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Capone I, Bozzi F, Dagrada GP, Verderio P, Conca E, Busico A, Testi MA, Monti V, Duca M, Proto C, Damian S, Piccolo A, Perrone F, Tamborini E, Devecchi A, Collini P, Lorenzini D, Vingiani A, Agnelli L, Pruneri G. Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:582-597. [PMCID: PMC9630092 DOI: 10.37349/etat.2022.00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/02/2022] [Indexed: 11/07/2022] Open
Abstract
Aim: Diagnostic laboratories are progressively introducing next-generation sequencing (NGS) technologies in the routine workflow to meet the increasing clinical need for comprehensive molecular characterization in cancer patients for diagnosis and precision medicine, including fusion-transcripts detection. Nevertheless, the low quality of messenger RNA (mRNA) extracted from formalin-fixed paraffin-embedded (FFPE) samples may affect the transition from traditional single-gene testing approaches [like fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), or polymerase chain reaction (PCR)] to NGS. The present study is aimed at assessing the overall accuracy of RNA fusion transcripts detection by NGS analysis in FFPE samples in real-world diagnostics. Methods: Herein, NGS data from 190 soft tissue tumors (STTs) and carcinoma cases, discussed in the context of the institutional Molecular Tumor Board, are reported and analyzed by FusionPlex© Solid tumor kit through the manufacturer’s pipeline and by two well-known fast and accurate open-source tools [Arriba (ARR) and spliced transcripts alignment to reference (STAR)-fusion (SFU)]. Results: The combination of FusionPlex© Solid tumor with ArcherDX® Analysis suite (ADx) analysis package has been proven to be sensitive and specific in STT samples, while partial loss of sensitivity has been found in carcinoma specimens. Conclusions: Albeit ARR and SFU showed lower sensitivity, the use of additional fusion-detection tools can contribute to reinforcing or extending the output obtained by ADx, particularly in the case of low-quality input data. Overall, our results sustain the clinical use of NGS for the detection of fusion transcripts in FFPE material.
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Affiliation(s)
- Iolanda Capone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Fabio Bozzi
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Gian Paolo Dagrada
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Paolo Verderio
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Elena Conca
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Adele Busico
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Maria Adele Testi
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Valentina Monti
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Matteo Duca
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Claudia Proto
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Silvia Damian
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Alberta Piccolo
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Federica Perrone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Elena Tamborini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Andrea Devecchi
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Paola Collini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Daniele Lorenzini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Andrea Vingiani
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, Italy
| | - Luca Agnelli
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Correspondence: Luca Agnelli, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy.
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, Italy
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Alternative PDGFD rearrangements in dermatofibrosarcomas protuberans without PDGFB fusions. Mod Pathol 2018; 31:1683-1693. [PMID: 29955147 DOI: 10.1038/s41379-018-0089-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 12/20/2022]
Abstract
Dermatofibrosarcoma protuberans is underlined by recurrent collagen type I alpha 1 chain-platelet-derived growth factor B chain (COL1A1-PDGFB) fusions but ~ 4% of typical dermatofibrosarcoma protuberans remain negative for this translocation in routine molecular screening. We investigated a series of 21 cases not associated with the pathognomonic COL1A1-PDGFB fusion on routine fluorescence in situ hybridization (FISH) testing. All cases displayed morphological and clinical features consistent with the diagnosis of dermatofibrosarcoma protuberans. RNA-sequencing analysis was successful in 20 cases. The classical COL1A1-PDGFB fusion was present in 40% of cases (n = 8/20), and subsequently confirmed with a COL1A1 break-apart FISH probe in all but one case (n = 7/8). 55% of cases (n = 11/20) displayed novel PDGFD rearrangements; PDGFD being fused either to the 5' part of COL6A3 (2q37.3) (n = 9/11) or EMILIN2 (18p11) (n = 2/11). All rearrangements led to in-frame fusion transcripts and were confirmed at genomic level by FISH and/or array-comparative genomic hybridization. PDGFD-rearranged dermatofibrosarcoma protuberans presented clinical outcomes similar to typical dermatofibrosarcoma protuberans. Notably, the two EMILIN2-PDGFD cases displayed fibrosarcomatous transformation and homozygous deletions of CDKN2A at genomic level. We report the first recurrent molecular variant of dermatofibrosarcoma protuberans involving PDGFD, which functionally mimic bona fide COL1A1-PDGFB fusions, leading presumably to a similar autocrine loop-stimulating PDGFRB. This study also emphasizes that COL1A1-PDGFB fusions can be cytogenetically cryptic on FISH testing in a subset of cases, thereby representing a diagnostic pitfall that pathologists should be aware of.
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Peng C, Zhao H, Chen W, Song Y, Wang X, Li J, Qiao Y, Wu D, Ma S, Wang X, Gao C. Identification of SHCBP1 as a novel downstream target gene of SS18-SSX1 and its functional analysis in progression of synovial sarcoma. Oncotarget 2018; 7:66822-66834. [PMID: 27572315 PMCID: PMC5341840 DOI: 10.18632/oncotarget.11651] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 08/21/2016] [Indexed: 01/10/2023] Open
Abstract
The SS18-SSX1 fusion gene has been shown to play important roles in the development of synovial sarcoma (SS), but the underlying molecular mechanisms and its downstream target genes are still not clear. Here SHC SH2-domain binding protein 1 (SHCBP1) was identified and validated to be a novel downstream target gene of SS18-SSX1 by using microarray assay, quantitative real-time (qPCR) and western blot. Expression of SHCBP1 was firstly confirmed in SS cell line and SS tissues. The effects of SHCBP1 overexpression or knockdown on SS cell proliferation and tumorigenicity were then studied by cell proliferation, DNA replication, colony formation, flow cytometric assays, and its in vivo tumorigenesis was determined in the nude mice. Meanwhile, the related signaling pathways of SHCBP1 were also examined in SS cells. The results indicated that SHCBP1 was significantly increased in SS cells and SS tissues compared with adjacent noncancerous tissues. The expression of SHCBP1 was demonstrated to be positively correlated with the SS18-SSX1 level. Overexpression and ablation of SHCBP1 promoted and inhibited, respectively, the proliferation and tumorigenicity of SS cells in vitro. SHCBP1 knockdown also significantly inhibited SS cell growth in nude mice, and lowered the MAPK/ERK and PI3K/AKT/mTOR signaling pathways and cyclin D1 expression. Our findings disclose that SHCBP1 is a novel downstream target gene of SS18-SSX1, and demonstrate that the oncogene SS18-SSX1 promotes tumorigenesis by increasing the expression of SHCBP1, which normally acts as a tumor promoting factor.
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Affiliation(s)
- Changliang Peng
- Department of Orthopaedics, Shandong University Second Hospital, Jinan, China
| | - Hui Zhao
- Department of Orthopaedics, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Wei Chen
- Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Yan Song
- Nephrology Research Institute, Shandong University Second Hospital, Jinan, China
| | - Xiaoying Wang
- Department of Pathology, Shandong University Second Hospital, Jinan, China
| | - Ji Li
- Department of Orthopaedics, Shandong University Second Hospital, Jinan, China
| | - Yong Qiao
- Department of Orthopaedics, Shandong University Second Hospital, Jinan, China
| | - Dongjin Wu
- Department of Orthopaedics, Shandong University Second Hospital, Jinan, China
| | - Shengzhong Ma
- Department of Orthopaedics, Shandong University Second Hospital, Jinan, China
| | - Xiuwen Wang
- Department of Orthopaedics, Shandong University Second Hospital, Jinan, China
| | - Chunzheng Gao
- Department of Orthopaedics, Shandong University Second Hospital, Jinan, China
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Advances in chromosomal translocations and fusion genes in sarcomas and potential therapeutic applications. Cancer Treat Rev 2017; 63:61-70. [PMID: 29247978 DOI: 10.1016/j.ctrv.2017.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/12/2022]
Abstract
Chromosomal translocations and fusion genes are very common in human cancer especially in subtypes of sarcomas, such as rhabdomyosarcoma, Ewing's sarcoma, synovial sarcoma and liposarcoma. The discovery of novel chromosomal translocations and fusion genes in different tumors are due to the advancement of next-generation sequencing (NGS) technologies such as whole genome sequencing. Recently, many novel chromosomal translocations and gene fusions have been identified in different types of sarcoma through NGS approaches. In addition to previously known sarcoma fusion genes, these novel specific fusion genes and associated molecular events represent important targets for novel therapeutic approaches in the treatment of sarcomas. This review focuses on recent advances in chromosomal translocations and fusion genes in sarcomas and their potential therapeutic applications in the treatment of sarcomas.
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Zorzan E, Da Ros S, Musetti C, Shahidian LZ, Coelho NFR, Bonsembiante F, Létard S, Gelain ME, Palumbo M, Dubreuil P, Giantin M, Sissi C, Dacasto M. Screening of candidate G-quadruplex ligands for the human c-KIT promotorial region and their effects in multiple in-vitro models. Oncotarget 2017; 7:21658-75. [PMID: 26942875 PMCID: PMC5008313 DOI: 10.18632/oncotarget.7808] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/20/2016] [Indexed: 12/11/2022] Open
Abstract
Stabilization of G-quadruplex (G4) structures in promoters is a novel promising strategy to regulate gene expression at transcriptional and translational levels. c-KIT proto-oncogene encodes for a tyrosine kinase receptor. It is involved in several physiological processes, but it is also dysregulated in many diseases, including cancer. Two G-rich sequences able to fold into G4, have been identified in c-KIT proximal promoter, thus representing suitable targets for anticancer intervention. Herein, we screened an “in house” library of compounds for the recognition of these G4 elements and we identified three promising ligands. Their G4-binding properties were analyzed and related to their antiproliferative, transcriptional and post-transcriptional effects in MCF7 and HGC27 cell lines. Besides c-KIT, the transcriptional analysis covered a panel of oncogenes known to possess G4 in their promoters. From these studies, an anthraquinone derivative (AQ1) was found to efficiently downregulate c-KIT mRNA and protein in both cell lines. The targeted activity of AQ1 was confirmed using c-KIT–dependent cell lines that present either c-KIT mutations or promoter engineered (i.e., α155, HMC1.2 and ROSA cells). Present results indicate AQ1 as a promising compound for the target therapy of c-KIT-dependent tumors, worth of further and in depth molecular investigations.
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Affiliation(s)
- Eleonora Zorzan
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Silvia Da Ros
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Caterina Musetti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Lara Zorro Shahidian
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Nuno Filipe Ramos Coelho
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Federico Bonsembiante
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Sébastien Létard
- Centre de Recherche en Cancerologie de Marseille, INSERM (U1068), CNRS (U7258), Université Aix-Marseille (UM105), Marseille, France
| | - Maria Elena Gelain
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Patrice Dubreuil
- Centre de Recherche en Cancerologie de Marseille, INSERM (U1068), CNRS (U7258), Université Aix-Marseille (UM105), Marseille, France
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
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Puls F, Niblett AJ, Mangham DC. Molecular pathology of bone tumours: diagnostic implications. Histopathology 2013; 64:461-76. [DOI: 10.1111/his.12275] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/04/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Florian Puls
- Department of Musculoskeletal Pathology; Royal Orthopaedic Hospital NHS Trust; Robert Aitken Institute of Clinical Research; Birmingham UK
| | - Angela J Niblett
- Department of Musculoskeletal Pathology; Royal Orthopaedic Hospital NHS Trust; Robert Aitken Institute of Clinical Research; Birmingham UK
| | - D Chas Mangham
- Department of Musculoskeletal Pathology; Royal Orthopaedic Hospital NHS Trust; Robert Aitken Institute of Clinical Research; Birmingham UK
- Department of Musculoskeletal Pathology; Robert Jones & Agnes Hunt Orthopaedic Hospital NHS Trust; Oswestry Shropshire UK
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Martín Liberal J, Lagares-Tena L, Sáinz-Jaspeado M, Mateo-Lozano S, García del Muro X, Tirado OM. Targeted therapies in sarcomas: challenging the challenge. Sarcoma 2012; 2012:626094. [PMID: 22701332 PMCID: PMC3372278 DOI: 10.1155/2012/626094] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 03/27/2012] [Indexed: 12/16/2022] Open
Abstract
Sarcomas are a heterogeneous group of mesenchymal malignancies that very often lead to death. Nowadays, chemotherapy is the only available treatment for most sarcomas but there are few active drugs and clinical results still remain very poor. Thus, there is an imperious need to find new therapeutic alternatives in order to improve sarcoma patient's outcome. During the last years, there have been described a number of new molecular pathways that have allowed us to know more about cancer biology and tumorigenesis. Sarcomas are one of the tumors in which more advances have been made. Identification of specific chromosomal translocations, some important pathways characterization such as mTOR pathway or the insulin-like growth factor pathway, the stunning development in angiogenesis knowledge, and brand new agents like viruses have lead to the development of new therapeutic options with promising results. This paper makes an exhaustive review of preclinical and clinical evidence of the most recent targeted therapies in sarcomas and provides a future view of treatments that may lead to improve prognosis of patients affected with this disease.
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Affiliation(s)
- Juan Martín Liberal
- Laboratori d'Oncología Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Laura Lagares-Tena
- Laboratori d'Oncología Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Miguel Sáinz-Jaspeado
- Laboratori d'Oncología Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Silvia Mateo-Lozano
- Nanomedicine Research Program, Molecular Biology and Biochemistry Research Center, CIBBIM-Nanomedicine, Vall d'Hebron Hospital Research Institute, 08035 Barcelona, Spain
| | - Xavier García del Muro
- Laboratori d'Oncología Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Oscar M. Tirado
- Laboratori d'Oncología Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
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Seo SW, Lee H, Lee HI, Kim HS. The role of TLE1 in synovial sarcoma. J Orthop Res 2011; 29:1131-6. [PMID: 21319215 DOI: 10.1002/jor.21318] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Accepted: 10/28/2010] [Indexed: 02/04/2023]
Abstract
The treatment outcome of synovial sarcoma is poor owing to its resistance to radiation and chemotherapy. The transducin-like enhancer of split 1 (TLE1) is a co-repressor that involves many signaling pathways like cell survival, hematopoiesis and differentiation. Although TLE1 is uniquely expressed in synovial sarcomas, the biological role of TLE1 is not completely understood. This study evaluated the function of TLE1 in synovial sarcomas using knock-down of TLE1, and examined whether the inhibition of TLE1 suppresses the proliferation of synovial sarcomas and enhances the cytotoxicity caused by doxorubicin (doxo). The over-expression of TLE1 was first confirmed in synovial sarcoma cells (HS-SYII). When the HS-SYII cells and normal fibroblast were transiently transfected with TLE1 siRNA, the MTT assay revealed growth inhibition in the HS-SY-11 cells but not in the normal fibroblast. TLE1 silencing also potentiated the cytotoxic effects of doxo against HS-SYII cells. This effect of TLE1 silencing was attributed mainly to the induction of apoptosis. Subsequent analysis revealed that Bcl-2 is a possible downstream target of TLE1 signaling. This study demonstrated that TLE1 is a critical factor for the survival of synovial sarcomas. Overall, the inhibition of TLE1 affects cell proliferation and the apoptosis pathway by suppressing the expression of Bcl-2.
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Affiliation(s)
- Sung Wook Seo
- Department of Orthopaedic Surgery, Samsung Medical Center, Sungkyunkwan University, #50, Ilwon-dong, Gangnam-gu, 135-710, Seoul, South Korea
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