Identification of novel NUP98::RARA fusion transcripts in acute promyelocytic leukemia with i(17)(q10) abnormality

Abstract

Acute promyelocytic leukemia (APL) is one subtype of acute myeloid leukemia (AML) primarily associated with the typical fusion gene PML::RARA/t(15;17). A small percentage of APL cases are caused by atypical gene transcript variants lacking the PML::RARA. We report one case with two novel NUP98::RARA fusion transcripts in APL lacking the fusion gene PML::RARA/t(15;17). These NUP98::RARA fusion transcripts were identified using next-generation sequencing (NGS), which were confirmed by Sanger sequencing. One of the transcripts differs from the previously reported transcript in terms of break sites and transcript length, which identified as subtype of NUP98::RARA fusion transcript. The other one is the same as previously reported, demonstrating reproducible abnormality of this fusion gene. The patient was treated with all-trans retinoic acid (ATRA), realgar-Indigo naturalis formula (RIF) and chemotherapy. According to the published paper, this is the second report of NUP98::RARA fusion transcript in APL. It is also the first variant APL with der(11)(p15)t(11;17)(p15;q21) and i(17)(q10) chromosome abnormalities. Therefore, we compared and summarized these two cases.

Keywords: APL; NUP98::RARA; i(17)(q10); t(11;17)(p15;q21).

Figure 1

Morphology, FISH, mRNA sequencing and karyotype of patient’s myeloid blasts. A. Bone marrow smear: APL with large promyelocytes, full cytoplasm with purple-red azurophilic granules (partially), non-lobulated nuclei and nucleoli, and few Auer rods (top. Wright-Giemsa, ×1000); The peroxidase stain shows strong positivity (bottom, ×1000). B. FISH showed 4 red and 2 green signals using PML::RARA dual-color dual-fusion probe, PML::RARA was negative (×1000). C. FISH showed 3 yellow signals and 1 green signal using RARA break-apart probe, RARA rearrangement was positive(×1000). D. NGS of NUP98::RARA fusion gene with ruptured sites: (11: 3759570: -, 17: 38496727: +). E. NGS of NUP98::RARA fusion gene with ruptured sites (11: 3765739: -, 17: 38504568: +). F. R-banding karyotype analysis: 46,XY,der(11)(p15)t(11;17)(p15;q21),i(17)(q10).

Figure 2

Gel electrophoresis and Sanger sequencing of PCR products, pattern of transcripts. (A) Gel electrophoresis of PCR products: 1: transcript of NUP98::RARA with a breakpoint in the recombination region of NUP98; 2: transcript of NUP98::RARA with a breakpoint in exon 12 of NUP98. (B, C) Sanger sequencing: two NUP98::RARA fusion transcripts, the NUP98::RARA transcript 1 with a breakpoint in the recombination region of NUP98 (B); the NUP98::RARA transcript 2 with a breakpoint in exon 12 of NUP98 (C). Both of the transcripts were bidirectionally sequenced and confirmed via BLAST. (D) NUP98::RARA transcripts: breakpoints in exon 12 and recombination region of the NUP98; breakpoints in exon 3 and intron 2 of the RARA; ligand-binding domain (LBD); DNA-binding domain (DBD); 5’-untranslated region (5’-UTR); glycine-leucine-phenylalanine-glycine (GLFG); Gle2/Rae1-binding sequence (GLEBS).