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MacKeracher A, Arnoldo A, Siddaway R, Surrey LF, Somers GR. The Incidence of Multiple Fusions in a Series of Pediatric Soft Tissue and Bone Tumors. Pediatr Dev Pathol 2024; 27:3-12. [PMID: 37771132 PMCID: PMC10800079 DOI: 10.1177/10935266231199928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) has increased the detection of fusion genes in cancer. NGS has found multiple fusions in single tumor samples; however, the incidence of this in pediatric soft tissue and bone tumors (PSTBTs) is not well documented. The aim of this study is to catalogue the incidence of multiple fusions in a series of PSTBTs, and apply a modified gene fusion classification system to determine clinical relevance. METHODOLOGY RNA from 78 bone and soft tissue tumors and 7 external quality assessment samples were sequenced and analyzed using recently-described Metafusion (MF) software and classified using a modification of previously-published schema for fusion classification into 3 tiers: 1, strong clinical significance; 2, potential clinical significance; and 3, unknown clinical significance. RESULTS One-hundred forty-five fusions were detected in 85 samples. Fifty-five samples (65%) had a single fusion and 30 (35%) had more than 1 fusion. No samples contained more than 1 tier 1 fusion. There were 40 tier 1 (28%), 36 tier 2 (24%), and 69 (48%) tier 3 fusions. CONCLUSIONS A significant percentage of PSTBTs harbor more than 1 fusion, and by applying a modified fusion classification scheme, the potential clinical relevance of such fusions can be determined.
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Affiliation(s)
- Anastasia MacKeracher
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Anthony Arnoldo
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Robert Siddaway
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Lea F. Surrey
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Gino R. Somers
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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Li Y, Liu Y, Gao X, Zhao W, Zhou F, Liu H, Wang W. Identification of novel PIEZO1::CBFA2T3 and INO80C::SETBP1 fusion genes in an acute myeloid leukemia patient by RNA-seq. Mol Biol Rep 2023; 50:1961-1966. [PMID: 36472727 DOI: 10.1007/s11033-022-08138-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Fusion genes are recurrent molecular aberrations in acute myeloid leukemia, with significant diagnostic and therapeutic value. The identification of novel fusion genes provides advanced biomarkers for diagnosis and facilitates the discovery of drug targets. METHODS Bone marrow sample was extracted from an acute myeloid leukemia patient and RNA-sequencing was performed. Several bioinformatic methods, including differential analysis and Gene Set Enrichment Analysis (GSEA) pathway analyses were conducted based on the expression data. RESULTS Two novel fusion genes, PIEZO1::CBFA2T3 and INO80C::SETBP1, were identified by RNA-seq. Differential analysis found that SETBP1 and CBFA2T3 were overexpressed, and GSEA analysis showed the activation of immune-related pathways. These findings indicate dysfunction of the fusion related- genes and possible pathogenic effect of the fusion genes. CONCLUSION We reported a male AML patient with presence of PIEZO1::CBFA2T3 and INO80C::SETBP1 fusion genes.
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Affiliation(s)
- Yanling Li
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yao Liu
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinyu Gao
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Weiwei Zhao
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fanghui Zhou
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongxing Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, 065201, China.
- Beijing Lu Daopei Institute of Hematology, Beijing, 100076, China.
- Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, Beijing, 100076, China.
| | - Wei Wang
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
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Di Giacomo D, Quintini M, Pierini V, Pellanera F, La Starza R, Gorello P, Matteucci C, Crescenzi B, Fiumara PF, Veltroni M, Borlenghi E, Albano F, Forghieri F, Maccaferri M, Bettelli F, Luppi M, Cuneo A, Rossi G, Mecucci C. Genomic and clinical findings in myeloid neoplasms with PDGFRB rearrangement. Ann Hematol 2021; 101:297-307. [PMID: 34859285 PMCID: PMC8742810 DOI: 10.1007/s00277-021-04712-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/08/2022]
Abstract
Platelet-derived growth factor receptor B (PDGFRB) gene rearrangements define a unique subgroup of myeloid and lymphoid neoplasms frequently associated with eosinophilia and characterized by high sensitivity to tyrosine kinase inhibition. To date, various PDGFRB/5q32 rearrangements, involving at least 40 fusion partners, have been reported. However, information on genomic and clinical features accompanying rearrangements of PDGFRB is still scarce. Here, we characterized a series of 14 cases with a myeloid neoplasm using cytogenetic, single nucleotide polymorphism array, and next-generation sequencing. We identified nine PDGFRB translocation partners, including the KAZN gene at 1p36.21 as a novel partner in a previously undescribed t(1;5)(p36;q33) chromosome change. In all cases, the PDGFRB recombination was the sole cytogenetic abnormality underlying the phenotype. Acquired somatic variants were mainly found in clinically aggressive diseases and involved epigenetic genes (TET2, DNMT3A, ASXL1), transcription factors (RUNX1 and CEBPA), and signaling modulators (HRAS). By using both cytogenetic and nested PCR monitoring to evaluate response to imatinib, we found that, in non-AML cases, a low dosage (100–200 mg) is sufficient to induce and maintain longstanding hematological, cytogenetic, and molecular remissions.
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Affiliation(s)
- Danika Di Giacomo
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Martina Quintini
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Valentina Pierini
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Fabrizia Pellanera
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Roberta La Starza
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Paolo Gorello
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy.,Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Caterina Matteucci
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Barbara Crescenzi
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | | | - Marinella Veltroni
- Department of Pediatric Oncology-Hematology, Meyer Children's Hospital, Florence, Italy
| | | | - Francesco Albano
- Hematology Unit, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Forghieri
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Monica Maccaferri
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Francesca Bettelli
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Mario Luppi
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Antonio Cuneo
- Hematology, Department of Medical Sciences, St. Anna University Hospital, 44124, Ferrara, Italy
| | | | - Cristina Mecucci
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy.
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Cho Y, Hyun J, Kim M, Han B, Lee YK. Acute Promyelocytic Leukemia with a BCR-ABL1 Rearrangement in a Minor Clone. Lab Med 2021; 53:326-329. [PMID: 34725711 DOI: 10.1093/labmed/lmab097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Acute promyelocytic leukemia (APL) is a type of acute myeloid leukemia characterized by predominating abnormal promyelocytes with a PML-RARA rearrangement or a variant thereof. BCR-ABL1 rearrangement is an oncogenic event that is usually associated with chronic myeloid leukemia but also occurs in both acute lymphoblastic and acute myeloid leukemias and in healthy individuals. However, APL with concurrent PML-RARA and BCR-ABL1 rearrangements has rarely been reported. Herein, we describe a patient with APL exhibiting a BCR-ABL1 rearrangement in a minor clone and discuss the importance of evaluating this genetic alteration in terms of pathogenesis and treatment.
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Affiliation(s)
- Yonggeun Cho
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Republic of Korea
| | - Jungwon Hyun
- Department of Laboratory Medicine, Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Republic of Korea
| | - Miyoung Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Boram Han
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Republic of Korea
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Republic of Korea
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Chen X, Wang F, Zhang Y, Ma X, Cao P, Yuan L, Wang L, Chen J, Zhou X, Wu Q, Liu M, Jin D, Liu H. Fusion gene map of acute leukemia revealed by transcriptome sequencing of a consecutive cohort of 1000 cases in a single center. Blood Cancer J 2021; 11:112. [PMID: 34135310 PMCID: PMC8209121 DOI: 10.1038/s41408-021-00504-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/15/2021] [Accepted: 05/26/2021] [Indexed: 12/28/2022] Open
Abstract
Fusion genes (FGs) are important genetic abnormalities in acute leukemias, but their variety and occurrence in acute leukemias remain to be systematically described. Whole transcriptome sequencing (WTS) provides a powerful tool for analyzing FGs. Here we report the FG map revealed by WTS in a consecutive cohort of 1000 acute leukemia cases in a single center, including 539 acute myeloid leukemia (AML), 437 acute lymphoblastic leukemia (ALL), and 24 mixed-phenotype acute leukemia (MPAL) patients. Bioinformatic analysis identified 792 high-confidence in-frame fusion events (296 distinct fusions) which were classified into four tiers. Tier A (pathogenic), B (likely pathogenic), and C (uncertain significance) FGs were identified in 61.8% cases of the total cohort (59.7% in AML, 64.5% in ALL, and 63.6% in MPAL). FGs involving protein kinase, transcription factor, and epigenetic genes were detected in 10.7%, 48.5%, and 15.1% cases, respectively. A considerable amount of novel FGs (82 in AML, 88 in B-ALL, 13 in T-ALL, and 9 in MPAL) was identified. This comprehensively described real map of FGs in acute leukemia revealed multiple FGs with clinical relevance that have not been previously recognized. WTS is a valuable tool and should be widely used in the routine diagnostic workup of acute leukemia.
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Affiliation(s)
- Xue Chen
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Fang Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Yang Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Xiaoli Ma
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Panxiang Cao
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Lili Yuan
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Lan Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Jiaqi Chen
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Xiaosu Zhou
- Beijing Lu Daopei Institute of Hematology, 100176, Beijing, China
| | - Qisheng Wu
- Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, 100176, Beijing, China
| | - Ming Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - David Jin
- Beijing Lu Daopei Institute of Hematology, 100176, Beijing, China
| | - Hongxing Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China. .,Beijing Lu Daopei Institute of Hematology, 100176, Beijing, China. .,Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, 100176, Beijing, China.
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