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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Sahin Y, Pei J, Baldwin DA, Mansoor N, Koslosky L, Abdelmessieh P, Wang YL, Nejati R, Testa JR. Acute myeloid leukemia with a novel AKAP9::PDGFRA fusion transformed from essential thrombocythemia: A case report and mini review. Leuk Res Rep 2024; 21:100465. [PMID: 38952949 PMCID: PMC11215950 DOI: 10.1016/j.lrr.2024.100465] [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: 02/07/2024] [Revised: 05/07/2024] [Accepted: 05/30/2024] [Indexed: 07/03/2024] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy associated with various combinations of gene mutations, epigenetic abnormalities, and chromosome rearrangement-related gene fusions. Despite the significant degree of heterogeneity in its pathogenesis, many gene fusions and point mutations are recurrent in AML and have been employed in risk stratification over the last several decades. Gene fusions have long been recognized for understanding tumorigenesis and their proven roles in clinical diagnosis and targeted therapies. Advances in DNA sequencing technologies and computational biology have contributed significantly to the detection of known fusion genes as well as for the discovery of novel ones. Several recurring gene fusions in AML have been linked to prognosis, treatment response, and disease progression. In this report, we present a case with a long history of essential thrombocythemia and hallmark CALR mutation transforming to AML characterized by a previously unreported AKAP9::PDGFRA fusion gene. We propose mechanisms by which this fusion may contribute to the pathogenesis of AML and its potential as a molecular target for tyrosine kinase inhibitors.
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Affiliation(s)
- Yavuz Sahin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jianming Pei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Don A. Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Nashwa Mansoor
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Lori Koslosky
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Peter Abdelmessieh
- Department of Bone Marrow Transplant and Cellular Therapies, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Y. Lynn Wang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Joseph. R. Testa
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Casuso A, Benavente BP, Leal Y, Carrera-Naipil C, Valenzuela-Muñoz V, Gallardo-Escárate C. Sex-Biased Transcription Expression of Vitellogenins Reveals Fusion Gene and MicroRNA Regulation in the Sea Louse Caligus rogercresseyi. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:243-260. [PMID: 38294574 DOI: 10.1007/s10126-024-10291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
The caligid ectoparasite, Caligus rogercresseyi, is one of the main concerns in the Chilean salmon industry. The molecular mechanisms displayed by the parasite during the reproductive process represent an opportunity for developing novel control strategies. Vitellogenin is a multifunctional protein recognized as a critical player in several crustaceans' biological processes, including reproduction, embryonic development, and immune response. This study aimed to characterize the C. rogercresseyi vitellogenins, including discovering novel transcripts and regulatory mechanisms associated with microRNAs. Herein, vitellogenin genes were identified by homology analysis using the reference sea louse genome, transcriptome database, and arthropods vitellogenin-protein database. The validation of expression transcripts was conducted by RNA nanopore sequencing technology. Moreover, fusion gene profiling, miRNA target analysis, and functional validation were performed using luciferase assay. Six putative vitellogenin genes were identified in the C. rogercresseyi genome with high homology with other copepods vitellogenins. Furthermore, miR-996 showed a putative role in regulating the Cr_Vitellogenin1 gene, which is highly expressed in females. Moreover, vitellogenin-fusion genes were identified in adult stages and highly regulated in males, demonstrating sex-related expression patterns. In females, the identified fusion genes merged with several non-vitellogenin genes involved in biological processes of ribosome assembly, BMP signaling pathway, and biosynthetic processes. This study reports the genome array of vitellogenins in C. rogercresseyi for the first time, revealing the putative role of fusion genes and miRNA regulation in sea lice biology.
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Affiliation(s)
- Antonio Casuso
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Bárbara P Benavente
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Yeny Leal
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Crisleri Carrera-Naipil
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile.
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile.
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Raghav Y, Dilliott AA, Petrozziello T, Kim SE, Berry JD, Cudkowicz ME, Vakili K, Fraenkel E, Farhan SMK, Sadri-Vakili G. Identification of gene fusions associated with amyotrophic lateral sclerosis. Muscle Nerve 2024; 69:477-489. [PMID: 38305586 DOI: 10.1002/mus.28043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
INTRODUCTION/AIMS Genetics is an important risk factor for amyotrophic lateral sclerosis (ALS), a neurodegenerative disease affecting motor neurons. Recent findings demonstrate that in addition to specific genetic mutations, structural variants caused by genetic instability can also play a causative role in ALS. Genomic instability can lead to deletions, duplications, insertions, inversions, and translocations in the genome, and these changes can sometimes lead to fusion of distinct genes into a single transcript. Gene fusion events have been studied extensively in cancer; however, they have not been thoroughly investigated in ALS. The aim of this study was to determine whether gene fusions are present in ALS. METHODS Gene fusions were identified using STAR Fusion v1.10.0 software in bulk RNA-Seq data from human postmortem samples from publicly available data sets from Target ALS and the New York Genome Center ALS Consortium. RESULTS We report the presence of gene fusion events in several brain regions as well as in spinal cord samples in ALS. Although most gene fusions were intra-chromosomal events between neighboring genes and present in both ALS and control samples, there was a significantly greater number of unique gene fusions in ALS compared to controls. Lastly, we identified specific gene fusions with a significant burden in ALS, that were absent from both control samples and known cancer gene fusion databases. DISCUSSION Collectively, our findings reveal an enrichment of gene fusions in ALS and suggest that these events may be an additional genetic cause linked to ALS pathogenesis.
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Affiliation(s)
- Yogindra Raghav
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Allison A Dilliott
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Tiziana Petrozziello
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Spencer E Kim
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James D Berry
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Merit E Cudkowicz
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Khashayar Vakili
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sali M K Farhan
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Genetics, McGill University, Montreal, Quebec, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Ghazaleh Sadri-Vakili
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
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Xu SM, Cheng Y, Fisher H, Janitz M. Recent advances in the investigation of fusion RNAs and their role in molecular pathology of cancer. Int J Biochem Cell Biol 2024; 168:106529. [PMID: 38246262 DOI: 10.1016/j.biocel.2024.106529] [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: 09/23/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Gene fusions have had a significant role in the development of various types of cancer, oftentimes involved in oncogenic activities through dysregulation of gene expression or signalling pathways. Some cancer-associated chromosomal translocations can undergo backsplicing, resulting in fusion-circular RNAs, a more stable isoform immune to RNase degradation. This stability makes fusion circular RNAs a promising diagnostic biomarker for cancer. While the detection of linear fusion RNAs and their function in certain cancers have been described in literature, fusion circular RNAs lag behind due to their low abundance in cancer cells. This review highlights current literature on the role of linear and circular fusion transcripts in cancer, tools currently available for detecting of these chimeric RNAs and their function and how they play a role in tumorigenesis.
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Affiliation(s)
- Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Harry Fisher
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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Yang Z, Shi M, Liang Y, Zhang F, Li C, Lu Y, Yin T, Wang Z, Li Y, Hao M, Guo R, Yang H, Lei G, Sun F, Zhang Y, Deng Z, Tian Y, Yu L, Bai C, Wang L, Wan C, Wang H, Yang P. Three-dimensional chromatin landscapes in hepatocellular carcinoma associated with hepatitis B virus. J Gastroenterol 2024; 59:119-137. [PMID: 37925679 DOI: 10.1007/s00535-023-02053-z] [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: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Three-dimensional (3D) chromatin architecture frequently altered in cancer. However, its changes during the pathogenesis of hepatocellular carcinoma (HCC) remained elusive. METHODS Hi-C and RNA-seq were applied to study the 3D chromatin landscapes and gene expression of HCC and ANHT. Hi-C Pro was used to generate genome-wide raw interaction matrices, which were normalized via iterative correction (ICE). Moreover, the chromosomes were divided into different compartments according to the first principal component (E1). Furthermore, topologically associated domains (TADs) were visualized via WashU Epigenome Browser. Furthermore, differential expression analysis of ANHT and HCC was performed using the DESeq2 R package. Additionally, dysregulated genes associated with 3D genome architecture altered were confirmed using TCGA, qRT-PCR, immunohistochemistry (IHC), etc. RESULTS: First, the intrachromosomal interactions of chr1, chr2, chr5, and chr11 were significantly different, and the interchromosomal interactions of chr4-chr10, chr13-chr21, chr15-chr22, and chr16-chr19 are remarkably different between ANHT and HCC, which resulted in the up-regulation of TP53I3 and ZNF738 and the down-regulation of APOC3 and APOA5 in HCC. Second, 49 compartment regions on 18 chromosomes have significantly switched (A-B or B-A) during HCC tumorigenesis, contributing to up-regulation of RAP2A. Finally, a tumor-specific TAD boundary located on chr5: 6271000-6478000 and enhancer hijacking were identified in HCC tissues, potentially associated with the elevated expression of MED10, whose expression were associated with poor prognosis of HCC patients. CONCLUSION This study demonstrates the crucial role of chromosomal structure variation in HCC oncogenesis and potential novel biomarkers of HCC, laying a foundation for cancer precision medicine development.
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Affiliation(s)
- Zhao Yang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China.
| | - Mengran Shi
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Youfeng Liang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fuhan Zhang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Cong Li
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yinying Lu
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Taian Yin
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhaohai Wang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yongchao Li
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China
| | - Mingxuan Hao
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Rui Guo
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hao Yang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Guanglin Lei
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Fang Sun
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Yu Zhang
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Zhuoya Deng
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yuying Tian
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Linxiang Yu
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Changqing Bai
- Department of Respiratory, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Lei Wang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chuanxing Wan
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China
| | - Haifeng Wang
- Department of Urology, Second Affiliated Hospital of Kunming Medical University, Kunming, 650504, China.
| | - Penghui Yang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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Emon IM, Al-Qazazi R, Rauh MJ, Archer SL. The Role of Clonal Hematopoiesis of Indeterminant Potential and DNA (Cytosine-5)-Methyltransferase Dysregulation in Pulmonary Arterial Hypertension and Other Cardiovascular Diseases. Cells 2023; 12:2528. [PMID: 37947606 PMCID: PMC10650407 DOI: 10.3390/cells12212528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
DNA methylation is an epigenetic mechanism that regulates gene expression without altering gene sequences in health and disease. DNA methyltransferases (DNMTs) are enzymes responsible for DNA methylation, and their dysregulation is both a pathogenic mechanism of disease and a therapeutic target. DNMTs change gene expression by methylating CpG islands within exonic and intergenic DNA regions, which typically reduces gene transcription. Initially, mutations in the DNMT genes and pathologic DNMT protein expression were found to cause hematologic diseases, like myeloproliferative disease and acute myeloid leukemia, but recently they have been shown to promote cardiovascular diseases, including coronary artery disease and pulmonary hypertension. We reviewed the regulation and functions of DNMTs, with an emphasis on somatic mutations in DNMT3A, a common cause of clonal hematopoiesis of indeterminant potential (CHIP) that may also be involved in the development of pulmonary arterial hypertension (PAH). Accumulation of somatic mutations in DNMT3A and other CHIP genes in hematopoietic cells and cardiovascular tissues creates an inflammatory environment that promotes cardiopulmonary diseases, even in the absence of hematologic disease. This review summarized the current understanding of the roles of DNMTs in maintenance and de novo methylation that contribute to the pathogenesis of cardiovascular diseases, including PAH.
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Affiliation(s)
- Isaac M. Emon
- Department of Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (I.M.E.); (R.A.-Q.)
| | - Ruaa Al-Qazazi
- Department of Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (I.M.E.); (R.A.-Q.)
| | - Michael J. Rauh
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada;
| | - Stephen L. Archer
- Department of Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (I.M.E.); (R.A.-Q.)
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Panicker S, Chengizkhan G, Gor R, Ramachandran I, Ramalingam S. Exploring the Relationship between Fusion Genes and MicroRNAs in Cancer. Cells 2023; 12:2467. [PMID: 37887311 PMCID: PMC10605240 DOI: 10.3390/cells12202467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Fusion genes are key cancer driver genes that can be used as potential drug targets in precision therapies, and they can also serve as accurate diagnostic and prognostic biomarkers. The fusion genes can cause microRNA (miRNA/miR) aberrations in many types of cancer. Nevertheless, whether fusion genes incite miRNA aberrations as one of their many critical oncogenic functionalities for driving carcinogenesis needs further investigation. Recent discoveries of miRNA genes that are present within the regions of genomic rearrangements that initiate fusion gene-based intronic miRNA dysregulation have brought the fusion genes into the limelight and revealed their unexplored potential in the field of cancer biology. Fusion gene-based 'promoter-switch' event aberrantly activate the miRNA-related upstream regulatory signals, while fusion-based coding region alterations disrupt the original miRNA coding loci. Fusion genes can potentially regulate the miRNA aberrations regardless of the protein-coding capability of the resultant fusion transcript. Studies on out-of-frame fusion and nonrecurrent fusion genes that cause miRNA dysregulation have attracted the attention of researchers on fusion genes from an oncological perspective and therefore could have potential implications in cancer therapies. This review will provide insights into the role of fusion genes and miRNAs, and their possible interrelationships in cancer.
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Affiliation(s)
- Saurav Panicker
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
| | - Gautham Chengizkhan
- Department of Endocrinology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600113, Tamil Nadu, India;
| | - Ravi Gor
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
| | - Ilangovan Ramachandran
- Department of Endocrinology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600113, Tamil Nadu, India;
| | - Satish Ramalingam
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
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Smirnov D, Konstantinovskiy N, Prokisch H. Integrative omics approaches to advance rare disease diagnostics. J Inherit Metab Dis 2023; 46:824-838. [PMID: 37553850 DOI: 10.1002/jimd.12663] [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: 03/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
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Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Nikita Konstantinovskiy
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
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10
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Yang Y, Shi L, Xu X, Wen J, Xie T, Li H, Li X, Chen M, Dou X, Yuan C, Song H, Xie B, Tao Y. Spermidine Synthase and Saccharopine Reductase Have Co-Expression Patterns Both in Basidiomycetes with Fusion Form and Ascomycetes with Separate Form. J Fungi (Basel) 2023; 9:jof9030352. [PMID: 36983520 PMCID: PMC10051792 DOI: 10.3390/jof9030352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
Gene fusion is a process through which two or more distinct genes are fused into a single chimeric gene. Unlike most harmful fusion genes in cancer cells, in this study, we first found that spermidine synthetase- (SPDS, catalyst of spermidine biosynthesis) and saccharopine reductase- (SR, catalyst of the penultimate step of lysine biosynthesis) encoding genes form a natural chimeric gene, FfSpdsSr, in Flammulina filiformis. Through the cloning of full-length ORFs in different strains and the analysis of alternative splicing in developmental stages, FfSpdsSr has only one copy and unique transcript encoding chimeric SPDS-SR in F. filiformis. By an orthologous gene search of SpdsSr in more than 80 fungi, we found that the chimeric SpdsSr exists in basidiomycetes, while the two separate Spds and Sr independently exist in ascomycetes, chytridiomycetes, and oomycetes. Further, the transcript level of FfSpdsSr was investigated in different developmental stages and under some common environmental factors and stresses by RT-qPCR. The results showed that FfSpdsSr mainly up-regulated in the elongation stage and pileus development of F. filiformis, as well as under blue light, high temperature, H2O2, and MeJA treatments. Moreover, a total of 15 sets of RNA-Seq data, including 218 samples of Neurospora crassa, were downloaded from the GEO database and used to analyze the expression correlation of NcSpds and NcSr. The results showed that the separate NcSpds and NcSr shared highly similar co-expression patterns in the samples with different strains and different nutritional and environmental condition treatments. The chimeric SpdsSr in basidiomycetes and the co-expression pattern of the Spds and Sr in N. crassa indicate the special link of spermidine and lysine in fungi, which may play an important role in the growth and development of fruiting body and in response to the multiple environmental factors and abiotic stresses.
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Affiliation(s)
- Yayong Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyu Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jin Wen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianyue Xie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hui Li
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Xiaoyu Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengyu Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyi Dou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengjin Yuan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hanbing Song
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baogui Xie
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongxin Tao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: ; Tel.: +86-0591-83789281
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11
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Zeng C, Zhong L, Liu W, Zhang Y, Yu X, Wang X, Zhang R, Kang T, Liao D. Targeting the Lysosomal Degradation of Rab22a-NeoF1 Fusion Protein for Osteosarcoma Lung Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205483. [PMID: 36529692 PMCID: PMC9929137 DOI: 10.1002/advs.202205483] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Rab22a-NeoF fusion protein has recently been reported as a promising target for osteosarcoma lung metastasis. However, how this fusion protein is regulated in cells remains unknown. Here, using multiple screenings, it is reported that Rab22a-NeoF1 fusion protein is degraded by an E3 ligase STUB1 via the autophagy receptor NDP52-mediated lysosome pathway, which is facilitated by PINK1 kinase. Mechanistically, STUB1 catalyzes the K63-linked ubiquitin chains on lysine112 of Rab22a-NeoF1, which is responsible for the binding of Rab22a-NeoF1 to NDP52, resulting in lysosomal degradation of Rab22a-NeoF1. PINK1 is able to phosphorylate Rab22a-NeoF1 at serine120, which promotes ubiquitination and degradation of Rab22a-NeoF1. Consistently, by upregulating PINK1, Sorafenib and Regorafenib can inhibit osteosarcoma lung metastasis induced by Rab22a-NeoF1. These findings reveal that the lysosomal degradation of Rab22a-NeoF1 fusion protein is targetable for osteosarcoma lung metastasis, proposing that Sorafenib and Regorafenib may benefit cancer patients who are positive for the RAB22A-NeoF1 fusion gene.
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Affiliation(s)
- Cuiling Zeng
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
| | - Li Zhong
- Center of Digestive DiseasesThe Seventh Affiliated Hospital, Sun Yat‐sen UniversityShenzhen518107China
- Scientific Research CenterThe Seventh Affiliated Hospital, Sun Yat‐sen UniversityShenzhenChina
| | - Wenqiang Liu
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
- Department of OncologyThe Fifth Affiliated Hospital, Sun Yat‐sen UniversityZhuhai519000China
| | - Yu Zhang
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
| | - Xinhao Yu
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
| | - Xin Wang
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
| | - Dan Liao
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterCollaborative Innovation Center for Cancer MedicineGuangzhou510060China
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12
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Shah S, Al-Omari A, Cook KW, Paston SJ, Durrant LG, Brentville VA. What do cancer-specific T cells 'see'? DISCOVERY IMMUNOLOGY 2022; 2:kyac011. [PMID: 38567060 PMCID: PMC10917189 DOI: 10.1093/discim/kyac011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 04/04/2024]
Abstract
Complex cellular interactions between the immune system and cancer can impact tumour development, growth, and progression. T cells play a key role in these interactions; however, the challenge for T cells is to recognize tumour antigens whilst minimizing cross-reactivity with antigens associated with healthy tissue. Some tumour cells, including those associated with viral infections, have clear, tumour-specific antigens that can be targeted by T cells. A high mutational burden can lead to increased numbers of mutational neoantigens that allow very specific immune responses to be generated but also allow escape variants to develop. Other cancer indications and those with low mutational burden are less easily distinguished from normal tissue. Recent studies have suggested that cancer-associated alterations in tumour cell biology including changes in post-translational modification (PTM) patterns may also lead to novel antigens that can be directly recognized by T cells. The PTM-derived antigens provide tumour-specific T-cell responses that both escape central tolerance and avoid the necessity for individualized therapies. PTM-specific CD4 T-cell responses have shown tumour therapy in murine models and highlight the importance of CD4 T cells as well as CD8 T cells in reversing the immunosuppressive tumour microenvironment. Understanding which cancer-specific antigens can be recognized by T cells and the way that immune tolerance and the tumour microenvironment shape immune responses to cancer is vital for the future development of cancer therapies.
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Affiliation(s)
- Sabaria Shah
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Abdullah Al-Omari
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Katherine W Cook
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Samantha J Paston
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Lindy G Durrant
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Victoria A Brentville
- Scancell Limited, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
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13
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Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent. BIOLOGY 2022; 11:biology11050625. [PMID: 35625354 PMCID: PMC9137560 DOI: 10.3390/biology11050625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/21/2022]
Abstract
Simple Summary Men of African origin have a 2–3 times greater chance of developing prostate cancer than those of European origin, and of patients that are diagnosed with the disease, men of African descent are 2 times more likely to die compared to white men. Men of African origin are still greatly underrepresented in genetic studies and clinical trials. This, unfortunately, means that new discoveries in cancer treatment are missing key information on the group with a greater chance of mortality. A fusion gene is a hybrid gene formed from two previously independent genes. Fusion genes have been found to be common in all main types of human cancer. The objective of this study was to increase our knowledge of fusion genes in prostate cancer using computational approaches and to compare fusion genes between men of African and European origin. This identified novel gene fusions unique to men of African origin and suggested that this group has a greater number of fusion genes. Abstract Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a western lifestyle and of African descent, suggesting risk factors that are genetic, environmental, and socioeconomic in nature. In the USA, African American (AA) men are disproportionately affected, on average suffering from a higher grade of the disease and at a younger age compared to men of European descent (EA). Fusion genes are chimeric products formed by the merging of two separate genes occurring as a result of chromosomal structural changes, for example, inversion or trans/cis-splicing of neighboring genes. They are known drivers of cancer and have been identified in 20% of cancers. Improvements in genomics technologies such as RNA-sequencing coupled with better algorithms for prediction of fusion genes has added to our knowledge of specific gene fusions in cancers. At present AA are underrepresented in genomic studies of prostate cancer. The primary goal of this study was to examine molecular differences in predicted fusion genes in a cohort of AA and EA men in the context of prostate cancer using computational approaches. RNA was purified from prostate tissue specimens obtained at surgery from subjects enrolled in the study. Fusion gene predictions were performed using four different fusion gene detection programs. This identified novel putative gene fusions unique to AA and suggested that the fusion gene burden was higher in AA compared to EA men.
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Lang F, Schrörs B, Löwer M, Türeci Ö, Sahin U. Identification of neoantigens for individualized therapeutic cancer vaccines. Nat Rev Drug Discov 2022; 21:261-282. [PMID: 35105974 PMCID: PMC7612664 DOI: 10.1038/s41573-021-00387-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 02/07/2023]
Abstract
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are recognized by autologous T cells in the host. As neoepitopes are not subject to central immune tolerance and are not expressed in healthy tissues, they are attractive targets for therapeutic cancer vaccines. Because the vast majority of cancer mutations are unique to the individual patient, harnessing the full potential of this rich source of targets requires individualized treatment approaches. Many computational algorithms and machine-learning tools have been developed to identify mutations in sequence data, to prioritize those that are more likely to be recognized by T cells and to design tailored vaccines for every patient. In this Review, we fill the gaps between the understanding of basic mechanisms of T cell recognition of neoantigens and the computational approaches for discovery of somatic mutations and neoantigen prediction for cancer immunotherapy. We present a new classification of neoantigens, distinguishing between guarding, restrained and ignored neoantigens, based on how they confer proficient antitumour immunity in a given clinical context. Such context-based differentiation will contribute to a framework that connects neoantigen biology to the clinical setting and medical peculiarities of cancer, and will enable future neoantigen-based therapies to provide greater clinical benefit.
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Affiliation(s)
- Franziska Lang
- TRON Translational Oncology, Mainz, Germany
- Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | | | - Ugur Sahin
- BioNTech, Mainz, Germany.
- University Medical Center, Johannes Gutenberg University, Mainz, Germany.
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15
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Roles of fusion genes in digestive system cancers: dawn for cancer precision therapy. Crit Rev Oncol Hematol 2022; 171:103622. [PMID: 35124200 DOI: 10.1016/j.critrevonc.2022.103622] [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: 11/02/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
For advanced and advanced tumors of the digestive system, personalized, precise treatment could be a lifesaving medicine. With the development of next-generation sequencing technology, detection of fusion genes in solid tumors has become more extensive. Some fusion gene targeting therapies have been written into the guidelines for digestive tract tumors, such as for neurotrophic receptor tyrosine kinase, fibroblast growth factor receptor 2. There are also many fusion genes being investigated as potential future therapeutic targets. This review focuses on the current detection methods for fusion genes, fusion genes written into the digestive system tumor guidelines, and potential fusion gene therapy targets in different organs to discuss the possibility of clinical treatments for these targets in digestive system tumors.
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16
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Fixing the GAP: the role of RhoGAPs in cancer. Eur J Cell Biol 2022; 101:151209. [DOI: 10.1016/j.ejcb.2022.151209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/29/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
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17
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Nagasawa S, Ikeda K, Shintani D, Yang C, Takeda S, Hasegawa K, Horie K, Inoue S. Identification of a Novel Oncogenic Fusion Gene SPON1-TRIM29 in Clinical Ovarian Cancer That Promotes Cell and Tumor Growth and Enhances Chemoresistance in A2780 Cells. Int J Mol Sci 2022; 23:689. [PMID: 35054873 PMCID: PMC8776205 DOI: 10.3390/ijms23020689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
Gene structure alterations, such as chromosomal rearrangements that develop fusion genes, often contribute to tumorigenesis. It has been shown that the fusion genes identified in public RNA-sequencing datasets are mainly derived from intrachromosomal rearrangements. In this study, we explored fusion transcripts in clinical ovarian cancer specimens based on our RNA-sequencing data. We successfully identified an in-frame fusion transcript SPON1-TRIM29 in chromosome 11 from a recurrent tumor specimen of high-grade serous carcinoma (HGSC), which was not detected in the corresponding primary carcinoma, and validated the expression of the identical fusion transcript in another tumor from a distinct HGSC patient. Ovarian cancer A2780 cells stably expressing SPON1-TRIM29 exhibited an increase in cell growth, whereas a decrease in apoptosis was observed, even in the presence of anticancer drugs. The siRNA-mediated silencing of SPON1-TRIM29 fusion transcript substantially impaired the enhanced growth of A2780 cells expressing the chimeric gene treated with anticancer drugs. Moreover, a subcutaneous xenograft model using athymic mice indicated that SPON1-TRIM29-expressing A2780 cells rapidly generated tumors in vivo compared to control cells, whose growth was significantly repressed by the fusion-specific siRNA administration. Overall, the SPON1-TRIM29 fusion gene could be involved in carcinogenesis and chemotherapy resistance in ovarian cancer, and offers potential use as a diagnostic and therapeutic target for the disease with the fusion transcript.
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Affiliation(s)
- Saya Nagasawa
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Kazuhiro Ikeda
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
| | - Daisuke Shintani
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Saitama 350-1298, Japan; (D.S.); (K.H.)
| | - Chiujung Yang
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Kosei Hasegawa
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Saitama 350-1298, Japan; (D.S.); (K.H.)
| | - Kuniko Horie
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
| | - Satoshi Inoue
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
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18
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Pang Y, Yu G, Butler M, Sindiri S, Song YK, Wei JS, Wen X, Chou HC, Quezado M, Pack S, Xi L, Abdullaev Z, Kim O, Ranjan A, Merchant M, Antony R, Boris L, Aboud O, Kamson D, Kaplan R, Mackey M, Camphausen K, Zaghloul K, Armstrong TS, Gilbert MR, Aldape K, Holdhoff M, Khan J, Wu J. Report of Canonical BCR- ABL1 Fusion in Glioblastoma. JCO Precis Oncol 2021; 5:PO.20.00519. [PMID: 34485806 DOI: 10.1200/po.20.00519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Ying Pang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Guangyang Yu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Madison Butler
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Sivasish Sindiri
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Young K Song
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jun S Wei
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Xinyu Wen
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Hisen-Chao Chou
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Svetlana Pack
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Liqiang Xi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Olga Kim
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Alice Ranjan
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Mythili Merchant
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Ramya Antony
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Lisa Boris
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Orwa Aboud
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David Kamson
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rosandra Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Megan Mackey
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD
| | - Kevin Camphausen
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD
| | - Kareem Zaghloul
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD
| | - Terri S Armstrong
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Matthias Holdhoff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jing Wu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
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19
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He F, Song K, Guan G, Huo J, Xin Y, Li T, Liu C, Zhu Q, Fan N, Guo Y, Wu L. The Phenomenon of Gene Rearrangement is Frequently Associated with TP53 Mutations and Poor Disease-Free Survival in Hepatocellular Carcinoma. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:723-736. [PMID: 34188519 PMCID: PMC8233541 DOI: 10.2147/pgpm.s313848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/03/2021] [Indexed: 01/05/2023]
Abstract
Purpose Gene rearrangements (GRs) have been reported to be related to adverse prognosis in some tumours, but the relationship in hepatocellular carcinoma (HCC) remains less studied. The objective of our study was to explore the clinicopathological characteristics and prognosis of HCC patients (HCCs) with GRs (GR-HCCs). Patients and Methods This retrospective study included 297 HCCs who underwent hepatectomy and had their tumours sequenced by next-generation sequencing. Categorical variables between groups were compared by the chi-square test. The impact of variables on disease-free survival (DFS) and survival after relapse (SAR) was analysed by the Kaplan–Meier method and Cox regression. Results We observed four repetitive GR events in 297 HCCs: BRD9/TERT, ARID2/intergenic, CDKN2A/intergenic and OBSCN truncation. GR-HCCs frequently presented with low tumour differentiation, tumour necrosis, microvascular invasion, elevated AFP and gene mutations (TP53, NTRK3 and BRD9). The 1-, 2-, and 3-year cumulative DFS rates in GR-HCCs were 45.1%, 31.9%, 31.9%, respectively, which were significantly lower than those of GR-negative HCCs (NGR-HCCs) (72.5%, 57.9%, and 49.0%, respectively; P = 0.001). GR was identified as an independent risk factor for inferior DFS in HCCs (HR = 1.980, 95% CI = 1.246–3.147; P = 0.004). However, there was no significant difference in SAR between GR-HCCs and NGR-HCCs receiving targeted therapy or immunotherapy. Conclusion GR is frequently associated with TP53 mutations and significantly affects DFS following radical resection for HCC. We recommend that GR-HCCs should be closely followed up as a high-risk group for postoperative recurrence.
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Affiliation(s)
- Fu He
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Kangjian Song
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Ge Guan
- Organ Transplant Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Junyu Huo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Yang Xin
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Tianxiang Li
- Organ Transplant Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Chao Liu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Qingwei Zhu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Ning Fan
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Yuan Guo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Liqun Wu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
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20
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Wang MY, Huang M, Wang CY, Tang XY, Wang JG, Yang YD, Xiong X, Gao CW. Transcriptome Analysis Reveals MFGE8-HAPLN3 Fusion as a Novel Biomarker in Triple-Negative Breast Cancer. Front Oncol 2021; 11:682021. [PMID: 34211850 PMCID: PMC8239224 DOI: 10.3389/fonc.2021.682021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/24/2021] [Indexed: 12/27/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a highly aggressive cancer with poor prognosis. The lack of effective targeted therapies for TNBC remains a profound clinical challenge. Fusion transcripts play critical roles in carcinogenesis and serve as valuable diagnostic and therapeutic targets in cancer. The present study aimed to identify novel fusion transcripts in TNBC. Methods We analyzed the RNA sequencing data of 360 TNBC samples to identify and filter fusion candidates through SOAPfuse and ChimeraScan analysis. The characteristics, including recurrence, fusion type, chromosomal localization, TNBC subgroup distribution, and clinicopathological correlations, were analyzed in all candidates. Furthermore, we selected the promising fusion transcript and predicted its fusion type and protein coding capacity. Results Using the RNA sequencing data, we identified 189 fusion transcripts in TNBC, among which 22 were recurrent fusions. Compared to para-tumor tissues, TNBC tumor tissues accumulated more fusion events, especially in high-grade tumors. Interestingly, these events were enriched at specific chromosomal loci, and the distribution pattern varied in different TNBC subtypes. The vast majority of fusion partners were discovered on chromosomes 1p, 11q, 19p, and 19q. Besides, fusion events mainly clustered on chromosome 11 in the immunomodulatory subtype and chromosome 19 in the luminal androgen receptor subtype of TNBC. Considering the tumor specificity and frameshift mutation, we selected MFGE8-HAPLN3 as a novel biomarker and further validated it in TNBC samples using PCR and Sanger sequencing. Further, we successfully identified three types of MFGE8-HAPLN3 (E6-E2, E5-E3, and E6-E3) and predicted the ORF of E6-E2, which could encode a protein of 712 amino acids, suggesting its critical role in TNBC. Conclusions Improved bioinformatic stratification and comprehensive analysis identified the fusion transcript MFGE8-HAPLN3 as a novel biomarker with promising clinical application in the future.
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Affiliation(s)
- Meng-Yuan Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Man Huang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Chao-Yi Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Xiao-Ying Tang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Jian-Gen Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yong-De Yang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Xin Xiong
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Chao-Wei Gao
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
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21
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Panicker S, Venkatabalasubramanian S, Pathak S, Ramalingam S. The impact of fusion genes on cancer stem cells and drug resistance. Mol Cell Biochem 2021; 476:3771-3783. [PMID: 34095988 DOI: 10.1007/s11010-021-04203-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
With ever increasing evidences on the role of fusion genes as the oncogenic protagonists in myriad cancers, it's time to explore if fusion genes can be the next generational drug targets in meeting the current demands of higher drug efficacy. Eliminating cancer stem cells (CSC) has become the current focus; however, we have reached a standstill in drug development owing to the lack of effective strategies to eradicate CSC. We believe that fusion genes could be the novel targets to overcome this limitation. The intriguing feature of fusion genes is that it dominantly impacts every aspect of CSC including self-renewal, differentiation, lineage commitment, tumorigenicity and stemness. Given the clinical success of fusion gene-based drugs in hematological cancers, our attempt to target fusion genes in eradicating CSC can be rewarding. As fusion genes are expressed explicitly in cancer cells, eradicating CSC by targeting fusion genes provides yet an another advantage of negligible patient side effects since normal cells remain unaffected by the drug. We hereby delineate the latest evidences on how fusion genes regulate CSC and drug resistance.
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Affiliation(s)
- Saurav Panicker
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India
| | | | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Chennai, 603103, Tamil Nadu, India
| | - Satish Ramalingam
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, 603203, Tamil Nadu, India.
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22
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Schlieben LD, Prokisch H, Yépez VA. How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data. Front Mol Biosci 2021; 8:647277. [PMID: 34141720 PMCID: PMC8204083 DOI: 10.3389/fmolb.2021.647277] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Rare diseases, although individually rare, collectively affect approximately 350 million people worldwide. Currently, nearly 6,000 distinct rare disorders with a known molecular basis have been described, yet establishing a specific diagnosis based on the clinical phenotype is challenging. Increasing integration of whole exome sequencing into routine diagnostics of rare diseases is improving diagnostic rates. Nevertheless, about half of the patients do not receive a genetic diagnosis due to the challenges of variant detection and interpretation. During the last years, RNA sequencing is increasingly used as a complementary diagnostic tool providing functional data. Initially, arbitrary thresholds have been applied to call aberrant expression, aberrant splicing, and mono-allelic expression. With the application of RNA sequencing to search for the molecular diagnosis, the implementation of robust statistical models on normalized read counts allowed for the detection of significant outliers corrected for multiple testing. More recently, machine learning methods have been developed to improve the normalization of RNA sequencing read count data by taking confounders into account. Together the methods have increased the power and sensitivity of detection and interpretation of pathogenic variants, leading to diagnostic rates of 10-35% in rare diseases. In this review, we provide an overview of the methods used for RNA sequencing and illustrate how these can improve the diagnostic yield of rare diseases.
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Affiliation(s)
- Lea D. Schlieben
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Vicente A. Yépez
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
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23
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Tolomeo D, Agostini A, Visci G, Traversa D, Storlazzi CT. PVT1: A long non-coding RNA recurrently involved in neoplasia-associated fusion transcripts. Gene 2021; 779:145497. [PMID: 33600954 DOI: 10.1016/j.gene.2021.145497] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022]
Abstract
NGS technologies and bioinformatics tools allow the rapid identification of chimeric transcripts in cancer. More than 40,000 fusions are so far reported in the literature; however, for most of them, the role in oncogenesis is still not fully understood. This is the case for fusions involving the long non-coding RNA (lncRNA) Plasmacytoma variant translocation 1 (PVT1) (8q24.21). This lncRNA displays oncogenic functions in several cancer types interacting with microRNAs and proteins, but the role of PVT1 fusion transcripts is more obscure. These chimeras have been identified in both hematological malignancies and solid tumors, mainly arising from rearrangements and/or amplification of the 8q24 chromosomal region. In this review, we detail the full spectrum of PVT1 fusions in cancer, summarizing current knowledge about their genesis, function, and role as biomarkers.
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Affiliation(s)
- Doron Tolomeo
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
| | - Antonio Agostini
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124 Bari, Italy.
| | - Grazia Visci
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
| | - Debora Traversa
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
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24
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Taniue K, Akimitsu N. Fusion Genes and RNAs in Cancer Development. Noncoding RNA 2021; 7:10. [PMID: 33557176 PMCID: PMC7931065 DOI: 10.3390/ncrna7010010] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
Abstract
Fusion RNAs are a hallmark of some cancers. They result either from chromosomal rearrangements or from splicing mechanisms that are non-chromosomal rearrangements. Chromosomal rearrangements that result in gene fusions are particularly prevalent in sarcomas and hematopoietic malignancies; they are also common in solid tumors. The splicing process can also give rise to more complex RNA patterns in cells. Gene fusions frequently affect tyrosine kinases, chromatin regulators, or transcription factors, and can cause constitutive activation, enhancement of downstream signaling, and tumor development, as major drivers of oncogenesis. In addition, some fusion RNAs have been shown to function as noncoding RNAs and to affect cancer progression. Fusion genes and RNAs will therefore become increasingly important as diagnostic and therapeutic targets for cancer development. Here, we discuss the function, biogenesis, detection, clinical relevance, and therapeutic implications of oncogenic fusion genes and RNAs in cancer development. Further understanding the molecular mechanisms that regulate how fusion RNAs form in cancers is critical to the development of therapeutic strategies against tumorigenesis.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Cancer Genomics and Precision Medicine, Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido 078-8510, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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25
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Detection of aberrant gene expression events in RNA sequencing data. Nat Protoc 2021; 16:1276-1296. [PMID: 33462443 DOI: 10.1038/s41596-020-00462-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 11/06/2020] [Indexed: 12/20/2022]
Abstract
RNA sequencing (RNA-seq) has emerged as a powerful approach to discover disease-causing gene regulatory defects in individuals affected by genetically undiagnosed rare disorders. Pioneering studies have shown that RNA-seq could increase the diagnosis rates over DNA sequencing alone by 8-36%, depending on the disease entity and tissue probed. To accelerate adoption of RNA-seq by human genetics centers, detailed analysis protocols are now needed. We present a step-by-step protocol that details how to robustly detect aberrant expression levels, aberrant splicing and mono-allelic expression in RNA-seq data using dedicated statistical methods. We describe how to generate and assess quality control plots and interpret the analysis results. The protocol is based on the detection of RNA outliers pipeline (DROP), a modular computational workflow that integrates all the analysis steps, can leverage parallel computing infrastructures and generates browsable web page reports.
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26
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Liu M, Chen P, Hu HY, Ou-Yang DJ, Khushbu RA, Tan HL, Huang P, Chang S. Kinase gene fusions: roles and therapeutic value in progressive and refractory papillary thyroid cancer. J Cancer Res Clin Oncol 2021; 147:323-337. [PMID: 33387037 DOI: 10.1007/s00432-020-03491-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022]
Abstract
The incidence of papillary thyroid cancer (PTC), the major type of thyroid cancer, is increasing rapidly around the world, and its pathogenesis is still unclear. There is poor prognosis for PTC involved in rapidly progressive tumors and resistance to radioiodine therapy. Kinase gene fusions have been discovered to be present in a wide variety of malignant tumors, and an increasing number of novel types have been detected in PTC, especially progressive tumors. As a tumor-driving event, kinase fusions are constitutively activated or overexpress their kinase function, conferring oncogenic potential, and their frequency is second only to BRAFV600E mutation in PTC. Diverse forms of kinase fusions have been observed and are associated with specific pathological features of PTC (usually at an advanced stage), and clinical trials of therapeutic strategies targeting kinase gene fusions are feasible for radioiodine-resistant PTC. This review summarizes the roles of kinase gene fusions in PTC and the value of clinical therapy of targeting fusions in progressive or refractory PTC, and discusses the future perspectives and challenges related to kinase gene fusions in PTC patients.
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Affiliation(s)
- Mian Liu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Pei Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Hui-Yu Hu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Deng-Jie Ou-Yang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Rooh-Afza Khushbu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Hai-Long Tan
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Peng Huang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Shi Chang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China.
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27
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CircRNAs and Fusion-circRNAs in cancer: New players in an old game. Cell Signal 2020; 75:109747. [DOI: 10.1016/j.cellsig.2020.109747] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022]
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28
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Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, Quintana-Bustamante O, Garcia-Silva S, Carcaboso AM, Petazzi P, Bueno C, Mora J, Peinado H, Segovia JC, Menendez P, Rodriguez-Perales S. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Commun 2020. [PMID: 33033246 DOI: 10.1038/s41467-020-18875-x.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fusion oncogenes (FOs) are common in many cancer types and are powerful drivers of tumor development. Because their expression is exclusive to cancer cells and their elimination induces cell apoptosis in FO-driven cancers, FOs are attractive therapeutic targets. However, specifically targeting the resulting chimeric products is challenging. Based on CRISPR/Cas9 technology, here we devise a simple, efficient and non-patient-specific gene-editing strategy through targeting of two introns of the genes involved in the rearrangement, allowing for robust disruption of the FO specifically in cancer cells. As a proof-of-concept of its potential, we demonstrate the efficacy of intron-based targeting of transcription factors or tyrosine kinase FOs in reducing tumor burden/mortality in in vivo models. The FO targeting approach presented here might open new horizons for the selective elimination of cancer cells.
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Affiliation(s)
- M Martinez-Lage
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - R Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain. .,Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.
| | - P Puig-Serra
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - P Moreno-Gaona
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - M C Martin
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - F J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - O Quintana-Bustamante
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain.,Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - S Garcia-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - A M Carcaboso
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - P Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - H Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - J C Segovia
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain.,Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, 08010, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - S Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
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29
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Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, Quintana-Bustamante O, Garcia-Silva S, Carcaboso AM, Petazzi P, Bueno C, Mora J, Peinado H, Segovia JC, Menendez P, Rodriguez-Perales S. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Commun 2020; 11:5060. [PMID: 33033246 PMCID: PMC7544871 DOI: 10.1038/s41467-020-18875-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Fusion oncogenes (FOs) are common in many cancer types and are powerful drivers of tumor development. Because their expression is exclusive to cancer cells and their elimination induces cell apoptosis in FO-driven cancers, FOs are attractive therapeutic targets. However, specifically targeting the resulting chimeric products is challenging. Based on CRISPR/Cas9 technology, here we devise a simple, efficient and non-patient-specific gene-editing strategy through targeting of two introns of the genes involved in the rearrangement, allowing for robust disruption of the FO specifically in cancer cells. As a proof-of-concept of its potential, we demonstrate the efficacy of intron-based targeting of transcription factors or tyrosine kinase FOs in reducing tumor burden/mortality in in vivo models. The FO targeting approach presented here might open new horizons for the selective elimination of cancer cells.
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Affiliation(s)
- M Martinez-Lage
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - R Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.
| | - P Puig-Serra
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - P Moreno-Gaona
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - M C Martin
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - F J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - O Quintana-Bustamante
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - S Garcia-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - A M Carcaboso
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - P Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - H Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - J C Segovia
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, 08010, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - S Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
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30
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Biswas A, Rajesh Y, Mitra P, Mandal M. ETV6 gene aberrations in non-haematological malignancies: A review highlighting ETV6 associated fusion genes in solid tumors. Biochim Biophys Acta Rev Cancer 2020; 1874:188389. [PMID: 32659251 DOI: 10.1016/j.bbcan.2020.188389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/23/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
ETV6 (translocation-Ets-leukemia virus) gene is a transcriptional repressor mainly involved in haematopoiesis and maintenance of vascular networks and has developed to be a major oncogene with the potential ability of forming fusion partners with many other genes with carcinogenic consequences. ETV6 fusions function primarily by constitutive activation of kinase activity of the fusion partners, modifications in the normal functions of ETV6 transcription factor, loss of function of ETV6 or the partner gene and activation of a proto-oncogene near the site of translocation. The role of ETV6 fusion gene in tumorigenesis has been well-documented and more variedly found in haematological malignancies. However, the role of the ETV6 oncogene in solid tumors has also risen to prominence due to an increasing number of cases being reported with this malignancy. Since, solid tumors can be well-targeted, the diagnosis of this genre of tumors based on ETV6 malignancy is of crucial importance for treatment. This review highlights the important ETV6 associated fusions in solid tumors along with critical insights as to existing and novel means of targeting it. A consolidation of novel therapies such as immune, gene, RNAi, stem cell therapy and protein degradation hitherto unused in the case of ETV6 solid tumor malignancies may open further therapeutic avenues.
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Affiliation(s)
- Angana Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Yetirajam Rajesh
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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31
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Barua S, Wang G, Mansukhani M, Hsiao S, Fernandes H. Key considerations for comprehensive validation of an RNA fusion NGS panel. Pract Lab Med 2020; 21:e00173. [PMID: 32613069 PMCID: PMC7322345 DOI: 10.1016/j.plabm.2020.e00173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/19/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
Objectives Validation of RNA-based NGS assays for the detection of therapeutically targetable gene fusions is challenging. Here, we report systematic validation and quality control monitoring of our targeted fusion panel for the detection of 17 clinically relevant fusion transcripts across several tumor types. We implemented this RNA Fusion Panel as a reflex test for tumors lacking DNA driver mutations. Design Forty-four formalin-fixed, paraffin-embedded (FFPE) or fresh-frozen lung, brain, soft tissue and skin tumors were used to determine the accuracy of the assay. Additional fusion-positive specimens and a calibrated reference standard were used to establish the precision, reproducibility and sensitivity of the assay. All aspects of the validation, including quality control metrics, were performed according to New York State guidelines. Results For the RNA fusion panel, accuracy, reproducibility and precision studies were above 99%. Reproducibility and sensitivity studies with the reference standard were helpful in identifying inconsistencies. The limit of detection for most RNA fusion transcripts was 50 copies. Application of the RNA fusion assay as a reflex test to 450 tumor samples lacking DNA driver mutations resulted in a 10% increase in diagnostic yield with minimal additional processing time. Conclusions The validated RNA fusion panel provides clinical utility in therapy selection for patients with solid tumors. By using a sequential testing approach, the RNA fusion assay complements the DNA hotspot assay in identifying clinically relevant variants across many tumor types with minimal additional increase in processing time. RNA fusion NGS panel uses anchored multiplex PCR to detect known and novel fusions. Pre- and post-sequencing quality control increases accuracy of results. Sequential testing of RNA, on samples without DNA variants is practical and cost-effective. Detection of novel RNA fusions expands the therapeutic landscape of tumors.
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Affiliation(s)
- Subit Barua
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Gary Wang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Mahesh Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Susan Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
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32
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Abstract
Supplemental Digital Content is available in the text Background: Fusion genes may play an important role in tumorigenesis, prognosis, and drug resistance; however, studies on fusion genes in endometrial cancer (EC) are rare. This study aimed to identify new fusion genes and to explore their clinical significance in EC. Methods: A total of 28 patients diagnosed with EC were enrolled in this study. RNA sequencing was used to obtain entire genomes and transcriptomes. STAR-comparison and STAR-fusion prediction were applied to predict the fusion genes. Chi-square tests and Student t tests were used to verify the clinical significance with SPSS 13.0 software. Results: New fusion genes were found, and the number of fusion genes varied from 3 to 110 among all patients with EC. The type of fusion genes varied and included messenger RNA (mRNA)-mRNA, long non-coding RNA (lncRNA)-lncRNA, and lncRNA-mRNA. There were six fusion genes with high fusion rates, namely, RP11–123O10.4–GRIP1, RP11–444D3.1–SOX5, RP11–680G10.1–GSE1, NRIP1–AF127936.7, RP11–96H19.1–RP11–446N19.1, and DPH7–PTP4A3. Further studies showed that these fusion genes are related to stage, grade, and recurrence, in which NRIP1–AF127936.7 and DPH7–PTP4A3 were found only in stage III patients with EC. DPH7–PTP4A3 was found in grades 2 and 3, and recurrent patients with EC. Conclusion: Fusion genes play an essential role in EC. Six genes that are overexpressed with high fusion rates are identified. NRIP1–AF127936.7 and DPH7–PTP4A3 might be related to stage, and DPH7–PTP4A3 be related to grade and recurrence.
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Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS One 2019; 14:e0223337. [PMID: 31577830 PMCID: PMC6774566 DOI: 10.1371/journal.pone.0223337] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5-35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as having diagnostic, prognostic or therapeutic relevance. Isolated reports exist of fusion transcripts being detected in cases of developmental and neurological phenotypes, and thus, systematic application of fusion detection to germline conditions may further increase diagnostic rates. However, current fusion detection methods are unsuited to the investigation of germline disease due to performance biases arising from their development using tumor, cell-line or in-silico data. METHODS We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering steps, and instead, prioritize candidates using a custom workflow that integrates genomic and transcriptomic sequence alignment, biological and technical annotations, customized categorization logic, and phenotypic prioritization. RESULTS We demonstrate that our approach to fusion transcript identification and prioritization detects genuine fusion events excluded by standard analyses and efficiently removes phenotypically unimportant candidates and false positive events, resulting in a reduced candidate list enriched for events with potential phenotypic relevance. We describe the successful genetic resolution of two previously undiagnosed disease cases through the detection of pathogenic fusion transcripts. Furthermore, we report the experimental validation of five additional cases of fusion transcripts with potential phenotypic relevance. CONCLUSIONS The approach we describe can be implemented to enable the detection of phenotypically relevant fusion transcripts in studies of rare inherited disease. Fusion transcript detection has the potential to increase diagnostic rates in rare inherited disease and should be included in RNA-based analytical pipelines aimed at genetic diagnosis.
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Affiliation(s)
- Gavin R. Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Laura E. Schultz-Rogers
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - W. Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Krutika Gaonkar
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Pritha Chanana
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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Kim SC, Shin R, Seo HY, Kim M, Park JW, Jeong SY, Ku JL. Identification of a Novel Fusion Gene, FAM174A-WWC1, in Early-Onset Colorectal Cancer: Establishment and Characterization of Four Human Cancer Cell Lines from Early-Onset Colorectal Cancers. Transl Oncol 2019; 12:1185-1195. [PMID: 31228769 PMCID: PMC6600802 DOI: 10.1016/j.tranon.2019.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer diagnosed worldwide and represents the second most common cause of all cancer-related deaths in Korea. Although epidemiological data indicate a sharp increase in the incidence of CRC among individuals older than 50 years, more than 10% of CRCs occur before reaching 50. These are known as early-onset CRCs (EOCRCs) and are likely to be suggestive of hereditary predisposition. However, known familial CRC syndromes account for only 20% of genetic aberrations of EOCRC, and the remaining 80% are still in question. Therefore, we aimed to establish reproducible biological resources and contribute to expand the mutation database of EOCRC. Four cell lines derived from the original tumor mass of CRC patients diagnosed under age 30 years were established, and next-generation sequencing technique was used to identify the genetic features of EOCRC. We have identified one novel fusion gene, FAM174A-WWC1, and analyzed its functional role. The induction of FAM174A-WWC1 to normal fibroblast caused alternations in cellular morphology as well as intercellular expression of E-cadherin and N-cadherin. Moreover, WWC1 carrying the fused FAM174A domain not only abrogated the membrane expression of YAP1 but also significantly increased the levels of nucleic YAP1. As a result, the FAM174A-WWC1 expression increased the oncogenic capacity and invasiveness of normal fibroblasts, which suggests its role as a potential driver mutation of EOCRC.
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Affiliation(s)
- Soon-Chan Kim
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Rumi Shin
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul 07061
| | - Ha-Young Seo
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Minjung Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Ji Won Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Seung-Yong Jeong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Republic of Korea.
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
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35
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Abstract
Fusion transcripts are used as biomarkers in companion diagnoses. Although more than 15,000 fusion RNAs have been identified from diverse cancer types, few common features have been reported. Here, we compared 16,410 fusion transcripts detected in cancer (from a published cohort of 9,966 tumor samples of 33 cancer types) with genome-wide RNA-DNA interactions mapped in two normal, noncancerous cell types [using iMARGI, an enhanced version of the mapping of RNA-genome interactions (MARGI) assay]. Among the top 10 most significant RNA-DNA interactions in normal cells, 5 colocalized with the gene pairs that formed fusion RNAs in cancer. Furthermore, throughout the genome, the frequency of a gene pair to exhibit RNA-DNA interactions is positively correlated with the probability of this gene pair to present documented fusion transcripts in cancer. To test whether RNA-DNA interactions in normal cells are predictive of fusion RNAs, we analyzed these in a validation cohort of 96 lung cancer samples using RNA sequencing (RNA-seq). Thirty-seven of 42 fusion transcripts in the validation cohort were found to exhibit RNA-DNA interactions in normal cells. Finally, by combining RNA-seq, single-molecule RNA FISH, and DNA FISH, we detected a cancer sample with EML4-ALK fusion RNA without forming the EML4-ALK fusion gene. Collectively, these data suggest an RNA-poise model, where spatial proximity of RNA and DNA could poise for the creation of fusion transcripts.
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