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Rausio H, Cervera A, Heuser VD, West G, Oikkonen J, Pianfetti E, Lovino M, Ficarra E, Taimen P, Hynninen J, Lehtonen R, Hautaniemi S, Carpén O, Huhtinen K. PIK3R1 fusion drives chemoresistance in ovarian cancer by activating ERK1/2 and inducing rod and ring-like structures. Neoplasia 2024; 51:100987. [PMID: 38489912 PMCID: PMC10955102 DOI: 10.1016/j.neo.2024.100987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/17/2024]
Abstract
Gene fusions are common in high-grade serous ovarian cancer (HGSC). Such genetic lesions may promote tumorigenesis, but the pathogenic mechanisms are currently poorly understood. Here, we investigated the role of a PIK3R1-CCDC178 fusion identified from a patient with advanced HGSC. We show that the fusion induces HGSC cell migration by regulating ERK1/2 and increases resistance to platinum treatment. Platinum resistance was associated with rod and ring-like cellular structure formation. These structures contained, in addition to the fusion protein, CIN85, a key regulator of PI3K-AKT-mTOR signaling. Our data suggest that the fusion-driven structure formation induces a previously unrecognized cell survival and resistance mechanism, which depends on ERK1/2-activation.
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Affiliation(s)
- Heidi Rausio
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland; Drug Research Doctoral Programme (DRDP), University of Turku, Turku, Finland.
| | - Alejandra Cervera
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Vanina D Heuser
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland
| | - Gun West
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Elena Pianfetti
- Department of Engineering, Enzo Ferrari, University of Modena and Reggio Emilia, Modena, Italy
| | - Marta Lovino
- Department of Engineering, Enzo Ferrari, University of Modena and Reggio Emilia, Modena, Italy
| | - Elisa Ficarra
- Department of Engineering, Enzo Ferrari, University of Modena and Reggio Emilia, Modena, Italy
| | - Pekka Taimen
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland; Department of Pathology, Turku University Hospital, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Rainer Lehtonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Pathology, University of Helsinki and HUSLAB, University Hospital, Helsinki, Finland
| | - Kaisa Huhtinen
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland; Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Osaki J, Noguchi R, Yanagihara K, Ono T, Adachi Y, Iwata S, Toda Y, Sekita T, Kobayashi E, Kojima N, Yoshida A, Kawai A, Kondo T. Establishment and characterization of NCC-ASPS2-C1: a novel patient-derived cell line of alveolar soft part sarcoma. Hum Cell 2024; 37:865-873. [PMID: 38478355 DOI: 10.1007/s13577-024-01039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/29/2024] [Indexed: 04/15/2024]
Abstract
Alveolar soft part sarcoma (ASPS) is a rare mesenchymal tumor characterized by rearrangement of the ASPSCR1 and TFE3 genes and a histologically distinctive pseudoalveolar pattern. ASPS progresses slowly, but is prone to late metastasis. As ASPS is refractory to conventional chemotherapy, the only curative treatment is complete surgical resection. The prognosis of advanced and metastatic cases is poor, highlighting the need for preclinical research to develop appropriate treatment options. However, ASPS is extremely rare, accounting for < 1% of all soft tissue sarcomas, and only one patient-derived ASPS cell line is available from public cell banks worldwide for research. This study reports the establishment of a novel ASPS cell line derived from the primary tumor tissue of an ASPS patient, named NCC-ASPS2-C1. This cell line retains the ASPSCR1-TFE3 fusion gene, which is characteristic of ASPS. The characterization of this cell line revealed stable growth, spheroid formation, and invasive properties. By screening a drug library using NCC-ASPS2-C1, we identified several drugs that inhibited the proliferation of ASPS cells. In conclusion, the establishment of NCC-ASPS2-C1 provides a valuable resource for advancing ASPS research and developing novel treatments for this challenging disease.
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Affiliation(s)
- Julia Osaki
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Rei Noguchi
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Kazuyoshi Yanagihara
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Takuya Ono
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Yuki Adachi
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shuhei Iwata
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Yu Toda
- Department of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Tetsuya Sekita
- Department of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Eisuke Kobayashi
- Department of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Naoki Kojima
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
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Ono T, Noguchi R, Osaki J, Akiyama T, Adachi Y, Kojima N, Toda Y, Fukushima S, Yoshimatsu Y, Yoshida A, Kawai A, Kondo T. Establishment and characterization of NCC-DFSP5-C1: a novel patient-derived dermatofibrosarcoma protuberans cell line. Hum Cell 2024; 37:854-864. [PMID: 38372888 DOI: 10.1007/s13577-024-01030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/12/2024] [Indexed: 02/20/2024]
Abstract
Dermatofibrosarcoma protuberans (DFSP) is the most prevalent dermal sarcoma, characterized by the presence of the fusion of the collagen type I alpha 1 (COL1A1) gene with the platelet-derived growth factor beta chain (PDGFB) gene. Although PDGF receptor inhibitor imatinib mesylate was approved for the treating patients with unresectable or metastatic DFSP, disease progression was shown in 9.2% of the patients. Therefore, developing novel therapeutic strategies is crucial for improving the prognosis of DFSP. Patient-derived cell lines play a vital role in preclinical studies; however, only a limited number of DFSP cell lines are currently available in public cell banks. Here, we successfully established a novel DFSP cell line (NCC-DFSP5-C1) using surgically resected tumor tissue from a patient with DFSP. NCC-DFSP5-C1 cells were confirmed to carry the COL1A1-PDGFB translocation and maintain the same mutation as the original tumor tissue. They exhibited consistent growth, formed spheroids, and were invasive. By screening a drug library using NCC-DFSP5-C1 and four previously established DFSP cell lines, we identified anti-cancer drugs that inhibit DFSP cell proliferation. Our observations suggest that the NCC-DFSP5-C1 cell line holds promise as a valuable tool for conducting fundamental and preclinical studies for DFSP.
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Affiliation(s)
- Takuya Ono
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Rei Noguchi
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Julia Osaki
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Taro Akiyama
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Taro Akiyama, Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, 260-8670, Japan
| | - Yuki Adachi
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Naoki Kojima
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yu Toda
- Department of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Suguru Fukushima
- Department of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yuki Yoshimatsu
- Department of Patient-Derived Cancer Model, Tochigi Cancer Center, 4-9-13 Yohnan, Utsunomiya, Tochigi, 320-0834, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology and Rehabilitation Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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Okamoto T, Mizuta R, Takahashi Y, Otani Y, Sasaki E, Horio Y, Kuroda H, Matsushita H, Date I, Hashimoto N, Masago K. Genomic landscape of glioblastoma without IDH somatic mutation in 42 cases: a comprehensive analysis using RNA sequencing data. J Neurooncol 2024:10.1007/s11060-024-04628-z. [PMID: 38653957 DOI: 10.1007/s11060-024-04628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/29/2024] [Indexed: 04/25/2024]
Abstract
PURPOSE Glioblastoma is a malignant brain tumor with a poor prognosis. Genetic mutations associated with this disease are complex are not fully understood and require further elucidation for the development of new treatments. The purpose of this study was to comprehensively analyze genetic mutations in glioblastomas and evaluate the usefulness of RNA sequencing. PATIENTS AND METHODS We analyzed 42 glioblastoma specimens that were resected in routine clinical practice and found wild-type variants of the IDH1 and IDH2 genes. RNA was extracted from frozen specimens and sequenced, and genetic analyses were performed using the CLC Genomics Workbench. RESULTS The most common genetic alterations in the 42 glioblastoma specimens were TP53 mutation (28.6%), EGFR splicing variant (16.7%), EGFR mutation (9.5%), and FGFR3 fusion (9.5%). Novel genetic mutations were detected in 8 patients (19%). In 12 cases (28.6%), driver gene mutations were not detected, suggesting an association with PPP1R14A overexpression. Our findings suggest the transcription factors SOX10 and NKX6-2 are potential markers in glioblastoma. CONCLUSION RNA sequencing is a promising approach for genotyping glioblastomas because it provides comprehensive information on gene expression and is relatively cost-effective.
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Affiliation(s)
- Takanari Okamoto
- Department of Neurosurgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Ryo Mizuta
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Yoshinobu Takahashi
- Department of Neurosurgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshihiro Otani
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Yoshitsugu Horio
- Department of Thoracic oncology, Aichi Cancer Center Hospital, Aichi, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Hiroaki Kuroda
- Department of Thoracic Surgery, Teikyo University Mizonokuchi Hospital, Kanagawa, Japan
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Hirokazu Matsushita
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Isao Date
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Naoya Hashimoto
- Department of Neurosurgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan.
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan.
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Casuso A, Benavente BP, Leal Y, Carrera-Naipil C, Valenzuela-Muñoz V, Gallardo-Escárate C. Sex-Biased Transcription Expression of Vitellogenins Reveals Fusion Gene and MicroRNA Regulation in the Sea Louse Caligus rogercresseyi. Mar Biotechnol (NY) 2024; 26:243-260. [PMID: 38294574 DOI: 10.1007/s10126-024-10291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
The caligid ectoparasite, Caligus rogercresseyi, is one of the main concerns in the Chilean salmon industry. The molecular mechanisms displayed by the parasite during the reproductive process represent an opportunity for developing novel control strategies. Vitellogenin is a multifunctional protein recognized as a critical player in several crustaceans' biological processes, including reproduction, embryonic development, and immune response. This study aimed to characterize the C. rogercresseyi vitellogenins, including discovering novel transcripts and regulatory mechanisms associated with microRNAs. Herein, vitellogenin genes were identified by homology analysis using the reference sea louse genome, transcriptome database, and arthropods vitellogenin-protein database. The validation of expression transcripts was conducted by RNA nanopore sequencing technology. Moreover, fusion gene profiling, miRNA target analysis, and functional validation were performed using luciferase assay. Six putative vitellogenin genes were identified in the C. rogercresseyi genome with high homology with other copepods vitellogenins. Furthermore, miR-996 showed a putative role in regulating the Cr_Vitellogenin1 gene, which is highly expressed in females. Moreover, vitellogenin-fusion genes were identified in adult stages and highly regulated in males, demonstrating sex-related expression patterns. In females, the identified fusion genes merged with several non-vitellogenin genes involved in biological processes of ribosome assembly, BMP signaling pathway, and biosynthetic processes. This study reports the genome array of vitellogenins in C. rogercresseyi for the first time, revealing the putative role of fusion genes and miRNA regulation in sea lice biology.
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Affiliation(s)
- Antonio Casuso
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Bárbara P Benavente
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Yeny Leal
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Crisleri Carrera-Naipil
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile.
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile.
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Huang XT, Wang CJ, Gao C, Xue TL, Zhao ZJ, Wang TY, Wu MY, Cui L, Zhang RD, Li ZG. Relationship between subtype-specific minimal residual disease level and long-term prognosis in children with acute lymphoblastic leukemia. Ann Hematol 2024:10.1007/s00277-024-05687-y. [PMID: 38494553 DOI: 10.1007/s00277-024-05687-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Minimal residual disease (MRD) based risk stratification criteria for specific genetic subtypes remained unclear in childhood acute lymphoblastic leukemia (ALL). Among 723 children with newly diagnosed ALL treated with the Chinese Children Leukemia Group CCLG-2008 protocol, MRD was assessed at time point 1 (TP1, at the end of induction) and TP2 (before consolidation treatment) and the MRD levels significantly differed in patients with different fusion genes or immunophenotypes (P all < 0.001). Moreover, the prognostic impact of MRD varied by distinct molecular subtypes. We stratified patients in each molecular subtype into two MRD groups based on the results. For patients carrying BCR::ABL1 or KMT2A rearrangements, we classified patients with MRD < 10-2 at both TP1 and TP2 as the low MRD group and the others as the high MRD group. ETV6::RUNX1+ patients with TP1 MRD < 10-3 and TP2 MRD-negative were classified as the low MRD group and the others as the high MRD group. For T-ALL, We defined children with TP1 MRD ≥ 10-3 as the high MRD group and the others as the low MRD group. The 10-year relapse-free survival of low MRD group was significantly better than that of high MRD group. We verified the prognostic impact of the subtype-specific MRD-based stratification in patients treated with the BCH-ALL2003 protocol. In conclusion, the subtype-specific MRD risk stratification may contribute to the precise treatment of childhood ALL.
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Affiliation(s)
- Xiao-Tong Huang
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chan-Juan Wang
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chao Gao
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tian-Lin Xue
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Zi-Jing Zhao
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tian-You Wang
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Min-Yuan Wu
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Lei Cui
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China.
| | - Rui-Dong Zhang
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China.
| | - Zhi-Gang Li
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China.
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Mejbel HA, Zein-Sabatto B, Wei S, Siegal GP. An Aneurysmal bone cyst harboring a novel ACSL4::USP6 fusion gene. J Orthop Sci 2024; 29:690-694. [PMID: 37349178 DOI: 10.1016/j.jos.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Haider A Mejbel
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Bassel Zein-Sabatto
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Shi Wei
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA; Department of Pathology & Laboratory Medicine, University of Kansas School of Medicine, Kansas City, KS 66160, USA.
| | - Gene P Siegal
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35249, USA.
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8
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Rai S, Singh MP, Sinha A, Srivastava A, Datta D, Srivastava S. Unravelling a novel CTNND1-RAB6A fusion transcript: Implications in colon cancer cell migration. Int J Biol Macromol 2024; 262:129981. [PMID: 38336316 DOI: 10.1016/j.ijbiomac.2024.129981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
The interchange of DNA sequences between genes may occur because of chromosomal rearrangements leading to the formation of chimeric genes. These chimeric genes have been linked to various cancers, accumulated significant interest in recent times. We used paired-end RNA-seq. data of four CRC and one normal sample generated from our previous study. The STAR-Fusion pipeline was utilized to identify the fusion genes unique to CRC. The in-silico identified fusion gene(s) were explored for their diagnostic, prognostic and therapeutic biomarker potential using TCGA-datasets, then validated through PCR and DNA sequencing. Further, cell line-based studies were performed to gain functional insights of the novel fusion transcript CTNND1-RAB6A, which was amplified in one sample. Sequencing revealed that there was a total loss of the CTNND1 gene, whereas RAB6A retained its coding sequence. Further, RAB6A was functionally characterized for its oncogenic potential in HCT116 cell line. RAB6A under-expression was found to be significantly associated with increased cell migration and is proposed to be regulated via the RAB6A-ECR1-Liprin-α axis. We conclude that RAB6A gene may play significant role in CRC oncogenesis, and could be used as a potential biomarker and therapeutic target in future for better management of a subset of CRCs harbouring this fusion.
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Affiliation(s)
- Sandhya Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India
| | - Manish Pratap Singh
- Department of Zoology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, (U.P.) 273009, India
| | - Abhipsa Sinha
- Division of cancer biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Ankit Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India
| | - Dipak Datta
- Division of cancer biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India.
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9
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Abstract
CIC-rearranged sarcoma is a rare type of small round cell sarcoma. The tumors often affect the deep soft tissues of patients in a wide age range. They are highly aggressive, respond poorly to chemotherapy, and have a worse outcome than Ewing sarcoma. CIC-rearranged sarcoma has characteristic and recognizable histology, including lobulated growth, focal myxoid changes, round to epithelioid cells, and minimal variation of nuclear size and shape. Nuclear ETV4 and WT1 expression are useful immunohistochemical findings. CIC fusion can be demonstrated using various methods; however, even next-generation sequencing suffers from imperfect sensitivity, especially for CIC::DUX4.
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Affiliation(s)
- Naohiro Makise
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-cho, Chuo-ku, Chiba-shi, Chiba, 260-8717, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan; Rare Cancer Center, National Cancer Center, Tokyo, Japan.
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Toda S, Iwasaki H, Okubo Y, Hayashi H, Kadoya M, Takahashi H, Yokose T, Hiroshima Y, Masudo K. The frequency of mutations in advanced thyroid cancer in Japan: a single-center study. Endocr J 2024; 71:31-37. [PMID: 38044137 DOI: 10.1507/endocrj.ej23-0342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
We analyzed the outcomes of genetic testing to study the frequency of mutations in advanced thyroid cancer in Japan. Patients (n = 96) with unresectable or metastatic thyroid carcinoma were included for retrospective chart review. Results of gene panel testing, which was performed between May 2020 and April 2023, were analyzed. The median age of the patients was 73.5 years (range, 17-88); 59 were women, and 39 were men. Overall, 17 patients had anaplastic thyroid carcinoma (ATC), 68 had papillary thyroid carcinoma (PTC), 7 had follicular thyroid carcinoma, and 6 had poorly differentiated thyroid carcinoma (PDTC). Of the 81 patients with differentiated thyroid carcinoma (DTC) and PDTC, 88.9% were radioactive iodine-refractory, and 32.7% of all cases had previously been treated with multiple kinase inhibitors. Of ATC cases, 52.9% had BRAF mutations, and 5.9% had RET fusion. Of PTC cases, 83.1% had BRAF mutations, 9.2% had RET fusion, and 1.5% had NTRK fusion. One case each of ATC and PTC had a tumor mutation burden of ≥10. ATC cases had a significantly higher prevalence of TP53 alterations than the other cases (82.3% vs. 11.8%), whereas the frequencies of TERT promoter mutations were 88.2% in ATC cases and 64.7% in the other cases, albeit without a significant difference. In conclusion, 58.8% of ATC, 93.8% of PTC, and 42.9% of PDTC had genetic alterations linked to therapeutic agents. Active gene panel testing is required to increase treatment options.
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Affiliation(s)
- Soji Toda
- Department of Endocrine Surgery, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
| | - Hiroyuki Iwasaki
- Department of Endocrine Surgery, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
| | - Yoichiro Okubo
- Department of Pathology, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
| | - Hiroyuki Hayashi
- Department of Pathology, Yokohama Municipal Citizen's Hospital, Kanagawa 221-0855, Japan
| | - Mei Kadoya
- Department of Endocrine Surgery, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Kanagawa 232-0024, Japan
| | - Hiroyuki Takahashi
- Department of Hematology and Medical Oncology, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
| | - Yukihiko Hiroshima
- Department of Cancer Genome Medicine, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
- Research Institute Division of Advanced Cancer Therapeutics, Kanagawa Cancer Center Research Institute, Kanagawa, 241-8515, Japan
| | - Katsuhiko Masudo
- Department of Endocrine Surgery, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
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11
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Qijun C, Wei W, Cheng W, Dongni L. Clinicopathological features and molecular genetic changes in 17 cases of uterine tumor resembling ovarian sex cord tumor. Hum Pathol 2024; 143:33-41. [PMID: 38000680 DOI: 10.1016/j.humpath.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Uterine tumor resembling ovarian sex cord tumor (UTROSCT) is a rare mesenchymal neoplasm that was recently reported to exhibit recurrent NCOA1-3rearrangement with the most frequent partners ESR1 and GREB1. In this study, the clinicopathological characteristics of 17 UTROSCT cases were summarized; among them, the fusion genes of 12 cases were retrospectively analyzed by targeted RNA sequencing. The mean age of our cohort was 47 years (19-67 y). Although the majority of UTROSCTs had clear boundaries on gross examination, microscopic infiltration into the myometrium was observed in 82.4 % of cases. The tumor cells showed diffuse, trabecular, nested, reticular, pseudopapillary, hollow and solid tubular patterns, expressing sex cord, epithelial, and myogenic markers. Six fusion genes, including ESR1::NCOA3 (n = 4), ESR1::NCOA2 (n = 2), ESR1::CITED2 (n = 2), GREB1::NCOA2 (n = 2), GREB1::NCOA1 (n = 1), and GREB1::NCOA3 (n = 1), were identified. The fusion genes of the three cases with recurrence and metastasis were GREB1::NCOA2, ESR1::NCOA3, and ESR1::CITED2. All 3 cases of recurrent tumors showed infiltrative growth, with moderate to severe dysplasia of tumor cells and different degrees of rhabdomyoid differentiation. This is the first report of the ESR1::CITED2 fusion genes in UTROSCT, and one of the two patients had recurrence and metastasis. Compared with UTROSCT withESR1 rearrangement, UTROSCT with GREB1 rearrangement was more common in elderly patientsand was more likely to present with intramural masses, less sex cord differentiation, poor prognosis, and relapse and metastasis.
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Affiliation(s)
- Chen Qijun
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
| | - Wang Wei
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
| | - Wang Cheng
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
| | - Liang Dongni
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
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12
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Shang YK, Pan XA, Chang YJ, Qin YQ, Wang Y, Yan CH, Sun YQ, Huang XJ, Zhao XS. [Clinical significance of monitoring NUP98::NSD1 fusion genes before and after allogeneic hematopoietic stem cell transplantation]. Zhonghua Xue Ye Xue Za Zhi 2023; 44:1010-1015. [PMID: 38503524 PMCID: PMC10834866 DOI: 10.3760/cma.j.issn.0253-2727.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Indexed: 03/21/2024]
Abstract
Objective: This study aimed to observe the dynamic changes of NUP98::NSD1 expression before and after allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Moreover, the clinical value of measurable residual disease (MRD) was analyzed. Methods: Sixteen AML patients who were diagnosed with the NUP98::NSD1 fusion gene and received allo-HSCT at Peking University People's Hospital were included. The NUP98::NSD1 fusion gene and leukemia-associated immunophenotype (LAIP) were monitored before and after transplantation to evaluate their MRD status. Results: The median follow-up time for all patients was 526 days (139-1136 days) , with four patients (25.0%) experiencing hematological recurrence at a median of 474 days (283-607 days) after transplantation. Three patients (18.8%) died, two of whom (12.5%) died of leukemia recurrence. The median expression level of NUP98::NSD1 in newly diagnosed patients with complete data was 78.5% (18.9%-184.4%) at the time of initial diagnosis. The recurrence rate was higher in NUP98::NSD1-positive patients after transplantation, with 44.4% of patients experiencing recurrence, whereas no recurrence occurred in NUP98::NSD1-negative patients after transplantation. The area under the receiver operating characteristic curve predicted by the NUP98::NSD1 level after transplantation was 1.000 (95% confidence interval: 1.000-1.000, P=0.003) . Among the four patients with recurrence, NUP98::NSD1 was more sensitive than flow cytometry residual (FCM) and Wilms' tumor gene 1 (WT1) . Conclusions: The NUP98::NSD1 fusion gene can be used to evaluate the MRD status of allo-HSCT. NUP98::NSD1-positive patients after transplantation have a high relapse rate and poor prognosis. NUP98::NSD1 was more sensitive than FCM and WT1 in predicting posttransplant relapse.
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Affiliation(s)
- Y K Shang
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - X A Pan
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - Y J Chang
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - Y Q Qin
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - Y Wang
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - C H Yan
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - Y Q Sun
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - X J Huang
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - X S Zhao
- Peking University People's Hospital & Peking University Institute of Hematology, National Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
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13
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Shen C, Zhong L, Wan P, Jia H, Liu B. Enzyme-free dual amplification biosensor based on functional nucleic acid and CDs/CoOOH for detection of leukemia fusion gene. Anal Chim Acta 2023; 1276:341623. [PMID: 37573112 DOI: 10.1016/j.aca.2023.341623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 08/14/2023]
Abstract
Acute promyelocytic leukemia (APL) is an acute myeloid leukemia (AML) with a specific fusion gene target, PML/RARα fusion gene (PML/RARα), which is formed by the translocation of chromosomes 15 and 17. Detection of PML/RARα is the most reliable parameter for the diagnosis, treatment adjustment, efficacy evaluation, prognosis analysis and relapse prediction of APL. In this study, a novel biosensor was constructed for rapid enzyme-free detection of PML/RARα using DNAzyme and carbon dots/cobalt oxhydroxide nanosheet complexs (CDs/CoOOH). In the detection system, the separated DNAzymes could specifically recognize and bind together by the PML/RARα to form a complete DNAzyme for shearing hairpin probe (HP), then generated trigger, which was the first signal amplification. Then, trigger could hybridize with the capture probe (CP) anchored to streptavidin (SA) modified microplate as well as fluorescence quenching signal probe (SP@CDs/CoOOH). Finally, ascorbic acid (AA) was added to decompose CoOOH and the fluorescence of CDs was released, which was the second signal amplification. Through the dual signal amplification of DNAzyme and CDs/CoOOH, PML/RARα could be detected quickly and sensitively, which overcame the limitation of protein enzyme in traditional fluorescence methods, showing potential clinical application value in the diagnosis and treatment of leukemia.
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Affiliation(s)
- Chenlan Shen
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Precision Medicine Industrial Technology Institute, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China; Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Liang Zhong
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Peng Wan
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China; Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Hengke Jia
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Precision Medicine Industrial Technology Institute, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Beizhong Liu
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China; Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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14
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May PC, Reid AG, Robinson ME, Khorashad JS, Milojkovic D, Claudiani S, Willis F, Apperley JF, Innes AJ. FISH-negative BCR::ABL1-positive e19a2 chronic myeloid leukaemia: the most cryptic of insertions. BMC Med Genomics 2023; 16:172. [PMID: 37496024 PMCID: PMC10369825 DOI: 10.1186/s12920-023-01607-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Chronic myeloid leukaemia (CML) is one of the most well characterised human malignancies. Most patients have a cytogenetically visible translocation between chromosomes 9 and 22 which generates the pathognomonic BCR::ABL1 fusion gene. The derivative chromosome 22 ('Philadelphia' or Ph chromosome) usually harbours the fusion gene encoding a constitutively active ABL1 kinase domain. A small subset of patients have no visible translocation. Historically, these 'Philadelphia chromosome negative' patients caused diagnostic confusion between CML and other myeloproliferative neoplasms; it is now well established that the BCR::ABL1 fusion gene can be generated via submicroscopic intrachromosomal insertion of ABL1 sequence into BCR, or, more rarely, of BCR into ABL1. The fusion genes arising from cryptic insertions are not detectable via G-banded chromosome analysis [karyotype] but can nevertheless always be detected using fluorescence in situ hybridisation (FISH) and/or qualitative reverse transcriptase PCR. CASE PRESENTATION A 43-year-old female presented with suspected CML in 2007; however, contemporaneous gold standard laboratory investigations, G-banded chromosome analysis and FISH, were both negative. The reverse transcriptase quantitative PCR (RT-qPCR) assay available at the time, which was capable of detecting the common BCR::ABL1 transcripts (e13a2/e14a2), was also negative. Upon review in 2009, the newly recommended reverse transcriptase multiplex PCR (capable of detecting all BCR::ABL1 transcripts including the atypical ones) subsequently detected an e19a2 fusion. The patient then responded to tyrosine kinase inhibitor therapy. In contrast, FISH studies of both samples with three commercially available probes remained consistently negative. Retrospective whole genome sequencing, undertaken as part of the 100,000 Genomes Project, has now revealed that the patient's BCR::ABL1 fusion gene arose via a uniquely small insertion of 122 kb ABL1 sequences into BCR. CONCLUSIONS We present a patient with suspected chronic myeloid leukaemia whose genetic investigations were originally negative at the time of diagnosis despite the use of contemporaneous gold standard methods. This is the first report of a FISH-negative, BCR::ABL1 positive CML which demonstrates that, even after sixty years of research into one of the most well understood human malignancies, whole genome sequencing can yield novel diagnostic findings in CML.
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Affiliation(s)
- Philippa C May
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
- Specialist Integrated Haematological Malignancy Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Alistair G Reid
- North West Genomic Laboratory Hub, Manchester NHS Foundation Trust, Manchester, UK
| | - Mark E Robinson
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Jamshid S Khorashad
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Dragana Milojkovic
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Simone Claudiani
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Fenella Willis
- Department of Haematology, St George's University NHS Foundation Trust, London, UK
| | - Jane F Apperley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Andrew J Innes
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK.
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK.
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15
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Lee H, Seo J, Shin S, Lee ST, Choi JR. Development and validation of sensitive BCR::ABL1 fusion gene quantitation using next-generation sequencing. Cancer Cell Int 2023; 23:106. [PMID: 37248544 DOI: 10.1186/s12935-023-02938-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND BCR::ABL1 fusion has significant prognostic value and is screened for chronic myeloid leukemia (CML) disease monitoring as a part of routine molecular testing. To overcome the limitations of the current standard real-time quantitative polymerase chain reaction (RQ-PCR), we designed and validated a next-generation sequencing (NGS)-based assay to quantify BCR::ABL1 and ABL1 transcript copy numbers. METHODS After PCR amplification of the target sequence, deep sequencing was performed using an Illumina Nextseq 550Dx sequencer and in-house-designed bioinformatics pipeline. The Next-generation Quantitative sequencing (NQ-seq) assay was validated for its analytical performance, including precision, linearity, and limit of detection, using serially diluted control materials. A comparison with conventional RQ-PCR was performed with 145 clinical samples from 77 patients. RESULTS The limit of detection of the NQ-seq was the molecular response (MR) 5.6 [BCR::ABL1 0.00028% international scale (IS)]. The NQ-seq exhibited excellent precision and linear range from MR 2.0 to 5.0. The IS value from the NQ-seq was highly correlated with conventional RQ-PCR. CONCLUSIONS We conclude that the NQ-seq is an effective tool for monitoring BCR::ABL1 transcripts in CML patients with high sensitivity and reliability. Prospective assessment of the unselected large series is required to validate the clinical impact of this NGS-based monitoring strategy.
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Affiliation(s)
- Hyeonah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Seo
- Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
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16
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Liu Z, Yan W, Liu S, Liu Z, Xu P, Fang W. Regulatory network and targeted interventions for CCDC family in tumor pathogenesis. Cancer Lett 2023; 565:216225. [PMID: 37182638 DOI: 10.1016/j.canlet.2023.216225] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
CCDC (coiled-coil domain-containing) is a coiled helix domain that exists in natural proteins. There are about 180 CCDC family genes, encoding proteins that are involved in intercellular transmembrane signal transduction and genetic signal transcription, among other functions. Alterations in expression, mutation, and DNA promoter methylation of CCDC family genes have been shown to be associated with the pathogenesis of many diseases, including primary ciliary dyskinesia, infertility, and tumors. In recent studies, CCDC family genes have been found to be involved in regulation of growth, invasion, metastasis, chemosensitivity, and other biological behaviors of malignant tumor cells in various cancer types, including nasopharyngeal carcinoma, lung cancer, colorectal cancer, and thyroid cancer. In this review, we summarize the involvement of CCDC family genes in tumor pathogenesis and the relevant upstream and downstream molecular mechanisms. In addition, we summarize the potential of CCDC family genes as tumor therapy targets. The findings discussed here help us to further understand the role and the therapeutic applications of CCDC family genes in tumors.
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Affiliation(s)
- Zhen Liu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
| | - Weiwei Yan
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China
| | - Shaohua Liu
- Department of General Surgery, Pingxiang People's Hospital, Pingxiang, Jiangxi, 337000, China
| | - Zhan Liu
- Department of Gastroenterology and Clinical Nutrition, The First Affiliated Hospital (People's Hospital of Hunan Province), Hunan Normal University, Changsha, 410002, China
| | - Ping Xu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China; Respiratory Department, Peking University Shenzhen Hospital, Shenzhen, 518034, China.
| | - Weiyi Fang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
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17
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Liu G, Xin S, Geng S, Zheng W, Xu T, Sun Y. Identification of a novel fusion gene NLRC3-NLRP12 in miiuy croaker (Miichthys miiuy). Fish Shellfish Immunol 2023; 136:108697. [PMID: 36965609 DOI: 10.1016/j.fsi.2023.108697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/04/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Fusion gene is a new gene formed by the fusion of all or part of the sequences of two genes, it is caused by chromosome translocation, middle deletion or chromosome inversion. Numerous studies in the past have continuously shown that gene fusions are tightly associated with the occurrence and development of various diseases, especially cancer. Many fusion genes have been identified in humans. However, few fusion genes have been identified in fish. In this study, a novel NLRC3-NLRP12 fusion gene was identified in the Miichthys miiuy (miiuy croaker) by quantitative real-time PCR (qRT-PCR), PCR, and Sanger sequencing. This fusion gene is fused by two genes related to NLRs (nucleotide binding domain and oligomerization domain like receptors). We found that the expression of the NLRC3-NLRP12 fusion gene was significantly upregulated after infection with Vibrio anguillarum (V. anguillarum) or stimulation with lipopolysaccharide (LPS). In addition, the NLRC3-NLRP12 fusion gene was strongly induced by V. anguillarum infection, peaking within the kidney and liver at 12 h post infection. Further functional experiments showed that overexpression of NLRC3-NLRP12 significantly inhibited nuclear factor kappa-B (NF-κB) activation. This study suggests that the newly discovered NLRC3-NLRP12 fusion genes may play an important role in innate immunity in miiuy croaker.
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Affiliation(s)
- Guiliang Liu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shiying Xin
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shang Geng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China.
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18
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Nanishi K, Hino H, Hatakeyama K, Shiomi A, Kagawa H, Manabe S, Yamaoka Y, Nagashima T, Ohshima K, Urakami K, Akiyama Y, Yamaguchi K. Incidence and clinical significance of 491 known fusion genes in a large cohort of Japanese patients with colorectal cancer. Int J Clin Oncol 2023; 28:785-793. [PMID: 37022622 DOI: 10.1007/s10147-023-02335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023]
Abstract
BACKGROUND The clinical significance of fusion genes in colorectal cancer remains unclear. The purpose of this study was to determine the incidence of fusion genes in colorectal cancer and explore their clinical significance by screening for common fusion genes in a large Japanese cohort. METHODS This study involved 1588 patients. The incidence of 491 fusion genes was examined using a designed fusion panel. In addition, the patients were classified into two groups (RSPO fusion-positive or -negative) according to the presence of RSPO fusions, and the clinicopathological and genetic characteristics of both groups were compared. Long-term outcomes were analyzed in patients without distant metastases. RESULTS Fusion genes were detected in 2% (31/1588) of colorectal cancers. The incidence of RSPO fusions (such as PTPRK-RSPO3 and EIF3E-RSPO2) was 1.5% (24/1588), making them the most common fusions, whereas the incidence of other fusion genes was extremely low. The distribution of consensus molecular subtypes and frequency of APC mutations were significantly different between the RSPO fusion-positive and -negative groups. The 3-year cumulative incidence rate of recurrence was higher in the RSPO fusion-positive group than in the RSPO fusion-negative group (positive, 31.2% vs. negative, 13.5%, hazard ratio = 2.357; p = 0.040). CONCLUSION Broad screening for fusion genes showed that RSPO fusions were the most common in colorectal cancer, with an incidence of 1.5%. RSPO fusions may be clinically significant in identifying patients at a high risk of recurrence who would be responsive to specific treatments.
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Affiliation(s)
- Kenji Nanishi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Hitoshi Hino
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan.
| | - Keiichi Hatakeyama
- Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Hiroyasu Kagawa
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Shoichi Manabe
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Yusuke Yamaoka
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
- SRL Inc., Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
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Berking AC, Flaadt T, Behrens YL, Yoshimi A, Leipold A, Holzer U, Lang P, Quintanilla-Martinez L, Schlegelberger B, Reiter A, Niemeyer C, Strahm B, Göhring G. Rare and potentially fatal - Cytogenetically cryptic TNIP1::PDGFRB and PCM1::FGFR1 fusion leading to myeloid/lymphoid neoplasms with eosinophilia in children. Cancer Genet 2023; 272-273:29-34. [PMID: 36657267 DOI: 10.1016/j.cancergen.2023.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/11/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Myeloid/lymphoid neoplasms with eosinophilia (MLN-eos) are rare haematological neoplasms primarily affecting adults. The heterogeneous clinical picture and the rarity of the disease, especially in children, may delay an early diagnosis. MLN-eos are characterized by constitutive tyrosine kinase (TK) activity due to gene fusions. It is thus of importance to obtain a prompt genetic diagnosis to start a specific therapy. Here, we outline the clinical, genetic, and biochemical background of TK driven MLN-eos and report two extremely rare paediatric cases of MLN-eo, the used diagnostic methods, therapy and clinical outcomes. Our results demonstrate that, standard cytogenetic and molecular methods may not be sufficient to diagnose MLN-eo due to cytogenetically cryptic aberrations. We therefore recommend performing additional evaluation with fluorescence in-situ hybridization and molecular genetic methods (array-based comparative genomic hybridization and RNA sequencing) which will lead to the correct diagnosis. Following this diagnostic route we detected a TNIP1::PDGFRB and a PCM1::FGFR1 fusion in our patients. Thus, genetic diagnosis must be precise and quick in order to initiate adequate therapies with tyrosine kinase inhibitors or HSCT.
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Affiliation(s)
| | - Tim Flaadt
- Department of Hematology and Oncology, University Children's Hospital, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | | | - Ayami Yoshimi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Ursula Holzer
- Department of Hematology and Oncology, University Children's Hospital, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Peter Lang
- Department of Hematology and Oncology, University Children's Hospital, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tuebingen-Comprehensive Cancer Center, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Andreas Reiter
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Charlotte Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Brigitte Strahm
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany.
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20
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Zhang X, Hou Z, Huang D, Wang F, Gao B, Zhang C, Zhou D, Lou J, Wang H, Gao Y, Kang Z, Lu Y, Liu Q, Yan J. Single-cell heterogeneity and dynamic evolution of Ph-like acute lymphoblastic leukemia patient with novel TPR-PDGFRB fusion gene. Exp Hematol Oncol 2023; 12:19. [PMID: 36797781 PMCID: PMC9936632 DOI: 10.1186/s40164-023-00380-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a refractory and recurrent subtype of B-cell ALL enriched with kinase-activating rearrangements. Incomplete understanding of the heterogeneity within the tumor cells presents a major challenge for the diagnosis and therapy of Ph-like ALL. Here, we exhibited a comprehensive cell atlas of one Ph-like ALL patient with a novel TPR-PDGFRB fusion gene at diagnosis and relapse by using single-cell RNA sequencing (scRNA-seq). Twelve heterogeneous B-cell clusters, four with strong MKI67 expression indicating highly proliferating B cells, were identified. A relapse-enriched B-cell subset associated with poor prognosis was discovered, implicating the transcriptomic evolution during disease progression. Integrative single-cell analysis was performed on Ph-like ALL and Ph+ ALL patients, and revealed Ph-like specific B-cell subpopulations and shared malignant B cells characterized by the ectopic expression of the inhibitory receptor CLEC2D. Collectively, scRNA-seq of Ph-like ALL with a novel TPR-PDGFRB fusion gene provides valuable insights into the underlying heterogeneity associated with disease progression and offers useful information for the development of immunotherapeutic techniques in the future.
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Affiliation(s)
- Xuehong Zhang
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China. .,Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.
| | - Zhijie Hou
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China ,grid.411971.b0000 0000 9558 1426Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Dan Huang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Furong Wang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Beibei Gao
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Chengtao Zhang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Dong Zhou
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Jiacheng Lou
- grid.452828.10000 0004 7649 7439Department of Neurosurgery, the Second Hospital of Dalian Medical University, Dalian, China
| | - Haina Wang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Yuan Gao
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Zhijie Kang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Ying Lu
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China. .,Institute of Dermatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Quentin Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China. .,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jinsong Yan
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China.
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Khabiri A, Toroghi R, Mohammadabadi M, Tabatabaeizadeh SE. Introduction of a Newcastle disease virus challenge strain (sub-genotype VII.1.1) isolated in Iran. Vet Res Forum 2023; 14:221-228. [PMID: 37181855 PMCID: PMC10170471 DOI: 10.30466/vrf.2022.548152.3373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/29/2022] [Indexed: 05/16/2023]
Abstract
Newcastle disease virus (NDV) sub-genotype VII.1.1 is the most common circulating NDV in Iran. In this study, a velogenic NDV isolate was plaque purified and then characterized according to Office International des Epizooties (OIE) standard protocols. The biological properties of the purified isolate named CH/RT40/IR/2011 were characterized using sequencing and phylogenetic analysis, measurement of pathogenicity indexes and challenge studies. The isolate was plaque purified on chicken embryo fibroblast cells for three rounds and then characterized using molecular and biological approaches. Phylogenetic and evolutionary distance analysis of fusion and hemagglutinin-neuraminidase genes classified the virus in sub-genotype VII.1.1. No mutation was observed in the glycosylation and neutralizing epitope sites of the fusion and hemagglutinin-neuraminidase proteins compared to other reported Iranian NDV VII.1.1 isolates. The presence of the 112RRQKRF117 motif in the fusion protein cleavage site together with mean death time, intracerebral pathogenicity index and intravenous pathogenicity index of 57 hr, 1.80 and 2.50 respectively, revealed that the RT40 isolate was a velogenic NDV. In the challenge study, all chickens were inoculated via eye drop, and intranasal route with RT40 isolate died within a week. While all chickens in the vaccinated and challenged group survived and showed no clinical signs. In conclusion, according to genetic analysis, pathotyping and challenge study, the RT40 isolate was similar to virulent NDVs in Iran and was a suitable candidate for a national standard challenge strain, vaccine trials and vaccine production in commercial levers.
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Affiliation(s)
- Aliakbar Khabiri
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran;
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Reza Toroghi
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran;
- Correspondence Reza Toroghi. DVM, PhD Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran E-mail:
| | - Mohammadreza Mohammadabadi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Seyed-Elias Tabatabaeizadeh
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran;
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22
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Kato H, Kano S, Yasui Y, Nojiri Y, Yoshimitsu M, Nakamura M, Morita A. Effectiveness Treatment of a BRAF-ZKSCAN5 Fusion Gene Melanoma Case with Dabrafenib/Trametinib. Case Rep Oncol 2023; 16:1007-1012. [PMID: 37900828 PMCID: PMC10601785 DOI: 10.1159/000533822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/24/2023] [Indexed: 10/31/2023] Open
Abstract
The most important driver gene in malignant melanoma is the BRAF mutation, and molecularly targeted therapies targeting mutations, mainly V600E and V600k, are used in clinical practice. In this report, we treated a patient with malignant melanoma expressing a rare BRAF-ZKSCAN5 fusion gene with dabrafenib/trametinib. The patient was a 71-year-old female. She was diagnosed with malignant melanoma (pT4aN3M0, STAGE IIIC) of the abdomen with axillary lymph node metastasis. She underwent extended resection and axillary lymph node dissection and was treated with adjuvant therapy, but lung and mediastinal lymph node metastases developed. The patient was treated with immune checkpoint inhibitors for metastatic lesions and achieved complete remission, but relapsed and metastatic lesions appeared in the cervical lymph nodes. Next-generation sequencing revealed the BRAF-ZKSCAN5 fusion gene, and treatment with dabrafenib/trametinib was initiated. After 1 month of treatment, tumor growth stopped and the length of the tumor shrank by 22.2%, but she developed grade 3 adverse events of nausea, fatigue, and diarrhea and had difficulty exercising, forcing her to discontinue treatment after 6 weeks. The tumor continued to shrink during drug administration. This case report may provide insight into treatment options for cases in which the BRAF fusion gene was observed, which is expected to be detected in large numbers by next-generation sequencing in the future.
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Affiliation(s)
- Hiroshi Kato
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinji Kano
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yukiko Yasui
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuka Nojiri
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Maki Yoshimitsu
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Motoki Nakamura
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akimichi Morita
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Zhang H, Zhan Q, Wang X, Gao F, Yu J, Wang J, Fu W, Wang P, Wei X, Zhang L. TLS/FUS-ERG fusion gene in acute leukemia and myelodysplastic syndrome evolved to acute leukemia: report of six cases and a literature review. Ann Hematol 2022. [PMID: 36181538 DOI: 10.1007/s00277-022-04979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 09/08/2022] [Indexed: 11/01/2022]
Abstract
To investigate the pathogenesis and the refractory/relapse mechanisms in patients with t(16;21)(p11;q22), we retrospectively analyzed the clinical data of six cases in our hospital and sixty-two cases reported in the literature. Among the patients in our hospital, five cases were diagnosed as acute leukemia, and one was myelodysplastic syndrome evolved to acute myeloid leukemia, harboring TLS/FUS-ERG fusion gene; all the cases were detected t(16;21)(p11;q22) translocation, and five cases showed additional chromosomal abnormalities. We firstly report a novel three-way translocation t(11;16;21)(q13;p11;q22), which may affect the prognosis of leukemia with TLS-ERG fusion gene because this patient shows a more satisfactory treatment effect and deeper remission. And we found patients with TLS-ERG are more likely to have bone and arthrosis pain. Besides, CD56 and CD123 were positive in these cases, which are related to poor prognosis and the character of refractory. Moreover, some gene mutations are involved, and GATA2 and SMAD4 mutations were identified when the disease progressed from myelodysplastic syndrome to leukemia. Among sixty-two patients reported in the literature, valid positive percent of CD56 and CD123 were 81% and 14.3%, respectively. Mutation of the RUNX1 gene was detected in four cases, and one patient had multiple mutations, including BCOR, PLCG1, DIS3, BRAF, JAK2, and JAK3. The prominent feature of leukemia carrying the TLS/FUS-ERG gene is its poor prognosis. The relevant mechanism includes new mutation, jumping translocation, different transcripts, and so on. The mechanism still acquaints scarcely, which requires further study.
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Moudgil P, Kumar R, Jangir BL, Gupta R, Vaishali, Jindal N. Epidemiology, risk factors and molecular characterization of small ruminant morbillivirus in Haryana, India. Res Vet Sci 2022; 151:164-174. [PMID: 36041310 DOI: 10.1016/j.rvsc.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/02/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
Abstract
Peste des petitis ruminants is an economically important transboundary and notifiable viral disease of sheep and goats. In this study, 14 PPR suspected outbreaks among sheep and goats were investigated in four districts of Haryana, India, during July 2020 to October, 2021. The causative agent of the disease; small ruminant morbillivirus was detected by Reverse Transcription Polymerase Chain Reaction targeting full gene sequences of fusion protein gene and confirmed by sequencing. The overall morbidity and cumulative mortality in these outbreaks were 37.56% and 12.09%, respectively. Risk factor analysis identified significant difference in mortality based on age with higher mortality in young ones; 21% as compared to adults; 7.55%. Analysis of the vaccination status revealed significant difference in morbidity and mortality with higher morbidity and mortality in un-vaccinated animals as compared to vaccinated ones. The sequencing and phylogenetic analysis of representative samples revealed that the strains of the present study fall in lineage IV (96.6-99.1%) along with other Indian isolates but made a separate cluster (sub-lineage). The comparison of deduced amino acid (aa) sequence analysis of fusion protein of circulating field strains with reference vaccine strain and other lineage IV strains revealed four N-linked glycosylation sites instead of three. The findings of the present study revealed changes in fusion protein of some of the circulating field strains of SRMV in Haryana, India. Further detailed studies are warranted to delineate the molecular details of these circulating field strains and to evaluate the effectiveness of currently used vaccine against these mutated strains.
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Affiliation(s)
- Pallavi Moudgil
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Ramesh Kumar
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Babu Lal Jangir
- Department of Veterinary Pathology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Renu Gupta
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India.
| | - Vaishali
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
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Alfaro-Cervelló C, Nieto G, Navarro S. Differential diagnosis of myxoid soft tissue tumors. Experience in the Clinical University Hospital of Valencia. Rev Esp Patol 2022; 55:185-191. [PMID: 35779885 DOI: 10.1016/j.patol.2019.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 06/04/2019] [Accepted: 07/18/2019] [Indexed: 06/15/2023]
Abstract
Soft tissue tumors with myxoid components are often a diagnostic challenge for the pathologist. We retrospectively reviewed 41 cases of soft tissue tumors with myxoid components diagnosed in our center over a five-year period. The most frequent diagnoses were myxofibrosarcoma and myxoid liposarcoma, followed by low-grade fibromyxoid sarcoma, low-grade fibromyxoid tumor and myxoid neurofibroma. Other diagnoses included were extraskeletal myxoid chondrosarcoma, myxoinflammatory fibroblastic sarcoma, low-grade myxoliposarcoma, myofibrosarcoma, fibromatosis, solitary fibrous tumor, non-ossifying variant of ossifying fibromyxoid tumor and ancient neurinoma with myxoid degeneration. Immunohistochemical and molecular biology studies contributed significantly to the diagnosis. We highlight the importance of immunohistochemistry for MUC4 in the diagnosis of low-grade fibromyxoid sarcoma, and underscore the need for molecular studies in selected cases. Furthermore, several myxoid neoplasms present specific chromosomal translocations, therefore molecular biology studies to detect fusion genes are usually essential for the diagnosis. When the characteristics of the sample are not adequate for molecular biology, or no specific alterations are described, an in-depth knowledge of the histology of these lesions is still necessary to decide the most accurate diagnosis.
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Affiliation(s)
- Clara Alfaro-Cervelló
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Valencia, Spain; Departamento de Patología, Facultad de Medicina, Universidad de Valencia, Spain.
| | - Gema Nieto
- Departamento de Patología, Facultad de Medicina, Universidad de Valencia, Spain
| | - Samuel Navarro
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Valencia, Spain; Departamento de Patología, Facultad de Medicina, Universidad de Valencia, Spain
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Hino H, Shiomi A, Hatakeyama K, Kagawa H, Manabe S, Yamaoka Y, Nagashima T, Ohshima K, Urakami K, Akiyama Y, Yamaguchi K. Comprehensive genetic characterization of rectal cancer in a large cohort of Japanese patients: differences according to tumor location. J Gastroenterol 2022; 57:476-485. [PMID: 35449312 DOI: 10.1007/s00535-022-01875-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/03/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND In clinical practice, rectal cancer (RC) is classified according to tumor location. However, RC's genetic characteristics according to tumor location remain unclear. Therefore, we aimed to compare RC's genetic characteristics according to tumor location. METHODS In 611 patients with surgically resected RC, we performed genetic analyses and compared the results between low and other RCs. Low RC was defined according to the European Society for Medical Oncology (ESMO) guidelines and Japanese Classification of Colorectal, Appendiceal, and Anal Carcinoma (JCCRC). RESULTS KRAS mutation accumulation was significantly higher in low RC under the ESMO classification. Gene expression levels significantly differed between the groups for CTNNB1, KRAS, and ERBB2, under the ESMO classification and for TP53, KRAS, and ERBB2 under the JCCRC. Under the JCCRC, low RC had a significantly higher prevalence of fusion genes, such as EIF3E-RSPO2, PTPRK-RSPO3, and VTI1A-TCF7L2. Consensus molecular subtype (CMS) distribution was significantly different between the groups under both classifications. In particular, low RC had lower and higher frequencies of CMS2 and CMS4, respectively. CMS2 and CMS4 frequencies in low RC were 14.8% and 41.5% under the ESMO classification and 14.5% and 41.6% under the JCCRC, respectively. Multivariate Cox regression analysis demonstrated that pT3-4, pN1-2, and CMS4 were associated with poor relapse-free survival. CONCLUSIONS Low RC exhibited distinct genetic characteristics from other RCs. In particular, CMS4 was more frequent in low RC and was a risk factor for poor prognosis. These findings potentially avail further information regarding tumor biology and could lead to improvements in RC treatment.
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Affiliation(s)
- Hitoshi Hino
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Hiroyasu Kagawa
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Shoichi Manabe
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yusuke Yamaoka
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.,SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
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Zhou Y, Zhang C, Zhang L, Ye Q, Liu N, Wang M, Long G, Fan W, Long M, Wing RA. Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biol 2022; 23:130. [PMID: 35706016 PMCID: PMC9199173 DOI: 10.1186/s13059-022-02696-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. Results We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion genes across four Oryza species. The estimated rate of origination of fusion genes in the Oryza genus is as high as 63 fusion genes per species per million years, which is fixed at 16 fusion genes per species per million years and much higher than that in flies. By RNA sequencing analysis, we find more than 44% of the fusion genes are expressed and 90% of gene pairs show strong signals of purifying selection. Further analysis of CRISPR/Cas9 knockout lines indicates that newly formed fusion genes regulate phenotype traits including seed germination, shoot length and root length, suggesting the functional significance of these genes. Conclusions We detect new fusion genes that may drive phenotype evolution in Oryza. This study provides novel insights into the genome evolution of Oryza. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02696-w.
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Affiliation(s)
- Yanli Zhou
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Chengjun Zhang
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China. .,Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.
| | - Li Zhang
- Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.,Chinese Institute for Brain Research, (CIBR), Beijing, 102206, China
| | - Qiannan Ye
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Ningyawen Liu
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guangqiang Long
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Wei Fan
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA. .,Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Mukherjee SB, Mukherjee S, Frenkel-Morgenstern M. Fusion proteins mediate alternation of protein interaction networks in cancers. Adv Protein Chem Struct Biol 2022; 131:165-176. [PMID: 35871889 DOI: 10.1016/bs.apcsb.2022.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fusions of two different genes could lead to the production of chimeric RNAs, which could be translated into novel fusion (or chimeric) proteins. Fusion proteins often act as oncoproteins and drive cancer development, particularly in leukemia and lymphomas. Fusion proteins modify the existing protein-protein interaction (PPI) networks, which could eliminate some PPIs by removing protein domains in such fusions. This alternation of protein interaction networks could impact the signaling pathways and switch on the cancer-promoting activity that could drive the generation of cancer phenotypes and/or loss of controlled apoptosis. Thus, knowledge of the fusion proteins and their protein interaction networks could facilitate a deeper molecular understanding of cancer development, which could help to design new approaches for cancer therapies. Here, we discuss the structural features of fusion proteins and how they impact the PPI networks in cancers. Further, we discuss how to analyze the fusion protein-mediated alternation of PPI networks in cancers.
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Affiliation(s)
- Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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29
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Jiang F, Mao AP, Liu YY, Liu FZ, Li YL, Li J, Zhou JY, Tang XW, Ju AP, Li FT, Wan JH, Zuo LD, Li DZ. Detection of rare thalassemia mutations using long-read single-molecule real-time sequencing. Gene 2022; 825:146438. [PMID: 35306112 DOI: 10.1016/j.gene.2022.146438] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
Gap- polymerase chain reaction (PCR), reverse dot-blot assay (RDB), real-time PCR based multicolor melting curve analysis (MMCA assay), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing are conventional methods to diagnose thalassemia but all of them have limitations. In this study, we applied single-molecule real-time (SMRT) sequencing following multiplex long-range PCR to uncover rare mutations in nine patients and their family members. The patients with different results between Gap-PCR and MMCA assay or with phenotype not matching genotype were included. Using SMRT sequencing, we first identified the carriers with αααanti3.7/HKαα, -α762bpα/αα (chr16:172,648-173,409), ααfusion/αQSα (in a trans configuration), two cases with novel gene rearrangements and another case with a novel 341 bp insertion in α-globin gene cluster, respectively. One carrier with --SEA/αααanti4.2, and two carriers with the coexistence of globin variant and an α-globin gene duplication were also found. Most importantly, we could determine two defects in α-globin gene cluster being a cis or trans configuration in a single test. Our results showed that SMRT has great advantages in detection of α-globin gene triplications, rare deletions and determination of a cis or trans configuration. SMRT is a comprehensive and one-step method for thalassemia screening and diagnosis, especially for detection of rare thalassemia mutations.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Mao
- Berry Genomics Corporation, Beijing, 102200, China
| | - Yin-Yin Liu
- Berry Genomics Corporation, Beijing, 102200, China
| | - Feng-Zhi Liu
- Medical Genetics Laboratory, Foshan Maternal and Child Health Hospital, Foshan, Guangdong, China
| | - Yan-Lin Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Ju
- Clinical Laboratory, Huadu District Maternal and Neonatal Healthcare Hospital of Guangzhou, Hu Zhong Hospital, Guangzhou, Guangdong, China
| | - Fa-Tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jun-Hui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Lian-Dong Zuo
- Scientific Research Department, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China.
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30
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Hindupur A, Menon T, Dhandapani P. Molecular investigation of human metapneumovirus in children with acute respiratory infections in Chennai, South India, from 2016-2018. Braz J Microbiol 2022; 53:655-661. [PMID: 35118597 PMCID: PMC9151977 DOI: 10.1007/s42770-022-00689-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Human metapneumovirus (hMPV) has emerged as a frequent cause of acute respiratory infections (ARI) among young children. The prevalence and genetic diversity of hMPV circulating in Chennai, Southern India, has not been studied yet. Hence, this study was aimed to investigate the prevalence, co-infection with other respiratory viruses like HRSV A and B, influenza A and B, hRV and HPIV 1-4 viruses, socio-demographic associations, and genotypes of hMPV among children in Chennai. A total of 350 nasal swab specimens were collected from children with ARI during April 2016 to August 2018 and tested for hMPV by real time PCR method. In this study, hMPV was detected in 4% (14/350) of the samples. One hMPV positive sample was found to be co-infected with influenza B virus. The mean and median ages of the children with hMPV infection were 61.5 months (5.1 years) and 83 months (6.9 years), respectively. Phylogenetic analysis of the partial F gene revealed the presence of A2c subcluster among the study strains as well as with B1 and B2 lineages. The prevalence data obtained in this study is important in evaluating the role of hMPV in childhood ARI and emphasizes the importance of routine viral diagnosis in hospitals. To the best of our knowledge, this is the first study to report the prevalence, seasonality, and genetic diversity of hMPV in Chennai as well as the first study to report A2c subcluster of hMPV among children in India.
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Affiliation(s)
- Anusha Hindupur
- grid.413015.20000 0004 0505 215XDepartment of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu India
| | - Thangam Menon
- Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu India
| | - Prabu Dhandapani
- grid.413015.20000 0004 0505 215XDepartment of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu India
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Ueno-Yokohata H, Okita H, Nakasato K, Kiyotani C, Kato M, Matsumoto K, Kiyokawa N, Nakazawa A, Yoshioka T. Establishment of multiplex RT-PCR to detect fusion genes for the diagnosis of Ewing sarcoma. Diagn Pathol 2021; 16:102. [PMID: 34749732 DOI: 10.1186/s13000-021-01164-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/18/2021] [Indexed: 11/29/2022] Open
Abstract
Background Detection of the tumor-specific EWSR1/FUS-ETS fusion gene is essential to diagnose Ewing sarcoma. Reverse transcription–polymerase chain reaction (RT–PCR) and fluorescence in situ hybridization are commonly used to detect the fusion gene, and assays using next-generation sequencing have recently been reported. However, at least 28 fusion transcript variants have been reported, making rapid and accurate detection difficult. Methods We constructed two sets of multiplex PCR assays and evaluated their utility using cell lines and clinical samples. Results EWSR1/FUS-ETS was detected in five of six tumors by the first set, and in all six tumors by the second set. The fusion gene detected only by the latter was EWSR1-ERG, which completely lacked exon 7 of EWSR1. The fusion had a short N-terminal region of EWSR1 and showed pathologically atypical features. Conclusions We developed multiplex RT–PCR assays to detect EWSR1-ETS and FUS-ETS simultaneously. These assays will aid the rapid and accurate diagnosis of Ewing sarcoma. In addition, variants of EWSR1/FUS-ETS with a short N-terminal region that may have been previously missed can be easily detected. Supplementary Information The online version contains supplementary material available at 10.1186/s13000-021-01164-6.
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32
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Zou C, Ru GQ, Zhao M. A PHF1-TFE3 fusion atypical ossifying fibromyxoid tumor with prominent collagenous rosettes: Case report with a brief review. Exp Mol Pathol 2021; 123:104686. [PMID: 34560087 DOI: 10.1016/j.yexmp.2021.104686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
Ossifying fibromyxoid tumor (OFMT) is a rare mesenchymal neoplasm of uncertain line of differentiation that can be subdivided into typical, atypical, and malignant tumors. Cytogenetically, OFMT is characterized by recurrent gene rearrangement involving PHF1 in up to 85% of cases. The most common PHF1 fusion partner is EP400, present in approximately half of cases. Most recently, a novel fusion of PHF1-TFE3 was identified in about 10% of PHF1-rearranged OFMTs. Herein, we report a unique case of PHF1-TFE3 fusion atypical OFMT with prominent collagenous rosettes. A 50-year-old male patient presented with a slowly growing, painless mass in the right foot for 4 years. Gross examination showed a 3.5-cm, subcutaneous well-circumscribed, lobulated mass. Microscopic examination revealed a well-demarcated but un-encapsulated tumor without a peripheral bony shell. The neoplasm was composed of mildly atypical spindle to ovoid cells with increased mitosis (2 mitoses per 10 high-power fields) arranged in a multinodular manner within a fibromyxoid stroma, which contained numerous small, irregular collagenous rosettes surrounded by radiating growth of tumor cells. The neoplastic cells were diffusely positive for TFE3 and CD10. RNA sequencing revealed an in-frame fusion between PHF1 exon 12 and TFE3 exon 7. Subsequent Fluorescence in-situ hybridization analyses demonstrated positive for rearrangements of both the PHF1 and TFE3 loci. The patient was free of disease at 63 months' follow-up. Our case exhibits atypical features and prominent collagenous rosettes, expanding the morphological spectrum of OFMT with PHF1-TFE3 fusion.
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Affiliation(s)
- Cheng Zou
- Department of Orthopedics, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Guo-Qing Ru
- Department of Pathology, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Ming Zhao
- Department of Pathology, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China.
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Yoshimatsu Y, Noguchi R, Sin Y, Tsuchiya R, Ono T, Sei A, Sugaya J, Iwata S, Yoshida A, Kawai A, Kondo T. Establishment and characterization of NCC-LGFMS1-C1: a novel patient-derived cell line of low-grade fibromyxoid sarcoma. Hum Cell 2021; 34:1919-1928. [PMID: 34535876 DOI: 10.1007/s13577-021-00612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Low-grade fibromyxoid sarcoma (LGFMS) is a rare soft-tissue sarcoma genetically characterized by the presence of the FUS-CREB3L2 gene fusion. While LGFMS exhibits indolent features during its early stages, the rates of recurrence, metastasis, and death from the disease are high. Presently, the role of FUS-CREB3L2 gene fusions in the unique features of LGFMS is not clear, and there is no modality to improve the clinical outcomes of patients with LGFMS; thus, extensive studies on LGFMS are required. Patient-derived cancer cell lines are critical tools for cancer research. However, no cell line has been established for LGFMS. Here, we aimed to develop a novel cell line for LGFMS and successfully established it using surgically resected tumor tissues. The cells, named NCC-LGFMS1-C1, possessed the same fusion genes as their original tumor and visible copy number variations. The cells had a fibroblastic appearance, formed spheroids when they were seeded in a low-attachment dish, and exhibited constant growth and invasion. Additionally, we demonstrated the feasibility of high-throughput drug screening using these cells. In conclusion, the NCC-LGFMS1-C1 cell line is a useful tool for studying LGFMS.
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Affiliation(s)
- Yuki Yoshimatsu
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Rei Noguchi
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yooksil Sin
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Ryuto Tsuchiya
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takuya Ono
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akane Sei
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Jun Sugaya
- Division of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shintaro Iwata
- Division of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akira Kawai
- Division of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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Eguchi M. [Acute leukemia of infants and neonates]. Rinsho Ketsueki 2021; 62:1308-1318. [PMID: 34497221 DOI: 10.11406/rinketsu.62.1308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Leukemias diagnosed in <1-year-old infants generally have an aggressive clinical nature and unique biological characteristics. Acute lymphoblastic leukemia (ALL) in infants is still intractable and difficult to treat as compared with other pediatric ALLs, for which considerable progress in treatment outcomes has been recently achieved. Infant leukemia cells frequently carry chromosome translocations involving the 11q23 locus, resulting in the rearrangement and fusion of the KMT2A (MLL) gene. Among several KMT2A fusion genes, KMT2A-AFF1 (MLL-AF4) fusion is characteristically observed in neonatal and infant ALL, representing a hallmark of poor prognosis. The cytogenetic/molecular abnormalities t (1;22)(p13.3;q13.1)/RBM15-MKL1 and t (8;16)(p11.2;p13.3)/KAT6A-CREBBP (MOZ-CBP) are also well-known in acute myeloblastic leukemia in this population. Although many neonatal leukemias occurring within the first 28 days of birth are refractory, spontaneous remissions are occasionally observed, especially in the case of t (8;16). Therefore, international collaborative studies are necessary to improve understanding and facilitate the development of better treatment for this rare disease. Thus, this study summarizes the recently reported clinical, cytogenetic, and molecular biology aspects of neonatal and infant leukemias.
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Affiliation(s)
- Mariko Eguchi
- Department of Pediatrics, Ehime University Graduate School of Medicine
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Jiang F, Tang XW, Li J, Zhou JY, Zuo LD, Li DZ. Hb Lepore-Hong Kong: First Report of a Novel δ/β-Globin Gene Fusion in a Chinese Family. Hemoglobin 2021; 45:220-224. [PMID: 34309467 DOI: 10.1080/03630269.2021.1956945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We describe a new δ/β fusion gene causing β-thalassemia (β-thal) trait and its formation mechanism. The proband was a 39-year-old woman who presented with persistent microcytic microcytosis without iron deficiency. Molecular diagnoses revealed a δβ configuration within a 54 bp region between the Cap site (+22) and codon 8, causing a deletion (NG_000007.3: g.63154_70565del). This results in a variant that has been named Hb Lepore-Hong Kong and shows a decreased β-globin mRNA in carriers compared to that of normal subjects. It is assumed that combination of this variant with β-thal may cause severe β-thal syndrome.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lian-Dong Zuo
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
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Chen Y, Shi YZ, Feng XH, Wang XT, He XL, Zhao M. Novel TNC-PDGFD fusion in fibrosarcomatous dermatofibrosarcoma protuberans: a case report. Diagn Pathol 2021; 16:63. [PMID: 34256767 PMCID: PMC8276425 DOI: 10.1186/s13000-021-01123-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022] Open
Abstract
Background Dermatofibrosarcoma protuberans (DFSP) is a superficial fibroblastic tumor characterized by high rate of local recurrence and low metastatic potential. Fibrosarcomatous transformation can rarely arise in DFSP either de novo or as recurrent, which represents a form of tumor progression and carries an increased risk of metastasis over classic DFSP. Cytogenetically, DFSP is characterized by a recurrent unbalanced chromosome translocation t (17;22)(q22;q13), leading to the formation of COL1A1-PDGFB fusion transcript that is present in more than 90% of cases. Alternative fusions involving the PDGFD with partners of COL6A3 or EMILIN2 have recently been documented in less than 2% of cases. Herein, we report a DFSP with fibrosarcomtous morphology harboring a novel TNC-PDGFD fusion. Case presentation A 54-year-old female presented with a slowly growing mass in the right thigh. Excision demonstrated a 2-cm ovoid, well-circumscribed, gray-white, mass. Microscopic examination revealed a partially encapsulated subcutaneous nodule without dermal connection. The neoplasm was composed of cellular and fairly uniform spindle cells with brisk mitoses, arranged in elongated fascicles and herringbone patterns, with focal collagenized stroma. The neoplastic cells were positive for CD34 and smooth muscle actin. Fluorescence in-situ hybridization analyses showed negative for COL1A1-PDGFB fusion as well as NTRK1/2/3 rearrangements. A subsequent RNA sequencing detected an in-frame fusion between exon 15 of TNC and exon 6 of PDGFD. This fusion was further confirmed by nested reverse transcription polymerase chain reaction amplification followed by Sanger sequencing. A diagnosis of fibrosarcomatous DFSP was rendered and the patient was in good status at a follow-up of 12 months after the operation. Conclusions We report a fibrosarcomatous DFSP with novel TNC-PDGFD fusion, which adds to the pathologic and genetic spectrum of PDGFD-rearranged DFSP.
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Affiliation(s)
- Yuan Chen
- Department of Pathology, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, Gongshu District, Hangzhou, 310014, Zhejiang, China
| | - Ying-Zhou Shi
- Department of Pathology, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, Gongshu District, Hangzhou, 310014, Zhejiang, China
| | - Xiao-He Feng
- Department of Pathology, Haining Central Hospital, Jiaxing, Zhejiang, China
| | - Xiao-Tong Wang
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Xiang-Lei He
- Department of Pathology, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, Gongshu District, Hangzhou, 310014, Zhejiang, China
| | - Ming Zhao
- Department of Pathology, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, Gongshu District, Hangzhou, 310014, Zhejiang, China.
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Zheng Y, Jiang W, Chen D, Li Y, Dai L, Huang L, Wang M. [Research Progress of Fusion Genes RET in Non-small Cell Lung Cancer]. Zhongguo Fei Ai Za Zhi 2021; 24:591-597. [PMID: 34120433 PMCID: PMC8387645 DOI: 10.3779/j.issn.1009-3419.2021.102.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
过去的20年来,随着分子生物学研究的不断进展,非小细胞肺癌(non-small cell lung cancer, NSCLC)的治疗方法不断发展,靶向治疗使驱动基因突变阳性患者的生存期得到了改善。越来越多的靶点逐渐被发现,针对不同驱动基因的药物将NSCLC的治疗带入了一个前景广阔的靶向时代。在NSCLC的诸多驱动基因中,转染原癌基因(transfection proto-oncogene gene, RET)融合是除了表皮生长因子受体(epidermal growth factor receptor, EGFR)、间变淋巴瘤激酶(anaplastic lymphoma kinase, ALK)及c-ros原癌基因1-受体酪氨酸激酶(c-ros oncogene 1, receptor tyrosine kinase, ROS1)以外又一个重要的新兴靶点,针对RET基因融合的靶向药物不断推陈出新,近来新型高选择性RET抑制剂BLU-667和LOXO-292获得了重要突破。本文将对NSCLC中RET基因融合突变的概述、检测方法、临床病理特征、靶向治疗及耐药后的研究进展进行综述。
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Affiliation(s)
- Yujun Zheng
- Department of Oncology, The Friendship Hospital of Dalian, Dalian 116001, China
| | - Wei Jiang
- Department of Oncology, The Friendship Hospital of Dalian, Dalian 116001, China
| | - Dongyan Chen
- Department of Oncology, The Friendship Hospital of Dalian, Dalian 116001, China
| | - Yanjun Li
- Department of Oncology, The Friendship Hospital of Dalian, Dalian 116001, China
| | - Lulu Dai
- Department of Oncology, The Friendship Hospital of Dalian, Dalian 116001, China
| | - Lei Huang
- Department of Oncology, The Friendship Hospital of Dalian, Dalian 116001, China
| | - Mingji Wang
- Department of Oncology, The Friendship Hospital of Dalian, Dalian 116001, China
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Rodríguez‐Antolín C, Rosas‐Alonso R, Cruz P, Higuera O, Sánchez‐Cabrero D, Esteban‐Rodríguez I, Peláez‐García A, Fernández Montaño VE, Rodríguez‐Jiménez C, Ibáñez de Cáceres I, de Castro J. Novel SLC12A2-ROS1 Fusion in Non-Small Cell Lung Cancer with a Significant Response to Crizotinib: The Importance of Choosing the Appropriate Next-Generation Sequencing Assay. Oncologist 2021; 26:e908-e912. [PMID: 33682977 PMCID: PMC8176992 DOI: 10.1002/onco.13745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/25/2021] [Indexed: 01/05/2023] Open
Abstract
Identifying the druggable target is crucial for patients with nonsquamous advanced non-small cell lung cancer (NSCLC). This article adds to the spectrum of ROS1 fusion cases described in NSCLC. We describe a novel SLC12A2-ROS1 rearrangement that has not been previously reported in other cancers: a fusion that has clinical and radiological sensitivity to crizotinib. Fluorescence in situ hybridization detected the SLC12A2-ROS1 fusion and it was confirmed through hybrid capture-based next-generation sequencing (NGS); however, the fusion could not be detected by amplicon-based assay. The success of implementing NGS into routine clinical practice depends on the accuracy of testing. The test's methodological features should then be considered because they significantly affect the results. Given this patient's response to crizotinib, identifying patients with undescribed ROS1 fusions has important therapeutic implications. KEY POINTS: This is the first known description of an SLC12A2-ROS1 fusion. Considering the patient's clinical features and tumor response observed after crizotinib therapy, the authors confirm that this new rearrangement has relevant clinical impact for patients with non-small cell lung cancer. The success of implementing next-generation sequencing (NGS) into routine clinical practice depends on the accuracy of the testing. Different assays and NGS platforms can achieve differing results. Each assay's limitations need to be considered to ensure the quality of precision medicine in clinical practice.
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Affiliation(s)
- Carlos Rodríguez‐Antolín
- Epigenetics Laboratory, Department of Genetics, Hospital Universitario La PazMadridSpain
- Experimental Therapies and Novel Biomarkers in Cancer, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | - Rocío Rosas‐Alonso
- Epigenetics Laboratory, Department of Genetics, Hospital Universitario La PazMadridSpain
- Experimental Therapies and Novel Biomarkers in Cancer, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | - Patricia Cruz
- Department of Medical Oncology, Hospital Universitario La PazMadridSpain
- Experimental Therapies and Novel Biomarkers in Cancer, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | - Oliver Higuera
- Department of Medical Oncology, Hospital Universitario La PazMadridSpain
- Experimental Therapies and Novel Biomarkers in Cancer, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | - Darío Sánchez‐Cabrero
- Department of Medical Oncology, Hospital Universitario La PazMadridSpain
- Experimental Therapies and Novel Biomarkers in Cancer, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | - Isabel Esteban‐Rodríguez
- Department of Medical Oncology, Hospital Universitario La PazMadridSpain
- Department of Pathology, Hospital Universitario La PazMadridSpain
| | - Alberto Peláez‐García
- Molecular Pathology and Therapeutic Targets, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | | | - Carmen Rodríguez‐Jiménez
- Genetics of Metabolic Diseases, Department of Genetics, Hospital Universitario La PazMadridSpain
| | - Inmaculada Ibáñez de Cáceres
- Epigenetics Laboratory, Department of Genetics, Hospital Universitario La PazMadridSpain
- Experimental Therapies and Novel Biomarkers in Cancer, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | - Javier de Castro
- Department of Medical Oncology, Hospital Universitario La PazMadridSpain
- Experimental Therapies and Novel Biomarkers in Cancer, Hospital Universitario La Paz Institute for Health Research (IdiPAZ)MadridSpain
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Li B, Marques S, Wang J, Pelechano V. Using TIF-Seq2 to investigate association between 5´ and 3´mRNA ends. Methods Enzymol 2021; 655:85-118. [PMID: 34183135 DOI: 10.1016/bs.mie.2021.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The development of high-throughput technologies has revealed pervasive transcription in all genomes that have been investigated so far. This has uncovered a highly interleaved transcriptome organization involving thousands of overlapping coding and non-coding RNA isoforms that challenge our traditional definitions of genes and functional regions of the genome. In this chapter, we discuss the application of an improved Transcript Isoform Sequencing approach (TIF-Seq2) able to concurrently determine the start and end sites of individual RNA molecules. We exemplify its use for the investigation of the human transcriptome and show how it is especially well suited to discriminate between overlapping molecules and accurately define their boundaries.
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Affiliation(s)
- Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
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Abstract
Sarcoma consists in a group of rare malignant tumours of mesenchymal origin characterized by their vast clinical, pathological and biological heterogeneity. The pathological diagnosis of sarcoma relies classically of the differentiation features of tumour cells, with dozens of different tumour subtypes described in the last international classifications. Over the last decades, the advances in the development of new techniques of molecular biology have led to a major complexification of sarcoma classification, with the identification of multiple and specific molecular alterations that have led to significant changes for patients diagnostic, prognostic and therapeutic management. This review aims at giving an overview on the current knowledge of the molecular biology of soft tissue sarcoma, and emphasizes on their consequences for the daily management of patients.
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Affiliation(s)
- Sarah Watson
- Institut Curie, département d'oncologie médicale, Inserm U830, 26, rue d'Ulm, 75005 Paris, France.
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Vellichirammal NN, Guda C. A compiled dataset of molecular pathways associated with fusion genes identified in pediatric cancers. Data Brief 2021; 35:106780. [PMID: 33553527 PMCID: PMC7848762 DOI: 10.1016/j.dib.2021.106780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/05/2022] Open
Abstract
Fusion genes can serve as actionable biomarkers for diagnosis, prognosis or therapeutic stratification in the clinic. Pathways associated with fusion genes identified in different pediatric cancers are compiled in this article. Fusion genes reported in each cancer were collected using the PubMed search option with the keywords 'fusion transcript', 'fusion gene,' 'chromosomal translocation,' or 'DNA translocation' along with the corresponding pediatric cancer type. Research articles that identified fusion genes using conventional Fluorescence in situ hybridization (FISH) or quantitative real-time polymerase chain reaction (RT-PCR) methods or high-throughput RNA or DNA sequencing were included. The collected fusion gene data were compiled for each cancer and analyzed to identify their functions related to cancer and associated pathways using Ingenuity Pathway Analysis (IPA) and ClueGO software programs. Similarities in associated pathways across different cancers were also analyzed using IPA to identify commonly affected genes and pathways. This value-added and functionally annotated dataset will be an excellent resource for pediatric cancer researchers and clinicians interested in exploring fusion genes in different cancers. This article is a companion article to 'Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy'[1].
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Affiliation(s)
- Neetha N. Vellichirammal
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
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Ozawa T, Kaneko S, Szulzewsky F, Qiao Z, Takadera M, Narita Y, Kondo T, Holland EC, Hamamoto R, Ichimura K. C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation. Acta Neuropathol Commun 2021; 9:36. [PMID: 33685520 PMCID: PMC7941712 DOI: 10.1186/s40478-021-01135-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022] Open
Abstract
Recurrent C11orf95-RELA fusions (RELAFUS) are the hallmark of supratentorial ependymomas. The presence of RELA as the fusion partner indicates a close association of aberrant NF-κB activity with tumorigenesis. However, the oncogenic role of the C11orf95 has not been determined. Here, we performed ChIP-seq analyses to explore genomic regions bound by RELAFUS and H3K27ac proteins in human 293T and mouse ependymoma cells. We then utilized published RNA-Seq data from human and mouse RELAFUS tumors and identified target genes that were directly regulated by RELAFUS in these tumors. Subsequent transcription factor motif analyses of RELAFUS target genes detected a unique GC-rich motif recognized by the C11orf95 moiety, that is present in approximately half of RELAFUS target genes. Luciferase assays confirmed that a promoter carrying this motif is sufficient to drive RELAFUS-dependent gene expression. Further, the RELAFUS target genes were found to be overlapped with Rela target genes primarily via non-canonical NF-κB binding sites. Using a series of truncation and substitution mutants of RELAFUS, we also show that the activation domain in the RELAFUS moiety is necessary for the regulation of gene expression of these RELAFUS target genes. Lastly, we performed an anti-cancer drug screening with mouse ependymoma cells and identified potential anti-ependymoma drugs that are related to the oncogenic mechanism of RELAFUS. These findings suggested that RELAFUS might induce ependymoma formation through oncogenic pathways orchestrated by both C11orf95 and RELA target genes. Thus, our study unveils a complex gene function of RELAFUS as an oncogenic transcription factor in RELAFUS positive ependymomas.
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Wang Y, Shi T, Song X, Liu B, Wei J. Gene fusion neoantigens: Emerging targets for cancer immunotherapy. Cancer Lett 2021; 506:45-54. [PMID: 33675984 DOI: 10.1016/j.canlet.2021.02.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022]
Abstract
Tumor neoantigens play an important role in current cancer immunotherapies. The most commonly studied class of tumor neoantigens contains those derived from single-nucleotide variants (SNVs) and insertions or deletions (Indels). However, gene fusions are also ideal sources of tumor neoantigens, as they can form new open reading frames (ORFs). Compared with SNV and Indel (SNV&Indel) neoantigens, fusion gene neoantigens tend to be more immunogenic, have more targets per mutation, and are more broadly shared across different cancer types. As a result, they are an important class of tumor neoantigens and emerging targets for cancer immunotherapies, with uses as prognostic biomarkers of immune checkpoint blockade (ICB) and in the development of tumor vaccines, adoptive cell therapies and tumor immune microenvironment modulation. In this review, we introduce the chromosomal basis and characteristics of gene fusions. Then, we summarize the predictive tools, mutation burden and immunogenicity of gene fusion neoantigens. Further, we discuss applications and future improvements of gene fusion neoantigens with respect to current cancer immunotherapies and novel developments in cancer treatment.
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Affiliation(s)
- Yue Wang
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School & Clinical Cancer Institute of Nanjing University, Nanjing, 210008, China
| | - Tao Shi
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School & Clinical Cancer Institute of Nanjing University, Nanjing, 210008, China
| | - Xueru Song
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School & Clinical Cancer Institute of Nanjing University, Nanjing, 210008, China
| | - Baorui Liu
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School & Clinical Cancer Institute of Nanjing University, Nanjing, 210008, China
| | - Jia Wei
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School & Clinical Cancer Institute of Nanjing University, Nanjing, 210008, China.
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Kubota Y, Tanaka K, Hisaoka M, Daa T, Iwasaki T, Kawano M, Itonaga I, Tsumura H. Primary clear cell sarcoma of the femur: a unique case with RT-PCR and direct sequencing confirmation of EWSR1/ATF1 fusion gene. BMC Musculoskelet Disord 2021; 22:99. [PMID: 33478436 PMCID: PMC7819310 DOI: 10.1186/s12891-021-03969-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Background It is very rare for clear cell sarcomas (CCS) to arise in the bone. During diagnosis, it is important to distinguish primary CCS of bone from bone metastasis of melanoma because this difference fundamentally changes the therapeutic options. Recently, characteristic fusion genes of CCS have been detected using reverse transcription polymerase chain reaction (RT-PCR) or direct sequencing which allowed to distinguish CCS from melanoma. However, there was no study applying these analyses with positive results. In this case, we describe the use of fusion gene analysis to diagnose a primary CCS of the bone. Case presentation A 36-year-old male presented with a four-months history of left knee pain. Magnetic resonance imaging showed a lesion in the left femoral medial epicondyle. Histological examination of the biopsy specimen revealed proliferating oval or rounded cells. These cells had clear cytoplasm arranged in fascicles or compact nests with frequent deposits of brown pigment. Furthermore, immunohistochemistry analysis revealed that tumor cells were positive for S-100 protein, HMB-45, Melan-A, and SOX10. It stained negative for CD34 and BRAF v600e. Conclusively, detection of the EWSR1/ATF1 fusion gene using RT-PCR and direct sequencing confirmed that the lesion was a primary CCS of the bone. Wide-margin resection and reconstruction with a tumor endoprosthesis were performed. Conclusions Herein, we diagnosed a rare case of primary CCS of the bone by detecting EWSR1/ATF1 fusion gene using RT-PCR and direct sequencing. Since fluorescence-in situ hybridization (FISH) and RT-PCR could show false positive by mainly due to technical problems, it is better to perform direct sequencing to confidently diagnose the tumor as a primary CCS especially at very rare site such as bone.
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Affiliation(s)
- Yuta Kubota
- Department of Orthopaedic Surgery, Faculty of Medicine, Oita University, 1-1 Idaigaoka Hasama, 879-5593, Yufu City, Oita, Japan
| | - Kazuhiro Tanaka
- Department of Orthopaedic Surgery, Faculty of Medicine, Oita University, 1-1 Idaigaoka Hasama, 879-5593, Yufu City, Oita, Japan.
| | - Masanori Hisaoka
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, 807-8555, Kitakyushu, Japan
| | - Tsutomu Daa
- Department of Diagnostic Pathology, Faculty of Medicine, Oita University, 1-1 Idaigaoka Hasama, 879-5593, Yufu City, Oita, Japan
| | - Tatsuya Iwasaki
- Department of Orthopaedic Surgery, Faculty of Medicine, Oita University, 1-1 Idaigaoka Hasama, 879-5593, Yufu City, Oita, Japan
| | - Masanori Kawano
- Department of Orthopaedic Surgery, Faculty of Medicine, Oita University, 1-1 Idaigaoka Hasama, 879-5593, Yufu City, Oita, Japan
| | - Ichiro Itonaga
- Department of Orthopaedic Surgery, Faculty of Medicine, Oita University, 1-1 Idaigaoka Hasama, 879-5593, Yufu City, Oita, Japan
| | - Hiroshi Tsumura
- Department of Orthopaedic Surgery, Faculty of Medicine, Oita University, 1-1 Idaigaoka Hasama, 879-5593, Yufu City, Oita, Japan
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Staaf J, Jönsson M, Karlsson AF. Detection of Non-Small Lung Cell Carcinoma-Associated Genetic Alterations Using a NanoString Gene Expression Platform Approach. Methods Mol Biol 2021; 2279:91-107. [PMID: 33683688 DOI: 10.1007/978-1-0716-1278-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In non-small cell lung cancer (NSCLC), mutation detection and fusion gene status are treatment predictive and, hence, key factors in clinical management. Lately, alternate splicing variants of MET have gained focus as NSCLC tumors harboring a MET exon 14 skipping event have proven sensitive toward targeted therapy. Reliable methods for detection of genetic alterations in NSCLC have proven to be of increased importance. This chapter provides with hands-on experience of the NanoString gene expression platform for detection of genetic alterations in NSCLC.
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Affiliation(s)
- Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Anna F Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
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Esmaeelzadeh Dizaji R, Ghalyanchilangeroudi A, Vasfi Marandi M, Hosseini H, Karimi V, Ziafatikafi Z, Molouki A, Fallah Mehrabadi MH. Complete genome sequence of a subgenotype XXI.1.1 pigeon paramyxovirus type 1 virus (PPMV‑1) isolated from Iran in 2018 and phylogenetic analysis of a possible novel, but unassigned, PPMV-1 group isolated in 2014. Comp Immunol Microbiol Infect Dis 2020; 73:101565. [PMID: 33126169 DOI: 10.1016/j.cimid.2020.101565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 10/03/2020] [Accepted: 10/08/2020] [Indexed: 11/30/2022]
Abstract
Newcastle disease (ND) is one of the most serious infectious and contagious viral diseases in avian species. Recently, several ND outbreaks in pigeon caused by pigeon paramyxovirus serotype-1 (PPMV-1) have been reported from Iran, but unfortunately, phylogenetic studies have been mostly conducted on partial sequence of NDV fusion (F) gene. In addition, a complete genome data of Iranian PPMV-1 strains are not available. In the present study, a PPMV-1, named Avian avulavirus 1/pigeon/Iran/UT-EGV/2018, isolated from an infected pigeon, was subjected to whole-genome sequencing. The isolate showed an MDT of 74 h, thus categorizing it as mesogenic. The phylogenetic analysis based on the F gene sequence revealed the isolate belongs to XXI.1.1 subgenotype (min 0.9 % and max 3 %). To our knowledge, our study is the first study to publish the complete genome of a PPMV-1 from Iran. According to BLAST results, the whole genome of UT-EGV had high homology with some Russian, Egyptian and Ukrainian strains (the highest was 96.55 %). Additionally, we conducted a phylogenetic analysis on five PPMV-1 that we isolated in 2014 to find that they may belong to a completely unreported subgenotype (6 % distance when compared as a group). The information obtained from this study can be useful in preventive measures, including constructing an effective vaccine against PPMV-1 in Iran.
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Affiliation(s)
- Reza Esmaeelzadeh Dizaji
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mehdi Vasfi Marandi
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Hossein Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Karaj Branch, Karaj, Iran
| | - Vahid Karimi
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Zahra Ziafatikafi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Aidin Molouki
- Department of Poultry Diseases, RAZI Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Mohammad Hossein Fallah Mehrabadi
- Department of Poultry Diseases, RAZI Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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Ngo C, Khneisser P, Kanaan C, Valent A, Dumont S, Adam J, Scoazec JY. [A new case report and review of the literature]. Ann Pathol 2021; 41:207-11. [PMID: 33077252 DOI: 10.1016/j.annpat.2020.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 11/22/2022]
Abstract
Sarcoma with EWSR1-PATZ1 gene fusion is an exceedingly rare and newly described Ewing-like sarcoma harboring EWSR1 rearrangements involving fusion partners other than ETS family genes. The clinical, histopathologic and immunophenotypic features of cases reported in literature are fairly diverse and not specific. We report a new case report posing real challenges for histological and molecular diagnosis.
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Jiang XW, Chen SZ, Zhu XY, Xu XX, Liu Y. Development and validation of a droplet digital PCR assay for the evaluation of PML-RARα fusion transcripts in acute promyelocytic leukemia. Mol Cell Probes 2020; 53:101617. [PMID: 32585184 DOI: 10.1016/j.mcp.2020.101617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 06/03/2020] [Indexed: 11/11/2022]
Abstract
Acute promyelocytic leukemia (APL) is an aggressive disease that requires prompt treatment. Promyelocytic leukemia protein-retinoic acid receptor α (PML-RARα) fusion genes resulting from reciprocal translocation are considered a molecular basis for diagnosing APL. Moreover, PML-RARα fusion gene testing is an essential tool for monitoring the response to therapy via minimal residual disease and providing a diagnosis before rapid disease progression in APL. The present study developed a novel droplet digital PCR (ddPCR) assay to rapidly detect two PML-RARα variants (bcr1 and bcr3) and compared its limit of detection (LOD) with quantitative PCR (qPCR). It was demonstrated that the LOD of ddPCR for PML-RARα reached 0.001%, and the evaluation of high copy number samples of PML-RARα by ddPCR correlated well with qPCR. Furthermore, clinical sample testing with ddPCR found that 34 and 24% samples were bcr-1-positive and bcr3-positive, respectively. However, according to qPCR, 30% of the samples were bcr1-positive and 20% were bcr3-positive. In addition, the concordance rate between ddPCR and qPCR reaction was 86%. While monitoring minimal residual disease, the PML-RARα mutation rate of three patients who recovered well decreased to 0.34%. However, one patient who was bcr3-positive and relapsed had a mutation rate of 13% while in remission, indicating that the bcr3 isoform may be an adverse prognostic factor affecting recovery. Therefore, the present results suggested that this novel ddPCR assay may be useful for monitoring and evaluating the treatment effects and prognosis of APL.
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Affiliation(s)
- Xi-Wen Jiang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China.
| | - Si-Ze Chen
- Central Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, China; The Precise Therapy Engineering Technology Research Cente of Guangdong Province for Esophageal Cancer, Guangzhou, 510080, China
| | - Xiao-Ya Zhu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| | - Xiao-Xie Xu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| | - Yue Liu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
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Khan AB, Gadot R, Shetty A, Bayley JC, Hadley CC, Cardenas MF, Jalali A, Harmanci AS, Harmanci AO, Wheeler DA, Klisch TJ, Patel AJ. Identification of novel fusion transcripts in meningioma. J Neurooncol 2020; 149:219-230. [PMID: 32949309 DOI: 10.1007/s11060-020-03599-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/08/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Meningiomas are the most common primary intracranial tumor. Recent next generation sequencing analyses have elaborated the molecular drivers of this disease. We aimed to identify and characterize novel fusion genes in meningiomas. METHODS We performed a secondary analysis of our RNA sequencing data of 145 primary meningioma from 140 patients to detect fusion genes. Semi-quantitative rt-PCR was performed to confirm transcription of the fusion genes in the original tumors. Whole exome sequencing was performed to identify copy number variations within each tumor sample. Comparative RNA seq analysis was performed to assess the clonality of the fusion constructs within the tumor. RESULTS We detected six fusion events (NOTCH3-SETBP1, NF2-SPATA13, SLC6A3-AGBL3, PHF19-FOXP2 in two patients, and ITPK1-FBP2) in five out of 145 tumor samples. All but one event (NF2-SPATA13) led to extremely short reading frames, making these events de facto null alleles. Three of the five patients had a history of childhood radiation. Four out of six fusion events were detected in expression type C tumors, which represent the most aggressive meningioma. We validated the presence of the RNA transcripts in the tumor tissue by semi-quantitative RT PCR. All but the two PHF19-FOXP2 fusions demonstrated high degrees of clonality. CONCLUSIONS Fusion genes occur infrequently in meningiomas and are more likely to be found in tumors with greater degree of genomic instability (expression type C) or in patients with history of cranial irradiation.
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Affiliation(s)
- A Basit Khan
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Ron Gadot
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Arya Shetty
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - James C Bayley
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Caroline C Hadley
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Maria F Cardenas
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Akdes S Harmanci
- School of Biomedical Informatics, Center for Computational Systems Medicine, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - Arif O Harmanci
- School of Biomedical Informatics, Center for Computational Systems Medicine, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tiemo J Klisch
- Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA.
- Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA.
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA.
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Grither WR, Dickson BC, Fuh KC, Hagemann IS. Detection of a somatic GREB1-NCOA1 gene fusion in a uterine tumor resembling ovarian sex cord tumor (UTROSCT). Gynecol Oncol Rep 2020; 34:100636. [PMID: 32964092 PMCID: PMC7490989 DOI: 10.1016/j.gore.2020.100636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023] Open
Abstract
Uterine tumor resembling ovarian sex cord tumor is a rare mesenchymal neoplasm. UTROSCT harbors recurrent rearrangements between NCOA1-3 and ESR1 or GREB1. RNA-sequencing can identify these rearrangements to support the diagnosis.
Uterine tumor resembling ovarian sex cord tumor (UTROSCT) is a rare uterine neoplasm of uncertain malignant potential. We present the case of a 69-year-old woman who underwent hysterectomy for postmenopausal bleeding and was found to have a myometrial UTROSCT. RNA-sequencing identified a somatic GREB1–NCOA1 fusion, supporting the diagnosis. Next-generation sequencing is increasingly being adopted in diagnostic pathology laboratories. This report highlights the value of RNA-sequencing in identifying rare fusion events to support pathologic diagnoses.
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Affiliation(s)
- Whitney R Grither
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Katherine C Fuh
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ian S Hagemann
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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