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Sheng M, Zhang Y, Wang Y, Liu W, Wang X, Ke T, Liu P, Wang S, Shao W. Decoding the role of aberrant RNA alternative splicing in hepatocellular carcinoma: a comprehensive review. J Cancer Res Clin Oncol 2023; 149:17691-17708. [PMID: 37898981 DOI: 10.1007/s00432-023-05474-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/10/2023] [Indexed: 10/31/2023]
Abstract
During eukaryotic gene expression, alternative splicing of messenger RNA precursors is critical in increasing protein diversity and regulatory complexity. Multiple transcript isoforms could be produced by alternative splicing from a single gene; they could eventually be translated into protein isoforms with deleted, added, or altered domains or produce transcripts containing premature termination codons that could be targeted by nonsense-mediated mRNA decay. Alternative splicing can generate proteins with similar, different, or even opposite functions. Increasingly strong evidence indicates that abnormal RNA splicing is a prevalent and crucial occurrence in cellular differentiation, tissue advancement, and the development and progression of cancer. Aberrant alternative splicing could affect cancer cell activities such as growth, apoptosis, invasiveness, drug resistance, angiogenesis, and metabolism. This systematic review provides a comprehensive overview of the impact of abnormal RNA alternative splicing on the development and progression of hepatocellular carcinoma.
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Affiliation(s)
- Mengfei Sheng
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yuanyuan Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yaoyun Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Weiyi Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xingyu Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Tiaoying Ke
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Pingyang Liu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sihan Wang
- Department of Clinical Medicine, Bengbu Medical College, Bengbu, China
| | - Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
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2
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Dong Y, Xue L, Zhang Y, Liu C, Zhang Y, Jiang N, Ma X, Chen F, Li L, Yu L, Liu X, Shao S, Guan S, Zhang J, Xiao Q, Li H, Dong A, Huang L, Shi C, Wang Y, Fu M, Lv N, Zhan Q. Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC). J Exp Clin Cancer Res 2022; 41:150. [PMID: 35449073 PMCID: PMC9027881 DOI: 10.1186/s13046-022-02355-9] [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: 09/21/2021] [Accepted: 04/02/2022] [Indexed: 02/02/2023] Open
Abstract
Abstract
Background
Oral squamous cell carcinoma (OSCC) is one of the common cancers worldwide. The lack of specific biomarkers and therapeutic targets leads to delayed diagnosis and hence the poor prognosis of OSCC patients. Thus, it is urgent to identify effective biomarkers and therapeutic targets for OSCC.
Methods
We established the golden hamster carcinogenic model of OSCC induced by 7,12-dimethylbenz(a) anthrancene (DMBA) and used mRNA microarrays to detect the differentially expressed genes (DEGs). DEGs were validated in OSCC clinical tissue microarrays using immunohistochemistry method. Whole transcriptome sequencing was performed to obtain an overview of biological functions of Lsm12. PCR assay and sequencing were employed to investigate the alternative splicing of genes regulated by Lsm12. Cell proliferation, colony formation, Transwell migration and invasion assay and in vivo tumor formation assay were performed to investigate the roles of Lsm12 and two transcript variants of USO1 in OSCC cells.
Results
Lsm12 was identified to be significantly up-regulated in the animal model of OSCC tumorigenesis, which was validated in the clinical OSCC samples. In the paired normal tissues, Lsm12 staining was negative (91%, 92/101) or weak, while in OSCC tissues, positive rate is 100% and strong staining spread over the whole tissues in 93 (93/101, 92%) cases. Lsm12 overexpression significantly promoted OSCC cell growth, colony formation, migration and invasion abilities, while Lsm12 knockdown showed the opposite trends on these phenotypes and obviously inhibited the tumor formation in vivo. Furthermore, Lsm12 overexpression caused the inclusion of USO1 exon 15 and Lsm12 knockdown induced exon 15 skipping. Exon 15-retained USO1 significantly promoted the malignant phenotypes of OSCC cells when compared with the exon 15-deleted USO1.
Conclusions
We identified Lsm12, a novel tumorigenesis-related gene, as an important regulator involved in OSCC tumorigenesis. Lsm12 is a novel RNA-splicing related gene and can regulate the alternative splicing of USO1 exon 15 which was associated closely with OSCC carcinogenesis. Our findings thus provide that Lsm12 might be a potent biomarker and potential therapeutic target for OSCC.
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3
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Long non-coding RNAs are involved in alternative splicing and promote cancer progression. Br J Cancer 2022; 126:1113-1124. [PMID: 34750493 PMCID: PMC9023592 DOI: 10.1038/s41416-021-01600-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 09/14/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS) is a key process in which precursor RNAs produce different mature RNAs, and the disorder of AS is a key factor in promoting cancer development. Compared with coding RNA, studies on the functions of long non-coding RNAs (lncRNAs) are far from enough. In fact, lncRNA is an important participant and regulator in the process of AS. On the one hand, lncRNAs regulate cancer progression as AS products of precursor messenger RNA (mRNA), but on the other hand, precursor lncRNA generates cancer-related abnormal splicing variants through AS. In addition, lncRNAs directly or indirectly regulate the AS events of downstream target genes, thus affecting the occurrence and development of cancer. Here, we reviewed how lncRNAs regulate AS and influence oncogenesis in different ways.
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An Alternatively Spliced Variant of METTL3 Mediates Tumor Suppression in Hepatocellular Carcinoma. Genes (Basel) 2022; 13:genes13040669. [PMID: 35456475 PMCID: PMC9031889 DOI: 10.3390/genes13040669] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
Many post-transcriptional mRNA processing steps play crucial roles in tumorigenesis and the progression of cancers, such as N6-methyladenosine (m6A) modification and alternative splicing. Upregulation of methyltransferase-like 3 (METTL3), the catalytic core of the m6A methyltransferase complex, increases m6A levels and results in significant effects on the progression of hepatocellular carcinoma (HCC). However, alternative splicing of METTL3 has not been fully investigated, and the functions of its splice variants remain unclear. Here, we analyzed both our and online transcriptomic data, obtaining 13 splice variants of METTL3 in addition to canonical full-length METTL3-A in HCC cell lines and tissues. Validated by RT–qPCR and Western blotting, we found that METTL3-D, one of the splice variants expressing a truncated METTL3 protein, exhibits higher levels than METTL3-A in normal human livers but lower levels than METTL3-A in HCC tumor tissues and cell lines. Further functional assays demonstrated that METTL3-D expression decreased cellular m6A modification, inhibited the proliferation, migration, and invasion of HCC cells, and was negatively associated with the malignancy of patient tumors, exhibiting functions opposite to those of full-length METTL3-A. This study demonstrates that the METTL3-D splice variant is a tumor suppressor that could potentially be used as a target for HCC therapy.
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5
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Baralle M, Baralle FE. Alternative splicing and liver disease. Ann Hepatol 2021; 26:100534. [PMID: 34547477 DOI: 10.1016/j.aohep.2021.100534] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 02/04/2023]
Abstract
Alternative splicing produces complex and dynamic changes in the protein isoforms that are necessary for the proper biological functioning of the metabolic pathways involved in liver development and hepatocyte homeostasis. Changes in the physiological state of alternatively spliced forms are increasingly linked to liver pathologies. This may occur when the expression or function of the set of proteins controlling the alternative splicing processes are altered by external effectors such as oxidative stress and other environmental variations. Studies addressing these modifications reveal a complex interplay between the expression levels of different proteins that regulate the alternative splicing process as well as the changes in alternative splicing. This interplay results in a cascade of different protein isoforms that correlate with the progression of non-alcoholic fatty liver disease, hepatocellular carcinoma, and alcoholic liver disease. However, research on the detailed molecular mechanism underlying the production of these isoforms is needed. It is imperative to identify the physiological processes affected by the differentially spliced isoforms and confirm their role on the onset and maintenance of the pathology. This is required to design potential therapeutic approaches targeting the key splicing changes to revert the pathological condition as well as identify prognostic markers. In this review, we describe the complexity of the splicing process through an example to encourage researchers to go down this path. Subsequently, rather than a catalog of splicing events we have hand-picked and discuss a few selected studies of specific liver pathologies and suggested ways to focus research on these areas.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Italy
| | - Francisco E Baralle
- Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, ss14, Km 163.5, Basovizza, 34149 Trieste, Italy.
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Nasiri-Aghdam M, Garcia-Garduño TC, Jave-Suárez LF. CELF Family Proteins in Cancer: Highlights on the RNA-Binding Protein/Noncoding RNA Regulatory Axis. Int J Mol Sci 2021; 22:11056. [PMID: 34681716 PMCID: PMC8537729 DOI: 10.3390/ijms222011056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional modifications to coding and non-coding RNAs are unquestionably a pivotal way in which human mRNA and protein diversity can influence the different phases of a transcript's life cycle. CELF (CUGBP Elav-like family) proteins are RBPs (RNA-binding proteins) with pleiotropic capabilities in RNA processing. Their responsibilities extend from alternative splicing and transcript editing in the nucleus to mRNA stability, and translation into the cytoplasm. In this way, CELF family members have been connected to global alterations in cancer proliferation and invasion, leading to their identification as potential tumor suppressors or even oncogenes. Notably, genetic variants, alternative splicing, phosphorylation, acetylation, subcellular distribution, competition with other RBPs, and ultimately lncRNAs, miRNAs, and circRNAs all impact CELF regulation. Discoveries have emerged about the control of CELF functions, particularly via noncoding RNAs, and CELF proteins have been identified as competing, antagonizing, and regulating agents of noncoding RNA biogenesis. On the other hand, CELFs are an intriguing example through which to broaden our understanding of the RBP/noncoding RNA regulatory axis. Balancing these complex pathways in cancer is undeniably pivotal and deserves further research. This review outlines some mechanisms of CELF protein regulation and their functional consequences in cancer physiology.
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Affiliation(s)
- Maryam Nasiri-Aghdam
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Texali C. Garcia-Garduño
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Ciencias Biomédicas, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Luis Felipe Jave-Suárez
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
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Razpotnik R, Nassib P, Kunej T, Rozman D, Režen T. Identification of Novel RNA Binding Proteins Influencing Circular RNA Expression in Hepatocellular Carcinoma. Int J Mol Sci 2021; 22:7477. [PMID: 34299096 PMCID: PMC8307310 DOI: 10.3390/ijms22147477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) are increasingly recognized as having a role in cancer development. Their expression is modified in numerous cancers, including hepatocellular carcinoma (HCC); however, little is known about the mechanisms of their regulation. The aim of this study was to identify regulators of circRNAome expression in HCC. Using publicly available datasets, we identified RNA binding proteins (RBPs) with enriched motifs around the splice sites of differentially expressed circRNAs in HCC. We confirmed the binding of some of the candidate RBPs using ChIP-seq and eCLIP datasets in the ENCODE database. Several of the identified RBPs were found to be differentially expressed in HCC and/or correlated with the overall survival of HCC patients. According to our bioinformatics analyses and published evidence, we propose that NONO, PCPB2, PCPB1, ESRP2, and HNRNPK are candidate regulators of circRNA expression in HCC. We confirmed that the knocking down the epithelial splicing regulatory protein 2 (ESRP2), known to be involved in the maintenance of the adult liver phenotype, significantly changed the expression of candidate circRNAs in a model HCC cell line. By understanding the systemic changes in transcriptome splicing, we can identify new proteins involved in the molecular pathways leading to HCC development and progression.
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Affiliation(s)
- Rok Razpotnik
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
| | - Petra Nassib
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1230 Domžale, Slovenia;
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
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8
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Villemin JP, Lorenzi C, Cabrillac MS, Oldfield A, Ritchie W, Luco RF. A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants. BMC Biol 2021; 19:70. [PMID: 33845831 PMCID: PMC8042689 DOI: 10.1186/s12915-021-01002-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Breast cancer is amongst the 10 first causes of death in women worldwide. Around 20% of patients are misdiagnosed leading to early metastasis, resistance to treatment and relapse. Many clinical and gene expression profiles have been successfully used to classify breast tumours into 5 major types with different prognosis and sensitivity to specific treatments. Unfortunately, these profiles have failed to subclassify breast tumours into more subtypes to improve diagnostics and survival rate. Alternative splicing is emerging as a new source of highly specific biomarkers to classify tumours in different grades. Taking advantage of extensive public transcriptomics datasets in breast cancer cell lines (CCLE) and breast cancer tumours (TCGA), we have addressed the capacity of alternative splice variants to subclassify highly aggressive breast cancers. RESULTS Transcriptomics analysis of alternative splicing events between luminal, basal A and basal B breast cancer cell lines identified a unique splicing signature for a subtype of tumours, the basal B, whose classification is not in use in the clinic yet. Basal B cell lines, in contrast with luminal and basal A, are highly metastatic and express epithelial-to-mesenchymal (EMT) markers, which are hallmarks of cell invasion and resistance to drugs. By developing a semi-supervised machine learning approach, we transferred the molecular knowledge gained from these cell lines into patients to subclassify basal-like triple negative tumours into basal A- and basal B-like categories. Changes in splicing of 25 alternative exons, intimately related to EMT and cell invasion such as ENAH, CD44 and CTNND1, were sufficient to identify the basal-like patients with the worst prognosis. Moreover, patients expressing this basal B-specific splicing signature also expressed newly identified biomarkers of metastasis-initiating cells, like CD36, supporting a more invasive phenotype for this basal B-like breast cancer subtype. CONCLUSIONS Using a novel machine learning approach, we have identified an EMT-related splicing signature capable of subclassifying the most aggressive type of breast cancer, which are basal-like triple negative tumours. This proof-of-concept demonstrates that the biological knowledge acquired from cell lines can be transferred to patients data for further clinical investigation. More studies, particularly in 3D culture and organoids, will increase the accuracy of this transfer of knowledge, which will open new perspectives into the development of novel therapeutic strategies and the further identification of specific biomarkers for drug resistance and cancer relapse.
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Affiliation(s)
- Jean-Philippe Villemin
- Institut de Génétique Humaine (IGH-UMR9002), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Claudio Lorenzi
- Institut de Génétique Humaine (IGH-UMR9002), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Marie-Sarah Cabrillac
- Institut de Génétique Humaine (IGH-UMR9002), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Andrew Oldfield
- Institut de Génétique Humaine (IGH-UMR9002), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - William Ritchie
- Institut de Génétique Humaine (IGH-UMR9002), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France.
| | - Reini F Luco
- Institut de Génétique Humaine (IGH-UMR9002), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France.
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Dong S, Lu LJ. An alternative splicing signature model for predicting hepatocellular carcinoma-specific survival. J Gastrointest Oncol 2020; 11:1054-1064. [PMID: 33209497 PMCID: PMC7657838 DOI: 10.21037/jgo-20-377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) is a transcriptional regulation mechanism, which can expand the coding ability of genome and contribute to the occurrence and development of cancer. A systematic analysis of AS in hepatocellular carcinoma (HCC) is lacking and urgently needed. METHODS Univariate and multivariate Cox regression analyses were used to distinguish survival-related AS events and to calculate the risk score. Kaplan-Meier analysis and receiver operating characteristic (ROC) curves were used to evaluate the AS events' clinical significance to build a risk model in HCC. RESULTS Data of AS events was obtained from the Splice-Seq database. The corresponding clinical information of HCC was downloaded from The Cancer Genome Atlas (TCGA) data portal. We analyzed 78,878 AS events from 13,045 genes in HCC patients. A total of 2,440 and 2,888 AS events were significantly related to HCC patients' disease-free survival (DFS) and overall survival (OS). The two prognostic models (DFS and OS) were constructed based on a total of seven AS types from survival-related AS events above. The area under the curve (AUC) of the ROC curves was 0.769 in the DFS cohort and 0.886 in the OS cohort. CONCLUSIONS The prognostic model constructed by AS events can be used to predict the prognosis of HCC patients and provide potential therapeutic targets for further validation.
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Affiliation(s)
- Sheng Dong
- Department of Surgery, Wuxi No.9 People's Hospital affiliated to Soochow University, Wuxi, China
| | - Li-Jun Lu
- Department of Surgery, Wuxi No.9 People's Hospital affiliated to Soochow University, Wuxi, China
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10
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Burenina OY, Lazarevich NL, Kustova IF, Shavochkina DA, Moroz EA, Kudashkin NE, Patyutko YI, Metelin AV, Kim EF, Skvortsov DA, Zatsepin TS, Rubtsova MP, Dontsova OA. Panel of potential lncRNA biomarkers can distinguish various types of liver malignant and benign tumors. J Cancer Res Clin Oncol 2020; 147:49-59. [PMID: 32918630 DOI: 10.1007/s00432-020-03378-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE Liver cancers are among the deadliest malignancies due to a limited efficacy of early diagnostics, the lack of appropriate biomarkers and insufficient discrimination of different types of tumors by classic and molecular methods. In this study, we searched for novel long non-coding RNA (lncRNA) as well as validated several known candidates suitable as probable biomarkers for primary liver tumors of various etiology. METHODS We described a novel lncRNA HELIS (aka "HEalthy LIver Specific") and estimated its expression by RT-qPCR in 82 paired tissue samples from patients with hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), combined HCC-CCA, pediatric hepatoblastoma (HBL) and non-malignant hepatocellular adenoma (HCA) and focal nodular hyperplasia (FNH). Additionally, we examined expression of cancer-associated lncRNAs HULC, MALAT1, UCA1, CYTOR, LINC01093 and H19, which were previously studied mainly in HCC. RESULTS We demonstrated that down-regulation of HELIS strongly correlates with carcinogenesis; whereas in tumors with non-hepatocyte origin (HBL, CCA) or in a number of poorly differentiated HCC, this lncRNA is not expressed. We showed that recently discovered LINC01093 is dramatically down-regulated in all malignant liver cancers; while in benign tumors LINC01093 expression is just twice decreased in comparison to adjacent samples. CONCLUSION Our study revealed that among all measured biomarkers only down-regulated HELIS and LINC01093, up-regulated CYTOR and dysregulated HULC are perspective for differential diagnostics of liver cancers; whereas others demonstrated discordant results and cannot be considered as potential universal biomarkers for this purpose.
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Affiliation(s)
- Olga Y Burenina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026.
| | - Natalia L Lazarevich
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
- Biology Department, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Inna F Kustova
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Daria A Shavochkina
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Ekaterina A Moroz
- Institute of Clinical Oncology, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Nikolay E Kudashkin
- Institute of Clinical Oncology, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Yuriy I Patyutko
- Institute of Clinical Oncology, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Alexey V Metelin
- Petrovsky National Research Centre of Surgery, Moscow, Russia, 119991
| | - Eduard F Kim
- Petrovsky National Research Centre of Surgery, Moscow, Russia, 119991
| | - Dmitry A Skvortsov
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia, 101000
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
| | - Maria P Rubtsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
| | - Olga A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
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11
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Wang J, Wang X, Bhat A, Chen Y, Xu K, Mo YY, Yi SS, Zhou Y. Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma. Front Genet 2020; 11:659. [PMID: 32760422 PMCID: PMC7373802 DOI: 10.3389/fgene.2020.00659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/29/2020] [Indexed: 01/18/2023] Open
Abstract
It is increasingly appreciated that long non-coding RNAs (lncRNAs) associated with alternative splicing (AS) could be involved in aggressive hepatocellular carcinoma. Although many recent studies show the alteration of RNA alternative splicing by deregulated lncRNAs in cancer, the extent to which and how lncRNAs impact alternative splicing at the genome scale remains largely elusive. We analyzed RNA-seq data obtained from 369 hepatocellular carcinomas (HCCs) and 160 normal liver tissues, quantified 198,619 isoform transcripts, and identified a total of 1,375 significant AS events in liver cancer. In order to predict novel AS-associated lncRNAs, we performed an integration of co-expression, protein-protein interaction (PPI) and epigenetic interaction networks that links lncRNA modulators (such as splicing factors, transcript factors, and miRNAs) along with their targeted AS genes in HCC. We developed a random walk-based multi-graphic (RWMG) model algorithm that prioritizes functional lncRNAs with their associated AS targets to computationally model the heterogeneous networks in HCC. RWMG shows a good performance evaluated by the ROC curve based on cross-validation and bootstrapping strategies. As a conclusion, our robust network-based framework has derived 31 AS-related lncRNAs that not only validates known cancer-associated cases MALAT1 and HOXA11-AS, but also reveals new players such as DNM1P35 and DLX6-AS1with potential functional implications. Survival analysis further provides insights into the clinical significance of identified lncRNAs.
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Affiliation(s)
- Junqing Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuquan Wang
- Department of Mathematics and Computer Science, Tougaloo College, Jackson, MS, United States
| | - Akshay Bhat
- Department of Oncology and Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Yixin Chen
- Department of Computer and Information Science, University of Mississippi, Oxford, MS, United States
| | - Keli Xu
- Department of Neurobiology and Anatomical Sciences, University of Mississippi Medical Center, Jackson, MS, United States
| | - Yin-yuan Mo
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Song Stephen Yi
- Department of Oncology and Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Yunyun Zhou
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, United States
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12
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Identification of prognostic alternative splicing signatures in hepatitis B or/and C viruses related hepatocellular carcinoma. Genomics 2020; 112:3396-3406. [PMID: 32525024 DOI: 10.1016/j.ygeno.2020.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Alternative splicing (AS) takes a crucial part in tumor process. We aim to analyze AS in Hepatitis B virus (HBV) or/and hepatitis C virus (HCV) related hepatocellular carcinoma (HCC). METHODS Cox regression analysis was conducted to screen survival-associated AS events. The receiver operating characteristic curve used to evaluate the predictive accuracy. Splicing network was built to investigate the relationship between splicing factors and AS events. RESULTS Ninety-six survival-associated AS events were obtained by univariate Cox regression. Final prognostic model could significantly distinguish the prognosis. We identified RBFOX2 as the hub gene in splicing network based on differentially expressed splicing factors, and obtained MAP3K13_AT as the key AS event in survival-related splicing network. CONCLUSION Our results highlight the AS signatures in HCC patients with HBV or/and HCV infection. Meanwhile, AS events and splicing factors in different virus-infected HCC subgroups can provide novel perspectives as biomarkers and individualized therapeutic targets.
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13
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Lee SE, Alcedo KP, Kim HJ, Snider NT. Alternative Splicing in Hepatocellular Carcinoma. Cell Mol Gastroenterol Hepatol 2020; 10:699-712. [PMID: 32389640 PMCID: PMC7490524 DOI: 10.1016/j.jcmgh.2020.04.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) accounts for the majority of primary liver cancer cases, with more than 850,000 new diagnoses per year globally. Recent trends in the United States have shown that liver cancer mortality has continued to increase in both men and women, while 5-year survival remains below 20%. Understanding key mechanisms that drive chronic liver disease progression to HCC can reveal new therapeutic targets and biomarkers for early detection of HCC. In that regard, many studies have underscored the importance of alternative splicing as a source of novel HCC prognostic markers and disease targets. Alternative splicing of pre-mRNA provides functional diversity to the genome, and endows cells with the ability to rapidly remodel the proteome. Genes that control fundamental processes, such as metabolism, cell proliferation, and apoptosis, are altered globally in HCC by alternative splicing. This review highlights the major splicing factors, RNA binding proteins, transcriptional targets, and signaling pathways that are of key relevance to HCC. We highlight primary research from the past 3-5 years involving functional interrogation of alternative splicing in rodent and human liver, using both large-scale transcriptomic and focused mechanistic approaches. Because this is a rapidly advancing field, we anticipate that it will be transformative for the future of basic liver biology, as well as HCC diagnosis and management.
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Affiliation(s)
- Seung Eun Lee
- Department of Surgery, Chung-Ang University, Seoul, Korea,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Karel P. Alcedo
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hong Jin Kim
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Natasha T. Snider
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,Correspondence Address correspondence to: Natasha Snider, PhD, Department of Cell Biology and Physiology, University of North Carolina–Chapel Hill, 5340C MBRB, 111 Mason Farm Road, Chapel Hill, North Carolina 27516. fax: (919) 966-6927.
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14
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Identification of Candidate Genes Associated with Susceptibility to Ovarian Clear Cell Adenocarcinoma Using cis-eQTL Analysis. J Clin Med 2020; 9:jcm9041137. [PMID: 32316112 PMCID: PMC7231141 DOI: 10.3390/jcm9041137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
Ovarian clear cell adenocarcinoma (Ov-CCA) has a higher prevalence in the Japanese ancestry than other populations. The ancestral disparities in Ov-CCA prevalence suggests the presence of Ov-CCA-specific genetic alterations and may provide an opportunity to identify the novel genes associated with Ov-CCA tumorigenesis. Using 94 previously reported genes as the phenotypic trait, we conducted multistep expression quantitative trait loci (eQTL) analysis with the HapMap3 project datasets. Four single-nucleotide polymorphisms (SNPs) (rs4873815, rs12976454, rs11136002, and rs13259097) that had different allele frequencies in the Japanese ancestry and seven genes associated in cis (APBA3, C8orf58, KIAA1967, NAPRT1, RHOBTB2, TNFRSF10B, and ZNF707) were identified. In silico functional annotation analysis and in vitro promoter assay validated the regulatory effect of rs4873815-TT on ZNF707 and rs11136002-TT on TNFRSF10B. Furthermore, ZNF707 was highly expressed in Ov-CCA and had a negative prognostic value in disease recurrence in our sample cohort. This prognostic power was consistently observed in The Cancer Genome Atlas (TCGA) clear cell renal cell carcinoma dataset, suggesting that ZNF707 may have prognostic value in clear cell histology regardless of tissue origin. In conclusion, rs4873815-TT/ZNF707 may have clinical significance in the prognosis and tumorigenesis of Ov-CCA, which may be more relevant to clear cell histology. Besides, this study may underpin the evidence that cis-eQTL analysis based on ancestral disparities can facilitate the discovery of causal genetic alterations in complex diseases, such as cancer.
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15
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Yosudjai J, Wongkham S, Jirawatnotai S, Kaewkong W. Aberrant mRNA splicing generates oncogenic RNA isoforms and contributes to the development and progression of cholangiocarcinoma. Biomed Rep 2019; 10:147-155. [PMID: 30906543 PMCID: PMC6403481 DOI: 10.3892/br.2019.1188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
Cholangiocarcinoma is a lethal biliary cancer, with an unclear molecular pathogenesis. Alternative splicing is a post-transcriptional modification that generates mature mRNAs, which are subsequently translated into proteins. Aberrant alternative splicing has been reported to serve a role in tumor initiation, maintenance and metastasis in several types of human cancer, including cholangiocarcinoma. In this review, the aberrant splicing of genes and the functional contributions of the spliced genes, in the carcinogenesis, progression and aggressiveness of cholangiocarcinoma are summarized. In addition, factors that influence this aberrant splicing that may be relevant as therapeutic targets or prognosis markers for cholangiocarcinoma are discussed.
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Affiliation(s)
- Juthamas Yosudjai
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Siwanon Jirawatnotai
- Siriraj Center for Research of Excellence (SiCORE) for System Pharmacology, Department of Pharmacology, Faculty of Medicine, Siriraj Medical School, Mahidol University, Bangkok 10700, Thailand
| | - Worasak Kaewkong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
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16
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Li S, Hu Z, Zhao Y, Huang S, He X. Transcriptome-Wide Analysis Reveals the Landscape of Aberrant Alternative Splicing Events in Liver Cancer. Hepatology 2019; 69:359-375. [PMID: 30014619 DOI: 10.1002/hep.30158] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/30/2018] [Indexed: 01/02/2023]
Abstract
Alternative splicing (AS) is assumed to be a pivotal determinant for the generation of diverse transcriptional variants in cancer. However, the comprehensive dysregulation of AS and the prospective biological and clinical relevance in hepatocellular carcinoma (HCC) remain obscure. Here, we identified and depicted the AS landscape in HCC by performing reference-based assembly of sequencing reads from over 600 RNA sequencing (RNA-seq) libraries. We detected various differentially spliced ASEs across patients covering not only protein-coding genes, but also considerable numbers of noncoding genes. Strikingly, alternative transcription initiation was found to frequently occur in HCC. These differential ASEs were highly related to "cancer hallmarks" and involved in metabolism-related pathways in particular. In addition, 243 differential ASEs were identified as risk predictors for HCC patient survival. The isoform switch of metabolism-related gene UGP2 (UDP-glucose pyrophosphorylase 2) might play an essential role in HCC. We further constructed regulatory networks between RNA-binding protein (RBP) genes and the corresponding ASEs. Further analysis demonstrated that the regulated networks were enriched in a variety of metabolism-related pathways. Conclusion: Differential ASEs are prevalent in HCC, where alternative transcription initiation was found to frequently occur. We found that genes having differential ASEs were significantly enriched in metabolism-related pathways. The expression variations, binding relations, and even mutations of RBP genes largely influenced differential ASEs in HCC.
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Affiliation(s)
- Shengli Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yingjun Zhao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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17
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Li J, Wei L. Increased expression of LINC01510 predicts poor prognosis and promotes malignant progression in human non-small cell lung cancer. Biomed Pharmacother 2018; 109:519-529. [PMID: 30399588 DOI: 10.1016/j.biopha.2018.10.136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/21/2018] [Accepted: 10/21/2018] [Indexed: 10/27/2022] Open
Abstract
Non-small cell lung cancer (NSCLC), the most prevalent type of lung cancer, is one of the most leading causes of cancer-related morbidity and mortality worldwide. Evidence is accumulating that long non-coding RNAs (lncRNAs) play vital regulatory roles in tumor development and progression. LINC01510, a novel tumor-related lncRNA, has been identified as an oncogene in colorectal cancer; however, its role in NSCLC remains poorly understood. This study aimed to characterize the biological role of LINC01510 in NSCLC and illuminate the molecular mechanisms. Here we found that LINC01510 was highly expressed in NSCLC tissues. Besides, Fisher's exact test showed that high expression of LINC01510 was associated with larger tumor size, advanced TNM stage and lymph node metastasis. Kaplan-Meier survival analysis showed that patients with high LINC01510 expression had a much lower overall survival rate. Gain- and loss-of-function approaches were employed to investigate the effects of LINC01510 on NSCLC cell phenotypes. Functional studies demonstrated that LINC01510 over-expression promoted NSCLC cell proliferation, cell cycle progression, migration and invasion, but shRNA-mediated LINC01510 depletion inhibited NSCLC cell proliferation, cell cycle progression, migration and invasion. Notably, LINC01510 ablation suppressed tumorigenicity of NSCLC cells in a murine xenograft model. Furthermore, mechanistic studies revealed that LINC01510 exerted its oncogenic functions in NSCLC through miR-339-5p-mediated regulation of CDK14. To sum up, our data indicate that increased expression of LINC01510 predicts poor prognosis and promotes tumorigenesis in NSCLC. Collectively, this study may provide a basis for LINC01510 as a candidate therapeutic target in NSCLC.
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Affiliation(s)
- Jiwei Li
- Department of Thoracic Surgery, Henan Provincial People's Hospital, Zhengzhou 450003, China
| | - Li Wei
- Department of Thoracic Surgery, Henan Provincial People's Hospital, Zhengzhou 450003, China.
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18
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Jimenez M, Arechederra M, Ávila MA, Berasain C. Splicing alterations contributing to cancer hallmarks in the liver: central role of dedifferentiation and genome instability. Transl Gastroenterol Hepatol 2018; 3:84. [PMID: 30505971 DOI: 10.21037/tgh.2018.10.11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide. HCCs are molecularly heterogeneous tumors, and this complexity is to a great extent responsible for their poor response to conventional and targeted therapies. In this review we summarize recent evidence indicating that imbalanced expression of mRNA splicing factors can be a relevant source for this heterogeneity. We also discuss how these alterations may play a driver role in hepatocarcinogenesis by impinging on the general hallmarks of cancer. Considering the natural history of HCC, we focused on two pathogenic features that are characteristic of liver tumors: chromosomal instability and phenotypic de-differentiation. We highlight mechanisms connecting splicing derangement with these two processes and the enabling capacities acquired by liver cells along their neoplastic transformation. A thorough understanding of the alterations in the splicing machinery may also help to identify new HCC biomarkers and to design novel therapeutic strategies.
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Affiliation(s)
- Maddalen Jimenez
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | | | - Matías A Ávila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain
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19
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Yang S, Jia R, Bian Z. SRSF5 functions as a novel oncogenic splicing factor and is upregulated by oncogene SRSF3 in oral squamous cell carcinoma. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1161-1172. [DOI: 10.1016/j.bbamcr.2018.05.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 10/25/2022]
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20
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Lin KT, Ma WK, Scharner J, Liu YR, Krainer AR. A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma. Genome Res 2018; 28:gr.227181.117. [PMID: 29449409 PMCID: PMC5848607 DOI: 10.1101/gr.227181.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/24/2018] [Indexed: 01/05/2023]
Abstract
Pre-mRNA splicing can contribute to the switch of cell identity that occurs in carcinogenesis. Here, we analyze a large collection of RNA-seq data sets and report that splicing changes in hepatocyte-specific enzymes, such as AFMID and KHK, are associated with HCC patients' survival and relapse. The switch of AFMID isoforms is an early event in HCC development and is associated with driver mutations in TP53 and ARID1A The switch of AFMID isoforms is human-specific and not detectable in other species, including primates. Finally, we show that overexpression of the full-length AFMID isoform leads to a higher NAD+ level, lower DNA-damage response, and slower cell growth in HepG2 cells. The integrative analysis uncovered a mechanistic link between splicing switches, de novo NAD+ biosynthesis, driver mutations, and HCC recurrence.
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Affiliation(s)
- Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Wai Kit Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Juergen Scharner
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yun-Ru Liu
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan 11031
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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21
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Aydemir TB, Cousins RJ. The Multiple Faces of the Metal Transporter ZIP14 (SLC39A14). J Nutr 2018; 148:174-184. [PMID: 29490098 PMCID: PMC6251594 DOI: 10.1093/jn/nxx041] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
The SLC39A family of metal transporters was identified through homologies with the Zrt- and Irt-like (ZIP) proteins from yeast and plants. Of all the ZIP transporters, ZIP14 is arguably the most robustly characterized in terms of function at the integrative level. Mice with a global knockout of Zip14 are viable, thus providing the opportunity to conduct physiologic experiments. In mice, Zip14 expression is highly tissue specific, with the greatest abundance in the jejunum > liver > heart > kidney > white adipose tissue > skeletal muscle > spleen > pancreas. A unique feature of Zip14 is its upregulation by proinflammatory conditions, particularly increased interleukin 6 (IL-6) and nitric oxide. The transcription factors AP-1, ATF4, and ATF6α are involved in Zip14 regulation. ZIP14 does not appear to be zinc-regulated. The Zip14 knockout phenotype shows multiple sites of ZIP14 function, including the liver, adipose tissue, brain, pancreas, and bone. A prominent feature of the Zip14 ablation is a reduction in intestinal barrier function and onset of metabolic endotoxemia. Many aspects of the phenotype are accentuated with age and accompany increased circulating IL-6. Studies with 65Zn, 59Fe [nontransferrin-bound iron (NTBI)] and 54Mn show that ZIP14 transports these metals. At a steady state, the plasma concentrations of zinc, NTBI, and manganese are such that zinc ions are the major substrate available for ZIP14 at the cell surface. Upregulation of ZIP14 accounts for the hypozincemia and hepatic zinc accumulation associated with acute inflammation and sepsis and is required for liver regeneration and resistance to endoplasmic reticulum (ER) stress. Zip14 ablation in mice produces a defect in manganese excretion that leads to excess manganese accumulation in the brain that produces characteristics of Parkinsonism.
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Affiliation(s)
- Tolunay B Aydemir
- Food Science and Human Nutrition Department and Center for Nutritional
Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville,
FL,Address correspondence to TBA (e-mail: )
| | - Robert J Cousins
- Food Science and Human Nutrition Department and Center for Nutritional
Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville,
FL
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22
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Recent Advances in the Role of SLC39A/ZIP Zinc Transporters In Vivo. Int J Mol Sci 2017; 18:ijms18122708. [PMID: 29236063 PMCID: PMC5751309 DOI: 10.3390/ijms18122708] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/27/2017] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
Zinc (Zn), which is an essential trace element, is involved in numerous mammalian physiological events; therefore, either a deficiency or excess of Zn impairs cellular machineries and influences physiological events, such as systemic growth, bone homeostasis, skin formation, immune responses, endocrine function, and neuronal function. Zn transporters are thought to mainly contribute to Zn homeostasis within cells and in the whole body. Recent genetic, cellular, and molecular studies of Zn transporters highlight the dynamic role of Zn as a signaling mediator linking several cellular events and signaling pathways. Dysfunction in Zn transporters causes various diseases. This review aims to provide an update of Zn transporters and Zn signaling studies and discusses the remaining questions and future directions by focusing on recent progress in determining the roles of SLC39A/ZIP family members in vivo.
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23
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Fujita T, Higashitsuji H, Higashitsuji H, Liu Y, Itoh K, Sakurai T, Kojima T, Kandori S, Nishiyama H, Fukumoto M, Fukumoto M, Shibasaki K, Fujita J. TRPV4-dependent induction of a novel mammalian cold-inducible protein SRSF5 as well as CIRP and RBM3. Sci Rep 2017; 7:2295. [PMID: 28536481 PMCID: PMC5442135 DOI: 10.1038/s41598-017-02473-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/11/2017] [Indexed: 02/06/2023] Open
Abstract
Cold-inducible RNA-binding protein (CIRP) and RNA-binding motif protein 3 (RBM3) are two evolutionarily conserved RNA-binding proteins that are structurally related to hnRNPs and upregulated in response to moderately low temperatures in mammalian cells. Although contributions of splicing efficiency, the gene promoters activated upon mild hypothermia and the transcription factor Sp1 to induction of CIRP have been reported, precise mechanisms by which hypothermia and other stresses induce the expression of mammalian cold-inducible proteins (CIPs) are poorly understood. By screening the serine/arginine-rich splicing factors (SRSFs), we report that the transcript and protein levels of SRSF5 were increased in mammalian cells cultured at 32 °C. Expression of SRSF5 as well as CIRP and RBM3 were also induced by DNA damage, hypoxia, cycloheximide and hypotonicity. Immunohistochemical studies demonstrated that SRSF5 was constitutively expressed in male germ cells and the level was decreased in human testicular germ cell tumors. SRSF5 facilitated production of p19 H-RAS, and increased sensitivity to doxorubicin in human U-2 OS cells. Induction of CIPs was dependent on transient receptor potential vanilloid 4 (TRPV4) channel protein, but seemed independent of its ion channel activity. These findings indicate a previously unappreciated role for the TRP protein in linking environmental stress to splicing.
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Affiliation(s)
- Takanori Fujita
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan.,School of Economics, Nagoya University, Nagoya, Nagoya, 464-8601, Japan
| | - Hiroaki Higashitsuji
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Hisako Higashitsuji
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Yu Liu
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Katsuhiko Itoh
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Toshiharu Sakurai
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takahiro Kojima
- Department of Urology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Shuya Kandori
- Department of Urology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Hiroyuki Nishiyama
- Department of Urology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Motoi Fukumoto
- Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Manabu Fukumoto
- Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan.,Department of Molecular Pathology, Tokyo Medical University, Shinjuku-ku, Tokyo, 160-8402, Japan
| | - Koji Shibasaki
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Jun Fujita
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan. .,Department of Rehabilitation Medicine, Biwako-Chuo Hospital, Otsu, Shiga, 520-0834, Japan.
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24
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Zhang L, Li S, Choi YL, Lee J, Gong Z, Liu X, Pei Y, Jiang A, Ye M, Mao M, Zhang X, Kim J, Chen R. Systematic identification of cancer-related long noncoding RNAs and aberrant alternative splicing of quintuple-negative lung adenocarcinoma through RNA-Seq. Lung Cancer 2017; 109:21-27. [PMID: 28577945 DOI: 10.1016/j.lungcan.2017.04.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Lung adenocarcinoma (LUAD) is a common subtype of non-small cell lung cancer prevalent in Asia. There is a dearth of understanding regarding the transcriptome landscape of LUAD without primary known driver mutations. In this study, LUAD samples without well-known driver mutations occurring in EGFR, KRAS, ALK, ROS1 or RET (quintuple-negative) were used for transcriptome study with a focus on long noncoding RNAs (lncRNAs), alternative splicing and gene fusions. MATERIALS AND METHODS 24 pairs of LUAD and adjacent normal samples and 13 tumor-only samples derived from 37 quintuple-negative patients were used. Differentially expressed lncRNA transcripts were detected by paired t-test and were validated by qPCR. Functions of lncRNAs were predicted by co-expressed mRNAs. Aberrant splicing events in LUAD were identified using MISO. In addition, gene fusions were screened by SOAPfuse. RESULTS AND CONCLUSION In total, 90 and 153 up- or down-regulated lncRNA transcripts were detected in LUAD samples in comparison with the adjacent normal samples. The most significantly differentially expressed lncRNA transcript was ENST00000598996.1 (FENDRR) down-regulated in LUAD. By lncRNA-mRNA co-expression analysis, functions of 14 lncRNAs were predicted. The predicted functions included vasculature development, immune response, cell cycle and respiratory gaseous exchange. Furthermore, six co-expressed pairs of lncRNAs and their nearby protein coding genes were identified as associated with lung development. This study also identified two highly recurrent (22 in 24) differential exon skipping events occurring in MYH14 and ESYT2 with exon including isoforms of both genes up-regulated in isoform percentage in LUAD samples. On the other hand, two out of 24 LUAD samples possessed the driver mutation exon 14 skipping of MET. The transcriptional alterations of LUAD samples without well-known driver mutations identified in the study can be used as references for future research. The translational values of these transcriptional changes are also worthy of further investigation.
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Affiliation(s)
- Lu Zhang
- Informatics, MSD China R&D, Beijing, China.
| | | | - Yoon-La Choi
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jinseon Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | | | | | - Yunfei Pei
- Informatics, MSD China R&D, Beijing, China
| | | | | | - Mao Mao
- Pfizer Oncology, San Diego, CA 92121, USA
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Jhingook Kim
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Ronghua Chen
- Informatics, MSD China R&D, Beijing, China; Global Research IT, MRL-IT, Merck & Co., Inc., Boston, MA, USA.
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25
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Villacis RAR, Basso TR, Canto LM, Pinheiro M, Santiago KM, Giacomazzi J, de Paula CAA, Carraro DM, Ashton-Prolla P, Achatz MI, Rogatto SR. Rare germline alterations in cancer-related genes associated with the risk of multiple primary tumor development. J Mol Med (Berl) 2017; 95:523-533. [PMID: 28093616 DOI: 10.1007/s00109-017-1507-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 12/07/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022]
Abstract
Multiple primary tumors (MPT) have been described in carriers of inherited cancer predisposition genes. However, the genetic etiology of a large proportion of MPT cases remains unclear. We reviewed 267 patients with hereditary cancer predisposition syndromes (HCPS) that underwent genetic counseling and selected 22 patients with MPT to perform genomic analysis (CytoScan HD Array, Affymetrix) aiming to identify new alterations related to a high risk of developing MPT. Twenty patients had a positive family history of cancer and 11 met phenotypic criteria for HCPS. Genetic testing for each of the genes associated with these syndromes revealed negative results for pathogenic mutations. Seventeen rare germline copy number variations (CNVs) covering 40 genes were identified in 11 patients, including an EPCAM/MSH2 deletion in one Lynch syndrome patient. An enrichment analysis revealed a significant number of genes (where the CNVs are mapped) associated with carcinogenesis and/or related to functions implicated with tumor development, such as proliferation and cell survival. An interaction network analysis highlighted the importance of TP53 pathway in cancer emergence. A high number of germline copy-neutral loss of heterozygosity (cnLOH) was identified in nine cases, particularly in two patients. Eighteen genes were covered by both rare CNVs and cnLOH, including 14 related to tumorigenesis and seven genes (ABCC1, KDM4C, KIAA0430, MYH11, NDE1, PIWIL2, and ULK2) specifically associated with cellular growth and proliferation. Overall, we identified 14 cases with rare CNVs and/or cnLOH that may contribute to the risk of MPT development. KEY MESSAGE CNVs may explain the risk of hereditary cancer syndromes in MPT patients. CNVs affecting genes related to cancer are candidates to be involved in MPT risk. EPCAM/MSH2 deletions should be investigated in patients suspected to have LS. Gene enrichment related to the TP53 network is associated with MPT development. cnLOH and CNVs contribute to the risk of MPT development.
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Affiliation(s)
- Rolando A R Villacis
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Tatiane R Basso
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Luisa M Canto
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Maísa Pinheiro
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Karina M Santiago
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Juliana Giacomazzi
- Department of Genetics, Federal University of Rio Grande do Sul (UFRGS) and Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Cláudia A A de Paula
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Dirce M Carraro
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Patrícia Ashton-Prolla
- Department of Genetics, Federal University of Rio Grande do Sul (UFRGS) and Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Maria I Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil.,Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI)/National Institutes of Health (NIH), Bethesda, MD, USA
| | - Silvia R Rogatto
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil. .,Department of Clinical Genetics, Vejle Sygehus, Kabbeltoft 25, 7100, Vejle, Denmark. .,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark.
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Ziegler C, Kretz M. The More the Merrier-Complexity in Long Non-Coding RNA Loci. Front Endocrinol (Lausanne) 2017; 8:90. [PMID: 28487673 PMCID: PMC5403818 DOI: 10.3389/fendo.2017.00090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/06/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Christian Ziegler
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
- *Correspondence: Markus Kretz,
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