Cryptic recurrent ACIN1‐NUTM1 fusions in non‐KMT2A‐rearranged infant acute lymphoblastic leukemia

• Published in: Genes chromosomes & cancer Vol. 59; no. 2; pp. 125 - 130
• Main Authors: Pincez, Thomas, Landry, Josette‐Renée, Roussy, Mathieu, Jouan, Loubna, Bilodeau, Mélanie, Laramée, Louise, Couture, Françoise, Sinnett, Daniel, Gendron, Patrick, Hébert, Josée, Oligny, Luc, Rouette, Alexandre, Tran, Thai H., Wilhelm, Brian T., Bittencourt, Henrique, Cellot, Sonia
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.02.2020; Wiley Subscription Services, Inc
• Subjects: Acute lymphoblastic leukemia; Bone marrow; Cell fusion; Chemotherapy; Chromosome Aberrations; Chromosome rearrangements; Cytogenetics; Deoxyribonucleic acid; DNA; Exons; Gene expression; Gene Fusion; Gene Rearrangement - genetics; Hematology; Histone-Lysine N-Methyltransferase - genetics; Histone-Lysine N-Methyltransferase - metabolism; Humans; Immunohistochemistry; infant leukemia; Infant, Newborn; Isoforms; Leukemia; Leukemia, Myeloid, Acute - genetics; Literature reviews; Lymphatic leukemia; Male; Minimal residual disease; Myeloid-Lymphoid Leukemia Protein - genetics; Myeloid-Lymphoid Leukemia Protein - metabolism; Neoplasm Proteins - genetics; Neoplasm Proteins - metabolism; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; NUTM1; Oncogene Proteins, Fusion - genetics; Oncogene Proteins, Fusion - metabolism; Precursor Cell Lymphoblastic Leukemia-Lymphoma - genetics; Ribonucleic acid; RNA; transcriptomics; transcriptomics; infant leukemia; NUTM1; minimal residual disease; acute lymphoblastic leukemia; gene fusion
• ISSN: 1045-2257; 1098-2264
• DOI: 10.1002/gcc.22808

Infant acute lymphoblastic leukemias (ALL) are rare hematological malignancies occurring in children younger than 1 year of age, most frequently associated with KMT2A rearrangements (KMT2A‐r). The smaller subset without KMT2A‐r, which represents 20% of infant ALL cases, is poorly characterized. Here we report two cases of chemotherapy‐sensitive non‐KMT2A‐r infant ALL. Transcriptome analyses revealed identical ACIN1‐NUTM1 gene fusions in both cases, derived from cryptic chromosomal rearrangements undetected by standard cytogenetic approaches. Two isoforms of the gene fusion, joining exons 3 or 4 of ACIN1 to exon 3 of NUTM1, were identified. Both fusion transcripts contained the functional DNA‐binding SAP (SAF‐A/B, Acinus, and PIAS) domain of ACIN1 and most of NUTM1. The detection of the ACIN1‐NUTM1 fusion by RT‐PCR allowed the molecular monitoring of minimal residual disease in a clinical setting. Based on publicly available genomic datasets and literature review, we predict that NUTM1 gene fusions are recurrent events in infant ALL. As such, we propose two clinically relevant assays to screen for NUTM1 rearrangements in bone marrow cells, independent of the fusion partner: NUMT1 immunohistochemistry and NUTM1 RNA expression. In sum, our study identifies ACIN1‐NUTM1 as a recurrent and possibly cryptic fusion in non‐KMT2A‐r infant ALL, provides clinical tools to screen for NUTM1‐rearranged leukemia and contributes to the refinement of this new subgroup.