Article

Letter to the Editor

Ann Lab Med 2021; 41(4): 443-446

Published online July 1, 2021 https://doi.org/10.3343/alm.2021.41.4.443

Copyright © Korean Society for Laboratory Medicine.

The First Korean Case of NUP98-NSD1 and a Novel SNRK-ETV6 Fusion in a Pediatric Therapy-related Acute Myeloid Leukemia Patient Detected by Targeted RNA Sequencing

Ha Jin Lim, M.D.1* , Jun Hyung Lee, M.D.1* , Young Eun Lee, M.S.1,2 , Hee-Jo Baek, M.D.3 , Hoon Kook, M.D.3 , Ju Heon Park, M.D.1 , Seung Yeob Lee, M.D.1 , Hyun-Woo Choi, M.D.1 , Hyun-Jung Choi, M.D.1 , Seung-Jung Kee, M.D.1 , Jong Hee Shin, M.D.1 , and Myung Geun Shin, M.D.1,2

1Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea; 2Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea; 3Department of Pediatrics, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea

Correspondence to: Myung-Geun Shin, M.D.
Department of Laboratory Medicine, Chonnam National University Hwasun Hospital, 322 Seoyang-ro, Hwasun-eup, Hwasun-gun, Jeollanam-do 58128, Korea
Tel: +82-61-379-7950, Fax: +82-61-379-7984,
E-mail: mgshin@chonnam.ac.kr

*These authors equally contributed to this study.

Received: June 29, 2020; Revised: October 5, 2020; Accepted: January 4, 2021

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Dear Editor,

Targeted RNA-sequencing (RNA-seq) using next-generation sequencing (NGS) technology is a highly accurate method for selecting and sequencing specific transcripts of interest [1]. We routinely applied a customized targeted RNA-seq system during the diagnostic phase of hematologic malignancies. Our system detected the first Korean case of NUP98-NSD1 and a novel SNRK-ETV6 fusion with therapy-related acute myeloid leukemia (t-AML) showing a dismal clinical course. NUP98-NSD1 accounts for approximately 4% of pediatric AML cases and shows a poor prognosis [2, 3]. It could be created by a cryptic t(5;11)(q35;p15.5) and exerts a leukemogenic function by binding near the HOX locus and MEIS1 to increase expression via histone modifications [4]. The Institutional Review Board of Chonnam National University Hwasun Hospital (CNUHH), Hwasun, Korea (CNUHH-2020-091) approved this study and granted a waiver of consent due to its retrospective nature. This report highlights the role of high-throughput parallel targeted RNA-seq in enhancing the diagnostic yield of hematologic malignancies.

In April 2020, a 14-year-old girl visited the outpatient clinic of CNUHH 1.5 years and 1.9 years after a matched unrelated peripheral blood stem cell transplantation and initial diagnosis of AML, respectively, for a follow-up bone marrow (BM) examination At initial diagnosis, the Korean AML 2012 regimen (double-induction strategy with idarubicin or mitoxantrone plus cytarabine, followed by consolidation therapy with cytarabine and etoposide) was administered and complete remission was achieved 28 days after the second induction. The laboratory findings showed a leukocyte count of 3.1×109/L, absolute neutrophil count of 0.58×109/L, hemoglobin of 114 g/L, and platelet count of 37×109/L. BM aspirates revealed 28% leukemic blasts corresponding to French-American-British (FAB) type M2. The BM karyotype was 45,XX,add(3)(p25),del(5)(q?),-12,add(12)(p13)[8]//46,XY[12], and the multiplex reverse transcription (RT)-PCR (HemaVision kit; DNA Technology, Aarhus, Denmark) finding was negative.

Targeted RNA-seq (HEMEaccuTest RNA; NGeneBio, Seoul, Korea) of the BM sample using STAR-Fusion (ver 1.8.1) and FusionCatcher (ver 1.20) revealed NUP98-NSD1 and a novel SNRK-ETV6 fusion, which were confirmed by direct sequencing (Fig. 1). DESeq2 (ver 1.18.1) analysis showed that WT1, ERG, and BAALC expression increased 7.1, 5.6, and 4.1-log2-fold, respectively, compared with 14 normal controls (Table 1). An additional tier II variant of WT1, NM_024426.3:c.1142C>A (p.Ser381*), and three tier III variants were detected by FreeBayes (ver 1.3.1) [5]. Further targeted DNA NGS (HEMEaccuTest DNA) confirmed the variants in targeted RNA-seq and additionally detected a tier II variant of KRAS, NM_033360.4:c.38G>A (p.Gly13Asp), and five tier III variants. However, no significant variant of FLT3, including FLT3-ITD, was detected. Donor lymphocyte infusion (DLI) was conducted on day 7 after the diagnosis; however, the BM blasts increased to 88% on day 29. The combination of fludarabine, cytarabine, idarubicin, and granulocyte colony-stimulating factor chemotherapy was started on day 35 and the BM blasts decreased to <5% on day 71 with sustained thrombocytopenia; however, the condition repeatedly relapsed on day 134 and the patient expired on day 223.

Table 1 . Morphological, phenotypic, cytogenetic, and molecular characteristics of the initial and present phase of the case

Initial phasePresent phase


FindingVAF (%)MethodFindingVAF (%)Method
WHO classificationAML, NOSt-AML
FAB, typeM2Microscopic observationM2Microscopic observation
Expressed markerCD33, CD34, CD117, HLA-DR, and MPOImmunophenotyping or cytochemical stainCD33, CD34, CD117, and MPOImmunophenotyping or cytochemical stain
Karyotype46,XX[20]Karyotyping45,XX,add(3)(p25),del(5)(q?),-12,add(12)(p13)[8]//46,XY[12]Karyotyping
Gene fusionNegativeMultiplex RT-PCRNUP98-NSD1Targeted RNA-seq
SNRK-ETV6
Upregulated geneWT1Real-time PCR*WT1Targeted RNA-seq
ERG
BAALC
TP63
FGFR3
CCND1
CRLF2
VariantsNM_024426.3(WT1):c.1142C>A (p.Ser381*)40.97DNA NGSNM_024426.3(WT1):c.1142C>A (p.Ser381*)12.61Targeted RNA-seq and DNA NGS
NM_016320.4(NUP98):c.3557T>G (p.Leu1186Trp)47.15NM_001166693.2(AFF1):c.1021A>G (p.Lys341Glu)§40.58
NM_006197.3(PCM1):c.4148A>G (p.Asp1383Gly)47.50NM_016320.4(NUP98):c.3557T>G (p.Leu1186Trp)10.45
NM_033360.4(KRAS):c.38G>A (p.Gly13Asp)17.39NM_006197.3(PCM1):c.4148A>G (p.Asp1383Gly)9.47
NM_002834.3(PTPN11):c.227A>C (p.Glu76Ala)3.89NM_033360.4(KRAS):c.38G>A (p.Gly13Asp)10.79DNA NGS
NM_018036.6(ATG2B):c.1586C>T (p.Thr529Met)§38.94
NM_000051.3(ATM):c.2117C>T (p.Ser706Leu)10.85
NM_022552.4(DNMT3A):c.920C>T (p.Pro307Leu)3.11
NM_000215.3(JAK3):c.2062A>T (p.Ile688Phe)§34.82
NM_017617.5(NOTCH1):c.4627G>A, (p.Gly1543Arg)§35.32

*Using the WT1 ProfileQuant kit (Ipsogen, Marseille, France). Tier II variants classified by the grading system according to the levels of evidence required to determine significance [5]. Increased gene expression was defined as a >2-log2-fold increase compared with 14 normal controls. HOXA/B expression could not be determined in the present case owing to the lack of a target RNA-seq panel. §Variants with a VAF of approximately 35% to 40% that could possibly be donor-derived germline variants rather than clonal evolution.

Abbreviations: FAB, French-American-British; AML, acute myeloid leukemia; NOS, not otherwise specified; VAF, variant allele frequency; RT-PCR, reverse transcription-PCR; NGS, next-generation sequencing; t-AML, therapy-related AML; RNA-seq, RNA-sequencing.


Figure 1. Schematic representation of the NUP98-NSD1 (A–C) and novel SNRK-ETV6 (D–F) gene fusions and proteins. (A) Integrative genomics viewer (IGV) image showing the NUP98-NSD1 breakpoints with 171 supporting junction read counts. (B) Direct sequencing confirmed the identical breakpoint causing an in-frame fusion of NUP98-NSD1. (C) The predicted fusion protein translated from the NUP98-NSD1 transcript based on a merged sequence produced by STAR-Fusion (ver 1.8.1), which contains domains similar to a previous report [2] but is shorter. (D) IGV image showing the novel SNRK-ETV6 fusion breakpoints with 484 supporting junction read counts. (E) Direct sequencing confirmed the identical breakpoint causing a novel in-frame fusion of SNRK-ETV6. (F) The predicted fusion protein translated from the SNRK-ETV6 transcript based on the merged sequence produced by STAR-Fusion (ver 1.8.1).

NUP98-NSD1+ AML is characterized by frequent FAB-type M4/M5, a normal karyotype, and HOXA/B upregulation [2]. Further, NUP98-NSD1 is mutually exclusive with other type II variants, but often co-occurs with type I variants such as FLT3-ITD or WT1 variants [2, 3]. FLT3-ITD is the most common variant in NUP98-NSD1+ AML (unlike our case), and its prognosis is dismal. Recent studies showed the promising therapeutic effects of dasatinib and navitoclax combination therapy and preemptive DLI based on minimal residual disease for NUP98-NSD1+/FLT3-ITD+ AML [6, 7]. Regarding the novel SNRK-ETV6 fusion, the defect in ETV6 is pathogenic in hematologic malignancies caused by rearrangement or deletions [8]. However, the partner SNRK gene defect at 3p22.1 has rarely been studied in hematologic malignancies but reportedly impacts hematopoietic cell proliferation and differentiation [9]. Further studies are needed to clarify the role of this novel fusion. This case also meets the criteria of t-AML, representing del(5q) with a complex karyotype and prior cytotoxic chemotherapy; both NUP98- and ETV6- rearrangements were reported in t-AMLs [10]. Additionally, the patient has a variant in TP53 (rs1042522), known to increase the risk of developing therapy-related myeloid neoplasms. Owing to the retrospective nature of this study, the NUP98-NSD1 and SNRK-ETV6 status at the initial diagnostic phase could not be ascertained.

Compared with previous studies using multiple diagnostic methods to characterize NUP98-NSD1+ AML [2], the advantage of the present case was the use of RNA-seq, representing a simplified diagnostic step for gene fusion, expression, and gene variant analyses. Additionally, this system might help uncover novel genetic characteristics in leukemias in future larger-scale studies.

Lim HJ and Lee JH conceived and designed the study and collected and analyzed the data; Baek HJ and Kook H contributed to the data; Lim HJ and Shin MG wrote the final manuscript; Lee YE, Park JH, Lee SY, Choi HW, Choi HJ, Kee SJ, and Shin JH participated in coordination and discussion. All authors have accepted their responsibility for the entire content of this manuscript and approved the submission.

No potential conflicts of interest relevant to this article were reported.

This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Ministry of Science and ICT (MSIT) and the Ministry of Health and Welfare (MOHW) (NRF-2019M3E5D1A02067952).

  1. Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of next generation sequencing in laboratory medicine. Ann Lab Med 2021; 41: 25-43.
    Pubmed KoreaMed CrossRef
  2. Hollink IH, van den Heuvel-Eibrink MM, Arentsen-Peters ST, Pratcorona M, Abbas S, Kuipers JE, et al. NUP98/NSD1 characterizes a novel poor prognostic group in acute myeloid leukemia with a distinct HOX gene expression pattern. Blood 2011; 118: 3645-56.
    Pubmed CrossRef
  3. Niktoreh N, Walter C, Zimmermann M, von Neuhoff C, von Neuhoff N, Rasche M, et al. Mutated WT1, FLT3-ITD, and NUP98-NSD1 fusion in various combinations define a poor prognostic group in pediatric acute myeloid leukemia. J Oncol 2019; 2019: 1609128.
    Pubmed KoreaMed CrossRef
  4. Franks TM, McCloskey A, Shokirev MN, Benner C, Rathore A, Hetzer MW. Nup98 recruits the Wdr82-Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes Dev 2017; 31: 2222-34.
    Pubmed KoreaMed CrossRef
  5. Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, et al. Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn 2017; 19: 4-23.
    Pubmed KoreaMed CrossRef
  6. Kivioja JL, Thanasopoulou A, Kumar A, Kontro M, Yadav B, Majumder MM, et al. Dasatinib and navitoclax act synergistically to target NUP98-NSD1(+)/FLT3-ITD(+) acute myeloid leukemia. Leukemia 2019; 33: 1360-72.
    Pubmed CrossRef
  7. Mitani Y, Hiwatari M, Seki M, Hangai M, Takita J. Successful treatment of acute myeloid leukemia co-expressing NUP98/NSD1 and FLT3/ITD with preemptive donor lymphocyte infusions. Int J Hematol 2019; 110: 512-6.
    Pubmed CrossRef
  8. De Braekeleer E, Douet-Guilbert N, Morel F, Le Bris MJ, Basinko A, De Braekeleer M. ETV6 fusion genes in hematological malignancies: a review. Leuk Res 2012; 36: 945-61.
    Pubmed CrossRef
  9. Kertesz N, Samson J, Debacker C, Wu H, Labastie MC. Cloning and characterization of human and mouse SNRK sucrose non-fermenting protein (SNF-1)-related kinases. Gene 2002; 294: 13-24.
    CrossRef
  10. Block AW, Carroll AJ, Hagemeijer A, Michaux L, van Lom K, Olney HJ, et al. Rare recurring balanced chromosome abnormalities in therapy-related myelodysplastic syndromes and acute leukemia: report from an international workshop. Genes Chromosomes Cancer 2002; 33: 401-12.
    Pubmed CrossRef