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Singh S, Li H. Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing. RNA Biol 2021; 18:254-267. [PMID: 34142643 DOI: 10.1080/15476286.2021.1940047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Chimeric RNAs are gaining more and more attention as they have broad implications in both cancer and normal physiology. To date, over 40 chimeric RNA prediction methods have been developed to facilitate their identification from RNA sequencing data. However, a limited number of studies have been conducted to compare the performance of these tools; additionally, previous studies have become outdated as more software tools have been developed within the last three years. In this study, we benchmarked 16 chimeric RNA prediction software, including seven top performers in previous benchmarking studies, and nine that were recently developed. We used two simulated and two real RNA-Seq datasets, compared the 16 tools for their sensitivity, positive prediction value (PPV), F-measure, and also documented the computational requirements (time and memory). We noticed that none of the tools are inclusive, and their performance varies depending on the dataset and objects. To increase the detection of true positive events, we also evaluated the pair-wise combination of these methods to suggest the best combination for sensitivity and F-measure. In addition, we compared the performance of the tools for the identification of three classes (read-through, inter-chromosomal and intra-others) of chimeric RNAs. Finally, we performed TOPSIS analyses and ranked the weighted performance of the 16 tools.
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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.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
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2
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Padella A, Simonetti G, Paciello G, Giotopoulos G, Baldazzi C, Righi S, Ghetti M, Stengel A, Guadagnuolo V, De Tommaso R, Papayannidis C, Robustelli V, Franchini E, Ghelli Luserna di Rorà A, Ferrari A, Fontana MC, Bruno S, Ottaviani E, Soverini S, Storlazzi CT, Haferlach C, Sabattini E, Testoni N, Iacobucci I, Huntly BJP, Ficarra E, Martinelli G. Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia. Cancers (Basel) 2019; 11:E1951. [PMID: 31817495 PMCID: PMC6966504 DOI: 10.3390/cancers11121951] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately 18% of acute myeloid leukemia (AML) cases express a fusion transcript. However, few fusions are recurrent across AML and the identification of these rare chimeras is of interest to characterize AML patients. Here, we studied the transcriptome of 8 adult AML patients with poorly described chromosomal translocation(s), with the aim of identifying novel and rare fusion transcripts. We integrated RNA-sequencing data with multiple approaches including computational analysis, Sanger sequencing, fluorescence in situ hybridization and in vitro studies to assess the oncogenic potential of the ZEB2-BCL11B chimera. We detected 7 different fusions with partner genes involving transcription factors (OAZ-MAFK, ZEB2-BCL11B), tumor suppressors (SAV1-GYPB, PUF60-TYW1, CNOT2-WT1) and rearrangements associated with the loss of NF1 (CPD-PXT1, UTP6-CRLF3). Notably, ZEB2-BCL11B rearrangements co-occurred with FLT3 mutations and were associated with a poorly differentiated or mixed phenotype leukemia. Although the fusion alone did not transform murine c-Kit+ bone marrow cells, 45.4% of 14q32 non-rearranged AML cases were also BCL11B-positive, suggesting a more general and complex mechanism of leukemogenesis associated with BCL11B expression. Overall, by combining different approaches, we described rare fusion events contributing to the complexity of AML and we linked the expression of some chimeras to genomic alterations hitting known genes in AML.
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Affiliation(s)
- Antonella Padella
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Giorgia Simonetti
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Giulia Paciello
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino, 10129 Turin, Italy; (G.P.); (E.F.)
| | - George Giotopoulos
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, UK; (G.G.); (B.J.P.H.)
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke’s Hospital, University of Cambridge, Cambridge CB2 0XY, UK
| | - Carmen Baldazzi
- Institute of Hematology “L. and A. Seràgnoli”, Sant’Orsola-Malpighi University Hospital, 40138 Bologna, Italy;
| | - Simona Righi
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Martina Ghetti
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Anna Stengel
- MLL-Munich Leukemia Laboratory, 81377 Munich, Germany; (A.S.); (C.H.)
| | - Viviana Guadagnuolo
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Rossella De Tommaso
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Valentina Robustelli
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Eugenia Franchini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Andrea Ghelli Luserna di Rorà
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Anna Ferrari
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Maria Chiara Fontana
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Samantha Bruno
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Emanuela Ottaviani
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Simona Soverini
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | | | - Claudia Haferlach
- MLL-Munich Leukemia Laboratory, 81377 Munich, Germany; (A.S.); (C.H.)
| | - Elena Sabattini
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Nicoletta Testoni
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Brian J. P. Huntly
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, UK; (G.G.); (B.J.P.H.)
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke’s Hospital, University of Cambridge, Cambridge CB2 0XY, UK
| | - Elisa Ficarra
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino, 10129 Turin, Italy; (G.P.); (E.F.)
| | - Giovanni Martinelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
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Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol 2019; 20:213. [PMID: 31639029 PMCID: PMC6802306 DOI: 10.1186/s13059-019-1842-9] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/28/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA-seq, based on either read mapping or de novo fusion transcript assembly. RESULTS We benchmark 23 different methods including applications we develop, STAR-Fusion and TrinityFusion, leveraging both simulated and real RNA-seq. Overall, STAR-Fusion, Arriba, and STAR-SEQR are the most accurate and fastest for fusion detection on cancer transcriptomes. CONCLUSION The lower accuracy of de novo assembly-based methods notwithstanding, they are useful for reconstructing fusion isoforms and tumor viruses, both of which are important in cancer research.
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Affiliation(s)
- Brian J. Haas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA
| | - Bo Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129 USA
| | | | - Nathalie Pochet
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Howard Hughes Medical Institute, and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140 USA
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He Y, Yuan C, Chen L, Lei M, Zellmer L, Huang H, Liao DJ. Transcriptional-Readthrough RNAs Reflect the Phenomenon of "A Gene Contains Gene(s)" or "Gene(s) within a Gene" in the Human Genome, and Thus Are Not Chimeric RNAs. Genes (Basel) 2018; 9:E40. [PMID: 29337901 PMCID: PMC5793191 DOI: 10.3390/genes9010040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/29/2017] [Accepted: 01/07/2018] [Indexed: 02/06/2023] Open
Abstract
Tens of thousands of chimeric RNAs, i.e., RNAs with sequences of two genes, have been identified in human cells. Most of them are formed by two neighboring genes on the same chromosome and are considered to be derived via transcriptional readthrough, but a true readthrough event still awaits more evidence and trans-splicing that joins two transcripts together remains as a possible mechanism. We regard those genomic loci that are transcriptionally read through as unannotated genes, because their transcriptional and posttranscriptional regulations are the same as those of already-annotated genes, including fusion genes formed due to genetic alterations. Therefore, readthrough RNAs and fusion-gene-derived RNAs are not chimeras. Only those two-gene RNAs formed at the RNA level, likely via trans-splicing, without corresponding genes as genomic parents, should be regarded as authentic chimeric RNAs. However, since in human cells, procedural and mechanistic details of trans-splicing have never been disclosed, we doubt the existence of trans-splicing. Therefore, there are probably no authentic chimeras in humans, after readthrough and fusion-gene derived RNAs are all put back into the group of ordinary RNAs. Therefore, it should be further determined whether in human cells all two-neighboring-gene RNAs are derived from transcriptional readthrough and whether trans-splicing truly exists.
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Affiliation(s)
- Yan He
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang City 443002, Hubei, China.
| | - Lichan Chen
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Mingjuan Lei
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, 435 E. River Road, Minneapolis, MN 55455, USA.
| | - Hai Huang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Dezhong Joshua Liao
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
- Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, Guizhou, China.
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5
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L'Abbate A, Iacobucci I, Lonoce A, Turchiano A, Ficarra E, Paciello G, Cattina F, Ferrari A, Imbrogno E, Agostinelli C, Zinzani P, Martinelli G, Derenzini E, Storlazzi CT. RALE051: a novel established cell line of sporadic Burkitt lymphoma. Leuk Lymphoma 2017; 59:1252-1255. [PMID: 28893133 DOI: 10.1080/10428194.2017.1372580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Affiliation(s)
| | - Ilaria Iacobucci
- b Department of Experimental, Diagnostic and Specialty Medicine , Institute of Hematology "Seràgnoli", University of Bologna , Bologna , Italy
| | - Angelo Lonoce
- a Department of Biology , University of Bari , Bari , Italy
| | | | - Elisa Ficarra
- c Department of Computer and Control Engineering , Politecnico di Torino , Torino , Italy
| | - Giulia Paciello
- c Department of Computer and Control Engineering , Politecnico di Torino , Torino , Italy
| | - Federica Cattina
- d Chair of Haematology, Stem Cell Transplantation Unit , University of Brescia , Piazzale Spedali Civili 1, Brescia , Italy
| | - Anna Ferrari
- b Department of Experimental, Diagnostic and Specialty Medicine , Institute of Hematology "Seràgnoli", University of Bologna , Bologna , Italy
| | - Enrica Imbrogno
- b Department of Experimental, Diagnostic and Specialty Medicine , Institute of Hematology "Seràgnoli", University of Bologna , Bologna , Italy
| | - Claudio Agostinelli
- b Department of Experimental, Diagnostic and Specialty Medicine , Institute of Hematology "Seràgnoli", University of Bologna , Bologna , Italy
| | - Pierluigi Zinzani
- b Department of Experimental, Diagnostic and Specialty Medicine , Institute of Hematology "Seràgnoli", University of Bologna , Bologna , Italy
| | - Giovanni Martinelli
- b Department of Experimental, Diagnostic and Specialty Medicine , Institute of Hematology "Seràgnoli", University of Bologna , Bologna , Italy
| | - Enrico Derenzini
- e Haemolymphopathology Unit, Department of Haematology and Oncology "Seràgnoli" , S. Orsola-Malpighi Hospital , Bologna , Italy
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