1
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Bhuva DD, Tan CW, Salim A, Marceaux C, Pickering MA, Chen J, Kharbanda M, Jin X, Liu N, Feher K, Putri G, Tilley WD, Hickey TE, Asselin-Labat ML, Phipson B, Davis MJ. Library size confounds biology in spatial transcriptomics data. Genome Biol 2024; 25:99. [PMID: 38637899 PMCID: PMC11025268 DOI: 10.1186/s13059-024-03241-7] [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: 07/12/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including normalization methods. Here, we demonstrate that library size is associated with tissue structure and that normalizing these effects out using commonly applied scRNA-seq normalization methods will negatively affect spatial domain identification. Spatial data should not be specifically corrected for library size prior to analysis, and algorithms designed for scRNA-seq data should be adopted with caution.
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Affiliation(s)
- Dharmesh D Bhuva
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Chin Wee Tan
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- The University of Queensland Fraser Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Agus Salim
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Melbourne School of Population and Global Health, School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Claire Marceaux
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
| | - Marie A Pickering
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Jinjin Chen
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Malvika Kharbanda
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Xinyi Jin
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ning Liu
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Kristen Feher
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Givanna Putri
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Marie-Liesse Asselin-Labat
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
| | - Belinda Phipson
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Melissa J Davis
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- The University of Queensland Fraser Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
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2
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Zhang Y, Lee RY, Tan CW, Guo X, Yim WWY, Lim JC, Wee FY, Yang WU, Kharbanda M, Lee JYJ, Ngo NT, Leow WQ, Loo LH, Lim TK, Sobota RM, Lau MC, Davis MJ, Yeong J. Spatial omics techniques and data analysis for cancer immunotherapy applications. Curr Opin Biotechnol 2024; 87:103111. [PMID: 38520821 DOI: 10.1016/j.copbio.2024.103111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
In-depth profiling of cancer cells/tissues is expanding our understanding of the genomic, epigenomic, transcriptomic, and proteomic landscape of cancer. However, the complexity of the cancer microenvironment, particularly its immune regulation, has made it difficult to exploit the potential of cancer immunotherapy. High-throughput spatial omics technologies and analysis pipelines have emerged as powerful tools for tackling this challenge. As a result, a potential revolution in cancer diagnosis, prognosis, and treatment is on the horizon. In this review, we discuss the technological advances in spatial profiling of cancer around and beyond the central dogma to harness the full benefits of immunotherapy. We also discuss the promise and challenges of spatial data analysis and interpretation and provide an outlook for the future.
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Affiliation(s)
- Yue Zhang
- Duke-NUS Medical School, Singapore 169856, Singapore
| | - Ren Yuan Lee
- Yong Loo Lin School of Medicine, National University of Singapore, 169856 Singapore; Singapore Thong Chai Medical Institution, Singapore 169874, Singapore
| | - Chin Wee Tan
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia
| | - Xue Guo
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Willa W-Y Yim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Jeffrey Ct Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Felicia Yt Wee
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - W U Yang
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Malvika Kharbanda
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jia-Ying J Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Nye Thane Ngo
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Wei Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Tony Kh Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Mai Chan Lau
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A⁎STAR), Singapore 138648, Singapore
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia; immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joe Yeong
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore.
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3
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Behrens K, Brajanovski N, Xu Z, Viney EM, DiRago L, Hediyeh-Zadeh S, Davis MJ, Pearson RB, Sanij E, Alexander WS, Ng AP. ERG and c-MYC regulate a critical gene network in BCR::ABL1-driven B cell acute lymphoblastic leukemia. Sci Adv 2024; 10:eadj8803. [PMID: 38457494 PMCID: PMC10923517 DOI: 10.1126/sciadv.adj8803] [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] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/31/2024] [Indexed: 03/10/2024]
Abstract
Philadelphia chromosome-positive B cell acute lymphoblastic leukemia (B-ALL), characterized by the BCR::ABL1 fusion gene, remains a poor prognosis cancer needing new therapeutic approaches. Transcriptomic profiling identified up-regulation of oncogenic transcription factors ERG and c-MYC in BCR::ABL1 B-ALL with ERG and c-MYC required for BCR::ABL1 B-ALL in murine and human models. Profiling of ERG- and c-MYC-dependent gene expression and analysis of ChIP-seq data established ERG and c-MYC coordinate a regulatory network in BCR::ABL1 B-ALL that controls expression of genes involved in several biological processes. Prominent was control of ribosome biogenesis, including expression of RNA polymerase I (POL I) subunits, the importance of which was validated by inhibition of BCR::ABL1 cells by POL I inhibitors, including CX-5461, that prevents promoter recruitment and transcription initiation by POL I. Our results reveal an essential ERG- and c-MYC-dependent transcriptional network involved in regulation of metabolic and ribosome biogenesis pathways in BCR::ABL1 B-ALL, from which previously unidentified vulnerabilities and therapeutic targets may emerge.
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Affiliation(s)
- Kira Behrens
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Natalie Brajanovski
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Zhen Xu
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Elizabeth M. Viney
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ladina DiRago
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Soroor Hediyeh-Zadeh
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Melissa J. Davis
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, Australia
- The Diamantina Institute, The University of Queensland, Woolloongabba, Australia
- The South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Richard B. Pearson
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Australia
| | - Elaine Sanij
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Australia
- St. Vincent’s Institute of Medical Research, Fitzroy, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Parkville, Australia
| | - Warren S. Alexander
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Ashley P. Ng
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
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4
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Tan CW, Chen J, Liu N, Bhuva DD, Blick T, Monkman J, Cooper C, Kharbanda M, Feher K, Phipson B, Killingbeck EE, Pan L, Kim Y, Liang Y, Nam A, Leon M, Souza-Fonseca-Guimaraes P, Nagashima S, Camargo Martins AP, Machado-Souza C, de Noronha L, Tang B, Short K, Fraser J, Belz GT, Souza-Fonseca-Guimaraes F, Kulasinghe A, Davis MJ. In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection. EBioMedicine 2024; 101:105016. [PMID: 38377798 PMCID: PMC10884333 DOI: 10.1016/j.ebiom.2024.105016] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024] Open
Abstract
The utilization of single-cell resolved spatial transcriptomics to delineate immune responses during SARS-CoV-2 infection was able to identify M1 macrophages to have elevated expression of IFI27 in areas of infection.
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Affiliation(s)
- Chin Wee Tan
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jinjin Chen
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ning Liu
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Dharmesh D Bhuva
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Tony Blick
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Caroline Cooper
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia; Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Malvika Kharbanda
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Kristen Feher
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia
| | - Belinda Phipson
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Liuliu Pan
- Nanostring Technologies, Inc, Seattle, WA, USA
| | - Youngmi Kim
- Nanostring Technologies, Inc, Seattle, WA, USA
| | - Yan Liang
- Nanostring Technologies, Inc, Seattle, WA, USA
| | - Andy Nam
- Nanostring Technologies, Inc, Seattle, WA, USA
| | | | | | - Seigo Nagashima
- Laboratório de Patologia Experimental, PPGCS da PUCPR, Curitiba, Brazil
| | | | - Cleber Machado-Souza
- Faculdades Pequeno Príncipe (FPP), Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), R. Silva Jardim, 1632-ÁguaVerde, Curitiba, 80230-020, PR, Brazil
| | - Lucia de Noronha
- Laboratório de Patologia Experimental, PPGCS da PUCPR, Curitiba, Brazil
| | - Benjamin Tang
- Westmead Institute for Medical Research, Sydney, Australia
| | - Kirsty Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Fraser
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia; Faculty of Medicine University of Queensland, Brisbane, QLD, Australia; St Andrew's War Memorial Hospital, UnitingCare, Spring Hill, QLD, Australia
| | - Gabrielle T Belz
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | | | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
| | - Melissa J Davis
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia; South Australian ImmunoGENomics Cancer Institute, The University of Adelaide, SA, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
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5
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Bhuva DD, Tan CW, Liu N, Whitfield HJ, Papachristos N, Lee SC, Kharbanda M, Mohamed A, Davis MJ. vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis. BMC Bioinformatics 2024; 25:64. [PMID: 38331751 PMCID: PMC10854147 DOI: 10.1186/s12859-024-05676-y] [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: 05/18/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upstream. This scale of results hinders extensive exploration by biologists and can lead to investigator biases due to previous knowledge and expectations. To address this issue, we present vissE, a flexible network-based analysis and visualisation tool that organises information into semantic categories and provides various visualisation modules to characterise them with respect to the underlying data, thus providing a comprehensive view of the biological system. We demonstrate vissE's versatility by applying it to three different technologies: bulk, single-cell and spatial transcriptomics. Applying vissE to a factor analysis of a breast cancer spatial transcriptomic data, we identified stromal phenotypes that support tumour dissemination. Its adaptability allows vissE to enhance all existing gene-set enrichment and pathway analysis workflows, empowering biologists during molecular discovery.
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Affiliation(s)
- Dharmesh D Bhuva
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Chin Wee Tan
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Fraser Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia
| | - Ning Liu
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Holly J Whitfield
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas Papachristos
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Samuel C Lee
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Malvika Kharbanda
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ahmed Mohamed
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Colonial Foundation Healthy Ageing Centre, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
| | - Melissa J Davis
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- Fraser Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
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6
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Goh W, Sudholz H, Foroutan M, Scheer S, Pfefferle A, Delconte RB, Meng X, Shen Z, Hennessey R, Kong IY, Schuster IS, Andoniou CE, Davis MJ, Hediyeh-Zadeh S, Souza-Fonseca-Guimaraes F, Parish IA, Beavis P, Thiele D, Chopin M, Degli-Esposti MA, Cursons J, Kallies A, Rautela J, Nutt SL, Huntington ND. IKAROS and AIOLOS directly regulate AP-1 transcriptional complexes and are essential for NK cell development. Nat Immunol 2024; 25:240-255. [PMID: 38182668 DOI: 10.1038/s41590-023-01718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/22/2023] [Indexed: 01/07/2024]
Abstract
Ikaros transcription factors are essential for adaptive lymphocyte function, yet their role in innate lymphopoiesis is unknown. Using conditional genetic inactivation, we show that Ikzf1/Ikaros is essential for normal natural killer (NK) cell lymphopoiesis and IKZF1 directly represses Cish, a negative regulator of interleukin-15 receptor resulting in impaired interleukin-15 receptor signaling. Both Bcl2l11 and BIM levels, and intrinsic apoptosis were increased in Ikzf1-null NK cells, which in part accounts for NK lymphopenia as both were restored to normal levels when Ikzf1 and Bcl2l11 were co-deleted. Ikzf1-null NK cells presented extensive transcriptional alterations with reduced AP-1 transcriptional complex expression and increased expression of Ikzf2/Helios and Ikzf3/Aiolos. IKZF1 and IKZF3 directly bound AP-1 family members and deletion of both Ikzf1 and Ikzf3 in NK cells resulted in further reductions in Jun/Fos expression and complete loss of peripheral NK cells. Collectively, we show that Ikaros family members are important regulators of apoptosis, cytokine responsiveness and AP-1 transcriptional activity.
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Affiliation(s)
- Wilford Goh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Harrison Sudholz
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Momeneh Foroutan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Sebastian Scheer
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Aline Pfefferle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiangpeng Meng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Zihan Shen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Robert Hennessey
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Iona S Schuster
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Christopher E Andoniou
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
- The South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Thiele
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Michael Chopin
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Joe Cursons
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Axel Kallies
- Department of Microbiology & Immunology, Faculty of Medicine, Dentistry and Health Sciences & Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jai Rautela
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas D Huntington
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia.
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7
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Zawieja SD, Pea GA, Broyhill SE, Bromert KH, Norton CE, Kim HJ, Li M, Castorena-Gonzalez JA, Drumm BT, Davis MJ. Lymphatic muscle cells are the innate pacemaker cells regulating mouse lymphatic collecting vessel contractions. bioRxiv 2023:2023.08.24.554619. [PMID: 37662284 PMCID: PMC10473772 DOI: 10.1101/2023.08.24.554619] [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] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Collecting lymphatic vessels (cLVs) exhibit spontaneous contractions with a pressure-dependent frequency, but the identity of the lymphatic pacemaker cell is still debated. By analogy to pacemakers in the GI and lower urinary tracts, proposed cLV pacemaker cells include interstitial cells of Cajal like cells (ICLC), pericytes, as well as the lymphatic muscle (LMCs) cells themselves. Here we tested the extent to which these cell types are invested into the mouse cLV wall and if any cell type exhibited morphological and functional processes characteristic of pacemaker cells: a contiguous network; spontaneous Ca2+ transients; and depolarization-induced propagated contractions. We employed inducible Cre (iCre) mouse models routinely used to target these specific cell populations including: c-kitCreERT2 to target ICLC; PdgfrβCreERT2 to target pericytes; PdgfrαCreER™ to target CD34+ adventitial fibroblast-like cells or ICLC; and Myh11CreERT2 to target LMCs. These specific inducible Cre lines were crossed to the fluorescent reporter ROSA26mT/mG, the genetically encoded Ca2+ sensor GCaMP6f, and the light-activated cation channel rhodopsin2 (ChR2). c-KitCreERT2 labeled both a sparse population of LECs and round adventitial cells that responded to the mast cell activator compound 48-80. PdgfrβCreERT2 drove recombination in both adventitial cells and LMCs, limiting its power to discriminate a pericyte specific population. PdgfrαCreER™ labeled a large population of interconnected, oak leaf-shaped cells primarily along the adventitial surface of the vessel. Titrated induction of the smooth muscle-specific Myh11CreERT2 revealed a LMC population with heterogeneous morphology. Only LMCs consistently, but heterogeneously, displayed spontaneous Ca2+ events during the diastolic period of the contraction cycle, and whose frequency was modulated in a pressure-dependent manner. Optogenetic depolarization through the expression of ChR2 by Myh11CreERT2, but not PdgfrαCreER™ or c-KitCreERT2, resulted in a propagated contraction. These findings support the conclusion that LMCs, or a subset of LMCs, are responsible for mouse cLV pacemaking.
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Affiliation(s)
- S D Zawieja
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - G A Pea
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - S E Broyhill
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - K H Bromert
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - C E Norton
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - H J Kim
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - M Li
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | | | - B T Drumm
- Smooth Muscle Research Centre, Dundalk Institute of Technology, Dundalk, Co. Louth, A91 K584, Ireland
| | - M J Davis
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
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8
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Sharma S, Chung CY, Uryu S, Petrovic J, Cao J, Rickard A, Nady N, Greasley S, Johnson E, Brodsky O, Khan S, Wang H, Wang Z, Zhang Y, Tsaparikos K, Chen L, Mazurek A, Lapek J, Kung PP, Sutton S, Richardson PF, Greenwald EC, Yamazaki S, Jones R, Maegley KA, Bingham P, Lam H, Stupple AE, Kamal A, Chueh A, Cuzzupe A, Morrow BJ, Ren B, Carrasco-Pozo C, Tan CW, Bhuva DD, Allan E, Surgenor E, Vaillant F, Pehlivanoglu H, Falk H, Whittle JR, Newman J, Cursons J, Doherty JP, White KL, MacPherson L, Devlin M, Dennis ML, Hattarki MK, De Silva M, Camerino MA, Butler MS, Dolezal O, Pilling P, Foitzik R, Stupple PA, Lagiakos HR, Walker SR, Hediyeh-Zadeh S, Nuttall S, Spall SK, Charman SA, Connor T, Peat TS, Avery VM, Bozikis YE, Yang Y, Zhang M, Monahan BJ, Voss AK, Thomas T, Street IP, Dawson SJ, Dawson MA, Lindeman GJ, Davis MJ, Visvader JE, Paul TA. Discovery of a highly potent, selective, orally bioavailable inhibitor of KAT6A/B histone acetyltransferases with efficacy against KAT6A-high ER+ breast cancer. Cell Chem Biol 2023; 30:1191-1210.e20. [PMID: 37557181 DOI: 10.1016/j.chembiol.2023.07.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/07/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023]
Abstract
KAT6A, and its paralog KAT6B, are histone lysine acetyltransferases (HAT) that acetylate histone H3K23 and exert an oncogenic role in several tumor types including breast cancer where KAT6A is frequently amplified/overexpressed. However, pharmacologic targeting of KAT6A to achieve therapeutic benefit has been a challenge. Here we describe identification of a highly potent, selective, and orally bioavailable KAT6A/KAT6B inhibitor CTx-648 (PF-9363), derived from a benzisoxazole series, which demonstrates anti-tumor activity in correlation with H3K23Ac inhibition in KAT6A over-expressing breast cancer. Transcriptional and epigenetic profiling studies show reduced RNA Pol II binding and downregulation of genes involved in estrogen signaling, cell cycle, Myc and stem cell pathways associated with CTx-648 anti-tumor activity in ER-positive (ER+) breast cancer. CTx-648 treatment leads to potent tumor growth inhibition in ER+ breast cancer in vivo models, including models refractory to endocrine therapy, highlighting the potential for targeting KAT6A in ER+ breast cancer.
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Affiliation(s)
- Shikhar Sharma
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA.
| | - Chi-Yeh Chung
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Sean Uryu
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Jelena Petrovic
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Joan Cao
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Amanda Rickard
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Nataliya Nady
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | | | - Eric Johnson
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Oleg Brodsky
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Showkhin Khan
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Hui Wang
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Zhenxiong Wang
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Yong Zhang
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | | | - Lei Chen
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Anthony Mazurek
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - John Lapek
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Pei-Pei Kung
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Scott Sutton
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | | | - Eric C Greenwald
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Shinji Yamazaki
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Rhys Jones
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Karen A Maegley
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Patrick Bingham
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Hieu Lam
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Alexandra E Stupple
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; CANThera Discovery, Melbourne, VIC 3000, Australia
| | - Aileen Kamal
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Anderly Chueh
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Anthony Cuzzupe
- SYNthesis Med Chem (Australia) Pty Ltd, Bio21 Institute, 30 Flemington Road, Parkville, VIC 3052, Australia
| | - Benjamin J Morrow
- Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia
| | - Bin Ren
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Catalina Carrasco-Pozo
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Discovery Biology, Centre for Cellular Phenomics, Griffith University, Brisbane QLD 4111, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dharmesh D Bhuva
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Elizabeth Allan
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Elliot Surgenor
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - François Vaillant
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Havva Pehlivanoglu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Hendrik Falk
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - James R Whittle
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Joseph Cursons
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Judy P Doherty
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Karen L White
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mark Devlin
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Matthew L Dennis
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Meghan K Hattarki
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Melanie De Silva
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Michelle A Camerino
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Miriam S Butler
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Olan Dolezal
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Patricia Pilling
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Richard Foitzik
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; OncologyOne Pty Ltd, Melbourne, VIC 3000, Australia
| | - Paul A Stupple
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; CANThera Discovery, Melbourne, VIC 3000, Australia
| | - H Rachel Lagiakos
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Scott R Walker
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Stewart Nuttall
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Sukhdeep K Spall
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Susan A Charman
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Theresa Connor
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Thomas S Peat
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Vicky M Avery
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Discovery Biology, Centre for Cellular Phenomics, Griffith University, Brisbane QLD 4111, Australia
| | - Ylva E Bozikis
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Yuqing Yang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ming Zhang
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Brendon J Monahan
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; CANThera Discovery, Melbourne, VIC 3000, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ian P Street
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; OncologyOne Pty Ltd, Melbourne, VIC 3000, Australia; Children's Cancer Institute, Randwick, NSW 2031, Australia; University of New South Wales, Randwick, NSW 2021, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Geoffrey J Lindeman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia; Parkville Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC 3050, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E Visvader
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Thomas A Paul
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA.
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9
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Orang A, Dredge BK, Liu CY, Bracken JM, Chen CH, Sourdin L, Whitfield HJ, Lumb R, Boyle ST, Davis MJ, Samuel MS, Gregory PA, Khew-Goodall Y, Goodall GJ, Pillman KA, Bracken CP. Basonuclin-2 regulates extracellular matrix production and degradation. Life Sci Alliance 2023; 6:e202301984. [PMID: 37536977 PMCID: PMC10400885 DOI: 10.26508/lsa.202301984] [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: 02/09/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Epithelial-mesenchymal transition is essential for tissue patterning and organization. It involves both regulation of cell motility and alterations in the composition and organization of the ECM-a complex environment of proteoglycans and fibrous proteins essential for tissue homeostasis, signaling in response to chemical and biomechanical stimuli, and is often dysregulated under conditions such as cancer, fibrosis, and chronic wounds. Here, we demonstrate that basonuclin-2 (BNC2), a mesenchymal-expressed gene, that is, strongly associated with cancer and developmental defects across genome-wide association studies, is a novel regulator of ECM composition and degradation. We find that at endogenous levels, BNC2 controls the expression of specific collagens, matrix metalloproteases, and other matrisomal components in breast cancer cells, and in fibroblasts that are primarily responsible for the production and processing of the ECM within the tumour microenvironment. In so doing, BNC2 modulates the motile and invasive properties of cancers, which likely explains the association of high BNC2 expression with increasing cancer grade and poor patient prognosis.
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Affiliation(s)
- Ayla Orang
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Chi Yau Liu
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Julie M Bracken
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Chun-Hsien Chen
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Laura Sourdin
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Holly J Whitfield
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Rachael Lumb
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Sarah T Boyle
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Melissa J Davis
- South Australian ImmunogGENomics Cancer Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Fraser Institute, University of Queensland, Wooloongabba, Australia
| | - Michael S Samuel
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Yeesim Khew-Goodall
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
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10
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White CL, Kinross KM, Moore MK, Rasouli E, Strong R, Jones JM, Cain JE, Sturm D, Sahm F, Jones DTW, Pfister SM, Robertson T, D'Arcy C, Rodriguez ML, Dyke JM, Junckerstorff R, Bhuva DD, Davis MJ, Wood P, Hassall T, Ziegler DS, Kellie S, McCowage G, Alvaro F, Kirby M, Heath JA, Tsui K, Dodgshun A, Eisenstat DD, Khuong-Quang DA, Wall M, Algar EM, Gottardo NG, Hansford JR. Implementation of DNA Methylation Array Profiling in Pediatric Central Nervous System Tumors: The AIM BRAIN Project: An Australian and New Zealand Children's Haematology/Oncology Group Study. J Mol Diagn 2023; 25:709-728. [PMID: 37517472 DOI: 10.1016/j.jmoldx.2023.06.013] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 08/01/2023] Open
Abstract
DNA methylation array profiling for classifying pediatric central nervous system (CNS) tumors is a valuable adjunct to histopathology. However, unbiased prospective and interlaboratory validation studies have been lacking. The AIM BRAIN diagnostic trial involving 11 pediatric cancer centers in Australia and New Zealand was designed to test the feasibility of routine clinical testing and ran in parallel with the Molecular Neuropathology 2.0 (MNP2.0) study at Deutsches Krebsforschungszentrum (German Cancer Research Center). CNS tumors from 269 pediatric patients were prospectively tested on Illumina EPIC arrays, including 104 cases co-enrolled on MNP2.0. Using MNP classifier versions 11b4 and 12.5, we report classifications with a probability score ≥0.90 in 176 of 265 (66.4%) and 213 of 269 (79.2%) cases, respectively. Significant diagnostic information was obtained in 130 of 176 (74%) for 11b4, and 12 of 174 (7%) classifications were discordant with histopathology. Cases prospectively co-enrolled on MNP2.0 gave concordant classifications (99%) and score thresholds (93%), demonstrating excellent test reproducibility and sensitivity. Overall, DNA methylation profiling is a robust single workflow technique with an acceptable diagnostic yield that is considerably enhanced by the extensive subgroup and copy number profile information generated by the platform. The platform has excellent test reproducibility and sensitivity and contributes significantly to CNS tumor diagnosis.
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Affiliation(s)
- Christine L White
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Kathryn M Kinross
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; Australian and New Zealand Children's Haematology/Oncology Group, Clayton, Victoria, Australia
| | - Molly K Moore
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Elnaz Rasouli
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Robyn Strong
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; Australian and New Zealand Children's Haematology/Oncology Group, Clayton, Victoria, Australia
| | - Janelle M Jones
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; Australian and New Zealand Children's Haematology/Oncology Group, Clayton, Victoria, Australia
| | - Jason E Cain
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Dominik Sturm
- Hopp Children's Cancer Centre Heidelberg, Heidelberg, Germany; Division of Pediatric Glioma Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Centre Heidelberg, Heidelberg, Germany; Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Centre Heidelberg, Heidelberg, Germany; Division of Pediatric Glioma Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Centre Heidelberg, Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Thomas Robertson
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Colleen D'Arcy
- Department of Pathology, Royal Children's Hospital, Parkville, Victoria, Australia
| | | | - Jason M Dyke
- PathWest Neuropathology, Royal Perth Hospital, Perth, Western Australia, Australia; Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
| | - Reimar Junckerstorff
- PathWest Neuropathology, Royal Perth Hospital, Perth, Western Australia, Australia; Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
| | - Dharmesh D Bhuva
- Walter and Eliza Hall Institute, Melbourne, Victoria, Australia; South Australia ImmunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Melissa J Davis
- Walter and Eliza Hall Institute, Melbourne, Victoria, Australia; South Australia ImmunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Paul Wood
- Monash Children's Hospital, Clayton, Victoria, Australia
| | - Tim Hassall
- Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia; Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales (UNSW), Kensington, New South Wales, Australia; School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Stewart Kellie
- The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Geoffrey McCowage
- The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Frank Alvaro
- John Hunter Children's Hospital, New Lambton Heights, New South Wales, Australia
| | - Maria Kirby
- Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - John A Heath
- Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Karen Tsui
- Starship Children's Hospital, Grafton, Auckland, New Zealand
| | - Andrew Dodgshun
- Christchurch Hospital, Christchurch Central City, Christchurch, New Zealand
| | - David D Eisenstat
- Children's Cancer Centre, Royal Children's Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Meaghan Wall
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Elizabeth M Algar
- Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia.
| | - Nicholas G Gottardo
- Perth Children's Hospital, Nedlands, Western Australia, Australia; Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Jordan R Hansford
- South Australia ImmunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia; Women's and Children's Hospital, North Adelaide, South Australia, Australia; Children's Cancer Centre, Royal Children's Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia; South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
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11
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Koldej RM, Prabahran A, Tan CW, Ludford-Menting M, Morgan H, Holzwart N, Davis MJ, Ritchie DS. Spatial proteomics identifies a spectrum of immune dysregulation in acquired bone marrow failure syndromes. Front Immunol 2023; 14:1213560. [PMID: 37818364 PMCID: PMC10560754 DOI: 10.3389/fimmu.2023.1213560] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Poor graft function (PGF), manifested by multilineage cytopenias and complete donor chimerism post-allogeneic stem cell transplantation (alloSCT), and acquired aplastic anaemia (AA) are immune-mediated acquired bone marrow (BM) failure syndromes with a similar clinical presentation. In this study, we used spatial proteomics to compare the immunobiology of the BM microenvironment and identify common mechanisms of immune dysregulation under these conditions. Archival BM trephines from patients exhibited downregulation of the immunoregulatory protein VISTA and the M2 macrophage marker and suppressor of T-cell activation ARG1 with increased expression of the immune checkpoint B7-H3 compared to normal controls. Increased CD163 and CD14 expression suggested monocyte/macrophage skewing, which, combined with dysregulation of STING and VISTA, is indicative of an environment of reduced immunoregulation resulting in the profound suppression of hematopoiesis in these two conditions. There were no changes in the immune microenvironment between paired diagnostic AA and secondary MDS/AML samples suggesting that leukaemic clones develop in the impaired immune microenvironment of AA without the need for further alterations. Of the eight proteins with dysregulated expression shared by diagnostic AA and PGF, the diagnostic AA samples had a greater fold change in expression than PGF, suggesting that these diseases represent a spectrum of immune dysregulation. Unexpectedly, analysis of samples from patients with good graft function post-alloSCT demonstrated significant changes in the immune microenvironment compared to normal controls, with downregulation of CD44, STING, VISTA, and ARG1, suggesting that recovery of multilineage haematopoiesis post-alloSCT does not reflect recovery of immune function and may prime patients for the development of PGF upon further inflammatory insult. The demonstrable similarities in the immunopathology of AA and PGF will allow the design of clinical interventions that include both patient cohorts to accelerate therapeutic discovery and translation.
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Affiliation(s)
- Rachel M. Koldej
- Australian Cancer Research Foundation (ACRF) Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Ashvind Prabahran
- Australian Cancer Research Foundation (ACRF) Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Chin Wee Tan
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Mandy Ludford-Menting
- Australian Cancer Research Foundation (ACRF) Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Huw Morgan
- Australian Cancer Research Foundation (ACRF) Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas Holzwart
- Australian Cancer Research Foundation (ACRF) Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa J. Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - David S. Ritchie
- Australian Cancer Research Foundation (ACRF) Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
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12
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Whitfield HJ, Berthelet J, Mangiola S, Bell C, Anderson RL, Pal B, Yeo B, Papenfuss AT, Merino D, Davis MJ. Single-cell RNA sequencing captures patient-level heterogeneity and associated molecular phenotypes in breast cancer pleural effusions. Clin Transl Med 2023; 13:e1356. [PMID: 37691350 PMCID: PMC10493486 DOI: 10.1002/ctm2.1356] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND Malignant pleural effusions (MPEs) are a common complication of advanced cancers, particularly those adjacent to the pleura, such as lung and breast cancer. The pathophysiology of MPE formation remains poorly understood, and although MPEs are routinely used for the diagnosis of breast cancer patients, their composition and biology are poorly understood. It is difficult to distinguish invading malignant cells from resident mesothelial cells and to identify the directionality of interactions between these populations in the pleura. There is a need to characterize the phenotypic diversity of breast cancer cell populations in the pleural microenvironment, and investigate how this varies across patients. METHODS Here, we used single-cell RNA-sequencing to study the heterogeneity of 10 MPEs from seven metastatic breast cancer patients, including three Miltenyi-enriched samples using a negative selection approach. This dataset of almost 65 000 cells was analysed using integrative approaches to compare heterogeneous cell populations and phenotypes. RESULTS We identified substantial inter-patient heterogeneity in the composition of cell types (including malignant, mesothelial and immune cell populations), in expression of subtype-specific gene signatures and in copy number aberration patterns, that captured variability across breast cancer cell populations. Within individual MPEs, we distinguished mesothelial cell populations from malignant cells using key markers, the presence of breast cancer subtype expression patterns and copy number aberration patterns. We also identified pleural mesothelial cells expressing a cancer-associated fibroblast-like transcriptomic program that may support cancer growth. CONCLUSIONS Our dataset presents the first unbiased assessment of breast cancer-associated MPEs at a single cell resolution, providing the community with a valuable resource for the study of MPEs. Our work highlights the molecular and cellular diversity captured in MPEs and motivates the potential use of these clinically relevant biopsies in the development of targeted therapeutics for patients with advanced breast cancer.
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Affiliation(s)
- Holly J. Whitfield
- Department of Medical Biology, The Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
| | - Jean Berthelet
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
- School of Cancer MedicineLa Trobe UniversityBundooraVictoriaAustralia
| | - Stefano Mangiola
- Department of Medical Biology, The Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
| | - Caroline Bell
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
- School of Cancer MedicineLa Trobe UniversityBundooraVictoriaAustralia
| | - Robin L. Anderson
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
- School of Cancer MedicineLa Trobe UniversityBundooraVictoriaAustralia
- Peter MacCallum Cancer CentreParkvilleVictoriaAustralia
- Department of Clinical Pathology, Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
| | - Bhupinder Pal
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
- School of Cancer MedicineLa Trobe UniversityBundooraVictoriaAustralia
| | - Belinda Yeo
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
- School of Cancer MedicineLa Trobe UniversityBundooraVictoriaAustralia
- Austin HealthHeidelbergVictoriaAustralia
| | - Anthony T. Papenfuss
- Department of Medical Biology, The Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Clinical Pathology, Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneCarltonVictoriaAustralia
| | - Delphine Merino
- Department of Medical Biology, The Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
- Olivia Newton‐John Cancer Research InstituteHeidelbergVictoriaAustralia
- School of Cancer MedicineLa Trobe UniversityBundooraVictoriaAustralia
- Immunology DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
| | - Melissa J. Davis
- Department of Medical Biology, The Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Clinical Pathology, Faculty of MedicineDentistry and Health Science, The University of MelbourneCarltonVictoriaAustralia
- The University of Queensland Diamantina InstituteThe University of QueenslandBrisbaneQueenslandAustralia
- The South Australian Immunogenomics Cancer InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
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13
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Hediyeh-Zadeh S, Webb AI, Davis MJ. MsImpute: Estimation of Missing Peptide Intensity Data in Label-Free Quantitative Mass Spectrometry. Mol Cell Proteomics 2023; 22:100558. [PMID: 37105364 PMCID: PMC10368900 DOI: 10.1016/j.mcpro.2023.100558] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 04/29/2023] Open
Abstract
Mass spectrometry (MS) enables high-throughput identification and quantification of proteins in complex biological samples and can provide insights into the global function of biological systems. Label-free quantification is cost-effective and suitable for the analysis of human samples. Despite rapid developments in label-free data acquisition workflows, the number of proteins quantified across samples can be limited by technical and biological variability. This variation can result in missing values which can in turn challenge downstream data analysis tasks. General purpose or gene expression-specific imputation algorithms are widely used to improve data completeness. Here, we propose an imputation algorithm designated for label-free MS data that is aware of the type of missingness affecting data. On published datasets acquired by data-dependent and data-independent acquisition workflows with variable degrees of biological complexity, we demonstrate that the proposed missing value estimation procedure by barycenter computation competes closely with the state-of-the-art imputation algorithms in differential abundance tasks while outperforming them in the accuracy of variance estimates of the peptide abundance measurements, and better controls the false discovery rate in label-free MS experiments. The barycenter estimation procedure is implemented in the msImpute software package and is available from the Bioconductor repository.
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Affiliation(s)
- Soroor Hediyeh-Zadeh
- Bioinformatics Division, WEHI, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia; Colonial Foundation Healthy Ageing Centre, WEHI, Melbourne, Australia
| | - Andrew I Webb
- Department of Medical Biology, University of Melbourne, Melbourne, Australia; Colonial Foundation Healthy Ageing Centre, WEHI, Melbourne, Australia; Advanced Technology and Biology Division, WEHI, Melbourne, Australia
| | - Melissa J Davis
- Bioinformatics Division, WEHI, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia; The Diamantina Institute, The University of Queensland, Brisbane, Australia; The South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia.
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14
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Mohamed A, Bhuva DD, Lee S, Liu N, Tan CW, Davis MJ. vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis. Nucleic Acids Res 2023:7157520. [PMID: 37158226 DOI: 10.1093/nar/gkad337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/13/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023] Open
Abstract
Gene-set analysis (GSA) dominates the functional interpretation of omics data and downstream hypothesis generation. Despite its ability to summarise thousands of measurements into semantically interpretable components, GSA often results in hundreds of significantly enriched gene-sets. However, summarisation and effective visualisation of GSA results to facilitate hypothesis generation is still lacking. While some webservers provide gene-set visualization tools, there is still a need for tools that can effectively summarize and guide exploration of GSA results. To enable versatility, webservers accept gene lists as input, however, none provide end-to-end solutions for emerging data types such as single-cell and spatial omics. Here, we present vissE.Cloud, a webserver for end-to-end gene-set analysis, offering gene-set summarisation and highly interactive visualisation. vissE.Cloud uses algorithms from our earlier R package vissE to summarise GSA results by identifying biological themes. We maintain versatility by allowing analysis of gene lists, as well as, analysis of raw single-cell and spatial omics data, including CosMx and Xenium data, making vissE.Cloud the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data. Structuring the results hierarchically allows swift interactive investigations of results at the gene, gene-set, and clusters level. vissE.Cloud is freely available at https://www.vissE.Cloud.
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Affiliation(s)
- Ahmed Mohamed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- Colonial Foundation Healthy Ageing Centre, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
| | - Dharmesh D Bhuva
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Sam Lee
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ning Liu
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Chin Wee Tan
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
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15
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Vo T, Balderson B, Jones K, Ni G, Crawford J, Millar A, Tolson E, Singleton M, Kojic M, Robertson T, Walters S, Mulay O, Bhuva DD, Davis MJ, Wainwright BJ, Nguyen Q, Genovesi LA. Spatial transcriptomic analysis of Sonic hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition. Genome Med 2023; 15:29. [PMID: 37127652 PMCID: PMC10150495 DOI: 10.1186/s13073-023-01185-4] [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: 07/06/2022] [Accepted: 04/20/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Medulloblastoma (MB) is a malignant tumour of the cerebellum which can be classified into four major subgroups based on gene expression and genomic features. Single-cell transcriptome studies have defined the cellular states underlying each MB subgroup; however, the spatial organisation of these diverse cell states and how this impacts response to therapy remains to be determined. METHODS Here, we used spatially resolved transcriptomics to define the cellular diversity within a sonic hedgehog (SHH) patient-derived model of MB and show that cells specific to a transcriptional state or spatial location are pivotal for CDK4/6 inhibitor, Palbociclib, treatment response. We integrated spatial gene expression with histological annotation and single-cell gene expression data from MB, developing an analysis strategy to spatially map cell type responses within the hybrid system of human and mouse cells and their interface within an intact brain tumour section. RESULTS We distinguish neoplastic and non-neoplastic cells within tumours and from the surrounding cerebellar tissue, further refining pathological annotation. We identify a regional response to Palbociclib, with reduced proliferation and induced neuronal differentiation in both treated tumours. Additionally, we resolve at a cellular resolution a distinct tumour interface where the tumour contacts neighbouring mouse brain tissue consisting of abundant astrocytes and microglia and continues to proliferate despite Palbociclib treatment. CONCLUSIONS Our data highlight the power of using spatial transcriptomics to characterise the response of a tumour to a targeted therapy and provide further insights into the molecular and cellular basis underlying the response and resistance to CDK4/6 inhibitors in SHH MB.
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Affiliation(s)
- Tuan Vo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Brad Balderson
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Kahli Jones
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Guiyan Ni
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Amanda Millar
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Elissa Tolson
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Matthew Singleton
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Marija Kojic
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Thomas Robertson
- Department of Pathology, Royal Brisbane and Women's Hospital, University of Queensland, Brisbane, QLD, 4029, Australia
| | - Shaun Walters
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Onkar Mulay
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dharmesh D Bhuva
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Faculty of Medicine, South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Melissa J Davis
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Faculty of Medicine, South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Brandon J Wainwright
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Laura A Genovesi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
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16
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Lonsdale A, Ceballos-Laita L, Takahashi D, Uemura M, Abadía J, Davis MJ, Bacic A, Doblin MS. LSPpred Suite: Tools for Leaderless Secretory Protein Prediction in Plants. Plants (Basel) 2023; 12:1428. [PMID: 37050054 PMCID: PMC10097205 DOI: 10.3390/plants12071428] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Plant proteins that are secreted without a classical signal peptide leader sequence are termed leaderless secretory proteins (LSPs) and are implicated in both plant development and (a)biotic stress responses. In plant proteomics experimental workflows, identification of LSPs is hindered by the possibility of contamination from other subcellar compartments upon purification of the secretome. Applying machine learning algorithms to predict LSPs in plants is also challenging due to the rarity of experimentally validated examples for training purposes. This work attempts to address this issue by establishing criteria for identifying potential plant LSPs based on experimental observations and training random forest classifiers on the putative datasets. The resultant plant protein database LSPDB and bioinformatic prediction tools LSPpred and SPLpred are available at lsppred.lspdb.org. The LSPpred and SPLpred modules are internally validated on the training dataset, with false positives controlled at 5%, and are also able to classify the limited number of established plant LSPs (SPLpred (3/4, LSPpred 4/4). Until such time as a larger set of bona fide (independently experimentally validated) LSPs is established using imaging technologies (light/fluorescence/electron microscopy) to confirm sub-cellular location, these tools represent a bridging method for predicting and identifying plant putative LSPs for subsequent experimental validation.
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Affiliation(s)
- Andrew Lonsdale
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Melissa J. Davis
- Bioinformatics, Walter and Eliza Hall Institute for Medical Research, Melbourne, VIC 3052, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Monika S. Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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17
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Kulasinghe A, Liu N, Tan CW, Monkman J, Sinclair JE, Bhuva DD, Godbolt D, Pan L, Nam A, Sadeghirad H, Sato K, Bassi GL, O'Byrne K, Hartmann C, Dos Santos Miggiolaro AFR, Marques GL, Moura LZ, Richard D, Adams M, de Noronha L, Baena CP, Suen JY, Arora R, Belz GT, Short KR, Davis MJ, Guimaraes FSF, Fraser JF. Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage. Immunology 2023; 168:403-419. [PMID: 36107637 PMCID: PMC9537957 DOI: 10.1111/imm.13577] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/16/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to present with pulmonary and extra-pulmonary organ complications. In comparison with the 2009 pandemic (pH1N1), SARS-CoV-2 infection is likely to lead to more severe disease, with multi-organ effects, including cardiovascular disease. SARS-CoV-2 has been associated with acute and long-term cardiovascular disease, but the molecular changes that govern this remain unknown. In this study, we investigated the host transcriptome landscape of cardiac tissues collected at rapid autopsy from seven SARS-CoV-2, two pH1N1, and six control patients using targeted spatial transcriptomics approaches. Although SARS-CoV-2 was not detected in cardiac tissue, host transcriptomics showed upregulation of genes associated with DNA damage and repair, heat shock, and M1-like macrophage infiltration in the cardiac tissues of COVID-19 patients. The DNA damage present in the SARS-CoV-2 patient samples, were further confirmed by γ-H2Ax immunohistochemistry. In comparison, pH1N1 showed upregulation of interferon-stimulated genes, in particular interferon and complement pathways, when compared with COVID-19 patients. These data demonstrate the emergence of distinct transcriptomic profiles in cardiac tissues of SARS-CoV-2 and pH1N1 influenza infection supporting the need for a greater understanding of the effects on extra-pulmonary organs, including the cardiovascular system of COVID-19 patients, to delineate the immunopathobiology of SARS-CoV-2 infection, and long term impact on health.
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Affiliation(s)
- Arutha Kulasinghe
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Ning Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - James Monkman
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Jane E Sinclair
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Dharmesh D Bhuva
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - David Godbolt
- Pathology Queensland, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Liuliu Pan
- Nanostring Technologies, Inc, Seattle, Washington, USA
| | - Andy Nam
- Nanostring Technologies, Inc, Seattle, Washington, USA
| | - Habib Sadeghirad
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Kei Sato
- Critical Care Research Group, Faculty of Medicine, University of Queensland and The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Gianluigi Li Bassi
- Critical Care Research Group, Faculty of Medicine, University of Queensland and The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Ken O'Byrne
- The Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Camila Hartmann
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | | | - Gustavo Lenci Marques
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | - Lidia Zytynski Moura
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | - Derek Richard
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Mark Adams
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | | | - Cristina Pellegrino Baena
- Pontifical Catholic University of Parana, Curitiba, Brazil.,Marcelino Champagnat Hospital, Curitiba, Brazil
| | - Jacky Y Suen
- Critical Care Research Group, Faculty of Medicine, University of Queensland and The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Rakesh Arora
- Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gabrielle T Belz
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Kirsty R Short
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | | | - John F Fraser
- Pathology Queensland, The Prince Charles Hospital, Chermside, Queensland, Australia
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18
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Shojaei M, Shamshirian A, Monkman J, Grice L, Tran M, Tan CW, Teo SM, Rodrigues Rossi G, McCulloch TR, Nalos M, Raei M, Razavi A, Ghasemian R, Gheibi M, Roozbeh F, Sly PD, Spann KM, Chew KY, Zhu Y, Xia Y, Wells TJ, Senegaglia AC, Kuniyoshi CL, Franck CL, dos Santos AFR, de Noronha L, Motamen S, Valadan R, Amjadi O, Gogna R, Madan E, Alizadeh-Navaei R, Lamperti L, Zuñiga F, Nova-Lamperti E, Labarca G, Knippenberg B, Herwanto V, Wang Y, Phu A, Chew T, Kwan T, Kim K, Teoh S, Pelaia TM, Kuan WS, Jee Y, Iredell J, O’Byrne K, Fraser JF, Davis MJ, Belz GT, Warkiani ME, Gallo CS, Souza-Fonseca-Guimaraes F, Nguyen Q, Mclean A, Kulasinghe A, Short KR, Tang B. IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational study. Front Immunol 2023; 13:1060438. [PMID: 36685600 PMCID: PMC9850159 DOI: 10.3389/fimmu.2022.1060438] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023] Open
Abstract
Purpose Robust biomarkers that predict disease outcomes amongst COVID-19 patients are necessary for both patient triage and resource prioritisation. Numerous candidate biomarkers have been proposed for COVID-19. However, at present, there is no consensus on the best diagnostic approach to predict outcomes in infected patients. Moreover, it is not clear whether such tools would apply to other potentially pandemic pathogens and therefore of use as stockpile for future pandemic preparedness. Methods We conducted a multi-cohort observational study to investigate the biology and the prognostic role of interferon alpha-inducible protein 27 (IFI27) in COVID-19 patients. Results We show that IFI27 is expressed in the respiratory tract of COVID-19 patients and elevated IFI27 expression in the lower respiratory tract is associated with the presence of a high viral load. We further demonstrate that the systemic host response, as measured by blood IFI27 expression, is associated with COVID-19 infection. For clinical outcome prediction (e.g., respiratory failure), IFI27 expression displays a high sensitivity (0.95) and specificity (0.83), outperforming other known predictors of COVID-19 outcomes. Furthermore, IFI27 is upregulated in the blood of infected patients in response to other respiratory viruses. For example, in the pandemic H1N1/09 influenza virus infection, IFI27-like genes were highly upregulated in the blood samples of severely infected patients. Conclusion These data suggest that prognostic biomarkers targeting the family of IFI27 genes could potentially supplement conventional diagnostic tools in future virus pandemics, independent of whether such pandemics are caused by a coronavirus, an influenza virus or another as yet-to-be discovered respiratory virus.
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Affiliation(s)
- Maryam Shojaei
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia,Department of Medicine, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Amir Shamshirian
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Grice
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia,School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Siok Min Teo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gustavo Rodrigues Rossi
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy R. McCulloch
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Marek Nalos
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Maedeh Raei
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Razavi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Roya Ghasemian
- Antimicrobial Resistance Research Centre, Department of Infectious Diseases, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mobina Gheibi
- Student Research Committee, School of Allied Medical Sciences, Mazandaran University of Medical Science, Sari, Iran
| | | | - Peter D. Sly
- Child Health Research Centre, The University of Queensland, South Brisbane, QLD, Australia
| | - Kirsten M. Spann
- Centre for Immunology and Infection Control, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yanshan Zhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yao Xia
- School of Science, Edith Cowan University; School of Biomedical Science, University of Western Australia, Perth, WA, Australia
| | - Timothy J. Wells
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Alexandra Cristina Senegaglia
- Complexo Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Brazil,Core for Cell Technology, School of Medicine, PontifìciaUniversidade Católica do Paraná, Curitiba, Brazil
| | - Carmen Lúcia Kuniyoshi
- Complexo Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Brazil,Core for Cell Technology, School of Medicine, PontifìciaUniversidade Católica do Paraná, Curitiba, Brazil
| | | | | | | | - Sepideh Motamen
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza Valadan
- Molecular and Cell Biology Research Centre, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran,Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Omolbanin Amjadi
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Rajan Gogna
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark,Novo Nordisk Foundation centre for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Esha Madan
- Campania Centre for the Unknown, Lisbon, Portugal
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Centre, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Liliana Lamperti
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile
| | - Felipe Zuñiga
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Gonzalo Labarca
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile,Faculty of Medicine, Universidad de Concepcion, Concepcion, Chile
| | - Ben Knippenberg
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Velma Herwanto
- Faculty of Medicine, Universitas Tarumanagara, Jakarta, Indonesia
| | - Ya Wang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia,Department of Medicine, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia
| | - Amy Phu
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Westmead Clinical School, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Tracy Chew
- Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, NSW, Australia
| | - Timothy Kwan
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Karan Kim
- Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Tiana M. Pelaia
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Win Sen Kuan
- Emergency Medicine Department, National University Hospital, National University Health System, Singapore, Singapore,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yvette Jee
- Emergency Medicine Department, National University Hospital, National University Health System, Singapore, Singapore
| | - Jon Iredell
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, NSW, Australia,Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Ken O’Byrne
- Queensland University of Technology, Centre for Genomics and PersonalisedHealth, School of Biomedical Sciences, Brisbane, QLD, Australia
| | - John F. Fraser
- Critical Care Research Group, The University of Queensland, Brisbane, QLD, Australia
| | - Melissa J. Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Gabrielle T. Belz
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Majid E. Warkiani
- Australia Centre for Health Technologies (CHT) & Institute for Biomedical Materials & Devices (IBMD), School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Carlos Salomon Gallo
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile,Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, The University of Queensland, Brisbane, QLD, Australia
| | | | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anthony Mclean
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia,*Correspondence: Arutha Kulasinghe, ; Kirsty R. Short, ; Maryam Shojaei,
| | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia
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19
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Kimothi D, Biyani P, Hogan JM, Davis MJ. Sequence Representations and Their Utility for Predicting Protein-Protein Interactions. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:646-657. [PMID: 34941517 DOI: 10.1109/tcbb.2021.3137325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein-Protein Interactions (PPIs) are a crucial mechanism underpinning the function of the cell. So far, a wide range of machine-learning based methods have been proposed for predicting these relationships. Their success is heavily dependent on the construction of the underlying feature vectors, with most using a set of physico-chemical properties derived from the sequence. Few work directly with the sequence itself. In this paper, we explore the utility of sequence embeddings for predicting protein-protein interactions. We construct a protein pair feature vector by concatenating the embeddings of their constituent sequence. These feature vectors are then used as input to a binary classifier to make predictions. To learn sequence embeddings, we use two established Word2Vec based methods - Seq2Vec and BioVec - and we also introduce a novel feature construction method called SuperVecNW. The embeddings generated through SuperVecNW capture some network information in addition to the contextual information present in the sequences. We test the efficacy of our proposed approach on human and yeast PPI datasets and on three well-known networks: CD9, the Ras-Raf-Mek-Erk-Elk-Srf pathway, and a Wnt-related network. We demonstrate that low dimensional sequence embeddings provide better results than most alternative representations based on physico-chemical properties while offering a far simple approach to feature vector construction.
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20
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Souza-Fonseca Guimaraes F, Rossi GR, Dagley LF, Foroutan M, McCulloch TR, Yousef J, Park HY, Gunter JH, Beavis PA, Lin CY, Hediyeh-Zadeh S, Camilleri T, Davis MJ, Huntington ND. TGF-β and CIS inhibition overcomes NK cell suppression to restore anti-tumor immunity. Cancer Immunol Res 2022; 10:1047-1054. [PMID: 35759796 DOI: 10.1158/2326-6066.cir-21-1052] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/21/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022]
Abstract
Antibodies targeting "immune checkpoints" have revolutionized cancer therapy by reactivating tumor-resident cytotoxic lymphocytes, primarily CD8+ T cells. Interest in targeting analogous pathways in other cytotoxic lymphocytes is growing. Natural killer (NK) cells are key to cancer immunosurveillance by eradicating metastases and driving solid tumor inflammation. NK cell anti-tumor function is dependent on the cytokine interleukin (IL)-15. Ablation of the IL-15 signaling inhibitor CIS (Cish) enhances NK cell anti-tumor immunity by increasing NK cell metabolism and persistence within the tumor microenvironment (TME). The TME has also been shown to impair NK cell fitness via the production of immunosuppressive TGF-β, a suppression which occurs even in the presence of high IL-15 signaling. Here, we identified an unexpected interaction between CIS and the TGF-β signaling pathway in NK cells. Independently, Cish- and Tgfbr2-deficient NK cells are both hyper-responsive to IL-15 and hypo-responsive to TGF-β, with dramatically enhanced anti-tumor immunity. Remarkably, when both these immunosuppressive genes are simultaneously deleted in NK cells, mice are largely resistant to tumor development, suggesting that combining suppression of these two pathways might represent a novel therapeutic strategy to enhance innate anti-cancer immunity.
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Affiliation(s)
| | | | - Laura F Dagley
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | | | | | - Jumana Yousef
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | | | | | - Paul A Beavis
- Peter MacCallum Cancer Research Centre, Melbourne, Victoria, Australia
| | - Cheng-Yu Lin
- University of Queensland, Woolloongabba, QLD, Australia
| | | | | | - Melissa J Davis
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
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21
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Gaik M, Kojic M, Stegeman MR, Öncü-Öner T, Kościelniak A, Jones A, Mohamed A, Chau PYS, Sharmin S, Chramiec-Głąbik A, Indyka P, Rawski M, Biela A, Dobosz D, Millar A, Chau V, Ünalp A, Piper M, Bellingham MC, Eichler EE, Nickerson DA, Güleryüz H, Abbassi NEH, Jazgar K, Davis MJ, Mercimek-Andrews S, Cingöz S, Wainwright BJ, Glatt S. Functional divergence of the two Elongator subcomplexes during neurodevelopment. EMBO Mol Med 2022; 14:e15608. [PMID: 35698786 PMCID: PMC9260213 DOI: 10.15252/emmm.202115608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/17/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022] Open
Abstract
The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have been reported in the catalytic Elp123 subcomplex, while no missense mutations in the accessory subcomplex Elp456 have been described. Here, we identify ELP4 and ELP6 variants in patients with developmental delay, epilepsy, intellectual disability, and motor dysfunction. We determine the structures of human and murine Elp456 subcomplexes and locate the mutated residues. We show that patient‐derived mutations in Elp456 affect the tRNA modification activity of Elongator in vitro as well as in human and murine cells. Modeling the pathogenic variants in mice recapitulates the clinical features of the patients and reveals neuropathology that differs from the one caused by previously characterized Elp123 mutations. Our study demonstrates a direct correlation between Elp4 and Elp6 mutations, reduced Elongator activity, and neurological defects. Foremost, our data indicate previously unrecognized differences of the Elp123 and Elp456 subcomplexes for individual tRNA species, in different cell types and in different key steps during the neurodevelopment of higher organisms.
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Affiliation(s)
- Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marija Kojic
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Megan R Stegeman
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Tülay Öncü-Öner
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ahmed Mohamed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Colonial Foundation Healthy Ageing Centre, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,The Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Pak Yan Stefanie Chau
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Sazia Sharmin
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Paulina Indyka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Amanda Millar
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Vann Chau
- Department of Paediatrics (Neurology), The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Aycan Ünalp
- Department of Pediatric Neurology, Dr. Behçet Uz Children's Hospital, İzmir, Turkey
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mark C Bellingham
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Handan Güleryüz
- Department of Pediatric Radiology, School of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Nour El Hana Abbassi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Konrad Jazgar
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Melissa J Davis
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,The Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia.,The Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Saadet Mercimek-Andrews
- The Hospital for Sick Children, Toronto, ON, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, The University of Alberta, Edmonton, AB, Canada
| | - Sultan Cingöz
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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22
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El-Saafin F, Bergamasco MI, Chen Y, May RE, Esakky P, Hediyeh-Zadeh S, Dixon M, Wilcox S, Davis MJ, Strasser A, Smyth GK, Thomas T, Voss AK. Loss of TAF8 causes TFIID dysfunction and p53-mediated apoptotic neuronal cell death. Cell Death Differ 2022; 29:1013-1027. [PMID: 35361962 PMCID: PMC9091217 DOI: 10.1038/s41418-022-00982-5] [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: 03/26/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/08/2022] Open
Abstract
Mutations in genes encoding general transcription factors cause neurological disorders. Despite clinical prominence, the consequences of defects in the basal transcription machinery during brain development are unclear. We found that loss of the TATA-box binding protein-associated factor TAF8, a component of the general transcription factor TFIID, in the developing central nervous system affected the expression of many, but notably not all genes. Taf8 deletion caused apoptosis, unexpectedly restricted to forebrain regions. Nuclear levels of the transcription factor p53 were elevated in the absence of TAF8, as were the mRNAs of the pro-apoptotic p53 target genes Noxa, Puma and Bax. The cell death in Taf8 forebrain regions was completely rescued by additional loss of p53, but Taf8 and p53 brains failed to initiate a neuronal expression program. Taf8 deletion caused aberrant transcription of promoter regions and splicing anomalies. We propose that TAF8 supports the directionality of transcription and co-transcriptional splicing, and that failure of these processes causes p53-induced apoptosis of neuronal cells in the developing mouse embryo.
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Affiliation(s)
- Farrah El-Saafin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Maria I Bergamasco
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yunshun Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rose E May
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
| | - Prabagaran Esakky
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Mathew Dixon
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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23
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Wang M, Zadeh S, Pizzolla A, Thia K, Gyorki DE, McArthur GA, Scolyer RA, Long G, Wilmott JS, Andrews MC, Au-Yeung G, Weppler A, Sandhu S, Trapani JA, Davis MJ, Neeson PJ. Characterization of the treatment-naive immune microenvironment in melanoma with BRAF mutation. J Immunother Cancer 2022; 10:jitc-2021-004095. [PMID: 35383113 PMCID: PMC8984014 DOI: 10.1136/jitc-2021-004095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Accepted: 03/14/2022] [Indexed: 12/13/2022] Open
Abstract
Background Patients with BRAF-mutant and wild-type melanoma have different response rates to immune checkpoint blockade therapy. However, the reasons for this remain unknown. To address this issue, we investigated the precise immune composition resulting from BRAF mutation in treatment-naive melanoma to determine whether this may be a driver for different response to immunotherapy. Methods In this study, we characterized the treatment-naive immune context in patients with BRAF-mutant and BRAF wild-type (BRAF-wt) melanoma using data from single-cell RNA sequencing, bulk RNA sequencing, flow cytometry and immunohistochemistry (IHC). Results In single-cell data, BRAF-mutant melanoma displayed a significantly reduced infiltration of CD8+ T cells and macrophages but also increased B cells, natural killer (NK) cells and NKT cells. We then validated this finding using bulk RNA-seq data from the skin cutaneous melanoma cohort in The Cancer Genome Atlas and deconvoluted the data using seven different algorithms. Interestingly, BRAF-mutant tumors had more CD4+ T cells than BRAF-wt samples in both primary and metastatic cohorts. In the metastatic cohort, BRAF-mutant melanoma demonstrated more B cells but less CD8+ T cell infiltration when compared with BRAF-wt samples. In addition, we further investigated the immune cell infiltrate using flow cytometry and multiplex IHC techniques. We confirmed that BRAF-mutant melanoma metastases were enriched for CD4+ T cells and B cells and had a co-existing decrease in CD8+ T cells. Furthermore, we then identified B cells were associated with a trend for improved survival (p=0.078) in the BRAF-mutant samples and Th2 cells were associated with prolonged survival in the BRAF-wt samples. Conclusions In conclusion, treatment-naive BRAF-mutant melanoma has a distinct immune context compared with BRAF-wt melanoma, with significantly decreased CD8+ T cells and increased B cells and CD4+ T cells in the tumor microenvironment. These findings indicate that further mechanistic studies are warranted to reveal how this difference in immune context leads to improved outcome to combination immune checkpoint blockade in BRAF-mutant melanoma.
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Affiliation(s)
- Minyu Wang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Soroor Zadeh
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Computing and Information Systems, University of Melbourne VCCC, Parkville, Victoria, Australia
| | - Angela Pizzolla
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin Thia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Centre for Cancer Immunotherapy, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David E Gyorki
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Richard A Scolyer
- The University of Sydney, Melanoma Institute Australia, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Georgina Long
- Melanoma Institute Australia, North Sydney, New South Wales, Australia.,Department of Medical Oncology, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Miles C Andrews
- Department of Medicine, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - George Au-Yeung
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ali Weppler
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Shahneen Sandhu
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa J Davis
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia .,Department of Computing and Information Systems, University of Melbourne VCCC, Parkville, Victoria, Australia
| | - Paul Joseph Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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24
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Hancock EJ, Zawieja SD, Macaskill C, Davis MJ, Bertram CD. Modelling the coupling of the M-clock and C-clock in lymphatic muscle cells. Comput Biol Med 2022; 142:105189. [PMID: 34995957 PMCID: PMC9132416 DOI: 10.1016/j.compbiomed.2021.105189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 10/17/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 01/01/2023]
Abstract
Chronic dysfunction of the lymphatic vascular system results in fluid accumulation between cells: lymphoedema. The condition is commonly acquired secondary to diseases such as cancer or the associated therapies. The primary driving force for fluid return through the lymphatic vasculature is provided by contractions of the muscularized lymphatic collecting vessels, driven by electrochemical oscillations. However, there is an incomplete understanding of the molecular and bioelectric mechanisms involved in lymphatic muscle cell excitation, hampering the development and use of pharmacological therapies. Modelling in silico has contributed greatly to understanding the contributions of specific ion channels to the cardiac action potential, but modelling of these processes in lymphatic muscle remains limited. Here, we propose a model of oscillations in the membrane voltage (M-clock) and intracellular calcium concentrations (C-clock) of lymphatic muscle cells. We modify a model by Imtiaz and colleagues to enable the M-clock to drive the C-clock oscillations. This approach differs from typical models of calcium oscillators in lymphatic and related cell types, but is required to fit recent experimental data. We include an additional voltage dependence in the gating variable control for the L-type calcium channel, enabling the M-clock to oscillate independently of the C-clock. We use phase-plane analysis to show that these M-clock oscillations are qualitatively similar to those of a generalised FitzHugh-Nagumo model. We also provide phase plane analysis to understand the interaction of the M-clock and C-clock oscillations. The model and methods have the potential to help determine mechanisms and find targets for pharmacological treatment of lymphoedema.
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Affiliation(s)
- E J Hancock
- School of Mathematics & Statistics, University of Sydney, NSW, 2006, Australia
| | - S D Zawieja
- Dept. of Medical Pharmacology & Physiology, Univ. of Missouri, Columbia, MI, 65212, USA
| | - C Macaskill
- School of Mathematics & Statistics, University of Sydney, NSW, 2006, Australia
| | - M J Davis
- Dept. of Medical Pharmacology & Physiology, Univ. of Missouri, Columbia, MI, 65212, USA
| | - C D Bertram
- School of Mathematics & Statistics, University of Sydney, NSW, 2006, Australia.
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25
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Elangovan A, Li Y, Pires DEV, Davis MJ, Verspoor K. Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. BMC Bioinformatics 2022; 23:4. [PMID: 34983371 PMCID: PMC8729035 DOI: 10.1186/s12859-021-04504-x] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
MOTIVATION Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. A range of protein functions are mediated and regulated by protein interactions through post-translational modifications (PTM). However, only 4% of PPIs are annotated with PTMs in biological knowledge databases such as IntAct, mainly performed through manual curation, which is neither time- nor cost-effective. Here we aim to facilitate annotation by extracting PPIs along with their pairwise PTM from the literature by using distantly supervised training data using deep learning to aid human curation. METHOD We use the IntAct PPI database to create a distant supervised dataset annotated with interacting protein pairs, their corresponding PTM type, and associated abstracts from the PubMed database. We train an ensemble of BioBERT models-dubbed PPI-BioBERT-x10-to improve confidence calibration. We extend the use of ensemble average confidence approach with confidence variation to counteract the effects of class imbalance to extract high confidence predictions. RESULTS AND CONCLUSION The PPI-BioBERT-x10 model evaluated on the test set resulted in a modest F1-micro 41.3 (P =5 8.1, R = 32.1). However, by combining high confidence and low variation to identify high quality predictions, tuning the predictions for precision, we retained 19% of the test predictions with 100% precision. We evaluated PPI-BioBERT-x10 on 18 million PubMed abstracts and extracted 1.6 million (546507 unique PTM-PPI triplets) PTM-PPI predictions, and filter [Formula: see text] (4584 unique) high confidence predictions. Of the 5700, human evaluation on a small randomly sampled subset shows that the precision drops to 33.7% despite confidence calibration and highlights the challenges of generalisability beyond the test set even with confidence calibration. We circumvent the problem by only including predictions associated with multiple papers, improving the precision to 58.8%. In this work, we highlight the benefits and challenges of deep learning-based text mining in practice, and the need for increased emphasis on confidence calibration to facilitate human curation efforts.
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Affiliation(s)
- Aparna Elangovan
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
| | - Yuan Li
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
| | - Douglas E. V. Pires
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
| | - Melissa J. Davis
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - Karin Verspoor
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
- School of Computing Technologies, RMIT University, Melbourne, Australia
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26
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Grisaru-Tal S, Dulberg S, Beck L, Zhang C, Itan M, Hediyeh-Zadeh S, Caldwell J, Rozenberg P, Dolitzky A, Avlas S, Hazut I, Gordon Y, Shani O, Tsuriel S, Gerlic M, Erez N, Jacquelot N, Belz GT, Rothenberg ME, Davis MJ, Yu H, Geiger T, Madi A, Munitz A. Metastasis-Entrained Eosinophils Enhance Lymphocyte-Mediated Antitumor Immunity. Cancer Res 2021; 81:5555-5571. [PMID: 34429328 DOI: 10.1158/0008-5472.can-21-0839] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/09/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022]
Abstract
The recognition of the immune system as a key component of the tumor microenvironment (TME) led to promising therapeutics. Because such therapies benefit only subsets of patients, understanding the activities of immune cells in the TME is required. Eosinophils are an integral part of the TME especially in mucosal tumors. Nonetheless, their role in the TME and the environmental cues that direct their activities are largely unknown. We report that breast cancer lung metastases are characterized by resident and recruited eosinophils. Eosinophil recruitment to the metastatic sites in the lung was regulated by G protein-coupled receptor signaling but independent of CCR3. Functionally, eosinophils promoted lymphocyte-mediated antitumor immunity. Transcriptome and proteomic analyses identified the TME rather than intrinsic differences between eosinophil subsets as a key instructing factor directing antitumorigenic eosinophil activities. Specifically, TNFα/IFNγ-activated eosinophils facilitated CD4+ and CD8+ T-cell infiltration and promoted antitumor immunity. Collectively, we identify a mechanism by which the TME trains eosinophils to adopt antitumorigenic properties, which may lead to the development of eosinophil-targeted therapeutics. SIGNIFICANCE: These findings demonstrate antitumor activities of eosinophils in the metastatic tumor microenvironment, suggesting that harnessing eosinophil activity may be a viable clinical strategy in patients with cancer.
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Affiliation(s)
- Sharon Grisaru-Tal
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shai Dulberg
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lir Beck
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chunyan Zhang
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Michal Itan
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Julie Caldwell
- Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Perri Rozenberg
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Avishay Dolitzky
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shmuel Avlas
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Inbal Hazut
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yaara Gordon
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ophir Shani
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shlomo Tsuriel
- Institute of Pathology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Neta Erez
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nicolas Jacquelot
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne VIC, Australia.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Gabrielle T Belz
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia.,The University of Queensland Diamantina Institute, Brisbane, Queensland, Australia
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Hua Yu
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Madi
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Munitz
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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27
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Kulasinghe A, Tan CW, Dos Santos Miggiolaro AFR, Monkman J, SadeghiRad H, Bhuva DD, da Silva Motta Junior J, Vaz de Paula CB, Nagashima S, Baena CP, Souza-Fonseca-Guimaraes P, de Noronha L, McCulloch T, Rodrigues Rossi G, Cooper C, Tang B, Short KR, Davis MJ, Souza-Fonseca-Guimaraes F, Belz GT, O'Byrne K. Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures. Eur Respir J 2021; 59:13993003.01881-2021. [PMID: 34675048 PMCID: PMC8542865 DOI: 10.1183/13993003.01881-2021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 01/07/2021] [Accepted: 10/07/2021] [Indexed: 01/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). A better definition of the pulmonary host response to SARS-CoV-2 infection is required to understand viral pathogenesis and to validate putative COVID-19 biomarkers that have been proposed in clinical studies. Here, we use targeted transcriptomics of FFPE tissue using the Nanostring GeoMX™ platform to generate an in-depth picture of the pulmonary transcriptional landscape of COVID-19, pandemic H1N1 influenza and uninfected control patients. Host transcriptomics showed a significant upregulation of genes associated with inflammation, type I interferon production, coagulation and angiogenesis in the lungs of COVID-19 patients compared to non-infected controls. SARS-CoV-2 was non-uniformly distributed in lungs (emphasising the advantages of spatial transcriptomics) with the areas of high viral load associated with an increased type I interferon response. Once the dominant cell type present in the sample, within patient correlations and patient-patient variation had been controlled for, only a very limited number of genes were differentially expressed between the lungs of fatal influenza and COVID-19 patients. Strikingly, the interferon-associated gene IFI27, previously identified as a useful blood biomarker to differentiate bacterial and viral lung infections, was significantly upregulated in the lungs of COVID-19 patients compared to patients with influenza. Collectively, these data demonstrate that spatial transcriptomics is a powerful tool to identify novel gene signatures within tissues, offering new insights into the pathogenesis of SARS-COV-2 to aid in patient triage and treatment.
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Affiliation(s)
- Arutha Kulasinghe
- Queensland University of Technology, School of Biomedical Sciences, Faculty of Health, Brisbane, Queensland, Australia .,Translational Research Institute, Brisbane, Queensland, Australia.,University of Queensland Diamantina Institute, University of Queensland, Woollongabba, Queensland, Australia.,co-first authors
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia.,co-first authors
| | - Anna Flavia Ribeiro Dos Santos Miggiolaro
- Postgraduate Program of Health Sciences - School of Medicine - Hospital Marcelino Champagnat - Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil.,co-first authors
| | - James Monkman
- Queensland University of Technology, School of Biomedical Sciences, Faculty of Health, Brisbane, Queensland, Australia.,Translational Research Institute, Brisbane, Queensland, Australia
| | - Habib SadeghiRad
- Queensland University of Technology, School of Biomedical Sciences, Faculty of Health, Brisbane, Queensland, Australia.,Translational Research Institute, Brisbane, Queensland, Australia
| | - Dharmesh D Bhuva
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Jarbas da Silva Motta Junior
- Postgraduate Program of Health Sciences - School of Medicine - Hospital Marcelino Champagnat - Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil
| | - Caroline Busatta Vaz de Paula
- Postgraduate Program of Health Sciences - School of Medicine - Hospital Marcelino Champagnat - Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil
| | - Seigo Nagashima
- Postgraduate Program of Health Sciences - School of Medicine - Hospital Marcelino Champagnat - Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil
| | - Cristina Pellegrino Baena
- School of Medicine & Center of Education, Research and Innovation - Hospital Marcelino Champagnat - Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Brazil
| | - Paulo Souza-Fonseca-Guimaraes
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Lucia de Noronha
- Laboratory of Experimental Pathology - School of Medicine - Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Brazil
| | - Timothy McCulloch
- Translational Research Institute, Brisbane, Queensland, Australia.,University of Queensland Diamantina Institute, University of Queensland, Woollongabba, Queensland, Australia
| | - Gustavo Rodrigues Rossi
- Translational Research Institute, Brisbane, Queensland, Australia.,University of Queensland Diamantina Institute, University of Queensland, Woollongabba, Queensland, Australia
| | - Caroline Cooper
- Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.,University of Queensland, Faculty of Medicine, Woolloongabba, Queensland, Australia
| | - Benjamin Tang
- Centre for Immunology and Allergy Research, the Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Kirsty R Short
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,co-senior authors
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, VIC, Australia.,co-senior authors
| | - Fernando Souza-Fonseca-Guimaraes
- Translational Research Institute, Brisbane, Queensland, Australia.,University of Queensland Diamantina Institute, University of Queensland, Woollongabba, Queensland, Australia.,co-senior authors
| | - Gabrielle T Belz
- Translational Research Institute, Brisbane, Queensland, Australia.,University of Queensland Diamantina Institute, University of Queensland, Woollongabba, Queensland, Australia.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,co-senior authors
| | - Ken O'Byrne
- Queensland University of Technology, School of Biomedical Sciences, Faculty of Health, Brisbane, Queensland, Australia.,Translational Research Institute, Brisbane, Queensland, Australia.,co-senior authors
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28
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Yao B, Gui T, Zeng X, Deng Y, Wang Z, Wang Y, Yang D, Li Q, Xu P, Hu R, Li X, Chen B, Wang J, Zen K, Li H, Davis MJ, Herold MJ, Pan HF, Jiang ZW, Huang DCS, Liu M, Ju J, Zhao Q. Correction to: PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling. Genome Med 2021; 13:154. [PMID: 34607606 PMCID: PMC8491380 DOI: 10.1186/s13073-021-00966-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Bing Yao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.,Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Tao Gui
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xiangwei Zeng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Yexuan Deng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Zhi Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Dongjun Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Qixiang Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Peipei Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ruifeng Hu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xinyu Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Bing Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Jin Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ke Zen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Hua-Feng Pan
- Department of General Surgery, the Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi-Wei Jiang
- Department of General Surgery, the Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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Koldej RM, Prabahran A, Tan CW, Ng AP, Davis MJ, Ritchie DS. Dissection of the bone marrow microenvironment in hairy cell leukaemia identifies prognostic tumour and immune related biomarkers. Sci Rep 2021; 11:19056. [PMID: 34561502 PMCID: PMC8463612 DOI: 10.1038/s41598-021-98536-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
Hairy cell leukaemia (HCL) is a rare CD20+ B cell malignancy characterised by rare "hairy" B cells and extensive bone marrow (BM) infiltration. Frontline treatment with the purine analogue cladribine (CDA) results in a highly variable response duration. We hypothesised that analysis of the BM tumour microenvironment would identify prognostic biomarkers of response to CDA. HCL BM immunology pre and post CDA treatment and healthy controls were analysed using Digital Spatial Profiling to assess the expression of 57 proteins using an immunology panel. A bioinformatics pipeline was developed to accommodate the more complex experimental design of a spatially resolved study. Treatment with CDA was associated with the reduction in expression of HCL tumour markers (CD20, CD11c) and increased expression of myeloid markers (CD14, CD68, CD66b, ARG1). Expression of HLA-DR, STING, CTLA4, VISTA, OX40L were dysregulated pre- and post-CDA. Duration of response to treatment was associated with greater reduction in tumour burden and infiltration by CD8 T cells into the BM post-CDA. This is the first study to provide a high multiplex analysis of HCL BM microenvironment demonstrating significant immune dysregulation and identify biomarkers of response to CDA. With validation in future studies, prospective application of these biomarkers could allow early identification and increased monitoring in patients at increased relapse risk post CDA.
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Affiliation(s)
- Rachel M Koldej
- ACRF Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, Australia.
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.
| | - Ashvind Prabahran
- ACRF Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Ashley P Ng
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - David S Ritchie
- ACRF Translational Research Laboratory, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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30
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Adolphe C, Millar A, Kojic M, Barkauskas DS, Sundström A, Swartling FJ, Hediyeh-Zadeh S, Tan CW, Davis MJ, Genovesi LA, Wainwright BJ. SOX9 Defines Distinct Populations of Cells in SHH Medulloblastoma but Is Not Required for Math1-Driven Tumor Formation. Mol Cancer Res 2021; 19:1831-1839. [PMID: 34330843 DOI: 10.1158/1541-7786.mcr-21-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/18/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
Medulloblastoma is the most common malignant pediatric brain tumor and there is an urgent need for molecularly targeted and subgroup-specific therapies. The stem cell factor SOX9, has been proposed as a potential therapeutic target for the treatment of Sonic Hedgehog medulloblastoma (SHH-MB) subgroup tumors, given its role as a downstream target of Hedgehog signaling and in functionally promoting SHH-MB metastasis and treatment resistance. However, the functional requirement for SOX9 in the genesis of medulloblastoma remains to be determined. Here we report a previously undocumented level of SOX9 expression exclusively in proliferating granule cell precursors (GCP) of the postnatal mouse cerebellum, which function as the medulloblastoma-initiating cells of SHH-MBs. Wild-type GCPs express comparatively lower levels of SOX9 than neural stem cells and mature astroglia and SOX9low GCP-like tumor cells constitute the bulk of both infant (Math1Cre:Ptch1lox/lox ) and adult (Ptch1LacZ/+ ) SHH-MB mouse models. Human medulloblastoma single-cell RNA data analyses reveal three distinct SOX9 populations present in SHH-MB and noticeably absent in other medulloblastoma subgroups: SOX9 + MATH1 + (GCP), SOX9 + GFAP + (astrocytes) and SOX9 + MATH1 + GFAP + (potential tumor-derived astrocytes). To functionally address whether SOX9 is required as a downstream effector of Hedgehog signaling in medulloblastoma tumor cells, we ablated Sox9 using a Math1Cre model system. Surprisingly, targeted ablation of Sox9 in GCPs (Math1Cre:Sox9lox/lox ) revealed no overt phenotype and loss of Sox9 in SHH-MB (Math1Cre:Ptch1lox/lox;Sox9lox/lox ) does not affect tumor formation. IMPLICATIONS: Despite preclinical data indicating SOX9 plays a key role in SHH-MB biology, our data argue against SOX9 as a viable therapeutic target.
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Affiliation(s)
- Christelle Adolphe
- The University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Amanda Millar
- The University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Marija Kojic
- The University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Deborah S Barkauskas
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Anders Sundström
- Department of Immunology, Genetics, and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik J Swartling
- Department of Immunology, Genetics, and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Victoria, Australia
| | - Chin Wee Tan
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Victoria, Australia
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Victoria, Australia
| | - Laura A Genovesi
- The University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia.
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31
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Sharma S, Chung J, Uryu S, Rickard A, Nady N, Khan S, Wang Z, Zhang Y, Zhang H, Kung PP, Greenwald E, Maegley K, Bingham P, Lam H, Bozikis YE, Falk H, Allan E, Avery VM, Butler MS, Camerino MA, Carrasco-Pozo C, Charman SA, Davis MJ, Dawson MA, Sarah-Jane D, de Silva M, Dennis ML, Dolezal O, Lagiakos R, Lindeman GJ, MacPherson L, Nuttall S, Peat TS, Ren B, Stupple AE, Surgenor E, Tan CW, Thomas T, Visvader JE, Voss AK, Vaillant F, White KL, Whittle J, Yang Y, Hediyeh-Zadeh S, Stupple PA, Street IP, Monahan BJ, Paul T. Abstract 1130: First-in-class KAT6A/KAT6B inhibitor CTx-648 (PF-9363) demonstrates potent anti-tumor activity in ER+ breast cancer with KAT6A dysregulation. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1130] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
KAT6A is a lysine histone acetyltransferase (HAT) of the MYST family of HATs. KAT6A, and its paralog KAT6B, have been shown to acetylate histone H3K23Ac and regulate diverse biological processes, including transcription, cell-cycle progression, stem cell maintenance and development. Molecular dysregulation of KAT6A has been observed in several cancers, including amplifications in breast, lung, ovarian cancer along with oncogenic fusions in AML. In breast cancer, KAT6A is amplified as part of the 8p11 amplicon in 10-15% of the patient population, which correlates with a worse clinical outcome in the estrogen receptor+ (ER+) subtype. Here we present identification of a first-in-class potent KAT6A/KAT6B tool inhibitor CTx-648 (PF-9363), that possesses high selectivity versus other MYST family members (KAT7, KAT5, KAT8) and other KATs, demonstrating anti-tumor activity in breast cancer. Using genetic and pharmacological approaches, we have demonstrated several ER+ breast cancer cell lines including KAT6A amplified and over-expressing models, are dependent on KAT6A enzymatic function. Epigenomic profiling studies using bulk and nascent RNA-seq combined with ATAC-seq revealed CTx-648 leads to downregulation of a specific set of genes involved in ESR1 pathway, cell cycle and stem cell pathways. In vivo target validation studies showed strong anti-tumor activity of CTx-648 in several ER+ breast cancer cell line and patient-derived xenograft models, including models harboring endocrine therapy resistance ESR1 mutations, highlighting promise for this novel therapy in ER+ breast cancer population. Based on the strength of the pre-clinical data, a selective KAT6 inhibitor (PF-07248144) is now commencing a Phase 1 clinical study in Advanced or Metastatic Solid Tumors.
Citation Format: Shikhar Sharma, Jay Chung, Sean Uryu, Amanda Rickard, Natalie Nady, Showkhin Khan, Zhenxiong Wang, Yong Zhang, Haikuo Zhang, Pei-Pei Kung, Eric Greenwald, Karen Maegley, Patrick Bingham, Hieu Lam, Ylva E. Bozikis, Hendrik Falk, Elizabeth Allan, Vicky M. Avery, Miriam S. Butler, Michelle A. Camerino, Catalina Carrasco-Pozo, Susan A. Charman, Melissa J. Davis, Mark A. Dawson, Dawson Sarah-Jane, Melanie de Silva, Matthew L. Dennis, Olan Dolezal, Rachel Lagiakos, Geoffrey J. Lindeman, Laura MacPherson, Stewart Nuttall, Thomas S. Peat, Bin Ren, Alexandra E. Stupple, Elliot Surgenor, Chin Wee Tan, Tim Thomas, Jane E. Visvader, Anne K. Voss, Francois Vaillant, Karen L. White, James Whittle, Yuqing Yang, Soroor Hediyeh-Zadeh, Paul A. Stupple, Ian P. Street, Brendon J. Monahan, Thomas Paul. First-in-class KAT6A/KAT6B inhibitor CTx-648 (PF-9363) demonstrates potent anti-tumor activity in ER+ breast cancer with KAT6A dysregulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1130.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Melissa J. Davis
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Mark A. Dawson
- 4The Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Melanie de Silva
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Matthew L. Dennis
- 7Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Australia
| | - Olan Dolezal
- 7Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Australia
| | - Rachel Lagiakos
- 7Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Australia
| | | | | | - Stewart Nuttall
- 7Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Australia
| | - Thomas S. Peat
- 7Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Australia
| | - Bin Ren
- 7Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Australia
| | | | - Elliot Surgenor
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Chin Wee Tan
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Tim Thomas
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jane E. Visvader
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Anne K. Voss
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Francois Vaillant
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | - James Whittle
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Yuqing Yang
- 6The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | - Paul A. Stupple
- 9Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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32
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Berthelet J, Wimmer VC, Whitfield HJ, Serrano A, Boudier T, Mangiola S, Merdas M, El-Saafin F, Baloyan D, Wilcox J, Wilcox S, Parslow AC, Papenfuss AT, Yeo B, Ernst M, Pal B, Anderson RL, Davis MJ, Rogers KL, Hollande F, Merino D. The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile. Sci Adv 2021; 7:eabf4408. [PMID: 34233875 PMCID: PMC8262813 DOI: 10.1126/sciadv.abf4408] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/25/2021] [Indexed: 05/03/2023]
Abstract
Intratumoral heterogeneity is a driver of breast cancer progression, but the nature of the clonal interactive network involved in this process remains unclear. Here, we optimized the use of optical barcoding to visualize and characterize 31 cancer subclones in vivo. By mapping the clonal composition of thousands of metastases in two clinically relevant sites, the lungs and liver, we found that metastases were highly polyclonal in lungs but not in the liver. Furthermore, the transcriptome of the subclones varied according to their metastatic niche. We also identified a reversible niche-driven signature that was conserved in lung and liver metastases collected during patient autopsies. Among this signature, we found that the tumor necrosis factor-α pathway was up-regulated in lung compared to liver metastases, and inhibition of this pathway affected metastasis diversity. These results highlight that the cellular and molecular heterogeneity observed in metastases is largely dictated by the tumor microenvironment.
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Affiliation(s)
- Jean Berthelet
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Verena C Wimmer
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Holly J Whitfield
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Antonin Serrano
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Thomas Boudier
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Stefano Mangiola
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Michal Merdas
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Farrah El-Saafin
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - David Baloyan
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jordan Wilcox
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Steven Wilcox
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Adam C Parslow
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Anthony T Papenfuss
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Belinda Yeo
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
- Austin Health, Heidelberg, VIC 3084, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Bhupinder Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Melissa J Davis
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Kelly L Rogers
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Frédéric Hollande
- Department of Clinical Pathology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Melbourne, VIC 3000, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Delphine Merino
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry, and Health Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
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33
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Jacquelot N, Seillet C, Wang M, Pizzolla A, Liao Y, Hediyeh-Zadeh S, Grisaru-Tal S, Louis C, Huang Q, Schreuder J, Souza-Fonseca-Guimaraes F, de Graaf CA, Thia K, Macdonald S, Camilleri M, Luong K, Zhang S, Chopin M, Molden-Hauer T, Nutt SL, Umansky V, Ciric B, Groom JR, Foster PS, Hansbro PM, McKenzie ANJ, Gray DHD, Behren A, Cebon J, Vivier E, Wicks IP, Trapani JA, Munitz A, Davis MJ, Shi W, Neeson PJ, Belz GT. Blockade of the co-inhibitory molecule PD-1 unleashes ILC2-dependent antitumor immunity in melanoma. Nat Immunol 2021; 22:851-864. [PMID: 34099918 PMCID: PMC7611091 DOI: 10.1038/s41590-021-00943-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/26/2021] [Indexed: 01/17/2023]
Abstract
Group 2 innate lymphoid cells (ILC2s) are essential to maintain tissue homeostasis. In cancer, ILC2s can harbor both pro-tumorigenic and anti-tumorigenic functions, but we know little about their underlying mechanisms or whether they could be clinically relevant or targeted to improve patient outcomes. Here, we found that high ILC2 infiltration in human melanoma was associated with a good clinical prognosis. ILC2s are critical producers of the cytokine granulocyte-macrophage colony-stimulating factor, which coordinates the recruitment and activation of eosinophils to enhance antitumor responses. Tumor-infiltrating ILC2s expressed programmed cell death protein-1, which limited their intratumoral accumulation, proliferation and antitumor effector functions. This inhibition could be overcome in vivo by combining interleukin-33-driven ILC2 activation with programmed cell death protein-1 blockade to significantly increase antitumor responses. Together, our results identified ILC2s as a critical immune cell type involved in melanoma immunity and revealed a potential synergistic approach to harness ILC2 function for antitumor immunotherapies.
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Affiliation(s)
- Nicolas Jacquelot
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
| | - Cyril Seillet
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Minyu Wang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Angela Pizzolla
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yang Liao
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Victoria, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sharon Grisaru-Tal
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Cynthia Louis
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Qiutong Huang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Jaring Schreuder
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
| | | | - Carolyn A de Graaf
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin Thia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sean Macdonald
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Mary Camilleri
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kylie Luong
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Shengbo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Chopin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Tristan Molden-Hauer
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Viktor Umansky
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
| | - Bogoljub Ciric
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Joanna R Groom
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul S Foster
- Priority Research Centres for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, New South Wales, Australia
| | - Philip M Hansbro
- Priority Research Centres for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, New South Wales, Australia
- Centre for Inflammation, Centenary Institute, Sydney, New South Wales, Australia
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | | | - Daniel H D Gray
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Victoria, Australia
- Department of Medicine, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Victoria, Australia
- Department of Medicine, The University of Melbourne, Melbourne, Victoria, Australia
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Melbourne, Victoria, Australia
| | - Eric Vivier
- Innate Pharma Research Labs, Marseille, France
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France
- Service d'Immunologie, Marseille Immunopole, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Ian P Wicks
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Rheumatology Unit, Royal Melbourne Hospital, Melbourne, Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ariel Munitz
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Victoria, Australia
- Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul J Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gabrielle T Belz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
- The University of Queensland Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia.
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34
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Huckstep H, Fearnley LG, Davis MJ. Measuring pathway database coverage of the phosphoproteome. PeerJ 2021; 9:e11298. [PMID: 34113485 PMCID: PMC8162239 DOI: 10.7717/peerj.11298] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry based phosphoproteomics in the last decade. However, data saturation is occurring and the bottleneck of assigning biologically relevant functionality to phosphosites needs to be addressed. There has been finite success in using data-driven approaches to reveal phosphosite functionality due to a range of limitations. The alternate, more suitable approach is making use of prior knowledge from literature-derived databases. Here, we analysed seven widely used databases to shed light on their suitability to provide functional insights into phosphoproteomics data. We first determined the global coverage of each database at both the protein and phosphosite level. We also determined how consistent each database was in its phosphorylation annotations compared to a global standard. Finally, we looked in detail at the coverage of each database over six experimental datasets. Our analysis highlights the relative strengths and weaknesses of each database, providing a guide in how each can be best used to identify biological mechanisms in phosphoproteomic data.
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Affiliation(s)
- Hannah Huckstep
- Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Liam G. Fearnley
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Division of Population Health, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Melissa J. Davis
- Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
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35
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Emery-Corbin SJ, Hamey JJ, Ansell BRE, Balan B, Tichkule S, Stroehlein AJ, Cooper C, McInerney BV, Hediyeh-Zadeh S, Vuong D, Crombie A, Lacey E, Davis MJ, Wilkins MR, Bahlo M, Svärd SG, Gasser RB, Jex AR. Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia. Mol Biol Evol 2021; 37:3525-3549. [PMID: 32702104 PMCID: PMC7743719 DOI: 10.1093/molbev/msaa186] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis-a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.
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Affiliation(s)
- Samantha J Emery-Corbin
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Swapnil Tichkule
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Crystal Cooper
- Central Analytical Research Facility (CARF), Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Bernie V McInerney
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW, Australia
| | - Soroor Hediyeh-Zadeh
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Andrew Crombie
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, Australia.,Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia
| | - Melissa J Davis
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
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36
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Kojic M, Gawda T, Gaik M, Begg A, Salerno-Kochan A, Kurniawan ND, Jones A, Drożdżyk K, Kościelniak A, Chramiec-Głąbik A, Hediyeh-Zadeh S, Kasherman M, Shim WJ, Sinniah E, Genovesi LA, Abrahamsen RK, Fenger CD, Madsen CG, Cohen JS, Fatemi A, Stark Z, Lunke S, Lee J, Hansen JK, Boxill MF, Keren B, Marey I, Saenz MS, Brown K, Alexander SA, Mureev S, Batzilla A, Davis MJ, Piper M, Bodén M, Burne THJ, Palpant NJ, Møller RS, Glatt S, Wainwright BJ. Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nat Commun 2021; 12:2678. [PMID: 33976153 PMCID: PMC8113450 DOI: 10.1038/s41467-021-22888-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are the most common neurodevelopmental disorders and are characterized by substantial impairment in intellectual and adaptive functioning, with their genetic and molecular basis remaining largely unknown. Here, we identify biallelic variants in the gene encoding one of the Elongator complex subunits, ELP2, in patients with ID and ASD. Modelling the variants in mice recapitulates the patient features, with brain imaging and tractography analysis revealing microcephaly, loss of white matter tract integrity and an aberrant functional connectome. We show that the Elp2 mutations negatively impact the activity of the complex and its function in translation via tRNA modification. Further, we elucidate that the mutations perturb protein homeostasis leading to impaired neurogenesis, myelin loss and neurodegeneration. Collectively, our data demonstrate an unexpected role for tRNA modification in the pathogenesis of monogenic ID and ASD and define Elp2 as a key regulator of brain development.
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Affiliation(s)
- Marija Kojic
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Tomasz Gawda
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alexander Begg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anna Salerno-Kochan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Nyoman D Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katarzyna Drożdżyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Maria Kasherman
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Laura A Genovesi
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rannvá K Abrahamsen
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Camilla G Madsen
- Centre for Functional and Diagnostic Imaging and Research, Hvidovre Hospital, Hvidovre, Denmark
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zornitza Stark
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Joy Lee
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Department of Metabolic Medicine, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jonas K Hansen
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Martin F Boxill
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Boris Keren
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Isabelle Marey
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Margarita S Saenz
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Kathleen Brown
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Suzanne A Alexander
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Sergey Mureev
- CSIRO-QUT Synthetic Biology Alliance, Centre for Tropical Crops and Bio-commodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Alina Batzilla
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- The Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Department for Regional Health Research, The University of Southern Denmark, Odense, Denmark
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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37
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Jolly MK, Murphy RJ, Bhatia S, Whitfield HJ, Redfern A, Davis MJ, Thompson EW. Measuring and Modelling the Epithelial- Mesenchymal Hybrid State in Cancer: Clinical Implications. Cells Tissues Organs 2021; 211:110-133. [PMID: 33902034 DOI: 10.1159/000515289] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 11/19/2022] Open
Abstract
The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.
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Affiliation(s)
- Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Ryan J Murphy
- Queensland University of Technology, School of Mathematical Sciences, Brisbane, Queensland, Australia
| | - Sugandha Bhatia
- Queensland University of Technology, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Brisbane, Queensland, Australia.,Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Holly J Whitfield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Redfern
- Department of Medicine, School of Medicine, University of Western Australia, Fiona Stanley Hospital Campus, Perth, Washington, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Erik W Thompson
- Queensland University of Technology, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Brisbane, Queensland, Australia.,Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia
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38
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Yao B, Gui T, Zeng X, Deng Y, Wang Z, Wang Y, Yang D, Li Q, Xu P, Hu R, Li X, Chen B, Wang J, Zen K, Li H, Davis MJ, Herold MJ, Pan HF, Jiang ZW, Huang DCS, Liu M, Ju J, Zhao Q. PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling. Genome Med 2021; 13:58. [PMID: 33853662 PMCID: PMC8048298 DOI: 10.1186/s13073-021-00871-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [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: 02/13/2020] [Accepted: 03/17/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Aberrant changes in epigenetic mechanisms such as histone modifications play an important role in cancer progression. PRMT1 which triggers asymmetric dimethylation of histone H4 on arginine 3 (H4R3me2a) is upregulated in human colorectal cancer (CRC) and is essential for cell proliferation. However, how this dysregulated modification might contribute to malignant transitions of CRC remains poorly understood. METHODS In this study, we integrated biochemical assays including protein interaction studies and chromatin immunoprecipitation (ChIP), cellular analysis including cell viability, proliferation, colony formation, and migration assays, clinical sample analysis, microarray experiments, and ChIP-Seq data to investigate the potential genomic recognition pattern of H4R3me2s in CRC cells and its effect on CRC progression. RESULTS We show that PRMT1 and SMARCA4, an ATPase subunit of the SWI/SNF chromatin remodeling complex, act cooperatively to promote colorectal cancer (CRC) progression. We find that SMARCA4 is a novel effector molecule of PRMT1-mediated H4R3me2a. Mechanistically, we show that H4R3me2a directly recruited SMARCA4 to promote the proliferative, colony-formative, and migratory abilities of CRC cells by enhancing EGFR signaling. We found that EGFR and TNS4 were major direct downstream transcriptional targets of PRMT1 and SMARCA4 in colon cells, and acted in a PRMT1 methyltransferase activity-dependent manner to promote CRC cell proliferation. In vivo, knockdown or inhibition of PRMT1 profoundly attenuated the growth of CRC cells in the C57BL/6 J-ApcMin/+ CRC mice model. Importantly, elevated expression of PRMT1 or SMARCA4 in CRC patients were positively correlated with expression of EGFR and TNS4, and CRC patients had shorter overall survival. These findings reveal a critical interplay between epigenetic and transcriptional control during CRC progression, suggesting that SMARCA4 is a novel key epigenetic modulator of CRC. Our findings thus highlight PRMT1/SMARCA4 inhibition as a potential therapeutic intervention strategy for CRC. CONCLUSION PRMT1-mediated H4R3me2a recruits SMARCA4, which promotes colorectal cancer progression by enhancing EGFR signaling.
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Affiliation(s)
- Bing Yao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.,Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Tao Gui
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xiangwei Zeng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Yexuan Deng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Zhi Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Dongjun Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Qixiang Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Peipei Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ruifeng Hu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xinyu Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Bing Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Jin Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ke Zen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Hua-Feng Pan
- Department of General Surgery, the Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi-Wei Jiang
- Department of General Surgery, the Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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39
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Huang Q, Jacquelot N, Preaudet A, Hediyeh-zadeh S, Souza-Fonseca-Guimaraes F, McKenzie ANJ, Hansbro PM, Davis MJ, Mielke LA, Putoczki TL, Belz GT. Type 2 Innate Lymphoid Cells Protect against Colorectal Cancer Progression and Predict Improved Patient Survival. Cancers (Basel) 2021; 13:559. [PMID: 33535624 PMCID: PMC7867134 DOI: 10.3390/cancers13030559] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/30/2022] Open
Abstract
Chronic inflammation of the gastrointestinal (GI) tract contributes to colorectal cancer (CRC) progression. While the role of adaptive T cells in CRC is now well established, the role of innate immune cells, specifically innate lymphoid cells (ILCs), is not well understood. To define the role of ILCs in CRC we employed complementary heterotopic and chemically-induced CRC mouse models. We discovered that ILCs were abundant in CRC tumours and contributed to anti-tumour immunity. We focused on ILC2 and showed that ILC2-deficient mice developed a higher tumour burden compared with littermate wild-type controls. We generated an ILC2 gene signature and using machine learning models revealed that CRC patients with a high intratumor ILC2 gene signature had a favourable clinical prognosis. Collectively, our results highlight a critical role for ILC2 in CRC, suggesting a potential new avenue to improve clinical outcomes through ILC2-agonist based therapeutic approaches.
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Affiliation(s)
- Qiutong Huang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Nicolas Jacquelot
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Adele Preaudet
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Soroor Hediyeh-zadeh
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne 3010, Australia
| | | | | | - Philip M. Hansbro
- Center for Inflammation, Centenary Institute and the School of Life Sciences, University of Technology Sydney, Sydney 2050, Australia;
| | - Melissa J. Davis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Lisa A. Mielke
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Heidelberg 3084, Australia
| | - Tracy L. Putoczki
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Gabrielle T. Belz
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Australia; (Q.H.); (N.J.); (A.P.); (S.H.-z.); (M.J.D.); (L.A.M.); (T.L.P.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne 3010, Australia
- The University of Queensland Diamantina Institute, 37 Kent Street, Woolloongabba, Brisbane 4102, Australia;
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40
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Louis C, Souza-Fonseca-Guimaraes F, Yang Y, D'Silva D, Kratina T, Dagley L, Hediyeh-Zadeh S, Rautela J, Masters SL, Davis MJ, Babon JJ, Ciric B, Vivier E, Alexander WS, Huntington ND, Wicks IP. NK cell-derived GM-CSF potentiates inflammatory arthritis and is negatively regulated by CIS. J Exp Med 2020; 217:133838. [PMID: 32097462 PMCID: PMC7201918 DOI: 10.1084/jem.20191421] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 07/31/2019] [Revised: 11/25/2019] [Accepted: 01/15/2020] [Indexed: 01/08/2023] Open
Abstract
Despite increasing recognition of the importance of GM-CSF in autoimmune disease, it remains unclear how GM-CSF is regulated at sites of tissue inflammation. Using GM-CSF fate reporter mice, we show that synovial NK cells produce GM-CSF in autoantibody-mediated inflammatory arthritis. Synovial NK cells promote a neutrophilic inflammatory cell infiltrate, and persistent arthritis, via GM-CSF production, as deletion of NK cells, or specific ablation of GM-CSF production in NK cells, abrogated disease. Synovial NK cell production of GM-CSF is IL-18–dependent. Furthermore, we show that cytokine-inducible SH2-containing protein (CIS) is crucial in limiting GM-CSF signaling not only during inflammatory arthritis but also in experimental allergic encephalomyelitis (EAE), a murine model of multiple sclerosis. Thus, a cellular cascade of synovial macrophages, NK cells, and neutrophils mediates persistent joint inflammation via production of IL-18 and GM-CSF. Endogenous CIS provides a key brake on signaling through the GM-CSF receptor. These findings shed new light on GM-CSF biology in sterile tissue inflammation and identify several potential therapeutic targets.
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Affiliation(s)
- Cynthia Louis
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Medical Biology, University of Melbourne, Parkville, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- Medical Biology, University of Melbourne, Parkville, Australia.,Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Yuyan Yang
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Medical Biology, University of Melbourne, Parkville, Australia
| | - Damian D'Silva
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Medical Biology, University of Melbourne, Parkville, Australia
| | - Tobias Kratina
- Medical Biology, University of Melbourne, Parkville, Australia.,Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Laura Dagley
- Medical Biology, University of Melbourne, Parkville, Australia.,Systems Biology and Personalized Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Soroor Hediyeh-Zadeh
- Medical Biology, University of Melbourne, Parkville, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jai Rautela
- Medical Biology, University of Melbourne, Parkville, Australia.,Molecular Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Seth Lucian Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Medical Biology, University of Melbourne, Parkville, Australia
| | - Melissa J Davis
- Medical Biology, University of Melbourne, Parkville, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jeffrey J Babon
- Medical Biology, University of Melbourne, Parkville, Australia.,Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Bogoljub Ciric
- Department of Neurology, Thomas Jefferson University. Philadelphia, PA
| | - Eric Vivier
- Innate Pharma Research Labs, Innate Pharma, Marseille, France.,Aix Marseille University, CNRS, INSERM, CIML, Marseille, France.,Service d'Immunologie, Marseille Immunopole, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Warren S Alexander
- Medical Biology, University of Melbourne, Parkville, Australia.,Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Nicholas D Huntington
- Medical Biology, University of Melbourne, Parkville, Australia.,Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Ian P Wicks
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Medical Biology, University of Melbourne, Parkville, Australia.,Rheumatology Unit, Royal Melbourne Hospital, Parkville, Australia
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41
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Bhuva DD, Cursons J, Davis MJ. Stable gene expression for normalisation and single-sample scoring. Nucleic Acids Res 2020; 48:e113. [PMID: 32997146 PMCID: PMC7641762 DOI: 10.1093/nar/gkaa802] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 05/25/2020] [Revised: 09/08/2020] [Accepted: 09/29/2020] [Indexed: 12/22/2022] Open
Abstract
Gene expression signatures have been critical in defining the molecular phenotypes of cells, tissues, and patient samples. Their most notable and widespread clinical application is stratification of breast cancer patients into molecular (PAM50) subtypes. The cost and relatively large amounts of fresh starting material required for whole-transcriptome sequencing has limited clinical application of thousands of existing gene signatures captured in repositories such as the Molecular Signature Database. We identified genes with stable expression across a range of abundances, and with a preserved relative ordering across thousands of samples, allowing signature scoring and supporting general data normalisation for transcriptomic data. Our new method, stingscore, quantifies and summarises relative expression levels of signature genes from individual samples through the inclusion of these ‘stably-expressed genes’. We show that our list of stable genes has better stability across cancer and normal tissue data than previously proposed gene sets. Additionally, we show that signature scores computed from targeted transcript measurements using stingscore can predict docetaxel response in breast cancer patients. This new approach to gene expression signature analysis will facilitate the development of panel-type tests for gene expression signatures, thus supporting clinical translation of the powerful insights gained from cancer transcriptomic studies.
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Affiliation(s)
- Dharmesh D Bhuva
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.,School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia
| | - Joseph Cursons
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Melissa J Davis
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
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42
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Goh W, Scheer S, Jackson JT, Hediyeh-Zadeh S, Delconte RB, Schuster IS, Andoniou CE, Rautela J, Degli-Esposti MA, Davis MJ, McCormack MP, Nutt SL, Huntington ND. Hhex Directly Represses BIM-Dependent Apoptosis to Promote NK Cell Development and Maintenance. Cell Rep 2020; 33:108285. [PMID: 33086067 DOI: 10.1016/j.celrep.2020.108285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 08/17/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
Hhex encodes a homeobox transcriptional regulator important for embryonic development and hematopoiesis. Hhex is highly expressed in NK cells, and its germline deletion results in significant defects in lymphoid development, including NK cells. To determine if Hhex is intrinsically required throughout NK cell development or for NK cell function, we generate mice that specifically lack Hhex in NK cells. NK cell frequency is dramatically reduced, while NK cell differentiation, IL-15 responsiveness, and function at the cellular level remain largely normal in the absence of Hhex. Increased IL-15 availability fails to fully reverse NK lymphopenia following conditional Hhex deletion, suggesting that Hhex regulates developmental pathways extrinsic to those dependent on IL-15. Gene expression and functional genetic approaches reveal that Hhex regulates NK cell survival by directly binding Bcl2l11 (Bim) and repressing expression of this key apoptotic mediator. These data implicate Hhex as a transcriptional regulator of NK cell homeostasis and immunity.
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Affiliation(s)
- Wilford Goh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Sebastian Scheer
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Jacob T Jackson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Iona S Schuster
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, 6009, Australia; Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Christopher E Andoniou
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, 6009, Australia; Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Jai Rautela
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia; oNKo-Innate Pty Ltd., 27 Norwood Cres, Moonee Ponds, Victoria, 3039, Australia
| | - Mariapia A Degli-Esposti
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, 6009, Australia; Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Matthew P McCormack
- The Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, 3004, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia; oNKo-Innate Pty Ltd., 27 Norwood Cres, Moonee Ponds, Victoria, 3039, Australia.
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43
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Wee K, Hediyeh-Zadeh S, Duszyc K, Verma S, N Nanavati B, Khare S, Varma A, Daly RJ, Yap AS, Davis MJ, Budnar S. Snail induces epithelial cell extrusion by regulating RhoA contractile signalling and cell-matrix adhesion. J Cell Sci 2020; 133:jcs235622. [PMID: 32467325 DOI: 10.1242/jcs.235622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 05/14/2020] [Indexed: 01/06/2023] Open
Abstract
Cell extrusion is a morphogenetic process that is implicated in epithelial homeostasis and elicited by stimuli ranging from apoptosis to oncogenic transformation. To explore whether the morphogenetic transcription factor Snail (SNAI1) induces extrusion, we inducibly expressed a stabilized Snail6SA transgene in confluent MCF-7 monolayers. When expressed in small clusters (less than three cells) within otherwise wild-type confluent monolayers, Snail6SA expression induced apical cell extrusion. In contrast, larger clusters or homogenous cultures of Snail6SA cells did not show enhanced apical extrusion, but eventually displayed sporadic basal delamination. Transcriptomic profiling revealed that Snail6SA did not substantively alter the balance of epithelial and mesenchymal genes. However, we identified a transcriptional network that led to upregulated RhoA signalling and cortical contractility in cells expressing Snail6SA Enhanced contractility was necessary, but not sufficient, to drive extrusion, suggesting that Snail collaborates with other factors. Indeed, we found that the transcriptional downregulation of cell-matrix adhesion cooperates with contractility to mediate basal delamination. This provides a pathway for Snail to influence epithelial morphogenesis independently of classic epithelial-to-mesenchymal transition.
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Affiliation(s)
- Kenneth Wee
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Kinga Duszyc
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Suzie Verma
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Bageshri N Nanavati
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | - Amrita Varma
- Viravecs Laboratories CCAMP, GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India
| | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University
| | - Alpha S Yap
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Srikanth Budnar
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
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44
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Louis C, Souza-Fonseca-Guimaraes F, Yang Y, D'Silva D, Kratina T, Dagley L, Hediyeh-Zadeh S, Rautela J, Masters SL, Davis MJ, Babon JJ, Ciric B, Vivier E, Alexander WS, Huntington ND, Wicks IP. Correction: NK cell-derived GM-CSF potentiates inflammatory arthritis and is negatively regulated by CIS. J Exp Med 2020; 217:151591. [PMID: 32221522 PMCID: PMC7201915 DOI: 10.1084/jem.2019142103192020c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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45
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Delconte RB, Guittard G, Goh W, Hediyeh-Zadeh S, Hennessy RJ, Rautela J, Davis MJ, Souza-Fonseca-Guimaraes F, Nunès JA, Huntington ND. NK Cell Priming From Endogenous Homeostatic Signals Is Modulated by CIS. Front Immunol 2020; 11:75. [PMID: 32082327 PMCID: PMC7005222 DOI: 10.3389/fimmu.2020.00075] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 11/05/2019] [Accepted: 01/13/2020] [Indexed: 12/22/2022] Open
Abstract
Natural killer (NK) cell activation is controlled by a balance of activating and inhibitory signals and cytokines such as IL-15. We previously identified cytokine-inducible SH2-containing protein (CIS) as a negative regulator of IL-15 signaling in NK cells under inflammatory conditions. While the functional effect of Cish-deficiency in NK cells was obvious by their increased anti-tumor immunity and hyper-proliferative response to IL-15, it remained unclear how CIS regulates NK cell biology in steady-state. Here, we investigated the role of CIS in the homeostatic maintenance of NK cells and found CIS-ablation promoted terminal differentiation of NK cells and increased turnover, suggesting that under steady-state conditions, CIS plays a role in maintaining IL-15 driven regulation of NK cells in vivo. However, hyper-responsiveness to IL-15 did not manifest in NK cell accumulation, even when the essential NK cell apoptosis mediator, Bcl2l11 (BIM) was deleted in addition to Cish. Instead, loss of CIS conferred a lower activation threshold, evidenced by augmented functionality on a per cell basis both in vitro and in vivo without prior priming. We conclude that Cish regulates IL-15 signaling in NK cells in vivo, and through the rewiring of several activation pathways leads to a reduction in activation threshold, decreasing the requirement for priming and improving NK cell anti-tumor function. Furthermore, this study highlights the tight regulation of NK cell homeostasis by several pathways which prevent NK cell accumulation when IL-15 signaling and intrinsic apoptosis are dysregulated.
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Affiliation(s)
- Rebecca B Delconte
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Geoffrey Guittard
- Centre de Recherche en Cancérologie de Marseille, CRCM, Immunity and Cancer Team, Institut Paoli-Calmettes, Inserm, CNRS, Aix Marseille Université, Marseille, France
| | - Wilford Goh
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Soroor Hediyeh-Zadeh
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia.,Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Robert J Hennessy
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Jai Rautela
- oNKo-Innate Pty Ltd., Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Melissa J Davis
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia.,Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, QLD, Australia
| | - Jacques A Nunès
- Centre de Recherche en Cancérologie de Marseille, CRCM, Immunity and Cancer Team, Institut Paoli-Calmettes, Inserm, CNRS, Aix Marseille Université, Marseille, France
| | - Nicholas D Huntington
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia.,oNKo-Innate Pty Ltd., Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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46
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Pillman KA, Scheer KG, Hackett-Jones E, Saunders K, Bert AG, Toubia J, Whitfield HJ, Sapkota S, Sourdin L, Pham H, Le TD, Cursons J, Davis MJ, Gregory PA, Goodall GJ, Bracken CP. Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA). Nucleic Acids Res 2019; 47:8606-8619. [PMID: 31372646 PMCID: PMC6895270 DOI: 10.1093/nar/gkz664] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 01/22/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 12/29/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate 'indirect' miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon-Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.
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Affiliation(s)
- Katherine A Pillman
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Kaitlin G Scheer
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Emily Hackett-Jones
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Klay Saunders
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - John Toubia
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Holly J Whitfield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Sunil Sapkota
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Laura Sourdin
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Hoang Pham
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Thuc D Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Joseph Cursons
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Melissa J Davis
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
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47
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Bhuva DD, Cursons J, Smyth GK, Davis MJ. Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer. Genome Biol 2019; 20:236. [PMID: 31727119 PMCID: PMC6857226 DOI: 10.1186/s13059-019-1851-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Elucidation of regulatory networks, including identification of regulatory mechanisms specific to a given biological context, is a key aim in systems biology. This has motivated the move from co-expression to differential co-expression analysis and numerous methods have been developed subsequently to address this task; however, evaluation of methods and interpretation of the resulting networks has been hindered by the lack of known context-specific regulatory interactions. RESULTS In this study, we develop a simulator based on dynamical systems modelling capable of simulating differential co-expression patterns. With the simulator and an evaluation framework, we benchmark and characterise the performance of inference methods. Defining three different levels of "true" networks for each simulation, we show that accurate inference of causation is difficult for all methods, compared to inference of associations. We show that a z-score-based method has the best general performance. Further, analysis of simulation parameters reveals five network and simulation properties that explained the performance of methods. The evaluation framework and inference methods used in this study are available in the dcanr R/Bioconductor package. CONCLUSIONS Our analysis of networks inferred from simulated data show that hub nodes are more likely to be differentially regulated targets than transcription factors. Based on this observation, we propose an interpretation of the inferred differential network that can reconstruct a putative causal network.
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Affiliation(s)
- Dharmesh D Bhuva
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Joseph Cursons
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gordon K Smyth
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
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48
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Jain M, Cai L, Fleites LA, Munoz-Bodnar A, Davis MJ, Gabriel DW. Liberibacter crescens Is a Cultured Surrogate for Functional Genomics of Uncultured Pathogenic ' Candidatus Liberibacter' spp. and Is Naturally Competent for Transformation. Phytopathology 2019; 109:1811-1819. [PMID: 31090497 DOI: 10.1094/phyto-04-19-0129-r] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
'Candidatus Liberibacter' spp. are uncultured insect endosymbionts and phloem-limited bacterial plant pathogens associated with diseases ranging from severe to nearly asymptomatic. 'Ca. L. asiaticus', causal agent of Huanglongbing or citrus "greening," and 'Ca. L. solanacearum', causal agent of potato zebra chip disease, respectively threaten citrus and potato production worldwide. Research on both pathogens has been stymied by the inability to culture these agents and to reinoculate into any host. Only a single isolate of a single species of Liberibacter, Liberibacter crescens, has been axenically cultured. L. crescens strain BT-1 is genetically tractable to standard molecular manipulation techniques and has been developed as a surrogate model for functional studies of genes, regulatory elements, promoters, and secreted effectors derived from the uncultured pathogenic Liberibacters. Detailed, step-by-step, and highly reproducible protocols for axenic culture, transformation, and targeted gene knockouts of L. crescens are described. In the course of developing these protocols, we found that L. crescens is also naturally competent for direct uptake and homology-guided chromosomal integration of both linear and circular plasmid DNA. The efficiency of natural transformation was about an order of magnitude higher using circular plasmid DNA compared with linearized fragments. Natural transformation using a replicative plasmid was obtained at a rate of approximately 900 transformants per microgram of plasmid, whereas electroporation using the same plasmid resulted in 6 × 104 transformants. Homology-guided marker interruptions using either natural uptake or electroporation of nonreplicative plasmids yielded 10 to 12 transformation events per microgram of DNA, whereas similar interruptions using linear fragments via natural uptake yielded up to 34 transformation events per microgram of DNA.
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Affiliation(s)
- M Jain
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - L Cai
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - L A Fleites
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - A Munoz-Bodnar
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - M J Davis
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - D W Gabriel
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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49
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Rautela J, Dagley LF, de Oliveira CC, Schuster IS, Hediyeh-Zadeh S, Delconte RB, Cursons J, Hennessy R, Hutchinson DS, Harrison C, Kita B, Vivier E, Webb AI, Degli-Esposti MA, Davis MJ, Huntington ND, Souza-Fonseca-Guimaraes F. Therapeutic blockade of activin-A improves NK cell function and antitumor immunity. Sci Signal 2019; 12:12/596/eaat7527. [PMID: 31455725 DOI: 10.1126/scisignal.aat7527] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Natural killer (NK) cells are innate lymphocytes that play a major role in immunosurveillance against tumor initiation and metastatic spread. The signals and checkpoints that regulate NK cell fitness and function in the tumor microenvironment are not well defined. Transforming growth factor-β (TGF-β) is a suppressor of NK cells that inhibits interleukin-15 (IL-15)-dependent signaling events and increases the abundance of receptors that promote tissue residency. Here, we showed that NK cells express the type I activin receptor ALK4, which, upon binding to its ligand activin-A, phosphorylated SMAD2/3 to suppress IL-15-mediated NK cell metabolism. Activin-A impaired human and mouse NK cell proliferation and reduced the production of granzyme B to impair tumor killing. Similar to TGF-β, activin-A also induced SMAD2/3 phosphorylation and stimulated NK cells to increase their cell surface expression of several markers of ILC1 cells. Activin-A also induced these changes in TGF-β receptor-deficient NK cells, suggesting that activin-A and TGF-β stimulate independent pathways that drive SMAD2/3-mediated NK cell suppression. Last, inhibition of activin-A by follistatin substantially slowed orthotopic melanoma growth in mice. These data highlight the relevance of examining TGF-β-independent SMAD2/3 signaling mechanisms as a therapeutic axis to relieve NK cell suppression and promote antitumor immunity.
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Affiliation(s)
- Jai Rautela
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Laura F Dagley
- Systems Biology and Personalized Medicine Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Carolina C de Oliveira
- Laboratório de Células Inflamatórias e Neoplásicas, Departamento de Biologia Celular, SCB, Centro Politecnico, Universidade Federal do Paraná, Curitiba, CEP 81531-980, PR, Brazil
| | - Iona S Schuster
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Rebecca B Delconte
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Joseph Cursons
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Robert Hennessy
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dana S Hutchinson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Craig Harrison
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Badia Kita
- Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288 Marseille, France
| | - Andrew I Webb
- Systems Biology and Personalized Medicine Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Nicholas D Huntington
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia. .,University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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50
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Andersen JC, Camp CP, Davis MJ, Havill NP, Elkinton JS. Development of microsatellite markers for an outbreaking species of oak gall wasp, Zapatella davisae (Hymenoptera: Cynipidae), in the northeastern United States. Bull Entomol Res 2019; 109:510-517. [PMID: 30488819 DOI: 10.1017/s0007485318000858] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Populations of the recently described black oak gall wasp, Zapatella davisae Buffington (Hymenoptera: Cynipidae), have been identified as the cause of extensive tree damage and mortality to black oaks, Quercus velutina Lamarck (Fagales: Fagaceae), in the northeastern United States. Relatively little is known, however, about the distribution, phylogenetic placement, and lifecycle of this important tree pest. Therefore, we conducted next-generation sequencing using the Ion Torrent™ PGM (ThermoFisher Scientific, Inc.) platform to develop genomic resources for the study of Z. davisae and for other closely related species of oak gall wasps. Individual sequence reads were aligned, assembled into unique contigs, and the contigs were then utilized for the in silico isolation and development of microsatellite markers. In total, we screened 36 candidate microsatellite loci, of which 23 amplified consistently (five polymorphic and 18 monomorphic). We then examined whether the polymorphic loci could be used to infer whether populations of Z. davisae from Cape Cod and Nantucket are sexual or asexual by calculating several metrics of genetic diversity that might indicate the mode of reproduction. These included testing for statistical deviations from Hardy-Weinberg equilibrium (HWE) and for linkage disequilibrium (LD), observations for the presence of the Meselson effect, and by calculating the probability that clonal individuals are more prevalent than would be expected in a randomly mating population. While we found significant deviations from HWE and more clonal individuals than expected, our estimates of the Meselson effect were inconclusive due to limited sampling, and we found no evidence of LD. Therefore, the sexual/asexual status of Z. davisae populations remains uncertain.
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Affiliation(s)
- J C Andersen
- Department of Environmental Conservation, University of Amherst Massachusetts, 160 Holdsworth Way, Amherst, MA 01003, USA
| | - C P Camp
- Department of Environmental Conservation, University of Amherst Massachusetts, 160 Holdsworth Way, Amherst, MA 01003, USA
| | - M J Davis
- Department of Environmental Conservation, University of Amherst Massachusetts, 160 Holdsworth Way, Amherst, MA 01003, USA
| | - N P Havill
- United States Department of Agriculture Forest Service Northern Research Station, Hamden, CT 06514, USA
| | - J S Elkinton
- Department of Environmental Conservation, University of Amherst Massachusetts, 160 Holdsworth Way, Amherst, MA 01003, USA
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