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Chen JW, Shrestha L, Green G, Leier A, Marquez-Lago TT. The hitchhikers' guide to RNA sequencing and functional analysis. Brief Bioinform 2023; 24:bbac529. [PMID: 36617463 PMCID: PMC9851315 DOI: 10.1093/bib/bbac529] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 01/10/2023] Open
Abstract
DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantification, but once sequencing has concluded researchers can be easily overwhelmed with questions such as how to go from raw data to differential expression (DE), pathway analysis and interpretation. Several pipelines and procedures have been developed to this effect. Even though there is no unique way to perform RNA-Seq analysis, it usually follows these steps: 1) raw reads quality check, 2) alignment of reads to a reference genome, 3) aligned reads' summarization according to an annotation file, 4) DE analysis and 5) gene set analysis and/or functional enrichment analysis. Each step requires researchers to make decisions, and the wide variety of options and resulting large volumes of data often lead to interpretation challenges. There also seems to be insufficient guidance on how best to obtain relevant information and derive actionable knowledge from transcription experiments. In this paper, we explain RNA-Seq steps in detail and outline differences and similarities of different popular options, as well as advantages and disadvantages. We also discuss non-coding RNA analysis, multi-omics, meta-transcriptomics and the use of artificial intelligence methods complementing the arsenal of tools available to researchers. Lastly, we perform a complete analysis from raw reads to DE and functional enrichment analysis, visually illustrating how results are not absolute truths and how algorithmic decisions can greatly impact results and interpretation.
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Affiliation(s)
- Jiung-Wen Chen
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lisa Shrestha
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
| | - George Green
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Leier
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
| | - Tatiana T Marquez-Lago
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
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Evolutionary Landscape of Tea Circular RNAs and Its Contribution to Chilling Tolerance of Tea Plant. Int J Mol Sci 2023; 24:ijms24021478. [PMID: 36674993 PMCID: PMC9861842 DOI: 10.3390/ijms24021478] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Chilling stress threatens the yield and distribution pattern of global crops, including the tea plant (Camellia sinensis), one of the most important cash crops around the world. Circular RNA (circRNA) plays roles in regulating plant growth and biotic/abiotic stress responses. Understanding the evolutionary characteristics of circRNA and its feedbacks to chilling stress in the tea plant will help to elucidate the vital roles of circRNAs. In the current report, we systematically identified 2702 high-confidence circRNAs under chilling stress in the tea plant, and interestingly found that the generation of tea plant circRNAs was associated with the length of their flanking introns. Repetitive sequences annotation and DNA methylation analysis revealed that the longer flanking introns of circRNAs present more repetitive sequences and higher methylation levels, which suggested that repeat-elements-mediated DNA methylation might promote the circRNAs biogenesis in the tea plant. We further detected 250 differentially expressed circRNAs under chilling stress, which were functionally enriched in GO terms related to cold/stress responses. Constructing a circRNA-miRNA-mRNA interaction network discovered 139 differentially expressed circRNAs harboring potential miRNA binding sites, which further identified 14 circRNAs that might contribute to tea plant chilling responses. We further characterized a key circRNA, CSS-circFAB1, which was significantly induced under chilling stress. FISH and silencing experiments revealed that CSS-circFAB1 was potentially involved in chilling tolerance of the tea plant. Our study emphasizes the importance of circRNA and its preliminary role against low-temperature stress, providing new insights for tea plant cold tolerance breeding.
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Buratin A, Bortoluzzi S, Gaffo E. Systematic benchmarking of statistical methods to assess differential expression of circular RNAs. Brief Bioinform 2023; 24:6966517. [PMID: 36592056 PMCID: PMC9851295 DOI: 10.1093/bib/bbac612] [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: 09/26/2022] [Revised: 11/28/2022] [Accepted: 12/11/2022] [Indexed: 01/03/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA expression measured with RNA-seq has particular characteristics that might hamper the performance of standard biostatistical differential expression assessment methods (DEMs). We compared 38 DEM pipelines configured to fit circRNA expression data's statistical properties, including bulk RNA-seq, single-cell RNA-seq (scRNA-seq) and metagenomics DEMs. The DEMs performed poorly on data sets of typical size. Widely used DEMs, such as DESeq2, edgeR and Limma-Voom, gave scarce results, unreliable predictions or even contravened the expected behaviour with some parameter configurations. Limma-Voom achieved the most consistent performance throughout different benchmark data sets and, as well as SAMseq, reasonably balanced false discovery rate (FDR) and recall rate. Interestingly, a few scRNA-seq DEMs obtained results comparable with the best-performing bulk RNA-seq tools. Almost all DEMs' performance improved when increasing the number of replicates. CircRNA expression studies require careful design, choice of DEM and DEM configuration. This analysis can guide scientists in selecting the appropriate tools to investigate circRNA differential expression with RNA-seq experiments.
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Affiliation(s)
- Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Enrico Gaffo
- Corresponding author: Enrico Gaffo, Department of Molecular Medicine, University of Padova - Via G. Colombo, 3—35131 Padova, Italy. Phone +39 049 827 6502; Fax +39 049 827 6209; E-mail:
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Stefanov SR, Meyer IM. CYCLeR-a novel tool for the full isoform assembly and quantification of circRNAs. Nucleic Acids Res 2022; 51:e10. [PMID: 36478276 PMCID: PMC9881126 DOI: 10.1093/nar/gkac1100] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022] Open
Abstract
Splicing is one key mechanism determining the state of any eukaryotic cell. Apart from linear splice variants, circular splice variants (circRNAs) can arise via non-canonical splicing involving a back-splice junction (BSJ). Most existing methods only identify circRNAs via the corresponding BSJ, but do not aim to estimate their full sequence identity or to identify different, alternatively spliced circular isoforms arising from the same BSJ. We here present CYCLeR, the first computational method for identifying the full sequence identity of new and alternatively spliced circRNAs and their abundances while simultaneously co-estimating the abundances of known linear splicing isoforms. We show that CYCLeR significantly outperforms existing methods in terms of F score and quantification of transcripts in simulated data. In a in a comparative study with long-read data, we also show the advantages of CYCLeR compared to existing methods. When analysing Drosophila melanogaster data, CYCLeR uncovers biological patterns of circRNA expression that other methods fail to observe.
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Affiliation(s)
- Stefan R Stefanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany,Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Thielallee 63, 14195 Berlin, Germany
| | - Irmtraud M Meyer
- To whom correspondence should be addressed. Tel: +49 30 9406 3292; Fax: +49 30 9406 3291;
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Expression Profiles and Functional Analysis of Plasma Exosomal Circular RNAs in Acute Myocardial Infarction. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3458227. [PMID: 36221294 PMCID: PMC9547997 DOI: 10.1155/2022/3458227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/20/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
Acute myocardial infarction (AMI) is a common cardiovascular disease with high rates of morbidity and mortality globally. The dysregulation of circular RNAs (circRNAs) has been shown to be closely related to various pathological aspects of AMI. However, the function of exosomal circRNAs in AMI has yet to be investigated. The purpose of this study was to investigate the expression profiles of plasma exosomal circRNAs in AMI and explore their potential functionality. The expression profiles of plasma exosomal circRNAs in patients with AMI, stable coronary heart atherosclerotic disease (CAD), and healthy controls were obtained from a GEO expression dataset (GSE159657). We also analyzed bioinformatics functionality, potential pathways, and interaction networks related to the microRNAs associated with the differentially expressed circRNAs. A total of 253 exosomal circRNAs (184 up- and 69 down-regulated) and 182 exosomal circRNAs (94 up- and 88 down-regulated) were identified as being differentially expressed between the control group and the AMI and CAD patients, respectively. Compared with the CAD group, 231 different exosomal circRNAs (177 up- and 54 down-regulated) were identified in the AMI group. Functional analysis suggested that the parental genes of exosomal has_circ_0061776 were significantly enriched in the biological process of lysine degradation. Pathway interaction network analysis further indicated that exosomal has_circ_0061776 was associated with has-miR-133a, has-miR-214, has-miR-423, and has-miR-217 and may play a role in the pathogenesis of AMI through the MAPK signaling pathway. This study identified the differential expression and functionality of exosomal circRNAs in AMI and provided further understanding of the potential pathogenesis of an exosomal circRNA-related competing endogenous RNA (ceRNA) network in AMI.
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Association of Circular RNA and Long Non-Coding RNA Dysregulation with the Clinical Response to Immune Checkpoint Blockade in Cutaneous Metastatic Melanoma. Biomedicines 2022; 10:biomedicines10102419. [DOI: 10.3390/biomedicines10102419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Cutaneous melanoma (CM) is the most lethal form of skin cancer if it becomes metastatic, where treatment options and survival chances decrease dramatically. Immunotherapy treatments based on the immunologic checkpoint inhibitors programmed death cell protein 1 (PD-1) and cytotoxic T-lymphocyte antigen 4 (CTLA-4) constituted a main breakthrough in the treatment of metastatic CM, particularly for the achievement of long-term benefits. Even though it is a very promising therapy, resistance to primary immune checkpoint blockade (ICB) arises in about 70% of CM patients treated with a CTLA-4 inhibitor, and 40–65% of CM patients administered with a PD-1-targeting treatment. Some long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) are implicated in triggering pro- and anti-tumorigenic responses to various cancer treatments. The relationship between lncRNAs, circRNAs and ICB immunotherapy has not been explored in cutaneous metastatic melanoma (CMM). The aim of this pilot study is to evaluate the potential role of circRNA and lncRNA expression as pre-treatment predictors of the clinical response to immunotherapy in CMM patients. RNA-seq from 12 formalin-fixed paraffin-embedded (FFPE) samples from the metastatic biopsies of CMM patients treated with nivolumab was used to identify response-associated transcripts. Our findings indicate that specific lncRNAs and circRNAs, probably acting as competitive endogenous RNAs (ceRNAs), are involved in the regulatory networks of the immune response against metastatic melanoma that these patients have under treatment with nivolumab. Moreover, we established a risk score that yields predictions of the overall survival (OS) and progression-free survival (PFS) of CMM patients with high accuracy. This proof-of-principle work provides a possible insight into the function of ceRNAs, contributing to efforts to decipher the complex molecular mechanisms of ICB cancer treatment response.
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Chen Y, Zhou J, Wei Z, Cheng Y, Tian G, Quan Y, Kong Q, Wu W, Liu X. Identification of circular RNAs in cardiac hypertrophy and cardiac fibrosis. Front Pharmacol 2022; 13:940768. [PMID: 36003513 PMCID: PMC9393479 DOI: 10.3389/fphar.2022.940768] [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: 05/12/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Cardiac hypertrophy initially serves as an adaptive response to physiological and pathological stimuli. Sustained hypertrophy progress to pathological cardiac hypertrophy, cardiac fibrosis and ultimately lead to heart failure, one of the leading medical causes of mortality worldwide. Intervention of pathological cardiac hypertrophy can effectively reduce the occurrence of heart failure. Abundant factors, such as adrenergic, angiotensin, and endothelin (ET-1) receptors, have been shown to participate in the regulation of pathological cardiac hypertrophy. Recently, an increasing number of studies have indicated that circRNA and circRNA-miRNA–mRNA network regulation is indispensable for the posttranscriptional regulation of mRNA in cardiac hypertrophy. In our study, the morphological, cardiac function and pathological changes during cardiac hypertrophy were investigated. RNA sequencing identified 93 circRNAs that were differentially expressed in the TAC_2w group, and 55 circRNAs in the TAC_4w group compared with the sham group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses identified several significant pathways, including hypertrophic cardiomyopathy, extracellular matrix (ECM)-receptor interaction and focal adhesion. Coexpression analyses were performed for differentially expressed circRNAs and differentially expressed mRNAs. Based on gene set enrichment analysis (GSEA), 8 circRNAs (mmu-Nfkb1_0001, mmu-Smad4_0007, mmu-Hecw2_0009, mmu-Itgbl1_0002, mmu-Lrrc2_0005, mmu-Cpeb3_0007, mmu-Ryr2_0040, and mmu-Rtn4_0001) involved in cardiac hypertrophy and cardiac fibrosis were identified. We validated some key circRNAs by qPCR. The crucial coexpression of circRNA–mRNA and its interaction with miRNA showed the possible mechanism of circRNAs in the process of cardiac dysfunction. Our results may provide promising targets for the treatment of pathological cardiac hypertrophy and fibrosis.
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Affiliation(s)
- Yan Chen
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Junteng Zhou
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
- Health Management Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Cardiovascular Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Zisong Wei
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Cheng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
| | - Geer Tian
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Quan
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qihang Kong
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wenchao Wu
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaojing Liu
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Xiaojing Liu,
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58
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Johannsen EB, Just J, Viuff MH, Okholm TLH, Pedersen SB, Meyer Lauritsen K, Trolle C, Pedersen MGB, Chang S, Fedder J, Skakkebæk A, Gravholt CH. Sex chromosome aneuploidies give rise to changes in the circular RNA profile: A circular transcriptome-wide study of Turner and Klinefelter syndrome across different tissues. Front Genet 2022; 13:928874. [PMID: 35938026 PMCID: PMC9355307 DOI: 10.3389/fgene.2022.928874] [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: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: The landscape of circular RNAs (circRNAs), an important class of non-coding RNAs that regulate gene expression, has never been described in human disorders of sex chromosome aneuploidies. We profiled circRNAs in Turner syndrome females (45,X; TS) and Klinefelter syndrome males (47,XXY; KS) to investigate how circRNAs respond to a missing or an extra X chromosome. Methods: Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. CircRNAs were identified using a combination of circRNA identification pipelines (CIRI2, CIRCexplorer2 and circRNA_finder). Results: Differential expression of circRNAs was observed throughout the genome in TS and KS, in all tissues. The host-genes from which several of these circRNAs were derived, were associated with known phenotypic traits. Furthermore, several differentially expressed circRNAs had the potential to capture micro RNAs that targeted protein-coding genes with altered expression in TS and KS. Conclusion: Sex chromosome aneuploidies introduce changes in the circRNA transcriptome, demonstrating that the genomic changes in these syndromes are more complex than hitherto thought. CircRNAs may help explain some of the genomic and phenotypic traits observed in these syndromes.
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Affiliation(s)
- Emma B. Johannsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Departments of Clinical Medicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Emma B. Johannsen,
| | - Jesper Just
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Departments of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mette H. Viuff
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Trine Line Hauge Okholm
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | | | - Katrine Meyer Lauritsen
- Steno Diabetes Center, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | - Christian Trolle
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Simon Chang
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Fedder
- Centre of Andrology and Fertility Clinic, Department D, Odense University Hospital, Odense, Denmark
- Research Unit of Human Reproduction, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anne Skakkebæk
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Claus H. Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
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Yang S, Zhou H, Liu M, Jaijyan D, Cruz‐Cosme R, Ramasamy S, Subbian S, Liu D, Xu J, Niu X, Li Y, Xiao L, Tyagi S, Wang Q, Zhu H, Tang Q. SARS-CoV-2, SARS-CoV, and MERS-CoV encode circular RNAs of spliceosome-independent origin. J Med Virol 2022; 94:3203-3222. [PMID: 35318674 PMCID: PMC9088628 DOI: 10.1002/jmv.27734] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/01/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022]
Abstract
Circular RNAs (circRNAs) are a newly recognized component of the transcriptome with critical roles in autoimmune diseases and viral pathogenesis. To address the importance of circRNA in RNA viral transcriptome, we systematically identified and characterized circRNAs encoded by the RNA genomes of betacoronaviruses using both bioinformatical and experimental approaches. We predicted 351, 224, and 2764 circRNAs derived from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV, and Middle East respiratory syndrome coronavirus, respectively. We experimentally identified 75 potential SARS-CoV-2 circRNAs from RNA samples extracted from SARS-CoV-2-infected Vero E6 cells. A systematic comparison of viral and host circRNA features, including abundance, strand preference, length distribution, circular exon numbers, and breakpoint sequences, demonstrated that coronavirus-derived circRNAs had a spliceosome-independent origin. We further showed that back-splice junctions (BSJs) captured by inverse reverse-transcription polymerase chain reaction have different level of resistance to RNase R. Through northern blotting with a BSJ-spanning probe targeting N gene, we identified three RNase R-resistant bands that represent SARS-CoV-2 circRNAs that are detected cytoplasmic by single-molecule and amplified fluorescence in situ hybridization assays. Lastly, analyses of 169 sequenced BSJs showed that both back-splice and forward-splice junctions were flanked by homologous and reverse complementary sequences, including but not limited to the canonical transcriptional regulatory sequences. Our findings highlight circRNAs as an important component of the coronavirus transcriptome, offer important evaluation of bioinformatic tools in the analysis of circRNAs from an RNA genome, and shed light on the mechanism of discontinuous RNA synthesis.
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Affiliation(s)
- Shaomin Yang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain MedicineShenzhen Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science CenterShenzhenChina
- Department of Microbiology, College of PharmacyJinan UniversityGuangzhouGuangdongChina
| | - Hong Zhou
- Department of MicrobiologyHoward University College of MedicineWashingtonDistrict of ColumbiaUSA
| | - Mingde Liu
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, College of Veterinary MedicineThe Ohio State UniversityWoosterOhioUSA
| | - Dabbu Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical SchoolRutgers UniversityNewarkNew JerseyUSA
| | - Ruth Cruz‐Cosme
- Department of MicrobiologyHoward University College of MedicineWashingtonDistrict of ColumbiaUSA
| | - Santhamani Ramasamy
- Public Health Research Institute, Rutgers New Jersey Medical SchoolThe State University of New JerseyNewarkNew JerseyUSA
| | - Selvakumar Subbian
- Public Health Research Institute, Rutgers New Jersey Medical SchoolThe State University of New JerseyNewarkNew JerseyUSA
| | - Dongxiao Liu
- Department of MicrobiologyHoward University College of MedicineWashingtonDistrict of ColumbiaUSA
| | - Jiayu Xu
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, College of Veterinary MedicineThe Ohio State UniversityWoosterOhioUSA
| | - Xiaoyu Niu
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, College of Veterinary MedicineThe Ohio State UniversityWoosterOhioUSA
| | - Yaolan Li
- Department of Microbiology, College of PharmacyJinan UniversityGuangzhouGuangdongChina
| | - Lizu Xiao
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain MedicineShenzhen Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science CenterShenzhenChina
| | - Sanjay Tyagi
- Public Health Research Institute, Rutgers New Jersey Medical SchoolThe State University of New JerseyNewarkNew JerseyUSA
- Department of Medicine, New Jersey Medical SchoolRutgers UniversityNewarkNew JerseyUSA
| | - Qiuhong Wang
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, College of Veterinary MedicineThe Ohio State UniversityWoosterOhioUSA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical SchoolRutgers UniversityNewarkNew JerseyUSA
| | - Qiyi Tang
- Department of MicrobiologyHoward University College of MedicineWashingtonDistrict of ColumbiaUSA
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Naarmann-de Vries IS, Eschenbach J, Schudy S, Meder B, Dieterich C. Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq. Front Mol Biosci 2022; 9:875805. [PMID: 35755822 PMCID: PMC9214859 DOI: 10.3389/fmolb.2022.875805] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Recently, circular RNAs (circRNAs) have been extensively studied in animals and plants. circRNAs are generated by backsplicing from the same linear transcripts that are canonically spliced to produce, for example, mature mRNAs. circRNAs exhibit tissue-specific expression and are potentially involved in many diseases, among them cardiovascular diseases. The comprehensive analysis of circRNA expression patterns across larger patient cohorts requires a streamlined and cost-effective workflow designed to meet small input requirements. In this article, we present Lexo-circSeq, a targeted RNA sequencing approach that can profile up to 110 circRNAs and their corresponding linear transcripts in one experiment. We established Lexo-circSeq employing total human heart RNA and show that our protocol can detect depletion of a specific circRNA in hiPSC-derived cardiomyocytes. Finally, Lexo-circSeq was applied to biopsies from patients diagnosed with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), respectively. Interestingly, our results indicate that circular-to-linear-ratios for circSLC8A1 and circRBM33 are deregulated in cardiomyopathy.
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Affiliation(s)
- Isabel S Naarmann-de Vries
- Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Jessica Eschenbach
- Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah Schudy
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.,Department of Internal Medicine III, Institute for Cardiomyopathies, University Hospital Heidelberg, Heidelberg, Germany
| | - Benjamin Meder
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.,Department of Internal Medicine III, Institute for Cardiomyopathies, University Hospital Heidelberg, Heidelberg, Germany.,Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA, United States
| | - Christoph Dieterich
- Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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Usability evaluation of circRNA identification tools: Development of a heuristic-based framework and analysis. Comput Biol Med 2022; 147:105785. [PMID: 35780604 DOI: 10.1016/j.compbiomed.2022.105785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/23/2022] [Accepted: 06/26/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND AND OBJECTIVE Circular RNAs (circRNAs) are endogenous molecules of non-coding RNA that form a covalently closed loop at the 3' and 5' ends. Recently, the role of these molecules in the regulation of gene expression and their involvement in several human pathologies has gained notoriety. The identification of circRNAs is highly dependent on computational methods for analyzing RNA sequencing data. However, bioinformatics software is known to be problematic in terms of usability. Evidence points out that tools for identifying circRNAs can have such problems, negatively impacting researchers in this field. Here we present a heuristic-based framework for evaluating the usability of command-line circRNA identification software. METHODS We used heuristics evaluation to comprehensively identify the usability issues in a sample of circRNA identification tools. RESULTS We identified 46 usability issues presented individually in four tools. Most of the issues had cosmetic or minor severity. These are unlikely to challenge experienced users but may cause inconvenience for novice users. We also identified severe issues with the potential to harm users regardless of their experience. The areas most affected were the documentation and the installability of the tools. CONCLUSIONS With the proposed framework, we formally describe, for the first time, the usability problems that can affect users in this area of circRNA research. We hope that our framework can help researchers evaluate their software's usability during development.
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Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing. Nat Commun 2022; 13:3242. [PMID: 35688820 PMCID: PMC9187688 DOI: 10.1038/s41467-022-30963-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/24/2022] [Indexed: 12/30/2022] Open
Abstract
Previous studies have demonstrated the highly specific expression of circular RNAs (circRNAs) in different tissues and organisms, but the cellular architecture of circRNA has never been fully characterized. Here, we present a collection of 171 full-length single-cell RNA-seq datasets to explore the cellular landscape of circRNAs in human and mouse tissues. Through large-scale integrative analysis, we identify a total of 139,643 human and 214,747 mouse circRNAs in these scRNA-seq libraries. We validate the detected circRNAs with the integration of 11 bulk RNA-seq based resources, where 216,602 high-confidence circRNAs are uniquely detected in the single-cell cohort. We reveal the cell-type-specific expression pattern of circRNAs in brain samples, developing embryos, and breast tumors. We identify the uniquely expressed circRNAs in different cell types and validate their performance in tumor-infiltrating immune cell composition deconvolution. This study expands our knowledge of circRNA expression to the single-cell level and provides a useful resource for exploring circRNAs at this unprecedented resolution. Studies of circular RNAs have often been limited to the tissue or organism level. Here, authors investigate the comprehensive expression landscape of circRNAs in human and mouse at single-cell resolution, revealing highly specific and dynamic changes of circRNAs during multiple biological processes.
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63
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Liu Y, Wang L, Liu W. Roles of circRNAs in the Tumorigenesis and Metastasis of HCC: A Mini Review. Cancer Manag Res 2022; 14:1847-1856. [PMID: 35668744 PMCID: PMC9166687 DOI: 10.2147/cmar.s362594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/20/2022] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs with loop structures that are stable and widely distributed in different tumor tissues. The development of high-throughput sequencing and in silico tools has enabled the discovery of numerous functional circRNAs. Hepatocellular carcinoma (HCC) is a malignant tumor, and the mechanism involved in its progression has remained unclear. In recent years, an increasing number of circRNAs have been identified in HCC, contributing to tumorigenesis and metastasis and with the potential role as biomarkers through competitive endogenous RNAs (ceRNAs) as miRNA sponges or by interacting with RNA binding proteins (RBPs). In this review, we summarize the regulatory roles of circRNAs in HCC development as well as the use of bioinformatics tools in the annotation and prioritization of circRNA and highlight the participation of exosomal circRNAs in HCC metastasis and drug resistance.
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Affiliation(s)
- Yichen Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Lei Wang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
| | - Wen Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, People's Republic of China
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64
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Liu Z, Ding H, She J, Chen C, Zhang W, Yang E. DEBKS: A Tool to Detect Differentially Expressed Circular RNAs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:549-556. [PMID: 33631429 PMCID: PMC9801035 DOI: 10.1016/j.gpb.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 10/22/2020] [Accepted: 01/01/2021] [Indexed: 01/26/2023]
Abstract
Circular RNAs (circRNAs) are involved in various biological processes and disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that a circRNA is formed from the host gene by back-splicing (BS). To distinguish the expression difference originating from BS or the host gene, we present differentially expressed back-splicing (DEBKS), a software program to streamline the discovery of differential BS events between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying to real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.
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Affiliation(s)
- Zelin Liu
- Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Huiru Ding
- Department of Human Anatomy, Histology & Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianqi She
- Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chunhua Chen
- Department of Human Anatomy, Histology & Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Weiguang Zhang
- Department of Human Anatomy, Histology & Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Ence Yang
- Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Chinese Institute for Brain Research, Beijing 102206, China.
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65
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MacMillan HJ, Kong Y, Calvo-Roitberg E, Alonso LC, Pai AA. High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets. Sci Rep 2022; 12:7745. [PMID: 35546161 PMCID: PMC9095874 DOI: 10.1038/s41598-022-11668-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/20/2022] [Indexed: 01/05/2023] Open
Abstract
The antisense non-coding RNA in the INK locus (ANRIL) is a hotspot for genetic variants associated with cardiometabolic disease. We recently found increased ANRIL abundance in human pancreatic islets from donors with certain Type II Diabetes (T2D) risk-SNPs, including a T2D risk-SNP located within ANRIL exon 2 associated with beta cell proliferation. Recent studies have found that expression of circular species of ANRIL is linked to the regulation of cardiovascular phenotypes. Less is known about how the abundance of circular ANRIL may influence T2D phenotypes. Herein, we sequence circular RNA in pancreatic islets to characterize circular isoforms of ANRIL. We identify several consistently expressed circular ANRIL isoforms whose expression is correlated across dozens of individuals and characterize ANRIL splice sites that are commonly involved in back-splicing. We find that samples with the T2D risk allele in ANRIL exon 2 had higher ratios of circular to linear ANRIL compared to protective-allele carriers, and that higher circular:linear ANRIL was associated with decreased beta cell proliferation. Our study points to a combined involvement of both linear and circular ANRIL species in T2D phenotypes and opens the door for future studies of the molecular mechanisms by which ANRIL impacts cellular function in pancreatic islets.
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Affiliation(s)
- Hannah J MacMillan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Yahui Kong
- UMass Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Curia Global, Inc., Hopkinton, MA, 01748, USA
| | - Ezequiel Calvo-Roitberg
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Laura C Alonso
- Division of Endocrinology, Diabetes and Metabolism, Weill Cornell Medicine, New York, NY, 10021, USA.
- Weill Center for Metabolic Health, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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66
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Foruzandeh Z, Dorabadi DG, Sadeghi F, Zeinali-Sehrig F, Zaefizadeh M, Rahmati Y, Alivand MR. Circular RNAs as novel biomarkers in triple-negative breast cancer: a systematic review. Mol Biol Rep 2022; 49:9825-9840. [PMID: 35534586 DOI: 10.1007/s11033-022-07502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/21/2022] [Indexed: 11/25/2022]
Abstract
More effective prognostic and diagnostic tools are urgently required for early detecting and treating triple-negative breast cancer, which is the most acute type of breast cancer because of its lower survival rate, aggressiveness, and non-response to various common treatments. So, it remains the most harmful malignancy for women worldwide. Recently, circular RNAs, as a group of non-coding RNAs, with covalently closed loop and high stability have been discovered, which can modulate gene expression through competing with endogenous microRNA sponges. This finding provided further insight into novel approaches for controlling genes affected in many disorders and malignancies. This review concentrates on the dysregulated expression of circRNAs like their diagnostic and prognostic values in TNBC. This review aims to focus on the abnormal expression of circRNAs and their diagnostic and prognostic values in TNBC. We used PubMed, Embase, and Web of Science databases and ClinicalTrials.gov to systematically search for all relevant clinical studies. This review is based on articles published in databases up to April 2022 with the following keywords: "Circular RNA", "CircRNA", "Triple-Negative Breast Cancer" and "TNBC". We conducted a review of published CircRNA profiled-research articles to identify candidate CircRNA biomarkers for TNBC. The review is registered on JBI at https://jbi.global/systematic-review-register . Accumulating evidence has shown that several circRNAs are downregulated and some are upregulated in TNBC. The results of these studies confirm that circRNAs might be potential biomarkers with the diagnostic, prognostic, and therapeutic target value for TNBC. We also consider the connection between circRNAs and TNBC cell proliferation, apoptosis, metastasis, and chemotherapy resistance and sensitivity.
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Affiliation(s)
- Zahra Foruzandeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Davood Ghavi Dorabadi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Sadeghi
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Fatemeh Zeinali-Sehrig
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Yazdan Rahmati
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Eye Research Center, the Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
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67
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Almeida A, Gabriel M, Firlej V, Martin‐Jaular L, Lejars M, Cipolla R, Petit F, Vogt N, San‐Roman M, Dingli F, Loew D, Destouches D, Vacherot F, de la Taille A, Théry C, Morillon A. Urinary extracellular vesicles contain mature transcriptome enriched in circular and long noncoding RNAs with functional significance in prostate cancer. J Extracell Vesicles 2022; 11:e12210. [PMID: 35527349 PMCID: PMC9081490 DOI: 10.1002/jev2.12210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022] Open
Abstract
Long noncoding (lnc)RNAs modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, their ability to be transferred and control adjacent cells is unknown. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and antitumourigenic functions by controlling the immune response. In contrast to extracellular nonvesicular RNA, few studies have addressed the full RNA content within human fluids' EVs and have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on six Formalin-Fixed-Paraffin-Embedded (FFPE) prostate cancer (PCa) tumour tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. UEVs contain simplified transcriptome with intron-free cytoplasmic transcripts and enriched lnc/circular (circ)RNAs, strikingly common to an independent 20 patients' urinary cohort. Our full cellular and EVs transcriptome comparison within three PCa cell lines identified a set of overlapping 14 uEV-circRNAs characterized as essential for prostate cell proliferation in vitro and 28 uEV-lncRNAs belonging to the cancer-related lncRNA census (CLC2). In addition, we found 15 uEV-lncRNAs, predicted to encode 768 high-affinity neoantigens, and for which three of the encoded-ORF produced detectable unmodified peptides by mass spectrometry. Our dual analysis of EVs-lnc/circRNAs both in urines' and in vitro's EVs provides a fundamental resource for future uEV-lnc/circRNAs phenotypic characterization involved in PCa.
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Affiliation(s)
- Anna Almeida
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Departement de Recherche TranslationnellePSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Marc Gabriel
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Virginie Firlej
- AP‐HPHôpital H. MondorPlateforme de Ressources BiologiquesCréteilFrance
- Univ Paris Est CreteilUR TRePCaCréteilFrance
| | - Lorena Martin‐Jaular
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Matthieu Lejars
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Rocco Cipolla
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Floriane Petit
- Tumour BiologyINSERM U820, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Nicolas Vogt
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Mabel San‐Roman
- CNRS UMR3215, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | | | | | | | - Clotilde Théry
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Antonin Morillon
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
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68
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Liu H, Akhatayeva Z, Pan C, Liao M, Lan X. Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq. Bioinformatics 2022; 38:3037-3043. [PMID: 35482518 DOI: 10.1093/bioinformatics/btac302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Circular RNA is generally formed by the "back-splicing" process between the upstream splice acceptor and the downstream donor in/not in the regulation of the corresponding RNA-binding proteins or cis-elements. Therefore, more and more software packages have been developed and they are mostly based on the identification of the back-spliced junction reads. However, recent studies developed two software tools that can detect circRNA candidates by constructing k-mer table or/and de bruijn graph rather than reads mapping. RESULTS Here, we compared the precision, sensitivity and detection efficiency between software tools based on different algorithms. Eleven representative detection tools with two types of algorithm were selected for the overall pipeline analysis of RNA-seq datasets with/without RNase R treatment in two cell lines. Precision, sensitivity, AUC, F1 score and detection efficiency metrics were assessed to compare the prediction tools. Meanwhile, the sensitivity and distribution of highly expressed circRNAs before and after RNase R treatment were also revealed by their enrichment, unaffected and depleted candidate frequencies. Eventually, we found that compared to the k-mer based tools, CIRI2 and KNIFE based on reads mapping had relatively superior and more balanced detection performance regardless of the cell line or RNase R (-/+) datasets. AVAILABILITY AND IMPLEMENTATION All predicted results and source codes can be retrieved from https://github.com/luffy563/circRNA_tools_comparison. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hongfei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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69
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Yu W, Gu Q, Wu D, Zhang W, Li G, Lin L, Lowe JM, Hu S, Li TW, Zhou Z, Miao MZ, Gong Y, Zhao Y, Lu E. Identification of potentially functional circRNAs and prediction of circRNA-miRNA-mRNA regulatory network in periodontitis: Bridging the gap between bioinformatics and clinical needs. J Periodontal Res 2022; 57:594-614. [PMID: 35388494 PMCID: PMC9325354 DOI: 10.1111/jre.12989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023]
Abstract
Background and Objective Periodontitis is a multifactorial chronic inflammatory disease that can lead to the irreversible destruction of dental support tissues. As an epigenetic factor, the expression of circRNA is tissue‐dependent and disease‐dependent. This study aimed to identify novel periodontitis‐associated circRNAs and predict relevant circRNA‐periodontitis regulatory network by using recently developed bioinformatic tools and integrating sequencing profiling with clinical information for getting a better and more thorough image of periodontitis pathogenesis, from gene to clinic. Material and Methods High‐throughput sequencing and RT‐qPCR were conducted to identify differentially expressed circRNAs in gingival tissues from periodontitis patients. The relationship between upregulated circRNAs expression and probing depth (PD) was performed using Spearman's correlation analysis. Bioinformatic analyses including GO analysis, circRNA‐disease association prediction, and circRNA‐miRNA‐mRNA network prediction were performed to clarify potential regulatory functions of identified circRNAs in periodontitis. A receiver‐operating characteristic (ROC) curve was established to assess the diagnostic significance of identified circRNAs. Results High‐throughput sequencing identified 70 differentially expressed circRNAs (68 upregulated and 2 downregulated circRNAs) in human periodontitis (fold change >2.0 and p < .05). The top five upregulated circRNAs were validated by RT‐qPCR that had strong associations with multiple human diseases, including periodontitis. The upregulation of circRNAs were positively correlated with PD (R = .40–.69, p < .05, moderate). A circRNA‐miRNA‐mRNA network with the top five upregulated circRNAs, differentially expressed mRNAs, and overlapped predicted miRNAs indicated potential roles of circRNAs in immune response, cell apoptosis, migration, adhesion, and reaction to oxidative stress. The ROC curve showed that circRNAs had potential value in periodontitis diagnosis (AUC = 0.7321–0.8667, p < .05). Conclusion CircRNA‐disease associations were predicted by online bioinformatic tools. Positive correlation between upregulated circRNAs, circPTP4A2, chr22:23101560‐23135351+, circARHGEF28, circBARD1 and circRASA2, and PD suggested function of circRNAs in periodontitis. Network prediction further focused on downstream targets regulated by circRNAs during periodontitis pathogenesis.
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Affiliation(s)
- Weijun Yu
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Qisheng Gu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Department of Immunology, Bio Sorbonne Paris Cité, University of Paris, Paris, France
| | - Di Wu
- Division of Oral and Craniofacial Biomedicine, University of North Carolina Adams School of Dentistry, Chapel Hill, North Carolina, USA.,Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Weiqi Zhang
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Li
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Lu Lin
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jared M Lowe
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shucheng Hu
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tia Wenjun Li
- Division of Oral and Craniofacial Biomedicine, University of North Carolina Adams School of Dentistry, Chapel Hill, North Carolina, USA.,Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zhen Zhou
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael Z Miao
- Division of Oral and Craniofacial Biomedicine, University of North Carolina Adams School of Dentistry, Chapel Hill, North Carolina, USA
| | - Yuhua Gong
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yifei Zhao
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Eryi Lu
- Department of Stomatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
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70
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Sharma AR, Banerjee S, Bhattacharya M, Saha A, Lee SS, Chakraborty C. Recent progress of circular RNAs in different types of human cancer: Technological landscape, clinical opportunities and challenges (Review). Int J Oncol 2022; 60:56. [PMID: 35362541 DOI: 10.3892/ijo.2022.5346] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/10/2022] [Indexed: 11/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of endogenous non‑coding RNAs that have been recently regarded as functionally active. CircRNAs are remarkably stable and known to possess several biological functions such as microRNA sponging, regulating transcription and splicing and occasionally acting as polypeptide‑producing templates. CircRNAs show tissue‑specific expression and have been reported to be associated with the progression of several types of malignancies. Given the recent progress in genome sequencing and bioinformatics techniques, a rapid increment in the biological role of circRNAs has been observed. Concurrently, the patent search from different patent databases shows that the patent number of circRNA is increasing very quickly. These phenomena reveal a rapid development of the technological landscape. In the present review, the recent progress on circRNAs in various kinds of cancer has been investigated and their function as biomarkers or therapeutic targets and their technological landscape have been appreciated. A new insight into circRNAs structure and functional capabilities in cancer has been reviewed. Continually increasing knowledge on their critical role during cancer progression is projecting them as biomarkers or therapeutic targets for various kinds of cancer. Thus, recent updates on the functional role of circRNAs in terms of the technological landscape, clinical opportunities (biomarkers and therapeutic targets), and challenges in cancer have been illustrated.
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Affiliation(s)
- Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University‑Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon 24252, Republic of Korea
| | - Shreya Banerjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, Odisha 756020, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University‑Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon 24252, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
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71
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Zucko D, Hayir A, Grinde K, Boris-Lawrie K. Circular RNA Profiles in Viremia and ART Suppression Predict Competing circRNA–miRNA–mRNA Networks Exclusive to HIV-1 Viremic Patients. Viruses 2022; 14:v14040683. [PMID: 35458413 PMCID: PMC9027527 DOI: 10.3390/v14040683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 02/01/2023] Open
Abstract
Since the onset of the HIV-1/AIDS epidemic in 1981, 75 million people have been infected with the virus, and the disease remains a public health crisis worldwide. Circular RNAs (circRNAs) are derived from excised exons and introns during backsplicing, a form of alternative splicing. The relevance of unconventional, non-capped, and non-poly(A) transcripts to transcriptomics studies remains to be routinely investigated. Knowledge gaps to be filled are the interface between host-encoded circRNAs and viral replication in chronically progressed patients and upon treatment with antiviral drugs. We implemented a bioinformatic pipeline and repurpose publicly archived RNA sequence reads from the blood of 19 HIV-1-positive patients that previously compared transcriptomes during viremia and viremia suppression by antiretroviral therapy (ART). The in silico analysis identified viremic patients’ circRNA that became undetectable after ART. The circRNAs originated from a subset of host genes enriched in the HDAC biological pathway. These circRNAs and parental mRNAs held in common a small collection of miRNA response elements (MREs), some of which were present in HIV-1 mRNAs. The function of the MRE-containing target mRNA enriched the RNA polymerase II GO pathway. To visualize the interplay between individual circRNA–miRNA–target mRNA, important for HIV-1 and potentially other diseases, an Interactive Circos tool was developed to efficiently parse the intricately competing endogenous network of circRNA–miRNA–mRNA interactions originating from seven circRNA singled out in viremic versus non-viremic patients. The combined downregulation of the identified circRNAs warrants investigation as a novel antiviral targeting strategy.
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Affiliation(s)
- Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
| | - Abdullgadir Hayir
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA;
| | - Kelsey Grinde
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA;
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
- Correspondence:
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72
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De Palma FDE, Salvatore F, Pol JG, Kroemer G, Maiuri MC. Circular RNAs as Potential Biomarkers in Breast Cancer. Biomedicines 2022; 10:725. [PMID: 35327527 PMCID: PMC8945016 DOI: 10.3390/biomedicines10030725] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Due to the high heterogeneity and initially asymptomatic nature of breast cancer (BC), the management of this disease depends on imaging together with immunohistochemical and molecular evaluations. These tests allow early detection of BC and patient stratification as they guide clinicians in prognostication and treatment decision-making. Circular RNAs (circRNAs) represent a class of newly identified long non-coding RNAs. These molecules have been described as key regulators of breast carcinogenesis and progression. Moreover, circRNAs play a role in drug resistance and are associated with clinicopathological features in BC. Accumulating evidence reveals a clinical interest in deregulated circRNAs as diagnostic, prognostic and predictive biomarkers. Furthermore, due to their covalently closed structure, circRNAs are highly stable and easily detectable in body fluids, making them ideal candidates for use as non-invasive biomarkers. Herein, we provide an overview of the biogenesis and pleiotropic functions of circRNAs, and report on their clinical relevance in BC.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy;
- CEINGE-Biotecnologie Avanzate, 80145 Naples, Italy
| | - Francesco Salvatore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy;
- CEINGE-Biotecnologie Avanzate, 80145 Naples, Italy
- Inter-University Center for multifactorial and multi genetic chronic human diseases, “Federico II”-Naples, Tor Vergata-Roma II, and Chieti-Pescara Universities, 80131 Naples, Italy
| | - Jonathan G. Pol
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Guido Kroemer
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Maria Chiara Maiuri
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy
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73
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Huang HB, Luo HT, Wei NN, Liu ML, He F, Yang W, Dong J, Yang XF, Li FR. Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells. Stem Cell Res Ther 2022; 13:106. [PMID: 35279206 PMCID: PMC8917624 DOI: 10.1186/s13287-022-02792-5] [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: 09/22/2021] [Accepted: 02/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background The balance between osteogenesis and adipogenesis of mesenchymal stem cells (MSCs) is critical to skeletal development and diseases. As a research hotspot, circular RNAs (circRNAs) have expanded our understanding of a hidden layer of the transcriptome. Yet, their roles during adipo-osteogenesis remain poorly described. Methods The identity of human MSCs derived from bone marrow and adipose were first determined by flow cytometry, cellular staining, and quantitative polymerase chain reaction (qPCR). Multi-strategic RNA-sequencing was performed using Poly A, RiboMinus and RiboMinus/RNase R methods. Integrative analysis was performed to identify lineage-specific expressed circRNAs. The structural and expressional characteristics were identified by Sanger sequencing and qPCR, respectively. The regulatory effects of adipogenesis-specific circ-CRLF1 were confirmed using siRNA transcfection and qPCR. Results We generated a whole transcriptome map during adipo-osteogenesis based on 10 Poly A, 20 RiboMinus and 20 RiboMinus/ RNase R datasets. A total of 31,326 circRNAs were identified and quantified from ~ 3.4 billion paired-end reads. Furthermore, the integrative analysis revealed that 1166 circRNA genes exhibited strong lineage-specific expression patterns. Their host genes were enriched in distinct biological functions, such as cell adhesion, cytokine signaling, and cell division. We randomly selected and validated the back-spliced junction sites and expression patterns of 12 lineage-specific circRNAs. Functional analysis indicated that circ-CRLF1 negatively regulated adipogenesis. Conclusions Our integrative analysis reveals an accurate and generally applicable lineage-specific circRNA landscape for adipo-osteogenesis of MSCs and provides a potential therapeutic target, circ-CRLF1, for the treatment of skeleton-related disease. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02792-5.
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Affiliation(s)
- Hai-Bo Huang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Hai-Tao Luo
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Na-Na Wei
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.,Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China
| | - Miao-Ling Liu
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China
| | - Fei He
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China
| | - Wei Yang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China
| | - Jun Dong
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China. .,Department of Pathophysiology, Key Laboratory of the State Administration of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Xiao-Fei Yang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China. .,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.
| | - Fu-Rong Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China. .,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China. .,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China.
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Chen S, Cao X, Zhang J, Wu W, Zhang B, Zhao F. circVAMP3 Drives CAPRIN1 Phase Separation and Inhibits Hepatocellular Carcinoma by Suppressing c-Myc Translation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103817. [PMID: 35072355 PMCID: PMC8922094 DOI: 10.1002/advs.202103817] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/16/2021] [Indexed: 05/04/2023]
Abstract
Previous studies have identified the regulatory roles of circular RNAs (circRNAs) in human cancers. However, the molecular mechanisms of circRNAs in hepatocellular carcinoma (HCC) remain largely unknown. This study screens the expression profile of circRNAs in HCC and identifies circVAMP3 as a significantly downregulated circRNA in HCC tissues. HCC patients with low circVAMP3 expression present poor prognosis. circVAMP3 negatively regulates the proliferation and metastasis of HCC cells in vitro and in vivo by driving phase separation of CAPRIN1 and promoting stress granule formation in cells, which can downregulate the protein level of Myc proto-oncogene protein by inhibiting c-Myc translation. Furthermore, circVAMP3 is widely expressed in many human tissues and is downregulated in related cancers. Therefore, circVAMP3 is a potential prognostic indicator for HCC and may serve as a therapeutic target for HCC treatment.
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Affiliation(s)
- Shuai Chen
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Xiaofei Cao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- Key Laboratory of Systems BiologyHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310013China
| | - Jinyang Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
| | - Wanying Wu
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
| | - Bing Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
| | - Fangqing Zhao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Key Laboratory of Systems BiologyHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310013China
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming650223China
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75
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Wang P, Wang S, Wu Y, Nie W, Yiming A, Huang J, Ahmad I, Zhu B, Chen G. Identification and Characterization of Rice Circular RNAs Responding to Xanthomonas oryzae pv. oryzae Invasion. PHYTOPATHOLOGY 2022; 112:492-500. [PMID: 34420356 DOI: 10.1094/phyto-06-21-0235-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Emerging roles of circular RNAs (circRNAs) in various biological processes have advanced our knowledge of transcriptional and posttranscriptional gene regulation. To date, no research has been conducted to explore their roles in the rice-Xanthomonas oryzae pv. oryzae interaction. Therefore, we identified 3,517 circRNAs from rice leaves infected with the highly virulent X. oryzae pv. oryzae strain PXO99A by using rRNA depleted RNA sequencing technique coupled with the CIRI2 and CIRCexplorer2 pipeline. Characterization analyses showed that these circRNAs were distributed across the whole genome of rice, and most circRNAs arose from exons (85.13%), ranged from 200 to 1,000 bp, and were with a noncanonical GT/AG (including CT/AC equivalent) splicing signal. Functional annotation and enrichment analysis of the host genes that produced the differentially expressed circRNAs (DEcircRNAs) suggested that these identified circRNAs might play an important role in reprogramming rice responses to PXO99A invasion, mainly by mediating photorespiration and chloroplast, peroxisome, and diterpenoid biosynthesis. Moreover, 31 DEcircRNAs were predicted to act as microRNA decoys in rice. The expression profile of four DEcircRNAs were validated by quantitative real-time PCR with divergent primers, and the back-splicing sites of seven DEcircRNAs were verified by PCR analysis and Sanger sequencing. Collectively, these results inferred a potential functional role of circRNAs in the regulation of rice immunity and provide novel clues about the molecular mechanisms of rice-PXO99A interaction.
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Affiliation(s)
- Peihong Wang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Wu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhan Nie
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ayizekeranmu Yiming
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Huang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Iftikhar Ahmad
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Vehari 61100, Pakistan
| | - Bo Zhu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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76
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Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation. Genome Biol 2022; 23:48. [PMID: 35130952 PMCID: PMC8819885 DOI: 10.1186/s13059-022-02621-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/26/2022] [Indexed: 01/22/2023] Open
Abstract
Background Circular RNAs (circRNAs), a novel class of poorly conserved non-coding RNAs that regulate gene expression, are highly enriched in the human brain. Despite increasing discoveries of circRNA function in human neurons, the circRNA landscape and function in developing human oligodendroglia, the myelinating cells that govern neuronal conductance, remains unexplored. Meanwhile, improved experimental and computational tools for the accurate identification of circRNAs are needed. Results We adopt a published experimental approach for circRNA enrichment and develop CARP (CircRNA identification using A-tailing RNase R approach and Pseudo-reference alignment), a comprehensive 21-module computational framework for accurate circRNA identification and quantification. Using CARP, we identify developmentally programmed human oligodendroglia circRNA landscapes in the HOG oligodendroglioma cell line, distinct from neuronal circRNA landscapes. Numerous circRNAs display oligodendroglia-specific regulation upon differentiation, among which a subclass is regulated independently from their parental mRNAs. We find that circRNA flanking introns often contain cis-regulatory elements for RNA editing and are predicted to bind differentiation-regulated splicing factors. In addition, we discover novel oligodendroglia-specific circRNAs that are predicted to sponge microRNAs, which co-operatively promote oligodendroglia development. Furthermore, we identify circRNA clusters derived from differentiation-regulated alternative circularization events within the same gene, each containing a common circular exon, achieving additive sponging effects that promote human oligodendroglia differentiation. Conclusions Our results reveal dynamic regulation of human oligodendroglia circRNA landscapes during early differentiation and suggest critical roles of the circRNA-miRNA-mRNA axis in advancing human oligodendroglia development. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02621-1.
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77
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Xu D, Ma X, Sun C, Han J, Zhou C, Wong SH, Chan MTV, Wu WKK. Circular RNAs in Intervertebral Disc Degeneration: An Updated Review. Front Mol Biosci 2022; 8:781424. [PMID: 35071323 PMCID: PMC8770867 DOI: 10.3389/fmolb.2021.781424] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/13/2021] [Indexed: 01/26/2023] Open
Abstract
Low back pain, a common medical condition, could result in severe disability and inflict huge economical and public health burden. Its pathogenesis is attributed to multiple etiological factors, including intervertebral disc degeneration (IDD). Emerging evidence suggests that circular RNAs (circRNAs), a major type of regulatory non-coding RNA, play critical roles in cellular processes that are pertinent to IDD development, including nucleus pulposus cell proliferation and apoptosis as well as extracellular matrix deposition. Increasing number of translational studies also indicated that circRNAs could serve as novel biomarkers for the diagnosis of IDD and/or predicting its clinical outcomes. Our review aims to discuss the recent progress in the functions and mechanisms of newly discovered IDD-related circRNAs.
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Affiliation(s)
- Derong Xu
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xuexiao Ma
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chong Sun
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jialuo Han
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chuanli Zhou
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Sunny Hei Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - William K K Wu
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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78
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Pu Z, Lu J, Yang X. Emerging Roles of Circular RNAs in Vascular Smooth Muscle Cell Dysfunction. Front Genet 2022; 12:749296. [PMID: 35126447 PMCID: PMC8807483 DOI: 10.3389/fgene.2021.749296] [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: 07/29/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
Atherosclerosis is the major pathophysiological basis of cerebrovascular and cardiovascular diseases. Vascular smooth muscle cells (VSMCs) constitute the main structure of vasculature and play important roles in maintaining vascular tone and blood pressure. Many biological processes and cellular signaling events involved in atherosclerogenesis have been shown to converge on deregulating VSMC functions. However, the molecular mechanisms underlying dysfunctional VSMC in atherosclerosis are still poorly defined. Recent evidence revealed that circular RNAs (circRNAs) are closely related to diseases such as degenerative diseases, tumor, congenital diseases, endocrine diseases and cardiovascular diseases. Several studies demonstrated that circRNAs (e.g., circACTA2, Circ-SATB2, circDiaph3, circ_0020397, circTET3, circCCDC66) played critical roles in the regulation of VSMC proliferation, migration, invasion, and contractile-to-synthetic phenotype transformation by sponging microRNAs (e.g., miR-548f-5p, miR-939, miR-148a-5p, miR-138, miR-351-5p, miR-342-3p). This review describes recent progress in the profiling of circRNAs by transcriptome analysis in VSMCs and their molecular functions in regulating VSMC proliferation and migration.
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Affiliation(s)
| | - Jingbo Lu
- *Correspondence: Jingbo Lu, ; Xiaohan Yang,
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79
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Li P, Song R, Yin F, Liu M, Liu H, Ma S, Jia X, Lu X, Zhong Y, Yu L, Li X, Li X. circMRPS35 promotes malignant progression and cisplatin resistance in hepatocellular carcinoma. Mol Ther 2022; 30:431-447. [PMID: 34450251 PMCID: PMC8753434 DOI: 10.1016/j.ymthe.2021.08.027] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 01/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related death worldwide. Circular RNAs (circRNAs), a novel class of non-coding RNA, have been reported to be involved in the etiology of various malignancies. However, the underlying cellular mechanisms of circRNAs implicated in the pathogenesis of HCC remain unknown. In this study, we identified a functional RNA, hsa_circ_0000384 (circMRPS35), from public tumor databases using a set of computational analyses, and we further identified that circMRPS35 was highly expressed in 35 pairs of HCC from patients. Moreover, knockdown of the expression of circMRPS35 in Huh-7 and HCC-LM3 cells suppressed their proliferation, migration, invasion, clone formation, and cell cycle in vitro, and it suppressed tumor growth in vivo as well. Mechanically, circMRPS35 sponged microRNA-148a-3p (miR-148a), regulating the expression of Syntaxin 3 (STX3), which modulated the ubiquitination and degradation of phosphatase and tensin homolog (PTEN). Unexpectedly, we detected a peptide encoded by circMRPS35 (circMRPS35-168aa), which was significantly induced by chemotherapeutic drugs and promoted cisplatin resistance in HCC. These results demonstrated that circMRPS35 might be a novel mediator in HCC progress, and they raise the potential of a new biomarker for HCC diagnosis and prognosis, as well as a novel therapeutic target for HCC patients.
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Affiliation(s)
- Peng Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Runjie Song
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fan Yin
- Department of Oncology, The Second Medical Centre & National Clinical Research Center of Geriatric Disease, Chinese PLA General Hospital, Beijing 100071, China
| | - Mei Liu
- Department of Pathology, Chinese PLA General Hospital, Beijing 100071, China
| | - Huijiao Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuoqian Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaomeng Jia
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohui Lu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuting Zhong
- Department of Surgery, Chinese PLA General Hospital, Beijing, 100071, China
| | - Lei Yu
- Department of Thoracic Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100005, China
| | - Xiru Li
- Department of Surgery, Chinese PLA General Hospital, Beijing, 100071, China
| | - Xiangdong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland,Department of Nutrition and Health, China Agricultural University, Beijing 100193, China,Corresponding author: Xiangdong Li, State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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80
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Dai Q, Pu SS, Yang X, Li C, He Y, Liu X, Wang G. Whole Transcriptome Sequencing of Peripheral Blood Shows That Immunity/GnRH/PI3K-Akt Pathways Are Associated With Opioid Use Disorder. Front Psychiatry 2022; 13:893303. [PMID: 35800019 PMCID: PMC9253397 DOI: 10.3389/fpsyt.2022.893303] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Opioid use disorder (OUD), which is most commonly exhibited as addiction, is a persistent chronic disease that places a burden on families and society. Various peripheral traits have been linked to OUD in the past, but research on this topic is insufficient. METHODS Seven male patients with OUD and 7 male healthy controls with matched demographic and clinical data were enrolled in this study. Peripheral blood RNA was used to construct an rRNA-removed library and a small RNA library. The peripheral transcriptomic differences between the two groups were investigated using RNA-seq. Differentially expressed messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) were identified by bioinformatics methods, and functional enrichment analysis with differentially expressed RNAs was performed to investigate the potential biological mechanisms of OUD. RESULTS A total of 229 mRNAs (115 upregulated, 114 downregulated), 416 lncRNAs (191 upregulated, 225 downregulated), 17 circRNAs (16 upregulated, 1 downregulated) and 74 miRNAs (42 upregulated, 32 downregulated) were differentially expressed between the OUD group and the healthy control group. Functional enrichment analysis with differentially expressed mRNAs showed that immunity, GnRH secretion, and PI3K-Akt signaling pathways were associated with OUD. Immunity-, JAK-STAT-, and insulin-related pathways were enriched in functional enrichment analysis of target genes predicted by differentially expressed miRNAs. CONCLUSION We identified hundreds of differentially expressed genes that were enriched in immunity, GnRH secretion and PI3K-Akt signaling pathways. Some genes with significant changes might be used as potential biomarkers for progression and treatment of OUD.
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Affiliation(s)
- Qi Dai
- Affiliated Wuhan Mental Health Center, Jianghan University, Wuhan, China
| | - Shan-Shan Pu
- School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, China.,Department of Addiction, Wuhan Mental Health Center, Wuhan, China
| | - Xue Yang
- Department of Addiction, Wuhan Mental Health Center, Wuhan, China
| | - Chang Li
- Department of Psychiatry, Wuhan Mental Health Center, Wuhan, China
| | - Yafei He
- Department of Psychiatry, Wuhan Mental Health Center, Wuhan, China
| | - Xiaobo Liu
- Department of Psychiatry, Wuhan Mental Health Center, Wuhan, China
| | - Gang Wang
- Affiliated Wuhan Mental Health Center, Jianghan University, Wuhan, China.,Department of Addiction, Wuhan Mental Health Center, Wuhan, China
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Khashkhashi Moghadam S, Bakhshinejad B, Khalafizadeh A, Mahmud Hussen B, Babashah S. Non-coding RNA-associated competitive endogenous RNA regulatory networks: Novel diagnostic and therapeutic opportunities for hepatocellular carcinoma. J Cell Mol Med 2021; 26:287-305. [PMID: 34907642 PMCID: PMC8743668 DOI: 10.1111/jcmm.17126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC), as the most prevalent liver malignancy, is annually diagnosed in more than half a million people worldwide. HCC is strongly associated with hepatitis B and C viral infections as well as alcohol abuse. Obesity and nonalcoholic fatty liver disease (NAFLD) also significantly enhance the risk of liver cancer. Despite recent improvements in therapeutic approaches, patients diagnosed in advanced stages show poor prognosis. Accumulating evidence provides support for the regulatory role of non-coding RNAs (ncRNAs) in cancer. There are a variety of reports indicating the regulatory role of microRNAs (miRNAs) in different stages of HCC. Long non-coding RNAs (LncRNAs) exert their effects by sponging miRNAs and controlling the expression of miRNA-targeted genes. Circular RNAs (circRNAs) perform their biological functions by acting as transcriptional regulators, miRNA sponges and protein templates. Diverse studies have illustrated that dysregulation of competing endogenous RNA networks (ceRNETs) is remarkably correlated with HCC-causing diseases such as chronic viral infections, nonalcoholic steatohepatitis and liver fibrosis/cirrhosis. The aim of the current article was to provide an overview of the role and molecular mechanisms underlying the function of ceRNETs that modulate the characteristics of HCC such as uncontrolled cell proliferation, resistance to cell death, metabolic reprogramming, immune escape, angiogenesis and metastasis. The current knowledge highlights the potential of these regulatory RNA molecules as novel diagnostic biomarkers and therapeutic targets in HCC.
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Affiliation(s)
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Khalafizadeh
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Sadegh Babashah
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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82
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Wen ZJ, Xin H, Wang YC, Liu HW, Gao YY, Zhang YF. Emerging roles of circRNAs in the pathological process of myocardial infarction. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:828-848. [PMID: 34729251 PMCID: PMC8536508 DOI: 10.1016/j.omtn.2021.10.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Myocardial infarction (MI) is defined as cardiomyocyte death in a clinical context consistent with ischemic insult. MI remains one of the leading causes of morbidity and mortality worldwide. Although there are a number of effective clinical methods for the diagnosis and treatment of MI, further investigation of novel biomarkers and molecular therapeutic targets is required. Circular RNAs (circRNAs), novel non-coding RNAs, have been reported to function mainly by acting as microRNA (miRNA) sponges or binding to RNA-binding proteins (RBPs). The circRNA-miRNA-mRNA (protein) regulatory pathway regulates gene expression and affects the pathological mechanisms of various diseases. Undoubtedly, a more comprehensive understanding of the relationship between MI and circRNA will lay the foundation for the development of circRNA-based diagnostic and therapeutic strategies for MI. Therefore, this review summarizes the pathophysiological process of MI and various approaches to measure circRNA levels in MI patients, tissues, and cells; highlights the significance of circRNAs in the regulation MI pathogenesis and development; and provides potential clinical insight for the diagnosis, prognosis, and treatment of MI.
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Affiliation(s)
- Zeng-Jin Wen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Hui Xin
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yong-Chen Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Hao-Wen Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan-Yan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
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83
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Krishnamoorthy A, Kadener S. Using Drosophila to uncover molecular and physiological functions of circRNAs. Methods 2021; 196:74-84. [PMID: 33901645 PMCID: PMC8542058 DOI: 10.1016/j.ymeth.2021.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed RNA molecules generated by backsplicing. circRNAs are expressed in a tissue-specific manner, accumulate with age in neural tissues, and are highly stable. In many cases, circRNAs are generated at the expense of a linear transcript as back-splicing competes with linear splicing. Some circRNAs regulate gene expression in cis, and some circRNAs can be translated into protein. The advent of deep sequencing and new bioinformatic tools has allowed detection of thousands of circRNAs in eukaryotes. Studying the functions of circRNAs is done using a combination of molecular and genetic methods. The unique genetic tools that can be used in studies of Drosophila melanogaster are ideal for deciphering the functions of circRNAs in vivo. These tools include the GAL4-UAS system, which can be used to manipulate the levels of circRNAs with exquisite temporal and spatial control, and genetic interaction screening, which could be used to identify pathways regulated by circRNAs. Research performed in Drosophila has revealed circRNAs production mechanisms, details of their translation, and their physiological functions. Due to their short lifecycle and the existence of excellent neurodegeneration models, Drosophila can also be used to study the role of circRNAs in aging and age-related disorders. Here, we review molecular and genetic tools and methods for detecting, manipulating, and studying circRNAs in Drosophila.
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Affiliation(s)
| | - Sebastian Kadener
- Biology Department, Brandeis University, Waltham, MA 02454, United States.
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84
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Yu KHO, Shi CH, Wang B, Chow SHC, Chung GTY, Lung RWM, Tan KE, Lim YY, Tsang ACM, Lo KW, Yip KY. Quantifying full-length circular RNAs in cancer. Genome Res 2021; 31:2340-2353. [PMID: 34663689 PMCID: PMC8647826 DOI: 10.1101/gr.275348.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 10/12/2021] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discover and validate circRNA isoforms differentially expressed between the two groups. Compared with the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain substantially fewer microRNA response elements, showing the importance of quantifying full-length circRNA isoforms.
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Affiliation(s)
- Ken Hung-On Yu
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Christina Huan Shi
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Bo Wang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Savio Ho-Chit Chow
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Grace Tin-Yun Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Raymond Wai-Ming Lung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ke-En Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yat-Yuen Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Anna Chi-Man Tsang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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85
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Nong B, Guo M, Wang W, Songyang Z, Xiong Y. Comprehensive Analysis of Large-Scale Transcriptomes from Multiple Cancer Types. Genes (Basel) 2021; 12:1865. [PMID: 34946814 PMCID: PMC8701385 DOI: 10.3390/genes12121865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Various abnormalities of transcriptional regulation revealed by RNA sequencing (RNA-seq) have been reported in cancers. However, strategies to integrate multi-modal information from RNA-seq, which would help uncover more disease mechanisms, are still limited. Here, we present PipeOne, a cross-platform one-stop analysis workflow for large-scale transcriptome data. It was developed based on Nextflow, a reproducible workflow management system. PipeOne is composed of three modules, data processing and feature matrices construction, disease feature prioritization, and disease subtyping. It first integrates eight different tools to extract different information from RNA-seq data, and then used random forest algorithm to study and stratify patients according to evidences from multiple-modal information. Its application in five cancers (colon, liver, kidney, stomach, or thyroid; total samples n = 2024) identified various dysregulated key features (such as PVT1 expression and ABI3BP alternative splicing) and pathways (especially liver and kidney dysfunction) shared by multiple cancers. Furthermore, we demonstrated clinically-relevant patient subtypes in four of five cancers, with most subtypes characterized by distinct driver somatic mutations, such as TP53, TTN, BRAF, HRAS, MET, KMT2D, and KMT2C mutations. Importantly, these subtyping results were frequently contributed by dysregulated biological processes, such as ribosome biogenesis, RNA binding, and mitochondria functions. PipeOne is efficient and accurate in studying different cancer types to reveal the specificity and cross-cancer contributing factors of each cancer.It could be easily applied to other diseases and is available at GitHub.
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Affiliation(s)
- Baoting Nong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
| | - Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
| | - Weiwen Wang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510006, China;
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
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86
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Ghafouri-Fard S, Khoshbakht T, Taheri M, Jamali E. A Concise Review on the Role of CircPVT1 in Tumorigenesis, Drug Sensitivity, and Cancer Prognosis. Front Oncol 2021; 11:762960. [PMID: 34804965 PMCID: PMC8599443 DOI: 10.3389/fonc.2021.762960] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022] Open
Abstract
CircPVT1 (hsa_circ_0001821) is a cancer-related circular RNA (circRNA) that originated from a genomic locus on chromosome 8q24. This locus has been previously found to encode the oncogenic long non-coding RNA PVT1. Expression of this circRNA has been found to be upregulated in diverse neoplastic conditions. CircPVT1 acts as a sponge for miR-125a, miR-125b, miR-124-3p, miR-30a-5p, miR-205-5p, miR-423-5p, miR-526b, miR-137, miR-145-5p, miR-497, miR-30d/e, miR-455-5p, miR-29a-3p, miR-204-5p, miR-149, miR-106a-5p, miR-377, miR-3666, miR-203, and miR-199a-5p. Moreover, it can regulate the activities of PI3K/AKT, Wnt5a/Ror2, E2F2, and HIF-1α. Upregulation of circPVT1 has been correlated with decreased survival of patients with different cancer types. In the current review, we explain the oncogenic impact of circPVT1 in different tissues based on evidence from in vitro, in vivo, and clinical investigations.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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87
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Fatema K, Barrott JJ. Circling back to epigenetic regulation in osteosarcoma: Comment on 'Hsa_circ_0088212-mediated miR-520h/APOA1 axis inhibits the osteosarcoma progression' by ' Hao Peng'. Transl Oncol 2021; 15:101271. [PMID: 34801860 PMCID: PMC8605336 DOI: 10.1016/j.tranon.2021.101271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
CircRNAs are useful biomarkers and therapeutic targets in osteosarcoma. The circ_0088212/miR-520h/APOA1 signaling axis highlights dysregulation of opposing signals that facilitate tumor growth.
Osteosarcoma is a genetically complex cancer, thus there are increasing efforts to identify biomarkers and regulators within the epigenome that can better predict patient outcomes and provide new therapeutic targets. In this commentary, we have evaluated the work of Peng and colleagues on the identification and function of the signaling axis circ_0088212/miR_520 h/APOA1 in osteosarcoma. We provide the context of how novel it is to demonstrate the anti-tumor functions of APOA1 and not just correlative gene expression with patient outcome. We further postulate why some studies involving circRNAs in osteosarcoma contradict one another. We conclude that the study performed by Peng and colleagues was performed with enough rigor to give confidence that circ_0088212 is a bona fide tumor suppressor in osteosarcoma.
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Affiliation(s)
- Kaniz Fatema
- Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID, USA
| | - Jared J Barrott
- Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID, USA.
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88
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Gaffo E, Buratin A, Dal Molin A, Bortoluzzi S. Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2. Brief Bioinform 2021; 23:6409697. [PMID: 34698333 PMCID: PMC8769706 DOI: 10.1093/bib/bbab418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules originating by a process called back-splicing. CircRNAs are emerging as functional RNAs involved in the regulation of biological processes as well as in disease and cancer mechanisms. Current computational methods for circRNA identification from RNA-seq experiments are characterized by low discovery rates and performance dependent on the analysed data set. We developed CirComPara2 (https://github.com/egaffo/CirComPara2), a new automated computational pipeline for circRNA discovery and quantification, which consistently achieves high recall rates without losing precision by combining multiple circRNA detection methods. In our benchmark analysis, CirComPara2 outperformed state-of-the-art circRNA discovery tools and proved to be a reliable and robust method for comprehensive transcriptome characterization.
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Affiliation(s)
- Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy; Department of Biology, University of Padova, Padova, Italy
| | - Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy; Interdepartmental Center For Innovative Biotechnologies, University of Padova, Padova, Italy
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89
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Xiao Q, Dai J, Luo J. A survey of circular RNAs in complex diseases: databases, tools and computational methods. Brief Bioinform 2021; 23:6407737. [PMID: 34676391 DOI: 10.1093/bib/bbab444] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) are a category of novelty discovered competing endogenous non-coding RNAs that have been proved to implicate many human complex diseases. A large number of circRNAs have been confirmed to be involved in cancer progression and are expected to become promising biomarkers for tumor diagnosis and targeted therapy. Deciphering the underlying relationships between circRNAs and diseases may provide new insights for us to understand the pathogenesis of complex diseases and further characterize the biological functions of circRNAs. As traditional experimental methods are usually time-consuming and laborious, computational models have made significant progress in systematically exploring potential circRNA-disease associations, which not only creates new opportunities for investigating pathogenic mechanisms at the level of circRNAs, but also helps to significantly improve the efficiency of clinical trials. In this review, we first summarize the functions and characteristics of circRNAs and introduce some representative circRNAs related to tumorigenesis. Then, we mainly investigate the available databases and tools dedicated to circRNA and disease studies. Next, we present a comprehensive review of computational methods for predicting circRNA-disease associations and classify them into five categories, including network propagating-based, path-based, matrix factorization-based, deep learning-based and other machine learning methods. Finally, we further discuss the challenges and future researches in this field.
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Affiliation(s)
- Qiu Xiao
- Hunan Normal University and Hunan Xiangjiang Artificial Intelligence Academy, Changsha, China
| | - Jianhua Dai
- Hunan Normal University and Hunan Xiangjiang Artificial Intelligence Academy, Changsha, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
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90
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Nguyen DT, Trac QT, Nguyen TH, Nguyen HN, Ohad N, Pawitan Y, Vu TN. Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data. BMC Bioinformatics 2021; 22:495. [PMID: 34645386 PMCID: PMC8513298 DOI: 10.1186/s12859-021-04418-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circular RNA (circRNA) is an emerging class of RNA molecules attracting researchers due to its potential for serving as markers for diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and autoimmune diseases. Current methods for detection of circRNA from RNA sequencing (RNA-seq) focus mostly on improving mapping quality of reads supporting the back-splicing junction (BSJ) of a circRNA to eliminate false positives (FPs). We show that mapping information alone often cannot predict if a BSJ-supporting read is derived from a true circRNA or not, thus increasing the rate of FP circRNAs. RESULTS We have developed Circall, a novel circRNA detection method from RNA-seq. Circall controls the FPs using a robust multidimensional local false discovery rate method based on the length and expression of circRNAs. It is computationally highly efficient by using a quasi-mapping algorithm for fast and accurate RNA read alignments. We applied Circall on two simulated datasets and three experimental datasets of human cell-lines. The results show that Circall achieves high sensitivity and precision in the simulated data. In the experimental datasets it performs well against current leading methods. Circall is also substantially faster than the other methods, particularly for large datasets. CONCLUSIONS With those better performances in the detection of circRNAs and in computational time, Circall facilitates the analyses of circRNAs in large numbers of samples. Circall is implemented in C++ and R, and available for use at https://www.meb.ki.se/sites/biostatwiki/circall and https://github.com/datngu/Circall.
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Affiliation(s)
- Dat Thanh Nguyen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Quang Thinh Trac
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Thi-Hau Nguyen
- University of Engineering and Technology, Vietnam National University in Hanoi, Hanoi, Vietnam
| | - Ha-Nam Nguyen
- Information Technology Institute, Vietnam National University in Hanoi, Hanoi, Vietnam
| | - Nir Ohad
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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91
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Chen K, Chen C, Li H, Yang J, Xiang M, Wang H, Xie Z. Widespread translational control regulates retinal development in mouse. Nucleic Acids Res 2021; 49:9648-9664. [PMID: 34469513 PMCID: PMC8464051 DOI: 10.1093/nar/gkab749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022] Open
Abstract
Retinal development is tightly regulated to ensure the generation of appropriate cell types and the assembly of functional neuronal circuitry. Despite remarkable advances have been made in understanding regulation of gene expression during retinal development, how translational regulation guides retinogenesis is less understood. Here, we conduct a comprehensive translatome and transcriptome survey to the mouse retinogenesis from the embryonic to the adult stages. We discover thousands of genes that have dynamic changes at the translational level and pervasive translational regulation in a developmental stage-specific manner with specific biological functions. We further identify genes whose translational efficiencies are frequently controlled by changing usage in upstream open reading frame during retinal development. These genes are enriched for biological functions highly important to neurons, such as neuron projection organization and microtubule-based protein transport. Surprisingly, we discover hundreds of previously uncharacterized micropeptides, translated from putative long non-coding RNAs and circular RNAs. We validate their protein products in vitro and in vivo and demonstrate their potentials in regulating retinal development. Together, our study presents a rich and complex landscape of translational regulation and provides novel insights into their roles during retinogenesis.
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Affiliation(s)
- Kaining Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Congying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Huihui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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92
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Santos-Rodriguez G, Voineagu I, Weatheritt RJ. Evolutionary dynamics of circular RNAs in primates. eLife 2021; 10:e69148. [PMID: 34542404 PMCID: PMC8516421 DOI: 10.7554/elife.69148] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.
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Affiliation(s)
- Gabriela Santos-Rodriguez
- EMBL Australia, Garvan Institute of Medical ResearchDarlinghurstAustralia
- St. Vincent Clinical School, University of New South WalesDarlinghurstAustralia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydneyAustralia
| | - Robert J Weatheritt
- EMBL Australia, Garvan Institute of Medical ResearchDarlinghurstAustralia
- St. Vincent Clinical School, University of New South WalesDarlinghurstAustralia
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93
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Zhang J, Zhao F. Characterizing Circular RNAs Using Nanopore Sequencing. Trends Biochem Sci 2021; 46:785-786. [PMID: 34218979 DOI: 10.1016/j.tibs.2021.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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94
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Mahmoudi E, Green MJ, Cairns MJ. Dysregulation of circRNA expression in the peripheral blood of individuals with schizophrenia and bipolar disorder. J Mol Med (Berl) 2021; 99:981-991. [PMID: 33782720 DOI: 10.1007/s00109-021-02070-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are head-to-tail back-spliced RNA transcripts that have been linked to several biological processes and their perturbation is evident in human disease, including neurological disorders. There is also emerging research suggesting circRNA expression may also be altered in psychiatric and behavioural syndromes. Here, we provide a comprehensive analysis of circRNA expression in peripheral blood mononuclear cells (PBMCs) from 39 patients with schizophrenia and bipolar disorder as well as 20 healthy individuals using deep RNA-seq. We observed systematic alternative splicing leading to a complex and diverse profile of RNA transcripts including 8762 high confidence circRNAs. More specific scrutiny of the circular transcriptome in schizophrenia and bipolar disorder, compared to a non-psychiatric control group, revealed significant dysregulation of 55 circRNAs with a bias towards downregulation. These molecules were predicted to interact with a large number of miRNAs that target genes enriched in psychiatric disorders. Further replication and cross-validation to determine the specificity of these circRNAs across broader diagnostic groups and subgroups in psychiatry will enable their potential utility as biomarkers to be established. KEY MESSAGES: • We identified 8762 high confidence circRNAs with systematic alternative splicing in human PBMCs. • CircRNAs were dysregulated in schizophrenia and bipolar disorder, compared to a non-psychiatric control group. • The DE circRNAs were predicted to interact with miRNAs with target genes enriched in psychiatric disorders. • Some circRNAs have the potential to serve as biomarkers in psychiatry.
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Affiliation(s)
- Ebrahim Mahmoudi
- School of Biomedical Sciences and Pharmacy, University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Melissa J Green
- School of Psychiatry, University of New South Wales (UNSW), Sydney, NSW, Australia.,Neuroscience Research Australia (NeuRA), Randwick, NSW, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia. .,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW, 2308, Australia. .,Hunter Medical Research Institute, New Lambton Heights, Australia.
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95
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Zhang J, Hou L, Zuo Z, Ji P, Zhang X, Xue Y, Zhao F. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nat Biotechnol 2021; 39:836-845. [PMID: 33707777 DOI: 10.1038/s41587-021-00842-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/08/2023]
Abstract
Reconstructing the sequence of circular RNAs (circRNAs) from short RNA sequencing reads has proved challenging given the similarity of circRNAs and their corresponding linear messenger RNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length circRNAs. Here we describe a protocol for enrichment and full-length sequencing of circRNA isoforms using nanopore technology. Circular reverse transcription and size selection achieves a 20-fold higher enrichment of circRNAs from total RNA compared to previous methods. We developed an algorithm, called circRNA identifier using long-read sequencing data (CIRI-long), to reconstruct the sequence of circRNAs. The workflow was validated with simulated data and by comparison to Illumina sequencing as well as quantitative real-time RT-PCR. We used CIRI-long to analyze adult mouse brain samples and systematically profile circRNAs, including mitochondria-derived and transcriptional read-through circRNAs. We identified a new type of intronic self-ligated circRNA that exhibits special splicing and expression patterns. Our method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length circRNA sequences.
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Affiliation(s)
- Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lingling Hou
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Peifeng Ji
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaorong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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96
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Function of Circular RNAs in Fish and Their Potential Application as Biomarkers. Int J Mol Sci 2021; 22:ijms22137119. [PMID: 34281172 PMCID: PMC8268770 DOI: 10.3390/ijms22137119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.
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97
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Luo HT, Zheng YY, Tang J, Shao LJ, Mao YH, Yang W, Yang XF, Li Y, Tian RJ, Li FR. Dissecting the multi-omics atlas of the exosomes released by human lung adenocarcinoma stem-like cells. NPJ Genom Med 2021; 6:48. [PMID: 34127680 PMCID: PMC8203745 DOI: 10.1038/s41525-021-00217-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Lung adenocarcinoma is heterogeneous and hierarchically organized, with a subpopulation of stem-like cells (CSCs) that reside at the apex of the hierarchy, in which exosomes act as important mediators by transporting specific molecules among different cell populations. Although there have been numerous studies on tumor exosomes, the constituents and functional properties of CSC-derived exosomes are still poorly characterized. Here we present a detail transcriptome and proteome atlas of the exosomes released by human lung adenocarcinoma stem-like cells (LSLCs). The transcriptome analysis indicates the specific patterns of exosomal constituents, including the fragmentation of transcripts and the low-level presence of circular RNAs, and identifies multiple exosomal-enriched mRNAs and lncRNAs. Integrative analysis of transcriptome and proteome data reveals the diverse functions of exosomal-enriched RNAs and proteins, many of which are associated with tumorigenesis. Importantly, several LSLC markers we identified are highly expressed in LSLC-derived exosomes and associate with poor survival, which may serve as promising liquid biopsy biomarkers for lung adenocarcinoma diagnosis. Our study provides a resource for the future elucidation of the functions of tumor-derived exosomes and their regulatory mechanisms in mediating lung cancer development.
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Affiliation(s)
- Hai-Tao Luo
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Yuan-Yuan Zheng
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen, China
| | - Jun Tang
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China.,Institute of Oncology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Li-Juan Shao
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Yi-Heng Mao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
| | - Wei Yang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen, China
| | - Xiao-Fei Yang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen, China
| | - Yang Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen, China
| | - Rui-Jun Tian
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China.
| | - Fu-Rong Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China. .,Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen, China.
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98
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Wen G, Li M, Li F, Yang Z, Zhou T, Gu W. AQUARIUM: accurate quantification of circular isoforms using model-based strategy. Bioinformatics 2021; 37:4879-4881. [PMID: 34115093 DOI: 10.1093/bioinformatics/btab435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/11/2021] [Accepted: 06/08/2021] [Indexed: 01/22/2023] Open
Abstract
SUMMARY Currently, most computational methods estimate the expression of circular RNAs (circRNAs) using the number of sequencing reads that support back-splicing junctions (BSJ) in RNA-seq data, which may introduce biased estimation of circRNA expression due to the uneven distribution of sequencing reads. To overcome this, we previously developed a model-based strategy for circRNA quantification, enabling consideration of sequencing reads from the entire transcript. Yet, the lack of exact transcript structure of circRNAs may limit its accuracy. Here, we proposed a substantially improved circRNA quantification tool, AQUARIUM, by introducing the full-length RNA structure of circular isoforms. We assessed its performance in circRNA quantification using both biological and simulated rRNA-depleted RNA-seq datasets, and demonstrated its superior performance at both BSJ and isoform level. AVAILABILITY AND IMPLEMENTATION AQUARIUM is freely available at https://github.com/wanjun-group-seu/AQUARIUM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, 89557, USA
| | - Fuyu Li
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Zengyan Yang
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, 89557, USA
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.,Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing, Jiangsu, 210023, China.,School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
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99
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La Ferlita A, Alaimo S, Di Bella S, Martorana E, Laliotis GI, Bertoni F, Cascione L, Tsichlis PN, Ferro A, Bosotti R, Pulvirenti A. RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. BMC Bioinformatics 2021; 22:298. [PMID: 34082707 PMCID: PMC8173825 DOI: 10.1186/s12859-021-04211-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement. Results Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species. Conclusions RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04211-7.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | | | - Emanuele Martorana
- Regional Referral Centre for Rare Lung Diseases, A. O. U. "Policlinico-Vittorio Emanuele", Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Georgios I Laliotis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | | | | | - Philip N Tsichlis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | | | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy.
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100
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Haile S, Corbett RD, LeBlanc VG, Wei L, Pleasance S, Bilobram S, Nip KM, Brown K, Trinh E, Smith J, Trinh DL, Bala M, Chuah E, Coope RJN, Moore RA, Mungall AJ, Mungall KL, Zhao Y, Hirst M, Aparicio S, Birol I, Jones SJM, Marra MA. A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells. Front Genet 2021; 12:665888. [PMID: 34149808 PMCID: PMC8209500 DOI: 10.3389/fgene.2021.665888] [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: 02/09/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
RNA sequencing (RNAseq) has been widely used to generate bulk gene expression measurements collected from pools of cells. Only relatively recently have single-cell RNAseq (scRNAseq) methods provided opportunities for gene expression analyses at the single-cell level, allowing researchers to study heterogeneous mixtures of cells at unprecedented resolution. Tumors tend to be composed of heterogeneous cellular mixtures and are frequently the subjects of such analyses. Extensive method developments have led to several protocols for scRNAseq but, owing to the small amounts of RNA in single cells, technical constraints have required compromises. For example, the majority of scRNAseq methods are limited to sequencing only the 3' or 5' termini of transcripts. Other protocols that facilitate full-length transcript profiling tend to capture only polyadenylated mRNAs and are generally limited to processing only 96 cells at a time. Here, we address these limitations and present a novel protocol that allows for the high-throughput sequencing of full-length, total RNA at single-cell resolution. We demonstrate that our method produced strand-specific sequencing data for both polyadenylated and non-polyadenylated transcripts, enabled the profiling of transcript regions beyond only transcript termini, and yielded data rich enough to allow identification of cell types from heterogeneous biological samples.
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Affiliation(s)
- Simon Haile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Veronique G LeBlanc
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Lisa Wei
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Steve Bilobram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Kirstin Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Eva Trinh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jillian Smith
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Diane L Trinh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Miruna Bala
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Robin J N Coope
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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