARA, or KMT2A fusions and no deletion of 5q. Follow-up targeted probes confirmed persistence of the amplified clone and revealed additional abnormalities: deletion of 7q31 (D7S522) in 39 of 100 nuclei, trisomy 8 in 30 of 100 nuclei, and monoallelic CBFB signal loss in 64 of 100 nuclei. The CBFB pattern, one fused signal with a single green and orange signal, was consistent with deletion or monosomy rather than the three-signal rearrangement pattern typical of inv(16).

The variable distribution of these lesions across nuclei pointed to at least two related leukemic populations and suggested ongoing clonal evolution. Molecular testing added a further adverse marker. The NGS panel identified a pathogenic TP53 variant, NM_000546.4:c.584T>C resulting in p.Ile195Thr, at a high variant allele fraction of 62.6 percent based on 1,589 reads, while NPM1 and FLT3-ITD/TKD testing were negative.

The authors note that such a variant allele fraction may reflect loss of the wild-type TP53 allele, copy-neutral loss of heterozygosity, or an unrecognized germline mutation, and they recommend targeted testing in a non-tumor sample such as a buccal swab or skin fibroblast, together with genetic counseling, to clarify germline status. Treatment followed standard pathways but failed to control the disease. The patient received conventional 7 + 3 induction chemotherapy, and after multidisciplinary tumor board discussion, azacitidine combined with the BCL-2 inhibitor venetoclax.

Bone marrow blasts rose to 77 percent after induction and remained at 55 percent after reinduction, while the abnormal flow cytometric population persisted at 67 percent and then 53 percent, demonstrating refractory disease throughout. His course was complicated by febrile neutropenia driven by a perianal abscess with a sinus tract requiring surgical drainage and broad-spectrum antimicrobial therapy, along with subcutaneous nodules showing inflamed fat and superficial thrombophlebitis. Imaging revealed a right upper lobe ground-glass opacity, enlarged cervical and upper abdominal lymph nodes without hepatosplenomegaly, and mildly FDG-avid cervical nodes on a PET scan limited by brown fat activation.

The patient was discharged to seek follow-up in his home country, and no updated outcome information was available when the manuscript was finalized. In their discussion, the authors emphasize the unusual involvement of both subunits of the core-binding factor transcription complex through copy-number changes: very high-level RUNX1 amplification together with CBFB loss. Classic core-binding factor AML, defined by balanced RUNX1::RUNX1T1 or CBFB::MYH11 rearrangements, carries a favorable prognosis, making this copy-number-driven disruption of both subunits particularly notable.

The presence of del(7)(q31), an MDS-related cytogenetic abnormality, supports a classification of AML with myelodysplasia-related changes under the WHO framework, while the TP53 mutation at 62.6 percent variant allele fraction meets ICC criteria for AML with mutated TP53. Under ELN guidelines, del(7q), complex cytogenetics, and mutated TP53 each independently place the disease in the adverse-risk category. Comparing the case with previously published reports highlights its singularity.

Earlier series described iAMP21-like lesions in AML patients ranging from 26 to 77 years old, typically with lower amplification levels of 4 to 10 copies, often in therapy-related settings or with complex karyotypes involving chromosomes 5, 7, and 17. Xie and colleagues documented 13 AML cases with hsr(21)(q22) and very poor outcomes, all with complex karyotypes and a high frequency of TP53 deletion or mutation. To the authors' knowledge, no previously described AML case in a young adult has combined very high-level RUNX1 amplification exceeding ten copies with TP53 mutation, del(7q), trisomy 8, and CBFB loss.

The team concludes that comprehensive cytogenetic and molecular analysis should be performed upfront in suspected AML to identify such high-risk cases, and that further studies are needed to establish the prognostic and therapeutic significance of high-level RUNX1 amplification, particularly as azacitidine-venetoclax outcomes in TP53-mutated disease remain unfavorable and early consideration of allogeneic transplantation or investigational approaches is generally advised when feasible.

Subject of Research: A case report of refractory acute myeloid leukemia with high-level RUNX1/21q22 amplification, complex cytogenetic abnormalities, and a TP53 mutation

Article Title: Case Report: High-level RUNX1/21q22 amplification is associated with multiple cytogenetic abnormalities and TP53 gene mutation in a refractory AML patient with poor clinical outcome

Article References: Aldalaqan, S., Alomran, A. O., Albohigan, A., Aldakhil, K., Alsharif, R. A., Bafail, M., Altahan, R. M., Tashkandi, S. A., & Peer-Zada, A. A. (2026). Case Report: High-level RUNX1/21q22 amplification is associated with multiple cytogenetic abnormalities and TP53 gene mutation in a refractory AML patient with poor clinical outcome. Frontiers in Hematology, 5, Article 1928502. https://doi.org/10.3389/frhem.2026.1928502

Image Credits: AI Generated

DOI: 10.3389/frhem.2026.1928502

Keywords: acute myeloid leukemia, RUNX1 amplification, iAMP21, TP53 mutation, cytogenetics, FISH, refractory AML, chromosome 7q deletion, trisomy 8, CBFB loss, next-generation sequencing, adverse-risk AML