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Mukherjee S, Mukherjee SB, Frenkel-Morgenstern M. Functional and regulatory impact of chimeric RNAs in human normal and cancer cells. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1777. [PMID: 36633099 DOI: 10.1002/wrna.1777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity that might facilitate this cell to survive against new environmental stress. Several recent studies have demonstrated the functional roles of various chimeric RNAs in cancer progression and are considered as biomarkers for cancer diagnosis and sometimes even drug targets. Further, the growing evidence demonstrated the potential functional association of chimeric RNAs with cancer heterogeneity and drug resistance cancer evolution. Recent studies highlighted that chimeric RNAs also have functional potentiality in normal physiological processes. Several functionally potential chimeric RNAs were discovered in human cancer and normal cells in the last two decades. This could indicate that chimeric RNAs are the hidden layer of the human transcriptome that should be explored from the functional insights to better understand the functional evolution of the genome and disease development that could facilitate clinical practice improvements. This review summarizes the current knowledge of chimeric RNAs and highlights their functional, regulatory, and evolutionary impact on different cancers and normal physiological processes. Further, we will discuss the potential functional roles of a recently discovered novel class of chimeric RNAs named sense-antisense/cross-strand chimeric RNAs generated by the fusion of the bi-directional transcripts of the same gene. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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2
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Dorney R, Dhungel BP, Rasko JEJ, Hebbard L, Schmitz U. Recent advances in cancer fusion transcript detection. Brief Bioinform 2022; 24:6918739. [PMID: 36527429 PMCID: PMC9851307 DOI: 10.1093/bib/bbac519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Extensive investigation of gene fusions in cancer has led to the discovery of novel biomarkers and therapeutic targets. To date, most studies have neglected chromosomal rearrangement-independent fusion transcripts and complex fusion structures such as double or triple-hop fusions, and fusion-circRNAs. In this review, we untangle fusion-related terminology and propose a classification system involving both gene and transcript fusions. We highlight the importance of RNA-level fusions and how long-read sequencing approaches can improve detection and characterization. Moreover, we discuss novel bioinformatic tools to identify fusions in long-read sequencing data and strategies to experimentally validate and functionally characterize fusion transcripts.
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Affiliation(s)
- Ryley Dorney
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - Bijay P Dhungel
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lionel Hebbard
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
| | - Ulf Schmitz
- Corresponding author. Ulf Schmitz, Department of Molecular and Cell Biology, College of Public Health, Medical and Vet Sciences, James Cook University, Douglas, QLD 4811, Australia. E-mail:
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Zhou J, Guan X, Xu E, Zhou J, Xiong R, Yang Q. Chimeric RNA RRM2-C2orf48 plays an oncogenic role in the development of NNK-induced lung cancer. iScience 2022; 26:105708. [PMID: 36570773 PMCID: PMC9771722 DOI: 10.1016/j.isci.2022.105708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/24/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Chimeric RNAs have been used as biomarkers and therapeutic targets for multiple types of cancers. However, less attention has been paid to their mechanism of action in neoplasia. Here, we reported that high-expressed chimeric RNA RRM2-C2orf48 was found in malignantly transformed BEAS-2B cells induced by 4-(methyl nitrosamine)-1-(3-pyridinyl)-1-butanone (NNK) in 74 lung cancer patients and several lung cancer cell lines. The expression level of RRM2-C2orf48 was significantly correlated with lymph node metastasis, distant metastasis, tumor-lymph node-metastasis (TNM) stage, and smoking. Overexpressing RRM2-C2orf48 promoted cell growth and accelerated the process of NNK-induced lung cancer. RRM2-C2orf48 knockdown inhibited the growth of RRM2-C2orf48-overexpressing BEAS-2B cells. Finally, we identified miR-219a-2-3p as a potential target of RRM2-C2orf48 in lung cancer. In summary, chimeric RNA RRM2-C2orf48 accelerated the process of NNK-induced lung cancer, and miR-219a-2-3p may be involved in this process.
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Affiliation(s)
- Jiazhen Zhou
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Xinchao Guan
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, Guangzhou 510010, PR China
| | - Jiaxin Zhou
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Rui Xiong
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Qiaoyuan Yang
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China,Corresponding author
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The Fusion of CLEC12A and MIR223HG Arises from a trans-Splicing Event in Normal and Transformed Human Cells. Int J Mol Sci 2021; 22:ijms222212178. [PMID: 34830054 PMCID: PMC8625150 DOI: 10.3390/ijms222212178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
Chimeric RNAs are often associated with chromosomal rearrangements in cancer. In addition, they are also widely detected in normal tissues, contributing to transcriptomic complexity. Despite their prevalence, little is known about the characteristics and functions of chimeric RNAs. Here, we examine the genetic structure and biological roles of CLEC12A-MIR223HG, a novel chimeric transcript produced by the fusion of the cell surface receptor CLEC12A and the miRNA-223 host gene (MIR223HG), first identified in chronic myeloid leukemia (CML) patients. Surprisingly, we observed that CLEC12A-MIR223HG is not just expressed in CML, but also in a variety of normal tissues and cell lines. CLEC12A-MIR223HG expression is elevated in pro-monocytic cells resistant to chemotherapy and during monocyte-to-macrophage differentiation. We observed that CLEC12A-MIR223HG is a product of trans-splicing rather than a chromosomal rearrangement and that transcriptional activation of CLEC12A with the CRISPR/Cas9 Synergistic Activation Mediator (SAM) system increases CLEC12A-MIR223HG expression. CLEC12A-MIR223HG translates into a chimeric protein, which largely resembles CLEC12A but harbours an altered C-type lectin domain altering key disulphide bonds. These alterations result in differences in post-translational modifications, cellular localization, and protein-protein interactions. Taken together, our observations support a possible involvement of CLEC12A-MIR223HG in the regulation of CLEC12A function. Our workflow also serves as a template to study other uncharacterized chimeric RNAs.
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Mukherjee S, Frenkel-Morgenstern M. Evolutionary impact of chimeric RNAs on generating phenotypic plasticity in human cells. Trends Genet 2021; 38:4-7. [PMID: 34579972 DOI: 10.1016/j.tig.2021.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/18/2022]
Abstract
Chimeric RNAs are generated by the fusion of the exons or introns of two genes. The generation of chimeric RNAs is important for the functional expansion of cells. Here, we describe the functional implications of chimeric RNAs for generating phenotypic plasticity from an evolutionary perspective.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
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Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21197120. [PMID: 32992457 PMCID: PMC7582694 DOI: 10.3390/ijms21197120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 12/25/2022] Open
Abstract
Fusion genes and epigenetic regulators (i.e., miRNAs and long non-coding RNAs) constitute essential pieces of the puzzle of the tumor genomic landscape, in particular in mechanisms behind the adenoma-to-carcinoma progression of colorectal cancer (CRC). In this work, we aimed to identify molecular signatures of the different steps of sporadic CRC development in eleven patients, of which synchronous samples of adenomas, tumors, and normal tissues were analyzed by RNA-Seq. At a functional level, tumors and adenomas were all characterized by increased activity of the cell cycle, cell development, cell growth, and biological proliferation functions. In contrast, organic survival and apoptosis-related functions were inhibited both in tumors and adenomas at different levels. At a molecular level, we found that three individuals shared a tumor-specific fusion named MRPS31-SUGT1, generated through an intra-chromosomal translocation on chromosome 13, whose sequence resulted in being 100% identical to the long non-coding RNA (lncRNA) MRPS31P5. Our analyses suggest that MRPS31P5 could take part to a competitive endogenous (ce)RNA network by acting as a miRNA sponge or/and as an interactor of other mRNAs, and thus it may be an important gene expression regulatory factor and could be used as a potential biomarker for the detection of early CRC events.
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Abstract
Chimeric RNAs are hybrid transcripts containing exons from two separate genes. Chimeric RNAs are traditionally considered to be transcribed from fusion genes caused by chromosomal rearrangement. These canonical chimeric RNAs are well characterized to be expressed in a cancer-unique pattern and/or act as oncogene products. However, benefited by the development of advanced deep sequencing technologies, novel types of non-canonical chimeric RNAs have been discovered to be generated from intergenic splicing without genomic aberrations. They can be formed through trans-splicing or cis-splicing between adjacent genes (cis-SAGe) mechanisms. Non-canonical chimeric RNAs are widely detected in normal physiology, although several have been shown to have a cancer-specific expression pattern. Further studies have indicated that some of them play fundamental roles in controlling cell growth and motility, and may have functions independent of the parental genes. These discoveries are unveiling a new layer of the functional transcriptome and are also raising the possibility of utilizing non-canonical chimeric RNAs as cancer diagnostic markers and therapeutic targets. In this chapter, we will overview different categories of chimeric RNAs and their expression in various types of cancerous and normal samples. Acknowledging that chimeric RNAs are not unique to cancer, we will discuss both bioinformatic and biological methods to identify credible cancer-specific chimeric RNAs. Furthermore, we will describe downstream methods to explore their molecular processing mechanisms and potential functions. A better understanding of the biogenesis mechanisms and functional products of cancer-specific chimeric RNAs will pave ways for the development of novel cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Xinrui Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States.
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