Unusual Presentation of SET::NUP214-Associated Concomitant Hematological Neoplasm in a Child-Diagnostic and Treatment Struggle

Abstract

Simultaneous multilineage hematologic malignancies are uncommon and associated with poorer prognosis than single-lineage leukemia or lymphoma. Here, we describe a concomitant malignant neoplasm in a 4-year-old boy. The child presented with massive lymphoproliferative syndrome, nasal breathing difficulties, and snoring. Morphological, immunocytochemical, and flow cytometry diagnostics showed coexistence of acute myeloid leukemia (AML) and peripheral T-cell lymphoma (PTCL). Molecular examination revealed a rare t(9;9)(q34;q34)/SET::NUP214 translocation as well as common TCR clonal rearrangements in both the bone marrow and lymph nodes. The disease showed primary refractoriness to both lymphoid and myeloid high-dose chemotherapy as well as combined targeted therapy (trametinib + ruxolitinib). Hence, HSCT was performed, and the patient has since been in complete remission for over a year. This observation highlights the importance of molecular techniques for determining the united nature of complex SET::NUP214-positive malignant neoplasms arising from precursor cells with high lineage plasticity.

Keywords: HSCT; NUP214; fusion genes; pediatric leukemia and lymphoma.

Figure A1

Direct genomic DNA PCR for SET::NUP214 fusion. BM—bone marrow aspirate, LN—lymph node biopsy. BM populations are as follows: B—early myeloid blasts (CD45⁺CD33⁺CD14+), Mo—maturing and mature monocytes (CD45⁺CD33⁺CD14⁺), γδ-T 1—immature γδ-T lymphocytes considered leukemic (CD45^dimCD3^dim), γδ-T2—more mature γδ-T lymphocytes considered normal (CD45^highCD3^high) (color-coded as in Figure 2). For primers, see Table A2.

Figure A2

TRB locus rearrangements in the reported patient according to the distribution of clonal rearrangements in single cells—allele 1 simultaneously carries two DJ rearrangements (TRBD₁-TRBJ_1-2 and TRBD₂-TRBJ_2-2), allele 2 carries one DJ rearrangement (TRBD₂-TRBJ_2-1). V genes are in red, D genes are in blue, J genes are in green, C genes are in orange.

Figure 1

Bone marrow (BM) morphological examination with Romanowsky–Giemsa staining (a) and cytochemical examination for MPO (b), lipids (Sudan black staining) (c), glycogen (PAS reaction) (d) and non-specific esterase (e). Identified cells are marked as follows: B—blast, E—eosinophil, L—lymphocyte, Me—metamyelocyte, Mo—monocyte, My—myelocyte, N—neutrophil, P—promonocyte, 100× magnification.

Figure 2

Immunophenotypic description of the bone marrow (BM). A BM overview is presented in the “gray” panel; a brief description of early myeloid blasts is presented in the “red” panel; two populations of γδ-T lymphocytes are shown in blue and violet, while maturation of monocytic cells is shown in orange.

Figure 3

Lymph node biopsy examination with hematoxylin-eosin staining at 100× (a) and 400× (b) magnification, and immunohistochemical examination at 400× for MPO (c) and CD3 (d).

Figure 4

Conventional G-banded karyotype analysis showing the t(3;11)(q21;q23) translocation in whole BM. Rearranged chromosomes are marked with arrows.

Figure 5

CBL gene, exon 8 Sanger sequencing showing c.1186T>C, p.Cys396Arg missense variant (highlighted in yellow) in the BM (a), lymph node (b), and it’s absence in the nails (c).

Figure 6

Molecular findings on SET::NUP214 fusion in the BM: structure of SET::NUP214 fusion transcript in RNAseq data as depicted using the Arriba algorithm (a) and Sanger validation (SET::NUP214 exon 6—exon 18 junction is marked) (b); NUP214 gene rearrangement with 5′-partial deletion confirmed using FISH with NUP214 breakapart probe (CytoCell), 63× magnification, wild-type NUP214 is yellow, rearranged NUP214 3’-portion is green (c).

Figure 7

TCR repertoire: fraction of TRB (a) and TRD (b) clonal rearrangements in lymph node. BM—bone marrow aspirate, LN—lymph node biopsy. BM populations are as follows: B—early myeloid blasts (CD45⁺CD33⁺CD14⁻), Mo—maturing and mature monocytes (CD45⁺CD33⁺CD14⁺), γδ-T1—immature γδ-T lymphocytes considered leukemic (CD45^dimCD3^dim), γδ-T2—more mature γδ-T lymphocytes considered normal (CD45^highCD3^high).

Figure 8

CT scan data. (a) Initial CT scan on admission with massive lymphoproliferative syndrome. Red circles indicate lymph node conglomerates. (b) Computed tomography at 180 days after hematopoietic stem cell transplantation; no lymphadenopathy and recession of the lymphoproliferative syndrome are seen.

Figure 9

Continuity of the flow cytometric pattern of myeloid and T-lineage cells in BM of described patient, density plot of CD7 and CD33 expression (represented by color scale from red to blue). Mature neutrophils, erythroid precursors, NK cells, and B lymphocytes are excluded.