Novel NPM1 exon 5 mutations and gene fusions leading to aberrant cytoplasmic nucleophosmin in AML

Abstract

Nucleophosmin (NPM1) mutations in acute myeloid leukemia (AML) affect exon 12, but sporadically also exon 9 and 11, all causing changes at protein C-terminal end (loss of tryptophans and creation of a nuclear export signal-NES motif) that lead to aberrant cytoplasmic NPM1 (NPM1c+), detectable by immunohistochemistry. Combining immunohistochemistry and molecular analyses in 929 AML patients, we found non-exon 12 NPM1 mutations in 5/387 (1.3%) NPM1c+ cases. Besides mutations in exon 9 (n=1) and exon 11 (n=1), novel mutations in exon 5 were discovered (n=3). One more exon 5 mutation was identified in additional 141 AML patients selected for wild-type NPM1 exon 12. Furthermore, 3 NPM1 rearrangements (i.e. NPM1/RPP30, NPM1/SETBP1, NPM1/CCDC28A) were detected and characterized among 13,979 AML samples screened by cytogenetic/FISH and RNA sequencing. Functional studies demonstrated that in AML cases the new NPM1 proteins harboured an efficient extra NES, either newly created or already present in the fusion partner, ensuring its cytoplasmic accumulation. Our findings support NPM1 cytoplasmic relocation as critical for leukemogenesis and reinforce the role of immunohistochemistry in predicting any AML-associated NPM1 genetic lesions. Also, this study highlights the need for developing new specific assays for molecular diagnosis and monitoring of NPM1-mutated AML.

Atypical Rearrangements in APL-Like Acute Myeloid Leukemias: Molecular Characterization and Prognosis

“…Of note is that a NPM1-CCDC28A fusion transcript has been recently described in an adult patient whose features, however, resembled more an NPM1-mutated AML than APL ( 93 ). The similarities between APL and NPM1-mutated AML will be discussed in the dedicated paragraph.…”

New insights into the role of ribonuclease P protein subunit p30 from tumor to internal reference

“…have shown that the NPM1/RPP30 complex serves as one of three NPM1 rearrangements that have been found and analyzed in 13,979 AML samples ( 64 ). In patients with AML that have a NPM1 rearrangement, RPP30 is rearranged with NPM1 at exon 11, whereas the rearrangement of NPM1 with RPP30 is at the end of exon 9 ( 64 ). These data indicate RPP30 may help detect AML and monitor NPM1-mutated AML.…”

NPM1 exon 5 mutations in acute myeloid leukemia: Implications in diagnosis and minimal residual monitoring

“…Therefore, the vast majority of amplicon‐based assays currently used in clinical laboratories are designed to target the mutational hotspots in exon 12. However, emerging evidence suggests that other mutations besides the canonical exon 12 mutations may contribute to aberrant NPM1 cytoplasmic localization [ 5 ].…”