1
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Wright K, Han DJ, Song R, de Silva K, Plain KM, Purdie AC, Shepherd A, Chin M, Hortle E, Wong JJL, Britton WJ, Oehlers SH. Zebrafish tsc1 and cxcl12a increase susceptibility to mycobacterial infection. Life Sci Alliance 2024; 7:e202302523. [PMID: 38307625 PMCID: PMC10837051 DOI: 10.26508/lsa.202302523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024] Open
Abstract
Regulation of host miRNA expression is a contested node that controls the host immune response to mycobacterial infection. The host must counter subversive efforts of pathogenic mycobacteria to launch a protective immune response. Here, we examine the role of miR-126 in the zebrafish-Mycobacterium marinum infection model and identify a protective role for infection-induced miR-126 through multiple effector pathways. We identified a putative link between miR-126 and the tsc1a and cxcl12a/ccl2/ccr2 signalling axes resulting in the suppression of non-tnfa expressing macrophage accumulation at early M. marinum granulomas. Mechanistically, we found a detrimental effect of tsc1a expression that renders zebrafish embryos susceptible to higher bacterial burden and increased cell death via mTOR inhibition. We found that macrophage recruitment driven by the cxcl12a/ccl2/ccr2 signalling axis was at the expense of the recruitment of classically activated tnfa-expressing macrophages and increased cell death around granulomas. Together, our results delineate putative pathways by which infection-induced miR-126 may shape an effective immune response to M. marinum infection in zebrafish embryos.
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Affiliation(s)
- Kathryn Wright
- https://ror.org/0384j8v12 Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, Australia
- https://ror.org/0384j8v12 Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, Australia
- https://ror.org/0384j8v12 Directed Evolution Research Program at the Centenary Institute, The University of Sydney, Camperdown, Australia
- https://ror.org/0384j8v12 Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Darryl Jy Han
- https://ror.org/036wvzt09 A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Renhua Song
- https://ror.org/0384j8v12 Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
- https://ror.org/0384j8v12 Epigenetics and RNA Biology Laboratory, Charles Perkins Centre, The University of Sydney, Camperdown, Australia
| | - Kumudika de Silva
- https://ror.org/0384j8v12 Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Karren M Plain
- https://ror.org/0384j8v12 Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Auriol C Purdie
- https://ror.org/0384j8v12 Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Ava Shepherd
- https://ror.org/0384j8v12 Directed Evolution Research Program at the Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Maegan Chin
- https://ror.org/0384j8v12 Directed Evolution Research Program at the Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Elinor Hortle
- https://ror.org/0384j8v12 Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, Australia
- https://ror.org/0384j8v12 Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
- Faculty of Science, School of Life Sciences, Centre for Inflammation and University of Technology Sydney, Sydney, Australia
| | - Justin J-L Wong
- https://ror.org/0384j8v12 Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
- https://ror.org/0384j8v12 Epigenetics and RNA Biology Laboratory, Charles Perkins Centre, The University of Sydney, Camperdown, Australia
| | - Warwick J Britton
- https://ror.org/0384j8v12 Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, Australia
- https://ror.org/0384j8v12 Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
- Department of Clinical Immunology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Stefan H Oehlers
- https://ror.org/0384j8v12 Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, Australia
- https://ror.org/0384j8v12 Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
- https://ror.org/036wvzt09 A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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2
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Pinello N, Song R, Lee Q, Calonne E, Larance M, Fuks F, Wong JJL. A multiomics dataset for the study of RNA modifications in human macrophage differentiation and polarisation. Sci Data 2024; 11:252. [PMID: 38418823 PMCID: PMC10902381 DOI: 10.1038/s41597-024-03076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
RNA modifications have emerged as central regulators of gene expression programs. Amongst RNA modifications are N6-methyladenosine (m6A) and RNA 5-hydroxymethylcytosine (5hmC). While m6A is established as a versatile regulator of RNA metabolism, the functions of RNA 5hmC are unclear. Despite some evidence linking RNA modifications to immunity, their implications in gene expression control in macrophage development and functions remain unclear. Here we present a multi-omics dataset capturing different layers of the gene expression programs driving macrophage differentiation and polarisation. We obtained mRNA-Seq, m6A-IP-Seq, 5hmC-IP-Seq, Polyribo-Seq and LC-MS/MS data from monocytes and resting-, pro- and anti-inflammatory-like macrophages. We present technical validation showing high quality and correlation between samples for all datasets, and evidence of biological consistency of modelled macrophages at the transcriptomic, epitranscriptomic, translational and proteomic levels. This multi-omics dataset provides a resource for the study of RNA m6A and 5hmC in the context of macrophage biology and spans the gene expression process from transcripts to proteins.
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Affiliation(s)
- Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mark Larance
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, 2050, New South Wales, Australia
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.
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3
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Wong ACH, Wong JJL, Rasko JEJ, Schmitz U. SpliceWiz: interactive analysis and visualization of alternative splicing in R. Brief Bioinform 2023; 25:bbad468. [PMID: 38152981 PMCID: PMC10753292 DOI: 10.1093/bib/bbad468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 12/29/2023] Open
Abstract
Alternative splicing (AS) is a crucial mechanism for regulating gene expression and isoform diversity in eukaryotes. However, the analysis and visualization of AS events from RNA sequencing data remains challenging. Most tools require a certain level of computer literacy and the available means of visualizing AS events, such as coverage and sashimi plots, have limitations and can be misleading. To address these issues, we present SpliceWiz, an R package with an interactive Shiny interface that allows easy and efficient AS analysis and visualization at scale. A novel normalization algorithm is implemented to aggregate splicing levels within sample groups, thereby allowing group differences in splicing levels to be accurately visualized. The tool also offers downstream gene ontology enrichment analysis, highlighting ASEs belonging to functional pathways of interest. SpliceWiz is optimized for speed and efficiency and introduces a new file format for coverage data storage that is more efficient than BigWig. Alignment files are processed orders of magnitude faster than other R-based AS analysis tools and on par with command-line tools. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization. SpliceWiz is a Bioconductor package and is also available on GitHub (https://github.com/alexchwong/SpliceWiz).
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Affiliation(s)
- Alex C H Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, the University of Sydney, Camperdown, NSW 2050, Australia
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Biomedical Sciences and Molecular Biology, James Cook University, Townsville, QLD 4810, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4810, Australia
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4
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Lee Q, Song R, Phan DAV, Pinello N, Tieng J, Su A, Halstead JM, Wong ACH, van Geldermalsen M, Lee BSL, Rong B, Cook KM, Larance M, Liu R, Lan F, Tiffen JC, Wong JJL. Correction: Overexpression of VIRMA confers vulnerability to breast cancers via the m 6A-dependent regulation of unfolded protein response. Cell Mol Life Sci 2023; 80:204. [PMID: 37450040 PMCID: PMC10348946 DOI: 10.1007/s00018-023-04825-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Affiliation(s)
- Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Dang Anh Vu Phan
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jessica Tieng
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Anni Su
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - James M Halstead
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Alex C H Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Michelle van Geldermalsen
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Bob S-L Lee
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Kristina M Cook
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renjing Liu
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jessamy C Tiffen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Melanoma Epigenetics Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia.
- , Locked Bag 6, Newtown, NSW, 2042, Australia.
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5
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Zhang J, Yang J, Duval C, Edin ML, Williams A, Lei L, Tu M, Pourmand E, Song R, Graves JP, DeGraff LM, Wong JJL, Wang Y, Sun Q, Sanidad KZ, Wong S, Han Y, Zhang Z, Lee KSS, Park Y, Xiao H, Liu Z, Decker EA, Cui W, Zeldin DC, Zhang G. CYP eicosanoid pathway mediates colon cancer-promoting effects of dietary linoleic acid. FASEB J 2023; 37:e23009. [PMID: 37273180 DOI: 10.1096/fj.202300786r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023]
Abstract
Human and animal studies support that consuming a high level of linoleic acid (LA, 18:2ω-6), an essential fatty acid and key component of the human diet, increases the risk of colon cancer. However, results from human studies have been inconsistent, making it challenging to establish dietary recommendations for optimal LA intake. Given the importance of LA in the human diet, it is crucial to better understand the molecular mechanisms underlying its potential colon cancer-promoting effects. Using LC-MS/MS-based targeted lipidomics, we find that the cytochrome P450 (CYP) monooxygenase pathway is a major pathway for LA metabolism in vivo. Furthermore, CYP monooxygenase is required for the colon cancer-promoting effects of LA, since the LA-rich diet fails to exacerbate colon cancer in CYP monooxygenase-deficient mice. Finally, CYP monooxygenase mediates the pro-cancer effects of LA by converting LA to epoxy octadecenoic acids (EpOMEs), which have potent effects on promoting colon tumorigenesis via gut microbiota-dependent mechanisms. Overall, these results support that CYP monooxygenase-mediated conversion of LA to EpOMEs plays a crucial role in the health effects of LA, establishing a unique mechanistic link between dietary fatty acid intake and cancer risk. These results could help in developing more effective dietary guidelines for optimal LA intake and identifying subpopulations that may be especially vulnerable to LA's negative effects.
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Affiliation(s)
- Jianan Zhang
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jun Yang
- Department of Entomology and Comprehensive Cancer Center, University of California, Davis, California, USA
| | - Caroline Duval
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Matthew L Edin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Andrea Williams
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Lei Lei
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Maolin Tu
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Elham Pourmand
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, University of Sydney, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Joan P Graves
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Laura M DeGraff
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, University of Sydney, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Yige Wang
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore
| | - Quancai Sun
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore
| | - Katherine Z Sanidad
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Siu Wong
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Yanhui Han
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Zhenyu Zhang
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kin Sing Stephen Lee
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Yeonhwa Park
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Zhenhua Liu
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Nutrition and Cancer Prevention Laboratory, School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Eric A Decker
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Darryl C Zeldin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore
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6
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Lee Q, Song R, Phan DAV, Pinello N, Tieng J, Su A, Halstead JM, Wong ACH, van Geldermalsen M, Lee BSL, Rong B, Cook KM, Larance M, Liu R, Lan F, Tiffen JC, Wong JJL. Overexpression of VIRMA confers vulnerability to breast cancers via the m 6A-dependent regulation of unfolded protein response. Cell Mol Life Sci 2023; 80:157. [PMID: 37208522 DOI: 10.1007/s00018-023-04799-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023]
Abstract
Virilizer-like m6A methyltransferase-associated protein (VIRMA) maintains the stability of the m6A writer complex. Although VIRMA is critical for RNA m6A deposition, the impact of aberrant VIRMA expression in human diseases remains unclear. We show that VIRMA is amplified and overexpressed in 15-20% of breast cancers. Of the two known VIRMA isoforms, the nuclear-enriched full-length but not the cytoplasmic-localised N-terminal VIRMA promotes m6A-dependent breast tumourigenesis in vitro and in vivo. Mechanistically, we reveal that VIRMA overexpression upregulates the m6A-modified long non-coding RNA, NEAT1, which contributes to breast cancer cell growth. We also show that VIRMA overexpression enriches m6A on transcripts that regulate the unfolded protein response (UPR) pathway but does not promote their translation to activate the UPR under optimal growth conditions. Under stressful conditions that are often present in tumour microenvironments, VIRMA-overexpressing cells display enhanced UPR and increased susceptibility to death. Our study identifies oncogenic VIRMA overexpression as a vulnerability that may be exploited for cancer therapy.
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Affiliation(s)
- Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Dang Anh Vu Phan
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jessica Tieng
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Anni Su
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - James M Halstead
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Alex C H Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Michelle van Geldermalsen
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Bob S-L Lee
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Kristina M Cook
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renjing Liu
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jessamy C Tiffen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Melanoma Epigenetics Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- , Locked Bag 6, Newtown, NSW, 2042, Australia.
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7
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Hitchins MP, Alvarez R, Zhou L, Aguirre F, Dámaso E, Pineda M, Capella G, Wong JJL, Yuan X, Ryan SR, Sathe DS, Baxter MD, Cannon T, Biswas R, DeMarco T, Grzelak D, Hampel H, Pearlman R. MLH1-methylated endometrial cancer under 60 years of age as the "sentinel" cancer in female carriers of high-risk constitutional MLH1 epimutation. Gynecol Oncol 2023; 171:129-140. [PMID: 36893489 PMCID: PMC10153467 DOI: 10.1016/j.ygyno.2023.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/11/2023]
Abstract
OBJECTIVE Universal screening of endometrial carcinoma (EC) for mismatch repair deficiency (MMRd) and Lynch syndrome uses presence of MLH1 methylation to omit common sporadic cases from follow-up germline testing. However, this overlooks rare cases with high-risk constitutional MLH1 methylation (epimutation), a poorly-recognized mechanism that predisposes to Lynch-type cancers with MLH1 methylation. We aimed to determine the role and frequency of constitutional MLH1 methylation among EC cases with MMRd, MLH1-methylated tumors. METHODS We screened blood for constitutional MLH1 methylation using pyrosequencing and real-time methylation-specific PCR in patients with MMRd, MLH1-methylated EC ascertained from (i) cancer clinics (n = 4, <60 years), and (ii) two population-based cohorts; "Columbus-area" (n = 68, all ages) and "Ohio Colorectal Cancer Prevention Initiative (OCCPI)" (n = 24, <60 years). RESULTS Constitutional MLH1 methylation was identified in three out of four patients diagnosed between 36 and 59 years from cancer clinics. Two had mono-/hemiallelic epimutation (∼50% alleles methylated). One with multiple primaries had low-level mosaicism in normal tissues and somatic "second-hits" affecting the unmethylated allele in all tumors, demonstrating causation. In the population-based cohorts, all 68 cases from the Columbus-area cohort were negative and low-level mosaic constitutional MLH1 methylation was identified in one patient aged 36 years out of 24 from the OCCPI cohort, representing one of six (∼17%) patients <50 years and one of 45 patients (∼2%) <60 years in the combined cohorts. EC was the first/dual-first cancer in three patients with underlying constitutional MLH1 methylation. CONCLUSIONS A correct diagnosis at first presentation of cancer is important as it will significantly alter clinical management. Screening for constitutional MLH1 methylation is warranted in patients with early-onset EC or synchronous/metachronous tumors (any age) displaying MLH1 methylation.
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Affiliation(s)
- Megan P Hitchins
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine (Oncology), Stanford University, Stanford, CA, USA.
| | - Rocio Alvarez
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lisa Zhou
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Francesca Aguirre
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Estela Dámaso
- Department of Medicine (Oncology), Stanford University, Stanford, CA, USA; Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain; Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain
| | - Marta Pineda
- Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain; Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
| | - Gabriel Capella
- Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain; Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, and Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Xiaopu Yuan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shawnia R Ryan
- Hereditary Cancer Assessment Program, University of New Mexico Comprehensive Cancer Center, NM, USA
| | - Devika S Sathe
- Precision Medicine and Genetics, Frederick Health, MD, USA
| | | | - Timothy Cannon
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | - Rakesh Biswas
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | - Tiffani DeMarco
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | | | - Heather Hampel
- Department of Internal Medicine and the Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA; Division of Clinical Cancer Genomics, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Rachel Pearlman
- Department of Internal Medicine and the Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
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8
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Song R, J-L Wong J. Altered expression of m1A regulatory genes is associated with oncogenic pathways, overall survival, and infiltration of immune cells in diverse human cancers. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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9
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Hortle E, Tran VL, Wright K, Fontaine AR, Pinello N, O'Rourke MB, Wong JJL, Hansbro PM, Britton WJ, Oehlers SH. OXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection. Life Sci Alliance 2022; 5:5/9/e202201476. [PMID: 35545295 PMCID: PMC9107790 DOI: 10.26508/lsa.202201476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mycobacteria up-regulate host kinase OXSR1 preventing potassium efflux and inflammasome activation. Depletion or inhibition of OXSR1 potentiates inflammasome activation and decreases bacterial burden. Pathogenic mycobacteria inhibit inflammasome activation to establish infection. Although it is known that potassium efflux is a trigger for inflammasome activation, the interaction between mycobacterial infection, potassium efflux, and inflammasome activation has not been investigated. Here, we use Mycobacterium marinum infection of zebrafish embryos and Mycobacterium tuberculosis infection of THP-1 cells to demonstrate that pathogenic mycobacteria up-regulate the host WNK signalling pathway kinases SPAK and OXSR1 which control intracellular potassium balance. We show that genetic depletion or inhibition of OXSR1 decreases bacterial burden and intracellular potassium levels. The protective effects of OXSR1 depletion are at least partially mediated by NLRP3 inflammasome activation, caspase-mediated release of IL-1β, and downstream activation of protective TNF-α. The elucidation of this druggable pathway to potentiate inflammasome activation provides a new avenue for the development of host-directed therapies against intracellular infections.
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Affiliation(s)
- Elinor Hortle
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia .,The University of Sydney, Discipline of Infectious Diseases and Immunology and Sydney Institute for Infectious Diseases, Camperdown, Australia.,Centre for Inflammation and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Vi Lt Tran
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Kathryn Wright
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Angela Rm Fontaine
- Centenary Imaging and Sydney Cytometry at the Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia.,The University of Sydney, Faculty of Medicine and Health, Camperdown, Australia
| | - Matthew B O'Rourke
- Centre for Inflammation and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia.,The University of Sydney, Faculty of Medicine and Health, Camperdown, Australia
| | - Philip M Hansbro
- Centre for Inflammation and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Warwick J Britton
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Department of Clinical Immunology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Stefan H Oehlers
- Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, Australia .,The University of Sydney, Discipline of Infectious Diseases and Immunology and Sydney Institute for Infectious Diseases, Camperdown, Australia.,A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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10
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Song R, Tikoo S, Jain R, Pinello N, Au AY, Nagarajah R, Porse B, Rasko JEJ, Wong JJL. Dynamic intron retention modulates gene expression in the monocytic differentiation pathway. Immunology 2021; 165:274-286. [PMID: 34775600 DOI: 10.1111/imm.13435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/01/2022] Open
Abstract
Monocytes play a crucial role in maintaining homeostasis and mediating a successful innate immune response. They also act as central players in diverse pathological conditions, thus making them an attractive therapeutic target. Within the bone marrow, monocytes arise from a committed precursor termed cMoP (Common Monocyte Progenitor). However, molecular mechanisms that regulate the differentiation of cMoP to various monocytic subsets remain unclear. Herein, we purified murine myeloid precursors for deep poly-A enriched RNA sequencing to understand the role of alternative splicing in the development and differentiation of monocytes under homeostasis. Our analyses revealed intron retention to be the major alternative splicing mechanism involved in the monocyte differentiation cascade, especially in the differentiation of Ly6Chi monocytes to Ly6Clo monocytes. Furthermore, we found that the key genes regulated by intron retention in the differentiation of murine Ly6Chi to Ly6Clo monocytes were also conserved in humans. Our data highlight the unique role of intron retention in the regulation of the monocytic differentiation pathway.
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Affiliation(s)
- Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Shweta Tikoo
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Rohit Jain
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Amy Ym Au
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Rajini Nagarajah
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.,Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
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11
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Choi JP, Yang X, He S, Song R, Xu ZR, Foley M, Wong JJL, Xu CR, Zheng X. CCM2L (Cerebral Cavernous Malformation 2 Like) Deletion Aggravates Cerebral Cavernous Malformation Through Map3k3-KLF Signaling Pathway. Stroke 2021; 52:1428-1436. [PMID: 33657857 DOI: 10.1161/strokeaha.120.031523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jaesung P Choi
- Lab of Cardiovascular Signaling, Centenary Institute, Sydney Medical School (J.P.C., X.Z.), University of Sydney, NSW, Australia.,Centre for Inflammation, Centenary Institute, School of Life Sciences, University of Technology Sydney, NSW, Australia (J.P.C.)
| | - Xi Yang
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, China (X.Y., X.Z.)
| | - Shuang He
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing, China (S.H., Z.-R.X., C.-R.X.)
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, Sydney Medical School (R.S., J.J.-L.W.), University of Sydney, NSW, Australia
| | - Zi-Ran Xu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing, China (S.H., Z.-R.X., C.-R.X.)
| | - Matthew Foley
- Australian Centre for Microscopy and Microanalysis (M.F.), University of Sydney, NSW, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, Sydney Medical School (R.S., J.J.-L.W.), University of Sydney, NSW, Australia
| | - Cheng-Ran Xu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing, China (S.H., Z.-R.X., C.-R.X.)
| | - Xiangjian Zheng
- Lab of Cardiovascular Signaling, Centenary Institute, Sydney Medical School (J.P.C., X.Z.), University of Sydney, NSW, Australia.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, China (X.Y., X.Z.)
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12
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Green ID, Pinello N, Song R, Lee Q, Halstead JM, Kwok CT, Wong ACH, Nair SS, Clark SJ, Roediger B, Schmitz U, Larance M, Hayashi R, Rasko JEJ, Wong JJL. Macrophage development and activation involve coordinated intron retention in key inflammatory regulators. Nucleic Acids Res 2020; 48:6513-6529. [PMID: 32449925 PMCID: PMC7337907 DOI: 10.1093/nar/gkaa435] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/04/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022] Open
Abstract
Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA sequencing and proteomics analysis, we identify IR events that affect the expression of key genes/proteins involved in macrophage development and function. We demonstrate that decreased IR in nuclear-detained mRNA is coupled with increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts are rapidly spliced, enabling timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular factors controlling vital regulators of the innate immune response.
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Affiliation(s)
- Immanuel D Green
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - James M Halstead
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Chau-To Kwok
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Alex C H Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst 2010, Australia.,St. Vincent's Clinical School, UNSW, Sydney 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst 2010, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst 2010, Australia.,St. Vincent's Clinical School, UNSW, Sydney 2010, Australia
| | - Ben Roediger
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Ulf Schmitz
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Mark Larance
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown 2006, New South Wales, Australia
| | - Rippei Hayashi
- The John Curtin School of Medical Research, The Australian National University, ACT 2601, Australia
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
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13
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Gao D, Pinello N, Nguyen TV, Thoeng A, Nagarajah R, Holst J, Rasko JEJ, Wong JJL. DNA methylation/hydroxymethylation regulate gene expression and alternative splicing during terminal granulopoiesis. Epigenomics 2019; 11:95-109. [DOI: 10.2217/epi-2018-0050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Aim: To determine whether epigenetic modifications of DNA regulate gene expression and alternative splicing during terminal granulopoiesis. Materials & methods: Using whole genome bisulfite sequencing, reduced representation hydroxymethylation profiling and mRNA sequencing, we compare changes in DNA methylation, DNA hydroxymethylation, gene expression and alternative splicing in mouse promyelocytes and granulocytes. Results & conclusion: We show reduced DNA methylation at the promoters and enhancers of key granulopoiesis genes, indicating a regulatory role in the activation of lineage-specific genes during differentiation. Notably, increased DNA hydroxymethylation in exons is associated with preferential inclusion of specific exons in granulocytes. Overall, DNA methylation and hydroxymethylation changes at particular genomic loci may play specific roles in gene regulation or alternative splicing during terminal granulopoiesis. Data deposition: Whole genome bisulfite sequencing of mouse promyelocytes and granulocytes: Gene Expression Omnibus (GSE85517); mRNA sequencing of mouse promyelocytes and granulocytes: Gene Expression Omnibus (GSE48307); reduced representation 5-hydroxymethylation profiling of mouse promyelocytes and granulocytes: Bioproject (PRJNA495696).
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Affiliation(s)
- Dadi Gao
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Bioinformatics Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Natalia Pinello
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Gene Regulation in Cancer Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
| | - Trung V Nguyen
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Gene Regulation in Cancer Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
| | - Annora Thoeng
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Rajini Nagarajah
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Jeff Holst
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Origins of Cancer Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
| | - John EJ Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, NSW 2006, Australia
- Gene Regulation in Cancer Laboratory Centenary Institute, University of Sydney, Camperdown 2050, Australia
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14
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Roediger B, Lee Q, Tikoo S, Cobbin JCA, Henderson JM, Jormakka M, O'Rourke MB, Padula MP, Pinello N, Henry M, Wynne M, Santagostino SF, Brayton CF, Rasmussen L, Lisowski L, Tay SS, Harris DC, Bertram JF, Dowling JP, Bertolino P, Lai JH, Wu W, Bachovchin WW, Wong JJL, Gorrell MD, Shaban B, Holmes EC, Jolly CJ, Monette S, Weninger W. An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis. Cell 2018; 175:530-543.e24. [PMID: 30220458 PMCID: PMC6800251 DOI: 10.1016/j.cell.2018.08.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 07/23/2018] [Accepted: 08/07/2018] [Indexed: 11/19/2022]
Abstract
The occurrence of a spontaneous nephropathy with intranuclear inclusions in laboratory mice has puzzled pathologists for over 4 decades, because its etiology remains elusive. The condition is more severe in immunodeficient animals, suggesting an infectious cause. Using metagenomics, we identify the causative agent as an atypical virus, termed "mouse kidney parvovirus" (MKPV), belonging to a divergent genus of Parvoviridae. MKPV was identified in animal facilities in Australia and North America, is transmitted via a fecal-oral or urinary-oral route, and is controlled by the adaptive immune system. Detailed analysis of the clinical course and histopathological features demonstrated a stepwise progression of pathology ranging from sporadic tubular inclusions to tubular degeneration and interstitial fibrosis and culminating in renal failure. In summary, we identify a widely distributed pathogen in laboratory mice and establish MKPV-induced nephropathy as a new tool for elucidating mechanisms of tubulointerstitial fibrosis that shares molecular features with chronic kidney disease in humans.
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Affiliation(s)
- Ben Roediger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia.
| | - Quintin Lee
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Shweta Tikoo
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Joanna C A Cobbin
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - James M Henderson
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Mika Jormakka
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Matthew B O'Rourke
- Mass Spectrometry Core Facility, University of Sydney, Sydney, NSW 2006, Australia; Proteomics Core Facility, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Matthew P Padula
- Proteomics Core Facility, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Natalia Pinello
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Marisa Henry
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; Laboratory Animal Services, University of Sydney, Sydney, NSW 2006, Australia
| | - Maria Wynne
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; Laboratory Animal Services, University of Sydney, Sydney, NSW 2006, Australia
| | - Sara F Santagostino
- Laboratory of Comparative Pathology, Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY 10065, USA
| | - Cory F Brayton
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Leszek Lisowski
- Children's Medical Research Institute, University of Sydney, Sydney, NSW 2006, Australia; Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Centre, Puławy 24-100, Poland
| | - Szun S Tay
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - David C Harris
- Centre for Transplantation and Renal Research, Westmead Institute for Medical Research, University of Sydney, NSW 2006, Australia
| | - John F Bertram
- Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - John P Dowling
- Department of Anatomical Pathology, Monash Medical Centre, Clayton, VIC 3168, Australia
| | - Patrick Bertolino
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Jack H Lai
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Wengen Wu
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - William W Bachovchin
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Justin J-L Wong
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Mark D Gorrell
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Babak Shaban
- Australian Genomics Research Facility, Parkville, VIC 3000, Australia; Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Christopher J Jolly
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Sébastien Monette
- Laboratory of Comparative Pathology, Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wolfgang Weninger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; Discipline of Dermatology, Faculty of Medicine and Health, University of Sydney, NSW 2006, Australia; Department of Dermatology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria.
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15
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Nair SS, Luu PL, Qu W, Maddugoda M, Huschtscha L, Reddel R, Chenevix-Trench G, Toso M, Kench JG, Horvath LG, Hayes VM, Stricker PD, Hughes TP, White DL, Rasko JEJ, Wong JJL, Clark SJ. Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics Chromatin 2018; 11:24. [PMID: 29807544 PMCID: PMC5971424 DOI: 10.1186/s13072-018-0194-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 12/24/2022] Open
Abstract
Background Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. Results In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16–20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we developed a WGBS pipeline (METH10X) that is fast and can call SNPs. We performed WGBS on both high-quality intact DNA and degraded DNA from formalin-fixed paraffin-embedded tissue. First, we compared different library preparation methods on the HiSeq 2500 platform to identify the best method for sequencing on the HiSeq X Ten. Second, we optimised the PhiX and genome spike-ins to achieve higher quality and coverage of WGBS data on the HiSeq X Ten. Third, we performed integrated whole genome sequencing (WGS) and WGBS of the same DNA sample in a single lane of HiSeq X Ten to improve data output. Finally, we compared methylation data from the HiSeq 2500 and HiSeq X Ten and found high concordance (Pearson r > 0.9×). Conclusions Together we provide a systematic, efficient and complete approach to perform and analyse WGBS on the HiSeq X Ten. Our protocol allows for large-scale WGBS studies at reasonable processing time and cost on the HiSeq X Ten platform. Electronic supplementary material The online version of this article (10.1186/s13072-018-0194-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Phuc-Loi Luu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Madhavi Maddugoda
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Lily Huschtscha
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Roger Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | | | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.,Clinical Prostate Cancer Research, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Faculty of Health Science and Faculty of Science, University of Adelaide, Adelaide, SA, Australia.,Australian Genomic Health Alliance, Melbourne, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia. .,Epigenetics Research Program, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.
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16
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Rajasekhar M, Schmitz U, Flamant S, Wong JJL, Bailey CG, Ritchie W, Holst J, Rasko JEJ. Identifying microRNA determinants of human myelopoiesis. Sci Rep 2018; 8:7264. [PMID: 29739970 PMCID: PMC5940821 DOI: 10.1038/s41598-018-24203-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/23/2018] [Indexed: 01/05/2023] Open
Abstract
Myelopoiesis involves differentiation of hematopoietic stem cells to cellular populations that are restricted in their self-renewal capacity, beginning with the common myeloid progenitor (CMP) and leading to mature cells including monocytes and granulocytes. This complex process is regulated by various extracellular and intracellular signals including microRNAs (miRNAs). We characterised the miRNA profile of human CD34+CD38+ myeloid progenitor cells, and mature monocytes and granulocytes isolated from cord blood using TaqMan Low Density Arrays. We identified 19 miRNAs that increased in both cell types relative to the CMP and 27 that decreased. miR-125b and miR-10a were decreased by 10-fold and 100-fold respectively in the mature cells. Using in vitro granulopoietic differentiation of human CD34+ cells we show that decreases in both miR-125b and miR-10a correlate with a loss of CD34 expression and gain of CD11b and CD15 expression. Candidate target mRNAs were identified by co-incident predictions between the miRanda algorithm and genes with increased expression during differentiation. Using luciferase assays we confirmed MCL1 and FUT4 as targets of miR-125b and the transcription factor KLF4 as a target of miR-10a. Together, our data identify miRNAs with differential expression during myeloid development and reveal some relevant miRNA-target pairs that may contribute to physiological differentiation.
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Affiliation(s)
- Megha Rajasekhar
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephane Flamant
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Justin J-L Wong
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - William Ritchie
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Jeff Holst
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia.,Origins of Cancer Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia. .,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia. .,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia.
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17
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Schmitz U, Pinello N, Jia F, Alasmari S, Ritchie W, Keightley MC, Shini S, Lieschke GJ, Wong JJL, Rasko JEJ. Intron retention enhances gene regulatory complexity in vertebrates. Genome Biol 2017; 18:216. [PMID: 29141666 PMCID: PMC5688624 DOI: 10.1186/s13059-017-1339-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/13/2017] [Indexed: 01/22/2023] Open
Abstract
Background While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution. Results Our RNA-sequencing-based analysis suggests that IR increases gene regulatory complexity, which is indicated by a strong anti-correlation between the number of genes affected by IR and the number of protein-coding genes in the genome of individual species. Our results confirm that IR affects many orthologous or functionally related genes in granulocytes. Further analysis uncovers new and unanticipated conserved characteristics of intron-retaining transcripts. We find that intron-retaining genes are transcriptionally co-regulated from bidirectional promoters. Intron-retaining genes have significantly longer 3′ UTR sequences, with a corresponding increase in microRNA binding sites, some of which include highly conserved sequence motifs. This suggests that intron-retaining genes are highly regulated post-transcriptionally. Conclusions Our study provides unique insights concerning the role of IR as a robust and evolutionarily conserved mechanism of gene expression regulation. Our findings enhance our understanding of gene regulatory complexity by adding another contributor to evolutionary adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1339-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ulf Schmitz
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.,Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia
| | - Natalia Pinello
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.,Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia
| | - Fangzhi Jia
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.,Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia
| | - Sultan Alasmari
- Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia
| | | | | | - Shaniko Shini
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Justin J-L Wong
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.,Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia. .,Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia. .,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, NSW, Australia. .,, Locked Bag 6, Newtown, NSW, 2042, Australia.
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18
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Tan MC, Widagdo J, Chau YQ, Zhu T, Wong JJL, Cheung A, Anggono V. The Activity-Induced Long Non-Coding RNA Meg3 Modulates AMPA Receptor Surface Expression in Primary Cortical Neurons. Front Cell Neurosci 2017; 11:124. [PMID: 28515681 PMCID: PMC5413565 DOI: 10.3389/fncel.2017.00124] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 11/13/2022] Open
Abstract
Transcription of new RNA is crucial for maintaining synaptic plasticity, learning and memory. Although the importance of synaptic plasticity-related messenger RNAs (mRNAs) is well established, the role of a large group of long non-coding RNAs (lncRNAs) in long-term potentiation (LTP) is not known. In this study, we demonstrated the expression of a lncRNA cluster, namely maternally expressed gene 3 (Meg3), retrotransposon-like gene 1-anti-sense (Rtl1-AS), Meg8 and Meg9, which is located in the maternally imprinted Dlk1-Dio3 region on mouse chromosome 12qF1, in primary cortical neurons following glycine stimulation in an N-Methyl-D-aspartate receptor (NMDAR)-dependent manner. Importantly, we also validated the expression of Meg3, Meg8 and Meg9 in the hippocampus of mice following cued fear conditioning in vivo. Interestingly, Meg3 is the only lncRNA that is expressed in the nucleus and cytoplasm. Further analysis revealed that Meg3 loss of function blocked the glycine-induced increase of the GluA1 subunit of AMPA receptors on the plasma membrane, a major hallmark of LTP. This aberrant trafficking of AMPA receptors correlated with the dysregulation of the phosphatidylinoside-3-kinase (PI3K)/AKT signaling pathway and the downregulation of the lipid phosphatase and tensin homolog (PTEN). These findings provide the first evidence for a functional role of the lncRNA Meg3 in the intricate regulation of the PTEN/PI3K/AKT signaling cascade during synaptic plasticity in neurons.
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Affiliation(s)
- Men C Tan
- Clem Jones Centre for Ageing Dementia Research, The University of QueenslandBrisbane, QLD, Australia.,Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, The University of QueenslandBrisbane, QLD, Australia.,Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Yu Q Chau
- Clem Jones Centre for Ageing Dementia Research, The University of QueenslandBrisbane, QLD, Australia.,Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, The University of QueenslandBrisbane, QLD, Australia.,Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary InstituteSydney, NSW, Australia.,Sydney Medical School, University of SydneySydney, NSW, Australia
| | - Allen Cheung
- Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, The University of QueenslandBrisbane, QLD, Australia.,Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
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19
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Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJL, Bomane A, Cosson B, Eyras E, Rasko JEJ, Ritchie W. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol 2017; 18:51. [PMID: 28298237 PMCID: PMC5353968 DOI: 10.1186/s13059-017-1184-4] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/27/2017] [Indexed: 01/05/2023] Open
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.
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Affiliation(s)
- Robert Middleton
- Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia
| | - Dadi Gao
- Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.,Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Boston & Harvard Medical School, Boston, MA, USA.,Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia
| | | | - Babita Singh
- Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain
| | - Amy Au
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Justin J-L Wong
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, Australia
| | - Alexandra Bomane
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France
| | - Bertrand Cosson
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France
| | - Eduardo Eyras
- Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, E08010, Barcelona, Spain
| | - John E J Rasko
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - William Ritchie
- Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia. .,CNRS, UPR 1142, Montpellier, 34094, France. .,CNRS, UMR 5203, Montpellier, 34094, France.
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20
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Abstract
Since the discovery of microRNAs (miRNAs) in the early 1990s, these small molecules have been increasingly recognized as key players in the regulation of critical biological processes. They have also been implicated in many diverse human diseases. The canonical function of miRNAs is to target the 3′ untranslated region (3′ UTR) of cytoplasmic messenger RNA to post-transcriptionally regulate mRNA and protein levels. It has now been shown that miRNAs can also bind to the promoter regions of genes or primary miRNA transcripts to regulate gene expression. Such observations have indicated the presence of miRNAs in the nucleus and implied additional non-canonical functions. Nevertheless, the role(s) of nuclear miRNAs in normal hemopoiesis and cancer remains elusive despite a burgeoning literature. Herein, we review current knowledge concerning the abundance and/or functions of nuclear miRNAs during blood cell development and cancer biology. We also discuss ongoing challenges in order to provoke further studies into identifying key roles for nuclear miRNAs in the development of other cell lineages and human cancers.
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Affiliation(s)
- John E J Rasko
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2050, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - Justin J-L Wong
- Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, Australia. .,Sydney Medical School, University of Sydney, Camperdown, NSW, 2050, Australia. .,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, Australia. .,, Locked Bag 6, Newtown, NSW, 2042, Australia.
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21
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Wong JJL, Au AYM, Gao D, Pinello N, Kwok CT, Thoeng A, Lau KA, Gordon JEA, Schmitz U, Feng Y, Nguyen TV, Middleton R, Bailey CG, Holst J, Rasko JEJ, Ritchie W. RBM3 regulates temperature sensitive miR-142-5p and miR-143 (thermomiRs), which target immune genes and control fever. Nucleic Acids Res 2016; 44:2888-97. [PMID: 26825461 PMCID: PMC4824108 DOI: 10.1093/nar/gkw041] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/13/2016] [Indexed: 12/27/2022] Open
Abstract
Fever is commonly used to diagnose disease and is consistently associated with increased mortality in critically ill patients. However, the molecular controls of elevated body temperature are poorly understood. We discovered that the expression of RNA-binding motif protein 3 (RBM3), known to respond to cold stress and to modulate microRNA (miRNA) expression, was reduced in 30 patients with fever, and in THP-1-derived macrophages maintained at a fever-like temperature (40°C). Notably, RBM3 expression is reduced during fever whether or not infection is demonstrable. Reduced RBM3 expression resulted in increased expression of RBM3-targeted temperature-sensitive miRNAs, we termed thermomiRs. ThermomiRs such as miR-142–5p and miR-143 in turn target endogenous pyrogens including IL-6, IL6ST, TLR2, PGE2 and TNF to complete a negative feedback mechanism, which may be crucial to prevent pathological hyperthermia. Using normal PBMCs that were exogenously exposed to fever-like temperature (40°C), we further demonstrate the trend by which decreased levels of RBM3 were associated with increased levels of miR-142–5p and miR-143 and vice versa over a 24 h time course. Collectively, our results indicate the existence of a negative feedback loop that regulates fever via reduced RBM3 levels and increased expression of miR-142–5p and miR-143.
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Affiliation(s)
- Justin J-L Wong
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Amy Y M Au
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Dadi Gao
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia Bioinformatics Laboratory, Centenary Institute, Camperdown 2050, Australia
| | - Natalia Pinello
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Chau-To Kwok
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Annora Thoeng
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Katherine A Lau
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Jane E A Gordon
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Yue Feng
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Trung V Nguyen
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Robert Middleton
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia Bioinformatics Laboratory, Centenary Institute, Camperdown 2050, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Jeff Holst
- Sydney Medical School, University of Sydney, NSW 2006, Australia Origins of Cancer Program, Centenary Institute, Camperdown 2050, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - William Ritchie
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia Sydney Medical School, University of Sydney, NSW 2006, Australia Bioinformatics Laboratory, Centenary Institute, Camperdown 2050, Australia CNRS, UMR 5203, Montpellier 34094, France
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22
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Wang Q, Hardie RA, Hoy AJ, van Geldermalsen M, Gao D, Fazli L, Sadowski MC, Balaban S, Schreuder M, Nagarajah R, Wong JJL, Metierre C, Pinello N, Otte NJ, Lehman ML, Gleave M, Nelson CC, Bailey CG, Ritchie W, Rasko JEJ, Holst J. Targeting ASCT2-mediated glutamine uptake blocks prostate cancer growth and tumour development. J Pathol 2015; 236:278-89. [PMID: 25693838 PMCID: PMC4973854 DOI: 10.1002/path.4518] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/19/2015] [Accepted: 02/12/2015] [Indexed: 12/11/2022]
Abstract
Glutamine is conditionally essential in cancer cells, being utilized as a carbon and nitrogen source for macromolecule production, as well as for anaplerotic reactions fuelling the tricarboxylic acid (TCA) cycle. In this study, we demonstrated that the glutamine transporter ASCT2 (SLC1A5) is highly expressed in prostate cancer patient samples. Using LNCaP and PC‐3 prostate cancer cell lines, we showed that chemical or shRNA‐mediated inhibition of ASCT2 function in vitro decreases glutamine uptake, cell cycle progression through E2F transcription factors, mTORC1 pathway activation and cell growth. Chemical inhibition also reduces basal oxygen consumption and fatty acid synthesis, showing that downstream metabolic function is reliant on ASCT2‐mediated glutamine uptake. Furthermore, shRNA knockdown of ASCT2 in PC‐3 cell xenografts significantly inhibits tumour growth and metastasis in vivo, associated with the down‐regulation of E2F cell cycle pathway proteins. In conclusion, ASCT2‐mediated glutamine uptake is essential for multiple pathways regulating the cell cycle and cell growth, and is therefore a putative therapeutic target in prostate cancer. © 2015 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Qian Wang
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Rae-Anne Hardie
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Andrew J Hoy
- Discipline of Physiology, Bosch Institute and Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Michelle van Geldermalsen
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Dadi Gao
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia.,Bioinformatics, Centenary Institute, Camperdown, NSW, Australia
| | - Ladan Fazli
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Martin C Sadowski
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Australia
| | - Seher Balaban
- Discipline of Physiology, Bosch Institute and Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Mark Schreuder
- Discipline of Physiology, Bosch Institute and Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Rajini Nagarajah
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Justin J-L Wong
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Cynthia Metierre
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Natalia Pinello
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Nicholas J Otte
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Melanie L Lehman
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Australia
| | - Martin Gleave
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Australia
| | - Charles G Bailey
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - William Ritchie
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia.,Bioinformatics, Centenary Institute, Camperdown, NSW, Australia
| | - John E J Rasko
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Jeff Holst
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
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23
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Wang Q, Hardie RA, Hoy AJ, van Geldermalsen M, Gao D, Fazli L, Sadowski MC, Balaban S, Schreuder M, Nagarajah R, Wong JJL, Metierre C, Pinello N, Otte NJ, Lehman ML, Gleave M, Nelson CC, Bailey CG, Ritchie W, Rasko JEJ, Holst J. Targeting ASCT2-mediated glutamine uptake blocks prostate cancer growth and tumour development. J Pathol 2015. [PMID: 25693838 DOI: 10.1002/path.4518.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Glutamine is conditionally essential in cancer cells, being utilized as a carbon and nitrogen source for macromolecule production, as well as for anaplerotic reactions fuelling the tricarboxylic acid (TCA) cycle. In this study, we demonstrated that the glutamine transporter ASCT2 (SLC1A5) is highly expressed in prostate cancer patient samples. Using LNCaP and PC-3 prostate cancer cell lines, we showed that chemical or shRNA-mediated inhibition of ASCT2 function in vitro decreases glutamine uptake, cell cycle progression through E2F transcription factors, mTORC1 pathway activation and cell growth. Chemical inhibition also reduces basal oxygen consumption and fatty acid synthesis, showing that downstream metabolic function is reliant on ASCT2-mediated glutamine uptake. Furthermore, shRNA knockdown of ASCT2 in PC-3 cell xenografts significantly inhibits tumour growth and metastasis in vivo, associated with the down-regulation of E2F cell cycle pathway proteins. In conclusion, ASCT2-mediated glutamine uptake is essential for multiple pathways regulating the cell cycle and cell growth, and is therefore a putative therapeutic target in prostate cancer.
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Affiliation(s)
- Qian Wang
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Rae-Anne Hardie
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Andrew J Hoy
- Discipline of Physiology, Bosch Institute and Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Michelle van Geldermalsen
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Dadi Gao
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia.,Bioinformatics, Centenary Institute, Camperdown, NSW, Australia
| | - Ladan Fazli
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Martin C Sadowski
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Australia
| | - Seher Balaban
- Discipline of Physiology, Bosch Institute and Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Mark Schreuder
- Discipline of Physiology, Bosch Institute and Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Rajini Nagarajah
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Justin J-L Wong
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Cynthia Metierre
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Natalia Pinello
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Nicholas J Otte
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - Melanie L Lehman
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Australia
| | - Martin Gleave
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Australia
| | - Charles G Bailey
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
| | - William Ritchie
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia.,Bioinformatics, Centenary Institute, Camperdown, NSW, Australia
| | - John E J Rasko
- Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Jeff Holst
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, Australia
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Wong JJL, Lau KA, Pinello N, Rasko JEJ. Epigenetic modifications of splicing factor genes in myelodysplastic syndromes and acute myeloid leukemia. Cancer Sci 2014; 105:1457-63. [PMID: 25220401 PMCID: PMC4462368 DOI: 10.1111/cas.12532] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/28/2014] [Accepted: 09/01/2014] [Indexed: 12/19/2022] Open
Abstract
Somatic mutations in splicing factor genes have frequently been reported in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Although aberrant epigenetic changes are frequently implicated in blood cancers, their direct role in suppressing one or both alleles of critical splicing factors has not been previously examined. Here, we examined promoter DNA hypermethylation of nine splicing factors, SF3B1, SRSF2, U2AF1, ZRSR2, SF3A1, HNRNPR, MATR3, ZFR, and YBX3 in 10 leukemic cell lines and 94 MDS or AML patient samples from the Australasian Leukemia and Lymphoma Group Tissue Bank. The only evidence of epigenetic effects was hypermethylation of the YBX3 promoter in U937 cells in conjunction with an enrichment of histone marks associated with gene silencing. In silico analysis of DNA methylation data for 173 AML samples generated by the Cancer Genome Atlas Research Network revealed promoter hypermethylation of the gene encoding Y box binding protein 3, YBX3, in 11/173 (6.4%) AML cases, which was significantly associated with reduced mRNA expression (P < 0.0001). Hypermethylation of the ZRSR2 promoter was also detected in 7/173 (4%) cases but was not associated with decreased mRNA expression (P = 0.1204). Hypermethylation was absent at the promoter of seven other splicing factor genes in all cell lines and patient samples examined. We conclude that DNA hypermethylation does not frequently silence splicing factors in MDS and AML. However, in the case of YBX3, promoter hypermethylation-induced downregulation may contribute to the pathogenesis or maintenance of AML.
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Affiliation(s)
- Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
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25
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Wong JJL, Ritchie W, Ebner OA, Selbach M, Wong JWH, Huang Y, Gao D, Pinello N, Gonzalez M, Baidya K, Thoeng A, Khoo TL, Bailey CG, Holst J, Rasko JEJ. Orchestrated intron retention regulates normal granulocyte differentiation. Cell 2013; 154:583-95. [PMID: 23911323 DOI: 10.1016/j.cell.2013.06.052] [Citation(s) in RCA: 320] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 05/01/2013] [Accepted: 06/28/2013] [Indexed: 12/11/2022]
Abstract
Intron retention (IR) is widely recognized as a consequence of mis-splicing that leads to failed excision of intronic sequences from pre-messenger RNAs. Our bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control. IR regulates the expression of 86 functionally related genes, including those that determine the nuclear shape that is unique to granulocytes. Retention of introns in specific genes is associated with downregulation of splicing factors and higher GC content. IR, conserved between human and mouse, led to reduced mRNA and protein levels by triggering the nonsense-mediated decay (NMD) pathway. In contrast to the prevalent view that NMD is limited to mRNAs encoding aberrant proteins, our data establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis. Physiological IR may provide an energetically favorable level of dynamic gene expression control prior to sustained gene translation.
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Affiliation(s)
- Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia
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26
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Abstract
MicroRNAs (miRNAs) are key to the pathogenesis of human malignancies and increasingly recognized as potential biomarkers and therapeutic targets. Haematological malignancies, being the earliest human malignancies linked to aberrant miRNA expression, have consistently underpinned our understanding of the role that miRNAs play in cancer development. Here, we review the expanding roles attributed to miRNAs in the pathogenesis of different types of myeloid malignancies and highlight key findings.
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Affiliation(s)
- Jane E A Gordon
- Gene & Stem Cell Therapy Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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27
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Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJL, Rasko JEJ, Rokhsar DS, Degnan BM, Mattick JS. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol 2010; 17:1030-4. [PMID: 20622877 DOI: 10.1038/nsmb.1841] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 04/27/2010] [Indexed: 12/21/2022]
Abstract
We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences immediately downstream of transcription start sites. Here, using cytoplasmic and nuclear small RNA high-throughput sequencing datasets, we report the identification of a second class of nuclear-specific approximately 17- to 18-nucleotide small RNAs whose 3' ends map precisely to the splice donor site of internal exons in animals. These splice-site RNAs (spliRNAs) are associated with highly expressed genes and show evidence of developmental stage- and region-specific expression. We also show that tiRNAs are localized to the nucleus, are enriched at chromatin marks associated with transcription initiation and possess a 3'-nucleotide bias. Additionally, we find that microRNA-offset RNAs (moRNAs), the miR-15/16 cluster previously linked to oncosuppression and most small nucleolar RNA (snoRNA)-derived small RNAs (sdRNAs) are enriched in the nucleus, whereas most miRNAs and two H/ACA sdRNAs are cytoplasmically enriched. We propose that nuclear-localized tiny RNAs are involved in the epigenetic regulation of gene expression.
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Affiliation(s)
- Ryan J Taft
- Institute for Molecular Bioscience, School of Integrative Biology, University of Queensland, St. Lucia, Australia
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28
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Hawkins NJ, Lee JHF, Wong JJL, Kwok CT, Ward RL, Hitchins MP. MGMT methylation is associated primarily with the germline C>T SNP (rs16906252) in colorectal cancer and normal colonic mucosa. Mod Pathol 2009; 22:1588-99. [PMID: 19734844 DOI: 10.1038/modpathol.2009.130] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
O(6)-methylguanine DNA methyltransferase (MGMT) is a DNA repair protein that restores mutagenic O(6)-methylguanine to guanine. MGMT methylation is frequently observed in sporadic colorectal cancer and was recently correlated with the C>T allele at SNP rs16906252, within the transcriptional enhancer element of the promoter. MGMT methylation has also been associated with KRAS mutations, particularly G>A transitions. We studied 1123 colorectal carcinoma to define the molecular and clinicopathological profiles associated with MGMT methylation. Furthermore, we assessed factors contributing to MGMT methylation in the development of colorectal cancer by studying the allelic pattern of MGMT methylation using SNP rs16906252, and the methylation status of neighbouring genes within 10q26 in selected tumours and matched normal colonic mucosa. MGMT methylation was detected by combined bisulphite restriction analysis in 28% of tumours and was associated with a number of characteristics, including CDKN2A methylation, absent lymphovascular space invasion and KRAS mutations (but not specifically with KRAS G>A transitions). In a multivariate analysis adjusted for age and sex, MGMT methylation was associated with the T allele of SNP rs16906252 (P<0.0001, OR 5.5, 95% CI 3.8-7.9). Low-level methylation was detected by quantitative methylation-specific PCR in the normal colonic mucosa of cases, particularly those with a correspondingly methylated tumour, as well as controls without neoplasia, and this was also associated with the C>T SNP. We show that the T allele at SNP rs16906252 is a key determinant in the onset of MGMT methylation in colorectal cancer, whereas the association of methylation at MGMT and CDKN2A suggests that these loci may be targets of a common mechanism of epigenetic dysregulation.
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29
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Affiliation(s)
- J J L Wong
- School of Medical Sciences, University of NSW, Sydney, New South Wales, Australia
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