Cytogenetic and Molecular Analysis of a "Double-Hit" RUNX1 Including a RUNX1 p.Trp279* and a Cryptic Novel...

Alterations involving RUNX1 are recurrent in hematologic malignancies and contribute to disease pathogenesis via dysregulation of transcriptional factors essential for hematopoiesis. Here, we report an acquired alteration in both alleles of RUNX1; one is a truncating mutation and the second is a novel RUNX1::ARID1B identified in acute myeloid leukemia.

Bone marrow samples were assessed by morphologic examination and flow cytometry. Cytogenetic analysis was performed using conventional G-banded karyotyping and fluorescence in situ hybridization (FISH). Molecular profiling was performed using next-generation sequencing (NGS) for single nucleotide changes, copy number variations, gene fusions, and expression.

Morphology showed large-sized myeloblasts that are CD34+ and CD45+ (dim) consistent with acute myeloid leukemia. Genetic analysis of diagnostic specimen showed normal karyotype and FISH results but detected mutations in IDH1 and RUNX1. Cytogenetic analysis of a specimen at relapse showed complex abnormal karyotype and FISH detected RUNX1 rearrangement with 6q25. NGS identified this rearrangement as RUNX1::ARID1B. Thus, at this stage leukemia cells had "double-hit" abnormality in RUNX1. Gene transcript evaluation showed elevated levels of transcripts of both RUNX1 and ARIDB1.

This study expands the spectrum of RUNX1 fusions and highlights the integral diagnostic value of morphology, flow cytometry, cytogenetics, FISH, and NGS analyses for broad structural variant detection in clinical practice. Furthermore, the truncating mutation in one allele of RUNX1 and RUNX1::ARID1B of the second allele detected with advanced disease suggests the possibility of combined transcriptional and chromatin regulatory alterations in disease recurrence in the patient.