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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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2
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Liu D, Li J, Hao W, Lin X, Xia J, Zhu J, Yang S, Yang X. Chimeric RNA TNNI2-ACTA1-V1 Regulates Cell Proliferation by Regulating the Expression of NCOA3. Front Vet Sci 2022; 9:895190. [PMID: 35898549 PMCID: PMC9309209 DOI: 10.3389/fvets.2022.895190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Chimeric RNA is a crucial target for tumor diagnosis and drug therapy, also having its unique biological role in normal tissues. TNNI2-ACTA1-V1 (TA-V1), a chimeric RNA discovered by our laboratory in porcine muscle tissue, can inhibit the proliferation of Porcine Skeletal Muscle Satellite Cells (PSCs). The regulatory mechanism of TA-V1 in PSCs remains unclear, but we speculate that NCOA3, DDR2 and RDX may be the target genes of TA-V1. In this study, we explored the effects of NCOA3, DDR2 and RDX on cell viability and cell proliferation by CCK-8 assay, EdU staining and flow cytometry. Furthermore, the regulatory pathway of proliferation in PSCs mediated by TA-V1 through NCOA3 or CyclinD1 was elucidated by co-transfection and co-immunoprecipitation (Co-IP). The results revealed that overexpression of NCOA3 significantly increased cell viability and the expression level of CyclinD1, and also promotes cell proliferation by changing cells from the G1 phase to the S phase. In addition, inhibiting the expression of NCOA3 substantially reduced cell viability and inhibited cell proliferation. Overexpression of DDR2 and RDX had no significant effect on cell viability and proliferation. Co-transfection experiments showed that NCOA3 could rescue the proliferation inhibition of PSCs caused by TA-V1. Co-IP assay indicated that TA-V1 directly interacts with NCOA3. Our study explores the hypothesis that TA-V1 directly regulates NCOA3, indirectly regulating CyclinD1, thereby regulating PSCs proliferation. We provide new putative mechanisms of porcine skeletal muscle growth and lay the foundation for the study of chimeric RNA in normal tissues.
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Xie Z, Janczyk PL, Shi X, Wang Q, Singh S, Cornelison R, Xu J, Mandell JW, Barr FG, Li H. Rhabdomyosarcomas are oncogene addicted to the activation of AVIL. Proc Natl Acad Sci U S A 2022; 119:e2118048119. [PMID: 37146302 PMCID: PMC9214494 DOI: 10.1073/pnas.2118048119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/11/2022] [Indexed: 11/23/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is one of the most common pediatric soft-tissue cancer. Previously, we discovered a gene fusion, MARS-AVIL formed by chromosomal inversion in RMS. Suspecting that forming a fusion with a housekeeping gene may be one of the mechanisms to dysregulate an oncogene, we investigated AVIL expression and its role in RMS. We first showed that MARS-AVIL translates into an in-frame fusion protein, which is critical for RMS cell tumorigenesis. Besides forming a gene fusion with the housekeeping gene, MARS, the AVIL locus is often amplified, and its RNA and protein expression are overexpressed in the majority of RMSs. Tumors with AVIL dysregulation exhibit evidence of oncogene addiction: Silencing MARS-AVIL in cells harboring the fusion, or silencing AVIL in cells with AVIL overexpression, nearly eradicated the cells in culture, as well as inhibited in vivo xenograft growth in mice. Conversely, gain-of-function manipulations of AVIL led to increased cell growth and migration, enhanced foci formation in mouse fibroblasts, and most importantly transformed mesenchymal stem cells in vitro and in vivo. Mechanistically, AVIL seems to serve as a converging node functioning upstream of two oncogenic pathways, PAX3-FOXO1 and RAS, thus connecting two types of RMS associated with these pathways. Interestingly, AVIL is overexpressed in other sarcoma cells as well, and its expression correlates with clinical outcomes, with higher levels of AVIL expression being associated with worse prognosis. AVIL is a bona fide oncogene in RMS, and RMS cells are addicted to its activity.
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Affiliation(s)
- Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Pawel L. Janczyk
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Xinrui Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Qiong Wang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Urology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Robert Cornelison
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Jingjing Xu
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - James W. Mandell
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
| | - Frederic G. Barr
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908
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4
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Sun Y, Li H. Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases. Genes (Basel) 2022; 13:genes13050741. [PMID: 35627126 PMCID: PMC9140685 DOI: 10.3390/genes13050741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Chimeric RNAs are transcripts that are generated by gene fusion and intergenic splicing events, thus comprising nucleotide sequences from different parental genes. In the past, Northern blot analysis and RT-PCR were used to detect chimeric RNAs. However, they are low-throughput and can be time-consuming, labor-intensive, and cost-prohibitive. With the development of RNA-seq and transcriptome analyses over the past decade, the number of chimeric RNAs in cancer as well as in rare inherited diseases has dramatically increased. Chimeric RNAs may be potential diagnostic biomarkers when they are specifically expressed in cancerous cells and/or tissues. Some chimeric RNAs can also play a role in cell proliferation and cancer development, acting as tools for cancer prognosis, and revealing new insights into the cell origin of tumors. Due to their abilities to characterize a whole transcriptome with a high sequencing depth and intergenically identify spliced chimeric RNAs produced with the absence of chromosomal rearrangement, RNA sequencing has not only enhanced our ability to diagnose genetic diseases, but also provided us with a deeper understanding of these diseases. Here, we reviewed the mechanisms of chimeric RNA formation and the utility of RNA sequencing for discovering chimeric RNAs in several types of cancer and rare inherited diseases. We also discussed the diagnostic, prognostic, and therapeutic values of chimeric RNAs.
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Affiliation(s)
- Yunan Sun
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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Yurchenko AA, Pop OT, Ighilahriz M, Padioleau I, Rajabi F, Sharpe HJ, Poulalhon N, Dreno B, Khammari A, Delord M, Alberti A, Soufir N, Battistella M, Mourah S, Bouquet F, Savina A, Besse A, Mendez-Lopez M, Grange F, Monestier S, Mortier L, Meyer N, Dutriaux C, Robert C, Saiag P, Herms F, Lambert J, de Sauvage FJ, Dumaz N, Flatz L, Basset-Seguin N, Nikolaev SI. Frequency and Genomic Aspects of Intrinsic Resistance to Vismodegib in Locally Advanced Basal Cell Carcinoma. Clin Cancer Res 2022; 28:1422-1432. [PMID: 35078858 PMCID: PMC9365352 DOI: 10.1158/1078-0432.ccr-21-3764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/03/2021] [Accepted: 01/20/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Vismodegib is approved for the treatment of locally advanced basal cell carcinoma (laBCC), but some cases demonstrate intrinsic resistance (IR) to the drug. We sought to assess the frequency of IR to vismodegib in laBCC and its underlying genomic mechanisms. EXPERIMENTAL DESIGN Response to vismodegib was evaluated in a cohort of 148 laBCC patients. Comprehensive genomic and transcriptomic profiling was performed in a subset of five intrinsically resistant BCC (IR-BCC). RESULTS We identified that IR-BCC represents 6.1% of laBCC in the studied cohort. Prior treatment with chemotherapy was associated with IR. Genetic events that were previously associated with acquired resistance (AR) in BCC or medulloblastoma were observed in three out of five IR-BCC. However, IR-BCCs were distinct by highly rearranged polyploid genomes. Functional analyses identified hyperactivation of the HIPPO-YAP and WNT pathways at RNA and protein levels in IR-BCC. In vitro assay on the BCC cell line further confirmed that YAP1 overexpression increases the cell proliferation rate. CONCLUSIONS IR to vismodegib is a rare event in laBCC. IR-BCCs frequently harbor resistance mutations in the Hh pathway, but also are characterized by hyperactivation of the HIPPO-YAP and WNT pathways.
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Affiliation(s)
- Andrey A. Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Oltin T. Pop
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | | | - Ismael Padioleau
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Fatemeh Rajabi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | | | - Nicolas Poulalhon
- Service de dermatologie, Hôpital Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Brigitte Dreno
- Department of Dermato-Oncology, CHU Nantes, Nantes Université, CIC 1413, Inserm UMR 1302/EMR6001 INCIT, F-44000 Nantes, France
| | - Amir Khammari
- Department of Dermato-Oncology, CHU Nantes, Nantes Université, CIC 1413, Inserm UMR 1302/EMR6001 INCIT, F-44000 Nantes, France
| | - Marc Delord
- Université de Paris, Hôpital Saint-Louis, Paris, France.,Department of Population Health Sciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | | | - Maxime Battistella
- INSERM U976, Hôpital Saint-Louis, Paris, France.,Université de Paris, Hôpital Saint-Louis, Paris, France.,Service d'anatomie pathologique, Hôpital Saint-Louis, Claude Vellefaux, Paris, France
| | - Samia Mourah
- INSERM U976, Hôpital Saint-Louis, Paris, France.,Université de Paris, Hôpital Saint-Louis, Paris, France.,Département de Génomique des Tumeurs Solides, Hôpital Saint-Louis, Claude Vellefaux, Paris, France
| | | | | | - Andrej Besse
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Max Mendez-Lopez
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Florent Grange
- Service de dermatologie, CHU Reims, Rue du general Koenig, Reims, France.,Service de Dermatologie, centre hospitalier de Valence, Valence, France
| | | | - Laurent Mortier
- Service de dermatologie, CHU Lille, Clin Dermato Hop Huriez, Rue Michel Polonovski, Lille, France
| | - Nicolas Meyer
- Service de dermatologie, Institut Univeristaire du Cancer et CHU de Toulouse, Hôpital Larrey, Toulouse, France
| | | | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Department of Medical Oncology, Gustave Roussy and Paris-Saclay University, Villejuif, France
| | - Philippe Saiag
- Department of General and Oncologic Dermatology, Ambroise-Paré hospital, APHP, and EA 4340 “Biomarkers in Cancerology and Hemato-oncology,” UVSQ, Université Paris-Saclay, Boulogne-Billancourt, France
| | - Florian Herms
- Service de dermatologie, Hôpital Saint-Louis, Paris, France
| | - Jerome Lambert
- Université de Paris, Hôpital Saint-Louis, Paris, France.,Service de Biostatistique et Information Médicale, Hôpital Saint-Louis, Paris, France
| | | | | | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Nicole Basset-Seguin
- INSERM U976, Hôpital Saint-Louis, Paris, France.,Université de Paris, Hôpital Saint-Louis, Paris, France.,Service de dermatologie, Hôpital Saint-Louis, Paris, France.,Corresponding Authors: Sergey I. Nikolaev, U981 INSERM, Institut Gustave Roussy, 114 rue Edouard Vaillant, 94800 Villejuif, France. Phone: 33-142115775; E-mail: ; and Nicole Basset-Seguin, Service de dermatologie, unité d'oncodermatologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris. Phone: 33-153722066; Fax: 33-142355310; E-mail:
| | - Sergey I. Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Corresponding Authors: Sergey I. Nikolaev, U981 INSERM, Institut Gustave Roussy, 114 rue Edouard Vaillant, 94800 Villejuif, France. Phone: 33-142115775; E-mail: ; and Nicole Basset-Seguin, Service de dermatologie, unité d'oncodermatologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris. Phone: 33-153722066; Fax: 33-142355310; E-mail:
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6
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Pitolli C, Marini A, Sette C, Pagliarini V. Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer. Int J Mol Sci 2022; 23:ijms23052811. [PMID: 35269953 PMCID: PMC8911335 DOI: 10.3390/ijms23052811] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Alberto Marini
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
- Correspondence:
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Pillozzi S, Bernini A, Palchetti I, Crociani O, Antonuzzo L, Campanacci D, Scoccianti G. Soft Tissue Sarcoma: An Insight on Biomarkers at Molecular, Metabolic and Cellular Level. Cancers (Basel) 2021; 13:cancers13123044. [PMID: 34207243 PMCID: PMC8233868 DOI: 10.3390/cancers13123044] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Soft tissue sarcoma is a rare mesenchymal malignancy. Despite the advancements in the fields of radiology, pathology and surgery, these tumors often recur locally and/or with metastatic disease. STS is considered to be a diagnostic challenge due to the large variety of histological subtypes with clinical and histopathological characteristics which are not always distinct. One of the important clinical problems is a lack of useful biomarkers. Therefore, the discovery of biomarkers that can be used to detect tumors or predict tumor response to chemotherapy or radiotherapy could help clinicians provide more effective clinical management. Abstract Soft tissue sarcomas (STSs) are a heterogeneous group of rare tumors. Although constituting only 1% of all human malignancies, STSs represent the second most common type of solid tumors in children and adolescents and comprise an important group of secondary malignancies. Over 100 histologic subtypes have been characterized to date (occurring predominantly in the trunk, extremity, and retroperitoneum), and many more are being discovered due to molecular profiling. STS mortality remains high, despite adjuvant chemotherapy. New prognostic stratification markers are needed to help identify patients at risk of recurrence and possibly apply more intensive or novel treatments. Recent scientific advancements have enabled a more precise molecular characterization of sarcoma subtypes and revealed novel therapeutic targets and prognostic/predictive biomarkers. This review aims at providing a comprehensive overview of the most relevant cellular, molecular and metabolic biomarkers for STS, and highlight advances in STS-related biomarker research.
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Affiliation(s)
- Serena Pillozzi
- Medical Oncology Unit, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy;
- Correspondence:
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
| | - Ilaria Palchetti
- Department of Chemistry Ugo Schiff, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy;
| | - Olivia Crociani
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy;
| | - Lorenzo Antonuzzo
- Medical Oncology Unit, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy;
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy;
| | - Domenico Campanacci
- Department of Health Science, University of Florence, Largo Brambilla 3, 50134 Florence, Italy;
| | - Guido Scoccianti
- Department of Orthopaedic Oncology and Reconstructive Surgery, University of Florence, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy;
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8
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Ou MY, Xiao Q, Ju XC, Zeng PM, Huang J, Sheng AL, Luo ZG. The CTNNBIP1-CLSTN1 fusion transcript regulates human neocortical development. Cell Rep 2021; 35:109290. [PMID: 34192541 DOI: 10.1016/j.celrep.2021.109290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/17/2021] [Accepted: 06/02/2021] [Indexed: 12/21/2022] Open
Abstract
Fusion transcripts or RNAs have been found in both disordered and healthy human tissues and cells; however, their physiological functions in the brain development remain unknown. In the analysis of deposited RNA-sequence libraries covering early to middle embryonic stages, we identify 1,055 fusion transcripts present in the developing neocortex. Interestingly, 98 fusion transcripts exhibit distinct expression patterns in various neural progenitors (NPs) or neurons. We focus on CTNNBIP1-CLSTN1 (CTCL), which is enriched in outer radial glial cells that contribute to cortex expansion during human evolution. Intriguingly, downregulation of CTCL in cultured human cerebral organoids causes marked reduction in NPs and precocious neuronal differentiation, leading to impairment of organoid growth. Furthermore, the expression of CTCL fine-tunes Wnt/β-catenin signaling that controls cortex patterning. Together, this work provides evidence indicating important roles of fusion transcript in human brain development and evolution.
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Affiliation(s)
- Min-Yi Ou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Xiao
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang-Chun Ju
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Peng-Ming Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ai-Li Sheng
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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9
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Adamus A, Ali I, Vasileiadis V, Al-Hileh L, Lisec J, Frank M, Seitz G, Engel N. Vincetoxicum arnottianum modulates motility features and metastatic marker expression in pediatric rhabdomyosarcoma by stabilizing the actin cytoskeleton. BMC Complement Med Ther 2021; 21:136. [PMID: 33947373 PMCID: PMC8097906 DOI: 10.1186/s12906-021-03299-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/07/2021] [Indexed: 12/28/2022] Open
Abstract
Background Prevention of metastatic invasion is one of the main challenges in the treatment of alveolar rhabdomyosarcoma. Still the therapeutic options are limited. Therefore, an anti-tumor screening was initiated focusing on the anti-metastatic and anti-invasion properties of selected medicinal plant extracts and phytoestrogens, already known to be effective in the prevention and treatment of different cancer entities. Methods Treatment effects were first evaluated by cell viability, migration, invasion, and colony forming assays on the alveolar rhabdomyosarcoma cell line RH-30 in comparison with healthy primary cells. Results Initial anti-tumor screenings of all substances analyzed in this study, identified the plant extract of Vincetoxicum arnottianum (VSM) as the most promising candidate, harboring the highest anti-metastatic potential. Those significant anti-motility properties were proven by a reduced ability for migration (60%), invasion (99%) and colony formation (61%) under 48 h exposure to 25 μg/ml VSM. The restricted motility features were due to an induction of the stabilization of the cytoskeleton – actin fibers were 2.5-fold longer and were spanning the entire cell. Decreased proliferation (PCNA, AMT, GCSH) and altered metastasis (e. g. SGPL1, CXCR4, stathmin) marker expression on transcript and protein level confirmed the significant lowered tumorigenicity under VSM treatment. Finally, significant alterations in the cell metabolism were detected for 25 metabolites, with levels of uracil, N-acetyl serine and propanoyl phosphate harboring the greatest alterations. Compared to the conventional therapy with cisplatin, VSM treated cells demonstrated a similar metabolic shutdown of the primary cell metabolism. Primary control cells were not affected by the VSM treatment. Conclusions This study revealed the VSM root extract as a potential, new migrastatic drug candidate for the putative treatment of pediatric alveolar rhabdomyosarcoma with actin filament stabilizing properties and accompanied by a marginal effect on the vitality of primary cells. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03299-x.
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Affiliation(s)
- Anna Adamus
- Department of Pediatric Surgery, University Hospital, Marburg, Germany
| | - Iftikhar Ali
- Department of Chemistry, Karakoram International University, Gilgit, Pakistan.,Shandong Key Laboratory of TCM Quality Control Technology, Shandong Analysis and Test Center, Jinan, Shandong Province, P.R. China
| | | | - Luai Al-Hileh
- Department of Pediatric Surgery, University Hospital, Marburg, Germany
| | - Jan Lisec
- Division 1.7 Analytical Chemistry, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Marcus Frank
- Medical Biology and Electron Microscopy Center, Rostock University Medical Center, Rostock, Germany.,Department of Life, Light & Matter, University of Rostock, Rostock, Germany
| | - Guido Seitz
- Department of Pediatric Surgery, University Hospital, Marburg, Germany
| | - Nadja Engel
- Department of Oral and Maxillofacial Surgery, Facial Plastic Surgery, Rostock University Medical Center, Rostock, Germany.
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10
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Wang L, Xiong X, Yao Z, Zhu J, Lin Y, Lin W, Li K, Xu X, Guo Y, Chen Y, Pan Y, Zhou F, Fan J, Chen Y, Gao S, Jim Yeung SC, Zhang H. Chimeric RNA ASTN2-PAPPA as aggravates tumor progression and metastasis in human esophageal cancer. Cancer Lett 2021; 501:1-11. [PMID: 33388371 DOI: 10.1016/j.canlet.2020.10.052] [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: 07/31/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 02/05/2023]
Abstract
Transcription-induced chimeric RNAs are an emerging area of research into molecular signatures for disease biomarker and therapeutic target development. Despite their importance, little is known for chimeric RNAs-relevant roles and the underlying mechanisms for cancer pathogenesis and progression. Here we describe a unique ASTN2-PAPPAantisense chimeric RNA (A-PaschiRNA) that could be the first reported chimeric RNA derived from the splicing of exons and intron antisense of two neighboring genes, respectively. Aberrant A-PaschiRNA level in ESCC tissues was associated with tumor progression and patients' outcome. In vitro and in vivo studies demonstrated that A-PaschiRNA aggravated ESCC metastasis and enhanced stemness through modulating OCT4. Mechanistic studies demonstrated that ERK5-mediated non-canonical PAF1 activity was required for A-PaschiRNA-induced cancer malignancy. The study defined an undocumented function of chimeric RNAs in aggravating cancer stemness and metastasis.
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Affiliation(s)
- Lu Wang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiao Xiong
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Zhimeng Yao
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jianlin Zhu
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Yusheng Lin
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China; Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Wan Lin
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Kai Li
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiaozheng Xu
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yi Guo
- Endoscopy Center, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yuping Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Fuyou Zhou
- The Fourth Affiliated Hospital of Henan University of Science and Technology, Anyang, Henan, 455001, China; Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, Henan, 455001, China
| | - Jun Fan
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yan Chen
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Shegan Gao
- College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Henan Key Laboratory of Cancer Epigenetics, Luoyang, 471003, China.
| | - Sai-Ching Jim Yeung
- Department of Emergency Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China.
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11
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Abstract
Our work in rhabdomyosarcoma led us to the discovery of a novel oncogene, Advillin (AVIL) in glioblastoma. Multiple lines of evidence support that AVIL is an Achilles heel of glioblastoma, with its specific targeting potentially an effective treatment approach for the disease. A new signaling axis was also established.
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Affiliation(s)
- Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
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12
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Xie Z, Janczyk PŁ, Zhang Y, Liu A, Shi X, Singh S, Facemire L, Kubow K, Li Z, Jia Y, Schafer D, Mandell JW, Abounader R, Li H. A cytoskeleton regulator AVIL drives tumorigenesis in glioblastoma. Nat Commun 2020; 11:3457. [PMID: 32651364 PMCID: PMC7351761 DOI: 10.1038/s41467-020-17279-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma is a deadly cancer, with no effective therapies. Better understanding and identification of selective targets are urgently needed. We found that advillin (AVIL) is overexpressed in all the glioblastomas we tested including glioblastoma stem/initiating cells, but hardly detectable in non-neoplastic astrocytes, neural stem cells or normal brain. Glioma patients with increased AVIL expression have a worse prognosis. Silencing AVIL nearly eradicated glioblastoma cells in culture, and dramatically inhibited in vivo xenografts in mice, but had no effect on normal control cells. Conversely, overexpressing AVIL promoted cell proliferation and migration, enabled fibroblasts to escape contact inhibition, and transformed immortalized astrocytes, supporting AVIL being a bona fide oncogene. We provide evidence that the tumorigenic effect of AVIL is partly mediated by FOXM1, which regulates LIN28B, whose expression also correlates with clinical prognosis. AVIL regulates the cytoskeleton through modulating F-actin, while mutants disrupting F-actin binding are defective in its tumorigenic capabilities. Genes that modulate the cytoskeleton have been associated with increased cell proliferation and migration. Here, the authors show that AVIL, an actin regulatory protein, is overexpressed in glioblastomas and mediates oncogenic effects through regulation of FOXM1 stability and LIN28B expression.
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Affiliation(s)
- Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Pawel Ł Janczyk
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ying Zhang
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Aiqun Liu
- Tumor Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Xinrui Shi
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Loryn Facemire
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Kristopher Kubow
- Department of Biology, James Madison University, Harrisonburg, VA, 22807, USA
| | - Zi Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yuemeng Jia
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Dorothy Schafer
- Department of Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - James W Mandell
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Roger Abounader
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA. .,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
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13
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Elfman J, Pham LP, Li H. The relationship between chimeric RNAs and gene fusions: Potential implications of reciprocity in cancer. J Genet Genomics 2020; 47:341-348. [PMID: 33008771 DOI: 10.1016/j.jgg.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Justin Elfman
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA
| | - Lam-Phong Pham
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA.
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14
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Wu H, Singh S, Xie Z, Li X, Li H. Landscape characterization of chimeric RNAs in colorectal cancer. Cancer Lett 2020; 489:56-65. [PMID: 32534173 DOI: 10.1016/j.canlet.2020.05.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/31/2022]
Abstract
Gene fusions and their fusion products have been recognized as ideal biomarkers and drug targets for cancer. However, few recurrent gene fusions were found in colorectal cancer (CRC), despite comprehensive studies. We believe that chimeric RNAs, in the absence of chromosomal rearrangement, may represent a new repertoire of biomarkers and/or therapeutic targets in CRC. In this study, we aim to identify such recurrent chimeric RNAs, and investigate their clinical implications. To do so, we performed extensive data mining for chimeric RNAs using The Cancer Genome Atlas CRC RNA-Seq datasets. Multiple filtering criteria were applied, and the landscape of chimeric RNAs at multiple levels, from various angles, was analyzed. Eleven frequent, cancer biased chimeric RNAs were validated. The expression of RRM2-C2orf48 correlates with poor clinical outcomes, while the expression of parental RRM2 and C2orf48 correlates with positive clinical outcomes. Mechanistically, it is a product of cis-splicing between adjacent genes. Silencing of RRM2-C2orf48 resulted in reduced cellular proliferation in colon cancer cells, whereas overexpressed chimera promoted cell proliferation. These findings suggest that frequent chimeric RNAs are present in CRCs, and that chimeric RNAs may have different expression profiles and functions from parental genes, thus representing a new repertoire of biomarkers and therapeutic targets.
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Affiliation(s)
- Hao Wu
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, China; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA; Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
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15
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Heyer EE, Blackburn J. Sequencing Strategies for Fusion Gene Detection. Bioessays 2020; 42:e2000016. [DOI: 10.1002/bies.202000016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Erin E. Heyer
- The Kinghorn Cancer CentreGarvan Institute of Medical Research 384 Victoria Street Darlinghurst NSW 2010 Australia
| | - James Blackburn
- The Kinghorn Cancer CentreGarvan Institute of Medical Research 384 Victoria Street Darlinghurst NSW 2010 Australia
- Faculty of Medicine, St. Vincent's Clinical SchoolUNSW, St Vincent's Hospital Victoria Street Darlinghurst NSW 2010 Australia
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16
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Singh S, Qin F, Kumar S, Elfman J, Lin E, Pham LP, Yang A, Li H. The landscape of chimeric RNAs in non-diseased tissues and cells. Nucleic Acids Res 2020; 48:1764-1778. [PMID: 31965184 PMCID: PMC7038929 DOI: 10.1093/nar/gkz1223] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/13/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Shailesh Kumar
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Justin Elfman
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Lam-Phong Pham
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Amy Yang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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17
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Abstract
Chimeric RNAs as well as their fused protein products have therapeutic applications ranging from diagnostics to being used as therapeutic target. Many algorithms have been developed to identify chimeric RNAs, however, identification and validation of fused protein product of the chimeric RNA is still an emerging field. These chimeric proteins can be validated by searching and identifying them in publicly available proteomics datasets. Here we describe the detailed steps for (1) downloading and processing publicly available proteomics datasets, (2) developing fusion peptide database by performing in silico tryptic digestion of chimeric proteins, and (3) software used to identify chimeric peptides in the proteomics data.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA.
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18
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Wu H, Singh S, Shi X, Xie Z, Lin E, Li X, Li H. Functional heritage: the evolution of chimeric RNA into a gene. RNA Biol 2019; 17:125-134. [PMID: 31566065 DOI: 10.1080/15476286.2019.1670038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Once believed to be unique features of neoplasia, chimeric RNAs are now being discovered in normal physiology. We speculated that some chimeric RNAs may be functional precursors of genes, and that forming chimeric RNA at the transcriptional level may be a 'trial' mechanism before the functional element is fixed into the genome. Supporting this idea, we identified a chimeric RNA, HNRNPA1L2-SUGT1 (H-S), whose sequence is highly similar to that of a 'pseudogene' MRPS31P5. Sequence analysis revealed that MRPS31P5 transcript is more similar to H-S chimeric RNA than its 'parent' gene, MRPS31. Evolutionarily, H-S precedes MRPS31P5, as it can be detected bioinformatically and experimentally in marmosets, which do not yet possess MRPS31P5 in their genome. Conversely, H-S is minimally expressed in humans, while instead, MRPS31P5 is abundantly expressed. Silencing H-S in marmoset cells resulted in similar phenotype as silencing MRPS31P5 in human cells. In addition, whole transcriptome analysis and candidate downstream target validation revealed common signalling pathways shared by the two transcripts. Interestingly, H-S failed to rescue the phenotype caused by silencing MPRS31P5 in human and rhesus cells, whereas MRPS31P5 can at least partially rescue the phenotype caused by silencing H-S in marmoset cells, suggesting that MRPS31P5 may have further evolved into a distinct entity. Thus, multiple lines of evidence support that MRPS31P5 is not truly a pseudogene of MRPS31, but a likely functional descendent of H-S chimera. Instead being a gene fusion product, H-S is a product of cis-splicing between adjacent genes, while MRPS31P5 is likely produced by genome rearrangement.
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Affiliation(s)
- Hao Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China.,Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Xinrui Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
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19
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Thoenen E, Curl A, Iwakuma T. TP53 in bone and soft tissue sarcomas. Pharmacol Ther 2019; 202:149-164. [PMID: 31276706 DOI: 10.1016/j.pharmthera.2019.06.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022]
Abstract
Genomic and functional study of existing and emerging sarcoma targets, such as fusion proteins, chromosomal aberrations, reduced tumor suppressor activity, and oncogenic drivers, is broadening our understanding of sarcomagenesis. Among these mechanisms, the tumor suppressor p53 (TP53) plays significant roles in the suppression of bone and soft tissue sarcoma progression. Although mutations in TP53 were thought to be relatively low in sarcomas, modern techniques including whole-genome sequencing have recently illuminated unappreciated alterations in TP53 in osteosarcoma. In addition, oncogenic gain-of-function activities of missense mutant p53 (mutp53) have been reported in sarcomas. Moreover, new targeting strategies for TP53 have been discovered: restoration of wild-type p53 (wtp53) activity through inhibition of TP53 negative regulators, reactivation of the wtp53 activity from mutp53, depletion of mutp53, and targeting of vulnerabilities in cells with TP53 deletions or mutations. These discoveries enable development of novel therapeutic strategies for therapy-resistant sarcomas. We have outlined nine bone and soft tissue sarcomas for which TP53 plays a crucial tumor suppressive role. These include osteosarcoma, Ewing sarcoma, chondrosarcoma, rhabdomyosarcoma (RMS), leiomyosarcoma (LMS), synovial sarcoma, liposarcoma (LPS), angiosarcoma, and undifferentiated pleomorphic sarcoma (UPS).
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Affiliation(s)
- Elizabeth Thoenen
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66010, USA
| | - Amanda Curl
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66010, USA
| | - Tomoo Iwakuma
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66010, USA; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66010, USA; Translational Laboratory Oncology Research, Children's Mercy Research Institute, Kansas City, MO 64108, USA.
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20
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Tang Y, Ma S, Wang X, Xing Q, Huang T, Liu H, Li Q, Zhang Y, Zhang K, Yao M, Yang GL, Li H, Zang X, Yang B, Guan F. Identification of chimeric RNAs in human infant brains and their implications in neural differentiation. Int J Biochem Cell Biol 2019; 111:19-26. [DOI: 10.1016/j.biocel.2019.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/06/2019] [Accepted: 03/30/2019] [Indexed: 02/07/2023]
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21
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A comparison of adult rhabdomyosarcoma and high-grade neuroendocrine carcinoma of the urinary bladder reveals novel PPP1R12A fusions in rhabdomyosarcoma. Hum Pathol 2019; 88:48-59. [PMID: 30946934 DOI: 10.1016/j.humpath.2019.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/10/2019] [Accepted: 03/14/2019] [Indexed: 01/21/2023]
Abstract
Some rhabdomyosarcomas and sarcomatoid carcinomas with heterologous rhabdomyosarcomatous elements resemble high-grade neuroendocrine carcinoma, creating a diagnostic difficulty. The purpose of this study was to characterize the overlap of adult genitourinary rhabdomyosarcomas, excluding those occurring at paratesticular sites, with high-grade neuroendocrine carcinoma and identify features helpful in their separation. Seventeen cases of rhabdomyosarcoma (11 from the urinary bladder and 3 each from kidney and prostate) were compared to 10 cases of high-grade neuroendocrine carcinoma from the urinary bladder. These tumors were analyzed by immunohistochemistry for desmin, MyoD1, myogenin, chromogranin, synaptophysin, CD56, TTF1, and ASCL1, and RNA sequencing was performed on 4 cases of bladder rhabdomyosarcoma (2 rhabdomyosarcomas and 2 sarcomatoid-rhabdomyosarcoma) and 10 cases of bladder high-grade neuroendocrine carcinoma. This was compared to public data from 414 typical urothelial carcinomas from The Cancer Genome Atlas dataset. Morphologic and immunophenotypic overlap with high-grade neuroendocrine carcinoma was seen in half of the bladder tumors, which included 4 rhabdomyosarcomas and 2 sarcomatoid rhabdomyosarcomas. RNA sequencing confirmed expression of neuroendocrine markers in these cases (2 rhabdomyosarcomas and 2 sarcomatoid rhabdomyosarcomas). Differential neuroendocrine differentiation was highlighted by ASCL1 protein expression only in high-grade neuroendocrine carcinoma. Moreover, both a pure alveolar rhabdomyosarcoma and sarcomatoid rhabdomyosarcoma of the urinary bladder demonstrated a fusion involving PPP1R12A. In summary, adult rhabdomyosarcomas of the urinary bladder are molecularly distinct from high-grade neuroendocrine carcinomas based on specific patterns of expression of myogenic and epithelial to mesenchymal transition-related transcription factors as well as the presence of a novel PPP1R12A fusion which is seen in a subset of cases.
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22
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Adamus A, Peer K, Ali I, Lisec J, Falodun A, Frank M, Seitz G, Engel N. Berberis orthobotrys - A promising herbal anti-tumorigenic candidate for the treatment of pediatric alveolar rhabdomyosarcoma. JOURNAL OF ETHNOPHARMACOLOGY 2019; 229:262-271. [PMID: 30315865 DOI: 10.1016/j.jep.2018.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/04/2018] [Accepted: 10/07/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Berberis orthobotrys (BORM) is a medical plant with a long history in traditional usage for the treatment of wounds, cancer, gastrointestinal malady and several other diseases. Our previous studies identified the endemic Pakistani plant Berberis orthobotrys Bien. ex Aitch. as promising source for the treatment of breast cancer and osteosarcoma. AIM OF THE STUDY The present study was aimed to evaluate the anti-cancer properties of 26 plant derived extracts and compounds including the methanolic root extract of Berberis orthobotrys (BORM) on pediatric alveolar rhabdomyosarcoma (RMA), which is known to develop drug resistance, metastatic invasion and potential tumor progression. MATERIALS AND METHODS The main anti-tumor activity of BORM was verified by focusing on morphological, cell structural and metabolic alterations via metabolic profiling, cell viability measurements, flow cytometry, western blotting and diverse microscopy-based methods using the human RMA cell line Rh30. RESULTS Exposure of 25 µg/ml BORM exerts an influence on the cell stability, the degradation of oncosomes as well as the shutdown of the metabolic activity of RMA cells, primarily by downregulation of the energy metabolism. Therefore glycyl-aspartic acid and N-acetyl serine decreased moderately, and uracil increased intracellularly. On healthy, non-transformed muscle cells BORM revealed very low metabolic alterations and nearly no cytotoxic impact. Furthermore, BORM is also capable to reduce Rh30 cell migration (~50%) and proliferation (induced G2/M cycle arrest) as well as to initiate apoptosis confirmed by reduced Bcl-2, Bax and PCNA expression and induced PARP-1 cleavage. CONCLUSIONS The study provides the first evidence, that BORM treatment is effective against RMA cells with low side effects on healthy cells.
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Affiliation(s)
- Anna Adamus
- Department of Pediatric Surgery, University Hospital Marburg, Baldingerstraße, 35033 Marburg, Germany
| | - Katharina Peer
- Department of Pediatric Surgery, University Hospital Marburg, Baldingerstraße, 35033 Marburg, Germany
| | - Iftikhar Ali
- Department of Chemistry, Karakoram International University, 15100 Gilgit, Pakistan
| | - Jan Lisec
- Division 1.7 Analytical Chemistry, Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, Berlin 12489 Germany
| | - Abiodun Falodun
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Benin, Benin City 300001, Nigeria
| | - Marcus Frank
- Medical Biology and Electron Microscopy Centre, Rostock University Medical Center, Strempelstraße 14, Rostock 18057, Germany
| | - Guido Seitz
- Department of Pediatric Surgery, University Hospital Marburg, Baldingerstraße, 35033 Marburg, Germany
| | - Nadja Engel
- Department of Pediatric Surgery, University Hospital Marburg, Baldingerstraße, 35033 Marburg, Germany; Department of Oral and Maxillofacial Surgery, Facial Plastic Surgery, Rostock University Medical Center, Schillingallee 35, 18057 Rostock, Germany.
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23
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Chimeric RNA in Cancer and Stem Cell Differentiation. Stem Cells Int 2018; 2018:3178789. [PMID: 30510584 PMCID: PMC6230395 DOI: 10.1155/2018/3178789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/27/2018] [Indexed: 01/05/2023] Open
Abstract
Gene fusions are considered hallmarks of cancer which can be produced by chromosomal rearrangements. These DNA-level fusion events may result in the expression of chimeric RNAs; however, chimeric RNAs can be also produced by intergenic splicing events. Chimeric transcripts created by the latter mechanism are regulated at the transcriptional level and thus present additional modes of action and regulation. They have demonstrated importance in normal cell physiology, and their dysregulation can induce oncogenesis and impact cell differentiation. In this review, we outline proven mechanisms through which intergenically spliced chimeric RNAs are involved in carcinogenesis. We highlight their similarity to canonical chimeric RNAs resulting from gene fusions as well as their unique qualities. Additionally, we review known roles of chimeric RNA in cell differentiation and propose means through which chimeric RNAs may be valuable as stage-specific markers or as targets for expression profiling.
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24
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Nguyen TH, Barr FG. Therapeutic Approaches Targeting PAX3-FOXO1 and Its Regulatory and Transcriptional Pathways in Rhabdomyosarcoma. Molecules 2018; 23:E2798. [PMID: 30373318 PMCID: PMC6278278 DOI: 10.3390/molecules23112798] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is a family of soft tissue cancers that are related to the skeletal muscle lineage and predominantly occur in children and young adults. A specific chromosomal translocation t(2;13)(q35;q14) that gives rise to the chimeric oncogenic transcription factor PAX3-FOXO1 has been identified as a hallmark of the aggressive alveolar subtype of RMS. PAX3-FOXO1 cooperates with additional molecular changes to promote oncogenic transformation and tumorigenesis in various human and murine models. Its expression is generally restricted to RMS tumor cells, thus providing a very specific target for therapeutic approaches for these RMS tumors. In this article, we review the recent understanding of PAX3-FOXO1 as a transcription factor in the pathogenesis of this cancer and discuss recent developments to target this oncoprotein for treatment of RMS.
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Affiliation(s)
| | - Frederic G. Barr
- Laboratory of Pathology, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, USA;
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25
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Tang Y, Qin F, Liu A, Li H. Recurrent fusion RNA DUS4L-BCAP29 in non-cancer human tissues and cells. Oncotarget 2018; 8:31415-31423. [PMID: 28415823 PMCID: PMC5458218 DOI: 10.18632/oncotarget.16329] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 01/09/2023] Open
Abstract
Traditional gene fusions are involved in the development of various neoplasia. DUS4L-BCAP29, a chimeric fusion RNA, has been reported to be a cancer-fusion in prostate and gastric cancer, in addition to playing a tumorigenic role. Here, we showed that the DUS4L-BCAP29 fusion transcript exists in a variety of normal tissues. It is also present in non-cancer epithelial, as well as in fibroblast cell lines. Quantitatively, the fusion transcript has a comparable expression in non-cancerous, gastric and prostate cell lines and tissues as in the cancer cell lines and tissues. The loss-of-function approach as previously reported is not sufficient to prove the functionality of the fusion. On the other hand, the gain-of-function approach showed that overexpression of DUS4L-BCAP29 promotes cell growth and motility, even in non-cancer cells. Finally, we provide further evidence that the fusion transcript is a product of cis-splicing between adjacent genes. In summary, we believe that in contrast to traditional gene fusions, DUS4L-BCAP29 cannot be used as a cancer biomarker. Instead, it is a fusion transcript that exists in normal physiology and that its pro-growth effect is not unique to cancer cells.
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Affiliation(s)
- Yue Tang
- College of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450008, P.R. China.,Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, P.R. China
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Aiqun Liu
- Department of Endoscopy, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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26
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Huang R, Kumar S, Li H. Absence of Correlation between Chimeric RNA and Aging. Genes (Basel) 2017; 8:genes8120386. [PMID: 29240691 PMCID: PMC5748704 DOI: 10.3390/genes8120386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/06/2017] [Accepted: 12/07/2017] [Indexed: 11/16/2022] Open
Abstract
Chimeric RNAs have been recognized as a phenomenon not unique to cancer cells. They also exist in normal physiology. Aging is often characterized by deregulation of molecular and cellular mechanisms, including loss of heterochromatin, increased transcriptional noise, less tight control on alternative splicing, and more stress-induced changes. It is thus assumed that chimeric RNAs are more abundant in older people. In this study, we conducted a preliminary investigation to identify any chimeric RNAs with age-based trends in their expression levels in blood samples. A chimeric RNA candidate list generated by bioinformatic analysis indicated the possibility of both negative and positive trends in the expression of chimeric RNAs. Out of this candidate list, five novel chimeric RNAs were successfully amplified in multiple blood samples and then sequenced. Although primary smaller sample sizes displayed some weak trends with respect to age, analysis of quantitative PCR data from larger sample sizes showed essentially no relationship between expression levels and age. Altogether, these results indicate that, contradictory to the common assumption, chimeric RNAs as a group are not all higher in older individuals and that placing chimeric RNAs in the context of aging will be a much more complex task than initially anticipated.
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Affiliation(s)
- Reyna Huang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| | - Shailesh Kumar
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
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27
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Li Z, Qin F, Li H. Chimeric RNAs and their implications in cancer. Curr Opin Genet Dev 2017; 48:36-43. [PMID: 29100211 DOI: 10.1016/j.gde.2017.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/06/2017] [Accepted: 10/02/2017] [Indexed: 11/26/2022]
Abstract
Chimeric RNAs have been believed to be solely produced by gene fusions resulting from chromosomal rearrangement, thus unique features of cancer. Detected chimeric RNAs have also been viewed as surrogates for the presence of gene fusions. However, more and more research has demonstrated that chimeric RNAs in general are not a hallmark of cancer, but rather widely present in non-cancerous cells and tissues. At the same time, they may be produced by other mechanisms other than chromosomal rearrangement. The field of non-canonical chimeric RNAs is still in its infancy, with many challenges ahead, including the lack of a unified terminology. However, we believe that these non-canonical chimeric RNAs will have significant impacts in cancer detection and treatment.
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Affiliation(s)
- Zi Li
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA; Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Fujun Qin
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.
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28
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Diao S, Zheng Q, Gao J, Yao Y, Ren S, Liu Y, Xu Y. Trefoil factor 3 contributes to the malignancy of glioma via regulating HIF-1α. Oncotarget 2017; 8:76770-76782. [PMID: 29100347 PMCID: PMC5652741 DOI: 10.18632/oncotarget.20010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/27/2017] [Indexed: 12/22/2022] Open
Abstract
Trefoil factor 3 (TFF3) plays significant roles in several solid tumors. However, the expression pattern and function of TFF3 in glioblastoma (GBM) have not been reported. Here, we report that expression level of TFF3 significantly elevated in glioma and correlated with the prognosis of glioma patients. Then we found TFF3 promotes proliferation, invasion, and migration and inhibits apoptosis of glioma cells in vitro, and delayed tumor progression in subcutaneous xenograft nude mice, and prolonged the median survival time in orthotopic xenograft mice. Moreover, knockdown of TFF3 reduced the expression of HIF-1α through a hypoxia-independent manner. These findings suggest that targeting TFF3 may offer a novel strategy for therapeutic intervention of malignant gliomas.
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Affiliation(s)
- Shuo Diao
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
| | - Qianqian Zheng
- Department of Pathophysiology, Basic Medical College, China Medical University, Shenyang, People's Republic of China
| | - Jian Gao
- Center of Laboratory Technology and Experimental Medicine, China Medical University, Shenyang, People's Republic of China
| | - Yiqun Yao
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
| | - Siyang Ren
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
| | - Yongjian Liu
- Department of Interventional Therapy, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
| | - Yinghui Xu
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
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29
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Selfe JL, Shipley J. Fusion gene addiction: can tumours be forced to give up the habit? J Pathol 2017; 242:263-266. [PMID: 28378394 DOI: 10.1002/path.4902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/23/2017] [Indexed: 11/10/2022]
Abstract
Fusion of genes in tumours can have oncogenic roles in reprogramming cells through overexpression of oncogenes or the production of novel fusion proteins. A fundamental question in cancer biology is what genetic events are critical for initiation and whether these are also required for cancer progression. In recent work published in The Journal of Pathology, dependency on a fusion protein was addressed using a model of alveolar rhabdomyosarcomas - a sarcoma subtype with frequent fusion of PAX3 and FOXO1 genes that is associated with poor outcome. PAX3-FOXO1 encodes a potent transcription factor that together with MYCN alters the transcriptional landscape of cells. Building on previous work, an inducible model in human myoblast cells was used to show that PAX3-FOXO1 and MYCN can initiate rhabdomyosarcoma development but, contrary to current thinking, tumour recurrences occasionally arose independent of the fusion protein. Further work needs to identify the molecular nature of this independence and assess any relevance in human tumours. Such functional approaches are required together with computational modeling of molecular data to unravel spatial and temporal dependencies on specific genetic events. This may support molecular prognostic markers and therapeutic targets. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Joanna L Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
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30
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Xie Z, Li H. Fusion RNA profiling provides hints on cell of origin of mysterious tumor. Mol Cell Oncol 2016; 4:e1263714. [PMID: 28197537 DOI: 10.1080/23723556.2016.1263714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 01/06/2023]
Abstract
Biological samples can be grouped into separate clusters based on their gene expression profiles. This approach has yielded meaningful biological insights and facilitated biomarker discoveries. Recently, we developed another approach to study connections between biological samples based on their fusion RNA expression. We have used this approach to provide insights into the cell of origin for a mysterious tumor, alveolar rhabdomyosarcoma.
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Affiliation(s)
- Zhongqiu Xie
- Department of Pathology, University of Virginia , Charlottesville, VA, USA
| | - Hui Li
- Department of Pathology, University of Virginia, Charlottesville, VA, USA; University of Virginia Cancer Center, Charlottesville, VA, USA
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