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Summers BS, Thomas Broome S, Pang TWR, Mundell HD, Koh Belic N, Tom NC, Ng ML, Yap M, Sen MK, Sedaghat S, Weible MW, Castorina A, Lim CK, Lovelace MD, Brew BJ. A Review of the Evidence for Tryptophan and the Kynurenine Pathway as a Regulator of Stem Cell Niches in Health and Disease. Int J Tryptophan Res 2024; 17:11786469241248287. [PMID: 38757094 PMCID: PMC11097742 DOI: 10.1177/11786469241248287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024] Open
Abstract
Stem cells are ubiquitously found in various tissues and organs in the body, and underpin the body's ability to repair itself following injury or disease initiation, though repair can sometimes be compromised. Understanding how stem cells are produced, and functional signaling systems between different niches is critical to understanding the potential use of stem cells in regenerative medicine. In this context, this review considers kynurenine pathway (KP) metabolism in multipotent adult progenitor cells, embryonic, haematopoietic, neural, cancer, cardiac and induced pluripotent stem cells, endothelial progenitor cells, and mesenchymal stromal cells. The KP is the major enzymatic pathway for sequentially catabolising the essential amino acid tryptophan (TRP), resulting in key metabolites including kynurenine, kynurenic acid, and quinolinic acid (QUIN). QUIN metabolism transitions into the adjoining de novo pathway for nicotinamide adenine dinucleotide (NAD) production, a critical cofactor in many fundamental cellular biochemical pathways. How stem cells uptake and utilise TRP varies between different species and stem cell types, because of their expression of transporters and responses to inflammatory cytokines. Several KP metabolites are physiologically active, with either beneficial or detrimental outcomes, and evidence of this is presented relating to several stem cell types, which is important as they may exert a significant impact on surrounding differentiated cells, particularly if they metabolise or secrete metabolites differently. Interferon-gamma (IFN-γ) in mesenchymal stromal cells, for instance, highly upregulates rate-limiting enzyme indoleamine-2,3-dioxygenase (IDO-1), initiating TRP depletion and production of metabolites including kynurenine/kynurenic acid, known agonists of the Aryl hydrocarbon receptor (AhR) transcription factor. AhR transcriptionally regulates an immunosuppressive phenotype, making them attractive for regenerative therapy. We also draw attention to important gaps in knowledge for future studies, which will underpin future application for stem cell-based cellular therapies or optimising drugs which can modulate the KP in innate stem cell populations, for disease treatment.
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Affiliation(s)
- Benjamin Sebastian Summers
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia
| | - Sarah Thomas Broome
- Faculty of Science, Laboratory of Cellular and Molecular Neuroscience, School of Life Sciences, University of Technology Sydney, NSW, Australia
| | | | - Hamish D Mundell
- Faculty of Medicine and Health, New South Wales Brain Tissue Resource Centre, School of Medical Sciences, Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Naomi Koh Belic
- School of Life Sciences, University of Technology, Sydney, NSW, Australia
| | - Nicole C Tom
- Formerly of the Department of Physiology, University of Sydney, NSW, Australia
| | - Mei Li Ng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Maylin Yap
- Formerly of the Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Monokesh K Sen
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- School of Medicine, Western Sydney University, NSW, Australia
- Faculty of Medicine and Health, School of Medical Sciences, Charles Perkins Centre, The University of Sydney, NSW, Australia
| | - Sara Sedaghat
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Michael W Weible
- School of Environment and Science, Griffith University, Brisbane, QLD, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
| | - Alessandro Castorina
- Faculty of Science, Laboratory of Cellular and Molecular Neuroscience, School of Life Sciences, University of Technology Sydney, NSW, Australia
| | - Chai K Lim
- Faculty of Medicine, Macquarie University, Sydney, NSW, Australia
| | - Michael D Lovelace
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia
| | - Bruce J Brew
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia
- Departments of Neurology and Immunology, St. Vincent’s Hospital, Sydney, NSW, Australia
- University of Notre Dame, Darlinghurst, Sydney, NSW, Australia
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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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Wu Q, Wang P, Peng Q, Kang Z, Deng Y, Li J, Chen Y, Li J, Ge F. Adhesion G Protein-Coupled Receptor G2 Promotes Hepatocellular Carcinoma Progression and Serves as a Neutrophil-Related Prognostic Biomarker. Int J Mol Sci 2023; 24:16986. [PMID: 38069309 PMCID: PMC10707058 DOI: 10.3390/ijms242316986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Adhesion G protein-coupled receptor G2 (ADGRG2) is an orphan adhesion G protein-coupled receptor (GPCR), which performs a tumor-promoting role in certain cancers; however, it has not been systematically investigated in hepatocellular carcinoma (HCC). In the current study, we utilized multiple databases to analyze the expression and diagnostic and prognostic value of ADGRG2 in HCC and its correlation with immune infiltration and inflammatory factors. The function and upstream regulatory miRNA of ADGRG2 were validated through qPCR, Western blot, CCK8, wound healing, and dual luciferase assays. It turned out that ADGRG2 was significantly higher in HCC and had a poor survival rate, especially in AFP ≤ 400 ng/mL subgroups. Functional enrichment analysis suggested that ADGRG2 may be involved in cancer pathways and immune-related pathways. In vitro, siRNA-mediated ADGRG2 silencing could inhibit the proliferation and migration of Huh7 and HepG2 cells. There was a highly significant positive correlation between ADGRG2 and neutrophils. Moreover, NET-related genes were filtered and confirmed, such as ENO1 and S100A9. Meanwhile, the high expression of ADGRG2 was also accompanied by the highest number of inflammatory cytokines, chemokines, and chemokine receptors and good immunotherapy efficacy. Finally, AGDGR2 may be sensitive to two drugs (PIK-93 and NPK76-II-72-1) and can be targeted by miR-326. In conclusion, ADGRG2 may serve as a novel biomarker and drug target for HCC diagnosis, immunotherapy, and prognosis and was related to neutrophils and the inflammatory process of liver cancer development.
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Affiliation(s)
- Qian Wu
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Pei Wang
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Qihang Peng
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Zhongcui Kang
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Yiting Deng
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Jiayi Li
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Ying Chen
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Jin Li
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
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León-Letelier RA, Dou R, Vykoukal J, Sater AHA, Ostrin E, Hanash S, Fahrmann JF. The kynurenine pathway presents multi-faceted metabolic vulnerabilities in cancer. Front Oncol 2023; 13:1256769. [PMID: 37876966 PMCID: PMC10591110 DOI: 10.3389/fonc.2023.1256769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The kynurenine pathway (KP) and associated catabolites play key roles in promoting tumor progression and modulating the host anti-tumor immune response. To date, considerable focus has been on the role of indoleamine 2,3-dioxygenase 1 (IDO1) and its catabolite, kynurenine (Kyn). However, increasing evidence has demonstrated that downstream KP enzymes and their associated metabolite products can also elicit tumor-microenvironment immune suppression. These advancements in our understanding of the tumor promotive role of the KP have led to the conception of novel therapeutic strategies to target the KP pathway for anti-cancer effects and reversal of immune escape. This review aims to 1) highlight the known biological functions of key enzymes in the KP, and 2) provide a comprehensive overview of existing and emerging therapies aimed at targeting discrete enzymes in the KP for anti-cancer treatment.
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Affiliation(s)
- Ricardo A. León-Letelier
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rongzhang Dou
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jody Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ali Hussein Abdel Sater
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Zhou L, Wang Q, Hou J, Wu X, Wang L, Chen X. Upregulation of hsa_circ_0002003 promotes hepatocellular carcinoma progression. BMC Cancer 2023; 23:611. [PMID: 37400785 DOI: 10.1186/s12885-023-11086-9] [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: 02/16/2022] [Accepted: 06/19/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs), which are involved in various human malignancies, have emerged as promising biomarkers. The present study aimed to investigate unique expression profiles of circRNAs in hepatocellular carcinoma (HCC) and identify novel biomarkers associated with HCC development and progression. METHODS CircRNA expression profiles of HCC tissues were jointly analyzed to identify differentially expressed circRNAs. Overexpression plasmid and siRNA targeting candidate circRNAs were used in functional assays in vitro. CircRNA-miRNA interactions were predicted using miRNAs expressed in the miRNA-seq dataset GSE76903. To further screen downstream genes targeted by the miRNAs, survival analysis and qRT-PCR were conducted to evaluate their prognostic role in HCC and construct a ceRNA regulatory network. RESULTS Three significantly upregulated circRNAs, hsa_circ_0002003, hsa_circ_0002454, and hsa_circ_0001394, and one significantly downregulated circRNA, hsa_circ_0003239, were identified and validated by qRT-PCR. Our in vitro data indicated that upregulation of hsa_circ_0002003 accelerated cell growth and metastasis. Mechanistically, DTYMK, DAP3, and STMN1, which were targeted by hsa-miR-1343-3p, were significantly downregulated in HCC cells when hsa_circ_0002003 was silenced and were significantly correlated with poor prognosis in patients with HCC. CONCLUSION Hsa_circ_0002003 may play critical roles in HCC pathogenesis and serve as a potential prognostic biomarker for HCC. Targeting the hsa_circ_0002003/hsa-miR-1343-3p/STMN1 regulatory axis could be an effective therapeutic strategy in patients with HCC.
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Affiliation(s)
- Lisha Zhou
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing, China
| | - Qianwen Wang
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Jun Hou
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Xiangwei Wu
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Lianghai Wang
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
- Department of Pathology, the First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
| | - Xueling Chen
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
- Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
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Zhou D, Cao S, Xie H. Research on Predicting the Occurrence of Hepatocellular Carcinoma Based on Notch Signal-Related Genes Using Machine Learning Algorithms. THE TURKISH JOURNAL OF GASTROENTEROLOGY : THE OFFICIAL JOURNAL OF TURKISH SOCIETY OF GASTROENTEROLOGY 2023; 34:760-770. [PMID: 37051625 PMCID: PMC10441146 DOI: 10.5152/tjg.2023.22357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/12/2022] [Indexed: 04/14/2023]
Abstract
BACKGROUND/AIMS Hepatocellular carcinoma, a highly malignant tumor, is difficult to diagnose, treat, and predict the prognosis. Notch signaling pathway can affect hepatocellular carcinoma. We aimed to predict the occurrence of hepatocellular carcinoma based on Notch signal-related genes using machine learning algorithms. MATERIALS AND METHODS We downloaded hepatocellular carcinoma data from the Cancer Genome Atlas and Gene Expression Omnibus databases and used machine learning methods to screen the hub Notch signal-related genes. Machine learning classification was used to construct a prediction model for the classification and diagnosis of hepatocellular carcinoma cancer. Bioinformatics methods were applied to explore the expression of these hub genes in the hepatocellular carcinoma tumor immune microenvironment. RESULTS We identified 4 hub genes, namely, LAMA4, POLA2, RAD51, and TYMS, which were used as the final variables, and found that AdaBoostClassifie was the best algorithm for the classification and diagnosis model of hepatocellular carcinoma. The area under curve, accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1 score of this model in the training set were 0.976, 0.881, 0.877, 0.977, 0.996, 0.500, and 0.932; respectively. The area under curves were 0.934, 0.863, 0.881, 0.886, 0.981, 0.489, and 0.926. The area under curve in the external validation set was 0.934. Immune cell infiltration was related to the expression of 4 hub genes. Patients in the low-risk group of hepatocellular carcinoma were more likely to have an immune escape. CONCLUSION The Notch signaling pathway was closely related to the occurrence and development of hepatocellular carcinoma. The hepatocellular carcinoma classification and diagnosis model established based on this had a high degree of reliability and stability.
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Affiliation(s)
- Dingzhong Zhou
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, P. R. China
- Key Laboratory of Medical Imaging and Artifical Intelligence of Hunan Province, Chenzhou, P. R. China
| | - Sujuan Cao
- Department of Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, P. R. China
| | - Hui Xie
- Key Laboratory of Medical Imaging and Artifical Intelligence of Hunan Province, Chenzhou, P. R. China
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, P. R. China
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Kiyose H, Nakagawa H, Ono A, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Shimada M, Wong JH, Fujimoto A. Comprehensive analysis of full-length transcripts reveals novel splicing abnormalities and oncogenic transcripts in liver cancer. PLoS Genet 2022; 18:e1010342. [PMID: 35926060 PMCID: PMC9380957 DOI: 10.1371/journal.pgen.1010342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/16/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. Although long-reads sequencing technologies would enable the sequencing of full-length transcripts, the data analysis is difficult. In this study, we developed an analysis pipeline named SPLICE and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5%) were novel. A comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Interestingly, 746 genes with DETs, including the LINE1-MET transcript, were not found by a gene-level analysis. We also found that fusion transcripts of transposable elements and hepatitis B virus (HBV) were overexpressed in HCCs. In vitro experiments on DETs showed that LINE1-MET and HBV-human transposable elements promoted cell growth. Furthermore, fusion gene detection showed novel recurrent fusion events that were not detected in the short-reads. These results suggest the efficiency of full-length transcriptome studies and the importance of splicing variants in carcinogenesis. Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. In this study, we developed an analysis pipeline named SPLICE for long-read transcriptome sequencing and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC), and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 5,366 novel transcripts and 9,933 differentially expressed transcripts in 4,744 genes between HCCs and non-cancerous livers. An analysis of hepatitis B virus (HBV) transcripts showed that fusion transcripts of the HBV gene and human transposable elements were overexpressed in HBV-infected HCCs. We also identified fusion genes that were not found in the short-reads. These results suggest that long-reads sequencing technologies provide a fuller understanding of cancer transcripts and that our method contributes to the analysis of transcriptome sequences by such technologies.
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Affiliation(s)
- Hiroki Kiyose
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Ueno
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Shinya Hayami
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Yamaue
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Kazuaki Chayama
- Collaborative Research Laboratory of Medical Innovation, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Research Center for Hepatology and Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mihoko Shimada
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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The Kynurenine Pathway and Cancer: Why Keep It Simple When You Can Make It Complicated. Cancers (Basel) 2022; 14:cancers14112793. [PMID: 35681770 PMCID: PMC9179486 DOI: 10.3390/cancers14112793] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The kynurenine pathway has two main physiological roles: (i) it protects specific organs such as the eyes and placenta from strong immune reactions and (ii) it additionally generate in the liver and kidney a metabolite essential to all cells of human body. Abnormal activation of this pathway is recurrently observed in numerous cancer types. Its two functions are hijacked to promote tumor growth and cancer cell dissemination through multiple mechanisms. Clinical assays including administration of inhibitors of this pathway have not yet been successful. The complex regulation of this pathway is likely the reason behind this failure. In this review, we try to give an overview of the current knowledge about this pathway, to point out the next challenges, and to propose alternative therapeutic routes. Abstract The kynurenine pathway has been highlighted as a gatekeeper of immune-privileged sites through its ability to generate from tryptophan a set of immunosuppressive metabolic intermediates. It additionally constitutes an important source of cellular NAD+ for the organism. Hijacking of its immunosuppressive functions, as recurrently observed in multiple cancers, facilitates immune evasion and promotes tumor development. Based on these observations, researchers have focused on characterizing indoleamine 2,3-dioxygenase (IDO1), the main enzyme catalyzing the first and limiting step of the pathway, and on developing therapies targeting it. Unfortunately, clinical trials studying IDO1 inhibitors have thus far not met expectations, highlighting the need to unravel this complex signaling pathway further. Recent advances demonstrate that these metabolites additionally promote tumor growth, metastatic dissemination and chemoresistance by a combination of paracrine and autocrine effects. Production of NAD+ also contributes to cancer progression by providing cancer cells with enhanced plasticity, invasive properties and chemoresistance. A comprehensive survey of this complexity is challenging but necessary to achieve medical success.
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Ladewig E, Michelini F, Jhaveri K, Castel P, Carmona J, Fairchild L, Zuniga AG, Arruabarrena-Aristorena A, Cocco E, Blawski R, Kittane S, Zhang Y, Sallaku M, Baldino L, Hristidis V, Chandarlapaty S, Abdel-Wahab O, Leslie C, Scaltriti M, Toska E. The oncogenic PI3K-induced transcriptomic landscape reveals key functions in splicing and gene expression regulation. Cancer Res 2022; 82:2269-2280. [PMID: 35442400 DOI: 10.1158/0008-5472.can-22-0446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
The PI3K pathway regulates proliferation, survival, and metabolism and is frequently activated across human cancers. A comprehensive elucidation of how this signaling pathway controls transcriptional and co-transcriptional processes could provide new insights into the key functions of PI3K signaling in cancer. Here, we undertook a transcriptomic approach to investigate genome-wide gene expression and transcription factor (TF) activity changes, as well as splicing and isoform usage dynamics, downstream of PI3K. These analyses uncovered widespread alternatively spliced (AS) isoforms linked to proliferation, metabolism, and splicing in PIK3CA mutant cells, which were reversed by inhibition of PI3Kα. Analysis of paired tumor biopsies from PIK3CA-mutated breast cancer patients undergoing treatment with PI3Kα inhibitors identified widespread splicing alterations that affect specific isoforms in common with the preclinical models, and these alterations, namely PTK2/FRNK and AFMID isoforms, were validated as functional drivers of cancer cell growth or migration. Mechanistically, isoform-specific splicing factors mediated PI3K-dependent RNA splicing. Treatment with splicing inhibitors rendered breast cancer cells more sensitive to the PI3Kα inhibitor alpelisib, resulting in greater growth inhibition than alpelisib alone. This study provides the first comprehensive analysis of widespread splicing alterations driven by oncogenic PI3K in breast cancer. The atlas of PI3K-mediated splicing programs establishes a key role for the PI3K pathway in regulating splicing, opening new avenues for exploiting PI3K signaling as a therapeutic vulnerability in breast cancer.
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Affiliation(s)
- Erik Ladewig
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Komal Jhaveri
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | - Pau Castel
- NYU Langone, New York, NY, United States
| | - Javier Carmona
- Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Lauren Fairchild
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Adler G Zuniga
- Johns Hopkins University School of Medicine, United States
| | | | | | - Ryan Blawski
- Johns Hopkins University School of Medicine, United States
| | - Srushti Kittane
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Yuhan Zhang
- Johns Hopkins University, Baltimore, United States
| | | | - Laura Baldino
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Omar Abdel-Wahab
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Christina Leslie
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Eneda Toska
- Johns Hopkins University, Baltimore, United States
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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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Jun Y, Suh YS, Park S, Lee J, Kim JI, Lee S, Lee WP, Anczuków O, Yang HK, Lee C. Comprehensive Analysis of Alternative Splicing in Gastric Cancer Identifies Epithelial-Mesenchymal Transition Subtypes Associated with Survival. Cancer Res 2022; 82:543-555. [PMID: 34903603 PMCID: PMC9359730 DOI: 10.1158/0008-5472.can-21-2117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/25/2021] [Accepted: 12/03/2021] [Indexed: 01/07/2023]
Abstract
Alternatively spliced RNA isoforms are a hallmark of tumors, but their nature, prevalence, and clinical implications in gastric cancer have not been comprehensively characterized. We systematically profiled the splicing landscape of 83 gastric tumors and matched normal mucosa, identifying and experimentally validating eight splicing events that can classify all gastric cancers into three subtypes: epithelial-splicing (EpiS), mesenchymal-splicing (MesS), and hybrid-splicing. These subtypes were associated with distinct molecular signatures and epithelial-mesenchymal transition markers. Subtype-specific splicing events were enriched in motifs for splicing factors RBM24 and ESRP1, which were upregulated in MesS and EpiS tumors, respectively. A simple classifier based only on RNA levels of RBM24 and ESRP1, which can be readily implemented in the clinic, was sufficient to distinguish gastric cancer subtypes and predict patient survival in multiple independent patient cohorts. Overall, this study provides insights into alternative splicing in gastric cancer and the potential clinical utility of splicing-based patient classification. SIGNIFICANCE This study presents a comprehensive analysis of alternative splicing in the context of patient classification, molecular mechanisms, and prognosis in gastric cancer.
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Affiliation(s)
- Yukyung Jun
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul, Korea.,Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Korea
| | - Yun-Suhk Suh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.,Department of Surgery, Seoul National University Hospital, Seoul, Korea.,Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Jieun Lee
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Sanghyuk Lee
- Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Wan-Ping Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,School of Cyber Science and Engineering, Xi'an Jiaotong University, Xi'an, China.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
| | - Han-Kwang Yang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.,Department of Surgery, Seoul National University Hospital, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea.,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
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12
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Yu S, Hu C, Liu L, Cai L, Du X, Yu Q, Lin F, Zhao J, Zhao Y, Zhang C, Liu X, Li W. Comprehensive analysis and establishment of a prediction model of alternative splicing events reveal the prognostic predictor and immune microenvironment signatures in triple negative breast cancer. J Transl Med 2020; 18:286. [PMID: 32723333 PMCID: PMC7388537 DOI: 10.1186/s12967-020-02454-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is widely concerning because of high malignancy and poor prognosis. There is increasing evidence that alternative splicing (AS) plays an important role in the development of cancer and the formation of the tumour microenvironment. However, comprehensive analysis of AS signalling in TNBC is still lacking and urgently needed. Methods Transcriptome and clinical data of 169 TNBC tissues and 15 normal tissues were obtained and integrated from the cancer genome atlas (TCGA), and an overview of AS events was downloaded from the SpliceSeq database. Then, differential comparative analysis was performed to obtain cancer-associated AS events (CAAS). Metascape was used to perform parent gene enrichment analysis based on CAAS. Unsupervised cluster analysis was performed to analyse the characteristics of immune infiltration in the microenvironment. A splicing network was established based on the correlation between CAAS events and splicing factors (SFs). We then constructed prediction models and assessed the accuracy of these models by receiver operating characteristic (ROC) curve and Kaplan–Meier survival analyses. Furthermore, a nomogram was adopted to predict the individualized survival rate of TNBC patients. Results We identified 1194 cancer-associated AS events (CAAS) and evaluated the enrichment of 981 parent genes. The top 20 parent genes with significant differences were mostly related to cell adhesion, cell component connection and other pathways. Furthermore, immune-related pathways were also enriched. Unsupervised clustering analysis revealed the heterogeneity of the immune microenvironment in TNBC. The splicing network also suggested an obvious correlation between SFs expression and CAAS events in TNBC patients. Univariate and multivariate Cox regression analyses showed that the survival-related AS events were detected, including some significant participants in the carcinogenic process. A nomogram incorporating risk, AJCC and radiotherapy showed good calibration and moderate discrimination. Conclusion Our study revealed AS events related to tumorigenesis and the immune microenvironment, elaborated the potential correlation between SFs and CAAS, established a prognostic model based on survival-related AS events, and created a nomogram to better predict the individual survival rate of TNBC patients, which improved our understanding of the relationship between AS events and TNBC.
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Affiliation(s)
- Shanshan Yu
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Chuan Hu
- Department of Orthopaedic Surgery, the Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Lixiao Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Luya Cai
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xuedan Du
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Qiongjie Yu
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Fan Lin
- Department of Dermatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Jinduo Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Ye Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Cheng Zhang
- Department of Dermatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xuan Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Wenfeng Li
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China.
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13
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Zhu GQ, Yu L, Zhou YJ, Du JX, Dong SS, Wu YM, Shi YH, Zhou J, Fan J, Dai Z. Genetic Alterations and Transcriptional Expression of m 6A RNA Methylation Regulators Drive a Malignant Phenotype and Have Clinical Prognostic Impact in Hepatocellular Carcinoma. Front Oncol 2020; 10:900. [PMID: 32850303 PMCID: PMC7396691 DOI: 10.3389/fonc.2020.00900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 05/07/2020] [Indexed: 01/14/2023] Open
Abstract
Background: N6-methyladenosine (m6A) RNA methylation, associated with cancer initiation and progression, is dynamically regulated by the m6A RNA regulators. However, its role in liver carcinogenesis is poorly understood. Methods: Three hundred seventy-one hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas database with sequencing and copy number variations/mutations data were included. Survival analysis was performed using Cox regression model. We performed gene set enrichment analysis to explore the functions associated with different HCC groups. Finally, we used a machine-learning model on selected regulators for developing a risk signature (m6Ascore) The prognostic value of m6Ascore was finally validated in another two GEO datasets. Results: We demonstrated that 11 m6A RNA regulators are significantly differentially expressed among 371 HCC patients stratified by clinicopathological features (P<0.001). We then identified two distinct HCC clusters by applying consensus clustering to m6A RNA regulators. Compared with the cluster2 subgroup, the cluster1 subgroup correlates with poorer prognosis (P < 0.001). Moreover, the cell cycle, splicesome and notch signaling pathway are significantly enriched in the cluster1 subgroup. We further derived m6Ascore, using four m6A regulators, predicting HCC prognosis well at three (AUC = 0.7) or 5 years (AUC=0.7) in validation. The prognostic value of m6Ascore also was validated successfully in two GEO datasets (P < 0.05). Finally, we discovered that mutations and copy number variations of m6A regulators, conferring worse survival, are strongly associated with TP53 mutations in HCC. Conclusions: We find a significant relationship between the alterations and different expressions causing increased m6A level and worse survival, especially in TP53-mutated HCC patients. Genetic alterations of m6A genes might cooperate with TP53 and its regulator targets in the HCC pathogenesis. Our m6Ascore may be applied in the clinical trials for patient stratification in HCC.
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Affiliation(s)
- Gui-Qi Zhu
- State Key Laboratory of Genetic Engineering, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Lei Yu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu-Jie Zhou
- Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai, China.,Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuang-Shuang Dong
- State Key Laboratory of Genetic Engineering, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Yi-Ming Wu
- Department of Urology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ying-Hong Shi
- State Key Laboratory of Genetic Engineering, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Jian Zhou
- State Key Laboratory of Genetic Engineering, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Jia Fan
- State Key Laboratory of Genetic Engineering, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Zhi Dai
- State Key Laboratory of Genetic Engineering, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
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14
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Lin KT, Krainer AR. PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis. Bioinformatics 2020; 35:5048-5054. [PMID: 31135034 DOI: 10.1093/bioinformatics/btz438] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/24/2019] [Accepted: 05/22/2019] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e. precision, recall, false positive rate and correlation) in comparison with three leading tools (rMATS, SUPPA2 and Whippet). RESULTS PSI-Sigma outperformed these tools, especially in the case of AS events with multiple alternative exons and intron-retention events. We also briefly evaluated its performance in long-read RNA-seq analysis, by sequencing a mixture of human RNAs and RNA Sequins with nanopore long-read sequencers. AVAILABILITY AND IMPLEMENTATION PSI-Sigma is implemented is available at https://github.com/wososa/PSI-Sigma.
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Affiliation(s)
- Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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15
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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: 36] [Impact Index Per Article: 9.0] [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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16
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Sun J, Wang J, Zhang N, Yang R, Chen K, Kong D. Whole transcriptome analysis of chemically induced hepatocellular carcinoma using RNA-sequencing analysis. FEBS Open Bio 2019; 9:1900-1908. [PMID: 31433574 PMCID: PMC6823285 DOI: 10.1002/2211-5463.12724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/04/2019] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
RNA‐sequencing (RNA‐Seq) is a useful method to explore the molecular events in cells and tissues at the transcriptional level. However, comprehensive transcriptome analysis of hepatocarcinogenesis and progression is lacking. In this study, we aimed to characterize a dimethylnitrosamine (DEN) and carbon tetrachloride (CCl4; DEN+CCl4)‐induced hepatocellular carcinoma (HCC) mouse model by RNA‐Seq. In total, 2033 genes were up‐regulated and 841 genes were down‐regulated after DEN and CCl4 stimulation. The differentially expressed genes were highly enriched for the Gene Ontology terms oxoacid metabolic process, carboxylic acid metabolic process, and organic acid metabolic process. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the top five significantly overrepresented pathways were metabolic pathways, chemical carcinogenesis, steroid hormone biosynthesis, retinol metabolism and metabolism of xenobiotics by cytochrome P450. Moreover, a protein‐protein interaction network analysis indicated that Rous sarcoma oncogene (Src) may play a key role in DEN+CCl4‐induced HCC. These results provide a comprehensive overview of transcriptome events in DEN+CCl4‐induced HCC.
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Affiliation(s)
- Jie Sun
- Department of Gastroenterology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jing Wang
- Department of Gastroenterology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Na Zhang
- Department of Gastroenterology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Renjun Yang
- Department of Gastroenterology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Keyang Chen
- Department of Hygiene Inspection and Quarantine, School of Public Health, Anhui Medical University, Hefei, China
| | - Derun Kong
- Department of Gastroenterology, First Affiliated Hospital of Anhui Medical University, Hefei, China
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