1
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Yates ME, Waltermire H, Mori K, Li Z, Li Y, Guzolik H, Wang X, Liu T, Atkinson JM, Hooda J, Lee AV, Oesterreich S. ESR1 Fusions Invoke Breast Cancer Subtype-Dependent Enrichment of Ligand-Independent Oncogenic Signatures and Phenotypes. Endocrinology 2024; 165:bqae111. [PMID: 39207954 PMCID: PMC11384147 DOI: 10.1210/endocr/bqae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 08/15/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Breast cancer is a leading cause of female mortality and despite advancements in personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. The estrogen receptor (ER, ESR1) is expressed in two-thirds of all breast cancer, and under endocrine stress, somatic ESR1 mutations arise in approximately 30% of cases that result in endocrine resistance. We and others reported ESR1 fusions as a mechanism of ER-mediated endocrine resistance. ER fusions, which retain the activation function 1- and DNA-binding domains, harbor ESR1 exons 1 to 6 fused to an in-frame gene partner resulting in loss of the ER ligand-binding domain (LBD). We demonstrate that in a no-special type (invasive ductal carcinoma [IDC]-NST) and an invasive lobular carcinoma (ILC) cell line, ER fusions exhibit robust hyperactivation of canonical ER signaling pathways independent of estradiol or antiendocrine therapies. We employ cell line models stably overexpressing ER fusions with concurrent endogenous ER knockdown to minimize endogenous ER influence. Cell lines exhibited shared transcriptomic enrichment in pathways known to be drivers of metastatic disease, notably MYC signaling. Cells expressing the 3' fusion partners SOX9 and YAP1 consistently demonstrated enhanced growth and cell survival. ILC cells expressing the DAB2 fusion led to enhanced growth, survival, and migration, phenotypes not appreciated in the IDC-NST DAB2 model. Herein, we report that cell line activity is subtype-, fusion-, and assay-specific, suggesting that LBD loss, the fusion partner, and the cellular landscape all influence fusion activities. Therefore, it will be critical to assess fusion frequency in the context of the clinicopathology.
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MESH Headings
- Humans
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/metabolism
- Female
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Cell Line, Tumor
- Phenotype
- YAP-Signaling Proteins/genetics
- YAP-Signaling Proteins/metabolism
- SOX9 Transcription Factor/genetics
- SOX9 Transcription Factor/metabolism
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Signal Transduction/genetics
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/metabolism
- Carcinoma, Lobular/pathology
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Gene Expression Regulation, Neoplastic
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Ligands
- Cell Proliferation/genetics
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Affiliation(s)
- Megan E Yates
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hunter Waltermire
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Biomedical Masters Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Kanako Mori
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Physician Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Zheqi Li
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yiting Li
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Hannah Guzolik
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Tiantong Liu
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Jennifer M Atkinson
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jagmohan Hooda
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Adrian V Lee
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Human Genetics Graduate Program, University of Pittsburgh School of Public Health, Pittsburgh, PA 15213, USA
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA 15213, USA
| | - Steffi Oesterreich
- Women's Cancer Research Center, Magee-Women Research Institute, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Human Genetics Graduate Program, University of Pittsburgh School of Public Health, Pittsburgh, PA 15213, USA
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA 15213, USA
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2
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Patrichi AI, Gurzu S. Pathogenetic and molecular classifications of soft tissue and bone tumors: A 2024 update. Pathol Res Pract 2024; 260:155406. [PMID: 38878666 DOI: 10.1016/j.prp.2024.155406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 08/09/2024]
Abstract
Soft tissue and bone tumors comprise a wide category of neoplasms. Their diversity frequently raises diagnostic challenges, and therapeutic options are continuously developing. The therapeutic success rate and long-term prognosis of patients have improved substantially due to new advances in immunohistochemical and molecular biology techniques. A fundamental contribution to these achievements has been the study of the tumor microenvironment and the reclassification of new entities with the updating of the molecular pathogenesis in the revised 5th edition of the Classification of Soft Tissue Tumors, edited by the World Health Organization. The proposed molecular diagnostic techniques include the well-known in situ hybridization and polymerase chain reaction methods, but new techniques such as copy-number arrays, multiplex probes, single-nucleotide polymorphism, and sequencing are also proposed. This review aims to synthesize the most recent pathogenetic and molecular classifications of soft tissue and bone tumors, considering the major impact of these diagnostic tools, which are becoming indispensable in clinicopathological practice.
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Affiliation(s)
- Andrei Ionut Patrichi
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology, Targu-Mures, Romania; Research Center of Oncopathology and Translational Medicine (CCOMT), Targu-Mures, Romania
| | - Simona Gurzu
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology, Targu-Mures, Romania; Research Center of Oncopathology and Translational Medicine (CCOMT), Targu-Mures, Romania; Romanian Academy of Medical Sciences, Romania.
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3
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Alidousty C, Becker A, Binot E, Hillmer AM, Merkelbach-Bruse S, Budde B, Bäßmann I, Rappl G, Wolf J, Eich ML, Noh KW, Buettner R, Schultheis AM. Frequency and functional characterization of fusion genes in squamous cell carcinoma of the lung. Gene 2024; 895:148018. [PMID: 37981082 DOI: 10.1016/j.gene.2023.148018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/23/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023]
Abstract
INTRODUCTION In contrast to lung adenocarcinoma (LUAD), targetable genetic alterations are less frequently detected in squamous cell carcinoma of the lung (LUSC). Over the last years, gene fusions have become promising targets in many solid cancers. Here, we analysed a cohort of LUSC, identified recurrent fusion genes and functionally characterised these tumour genomes. METHODS A subset of 1608 squamous cell carcinomas of the lung was analysed by means of the FusionPlex® Lung Panel to identify potentially targetable gene fusions using targeted next-generation sequencing. Cases harbouring recurrent gene fusions were further analysed using FISH, Cytoscan HD arrays and cell culture experiments. RESULTS We found both, known and novel gene fusions in about 3 % of the cases. Known fusions occurring in lung cancer included ALK::EML4, EGFRvIII, EZR::ROS1 and FGFR3::TACC. We further identified recurrent gene fusions of currently unknown biological function, involving EGFR::VSTM2A and NSD3::FGFR1 and showed that the occurrence of the EGFR::VSTM2A fusion is accompanied by high-level amplification of EGFR. Our analyses further revealed that the genomes of these LUSC patients are chromosomally unstable, which leads us to believe that such non-actionable genomic rearrangements may be a result of "chromosomal chaos" most probably not representing exclusive cancer-driving genes in this cancer entity. CONCLUSIONS We emphasise that caution should be taken when novel fusions are found and that the appearance of new gene fusions should always be interpreted in the molecular context of the respective disease.
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Affiliation(s)
- Christina Alidousty
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Arvid Becker
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Elke Binot
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Axel M Hillmer
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Robert Koch Strasse 21, 50931 Cologne, Germany
| | - Sabine Merkelbach-Bruse
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Birgit Budde
- Cologne Center for Genomics, Medical Faculty of the University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Ingelore Bäßmann
- Cologne Center for Genomics, Medical Faculty of the University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Gunter Rappl
- Center for Molecular Medicine Cologne, University of Cologne, Robert Koch Strasse 21, 50931 Cologne, Germany
| | - Jürgen Wolf
- Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Marie-Lisa Eich
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Ka-Won Noh
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Reinhard Buettner
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Anne Maria Schultheis
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany.
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4
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Shim JW, Choi JY, Shim DM, Seo SW. Novel MFSD7-ATP5I fusion promotes migration and invasion of human sarcoma. J Orthop Res 2024; 42:443-452. [PMID: 37782287 DOI: 10.1002/jor.25689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/13/2023] [Indexed: 10/03/2023]
Abstract
Fusion genes have been implicated in the development and progression of several types of sarcomas, serving as valuable diagnostic and prognostic markers, as well as potential therapeutic targets. We discovered a novel major facilitator superfamily domain-containing 7 (MFSD7) and adenosine triphosphate 5I (ATP5I) gene fusion from sarcomas. In this study, the MFSD7-ATP5I fusion transcript was screened using RNA sequencing in 55 sarcoma samples and sixteen normal samples. The MFSD7-ATP5I fusion transcript was detected in 58% of sarcoma samples. The correlation between the expression of MFSD7-ATP5I fusion transcript and clinicopathological information was analyzed, and MFSD7-ATP5I expression is associated with marked pleomorphism and lower tumor necrosis. Cell migration and invasion was significantly reduced by knock-down of MFSD7-ATP5I. Cell migration and invasion was increased by overexpression of MFSD7-ATP5I. A phosphokinase assay demonstrated that MFSD7-ATP5I is involved in the GSK-3 pathway. The current study found that MFSD7-ATP5I is associated with increasing pleomorphism and decreasing necrosis of tumors. And our gain and loss of function experiments prove that MFSD7-ATP5I promotes the invasiveness of tumor cells.
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Affiliation(s)
- Jae Woo Shim
- Department of Orthopedic Surgery, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Korea
| | - Ji-Yoon Choi
- Department of Orthopedic Surgery, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Korea
| | - Da Mi Shim
- Department of Orthopedic Surgery, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Korea
| | - Sung Wook Seo
- Department of Orthopedic Surgery, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Korea
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5
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Teku G, Nilsson J, Magnusson L, Sydow S, Flucke U, Puls F, Mitra S, Mertens F. Insertion of the CXXC domain of KMT2A into YAP1: An unusual mechanism behind the formation of a chimeric oncogenic protein. Genes Chromosomes Cancer 2023; 62:633-640. [PMID: 37246732 DOI: 10.1002/gcc.23176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/30/2023] Open
Abstract
Most neoplasia-associated gene fusions are formed through the fusion of the 5'-part of one gene with the 3'-part of another. We here describe a unique mechanism, by which a part of the KMT2A gene through an insertion replaces part of the YAP1 gene. The resulting YAP1::KMT2A::YAP1 (YKY) fusion was verified by RT-PCR in three cases of sarcoma morphologically resembling sclerosing epithelioid fibrosarcoma (SEF-like sarcoma). In all cases, a portion (exons 4/5-6) encoding the CXXC domain of KMT2A was inserted between exon 4/5 and exon 8/9 of YAP1. The inserted sequence from KMT2A thus replaced exons 5/6-8 of YAP1, which encode an important regulatory sequence of YAP1. To evaluate the cellular impact of the YKY fusion, global gene expression profiles from fresh frozen and formalin-fixed YKY-expressing sarcomas were compared with control tumors. The effects of the YKY fusion, as well as YAP1::KMT2A and KMT2A::YAP1 fusion constructs, were further studied in immortalized fibroblasts. Analysis of differentially upregulated genes revealed significant overlap between tumors and cell lines expressing YKY, as well as with previously reported YAP1 fusions. Pathway analysis of upregulated genes in cells and tumors expressing YKY revealed an enrichment of genes included in key oncogenic signaling pathways, such as Wnt and Hedgehog. As these pathways are known to interact with YAP1, it seems likely that the pathogenesis of sarcomas with the YKY fusion is linked to distorted YAP1 signaling.
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Affiliation(s)
- Gabriel Teku
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Saskia Sydow
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Uta Flucke
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Florian Puls
- Department Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Shamik Mitra
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, Lund, Sweden
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6
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Hafstað V, Häkkinen J, Persson H. Fast and sensitive validation of fusion transcripts in whole-genome sequencing data. BMC Bioinformatics 2023; 24:359. [PMID: 37741966 PMCID: PMC10518092 DOI: 10.1186/s12859-023-05489-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND In cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or place one gene under the control of the promoter of another gene. These fusion genes can act as oncogenic drivers in tumor development and several fusions involving kinases have been successfully exploited as drug targets. Expressed fusions can be identified in RNA sequencing (RNA-Seq) data, but fusion prediction software often has a high fraction of false positive fusion transcript predictions. This is problematic for both research and clinical applications. RESULTS We describe a method for validation of fusion transcripts detected by RNA-Seq in matched whole-genome sequencing (WGS) data. Our pipeline uses discordant read pairs to identify supported fusion events and analyzes soft-clipped read alignments to determine genomic breakpoints. We have tested it on matched RNA-Seq and WGS data for both tumors and cancer cell lines and show that it can be used to validate both new predicted gene fusions and experimentally validated fusion events. It was considerably faster and more sensitive than using BreakDancer and Manta, software that is instead designed to detect many different types of structural variants on a genome-wide scale. CONCLUSIONS We have developed a fast and very sensitive pipeline for validation of gene fusions detected by RNA-Seq in matched WGS data. It can be used to identify high-quality gene fusions for further bioinformatic and experimental studies, including validation of genomic breakpoints and studies of the mechanisms that generate fusions. In a clinical setting, it could help find expressed gene fusions for personalized therapy.
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Affiliation(s)
- Völundur Hafstað
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Jari Häkkinen
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Helena Persson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden.
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7
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Yates ME, Li Z, Li Y, Guzolik H, Wang X, Liu T, Hooda J, Atkinson JM, Lee AV, Oesterreich S. ESR1 fusion proteins invoke breast cancer subtype-dependent enrichment of ligand independent pro-oncogenic signatures and phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558175. [PMID: 37790296 PMCID: PMC10542116 DOI: 10.1101/2023.09.18.558175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Breast cancer is a leading cause of female mortality and despite advancements in diagnostics and personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. Fortunately, identification of mechanisms of therapeutic resistance have rapidly transformed our understanding of cancer evasion and is enabling targeted treatment regimens. When the druggable estrogen receptor (ER, ESR1 ), expressed in two-thirds of all breast cancer, is exposed to endocrine therapy, there is risk of somatic mutation development in approximately 30% of cases and subsequent treatment resistance. A more recently discovered mechanism of ER mediated endocrine resistance is the expression of ER fusion proteins. ER fusions, which retain the protein's DNA binding domain, harbor ESR1 exons 1-6 fused to an in-frame gene partner resulting in loss of the 3' ER ligand binding domain (LBD). In this report we demonstrate that in no-special type (NST) and invasive lobular carcinoma (ILC) cell line models, ER fusion proteins exhibit robust hyperactivation of canonical ER signaling pathways independent of the ligand estradiol or anti-endocrine therapies such as Fulvestrant and Tamoxifen. We employ cell line models stably overexpressing ER fusion proteins with concurrent endogenous ER knockdown to minimize the influence of endogenous wildtype ER. Cell lines exhibited shared transcriptomic enrichment in pathways known to be drivers of metastatic disease, notably the MYC pathway. The heterogeneous 3' fusion partners, particularly transcription factors SOX9 and YAP1 , evoked varying degrees of transcriptomic and cistromic activity that translated into unique phenotypic readouts. Herein we report that cell line activity is subtype-, fusion-, and assay-specific suggesting that the loss of the LBD, the 3' fusion partner, and the cellular landscape all influence fusion activity. Therefore, it will be critical to generate additional data on frequency of the ER fusions, in the context of the clinicopathological features of the tumor. Significance ER fusion proteins exhibit diverse mechanisms of endocrine resistance in breast cancer cell lines representing the no special type (NST) and invasive lobular cancer (ILC) subtypes. Our emphasize upon both the shared and unique cellular adaptations imparted by ER fusions offers the foundation for further translational research and clinical decision making.
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8
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Wang J, Zheng J, Lee E, Aguilar B, Phan J, Abdilleh K, Taylor RC, Longabaugh W, Johansson B, Mertens F, Mitelman F, Pot D, LaFramboise T. A cloud-based resource for genome coordinate-based exploration and large-scale analysis of chromosome aberrations and gene fusions in cancer. Genes Chromosomes Cancer 2023; 62:441-448. [PMID: 36695636 PMCID: PMC10258157 DOI: 10.1002/gcc.23128] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023] Open
Abstract
Cytogenetic analysis provides important information on the genetic mechanisms of cancer. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer (Mitelman DB) is the largest catalog of acquired chromosome aberrations, presently comprising >70 000 cases across multiple cancer types. Although this resource has enabled the identification of chromosome abnormalities leading to specific cancers and cancer mechanisms, a large-scale, systematic analysis of these aberrations and their downstream implications has been difficult due to the lack of a standard, automated mapping from aberrations to genomic coordinates. We previously introduced CytoConverter as a tool that automates such conversions. CytoConverter has now been updated with improved interpretation of karyotypes and has been integrated with the Mitelman DB, providing a comprehensive mapping of the 70 000+ cases to genomic coordinates, as well as visualization of the frequencies of chromosomal gains and losses. Importantly, all CytoConverter-generated genomic coordinates are publicly available in Google BigQuery, a cloud-based data warehouse, facilitating data exploration and integration with other datasets hosted by the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) Resource. We demonstrate the use of BigQuery for integrative analysis of Mitelman DB with other cancer datasets, including a comparison of the frequency of imbalances identified in Mitelman DB cases with those found in The Cancer Genome Atlas (TCGA) copy number datasets. This solution provides opportunities to leverage the power of cloud computing for low-cost, scalable, and integrated analysis of chromosome aberrations and gene fusions in cancer.
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Affiliation(s)
- Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jeanne Zheng
- School of Public Health, Brown University, Providence, RI, USA
| | - Elaine Lee
- Institute for Systems Biology, Seattle, WA, USA
| | | | - John Phan
- General Dynamics Information Technology, Rockville, MD, USA
| | | | - Ronald C. Taylor
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | | | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - David Pot
- General Dynamics Information Technology, Rockville, MD, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
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9
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Drazdauskienė U, Kapustina Ž, Medžiūnė J, Dubovskaja V, Sabaliauskaitė R, Jarmalaitė S, Lubys A. Fusion sequencing via terminator-assisted synthesis (FTAS-seq) identifies TMPRSS2 fusion partners in prostate cancer. Mol Oncol 2023; 17:993-1006. [PMID: 37300660 DOI: 10.1002/1878-0261.13428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/26/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023] Open
Abstract
Genetic rearrangements that fuse an androgen-regulated promoter area with a protein-coding portion of an originally androgen-unaffected gene are frequent in prostate cancer, with the fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2-ERG fusion) being the most prevalent. Conventional hybridization- or amplification-based methods can test for the presence of expected gene fusions, but the exploratory analysis of currently unknown fusion partners is often cost-prohibitive. Here, we developed an innovative next-generation sequencing (NGS)-based approach for gene fusion analysis termed fusion sequencing via terminator-assisted synthesis (FTAS-seq). FTAS-seq can be used to enrich the gene of interest while simultaneously profiling the whole spectrum of its 3'-terminal fusion partners. Using this novel semi-targeted RNA-sequencing technique, we were able to identify 11 previously uncharacterized TMPRSS2 fusion partners and capture a range of TMPRSS2-ERG isoforms. We tested the performance of FTAS-seq with well-characterized prostate cancer cell lines and utilized the technique for the analysis of patient RNA samples. FTAS-seq chemistry combined with appropriate primer panels holds great potential as a tool for biomarker discovery that can support the development of personalized cancer therapies.
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Affiliation(s)
| | | | | | | | | | - Sonata Jarmalaitė
- National Cancer Institute, Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, Vilnius, Lithuania
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10
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Mandahl N, Mitelman F. Giemsa-negative chromosome bands preferentially recombine in cancer-associated translocations and gene fusions. Genes Chromosomes Cancer 2023; 62:61-74. [PMID: 36116030 PMCID: PMC10092824 DOI: 10.1002/gcc.23095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022] Open
Abstract
Chromosome abnormalities, in particular translocations, and gene fusions are hallmarks of neoplasia. Although both have been recognized as important drivers of cancer for decades, our knowledge of the characterizing features of the cytobands involved in recombinations is poorly understood. The present study, based on a comparative analysis of 10 442 translocation breakpoints and 30 762 gene fusions comprising 13 864 protein-coding genes, is the most comprehensive evaluation of the interactions of cytobands participating in the formation of such rearrangements in cancer. The major conclusion is that although large G-negative, gene-rich bands are most frequently involved, the greatest impact was seen for staining properties. Thus, 60% of the recombinations leading to the formation of both translocations and fusion genes take place between two G-negative bands whereas only about 10% involve two G-positive bands. There is compelling evidence that G-negative bands contain more genes than dark staining bands and it has previously been shown that breakpoints involved in structural chromosome rearrangements and in gene fusions preferentially affect gene-rich bands. The present study not only corroborates these findings but in addition demonstrates that the recombination processes favor the joining of two G-negative cytobands and that this feature may be a stronger factor than gene content. It is reasonable to assume that the formation of translocations and fusion genes in cancer cells, irrespective of whether they have a pathogenetically significant impact or not, may be mediated by some underlying mechanisms that either favor the origin or provide a selective advantage for recombinations of G-negative cytobands.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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11
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PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
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Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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12
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Lacambra MD, Antonescu CR, Chit C, Chiu WK, Demicco EG, Ferguson PC, Swanson D, To KF, Zhang L, Dickson BC. Expanding the spectrum of mesenchymal neoplasms with NR1D1‐rearrangement. Genes Chromosomes Cancer 2022; 61:420-426. [DOI: 10.1002/gcc.23032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Maribel D. Lacambra
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Cristina R. Antonescu
- Department of Pathology Memorial Sloan Kettering Cancer Center New York New York United States
| | - Chow Chit
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Wang Kei Chiu
- Department of Orthopedics and Traumatology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Elizabeth G. Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
| | - Peter C. Ferguson
- Department of Surgery, Mount Sinai Health System; Division of Orthopaedics, Department of Surgery University of Toronto Toronto Ontario Canada
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
| | - Ka Fai To
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Lei Zhang
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Brendan C. Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
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13
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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14
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Beg S, Bareja R, Ohara K, Eng KW, Wilkes DC, Pisapia DJ, Zoughbi WA, Kudman S, Zhang W, Rao R, Manohar J, Kane T, Sigouros M, Xiang JZ, Khani F, Robinson BD, Faltas BM, Sternberg CN, Sboner A, Beltran H, Elemento O, Mosquera JM. Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology. Transl Oncol 2020; 14:100944. [PMID: 33190043 PMCID: PMC7674614 DOI: 10.1016/j.tranon.2020.100944] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Frequency of clinically relevant mutations in solid tumors by targeted and whole-exome sequencing is ∼30%. Transcriptome analysis complements detection of actionable gene fusions in advanced cancer patients. Goal of this study was to determine the added value of anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) assay to identify further potential drug targets, when coupled with whole-exome sequencing (WES). METHODS Selected series of fifty-six samples from 55 patients enrolled in our precision medicine study were interrogated by WES and AMP-based NGS. RNA-seq was performed in 19 cases. Clinically relevant and actionable alterations detected by three methods were integrated and analyzed. RESULTS AMP-based NGS detected 48 fusions in 31 samples (55.4%); 31.25% (15/48) were classified as targetable based on published literature. WES revealed 29 samples (51.8%) harbored targetable alterations. TMB-high and MSI-high status were observed in 12.7% and 1.8% of cases. RNA-seq from 19 samples identified 8 targetable fusions (42.1%), also captured by AMP-based NGS. When number of actionable fusions detected by AMP-based NGS were added to WES targetable alterations, 66.1% of samples had potential drug targets. When both WES and RNA-seq were analyzed, 57.8% of samples had targetable alterations. CONCLUSIONS This study highlights importance of an integrative genomic approach for precision oncology, including use of different NGS platforms with complementary features. Integrating RNA data (whole transcriptome or AMP-based NGS) significantly enhances detection of potential targets in cancer patients. In absence of fresh frozen tissue, AMP-based NGS is a robust method to detect actionable fusions using low-input RNA from archival tissue.
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Affiliation(s)
- Shaham Beg
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Rohan Bareja
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Kentaro Ohara
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Kenneth Wha Eng
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - David C Wilkes
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - David J Pisapia
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Wael Al Zoughbi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Sarah Kudman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Wei Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Rema Rao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Jyothi Manohar
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Troy Kane
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Michael Sigouros
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Jenny Zhaoying Xiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Francesca Khani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States
| | - Bishoy M Faltas
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States; Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Cora N Sternberg
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States; Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States; Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and NewYork Presbyterian, New York, NY, United States.
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15
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Stengel A, Shahswar R, Haferlach T, Walter W, Hutter S, Meggendorfer M, Kern W, Haferlach C. Whole transcriptome sequencing detects a large number of novel fusion transcripts in patients with AML and MDS. Blood Adv 2020; 4:5393-5401. [PMID: 33147338 PMCID: PMC7656918 DOI: 10.1182/bloodadvances.2020003007] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/30/2020] [Indexed: 12/31/2022] Open
Abstract
Fusion transcripts are frequent genetic abnormalities in myeloid malignancies and are often the basis for risk stratification, minimal residual disease (MRD) monitoring, and targeted therapy. We comprehensively analyzed the fusion transcript landscape in 572 acute myeloid leukemia (AML) and 630 myelodysplastic syndrome (MDS) patients by whole transcriptome sequencing (WTS). Totally, 274 fusion events (131 unique fusions) were identified in 210/572 AML patients (37%). In 16/630 MDS patients, 16 fusion events (15 unique fusions) were detected (3%). In AML, 141 cases comprised entity-defining rearrangements (51% of all detected fusions) and 21 (8%) additional well-known fusions, all detected by WTS (control group). In MDS, only 1 fusion was described previously (NRIP1-MECOM, n = 2). Interestingly, a high number of so-far unreported fusions were found (41% [112/274] in AML, 88% [14/16] in MDS), all validated by cytogenetic and/or whole genome sequencing data. With 1 exception (CTDSP1-CFLAR, n = 2), all novel fusions were observed in 1 patient each. In AML, cases with novel fusions showed concomitantly a high frequency of TP53 mutations (67%) and of a complex karyotype (71%), which was also observed in MDS, but less pronounced (TP53, 26%; complex karyotype, 21%). A functional annotation of genes involved in novel fusions revealed many functional relevant genes (eg, transcription factors; n = 28 in AML, n = 2 in MDS) or enzymes (n = 42 in AML, n = 9 in MDS). Taken together, new genomic alterations leading to fusion transcripts were much more common in AML than in MDS. Any novel fusions might be of use for developing markers (eg, for MRD monitoring), particularly in cases without an entity-defining abnormality.
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Affiliation(s)
- Anna Stengel
- MLL Munich Leukemia Laboratory, Munich, Germany; and
| | - Rabia Shahswar
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | - Wencke Walter
- MLL Munich Leukemia Laboratory, Munich, Germany; and
| | | | | | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Munich, Germany; and
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16
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Sbaraglia M, Bellan E, Dei Tos AP. The 2020 WHO Classification of Soft Tissue Tumours: news and perspectives. Pathologica 2020; 113:70-84. [PMID: 33179614 PMCID: PMC8167394 DOI: 10.32074/1591-951x-213] [Citation(s) in RCA: 381] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal tumours represent one of the most challenging field of diagnostic pathology and refinement of classification schemes plays a key role in improving the quality of pathologic diagnosis and, as a consequence, of therapeutic options. The recent publication of the new WHO classification of Soft Tissue Tumours and Bone represents a major step toward improved standardization of diagnosis. Importantly, the 2020 WHO classification has been opened to expert clinicians that have further contributed to underline the key value of pathologic diagnosis as a rationale for proper treatment. Several relevant advances have been introduced. In the attempt to improve the prediction of clinical behaviour of solitary fibrous tumour, a risk assessment scheme has been implemented. NTRK-rearranged soft tissue tumours are now listed as an "emerging entity" also in consideration of the recent therapeutic developments in terms of NTRK inhibition. This decision has been source of a passionate debate regarding the definition of "tumour entity" as well as the consequences of a "pathology agnostic" approach to precision oncology. In consideration of their distinct clinicopathologic features, undifferentiated round cell sarcomas are now kept separate from Ewing sarcoma and subclassified, according to the underlying gene rearrangements, into three main subgroups (CIC, BCLR and not ETS fused sarcomas) Importantly, In order to avoid potential confusion, tumour entities such as gastrointestinal stroma tumours are addressed homogenously across the different WHO fascicles. Pathologic diagnosis represents the integration of morphologic, immunohistochemical and molecular characteristics and is a key element of clinical decision making. The WHO classification is as a key instrument to promote multidisciplinarity, stimulating pathologists, geneticists and clinicians to join efforts aimed to translate novel pathologic findings into more effective treatments.
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Affiliation(s)
- Marta Sbaraglia
- Department of Pathology, Azienda Ospedale Università Padova, Padova, Italy
| | - Elena Bellan
- Department of Pathology, Azienda Ospedale Università Padova, Padova, Italy
| | - Angelo P Dei Tos
- Department of Pathology, Azienda Ospedale Università Padova, Padova, Italy.,Department of Medicine, University of Padua School of Medicine, Padua, Italy
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17
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Pisapia DJ, Ohara K, Bareja R, Wilkes DC, Hissong E, Croyle JA, Kim JH, Saab J, MacDonald TY, Beg S, O’Reilly C, Kudman S, Rubin MA, Elemento O, Sboner A, Greenfield J, Mosquera JM. Fusions involving BCOR and CREBBP are rare events in infiltrating glioma. Acta Neuropathol Commun 2020; 8:80. [PMID: 32493417 PMCID: PMC7271411 DOI: 10.1186/s40478-020-00951-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/19/2020] [Indexed: 12/31/2022] Open
Abstract
BCOR has been recognized as a recurrently altered gene in a subset of pediatric tumors of the central nervous system (CNS). Here, we describe a novel BCOR-CREBBP fusion event in a case of pediatric infiltrating astrocytoma and further probe the frequency of related fusion events in CNS tumors. We analyzed biopsy samples taken from a 15-year-old male with an aggressive, unresectable and multifocal infiltrating astrocytoma. We performed RNA sequencing (RNA-seq) and targeted DNA sequencing. In the index case, the fused BCOR-CREBBP transcript comprises exons 1-4 of BCOR and exon 31 of CREBBP. The fused gene thus retains the Bcl6 interaction domain of BCOR while eliminating the domain that has been shown to interact with the polycomb group protein PCGF1. The fusion event was validated by FISH and reverse transcriptase PCR. An additional set of 177 pediatric and adult primary CNS tumors were assessed via FISH for BCOR break apart events, all of which were negative. An additional 509 adult lower grade infiltrating gliomas from the publicly available TCGA dataset were screened for BCOR or CREBBP fusions. In this set, one case was found to harbor a CREBBP-GOLGA6L2 fusion and one case a CREBBP-SRRM2 fusion. In a third patient, both BCOR-L3MBTL2 and EP300-BCOR fusions were seen. Of particular interest to this study, EP300 is a paralog of CREBBP and the breakpoint seen involves a similar region of the gene to that of the index case; however, the resultant transcript is predicted to be completely distinct. While this gene fusion may play an oncogenic role through the loss of tumor suppressor functions of BCOR and CREBBP, further screening over larger cohorts and functional validation is needed to determine the degree to which this or similar fusions are recurrent and to elucidate their oncogenic potential.
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18
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Vellichirammal NN, Albahrani A, Banwait JK, Mishra NK, Li Y, Roychoudhury S, Kling MJ, Mirza S, Bhakat KK, Band V, Joshi SS, Guda C. Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1379-1398. [PMID: 32160708 PMCID: PMC7044684 DOI: 10.1016/j.omtn.2020.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/03/2020] [Accepted: 01/14/2020] [Indexed: 01/26/2023]
Abstract
Gene fusions that contribute to oncogenicity can be explored for identifying cancer biomarkers and potential drug targets. To investigate the nature and distribution of fusion transcripts in cancer, we examined the transcriptome data of about 9,000 primary tumors from 33 different cancers in TCGA (The Cancer Genome Atlas) along with cell line data from CCLE (Cancer Cell Line Encyclopedia) using ChimeRScope, a novel fusion detection algorithm. We identified several fusions with sense (canonical, 39%) or antisense (non-canonical, 61%) transcripts recurrent across cancers. The majority of the recurrent non-canonical fusions found in our study are novel, unexplored, and exhibited highly variable profiles across cancers, with breast cancer and glioblastoma having the highest and lowest rates, respectively. Overall, 4,344 recurrent fusions were identified from TCGA in this study, of which 70% were novel. Additional analysis of 802 tumor-derived cell line transcriptome data across 20 cancers revealed significant variability in recurrent fusion profiles between primary tumors and corresponding cell lines. A subset of canonical and non-canonical fusions was validated by examining the structural variation evidence in whole-genome sequencing (WGS) data or by Sanger sequencing of fusion junctions. Several recurrent fusion genes identified in our study show promise for drug repurposing in basket trials and present opportunities for mechanistic studies.
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Affiliation(s)
| | - Abrar Albahrani
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jasjit K Banwait
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Bioinformatics and Systems Biology Core. University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nitish K Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - You Li
- HitGen, South Keyuan Road 88, Chengdu, China
| | - Shrabasti Roychoudhury
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mathew J Kling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shantaram S Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Bioinformatics and Systems Biology Core. University of Nebraska Medical Center, Omaha, NE 68198, USA.
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19
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McEvoy CR, Fox SB, Prall OWJ. Emerging entities in NUTM1-rearranged neoplasms. Genes Chromosomes Cancer 2020; 59:375-385. [PMID: 32060986 DOI: 10.1002/gcc.22838] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Structural alterations of NUTM1 were originally thought to be restricted to poorly differentiated carcinomas with variable squamous differentiation originating in the midline organs of children and adolescents. Termed NUT carcinomas (NCs), they were defined by a t(15;19) chromosomal rearrangement that was found to result in a BRD4-NUTM1 gene fusion. However, the use of DNA and RNA-based next-generation sequencing has recently revealed a multitude of new NUTM1 fusion partners in a diverse array of neoplasms including sarcoma-like tumors, poromas, and acute lymphoblastic leukemias (ALLs) that we propose to call NUTM1-rearranged neoplasms (NRNs). Intriguingly, the nosology of NRNs often correlates with the functional classification of the fusion partner, suggesting different oncogenic mechanisms within each NRN division. Indeed, whereas NCs are characterized by their aggressiveness and intransigence to standard therapeutic measures, the more positive clinical outcomes seen in some sarcoma and ALL NRNs may reflect these mechanistic differences. Here we provide a broad overview of the molecular, nosological, and clinical features in these newly discovered neoplastic entities. We describe how aberrant expression of NUTM1 due to fusion with an N-terminal DNA/chromatin-binding protein can generate a potentially powerful chromatin modifier that can give rise to oncogenic transformation in numerous cellular contexts. We also conclude that classification, clinical behavior, and therapeutic options may be best defined by the NUTM1 fusion partner rather than by tumor morphology or immunohistochemical profile.
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Affiliation(s)
- Christopher R McEvoy
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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20
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Arbajian E, Hofvander J, Magnusson L, Mertens F. Deep sequencing of myxoinflammatory fibroblastic sarcoma. Genes Chromosomes Cancer 2020; 59:309-317. [PMID: 31898851 DOI: 10.1002/gcc.22832] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/30/2019] [Accepted: 12/30/2019] [Indexed: 12/20/2022] Open
Abstract
Myxoinflammatory fibroblastic sarcoma (MIFS) has recurrent genetic features in the form of a translocation t(1;10)(p22-31;q24-25), BRAF gene fusions, and/or an amplicon in 3p11-12 including the VGLL3 gene. The breakpoints on chromosomes 1 and 10 in the t(1;10) cluster in or near the TGFBR3 and OGA genes, respectively. We here used a combination of deep sequencing of the genome (WGS), captured sequences (Cap-seq), and transcriptome (RNA-seq) and genomic arrays to investigate the molecular outcome of the t(1;10) and the VGLL3 amplicon, as well as to assess the spectrum of other recurrent genomic features in MIFS. Apart from a ROBO1-BRAF chimera in a t(1;10)-negative MIFS-like tumor, no fusion gene was found at RNA-seq. This was in line with WGS and Cap-seq results, revealing variable breakpoints in chromosomes 1 and 10 and genomic breakpoints that should not yield functional fusion transcripts. The most common genomic rearrangements were breakpoints in or around the OGA, NPM3, and FGF8 genes in chromosome band 10q24, and loss of 1p11-p21 and 10q26-qter (all simultaneously present in 6/7 MIFS); a breakpoint in or near TGFBR3 in chromosome 1 was found in four of these tumors. Amplification and overexpression of VGLL3 was a consistent feature in MIFS and MIFS-like tumors with amplicons in 3p11-12. The significant molecular genetic outcome of the recurrent t(1;10) could be loss of genetic material from 1p and 10q. Other recurrent genomic imbalances in MIFS, such as homozygous loss of CDKN2A and 3p- and 13q-deletions, are shared with other sarcomas, suggesting overlapping pathogenetic pathways.
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Affiliation(s)
- Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
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Neckles C, Sundara Rajan S, Caplen NJ. Fusion transcripts: Unexploited vulnerabilities in cancer? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1562. [PMID: 31407506 PMCID: PMC6916338 DOI: 10.1002/wrna.1562] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Gene fusions are an important class of mutations in several cancer types and include genomic rearrangements that fuse regulatory or coding elements from two different genes. Analysis of the genetics of cancers harboring fusion oncogenes and the proteins they encode have enhanced cancer diagnosis and in some cases patient treatment. However, the effect of the complex structure of fusion genes on the biogenesis of the resulting chimeric transcripts they express is not well studied. There are two potential RNA‐related vulnerabilities inherent to fusion‐driven cancers: (a) the processing of the fusion precursor messenger RNA (pre‐mRNA) to the mature mRNA and (b) the mature mRNA. In this study, we discuss the effects that the genetic organization of fusion oncogenes has on the generation of translatable mature RNAs and the diversity of fusion transcripts expressed in different cancer subtypes, which can fundamentally influence both tumorigenesis and treatment. We also discuss functional genomic approaches that can be utilized to identify proteins that mediate the processing of fusion pre‐mRNAs. Furthermore, we assert that an enhanced understanding of fusion transcript biogenesis and the diversity of the chimeric RNAs present in fusion‐driven cancers will increase the likelihood of successful application of RNA‐based therapies in this class of tumors. This article is categorized under:RNA Processing > RNA Editing and Modification RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
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