1
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Kontos CK, Karousi P, Artemaki PI, Abdelgawad A, Dimitriadou A, Machairas NP, Sideris DC, Pappa V, Scorilas A, Batish M, Papageorgiou SG. Novel circular RNAs of the apoptosis-related BAX and BCL2L12 genes identified in a chronic lymphocytic leukemia cell line using nanopore sequencing. FEBS Open Bio 2023; 13:1953-1966. [PMID: 37424436 PMCID: PMC10549219 DOI: 10.1002/2211-5463.13672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/13/2023] [Accepted: 07/07/2023] [Indexed: 07/11/2023] Open
Abstract
Circular RNAs (circRNAs), a novel RNA type generated by back-splicing, are key regulators of gene expression, with deregulated expression and established involvement in leukemia. The products of BCL2 and its homologs, including BAX and BCL2L12, are implicated in chronic lymphocytic leukemia (CLL). However, to the best of our knowledge, nothing is known about circRNAs produced by these two genes and their role in CLL. We sought to further elucidate the contribution of BAX and BCL2L12 in CLL by unraveling the identity, localization, and potential role of their circRNAs. Therefore, total RNA from the EHEB cell line and peripheral blood mononuclear cells (PBMCs) of CLL patients and non-leukemic blood donors was extracted and reverse-transcribed using random hexamers. Next, nested PCRs with divergent primers were performed and the purified PCR products were subjected to 3rd generation nanopore sequencing. Nested PCRs were also applied to first-strand cDNAs synthesized from total RNA extracts of PBMCs from CLL patients and non-leukemic blood donors. Lastly, a single-molecule resolution fluorescent in situ hybridization method called circFISH was used to visualize the circRNA distribution in EHEB cells. We discovered several novel circRNAs produced by BAX and BCL2L12, which were characterized by great exon structure diversity. In addition, intriguing findings regarding their formation emerged. Interestingly, visualization of the most abundant circRNAs showed distinct intracellular localization. Moreover, a complex BAX and BCL2L12 circRNA expression pattern was revealed in CLL patients and non-leukemic blood donors. Our data suggest a multifaceted role of BAX and BCL2L12 circRNAs in B-cell CLL.
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Affiliation(s)
- Christos K. Kontos
- Department of Biochemistry and Molecular Biology, Faculty of BiologyNational and Kapodistrian University of AthensGreece
| | - Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of BiologyNational and Kapodistrian University of AthensGreece
| | - Pinelopi I. Artemaki
- Department of Biochemistry and Molecular Biology, Faculty of BiologyNational and Kapodistrian University of AthensGreece
| | - Ahmed Abdelgawad
- Department of Medical and Molecular SciencesUniversity of DelawareNewarkDEUSA
| | - Aspasia Dimitriadou
- Department of Biochemistry and Molecular Biology, Faculty of BiologyNational and Kapodistrian University of AthensGreece
| | - Nikolaos P. Machairas
- Department of Biochemistry and Molecular Biology, Faculty of BiologyNational and Kapodistrian University of AthensGreece
| | - Diamantis C. Sideris
- Department of Biochemistry and Molecular Biology, Faculty of BiologyNational and Kapodistrian University of AthensGreece
| | - Vasiliki Pappa
- Second Department of Internal Medicine and Research UnitUniversity General Hospital “Attikon”AthensGreece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of BiologyNational and Kapodistrian University of AthensGreece
| | - Mona Batish
- Department of Medical and Molecular SciencesUniversity of DelawareNewarkDEUSA
| | - Sotirios G. Papageorgiou
- Second Department of Internal Medicine and Research UnitUniversity General Hospital “Attikon”AthensGreece
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2
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Zhang J, Zhang H, Ju Z, Peng Y, Pan Y, Xi W, Wei Y. JCcirc: circRNA full-length sequence assembly through integrated junction contigs. Brief Bioinform 2023; 24:bbad363. [PMID: 37833842 DOI: 10.1093/bib/bbad363] [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: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Recent studies have shed light on the potential of circular RNA (circRNA) as a biomarker for disease diagnosis and as a nucleic acid vaccine. The exploration of these functionalities requires correct circRNA full-length sequences; however, existing assembly tools can only correctly assemble some circRNAs, and their performance can be further improved. Here, we introduce a novel feature known as the junction contig (JC), which is an extension of the back-splice junction (BSJ). Leveraging the strengths of both BSJ and JC, we present a novel method called JCcirc (https://github.com/cbbzhang/JCcirc). It enables efficient reconstruction of all types of circRNA full-length sequences and their alternative isoforms using splice graphs and fragment coverage. Our findings demonstrate the superiority of JCcirc over existing methods on human simulation datasets, and its average F1 score surpasses CircAST by 0.40 and outperforms both CIRI-full and circRNAfull by 0.13. For circRNAs below 400 bp, 400-800 bp, 800 bp-1200 bp and above 1200 bp, the correct assembly rates are 0.13, 0.09, 0.04 and 0.03 higher, respectively, than those achieved by existing methods. Moreover, JCcirc also outperforms existing assembly tools on other five model species datasets and real sequencing datasets. These results show that JCcirc is a robust tool for accurately assembling circRNA full-length sequences, laying the foundation for the functional analysis of circRNAs.
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Affiliation(s)
- Jingjing Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institute of Advanced Technology, CAS, Shenzhen, China
| | - Huiling Zhang
- College of Mathematics and Information, South China Agriculture University, Guangzhou, China
| | - Zhen Ju
- University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institute of Advanced Technology, CAS, Shenzhen, China
| | - Yin Peng
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, China
| | - Yi Pan
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institute of Advanced Technology, CAS, Shenzhen, China
| | - Wenhui Xi
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institute of Advanced Technology, CAS, Shenzhen, China
| | - Yanjie Wei
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institute of Advanced Technology, CAS, Shenzhen, China
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3
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Selcen I, Prentice E, Casaccia P. The epigenetic landscape of oligodendrocyte lineage cells. Ann N Y Acad Sci 2023; 1522:24-41. [PMID: 36740586 PMCID: PMC10085863 DOI: 10.1111/nyas.14959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The epigenetic landscape of oligodendrocyte lineage cells refers to the cell-specific modifications of DNA, chromatin, and RNA that define a unique gene expression pattern of functionally specialized cells. Here, we focus on the epigenetic changes occurring as progenitors differentiate into myelin-forming cells and respond to the local environment. First, modifications of DNA, RNA, nucleosomal histones, key principles of chromatin organization, topologically associating domains, and local remodeling will be reviewed. Then, the relationship between epigenetic modulators and RNA processing will be explored. Finally, the reciprocal relationship between the epigenome as a determinant of the mechanical properties of cell nuclei and the target of mechanotransduction will be discussed. The overall goal is to provide an interpretative key on how epigenetic changes may account for the heterogeneity of the transcriptional profiles identified in this lineage.
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Affiliation(s)
- Ipek Selcen
- Graduate Program in Biochemistry, The Graduate Center of The City University of New York, New York, New York, USA.,Neuroscience Initiative, Advanced Science Research Center, The Graduate Center of The City University of New York, New York, New York, USA
| | - Emily Prentice
- Neuroscience Initiative, Advanced Science Research Center, The Graduate Center of The City University of New York, New York, New York, USA.,Graduate Program in Biology, The Graduate Center of The City University of New York, New York, New York, USA
| | - Patrizia Casaccia
- Graduate Program in Biochemistry, The Graduate Center of The City University of New York, New York, New York, USA.,Neuroscience Initiative, Advanced Science Research Center, The Graduate Center of The City University of New York, New York, New York, USA.,Graduate Program in Biology, The Graduate Center of The City University of New York, New York, New York, USA
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4
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Circular RNAs and tuberculosis infection. Int J Biol Macromol 2023; 226:1218-1225. [PMID: 36442574 DOI: 10.1016/j.ijbiomac.2022.11.235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/13/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is a deadly infectious disease caused by Mycobacterium tuberculosis (Mtb) that affects the immune system chronically. Therefore, effective control and treatment of tuberculosis requires rapid and accurate diagnostic strategies. Tuberculosis has always been a global burden on health, social and economic systems due to the lack of standard curative and diagnostic (bio)markers. Accordingly, the management and monitoring of patients with active TB at the primary care level may be possible through new, rapid and cost-effective non-sputum-based diagnostic procedures. Biomarkers can help diagnose various diseases, including circular RNA (circRNA), which has recently been introduced as an endogenous, abundant and stable RNA in the cytoplasm with unique tissue specificity. There are frequent reports of circRNA involvement in many pathological and physiological processes in human beings. Recent studies have highlighted the presence of circRNAs in serum and their role as promising biomarkers in the diagnosis of the disease, potentially due to the continuous, stable, closed covalent circular structures and lack of easy degradation by nucleases. The purpose of this review article is to scrutinize the behavior of circulating plasma RNAs in relation to the pathogenesis and diagnosis of tuberculosis.
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5
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Competing Endogenous RNA (ceRNA) Networks and Splicing Switches in Cervical Cancer: HPV Oncogenesis, Clinical Significance and Therapeutic Opportunities. Microorganisms 2022; 10:microorganisms10091852. [PMID: 36144454 PMCID: PMC9501168 DOI: 10.3390/microorganisms10091852] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/25/2022] [Accepted: 09/09/2022] [Indexed: 12/20/2022] Open
Abstract
Cervical cancer (CC) is the primary cause of female cancer fatalities in low-middle-income countries (LMICs). Persistent infections from the human papillomavirus (HPV) can result in cervical cancer. However, numerous different factors influence the development and progression of cervical cancer. Transcriptomic knowledge of the mechanisms with which HPV causes cervical cancer pathogenesis is growing. Nonetheless, there is an existing gap hindering the development of therapeutic approaches and the improvement of patient outcomes. Alternative splicing allows for the production of numerous RNA transcripts and protein isoforms from a single gene, increasing the transcriptome and protein diversity in eukaryotes. Cancer cells exhibit astounding transcriptome modifications by expressing cancer-specific splicing isoforms. High-risk HPV uses cellular alternative splicing events to produce viral and host splice variants and proteins that drive cancer progression or contribute to distinct cancer hallmarks. Understanding how viruses utilize alternative splicing to drive pathogenesis and tumorigenesis is essential. Although research into the role of miRNAs in tumorigenesis is advancing, the function of other non-coding RNAs, including lncRNA and circRNA, has been understudied. Through their interaction with mRNA, non-coding RNAs form a network of competing endogenous RNAs (ceRNAs), which regulate gene expression and promote cervical cancer development and advancement. The dysregulated expression of non-coding RNAs is an understudied and tangled process that promotes cervical cancer development. This review will present the role of aberrant alternative splicing and immunosuppression events in HPV-mediated cervical tumorigenesis, and ceRNA network regulation in cervical cancer pathogenesis will also be discussed. Furthermore, the therapeutic potential of splicing disruptor drugs in cervical cancer will be deliberated.
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6
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Xu X, Zou R, Liu X, Su Q. Alternative splicing signatures of congenital heart disease and induced pluripotent stem cell-derived cardiomyocytes from congenital heart disease patients. Medicine (Baltimore) 2022; 101:e30123. [PMID: 35984151 PMCID: PMC9388029 DOI: 10.1097/md.0000000000030123] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Congenital heart disease (CHD) is the most serious congenital defect in newborns with higher mortality. Alternative splicing (AS) plays an essential role in numerous heart diseases. However, our understanding of the link between mRNA splicing and CHD in humans is limited. Here, we try to investigate the genome-wide AS events in CHD using bioinformatics methods. We collected available RNA-seq datasets of CHD-induced pluripotent stem cell-cardiomyocytes (iPSC-CMs) (including single ventricle disease [SVD] and tetralogy of Fallot [TOF]) and non-CHD from the Gene Expression Omnibus database. Then, we unprecedentedly performed AS profiles in CHD-iPSC-CMs and non-CHD-iPSC-CMs. The rMAPS was used to generate RNA-maps for the analysis of RNA-binding proteins' (RBPs) binding sites. We used StringTie to identify and quantify the transcripts from aligned RNA-Seq reads. A quantification matrix was generated with respect to different groups by extracting the transcripts per million values from StringTie outputs. Then, this matrix was used for correlation analysis between the expression level of RBP and AS level. Finally, we validated our AS results using RNA-seq data from CHD and non-CHD patient tissue samples. We identified CHD-related AS events using CHD-iPSC-CMs and CHD samples from patients. The results showed that functional enrichment of abnormal AS in SVD and TOF was transcription factor-related. Using rMAPS, RNA-binding proteins which regulated these AS were also determined, and RBP-AS regulatory network was constructed. Overall, we identified abnormal AS in CHD-iPSC-CMs and CHD samples from patients. We predicted AS regulators in SVD and TOF, respectively. At last, we concluded that AS played a key role in the pathogenesis of CHD.
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Affiliation(s)
- Xiang Xu
- Department of Cardiology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Renchao Zou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Xiaoyong Liu
- Department of Cardiology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, China
| | - Qianqian Su
- Department of Laboratory Animal Science, Kunming Medical University, Kunming City, China
- *Correspondence: Qianqian Su, Department of Laboratory Animal Science, Kunming Medical University, Kunming City, Yunnan Province, China (e-mail: )
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7
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Asadi MR, Moslehian MS, Sabaie H, Sharifi-Bonab M, Hakimi P, Hussen BM, Taheri M, Rakhshan A, Rezazadeh M. CircRNA-Associated CeRNAs Regulatory Axes in Retinoblastoma: A Systematic Scoping Review. Front Oncol 2022; 12:910470. [PMID: 35865469 PMCID: PMC9294360 DOI: 10.3389/fonc.2022.910470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022] Open
Abstract
Retinoblastoma (RB) is one of the most common childhood cancers caused by RB gene mutations (tumor suppressor gene in various patients). A better understanding of molecular pathways and the development of new diagnostic approaches may lead to better treatment for RB patients. The number of studies on ceRNA axes is increasing, emphasizing the significance of these axes in RB. Circular RNAs (circRNAs) play a vital role in competing endogenous RNA (ceRNA) regulatory axes by sponging microRNAs and regulating gene expression. Because of the broadness of ceRNA interaction networks, they may assist in investigating treatment targets in RB. This study conducted a systematic scoping review to evaluate verified loops of ceRNA in RB, focusing on the ceRNA axis and its relationship to circRNAs. This scoping review was carried out using a six-step strategy and the Prisma guideline, and it involved systematically searching the publications of seven databases. Out of 363 records, sixteen articles were entirely consistent with the defined inclusion criteria and were summarized in the relevant table. The majority of the studies focused on the circRNAs circ_0000527, circ_0000034, and circTET1, with approximately two-fifths of the studies focusing on a single circRNA. Understanding the many features of this regulatory structure may help elucidate RB’s unknown causative factors and provide novel molecular potential therapeutic targets and medical fields.
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Affiliation(s)
- Mohammad Reza Asadi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziyeh Sadat Moslehian
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mirmohsen Sharifi-Bonab
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parvin Hakimi
- Woman’s Reproductive Health Research Center, Tabriz University of medical sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- *Correspondence: Mohammad Taheri, ; Azadeh Rakhshan, ; Maryam Rezazadeh,
| | - Azadeh Rakhshan
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Mohammad Taheri, ; Azadeh Rakhshan, ; Maryam Rezazadeh,
| | - Maryam Rezazadeh
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Woman’s Reproductive Health Research Center, Tabriz University of medical sciences, Tabriz, Iran
- *Correspondence: Mohammad Taheri, ; Azadeh Rakhshan, ; Maryam Rezazadeh,
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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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Zhang J, Hossain MT, Liu W, Peng Y, Pan Y, Wei Y. Evaluation of CircRNA Sequence Assembly Methods Using Long Reads. Front Genet 2022; 13:816825. [PMID: 35237301 PMCID: PMC8882733 DOI: 10.3389/fgene.2022.816825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
The functional study on circRNAs has been increasing in the past decade due to its important roles in micro RNA sponge, protein coding, the initiation, and progression of diseases. The study of circRNA functions depends on the full-length sequences of circRNA, and current sequence assembly methods based on short reads face challenges due to the existence of linear transcript. Long reads produced by long-read sequencing techniques such as Nanopore technology can cover full-length sequences of circRNA and therefore can be used to evaluate the correctness and completeness of circRNA full sequences assembled from short reads of the same sample. Using long reads of the same samples, one from human and the other from mouse, we have comprehensively evaluated the performance of several well-known circRNA sequence assembly algorithms based on short reads, including circseq_cup, CIRI_full, and CircAST. Based on the F1 score, the performance of CIRI-full was better in human datasets, whereas in mouse datasets CircAST was better. In general, each algorithm was developed to handle special situations or circumstances. Our results indicated that no single assembly algorithm generated better performance in all cases. Therefore, these assembly algorithms should be used together for reliable full-length circRNA sequence reconstruction. After analyzing the results, we have introduced a screening protocol that selects out exonic circRNAs with full-length sequences consisting of all exons between back splice sites as the final result. After screening, CIRI-full showed better performance for both human and mouse datasets. The average F1 score of CIRI-full over four circRNA identification algorithms increased from 0.4788 to 0.5069 in human datasets, and it increased from 0.2995 to 0.4223 in mouse datasets.
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Affiliation(s)
- Jingjing Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Centre for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Md. Tofazzal Hossain
- University of Chinese Academy of Sciences, Beijing, China
- Centre for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Weiguo Liu
- School of Software, Shandong University, Jinan, China
| | - Yin Peng
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, China
- *Correspondence: Yin Peng, ; Yanjie Wei,
| | - Yi Pan
- Centre for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Centre for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- *Correspondence: Yin Peng, ; Yanjie Wei,
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10
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Zhang S, Sun J, Gu M, Wang G, Wang X. Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer. Cancer Med 2021; 10:8725-8740. [PMID: 34796685 PMCID: PMC8683543 DOI: 10.1002/cam4.4398] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract. According to the research of circular RNAs in the CRC field, compared with linear RNAs, circular RNAs are a special type of noncoding RNA that are covalently closed circular structures, which have no 5' cap structure and 3' polyA tail and are not affected by RNA exonuclease and actinomycin D. Biological functions Notably, circular RNAs have a high degree of stability and potential effect on gene regulation. Meanwhile, circular RNAs are involved in the sponge action of microRNAs and mediate protein translation and direct binding, alternative splicing, and histone modification. Relationships with CRC Studies have shown that circular RNAs are related to the proliferation, invasion, recurrence, metastasis, ferroptosis, apoptosis, and chemotherapy resistance of CRC. Conclusions This article provides a brief review based on the source, structural characteristics, mechanisms, biological functions of circular RNAs, and the relationships between CRC.
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Affiliation(s)
- Shunhao Zhang
- Graduate School of Nantong University, Nantong, China
| | - Jing Sun
- Graduate School of Nantong University, Nantong, China
| | - Minqi Gu
- Graduate School of Nantong University, Nantong, China
| | - Guihua Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xudong Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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Babin L, Andraos E, Fuchs S, Pyronnet S, Brunet E, Meggetto F. From circRNAs to fusion circRNAs in hematological malignancies. JCI Insight 2021; 6:151513. [PMID: 34747369 PMCID: PMC8663548 DOI: 10.1172/jci.insight.151513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) represent a type of endogenous noncoding RNA generated by back-splicing events. Unlike the majority of RNAs, circRNAs are covalently closed, without a 5' end or a 3' poly(A) tail. A few circRNAs can be associated with polysomes, suggesting a protein-coding potential. CircRNAs are not degraded by RNA exonucleases or ribonuclease R and are enriched in exosomes. Recent developments in experimental methods coupled with evolving bioinformatic approaches have accelerated functional investigation of circRNAs, which exhibit a stable structure, a long half-life, and tumor specificity and can be extracted from body fluids and used as potential biological markers for tumors. Moreover, circRNAs may regulate the occurrence and development of cancers and contribute to drug resistance through a variety of molecular mechanisms. Despite the identification of a growing number of circRNAs, their effects in hematological cancers remain largely unknown. Recent studies indicate that circRNAs could also originate from fusion genes (fusion circRNAs, f-circRNAs) next to chromosomal translocations, which are considered the primary cause of various cancers, notably hematological malignancies. This Review will focus on circRNAs and f-circRNAs in hematological cancers.
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Affiliation(s)
- Loelia Babin
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
| | - Elissa Andraos
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
| | - Steffen Fuchs
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France.,Department of Pediatric Oncology, Charité University Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stéphane Pyronnet
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
| | - Erika Brunet
- Imagine Institute INSERM Joint Research Unit 1163, Laboratory of Genome Dynamics in the Immune System, Paris, France.,Paris Descartes-Sorbonne University, Imagine Institute, Paris, France
| | - Fabienne Meggetto
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
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Lin Z, Tang X, Wan J, Zhang X, Liu C, Liu T. Functions and mechanisms of circular RNAs in regulating stem cell differentiation. RNA Biol 2021; 18:2136-2149. [PMID: 33896374 DOI: 10.1080/15476286.2021.1913551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Stem cells are a class of undifferentiated cells with great self-renewal and differentiation capabilities that can differentiate into mature cells in specific tissue types. Stem cell differentiation plays critical roles in body homoeostasis, injury repair and tissue generation. The important functions of stem cell differentiation have resulted in numerous studies focusing on the complex molecular mechanisms and various signalling pathways controlling stem cell differentiation. Circular RNAs (circRNAs) are a novel class of noncoding RNAs with a covalently closed structure present in eukaryotes. Numerous studies have highlighted important biological functions of circRNAs, and they play multiple regulatory roles in various physiological and pathological processes. Importantly, multiple lines of evidence have shown the abnormal expression of numerous circRNAs during stem cell differentiation, and some play a role in regulating stem cell differentiation, highlighting the role of circRNAs as novel biomarkers of stem cell differentiation and novel targets for stem cell-based therapy. In this review, we systematically summarize and discuss recent advances in our understanding of the roles and underlying mechanisms of circRNAs in modulating stem cell differentiation, thus providing guidance for future studies to investigate stem cell differentiation and stem cell-based therapy.Abbreviations: CircRNAs: circular RNAs; ESCs: embryonic stem cells; ADSCs: adipose-derived mesenchymal stem cells; ecircRNAs: exonic circRNAs; EIciRNAs: exon-intron circRNAs; eiRNAs: circular intronic RNAs; tricRNAs: tRNA intronic circRNAs; pol II: polymerase II; snRNP: small nuclear ribonucleoprotein; m6A: N6-methyladenosine; AGO2: Argonaute 2; RBPs: RNA-binding proteins; MBNL: muscleblind-like protein 1; MSCs: mesenchymal stem cells; hiPSCs: human induced pluripotent stem cells; hiPSC-CMs: hiPSC-derived cardiomyocytes; hBMSCs: human bone marrow mesenchymal stem cells; hADSCs: human adipose-derived mesenchymal stem cells; hDPSCs: human dental pulp stem cells; RNA-seq: high-throughput RNA sequencing; HSCs: haematopoietic stem cells; NSCs: neural stem cells; EpSCs: epidermal stem cells; hESCs: human embryonic stem cells; mESCs: murine embryonic stem cells; MNs: motor neurons; SSUP: small subunit processome; BMSCs: bone marrow-derived mesenchymal stem cells; OGN: osteoglycin; GIOP: glucocorticoid‑induced osteoporosis; CDR1as: cerebellar degeneration-related protein 1 transcript; SONFH: steroid-induced osteogenesis of the femoral head; rBMSCs: rat bone marrow-derived mesenchymal stem cells; QUE: quercetin; AcvR1b: activin A receptor type 1B; BSP: bone sialoprotein; mADSCs: mouse ADSCs; PTBP1: polypyrimidine tract-binding protein; ER: endoplasmic reticulum; hUCMSCs: MSCs derived from human umbilical cord; MSMSCs: maxillary sinus membrane stem cells; SCAPs: stem cells from the apical papilla; MyoD: myogenic differentiation protein 1; MSTN: myostatin; MEF2C: myocyte enhancer factor 2C; BCLAF1: BCL2-associated transcription factor 1; EpSCs: epidermal stem cells; ISCs: intestinal stem cells; NSCs: neural stem cells; Lgr5+ ISCs: crypt base columnar cells; ILCs: innate lymphoid cells.
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Affiliation(s)
- Zhengjun Lin
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.,Xiangya School of Medicine, Central South University, Changsha, Hunan Province, China
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou No.1 People's Hospital, Chenzhou, Hunan, China
| | - Jia Wan
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xianghong Zhang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chunfeng Liu
- Department of Orthopedics, Suzhou Kowloon Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Suzhou, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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