1
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Wu Z, Shen S, Mizikovsky D, Cao Y, Naval-Sanchez M, Tan SZ, Alvarez YD, Sun Y, Chen X, Zhao Q, Kim D, Yang P, Hill TA, Jones A, Fairlie DP, Pébay A, Hewitt AW, Tam PPL, White MD, Nefzger CM, Palpant NJ. Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm. Dev Cell 2024; 59:705-722.e8. [PMID: 38354738 DOI: 10.1016/j.devcel.2024.01.019] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Wnt signaling is a critical determinant of cell lineage development. This study used Wnt dose-dependent induction programs to gain insights into molecular regulation of stem cell differentiation. We performed single-cell RNA sequencing of hiPSCs responding to a dose escalation protocol with Wnt agonist CHIR-99021 during the exit from pluripotency to identify cell types and genetic activity driven by Wnt stimulation. Results of activated gene sets and cell types were used to build a multiple regression model that predicts the efficiency of cardiomyocyte differentiation. Cross-referencing Wnt-associated gene expression profiles to the Connectivity Map database, we identified the small-molecule drug, tranilast. We found that tranilast synergistically activates Wnt signaling to promote cardiac lineage differentiation, which we validate by in vitro analysis of hiPSC differentiation and in vivo analysis of developing quail embryos. Our study provides an integrated workflow that links experimental datasets, prediction models, and small-molecule databases to identify drug-like compounds that control cell differentiation.
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Affiliation(s)
- Zhixuan Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Siew Zhuan Tan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yanina D Alvarez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Qiongyi Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Kim
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Pengyi Yang
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Timothy A Hill
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Patrick P L Tam
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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2
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Friedman CE, Cheetham SW, Negi S, Mills RJ, Ogawa M, Redd MA, Chiu HS, Shen S, Sun Y, Mizikovsky D, Bouveret R, Chen X, Voges HK, Paterson S, De Angelis JE, Andersen SB, Cao Y, Wu Y, Jafrani YMA, Yoon S, Faulkner GJ, Smith KA, Porrello E, Harvey RP, Hogan BM, Nguyen Q, Zeng J, Kikuchi K, Hudson JE, Palpant NJ. HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Dev Cell 2024; 59:91-107.e6. [PMID: 38091997 DOI: 10.1016/j.devcel.2023.11.012] [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: 05/26/2022] [Revised: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
Genomic regulation of cardiomyocyte differentiation is central to heart development and function. This study uses genetic loss-of-function human-induced pluripotent stem cell-derived cardiomyocytes to evaluate the genomic regulatory basis of the non-DNA-binding homeodomain protein HOPX. We show that HOPX interacts with and controls cardiac genes and enhancer networks associated with diverse aspects of heart development. Using perturbation studies in vitro, we define how upstream cell growth and proliferation control HOPX transcription to regulate cardiac gene programs. We then use cell, organoid, and zebrafish regeneration models to demonstrate that HOPX-regulated gene programs control cardiomyocyte function in development and disease. Collectively, this study mechanistically links cell signaling pathways as upstream regulators of HOPX transcription to control gene programs underpinning cardiomyocyte identity and function.
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Affiliation(s)
- Clayton E Friedman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sumedha Negi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Masahito Ogawa
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Meredith A Redd
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Romaric Bouveret
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Holly K Voges
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Scott Paterson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jessica E De Angelis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yohaann M A Jafrani
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sohye Yoon
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Kelly A Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Enzo Porrello
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Benjamin M Hogan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kazu Kikuchi
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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3
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Sun Y, Shim WJ, Shen S, Sinniah E, Pham D, Su Z, Mizikovsky D, White MD, Ho JK, Nguyen Q, Bodén M, Palpant N. Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. Nucleic Acids Res 2023; 51:e62. [PMID: 37125641 PMCID: PMC10287941 DOI: 10.1093/nar/gkad307] [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: 10/26/2022] [Accepted: 04/28/2023] [Indexed: 05/02/2023] Open
Abstract
Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential for biological interpretation of cell processes. Here, we present TRIAGE-Cluster which uses genome-wide epigenetic data from diverse bio-samples to identify genes demarcating cell diversity in scRNA-seq data. By integrating patterns of repressive chromatin deposited across diverse cell types with weighted density estimation, TRIAGE-Cluster determines cell type clusters in a 2D UMAP space. We then present TRIAGE-ParseR, a machine learning method which evaluates gene expression rank lists to define gene groups governing the identity and function of cell types. We demonstrate the utility of this two-step approach using atlases of in vivo and in vitro cell diversification and organogenesis. We also provide a web accessible dashboard for analysis and download of data and software. Collectively, genome-wide epigenetic repression provides a versatile strategy to define cell diversity and study gene regulation of scRNA-seq data.
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Affiliation(s)
- Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Duy Pham
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Zezhuo Su
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
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4
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Cao Y, Redd MA, Fang C, Mizikovsky D, Li X, Macdonald PS, King GF, Palpant NJ. New Drug Targets and Preclinical Modelling Recommendations for Treating Acute Myocardial Infarction. Heart Lung Circ 2023:S1443-9506(23)00139-7. [PMID: 37230806 DOI: 10.1016/j.hlc.2022.12.015] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/28/2022] [Accepted: 12/15/2022] [Indexed: 05/27/2023]
Abstract
Acute myocardial infarction (AMI) is the leading cause of morbidity and mortality worldwide and the primary underlying risk factor for heart failure. Despite decades of research and clinical trials, there are no drugs currently available to prevent organ damage from acute ischaemic injuries of the heart. In order to address the increasing global burden of heart failure, drug, gene, and cell-based regeneration technologies are advancing into clinical testing. In this review we highlight the burden of disease associated with AMI and the therapeutic landscape based on market analyses. New studies revealing the role of acid-sensitive cardiac ion channels and other proton-gated ion channels in cardiac ischaemia are providing renewed interest in pre- and post-conditioning agents with novel mechanisms of action that may also have implications for gene- and cell-based therapeutics. Furthermore, we present guidelines that couple new cell technologies and data resources with traditional animal modelling pipelines to help de-risk drug candidates aimed at treating AMI. We propose that improved preclinical pipelines and increased investment in drug target identification for AMI is critical to stem the increasing global health burden of heart failure.
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Affiliation(s)
- Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Meredith A Redd
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Chen Fang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Xichun Li
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Peter S Macdonald
- Cardiopulmonary Transplant Unit, St Vincent's Hospital, Sydney, NSW, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia.
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5
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Voges HK, Foster SR, Reynolds L, Parker BL, Devilée L, Quaife-Ryan GA, Fortuna PRJ, Mathieson E, Fitzsimmons R, Lor M, Batho C, Reid J, Pocock M, Friedman CE, Mizikovsky D, Francois M, Palpant NJ, Needham EJ, Peralta M, Monte-Nieto GD, Jones LK, Smyth IM, Mehdiabadi NR, Bolk F, Janbandhu V, Yao E, Harvey RP, Chong JJH, Elliott DA, Stanley EG, Wiszniak S, Schwarz Q, James DE, Mills RJ, Porrello ER, Hudson JE. Vascular cells improve functionality of human cardiac organoids. Cell Rep 2023:112322. [PMID: 37105170 DOI: 10.1016/j.celrep.2023.112322] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 09/14/2022] [Revised: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Crosstalk between cardiac cells is critical for heart performance. Here we show that vascular cells within human cardiac organoids (hCOs) enhance their maturation, force of contraction, and utility in disease modeling. Herein we optimize our protocol to generate vascular populations in addition to epicardial, fibroblast, and cardiomyocyte cells that self-organize into in-vivo-like structures in hCOs. We identify mechanisms of communication between endothelial cells, pericytes, fibroblasts, and cardiomyocytes that ultimately contribute to cardiac organoid maturation. In particular, (1) endothelial-derived LAMA5 regulates expression of mature sarcomeric proteins and contractility, and (2) paracrine platelet-derived growth factor receptor β (PDGFRβ) signaling from vascular cells upregulates matrix deposition to augment hCO contractile force. Finally, we demonstrate that vascular cells determine the magnitude of diastolic dysfunction caused by inflammatory factors and identify a paracrine role of endothelin driving dysfunction. Together this study highlights the importance and role of vascular cells in organoid models.
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Affiliation(s)
- Holly K Voges
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Paediatrics, School of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Simon R Foster
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Liam Reynolds
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Benjamin L Parker
- Charles Perkins Centre, School of Life and Environmental Science, The University of Sydney, Sydney, NSW 2006, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Lynn Devilée
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Gregory A Quaife-Ryan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Ellen Mathieson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Mary Lor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Christopher Batho
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Janice Reid
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark Pocock
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Clayton E Friedman
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, QLD, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, QLD, Australia
| | - Mathias Francois
- The Centenary Institute, David Richmond Program for Cardiovascular Research: Gene Regulation and Editing, Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, QLD, Australia
| | - Elise J Needham
- Charles Perkins Centre, School of Life and Environmental Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marina Peralta
- Australian Regenerative Medicine Institute. Monash University, Clayton, VIC 3800, Australia
| | | | - Lynelle K Jones
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedical Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedical Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Neda R Mehdiabadi
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Francesca Bolk
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Ernestene Yao
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - James J H Chong
- Centre for Heart Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia; Department of Cardiology, Westmead Hospital, Westmead, NSW 2145, Australia
| | - David A Elliott
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Paediatrics, School of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Edouard G Stanley
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Paediatrics, School of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Sophie Wiszniak
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5001, Australia
| | - Quenten Schwarz
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5001, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Science, The University of Sydney, Sydney, NSW 2006, Australia; Sydney Medical School, The University of Sydney, Sydney, 2010 NSW, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Paediatrics, School of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Enzo R Porrello
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, VIC 3052, Australia.
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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6
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Mizikovsky D, Naval Sanchez M, Nefzger CM, Cuellar Partida G, Palpant NJ. Organization of gene programs revealed by unsupervised analysis of diverse gene-trait associations. Nucleic Acids Res 2022; 50:e87. [PMID: 35716123 PMCID: PMC9410900 DOI: 10.1093/nar/gkac413] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/28/2022] [Accepted: 05/09/2022] [Indexed: 12/28/2022] Open
Abstract
Genome wide association studies provide statistical measures of gene–trait associations that reveal how genetic variation influences phenotypes. This study develops an unsupervised dimensionality reduction method called UnTANGLeD (Unsupervised Trait Analysis of Networks from Gene Level Data) which organizes 16,849 genes into discrete gene programs by measuring the statistical association between genetic variants and 1,393 diverse complex traits. UnTANGLeD reveals 173 gene clusters enriched for protein–protein interactions and highly distinct biological processes governing development, signalling, disease, and homeostasis. We identify diverse gene networks with robust interactions but not associated with known biological processes. Analysis of independent disease traits shows that UnTANGLeD gene clusters are conserved across all complex traits, providing a simple and powerful framework to predict novel gene candidates and programs influencing orthogonal disease phenotypes. Collectively, this study demonstrates that gene programs co-ordinately orchestrating cell functions can be identified without reliance on prior knowledge, providing a method for use in functional annotation, hypothesis generation, machine learning and prediction algorithms, and the interpretation of diverse genomic data.
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Affiliation(s)
- Dalia Mizikovsky
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Marina Naval Sanchez
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Nathan J Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
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