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Li K, Lv J, Wang J, Wei Y, Zhang Y, Lin J, Zhu Q. CircZNF609 inhibited bladder cancer immunotherapy sensitivity via enhancing fatty acid uptake through IGF2BP2/CD36 pathway. Int Immunopharmacol 2024; 137:112485. [PMID: 38878487 DOI: 10.1016/j.intimp.2024.112485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Circular RNAs (circRNAs) are gaining attention for their involvement in immune escape and immunotherapy sensitivity regulation. CircZNF609 is a well-known oncogene in various solid tumours. Our previous research revealed its role in reducing the chemosensitivity of bladder cancer (BCa) to cisplatin. However, the underlying role of circZNF609 in BCa immune escape and immunotherapy sensitivity remains unknown. We conducted BCa cells-CD8 + T cells co-culture assays, cell line-derived xenograft and patient-derived xenograft mouse models with human immune reconstitution to further confirm the role of circZNF609 in BCa immune escape and immunotherapy sensitivity. Overexpression of circZNF609 promoted BCa immune escape in vitro and in vivo. Mechanistically, circZNF609 was bound to IGF2BP2, enhancing its interaction with the 3'-untranslated region of CD36. This increased the stability of the CD36 mRNA, leading to enhanced fatty acid uptake by BCa cells and fatty acid depletion within the tumour microenvironment. Additionally, the nuclear export of circZNF609 was regulated by DDX39B. CircZNF609 promoted immune escape and suppressed BCa immunotherapy sensitivity by regulating the newly identified circZNF609/IGF2BP2/CD36 cascade. Therefore, circZNF609 holds potential as both a biomarker and therapeutic target in BCa immunotherapy.
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Affiliation(s)
- Kai Li
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiancheng Lv
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Wang
- Department of Urology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yong Wei
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yetao Zhang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Lin
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Qingyi Zhu
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Urology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
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Fang N, Liu B, Pan Q, Gong T, Zhan M, Zhao J, Wang Q, Tang Y, Li Y, He J, Xiang T, Sun F, Lu L, Xia J. SMG5 Inhibition Restrains Hepatocellular Carcinoma Growth and Enhances Sorafenib Sensitivity. Mol Cancer Ther 2024; 23:1188-1200. [PMID: 38647536 DOI: 10.1158/1535-7163.mct-23-0729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/25/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Hepatocellular carcinoma (HCC) has a pathogenesis that remains elusive with restricted therapeutic strategies and efficacy. This study aimed to investigate the role of SMG5, a crucial component in nonsense-mediated mRNA decay (NMD) that degrades mRNA containing a premature termination codon, in HCC pathogenesis and therapeutic resistance. We demonstrated an elevated expression of SMG5 in HCC and scrutinized its potential as a therapeutic target. Our findings revealed that SMG5 knockdown not only inhibited the migration, invasion, and proliferation of HCC cells but also influenced sorafenib resistance. Differential gene expression analysis between the control and SMG5 knockdown groups showed an upregulation of methionine adenosyltransferase 1A in the latter. High expression of methionine adenosyltransferase 1A, a catalyst for S-adenosylmethionine (SAM) production, as suggested by The Cancer Genome Atlas data, was indicative of a better prognosis for HCC. Further, an ELISA showed a higher concentration of SAM in SMG5 knockdown cell supernatants. Furthermore, we found that exogenous SAM supplementation enhanced the sensitivity of HCC cells to sorafenib alongside changes in the expression of Bax and Bcl-2, apoptosis-related proteins. Our findings underscore the important role of SMG5 in HCC development and its involvement in sorafenib resistance, highlighting it as a potential target for HCC treatment.
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Affiliation(s)
- Nan Fang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Bing Liu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Qiuzhong Pan
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Tingting Gong
- Department of Ultrasound, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, P. R. China
| | - Meixiao Zhan
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Jingjing Zhao
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Qijing Wang
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yan Tang
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yongqiang Li
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jia He
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Tong Xiang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Fengze Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Jianchuan Xia
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
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3
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Chong ZZ, Menkes DL, Souayah N. Pathogenesis underlying hexanucleotide repeat expansions in C9orf72 gene in amyotrophic lateral sclerosis. Rev Neurosci 2024; 35:85-97. [PMID: 37525497 DOI: 10.1515/revneuro-2023-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/07/2023] [Indexed: 08/02/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder. Mutations in C9orf72 and the resulting hexanucleotide repeat (GGGGCC) expansion (HRE) has been identified as a major cause of familial ALS, accounting for about 40 % of familial and 6 % of sporadic cases of ALS in Western patients. The pathological outcomes of HRE expansion in ALS have been recognized as the results of two mechanisms that include both the toxic gain-of-function and loss-of-function of C9ORF72. The gain of toxicity results from RNA and dipeptide repeats (DPRs). The HRE can be bidirectionally transcribed into RNA foci, which can bind to and disrupt RNA splicing, transport, and translation. The DPRs that include poly-glycine-alanine, poly-glycine-proline, poly-glycine- arginine, poly-proline-alanine, and poly-proline-arginine can induce toxicity by direct binding and sequestrating other proteins to interfere rRNA synthesis, ribosome biogenesis, translation, and nucleocytoplasmic transport. The C9ORF72 functions through binding to its partners-Smith-Magenis chromosome regions 8 (SMCR8) and WD repeat-containing protein (WDR41). Loss of C9ORF72 function results in impairment of autophagy, deregulation of autoimmunity, increased stress, and disruption of nucleocytoplasmic transport. Further insight into the mechanism in C9ORF72 HRE pathogenesis will facilitate identifying novel and effective therapeutic targets for ALS.
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Affiliation(s)
- Zhao Zhong Chong
- Department of Neurology, Rutgers University, New Jersey Medical School, 185 S. Orange Ave, Newark, NJ 07103, USA
| | - Daniel L Menkes
- Department of Neurology, Oakland University William Beaumont School of Medicine, 3555 West 13 Mile Road, Suite N120, Royal Oak, MI 48073, USA
| | - Nizar Souayah
- Department of Neurology, Rutgers University, New Jersey Medical School, 90 Bergen Street DOC 8100, Newark, NJ 07101, USA
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Mihaylov SR, Castelli LM, Lin YH, Gül A, Soni N, Hastings C, Flynn HR, Păun O, Dickman MJ, Snijders AP, Goldstone R, Bandmann O, Shelkovnikova TA, Mortiboys H, Ultanir SK, Hautbergue GM. The master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function. Nat Commun 2023; 14:5496. [PMID: 37679383 PMCID: PMC10485026 DOI: 10.1038/s41467-023-41304-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
PGC-1α plays a central role in maintaining mitochondrial and energy metabolism homeostasis, linking external stimuli to transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and an RNA recognition motif, however the RNA-processing function(s) were poorly investigated over the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export receptor NXF1. Inducible depletion of PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrate that its RNA/NXF1-binding activity is required for the nuclear export of some canonical mitochondrial-related mRNAs and mitochondrial homeostasis. Genome-wide investigations reveal that the nuclear export function is not strictly linked to promoter-binding, identifying in turn novel regulatory targets of PGC-1α in non-homologous end-joining and nucleocytoplasmic transport. These findings provide new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, aging and neurodegeneration.
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Affiliation(s)
- Simeon R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Aytac Gül
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Nikita Soni
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Christopher Hastings
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oana Păun
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Life Science Mass Spectrometry, Bruker Daltonics, Banner Lane, Coventry, CV4 9GH, UK
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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5
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Kulkarni V, Jayakumar S, Mohan M, Kulkarni S. Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections. Cells 2023; 12:987. [PMID: 37048060 PMCID: PMC10093752 DOI: 10.3390/cells12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets.
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Affiliation(s)
- Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Sahana Jayakumar
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Mahesh Mohan
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Smita Kulkarni
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
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6
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Castelli LM, Lin YH, Sanchez-Martinez A, Gül A, Mohd Imran K, Higginbottom A, Upadhyay SK, Márkus NM, Rua Martins R, Cooper-Knock J, Montmasson C, Cohen R, Walton A, Bauer CS, De Vos KJ, Mead RJ, Azzouz M, Dominguez C, Ferraiuolo L, Shaw PJ, Whitworth AJ, Hautbergue GM. A cell-penetrant peptide blocking C9ORF72-repeat RNA nuclear export reduces the neurotoxic effects of dipeptide repeat proteins. Sci Transl Med 2023; 15:eabo3823. [PMID: 36857431 DOI: 10.1126/scitranslmed.abo3823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Hexanucleotide repeat expansions in C9ORF72 are the most common genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Studies have shown that the hexanucleotide expansions cause the noncanonical translation of C9ORF72 transcripts into neurotoxic dipeptide repeat proteins (DPRs) that contribute to neurodegeneration. We show that a cell-penetrant peptide blocked the nuclear export of C9ORF72-repeat transcripts in HEK293T cells by competing with the interaction between SR-rich splicing factor 1 (SRSF1) and nuclear export factor 1 (NXF1). The cell-penetrant peptide also blocked the translation of toxic DPRs in neurons differentiated from induced neural progenitor cells (iNPCs), which were derived from individuals carrying C9ORF72-linked ALS mutations. This peptide also increased survival of iNPC-differentiated C9ORF72-ALS motor neurons cocultured with astrocytes. Oral administration of the cell-penetrant peptide reduced DPR translation and rescued locomotor deficits in a Drosophila model of mutant C9ORF72-mediated ALS/FTD. Intrathecal injection of this peptide into the brains of ALS/FTD mice carrying a C9ORF72 mutation resulted in reduced expression of DPRs in mouse brains. These findings demonstrate that disrupting the production of DPRs in cellular and animal models of ALS/FTD might be a strategy to ameliorate neurodegeneration in these diseases.
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Affiliation(s)
- Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Alvaro Sanchez-Martinez
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Aytaç Gül
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Kamallia Mohd Imran
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Santosh Kumar Upadhyay
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nóra M Márkus
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Raquel Rua Martins
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Claire Montmasson
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Rebecca Cohen
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Amy Walton
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Claudia S Bauer
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Kurt J De Vos
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Richard J Mead
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Cyril Dominguez
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
| | - Alexander J Whitworth
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield S10 2HQ, UK
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7
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Cheng Z, Qin W, Li S, Shao S, Liu B. Emerging roles of circular RNAs in cancer therapy-induced cardiotoxicity. Front Cardiovasc Med 2023; 10:1152436. [PMID: 37020518 PMCID: PMC10067915 DOI: 10.3389/fcvm.2023.1152436] [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: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Cancer therapy-induced cardiotoxicity (CTIC) is an important cause of death in cancer survivors which often results in the withdrawal or discontinuation of drugs. The underlying mechanisms of CTIC remain unclear. Circular RNAs (circRNAs) are a class of non-coding regulatory RNA molecules which have emerged in recent years. They are generated by back splicing and have powerful biological functions, including transcription and splicing, isolating or building macromolecular scaffolds to interfere with microRNA activity and signaling pathways, and acting as templates for translation. Moreover, circRNAs demonstrate high abundance and significant stability. CircRNAs can be used as novel biomarkers because they often function in a cell-type and tissue-specific manner. CircRNAs have attracted increasing attention in cardiovascular disease research, and recent studies exploring the role of circRNAs in CTIC have had promising results. This review will summarize the current understanding of circRNAs' biogenesis, regulation and function. Their clinical potential as biomarkers, therapeutic agents and drug targets will also be explored.
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Affiliation(s)
- Ziji Cheng
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wanting Qin
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shaoling Li
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shuijin Shao
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baonian Liu
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Correspondence: Baonian Liu
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8
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Chen L, Wang Y, Lin J, Song Z, Wang Q, Zhao W, Wang Y, Xiu X, Deng Y, Li X, Li Q, Wang X, Li J, Liu X, Liu K, Zhou J, Li K, Liu Y, Liao S, Deng Q, Xu C, Sun Q, Wu S, Zhang K, Guan MX, Zhou T, Sun F, Cai X, Huang C, Shan G. Exportin 4 depletion leads to nuclear accumulation of a subset of circular RNAs. Nat Commun 2022; 13:5769. [PMID: 36182935 PMCID: PMC9526749 DOI: 10.1038/s41467-022-33356-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/09/2022] [Indexed: 12/19/2022] Open
Abstract
Numerous RNAs are exported from the nucleus, abnormalities of which lead to cellular complications and diseases. How thousands of circular RNAs (circRNAs) are exported from the nucleus remains elusive. Here, we provide lines of evidence to demonstrate a link between the conserved Exportin 4 (XPO4) and nuclear export of a subset of circRNAs in metazoans. Exonic circRNAs (ecircRNAs) with higher expression levels, larger length, and lower GC content are more sensitive to XPO4 deficiency. Cellular insufficiency of XPO4 leads to nuclear circRNA accumulation, circRNA:DNA (ciR-loop) formation, linear RNA:DNA (liR-loop) buildup, and DNA damage. DDX39 known to modulate circRNA export can resolve ciR-loop, and splicing factors involved in the biogenesis of circRNAs can also affect the levels of ciR-loop. Testis and brain are two organs with high abundance of circRNAs, and insufficient XPO4 levels are detrimental, as Xpo4 heterozygous mice display male infertility and neural phenotypes. Increased levels of ciR-loop, R-loop, and DNA damage along with decreased cell numbers are observed in testis and hippocampus of Xpo4 heterozygotes. This study sheds light on the understandings of mechanism of circRNA export and reveals the significance of efficient nuclear export of circRNAs in cellular physiology. This study identifies the evolutionarily conserved Exportin 4 as an essential regulator in the nuclear export of circRNAs. Defective circRNA export results in R-loop formation and DNA damage in cells, as well as testis and neurological defects in mice.
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Affiliation(s)
- Liang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yucong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Qinwei Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Wenfang Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yan Wang
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China.,State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang, 325003, China
| | - Xiaoyu Xiu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China.,State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang, 325003, China
| | - Yuqi Deng
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Xiuzhi Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Qiqi Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaolin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jingxin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Xu Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Kunpeng Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuchan Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shanhui Liao
- Division of Life Science and Medicine, CAS Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei, 230027, China
| | - Qin Deng
- Analytical and Testing Center, Chongqing University, Chongqing, 400030, China
| | - Chao Xu
- Division of Life Science and Medicine, CAS Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei, 230027, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengzhou Wu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China.,State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang, 325003, China
| | - Kaiming Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Min-Xin Guan
- The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Tianhua Zhou
- Department of Cell Biology and Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Cancer Center, Institute of Gastroenterology, Zhejiang University, Hangzhou, 310016, China
| | - Fei Sun
- Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Xiujun Cai
- Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China. .,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| | - Ge Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China. .,Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
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9
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Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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10
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An M, Zheng H, Huang J, Lin Y, Luo Y, Kong Y, Pang M, Zhang D, Yang J, Chen J, Li Y, Chen C, Lin T. Aberrant Nuclear Export of circNCOR1 Underlies SMAD7-Mediated Lymph Node Metastasis of Bladder Cancer. Cancer Res 2022; 82:2239-2253. [PMID: 35395674 PMCID: PMC9359746 DOI: 10.1158/0008-5472.can-21-4349] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/28/2022] [Accepted: 04/06/2022] [Indexed: 01/07/2023]
Abstract
Circular RNAs (circRNA) containing retained introns are normally sequestered in the nucleus. Dysregulation of cellular homeostasis can drive their nuclear export, which may be involved in cancer metastasis. However, the mechanism underlying circRNA nuclear export and its role in lymph node (LN) metastasis of bladder cancer remain unclear. Here, we identify an intron-retained circRNA, circNCOR1, that is significantly downregulated in LN metastatic bladder cancer and is negatively associated with poor prognosis of patients. Overexpression of circNCOR1 inhibited lymphangiogenesis and LN metastasis of bladder cancer in vitro and in vivo. Nuclear circNCOR1 epigenetically promoted SMAD7 transcription by increasing heterogeneous nuclear ribonucleoprotein L (hnRNPL)-induced H3K9 acetylation in the SMAD7 promoter, leading to inhibition of the TGFβ-SMAD signaling pathway. Nuclear retention of circNCOR1 was regulated by small ubiquitin-like modifier (SUMO)ylation of DDX39B, an essential regulatory factor responsible for circRNA nuclear-cytoplasmic transport. Reduced SUMO2 binding to DDX39B markedly increased circNCOR1 retention in the nucleus to suppress bladder cancer LN metastasis. By contrast, SUMOylated DDX39B activated nuclear export of circNCOR1, impairing the suppressive role of circNCOR1 on TGFβ-SMAD cascade activation and bladder cancer LN metastasis. In patient-derived xenograft (PDX) models, overexpression of circNCOR1 and inhibition of TGFβ signaling significantly repressed tumor growth and LN metastasis. This study highlights SUMOylation-induced nuclear export of circNCOR1 as a key event regulating TGFβ-SMAD signaling and bladder cancer lymphangiogenesis, thus supporting circNCOR1 as a novel therapeutic agent for patients with LN metastatic bladder cancer. SIGNIFICANCE This study identifies the novel intron-retained circNCOR1 and elucidates a SUMOylation-mediated DDX39B-circNCOR1-SMAD7 axis that regulates lymph node metastasis of bladder cancer.
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Affiliation(s)
- Mingjie An
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Hanhao Zheng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jian Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yan Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yuming Luo
- Pancreatic Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yao Kong
- Pancreatic Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Mingrui Pang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Dingwen Zhang
- Pancreatic Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.,School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiabin Yang
- Pancreatic Center, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.,School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiancheng Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yuanlong Li
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Changhao Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.,Corresponding Authors: Tianxin Lin, Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiangyi Road, Yuexiu District, Guangzhou, Guangdong Province 510120, P. R. China. Phone: 8620-3407-0447; Fax: 8620-8133-2336; E-mail:; and Changhao Chen,
| | - Tianxin Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.,Corresponding Authors: Tianxin Lin, Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiangyi Road, Yuexiu District, Guangzhou, Guangdong Province 510120, P. R. China. Phone: 8620-3407-0447; Fax: 8620-8133-2336; E-mail:; and Changhao Chen,
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11
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Machine Learning analysis of high-grade serous ovarian cancer proteomic dataset reveals novel candidate biomarkers. Sci Rep 2022; 12:3041. [PMID: 35197484 PMCID: PMC8866540 DOI: 10.1038/s41598-022-06788-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/02/2022] [Indexed: 12/19/2022] Open
Abstract
Ovarian cancer is one of the most common gynecological malignancies, ranking third after cervical and uterine cancer. High-grade serous ovarian cancer (HGSOC) is one of the most aggressive subtype, and the late onset of its symptoms leads in most cases to an unfavourable prognosis. Current predictive algorithms used to estimate the risk of having Ovarian Cancer fail to provide sufficient sensitivity and specificity to be used widely in clinical practice. The use of additional biomarkers or parameters such as age or menopausal status to overcome these issues showed only weak improvements. It is necessary to identify novel molecular signatures and the development of new predictive algorithms able to support the diagnosis of HGSOC, and at the same time, deepen the understanding of this elusive disease, with the final goal of improving patient survival. Here, we apply a Machine Learning-based pipeline to an open-source HGSOC Proteomic dataset to develop a decision support system (DSS) that displayed high discerning ability on a dataset of HGSOC biopsies. The proposed DSS consists of a double-step feature selection and a decision tree, with the resulting output consisting of a combination of three highly discriminating proteins: TOP1, PDIA4, and OGN, that could be of interest for further clinical and experimental validation. Furthermore, we took advantage of the ranked list of proteins generated during the feature selection steps to perform a pathway analysis to provide a snapshot of the main deregulated pathways of HGSOC. The datasets used for this study are available in the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data portal (https://cptac-data-portal.georgetown.edu/).
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12
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Castelli LM, Cutillo L, Souza CDS, Sanchez-Martinez A, Granata I, Lin YH, Myszczynska MA, Heath PR, Livesey MR, Ning K, Azzouz M, Shaw PJ, Guarracino MR, Whitworth AJ, Ferraiuolo L, Milo M, Hautbergue GM. SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis. Mol Neurodegener 2021; 16:53. [PMID: 34376242 PMCID: PMC8353793 DOI: 10.1186/s13024-021-00475-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background Loss of motor neurons in amyotrophic lateral sclerosis (ALS) leads to progressive paralysis and death. Dysregulation of thousands of RNA molecules with roles in multiple cellular pathways hinders the identification of ALS-causing alterations over downstream changes secondary to the neurodegenerative process. How many and which of these pathological gene expression changes require therapeutic normalisation remains a fundamental question. Methods Here, we investigated genome-wide RNA changes in C9ORF72-ALS patient-derived neurons and Drosophila, as well as upon neuroprotection taking advantage of our gene therapy approach which specifically inhibits the SRSF1-dependent nuclear export of pathological C9ORF72-repeat transcripts. This is a critical study to evaluate (i) the overall safety and efficacy of the partial depletion of SRSF1, a member of a protein family involved itself in gene expression, and (ii) a unique opportunity to identify neuroprotective RNA changes. Results Our study shows that manipulation of 362 transcripts out of 2257 pathological changes, in addition to inhibiting the nuclear export of repeat transcripts, is sufficient to confer neuroprotection in C9ORF72-ALS patient-derived neurons. In particular, expression of 90 disease-altered transcripts is fully reverted upon neuroprotection leading to the characterisation of a human C9ORF72-ALS disease-modifying gene expression signature. These findings were further investigated in vivo in diseased and neuroprotected Drosophila transcriptomes, highlighting a list of 21 neuroprotective changes conserved with 16 human orthologues in patient-derived neurons. We also functionally validated the high neuroprotective potential of one of these disease-modifying transcripts, demonstrating that inhibition of ALS-upregulated human KCNN1–3 (Drosophila SK) voltage-gated potassium channel orthologs mitigates degeneration of human motor neurons and Drosophila motor deficits. Conclusions Strikingly, the partial depletion of SRSF1 leads to expression changes in only a small proportion of disease-altered transcripts, indicating that not all RNA alterations need normalization and that the gene therapeutic approach is safe in the above preclinical models as it does not disrupt globally gene expression. The efficacy of this intervention is also validated at genome-wide level with transcripts modulated in the vast majority of biological processes affected in C9ORF72-ALS. Finally, the identification of a characteristic signature with key RNA changes modified in both the disease state and upon neuroprotection also provides potential new therapeutic targets and biomarkers. Supplementary Information The online version contains supplementary material available at 10.1186/s13024-021-00475-y.
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Affiliation(s)
- Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Luisa Cutillo
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Cleide Dos Santos Souza
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Alvaro Sanchez-Martinez
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Ilaria Granata
- National Research Council of Italy, High Performance Computing and Networking Institute (ICAR-CNR), 111 Via Pietro Castellino, 80131, Naples, Italy
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Monika A Myszczynska
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Matthew R Livesey
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ke Ning
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mario R Guarracino
- National Research Council of Italy, High Performance Computing and Networking Institute (ICAR-CNR), 111 Via Pietro Castellino, 80131, Naples, Italy
| | - Alexander J Whitworth
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Marta Milo
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK. .,Present Address: AstraZeneca, Academy House, 136 Hills Road, Cambridge, CB2 8PA, UK.
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK. .,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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13
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Yeom KH, Pan Z, Lin CH, Lim HY, Xiao W, Xing Y, Black DL. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring. Genome Res 2021; 31:1106-1119. [PMID: 33832989 PMCID: PMC8168582 DOI: 10.1101/gr.273904.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/01/2021] [Indexed: 12/24/2022]
Abstract
Steps of mRNA maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution of processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track mRNA maturation across subcellular locations in mouse embryonic stem cells, neuronal progenitor cells, and postmitotic neurons. We find disparate patterns of RNA enrichment between the cytoplasmic, nucleoplasmic, and chromatin fractions, with some genes maintaining more polyadenylated RNA in chromatin than in the cytoplasm. We bioinformatically defined four regulatory groups for intron retention, including complete cotranscriptional splicing, complete intron retention in the cytoplasmic RNA, and two intron groups present in nuclear and chromatin transcripts but fully excised in cytoplasm. We found that introns switch their regulatory group between cell types, including neuronally excised introns repressed by polypyrimidine track binding protein 1 (PTBP1). Transcripts for the neuronal gamma-aminobutyric acid (GABA) B receptor, 1 (Gabbr1) are highly expressed in mESCs but are absent from the cytoplasm. Instead, incompletely spliced Gabbr1 RNA remains sequestered on chromatin, where it is bound by PTBP1, similar to certain long noncoding RNAs. Upon neuronal differentiation, Gabbr1 RNA becomes fully processed and exported for translation. Thus, splicing repression and chromatin anchoring of RNA combine to allow posttranscriptional regulation of Gabbr1 over development. For this and other genes, polyadenylated RNA abundance does not indicate functional gene expression. Our data sets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
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Affiliation(s)
- Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Zhicheng Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, California 90095, USA.,Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Han Young Lim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
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14
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Wang X, Lin L, Zhong Y, Feng M, Yu T, Yan Y, Zhou J, Liao M. Cellular hnRNPAB binding to viral nucleoprotein inhibits flu virus replication by blocking nuclear export of viral mRNA. iScience 2021; 24:102160. [PMID: 33681726 PMCID: PMC7918295 DOI: 10.1016/j.isci.2021.102160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/27/2020] [Accepted: 02/02/2021] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) play critical roles in the nuclear export, splicing, and sensing of RNA. However, the role of heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB) is poorly understood. In this study, we report that hnRNPAB cooperates with nucleoprotein (NP) to restrict viral mRNA nuclear export via inhibiting viral mRNA binding to ALY and NXF1. HnRNPAB restricts mRNA transfer from ALY to NXF1, inhibiting the mRNA nuclear export. Moreover, when cells are invaded by influenza A virus, NP interacts with hnRNPAB and interrupts the ALY-UAP56 interaction, leading to repression of ALY-viral mRNA binding, and then inhibits the viral mRNA binding to NXF1, leading to nuclear stimulation of viral mRNA. Collectively, these observations provide a new role of hnRNPAB to act as an mRNA nuclear retention factor, which is also effective for viral mRNA of influenza A virus, and NP cooperates with hnRNPAB to further restrict the viral mRNA nuclear export. HnRNPAB inhibits influenza A virus replication by repressing viral mRNA nuclear export HnRNPAB interrupts viral mRNA transferring from ALY to NXF1 NP cooperates with hnRNPAB to further restrict viral mRNA nuclear export The ALY-viral mRNA binding is restricted by NP-hnRNPAB complex
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Affiliation(s)
- Xingbo Wang
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Lulu Lin
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Yiye Zhong
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Mingfang Feng
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Tianqi Yu
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Yan Yan
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou 310003, P.R. China
- Corresponding author
| | - Min Liao
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
- Corresponding author
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15
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Jin Y, Qin X. Comprehensive Analysis of the Roles and Prognostic Value of RNA-Binding Proteins in Head and Neck Squamous Cell Carcinoma. DNA Cell Biol 2020; 39:1789-1798. [PMID: 32716650 DOI: 10.1089/dna.2020.5641] [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] [Indexed: 12/15/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a malignancy with relatively high incidence and poor prognosis. RNA-binding proteins (RBPs) were reported to be dysregulated in multiple cancers and were closely associated with tumor initiation and progression. However, an integrated analysis of the roles of RBPs in HNSCC has not been conducted. In the present study, we obtained transcriptome data and corresponding clinical information of HNSCC patients from The Cancer Genome Atlas database and screened out differentially expressed RBPs between tumor and normal tissues. Subsequently, we utilized a series of bioinformatics analyses to elucidate the potential functions and prognostic value of these RBPs in HNSCC. As a result, a total of 88 aberrantly expressed RBPs were identified, including 63 downregulated and 25 upregulated RBPs. Functional enrichment analysis suggested that the differentially expressed RBPs mainly participated in mRNA metabolic processes, RNA processing, RNA transport, regulation of RNA stability, RNA degradation, and mRNA surveillance pathway. Three RBP genes (NOVA1, EZH2, and RBM24) were determined as prognosis-related hub genes from which EZH2 and NOVA1 were selected to construct a prognostic signature based on LASSO Cox regression algorithm. Further analysis demonstrated that the high-risk patient group stratified by the risk signature has advanced tumor grade and poorer overall survival when compared with low-risk group. Moreover, univariate analysis showed that the risk score, tumor stage, T stage, and N stage were significantly associated with patient overall survival and the multivariate analysis results indicated that the risk score and age were greatly correlated with patient prognosis. Overall, this study provided a comprehensive landscape of RBPs in HNSCC and identified an effective gene signature for predicting the clinical outcomes of HNSCC patient, which may contribute to clinical decision making and individualized cancer treatment.
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Affiliation(s)
- Yu Jin
- Department of General Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, P.R. China
| | - Xing Qin
- Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, P.R. China.,Department of Oral and Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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16
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Bitetto G, Di Fonzo A. Nucleo-cytoplasmic transport defects and protein aggregates in neurodegeneration. Transl Neurodegener 2020; 9:25. [PMID: 32616075 PMCID: PMC7333321 DOI: 10.1186/s40035-020-00205-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
In the ongoing process of uncovering molecular abnormalities in neurodegenerative diseases characterized by toxic protein aggregates, nucleo-cytoplasmic transport defects have an emerging role. Several pieces of evidence suggest a link between neuronal protein inclusions and nuclear pore complex (NPC) damage. These processes lead to oxidative stress, inefficient transcription, and aberrant DNA/RNA maintenance. The clinical and neuropathological spectrum of NPC defects is broad, ranging from physiological aging to a suite of neurodegenerative diseases. A better understanding of the shared pathways among these conditions may represent a significant step toward dissecting their underlying molecular mechanisms, opening the way to a real possibility of identifying common therapeutic targets.
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Affiliation(s)
- Giacomo Bitetto
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Alessio Di Fonzo
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy.
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17
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Gao C, Wang Y. mRNA Metabolism in Cardiac Development and Disease: Life After Transcription. Physiol Rev 2020; 100:673-694. [PMID: 31751167 PMCID: PMC7327233 DOI: 10.1152/physrev.00007.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 09/06/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
The central dogma of molecular biology illustrates the importance of mRNAs as critical mediators between genetic information encoded at the DNA level and proteomes/metabolomes that determine the diverse functional outcome at the cellular and organ levels. Although the total number of protein-producing (coding) genes in the mammalian genome is ~20,000, it is evident that the intricate processes of cardiac development and the highly regulated physiological regulation in the normal heart, as well as the complex manifestation of pathological remodeling in a diseased heart, would require a much higher degree of complexity at the transcriptome level and beyond. Indeed, in addition to an extensive regulatory scheme implemented at the level of transcription, the complexity of transcript processing following transcription is dramatically increased. RNA processing includes post-transcriptional modification, alternative splicing, editing and transportation, ribosomal loading, and degradation. While transcriptional control of cardiac genes has been a major focus of investigation in recent decades, a great deal of progress has recently been made in our understanding of how post-transcriptional regulation of mRNA contributes to transcriptome complexity. In this review, we highlight some of the key molecular processes and major players in RNA maturation and post-transcriptional regulation. In addition, we provide an update to the recent progress made in the discovery of RNA processing regulators implicated in cardiac development and disease. While post-transcriptional modulation is a complex and challenging problem to study, recent technological advancements are paving the way for a new era of exciting discoveries and potential clinical translation in the context of cardiac biology and heart disease.
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Affiliation(s)
- Chen Gao
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
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18
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Zheleva A, Gómez-Orte E, Sáenz-Narciso B, Ezcurra B, Kassahun H, de Toro M, Miranda-Vizuete A, Schnabel R, Nilsen H, Cabello J. Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes.
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Affiliation(s)
- Angelina Zheleva
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Eva Gómez-Orte
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | | | - Begoña Ezcurra
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Henok Kassahun
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María de Toro
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, Germany
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Juan Cabello
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
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19
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Hwang SH, Yeom H, Eom SY, Lee YM, Lee M. Genome-wide DNA methylation changes in transformed foci induced by nongenotoxic carcinogens. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:576-587. [PMID: 30848857 DOI: 10.1002/em.22285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/15/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
In vitro cell transformation assays (CTA) have been proposed as a method to identify possible nongenotoxic carcinogens. However, the current protocols do not provide information on the mechanism of action of the test articles. In this study, we combined an in vitro Bhas 42 CTA and sequencing-based DNA methylation profiling analysis to elucidate the carcinogenic mechanism associated with nongenotoxic carcinogens. Three nongenotoxic carcinogens were evaluated: cadmium chloride, methyl carbamate, and lithocholic acid. Methylation profiles were generated for the two nongenotoxic carcinogens (cadmium chloride and lithocholic acid) that were positive in Bhas 42 CTA. Methyl carbamate did not exhibit any promoter activity. Approximately 9.8% of all differentially methylated regions (DMRs) identified in cadmium chloride-induced transformed foci overlapped with DMRs in lithocholic acid-induced transformed foci. Interestingly, overlapping DMRs showed more hypermethylation than individual DMRs. In addition, the DMRs in CpG island elements common to both nongenotoxic carcinogens showed considerably more bias toward hypermethylated DMRs than those unique to either cadmium chloride or lithocholic acid. Pathway enrichment analysis revealed that genes harboring hypermethylated DMRs were significantly enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including pathways in cancer, basal cell carcinoma, and Wnt signaling. The genes harboring hypomethylated DMRs were significantly related to mRNA surveillance pathway, RNA transport, and autophagy. Taken together, our preliminary results on genome-wide methylation analysis of cell clones from nongenotoxic carcinogen-induced foci could be exploited for CTAs improvement, but further research will be required to standardize and assess the specificity and sensitivity of this combined approach. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Sung-Hee Hwang
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Hojin Yeom
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Seong Yun Eom
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Yong-Moon Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheoungju-si, Chungcheongbuk-do 28160, Republic of Korea
| | - Michael Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
- INU Human Genome Center, Incheon National University, Incheon 22012, Republic of Korea
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20
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The Nuclear Export Receptors TbMex67 and TbMtr2 Are Required for Ribosome Biogenesis in Trypanosoma brucei. mSphere 2019; 4:4/4/e00343-19. [PMID: 31270172 PMCID: PMC6609230 DOI: 10.1128/msphere.00343-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The nuclear export of ribosomal subunits (60S and 40S) depends in part on the activity of the essential auxiliary export receptors TbMtr2 and TbMex67. When these proteins are individually depleted from the medically and agriculturally significant parasite Trypanosoma brucei, distinct alterations in the processing of the rRNAs of the large subunit (60S) are observed as well as aberrations in the assembly of functional ribosomes (polysomes). We also established that TbMex67 and TbMtr2 interact directly or indirectly with the protein components of the 5S RNP, including the trypanosome-specific P34/P37. The critical role that TbMex67 and TbMtr2 play in this essential biological process together with their parasite-specific interactions may provide new therapeutic targets against this important parasite. Ribosomal maturation is a complex and highly conserved biological process involving migration of a continuously changing RNP across multiple cellular compartments. A critical point in this process is the translocation of individual ribosomal subunits (60S and 40S) from the nucleus to the cytoplasm, and a number of export factors participate in this process. In this study, we characterize the functional role of the auxiliary export receptors TbMex67 and TbMtr2 in ribosome biogenesis in the parasite Trypanosoma brucei. We demonstrate that depletion of each of these proteins dramatically impacts the steady-state levels of other proteins involved in ribosome biogenesis, including the trypanosome-specific factors P34 and P37. In addition, we observe that the loss of TbMex67 or TbMtr2 leads to aberrant ribosome formation, rRNA processing, and polysome formation. Although the TbMex67-TbMtr2 heterodimer is structurally distinct from Mex67-Mtr2 complexes previously studied, our data show that they retain a conserved function in ribosome biogenesis. IMPORTANCE The nuclear export of ribosomal subunits (60S and 40S) depends in part on the activity of the essential auxiliary export receptors TbMtr2 and TbMex67. When these proteins are individually depleted from the medically and agriculturally significant parasite Trypanosoma brucei, distinct alterations in the processing of the rRNAs of the large subunit (60S) are observed as well as aberrations in the assembly of functional ribosomes (polysomes). We also established that TbMex67 and TbMtr2 interact directly or indirectly with the protein components of the 5S RNP, including the trypanosome-specific P34/P37. The critical role that TbMex67 and TbMtr2 play in this essential biological process together with their parasite-specific interactions may provide new therapeutic targets against this important parasite.
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21
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Carlevaro-Fita J, Johnson R. Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization. Mol Cell 2019; 73:869-883. [PMID: 30849394 DOI: 10.1016/j.molcel.2019.02.008] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/30/2019] [Accepted: 02/05/2019] [Indexed: 02/09/2023]
Abstract
The localization of long noncoding RNAs (lncRNAs) within the cell is the primary determinant of their molecular functions. LncRNAs are often thought of as chromatin-restricted regulators of gene transcription and chromatin structure. However, a rich population of cytoplasmic lncRNAs has come to light, with diverse roles including translational regulation, signaling, and respiration. RNA maps of increasing resolution and scope are revealing a subcellular world of highly specific localization patterns and hint at sequence-based address codes specifying lncRNA fates. We propose a new framework for analyzing sequencing-based data, which suggests that numbers of cytoplasmic lncRNA molecules rival those in the nucleus. New techniques promise to create high-resolution, transcriptome-wide maps associated with all organelles of the mammalian cell. Given its intimate link to molecular roles, subcellular localization provides a means of unlocking the mystery of lncRNA functions.
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Affiliation(s)
- Joana Carlevaro-Fita
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
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22
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Altered splicing and cytoplasmic levels of tRNA synthetases in SF3B1-mutant myelodysplastic syndromes as a therapeutic vulnerability. Sci Rep 2019; 9:2678. [PMID: 30804405 PMCID: PMC6390101 DOI: 10.1038/s41598-019-39591-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/24/2019] [Indexed: 12/19/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are haematopoietic malignancies that are characterised by a heterogeneous clinical course. In recent years, sequencing efforts have uncovered recurrent somatic mutations within RNA splicing factors, including SF3B1, SRSF2, U2AF1 and ZRSR2. The most frequently mutated gene is SF3B1, mutated in 17% of MDS patients. While SF3B1 mutations and their effects on splicing have been well characterised, much remains to be explored about their more far-reaching effects on cellular homeostasis. Given that mRNA splicing and nuclear export are coordinated processes, we hypothesised that SF3B1 mutation might also affect export of certain mRNAs and that this may represent a targetable pathway for the treatment of SF3B1-mutant MDS. We used CRISPR/Cas9-genome editing to create isogenic cellular models. Comprehensive transcriptome and proteome profiling of these cells identified alterations in the splicing and export of components of the translational machinery, primarily tRNA synthetases, in response to the SF3B1 K700E mutation. While steady-state protein synthesis was unaffected, SF3B1 mutant cells were more sensitive to the clinically-relevant purine analogue, 8-azaguanine. In this study, we also demonstrated that 8-azaguanine affects splicing. Our results suggest that the simultaneous targeting of RNA metabolism and splicing by 8-azaguanine represents a therapeutic opportunity for SF3B1-mutant myelodysplastic syndromes.
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23
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Wu Q, Li P, Wu M, Liu Q. Deregulation of Circular RNAs in Cancer From the Perspectives of Aberrant Biogenesis, Transport and Removal. Front Genet 2019; 10:16. [PMID: 30774645 PMCID: PMC6367250 DOI: 10.3389/fgene.2019.00016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/14/2019] [Indexed: 12/28/2022] Open
Abstract
CircRNAs (circular RNAs) are a class of RNAs generated from circularization with multiple novel functions. Recent studies have revealed the aberrant expression and aberrant functions of circRNAs in various tumors; thus, circRNAs have been recognized as promising cancer biomarkers. However, the underlying mechanisms behind their aberrant expression and functions remain unclear. In this review, we discuss at length the cancer-specific deregulation of circRNAs and the potential underlying aberrant events in circRNA biogenesis, localization and removal in cancer cells.
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Affiliation(s)
- Qiongqiong Wu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Peiyao Li
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Minghua Wu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Qiang Liu
- Third Xiangya Hospital, Central South University, Changsha, China
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24
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Neueder A. RNA-Mediated Disease Mechanisms in Neurodegenerative Disorders. J Mol Biol 2018; 431:1780-1791. [PMID: 30597161 DOI: 10.1016/j.jmb.2018.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 12/16/2022]
Abstract
RNA is accurately entangled in virtually all pathways that maintain cellular homeostasis. To name but a few, RNA is the "messenger" between DNA encoded information and the resulting proteins. Furthermore, RNAs regulate diverse processes by forming DNA::RNA or RNA::RNA interactions. Finally, RNA itself can be the scaffold for ribonucleoprotein complexes, for example, ribosomes or cellular bodies. Consequently, disruption of any of these processes can lead to disease. This review describes known and emerging RNA-based disease mechanisms like interference with regular splicing, the anomalous appearance of RNA-protein complexes and uncommon RNA species, as well as non-canonical translation. Due to the complexity and entanglement of the above-mentioned pathways, only few drugs are available that target RNA-based disease mechanisms. However, advances in our understanding how RNA is involved in and modulates cellular homeostasis might pave the way to novel treatments.
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Affiliation(s)
- Andreas Neueder
- Experimental Neurology, Department of Neurology, Ulm University, 89081 Ulm, Germany.
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25
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Is co-expression of USP22 and HSP90 more effective in predicting prognosis of gastric cancer? Pathol Res Pract 2018; 215:653-659. [PMID: 30598339 DOI: 10.1016/j.prp.2018.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/01/2018] [Accepted: 12/24/2018] [Indexed: 12/25/2022]
Abstract
The ubiquitin-specific peptidase 22 (USP22) belongs to the largest subfamily of deubiquitylases and recent studies indicate that overexpression of USP22 may promote gastric cancer progression and predict prognosis. But little is known about the interaction network of USP22 in gastric cancer. In this study, we applied bioinformatics methods and found that USP22 was correlated with the heat shock protein 90 (HSP90) which is now considered to be a biomarker to predict the prognosis of gastric cancer. Then the siRNA transfection and western blotting were used to testify the correlation of USP22 and HSP90 in gastric cancer cells. The immunohistochemistry staining of the microarrays was applied to confirm the correlation of USP22 and HSP90 expression in gastric cancer tissue and further analysis showed that co-expression of USP22 and HSP90 was related to lymph node metastasis and more effective in predicting the prognosis of gastric cancer. In summary, our data demonstrate that correlation exists between USP22 and HSP90 expressions in gastric cancer and co-expression of USP22 and HSP90 may be more effective in predicting prognosis of gastric cancer.
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26
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Culjkovic-Kraljacic B, Borden KLB. The Impact of Post-transcriptional Control: Better Living Through RNA Regulons. Front Genet 2018; 9:512. [PMID: 30455716 PMCID: PMC6230556 DOI: 10.3389/fgene.2018.00512] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Traditionally, cancer is viewed as a disease driven by genetic mutations and/or epigenetic and transcriptional dysregulation. While these are undoubtedly important drivers, many recent studies highlight the disconnect between the proteome and the genome or transcriptome. At least in part, this disconnect arises as a result of dysregulated RNA metabolism which underpins the altered proteomic landscape observed. Thus, it is important to understand the basic mechanisms governing post-transcriptional control and how these processes can be co-opted to drive cancer cell phenotypes. In some cases, groups of mRNAs that encode protein involved in specific oncogenic processes can be co-regulated at multiple processing levels in order to turn on entire biochemical pathways. Indeed, the RNA regulon model was postulated as a means to understand how cells coordinately regulate transcripts encoding proteins in the same biochemical pathways. In this review, we describe some of the basic mRNA processes that are dysregulated in cancer and the biological impact this has on the cell. This dysregulation can affect networks of RNAs simultaneously thereby underpinning the oncogenic phenotypes observed.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
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27
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Kumar R, Gardner A, Homan CC, Douglas E, Mefford H, Wieczorek D, Lüdecke HJ, Stark Z, Sadedin S, Nowak CB, Douglas J, Parsons G, Mark P, Loidi L, Herman GE, Mihalic Mosher T, Gillespie MK, Brady L, Tarnopolsky M, Madrigal I, Eiris J, Domènech Salgado L, Rabionet R, Strom TM, Ishihara N, Inagaki H, Kurahashi H, Dudding-Byth T, Palmer EE, Field M, Gecz J. Severe neurocognitive and growth disorders due to variation in THOC2, an essential component of nuclear mRNA export machinery. Hum Mutat 2018; 39:1126-1138. [PMID: 29851191 DOI: 10.1002/humu.23557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 12/12/2022]
Abstract
Highly conserved TREX-mediated mRNA export is emerging as a key pathway in neuronal development and differentiation. TREX subunit variants cause neurodevelopmental disorders (NDDs) by interfering with mRNA export from the cell nucleus to the cytoplasm. Previously we implicated four missense variants in the X-linked THOC2 gene in intellectual disability (ID). We now report an additional six affected individuals from five unrelated families with two de novo and three maternally inherited pathogenic or likely pathogenic variants in THOC2 extending the genotypic and phenotypic spectrum. These comprise three rare missense THOC2 variants that affect evolutionarily conserved amino acid residues and reduce protein stability and two with canonical splice-site THOC2 variants that result in C-terminally truncated THOC2 proteins. We present detailed clinical assessment and functional studies on a de novo variant in a female with an epileptic encephalopathy and discuss an additional four families with rare variants in THOC2 with supportive evidence for pathogenicity. Severe neurocognitive features, including movement and seizure disorders, were observed in this cohort. Taken together our data show that even subtle alterations to the canonical molecular pathways such as mRNA export, otherwise essential for cellular life, can be compatible with life, but lead to NDDs in humans.
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Affiliation(s)
- Raman Kumar
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Alison Gardner
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Claire C Homan
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Heather Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington & Seattle Children's Hospital, Seattle, Washington
| | - Dagmar Wieczorek
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany.,Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Hermann-Josef Lüdecke
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany.,Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, Australia
| | - Simon Sadedin
- Murdoch Children's Research Institute, Melbourne, Australia.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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- Broad's Center for Mendelian Genomics, Cambridge, Massachusetts
| | - Catherine Bearce Nowak
- The Feingold Center for Children at the Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Jessica Douglas
- The Feingold Center for Children at the Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | | | - Paul Mark
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | - Lourdes Loidi
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Gail E Herman
- Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio
| | | | - Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Lauren Brady
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - Irene Madrigal
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, Barcelona, Spain.,Centre for Biomedical Research on Rare Diseases (ISCIII), Barcelona, Spain
| | - Jesús Eiris
- Unidad de Neurología Pediátrica, Departamento de Pediatría, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura Domènech Salgado
- Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra and CIBERESP, Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Raquel Rabionet
- Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra and CIBERESP, Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Tim M Strom
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Naoko Ishihara
- Department of Pediatrics, Fujita Health University School of Medicine, Aichi, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, Japan
| | - Tracy Dudding-Byth
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia.,University of Newcastle, Australia Grow-Up-Well Priority Research Center, Callaghan, Australia
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
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28
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Corbett AH. Post-transcriptional regulation of gene expression and human disease. Curr Opin Cell Biol 2018; 52:96-104. [PMID: 29518673 PMCID: PMC5988930 DOI: 10.1016/j.ceb.2018.02.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 12/18/2022]
Abstract
A large number of mutations in genes that encode RNA binding proteins cause human disease. Many of these RNA binding proteins mediate key steps in post-transcriptional regulation of gene expression from mRNA processing to eventual decay in the cytoplasm. Surprisingly, these RNA binding proteins, which are ubiquitously expressed and play fundamental roles in gene expression, are often altered in tissue-specific disease. Mutations linked to disease impact nearly every post-transcriptional processing step and cause diverse disease phenotypes in a variety of specific tissues. This review summarizes steps in post-transcriptional regulation of gene expression that have been linked to disease providing specific examples of some of the many genes affected. Finally, recent advances that hold promise for treatment of some of these diseases are presented.
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Affiliation(s)
- Anita H Corbett
- Department of Biology, RRC 1021, Emory University, 1510 Clifton Road, NE, Atlanta 30322, GA, United States.
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29
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Li C, Liu L, Dinu V. Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma. PeerJ 2018; 6:e4571. [PMID: 29666752 PMCID: PMC5896492 DOI: 10.7717/peerj.4571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/14/2018] [Indexed: 01/01/2023] Open
Abstract
Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway's topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher's exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov-Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes of HCC are HCC subtype-associated specifically. In conclusion, PoTRA is a new approach to explore and discover pathways involved in cancer. PoTRA can be used as a complement to other existing methods to broaden our understanding of the biological mechanisms behind cancer at the system-level.
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Affiliation(s)
- Chaoxing Li
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Li Liu
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ, United States of America
| | - Valentin Dinu
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ, United States of America
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Chen Y, Cao B, Ou R, Wei Q, Chen X, Zhao B, Wu Y, Song W, Shang HF. Determining the Effect of the HNMT, STK39, and NMD3 Polymorphisms on the Incidence of Parkinson’s Disease, Amyotrophic Lateral Sclerosis, and Multiple System Atrophy in Chinese Populations. J Mol Neurosci 2018; 64:574-580. [DOI: 10.1007/s12031-018-1048-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/20/2018] [Indexed: 12/13/2022]
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31
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Coppin L, Leclerc J, Vincent A, Porchet N, Pigny P. Messenger RNA Life-Cycle in Cancer Cells: Emerging Role of Conventional and Non-Conventional RNA-Binding Proteins? Int J Mol Sci 2018; 19:ijms19030650. [PMID: 29495341 PMCID: PMC5877511 DOI: 10.3390/ijms19030650] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023] Open
Abstract
Functional specialization of cells and tissues in metazoans require specific gene expression patterns. Biological processes, thus, need precise temporal and spatial coordination of gene activity. Regulation of the fate of messenger RNA plays a crucial role in this context. In the present review, the current knowledge related to the role of RNA-binding proteins in the whole mRNA life-cycle is summarized. This field opens up a new angle for understanding the importance of the post-transcriptional control of gene expression in cancer cells. The emerging role of non-classic RNA-binding proteins is highlighted. The goal of this review is to encourage readers to view, through the mRNA life-cycle, novel aspects of the molecular basis of cancer and the potential to develop RNA-based therapies.
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Affiliation(s)
- Lucie Coppin
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Julie Leclerc
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Audrey Vincent
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Nicole Porchet
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Pascal Pigny
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
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