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Li Y, Deng K, Kaner J, Geyer JT, Ouseph M, Fang F, Xu K, Roboz G, Kluk MJ. Detection of Hybrid Fusion Transcripts, Aberrant Transcript Expression, and Specific Single Nucleotide Variants in Acute Leukemia and Myeloid Disorders with Recurrent Gene Rearrangements. Pathobiology 2023; 91:76-88. [PMID: 37490880 DOI: 10.1159/000532085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023] Open
Abstract
INTRODUCTION A variety of gene rearrangements and molecular alterations are key drivers in the pathobiology of acute leukemia and myeloid disorders; current classification systems increasingly incorporate these findings in diagnostic algorithms. Therefore, clinical laboratories require versatile tools, which can detect an increasing number and variety of molecular and cytogenetic alterations of clinical significance. METHODS We validated an RNA-based next-generation sequencing (NGS) assay that enables the detection of: (i) numerous hybrid fusion transcripts (including rare/novel gene partners), (ii) aberrantly expressed EVI1 (MECOM) and IKZF1 (Del exons 4-7) transcripts, and (iii) hotspot variants in KIT, ABL1, NPM1 (relevant in the context of gene rearrangement status). RESULTS For hybrid fusion transcripts, the assay showed 98-100% concordance for known positive and negative samples, with an analytical sensitivity (i.e., limit of detection) of approximately 0.8% cells. Samples with underlying EVI1 (MECOM) translocations demonstrated increased EVI1 (MECOM) expression. Aberrant IKZF1 (Del exons 4-7) transcripts detectable with the assay were also present on orthogonal reverse transcription PCR. Specific hotspot mutations in KIT, ABL1, and NPM1 detected with the assay showed 100% concordance with orthogonal testing. Lastly, several illustrative samples are included to highlight the assay's clinically relevant contributions to patient workup. CONCLUSION Through its ability to simultaneously detect various gene rearrangements, aberrantly expressed transcripts, and hotspot mutations, this RNA-based NGS assay is a valuable tool for clinical laboratories to supplement other molecular and cytogenetic methods used in the diagnostic workup and in clinical research for patients with acute leukemia and myeloid disorders.
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Affiliation(s)
- Yuewei Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kaifang Deng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Justin Kaner
- Department of Medicine, Hematology and Medical Oncology, Clinical and Translational Leukemia Program, Weill Cornell Medicine, New York, New York, USA
| | - Julia T Geyer
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Madhu Ouseph
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Frank Fang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kemin Xu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Gail Roboz
- Department of Medicine, Hematology and Medical Oncology, Clinical and Translational Leukemia Program, Weill Cornell Medicine, New York, New York, USA
| | - Michael J Kluk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
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de Oliveira Mota F, Gamba FT, de Carvalho Pires MG, de Toledo SRC, Gouveia JT, Oliveira ID, da Silva Santos N, Delbuono E, Rhein BN, da Costa Guimarães RF, de Sousa AVL. NUP214::ABL1: A Ph-like fusion found in a pediatric acute myeloid leukemia patient with normal karyotype. Pediatr Blood Cancer 2023; 70:e30203. [PMID: 36633225 DOI: 10.1002/pbc.30203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023]
Affiliation(s)
- Fernanda de Oliveira Mota
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Francine Tesser Gamba
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Michele Gaboardi de Carvalho Pires
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Silva Regina Caminada de Toledo
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Juliana Thomazini Gouveia
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Indhira Dias Oliveira
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Nancy da Silva Santos
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Elizabete Delbuono
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | - Bruno Nicolaz Rhein
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
| | | | - Ana Virginia Lopes de Sousa
- Department of Pediatric Oncology, Pediatric Oncology Institute - Grupo de Apoio ao Adolescente e à Criança com Câncer GRAACC/ Federal University of São Paulo UNIFESP, São Paulo, Brazil
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Stukaite-Ruibiene E, Norvilas R, Dirse V, Stankeviciene S, Vaitkeviciene GE. Case Report: Specific ABL-Inhibitor Imatinib Is an Effective Targeted Agent as the First Line Therapy to Treat B-Cell Acute Lymphoblastic Leukemia With a Cryptic NUP214::ABL1 Gene Fusion. Pathol Oncol Res 2022; 28:1610570. [PMID: 36172171 PMCID: PMC9510372 DOI: 10.3389/pore.2022.1610570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022]
Abstract
Acute lymphoblastic leukemia (ALL) with recurrent genetic lesions, affecting a series of kinase genes, is associated with unfavorable prognosis, however, it could benefit from treatment with tyrosine kinase inhibitors (TKI). NUP214::ABL1 fusion is detected in 6% of T-cell acute lymphoblastic leukemia (T-ALL), and is very rare in B-ALL. We present a case of adolescent with B-ALL and a cryptic NUP214::ABL1 fusion which was initially missed during diagnostic screening and was detected by additional RNA sequencing. Treatment with specific ABL-inhibitor Imatinib was added later in therapy with a good effect. Initial treatment according to conventional chemotherapy was complicated by severe side effects. At the end of Consolidation, the patient was stratified to a high risk group with allogeneic hematopoietic stem cell transplantation because of insufficient response to therapy. At that time, targeted RNA sequencing detected NUP214::ABL1 gene fusion which was previously missed due to a small microduplication in the 9q34 chromosome region. Gene variant analysis revealed no TKI-resistant ABL1 mutations; therefore, treatment with Imatinib was added to target the NUP214::ABL1 fusion protein. A negative minimal residual disease was achieved, and treatment was downgraded to intermediate risk protocol. Combining routine genetic assays with next-generation sequencing methods could prevent from missing atypical gene alterations. Identification of rare targetable genetic subtypes is of importance in order to introduce targeted therapy as early as possible that may improve survival and reduce toxicity. Treatment with ABL1 inhibitor imatinib mesylate revealed as a highly effective targeted therapy against the leukemia driving protein kinase.
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Affiliation(s)
- Egle Stukaite-Ruibiene
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- *Correspondence: Egle Stukaite-Ruibiene,
| | - Rimvydas Norvilas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Vaidas Dirse
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Sigita Stankeviciene
- Center for Pediatric Oncology and Hematology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Goda Elizabeta Vaitkeviciene
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Center for Pediatric Oncology and Hematology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
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Nardi V, McAfee SL, Dal Cin P, Tsai HK, Amrein PC, Hobbs GS, Brunner AM, Narayan R, Foster J, Fathi AT, Hock H. OUP accepted manuscript. Oncologist 2022; 27:82-86. [PMID: 35641210 PMCID: PMC8895729 DOI: 10.1093/oncolo/oyab052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
BCR-ABL1 kinase inhibitors have improved the prognosis of Philadelphia-chromosome-positive (Ph+)-acute lymphoblastic leukemia (ALL). Ph-like (or BCR-ABL1-like) ALL does not express BCR-ABL1 but commonly harbors other genomic alterations of signaling molecules that may be amenable to therapy. Here, we report a case with a NUP214-ABL1 fusion detected at relapse by multiplexed, targeted RNA sequencing. It had escaped conventional molecular work-up at diagnosis, including cytogenetic analysis and fluorescence in situ hybridization for ABL1 rearrangements. The patient had responded poorly to initial multi-agent chemotherapy and inotuzumab immunotherapy at relapse before the fusion was revealed. The addition of dasatinib targeting NUP214-ABL1 to inotuzumab resulted in complete molecular remission, but recurrence occurred rapidly with dasatinib alone. However, deep molecular remission was recaptured with a combination of blinatumomab and ponatinib, so he could proceed to allotransplantation. This case illustrates that next-generation sequencing approaches designed to discover cryptic gene fusions can benefit patients with Ph-like ALL.
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Affiliation(s)
- Valentina Nardi
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Steven L McAfee
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Paola Dal Cin
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Harrison K Tsai
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children’s Hospital, Boston, MA, USA
| | - Philip C Amrein
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Gabriela S Hobbs
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Andrew M Brunner
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Rupa Narayan
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Julia Foster
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Amir T Fathi
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Hanno Hock
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Corresponding author: Hanno Hock, Massachusetts General Hospital Cancer Center, 185 Cambridge Street CPZN 4212, Boston, MA 02114, USA. Tel: 617-643-3145;
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Wang HP, He JJ, Zhu QY, Wang L, Li JH, Huang JS, Xie WZ, Zhu HH, Jin J. Case Report: The First Report of NUP214-ABL1 Fusion Gene in Acute Myeloid Leukemia Patient Detected by Next-Generation Sequencing. Front Oncol 2021; 11:706798. [PMID: 34307175 PMCID: PMC8295748 DOI: 10.3389/fonc.2021.706798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The NUP214-ABL1 fusion gene is a constitutively active tyrosine kinase that can be detected in 6% of T-cell acute lymphoblastic leukemia (T-ALL) patients, and it can also be found in B-cell acute lymphoblastic leukaemia (B-ALL). However the NUP214-ABL1 fusion in acute myeloid leukemia (AML) has not yet been reported. Up to now, the sensitivity of NUP214-ABL1-positive patients to tyrosine kinase inhibitor (TKI) is still controversial. Here we report the first case of an AML patient carrying NUP214-ABL1 fusion gene. The conventional AML chemotherapy regimen for the patient was successful. Identification of additional AML patients with NUP214-ABL1 fusion gene will provide treatment experience and prognostic evaluation.
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Affiliation(s)
- Huan-Ping Wang
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Jun-Jun He
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qiao-Yun Zhu
- Central Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lin Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jian-Hu Li
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jian-Song Huang
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Wan-Zhuo Xie
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hong-Hu Zhu
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
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