1
|
PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
Collapse
Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
2
|
Single base substitution mutational signatures in pediatric acute myeloid leukemia based on whole genome sequencing. Leukemia 2021; 35:1485-1489. [PMID: 33864028 PMCID: PMC8102186 DOI: 10.1038/s41375-021-01242-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/09/2021] [Accepted: 03/23/2021] [Indexed: 01/18/2023]
|
3
|
Wang J, Dean DC, Hornicek FJ, Shi H, Duan Z. RNA sequencing (RNA-Seq) and its application in ovarian cancer. Gynecol Oncol 2018; 152:194-201. [PMID: 30297273 DOI: 10.1016/j.ygyno.2018.10.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022]
Abstract
Despite the surgical and chemotherapeutic advances over the past few decades, ovarian cancer remains the leading cause of gynecological cancer-related mortality. The absence of biomarkers in early detection and the development of drug resistance are principal causes of treatment failure in ovarian cancer. Recent progress in RNA sequencing (RNA-Seq) with Next Generation Sequencing technology has expanded the understanding of the molecular pathogenesis of ovarian cancer. As compared to previous hybridization-based microarray and Sanger sequence-based methods, RNA-Seq provides multiple layers of resolutions and transcriptome complexity, with less background noise and a broader dynamic range of RNA expression. Beyond quantifying gene expression, the data generated by RNA-Seq accelerates the identification of alternatively spliced genes, fusion genes, mutations/SNPs, allele-specific expression, novel transcripts and non-coding RNAs. RNA-Seq has been successfully applied in ovarian cancer research for earlier detection, ascertaining pathological origin, and defining the aberrant genes and dysregulated molecular pathways across patient groups. This review outlines the distinct advantages of RNA-Seq compared to other transcriptomics methods and its recent applications in ovarian cancer.
Collapse
Affiliation(s)
- Jinglu Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Dylan C Dean
- Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Francis J Hornicek
- Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Huirong Shi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
| | - Zhenfeng Duan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| |
Collapse
|
4
|
Brunetti M, Panagopoulos I, Gorunova L, Davidson B, Heim S, Micci F. RNA-sequencing identifies novel GREB1-NCOA2 fusion gene in a uterine sarcoma with the chromosomal translocation t(2;8)(p25;q13). Genes Chromosomes Cancer 2017; 57:176-181. [PMID: 29218853 PMCID: PMC5838407 DOI: 10.1002/gcc.22518] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 01/03/2023] Open
Abstract
Sarcomas account for 3% of all uterine malignancies and many of them are characterized by acquired, specific fusion genes whose detection has increased pathogenetic knowledge and diagnostic precision. We describe a novel fusion gene, GREB1-NCOA2, detected by transcriptome sequencing and validated by reverse transcriptase polymerase chain reaction and Sanger sequencing in an undifferentiated uterine sarcoma. The chimeric transcript was an in-frame fusion between exon 3 of GREB1 and exon 15 of NCOA2. The fusion is reported here for the first time, but it involves the GREB1 gene, an important promoter of tumor growth and progression, and NCOA2 which is known to be involved in transcriptional regulation. The alteration and recombination of these genes played a role in the tumorigenesis and/or progression of this sarcoma.
Collapse
Affiliation(s)
- Marta Brunetti
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ben Davidson
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
5
|
Wang Y, Wu N, Liu D, Jin Y. Recurrent Fusion Genes in Leukemia: An Attractive Target for Diagnosis and Treatment. Curr Genomics 2017; 18:378-384. [PMID: 29081694 PMCID: PMC5635644 DOI: 10.2174/1389202918666170329110349] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/23/2016] [Accepted: 02/14/2016] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Since the first fusion gene was discovered decades ago, a considerable number of fusion genes have been detected in leukemia. The majority of them are generated through chromosomal rearrangement or abnormal transcription. With the development of techniques, high-throughput sequencing method makes it possible to detect fusion genes systematically in multiple human cancers. Owing to their biological significance and tumor-specific expression, some of the fusion genes are attractive diagnostic tools and therapeutic targets. Tyrosine kinase inhibitors (TKI) targeting BCR-ABL1 fusions have been widely used to treat CML. The combination of ATRA and ATO targeting PML-RARA fusions has proven to be effective in acute promyelocytic leukemia (APL). Moreover, therapy with high dose cytarabine (HDAC) has significantly improved the prognosis of core binding factor (CBF) acute myeloid leukemia (AML) patients. Therefore, studies on fusion genes may benefit patients with leukemia by providing more diagnostic markers and therapies in the future. CONCLUSION The presented review focuses on the history of fusion genes, mechanisms of formation, and treatments against specific fusion genes in leukemia.
Collapse
Affiliation(s)
- Yuhui Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Nan Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Duo Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, P.R. China
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, P.R. China
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, P.R. China
| |
Collapse
|
6
|
Panagopoulos I, Gorunova L, Torkildsen S, Tierens A, Heim S, Micci F. FAM53B truncation caused by t(10;19)(q26;q13) chromosome translocation in acute lymphoblastic leukemia. Oncol Lett 2017; 13:2216-2220. [PMID: 28454383 PMCID: PMC5403202 DOI: 10.3892/ol.2017.5705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/17/2016] [Indexed: 11/18/2022] Open
Abstract
RNA-sequencing of the patient's bone marrow detected fusion transcripts in which the coding sequence of the FAM53B gene (from 10q26) was fused to a genomic sequence (from 19q13) that mapped upstream of the SLC7A10 locus. Reverse transcription-polymerase chain reaction together with Sanger sequencing verified the presence of this fusion transcript. The FAM53B fusion transcript is not expected to produce any chimeric protein. However, it may code for a truncated FAM53B protein consisting of the first 302 amino acids of FAM53B together with amino acids from the 19q13 sequence. Functionally, the truncated FAM53B would be similar to the protein encoded by the FAM53B sequence with accession no. BC031654.1 (FAM53B protein accession no. AAH31654.1). Furthermore, the truncated protein contains the entire conserved domain of the FAM53 protein family. The chromosome aberration t(10;19)(q26;q13) detected in this study was previously reported in a single case of ALL, in which it was also the sole karyotypic change. Both patients entered complete hematological and cytogenetic remission following treatment.
Collapse
Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, NO-0424 Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, NO-0424 Oslo, Norway
| | - Synne Torkildsen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, NO-0424 Oslo, Norway.,Department of Hematology, Oslo University Hospital, NO-0424 Oslo, Norway
| | - Anne Tierens
- Laboratory Medicine Program, Department of Haematopathology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, NO-0424 Oslo, Norway.,Faculty of Medicine, University of Oslo, NO-0316 Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, NO-0424 Oslo, Norway
| |
Collapse
|
7
|
Abstract
The association between chromosomal abnormalities and reduced fertility in domestic animals is well recorded and has been studied for decades. Chromosome aberrations directly affect meiosis, gametogenesis, and the viability of zygotes and embryos. In some instances, balanced structural rearrangements can be transmitted, causing fertility problems in subsequent generations. Here, we aim to give a comprehensive overview of the current status and future prospects of clinical cytogenetics of animal reproduction by focusing on the advances in molecular cytogenetics during the genomics era. We describe how advancing knowledge about animal genomes has improved our understanding of connections between gross structural or molecular chromosome variations and reproductive disorders. Further, we expand on a key area of reproduction genetics: cytogenetics of animal gametes and embryos. Finally, we describe how traditional cytogenetics is interfacing with advanced genomics approaches, such as array technologies and next-generation sequencing, and speculate about the future prospects.
Collapse
Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458;
| | | |
Collapse
|
8
|
Panagopoulos I, Gorunova L, Viset T, Heim S. Gene fusions AHRR-NCOA2, NCOA2-ETV4, ETV4-AHRR, P4HA2-TBCK, and TBCK-P4HA2 resulting from the translocations t(5;8;17)(p15;q13;q21) and t(4;5)(q24;q31) in a soft tissue angiofibroma. Oncol Rep 2016; 36:2455-2462. [PMID: 27633981 PMCID: PMC5055197 DOI: 10.3892/or.2016.5096] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/18/2016] [Indexed: 01/09/2023] Open
Abstract
We present an angiofibroma of soft tissue with the karyotype 46,XY,t(4;5)(q24;q31),t(5;8;17)(p15;q13;q21) [8]/46,XY,t(1;14)(p31;q32)[2]/46,XY[3]. RNA-sequencing showed that the t(4;5)(q24;q31) resulted in recombination of the genes TBCK on 4q24 and P4HA2 on 5q31.1 with generation of an in-frame TBCK-P4HA2 and the reciprocal but out-of-frame P4HA2-TBCK fusion transcripts. The putative TBCK-P4HA2 protein would contain the kinase, the rhodanese-like domain, and the Tre-2/Bub2/Cdc16 (TBC) domains of TBCK together with the P4HA2 protein which is a component of the prolyl 4-hydroxylase. The t(5;8;17)(p15;q13;q21) three-way chromosomal translocation targeted AHRR (on 5p15), NCOA2 (on 8q13), and ETV4 (on 17q21) generating the in-frame fusions AHRR-NCOA2 and NCOA2-ETV4 as well as an out-of-frame ETV4-AHRR transcript. In the AHRR-NCOA2 protein, the C-terminal part of AHRR is replaced by the C-terminal part of NCOA2 which contains two activation domains. The NCOA2-ETV4 protein would contain the helix-loop-helix, PAS_9 and PAS_11, CITED domains, the SRC-1 domain of NCOA2 and the ETS DNA-binding domain of ETV4. No fusion gene corresponding to t(1;14)(p31;q32) was found. Our findings indicate that, in spite of the recurrence of AHRR-NCOA2 in angiofibroma of soft tissue, additional genetic events (or fusion genes) might be required for the development of this tumor.
Collapse
Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Trond Viset
- Department of Pathology and Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
9
|
Micci F, Gorunova L, Agostini A, Johannessen LE, Brunetti M, Davidson B, Heim S, Panagopoulos I. Cytogenetic and molecular profile of endometrial stromal sarcoma. Genes Chromosomes Cancer 2016; 55:834-46. [PMID: 27219024 PMCID: PMC5113808 DOI: 10.1002/gcc.22380] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/13/2016] [Accepted: 04/13/2016] [Indexed: 01/01/2023] Open
Abstract
Recent cytogenetic and molecular investigations have improved our understanding of endometrial stromal tumors, including sarcomas (ESS), and helped redefine their classification into more pathogenetically meaningful categories. Because much more can be gained through such studies, we add information on another 22 ESS examined by karyotyping, PCR analysis, expression array analysis, and transcriptome sequencing. In spite of the known preference for certain pathogenetic pathways, we found considerable genetic heterogeneity in high‐grade (HG) as well as in low‐grade (LG) ESS. Not all HG tumors showed a YWHAE‐NUTM chimeric transcript and as many as six LGESS showed no hitherto known ESS‐related fusions. Among the transcripts identified by transcriptome sequencing and verified by Sanger sequencing, new variants of ZC3H7‐BCOR and its reciprocal BCOR‐ZC3H7 were identified as was involvement of the CREBBP and MLLT4 genes (both well known leukemia‐related genes) in two new fusions. FISH analysis identified a known EPC1‐PHF1 fusion which led to the identification of a new variant at the molecular level. The fact that around 70 genes were found differentially expressed, by microarray analysis, when comparing LGESS showing ESS‐related fusions with LGESS without such transcripts, underscores the biochemical importance of the observed genetic heterogeneity and hints that new subgroups/entities in LGESS still remain undiscovered. © 2016 The Authors. Genes, Chromosomes & Cancer Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. .,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Antonio Agostini
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Lene E Johannessen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Marta Brunetti
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Ben Davidson
- Department of Pathology, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| |
Collapse
|
10
|
Novel ZEB2-BCL11B Fusion Gene Identified by RNA-Sequencing in Acute Myeloid Leukemia with t(2;14)(q22;q32). PLoS One 2015; 10:e0132736. [PMID: 26186352 PMCID: PMC4505893 DOI: 10.1371/journal.pone.0132736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/17/2015] [Indexed: 01/31/2023] Open
Abstract
RNA-sequencing of a case of acute myeloid leukemia with the bone marrow karyotype 46,XY,t(2;14)(q22;q32)[5]/47,XY,idem,+?4,del(6)(q13q21)[cp6]/46,XY[4] showed that the t(2;14) generated a ZEB2-BCL11B chimera in which exon 2 of ZEB2 (nucleotide 595 in the sequence with accession number NM_014795.3) was fused to exon 2 of BCL11B (nucleotide 554 in the sequence with accession number NM_022898.2). RT-PCR together with Sanger sequencing verified the presence of the above-mentioned fusion transcript. All functional domains of BCL11B are retained in the chimeric protein. Abnormal expression of BCL11B coding regions subjected to control by the ZEB2 promoter seems to be the leukemogenic mechanism behind the translocation.
Collapse
|
11
|
Peng Z, Yuan C, Zellmer L, Liu S, Xu N, Liao DJ. Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers. J Cancer 2015; 6:555-67. [PMID: 26000048 PMCID: PMC4439942 DOI: 10.7150/jca.11997] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
Recent RNA-sequencing technology and associated bioinformatics have led to identification of tens of thousands of putative human chimeric RNAs, i.e. RNAs containing sequences from two different genes, most of which are derived from neighboring genes on the same chromosome. In this essay, we redefine "two neighboring genes" as those producing individual transcripts, and point out two known mechanisms for chimeric RNA formation, i.e. transcription from a fusion gene or trans-splicing of two RNAs. By our definition, most putative RNA chimeras derived from canonically-defined neighboring genes may either be technical artifacts or be cis-splicing products of 5'- or 3'-extended RNA of either partner that is redefined herein as an unannotated gene, whereas trans-splicing events are rare in human cells. Therefore, most authentic chimeric RNAs result from fusion genes, about 1,000 of which have been identified hitherto. We propose a hypothesis of "consecutive reverse transcriptions (RTs)", i.e. another RT reaction following the previous one, for how most spurious chimeric RNAs, especially those containing a short homologous sequence, may be generated during RT, especially in RNA-sequencing wherein RNAs are fragmented. We also point out that RNA samples contain numerous RNA and DNA shreds that can serve as endogenous random primers for RT and ensuing polymerase chain reactions (PCR), creating artifacts in RT-PCR.
Collapse
Affiliation(s)
- Zhiyu Peng
- 1. Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, P. R. China
| | - Chengfu Yuan
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Lucas Zellmer
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Siqi Liu
- 3. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Ningzhi Xu
- 4. Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, P. R. China
| | - D Joshua Liao
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| |
Collapse
|