A novel RUNX1::EWSR1 gene fusion in a young male acute myeloid leukemia (AML) patient: A case report
Cancer Genetics and Therapeutics
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Primary Categories:
- Cancer
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Secondary Categories:
- Cancer
Introduction
RUNX1, encoding the alpha subunit of the core-binding factor (CBF), is essential for normal hematopoiesis. RUNX1 mutations and fusions are frequently observed in hematologic malignancies. The RUNX1::RUNX1T1 fusion, resulting from the t(8;21)(q22;q22) translocation, is a well-characterized and defining genetic abnormality in acute myeloid leukemia (AML). Other common RUNX1 fusions include ETV6::RUNX1 fusion in pediatric acute lymphoblastic leukemia and RUNX1::MECOM fusion in therapy-related myeloid neoplasm. While various rare RUNX1 fusions with other partners have been described, the RUNX1::EWSR1 fusion identified in this patient has not been previously reported.
Case Presentation
Diagnostic Workup
Complete blood count revealed leukocytosis with white blood cell (WBC) count of 46.8 x 10³/µL, anemia with hemoglobin of 8.7 g/dL, and thrombocytopenia with platelets of 17 x 10³/µL. The WBC differential showed 78% blasts. Diagnostic bone marrow biopsy indicated AML with myelodysplasia-related changes in hypercellular bone marrow (90%) with decreased trilineage hematopoiesis, including dysgranulopoiesis and dysmegakaryopoiesis, and 67% blasts. Flow cytometry detected 75% immunophenotypically aberrant myeloid blasts with expression of monocytic markers CD11b, CD33, and CD64. Immunohistochemistry for CD42b highlighted a population of small, hypolobate megakaryocytes.
Cytogenetic karyotyping analysis of the bone marrow revealed two cell clones: one with a balanced t(2;21)(p23;q22) translocation and another with additional trisomies of chromosomes 10, 12, 21, and 22 (ISCN: 46,XY,t(2;21)(p23;q22)[14]/50,XY,t(2;21)(p23;q22),+10,+12,+21,+22[6]). Interphase FISH showed that approximately 50% of cells had an additional copy of RUNX1, and 40% had three extra copies of RUNX1. RNA-seq analysis identified a novel RUNX1::EWSR1 fusion, joining exon 7 of RUNX1 (N-terminus) with exon 10 of EWSR1 (C-terminus). AML Mutation Profiling assay detected a CBL mutation (c.1096-1G>T, VAF 11.5%) and two NRAS mutations (p.Q61R, VAF 31.2%; p.Q61K, VAF 12.5%) in trans configuration. To further characterize the RUNX1::EWSR1 fusion, metaphase and G-banded FISH were performed. Metaphase FISH with RUNX1 probe revealed one or two extra RUNX1 signals on the long arm of chromosome 22, while metaphase FISH for EWSR1 and G-banded FISH for 22q subtelomeric probe showed no abnormal localization of EWSR1 and 22q subtelomeric region. These findings suggest that the RUNX1::EWSR1 fusion likely arose from a cryptic insertion of RUNX1 on chromosome 22 rather than a translocation involving chromosomes 21 and 22 or a three-way translocation with chromosomes 2, 21, and 22.
Treatment and Management
The patient received initial intensive induction 7+3 chemotherapy (7 days of cytarabine and 3 days of daunorubicin). A follow-up bone marrow biopsy showed refractory disease prompting a re-induction with FLAG-Ida chemotherapy (fludarabine, cytarabine, idarubicin, and granulocyte colony-stimulating factor (G-CSF)), after which a complete remission was achieved.
Outcome and Follow-Up
His karyotyping, FISH and AML Mutation Profiling studies were unremarkable. A consolidative allogeneic stem cell transplant is planned as the definitive therapy based on high-risk, primary refractory disease.
Discussion
This represents the first reported AML case with a novel RUNX1::EWSR1 fusion. RUNX1 fusions generally contain either the N-terminal runt-homology domain (RHD) alone or both the RHD and C-terminal transactivation domain (TAD) of RUNX1. EWSR1 fusions are common alterations seen in bone and soft tissue tumors, which typically involve the N-terminal portion of EWSR1 (at least exons 1-7) fused to various C-terminal partners. In this patient, a novel RUNX1::EWSR1 fusion was identified, juxtaposing exon 7 of RUNX1 with exon 10 of EWSR1, producing a chimeric protein containing the RHD domain of RUNX1 and C-terminus of EWSR1.
Conclusion
RUNX1::EWSR1 fusion protein may exert a dominant-negative effect on wild-type RUNX1 and contribute to leukemogenesis. This case demonstrates the critical role of comprehensive cytogenetic and molecular genetic analyses in revealing complex genomic alterations in hematologic malignancies.
RUNX1, encoding the alpha subunit of the core-binding factor (CBF), is essential for normal hematopoiesis. RUNX1 mutations and fusions are frequently observed in hematologic malignancies. The RUNX1::RUNX1T1 fusion, resulting from the t(8;21)(q22;q22) translocation, is a well-characterized and defining genetic abnormality in acute myeloid leukemia (AML). Other common RUNX1 fusions include ETV6::RUNX1 fusion in pediatric acute lymphoblastic leukemia and RUNX1::MECOM fusion in therapy-related myeloid neoplasm. While various rare RUNX1 fusions with other partners have been described, the RUNX1::EWSR1 fusion identified in this patient has not been previously reported.
Case Presentation
A 26-year-old male presented with a three-week history of fatigue, easy bruising, and gingival bleeding prompting further hematologic evaluation.
Diagnostic Workup
Complete blood count revealed leukocytosis with white blood cell (WBC) count of 46.8 x 10³/µL, anemia with hemoglobin of 8.7 g/dL, and thrombocytopenia with platelets of 17 x 10³/µL. The WBC differential showed 78% blasts. Diagnostic bone marrow biopsy indicated AML with myelodysplasia-related changes in hypercellular bone marrow (90%) with decreased trilineage hematopoiesis, including dysgranulopoiesis and dysmegakaryopoiesis, and 67% blasts. Flow cytometry detected 75% immunophenotypically aberrant myeloid blasts with expression of monocytic markers CD11b, CD33, and CD64. Immunohistochemistry for CD42b highlighted a population of small, hypolobate megakaryocytes.
Cytogenetic karyotyping analysis of the bone marrow revealed two cell clones: one with a balanced t(2;21)(p23;q22) translocation and another with additional trisomies of chromosomes 10, 12, 21, and 22 (ISCN: 46,XY,t(2;21)(p23;q22)[14]/50,XY,t(2;21)(p23;q22),+10,+12,+21,+22[6]). Interphase FISH showed that approximately 50% of cells had an additional copy of RUNX1, and 40% had three extra copies of RUNX1. RNA-seq analysis identified a novel RUNX1::EWSR1 fusion, joining exon 7 of RUNX1 (N-terminus) with exon 10 of EWSR1 (C-terminus). AML Mutation Profiling assay detected a CBL mutation (c.1096-1G>T, VAF 11.5%) and two NRAS mutations (p.Q61R, VAF 31.2%; p.Q61K, VAF 12.5%) in trans configuration. To further characterize the RUNX1::EWSR1 fusion, metaphase and G-banded FISH were performed. Metaphase FISH with RUNX1 probe revealed one or two extra RUNX1 signals on the long arm of chromosome 22, while metaphase FISH for EWSR1 and G-banded FISH for 22q subtelomeric probe showed no abnormal localization of EWSR1 and 22q subtelomeric region. These findings suggest that the RUNX1::EWSR1 fusion likely arose from a cryptic insertion of RUNX1 on chromosome 22 rather than a translocation involving chromosomes 21 and 22 or a three-way translocation with chromosomes 2, 21, and 22.
Treatment and Management
The patient received initial intensive induction 7+3 chemotherapy (7 days of cytarabine and 3 days of daunorubicin). A follow-up bone marrow biopsy showed refractory disease prompting a re-induction with FLAG-Ida chemotherapy (fludarabine, cytarabine, idarubicin, and granulocyte colony-stimulating factor (G-CSF)), after which a complete remission was achieved.
Outcome and Follow-Up
His karyotyping, FISH and AML Mutation Profiling studies were unremarkable. A consolidative allogeneic stem cell transplant is planned as the definitive therapy based on high-risk, primary refractory disease.
Discussion
This represents the first reported AML case with a novel RUNX1::EWSR1 fusion. RUNX1 fusions generally contain either the N-terminal runt-homology domain (RHD) alone or both the RHD and C-terminal transactivation domain (TAD) of RUNX1. EWSR1 fusions are common alterations seen in bone and soft tissue tumors, which typically involve the N-terminal portion of EWSR1 (at least exons 1-7) fused to various C-terminal partners. In this patient, a novel RUNX1::EWSR1 fusion was identified, juxtaposing exon 7 of RUNX1 with exon 10 of EWSR1, producing a chimeric protein containing the RHD domain of RUNX1 and C-terminus of EWSR1.
Conclusion
RUNX1::EWSR1 fusion protein may exert a dominant-negative effect on wild-type RUNX1 and contribute to leukemogenesis. This case demonstrates the critical role of comprehensive cytogenetic and molecular genetic analyses in revealing complex genomic alterations in hematologic malignancies.