1
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Chew G, Mai AS, Ouyang JF, Qi Y, Chao Y, Wang Q, Petretto E, Tan EK. Transcriptomic imputation of genetic risk variants uncovers novel whole-blood biomarkers of Parkinson's disease. NPJ Parkinsons Dis 2024; 10:99. [PMID: 38719867 PMCID: PMC11078960 DOI: 10.1038/s41531-024-00698-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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/28/2024] [Indexed: 05/12/2024] Open
Abstract
Blood-based gene expression signatures could potentially be used as biomarkers for PD. However, it is unclear whether genetically-regulated transcriptomic signatures can provide novel gene candidates for use as PD biomarkers. We leveraged on the Genotype-Tissue Expression (GTEx) database to impute whole-blood transcriptomic expression using summary statistics of three large-scale PD GWAS. A random forest classifier was used with the consensus whole-blood imputed gene signature (IGS) to discriminate between cases and controls. Outcome measures included Area under the Curve (AUC) of Receiver Operating Characteristic (ROC) Curve. We demonstrated that the IGS (n = 37 genes) is conserved across PD GWAS studies and brain tissues. IGS discriminated between cases and controls in an independent whole-blood RNA-sequencing study (1176 PD, 254 prodromal, and 860 healthy controls) with mean AUC and accuracy of 64.8% and 69.4% for PD cohort, and 78.8% and 74% for prodromal cohort. PATL2 was the top-performing imputed gene in both PD and prodromal PD cohorts, whose classifier performance varied with biological sex (higher performance for males and females in the PD and prodromal PD, respectively). Single-cell RNA-sequencing studies (scRNA-seq) of healthy humans and PD patients found PATL2 to be enriched in terminal effector CD8+ and cytotoxic CD4+ cells, whose proportions are both increased in PD patients. We demonstrated the utility of GWAS transcriptomic imputation in identifying novel whole-blood transcriptomic signatures which could be leveraged upon for PD biomarker derivation. We identified PATL2 as a potential biomarker in both clinical and prodromic PD.
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Affiliation(s)
- Gabriel Chew
- Duke-National University of Singapore Medical School, Singapore, Singapore
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
| | - Aaron Shengting Mai
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John F Ouyang
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Yueyue Qi
- Duke-National University of Singapore Medical School, Singapore, Singapore
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
| | - Yinxia Chao
- Duke-National University of Singapore Medical School, Singapore, Singapore
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
- Department of Neurology, Singapore General Hospital, Singapore, Singapore
| | - Qing Wang
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Enrico Petretto
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Eng-King Tan
- Duke-National University of Singapore Medical School, Singapore, Singapore.
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore.
- Department of Neurology, Singapore General Hospital, Singapore, Singapore.
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2
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Ouyang JF, Mishra K, Xie Y, Park H, Huang KY, Petretto E, Behmoaras J. Systems level identification of a matrisome-associated macrophage polarisation state in multi-organ fibrosis. eLife 2023; 12:e85530. [PMID: 37706477 PMCID: PMC10547479 DOI: 10.7554/elife.85530] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
Tissue fibrosis affects multiple organs and involves a master-regulatory role of macrophages which respond to an initial inflammatory insult common in all forms of fibrosis. The recently unravelled multi-organ heterogeneity of macrophages in healthy and fibrotic human disease suggests that macrophages expressing osteopontin (SPP1) associate with lung and liver fibrosis. However, the conservation of this SPP1+ macrophage population across different tissues and its specificity to fibrotic diseases with different etiologies remain unclear. Integrating 15 single-cell RNA-sequencing datasets to profile 235,930 tissue macrophages from healthy and fibrotic heart, lung, liver, kidney, skin, and endometrium, we extended the association of SPP1+ macrophages with fibrosis to all these tissues. We also identified a subpopulation expressing matrisome-associated genes (e.g., matrix metalloproteinases and their tissue inhibitors), functionally enriched for ECM remodelling and cell metabolism, representative of a matrisome-associated macrophage (MAM) polarisation state within SPP1+ macrophages. Importantly, the MAM polarisation state follows a differentiation trajectory from SPP1+ macrophages and is associated with a core set of regulon activity. SPP1+ macrophages without the MAM polarisation state (SPP1+MAM-) show a positive association with ageing lung in mice and humans. These results suggest an advanced and conserved polarisation state of SPP1+ macrophages in fibrotic tissues resulting from prolonged inflammatory cues within each tissue microenvironment.
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Affiliation(s)
- John F Ouyang
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Kunal Mishra
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Yi Xie
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Harry Park
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Kevin Y Huang
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
| | - Enrico Petretto
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU)NanjingChina
| | - Jacques Behmoaras
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical SchoolSingaporeSingapore
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College LondonLondonUnited Kingdom
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3
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Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, Lister R. Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 2023; 620:863-872. [PMID: 37587336 PMCID: PMC10447250 DOI: 10.1038/s41586-023-06424-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 06/04/2021] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function1-8. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.
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Affiliation(s)
- Sam Buckberry
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Westlake Institute for Advanced Study, Hangzhou, China
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Ping Tan
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Trung Viet Nguyen
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Alex de Mendoza
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Thomas Frazer
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landín
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jacob M Paynter
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Nathan Smits
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hun S Chy
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Andrew L Laslett
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - James Breen
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia.
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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4
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Quah HS, Cao EY, Suteja L, Li CH, Leong HS, Chong FT, Gupta S, Arcinas C, Ouyang JF, Ang V, Celhar T, Zhao Y, Tay HC, Chan J, Takahashi T, Tan DSW, Biswas SK, Rackham OJL, Iyer NG. Single cell analysis in head and neck cancer reveals potential immune evasion mechanisms during early metastasis. Nat Commun 2023; 14:1680. [PMID: 36973261 PMCID: PMC10042873 DOI: 10.1038/s41467-023-37379-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identifies a subpopulation of pre-metastatic cells, driven by actionable pathways including AXL and AURK. Blocking these two proteins blunts tumor invasion in patient-derived cultures. Furthermore, scRNAseq analyses of tumor-infiltrating CD8 + T-lymphocytes show two distinct trajectories to T-cell dysfunction, corroborated by their clonal architecture based on single-cell T-cell receptor sequencing. By determining key modulators of these trajectories, followed by validation using external datasets and functional experiments, we uncover a role for SOX4 in mediating T-cell exhaustion. Finally, interactome analyses between pre-metastatic tumor cells and CD8 + T-lymphocytes uncover a putative role for the Midkine pathway in immune-modulation and this is confirmed by scRNAseq of tumors from humanized mice. Aside from specific findings, this study demonstrates the importance of tumor heterogeneity analyses in identifying key vulnerabilities during early metastasis.
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Affiliation(s)
- Hong Sheng Quah
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore
- Academic Clinical Program in Oncology, Duke-NUS Medical School, Singapore, Singapore
| | - Elaine Yiqun Cao
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Lisda Suteja
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Constance H Li
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore
- Academic Clinical Program in Oncology, Duke-NUS Medical School, Singapore, Singapore
| | - Hui Sun Leong
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore
| | - Fui Teen Chong
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore
| | - Shilpi Gupta
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Camille Arcinas
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore
- Academic Clinical Program in Oncology, Duke-NUS Medical School, Singapore, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Vivian Ang
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Teja Celhar
- HuNIT platform, Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yunqian Zhao
- HuNIT platform, Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hui Chen Tay
- HuNIT platform, Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jerry Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Takeshi Takahashi
- Laboratory Animal Research Department, Central Institute for Experimental Animals (CIEA), Kawasaki, Japan
| | - Daniel S W Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore
- Academic Clinical Program in Oncology, Duke-NUS Medical School, Singapore, Singapore
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Subhra K Biswas
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- The Alan Turing Institute, The British Library, London, United Kingdom
| | - N Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre, Singapore, Singapore.
- Academic Clinical Program in Oncology, Duke-NUS Medical School, Singapore, Singapore.
- Department of Head and Neck Surgery, National Cancer Centre, Singapore, Singapore.
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore.
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5
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Ouyang JF, Chothani S, Rackham OJ. Deep learning models will shape the future of stem cell research. Stem Cell Reports 2023; 18:6-12. [PMID: 36630908 PMCID: PMC9860061 DOI: 10.1016/j.stemcr.2022.11.007] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 01/12/2023] Open
Abstract
Our ability to understand and control stem cell biology is being augmented by developments on two fronts, our ability to collect more data describing cell state and our capability to comprehend these data using deep learning models. Here we consider the impact deep learning will have in the future of stem cell research. We explore the importance of generating data suitable for these methods, the requirement for close collaboration between experimental and computational researchers, and the challenges we face to do this fairly and effectively. Achieving this will ensure that the resulting deep learning models are biologically meaningful and computationally tractable.
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Affiliation(s)
- John F. Ouyang
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Singapore, Singapore
| | - Sonia Chothani
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Singapore, Singapore
| | - Owen J.L. Rackham
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Singapore, Singapore,School of Biological Sciences, University of Southampton, Southampton, UK,The Alan Turing Institute, The British Library, London, UK,Corresponding author
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6
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Chothani SP, Adami E, Widjaja AA, Langley SR, Viswanathan S, Pua CJ, Zhihao NT, Harmston N, D'Agostino G, Whiffin N, Mao W, Ouyang JF, Lim WW, Lim S, Lee CQE, Grubman A, Chen J, Kovalik JP, Tryggvason K, Polo JM, Ho L, Cook SA, Rackham OJL, Schafer S. A high-resolution map of human RNA translation. Mol Cell 2022; 82:2885-2899.e8. [PMID: 35841888 DOI: 10.1016/j.molcel.2022.06.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 09/19/2021] [Revised: 03/10/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.
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Affiliation(s)
- Sonia P Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Chee Jian Pua
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Nevin Tham Zhihao
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Giuseppe D'Agostino
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nicola Whiffin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Wang Mao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Wei Wen Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Shiqi Lim
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Cheryl Q E Lee
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - J P Kovalik
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore; London Institute of Medical Sciences, London W12 ONN, UK
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; School of Biological Sciences, University of Southampton, Southampton, UK.
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore.
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7
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Risbridger GP, Clark AK, Porter LH, Toivanen R, Bakshi A, Lister NL, Pook D, Pezaro CJ, Sandhu S, Keerthikumar S, Quezada Urban R, Papargiris M, Kraska J, Madsen HB, Wang H, Richards MG, Niranjan B, O'Dea S, Teng L, Wheelahan W, Li Z, Choo N, Ouyang JF, Thorne H, Devereux L, Hicks RJ, Sengupta S, Harewood L, Iddawala M, Azad AA, Goad J, Grummet J, Kourambas J, Kwan EM, Moon D, Murphy DG, Pedersen J, Clouston D, Norden S, Ryan A, Furic L, Goode DL, Frydenberg M, Lawrence MG, Taylor RA. The MURAL collection of prostate cancer patient-derived xenografts enables discovery through preclinical models of uro-oncology. Nat Commun 2021; 12:5049. [PMID: 34413304 PMCID: PMC8376965 DOI: 10.1038/s41467-021-25175-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
Preclinical testing is a crucial step in evaluating cancer therapeutics. We aimed to establish a significant resource of patient-derived xenografts (PDXs) of prostate cancer for rapid and systematic evaluation of candidate therapies. The PDX collection comprises 59 tumors collected from 30 patients between 2012-2020, coinciding with availability of abiraterone and enzalutamide. The PDXs represent the clinico-pathological and genomic spectrum of prostate cancer, from treatment-naïve primary tumors to castration-resistant metastases. Inter- and intra-tumor heterogeneity in adenocarcinoma and neuroendocrine phenotypes is evident from bulk and single-cell RNA sequencing data. Organoids can be cultured from PDXs, providing further capabilities for preclinical studies. Using a 1 x 1 x 1 design, we rapidly identify tumors with exceptional responses to combination treatments. To govern the distribution of PDXs, we formed the Melbourne Urological Research Alliance (MURAL). This PDX collection is a substantial resource, expanding the capacity to test and prioritize effective treatments for prospective clinical trials in prostate cancer.
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Affiliation(s)
- Gail P Risbridger
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia. .,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
| | - Ashlee K Clark
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Laura H Porter
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Roxanne Toivanen
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew Bakshi
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Natalie L Lister
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - David Pook
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC, Australia.,Department of Medical Oncology, Monash Health, Clayton, VIC, Australia
| | - Carmel J Pezaro
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Eastern Health and Monash University Eastern Health Clinical School, Box Hill, VIC, Australia.,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, England
| | - Shahneen Sandhu
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Cancer Tissue Collection After Death (CASCADE) Program, Melbourne, VIC, Australia
| | - Shivakumar Keerthikumar
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Rosalia Quezada Urban
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Melissa Papargiris
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Prostate Cancer Bioresource, VIC Node, Monash University, Clayton, VIC, Australia
| | - Jenna Kraska
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Australian Prostate Cancer Bioresource, VIC Node, Monash University, Clayton, VIC, Australia
| | - Heather B Madsen
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Australian Prostate Cancer Bioresource, VIC Node, Monash University, Clayton, VIC, Australia
| | - Hong Wang
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Michelle G Richards
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Birunthi Niranjan
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Samantha O'Dea
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Linda Teng
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - William Wheelahan
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Zhuoer Li
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Physiology, Monash University, Clayton, VIC, Australia
| | - Nicholas Choo
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Heather Thorne
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Lisa Devereux
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Rodney J Hicks
- Center for Molecular Imaging, Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Shomik Sengupta
- Eastern Health and Monash University Eastern Health Clinical School, Box Hill, VIC, Australia.,Department of Urology, Austin Hospital, The University of Melbourne, Heidelberg, VIC, Australia.,Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia.,Epworth Healthcare, Melbourne, VIC, Australia.,Epworth Freemasons, Epworth Health, East Melbourne, VIC, Australia
| | - Laurence Harewood
- Epworth Healthcare, Melbourne, VIC, Australia.,Department of Surgery, The University of Melbourne, Parkville, VIC, Australia
| | - Mahesh Iddawala
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Arun A Azad
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jeremy Goad
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Epworth Healthcare, Melbourne, VIC, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia
| | - Jeremy Grummet
- Epworth Healthcare, Melbourne, VIC, Australia.,Department of Surgery, Central Clinical School, Monash University, Clayton, VIC, Australia.,Australian Urology Associates, Melbourne, VIC, Australia
| | - John Kourambas
- Department of Medicine, Monash Health, Casey Hospital, Berwick, VIC, Australia
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC, Australia.,Department of Medical Oncology, Monash Health, Clayton, VIC, Australia
| | - Daniel Moon
- Epworth Healthcare, Melbourne, VIC, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia.,Australian Urology Associates, Melbourne, VIC, Australia.,Central Clinical School, Monash University, Clayton, VIC, Australia.,The Epworth Prostate Centre, Epworth Hospital, Richmond, VIC, Australia
| | - Declan G Murphy
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Epworth Healthcare, Melbourne, VIC, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia
| | - John Pedersen
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,TissuPath, Mount Waverley, VIC, Australia
| | | | - Sam Norden
- TissuPath, Mount Waverley, VIC, Australia
| | | | - Luc Furic
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - David L Goode
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Mark Frydenberg
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Epworth Healthcare, Melbourne, VIC, Australia.,Australian Urology Associates, Melbourne, VIC, Australia.,Department of Surgery, Monash University, Clayton, VIC, Australia.,Department of Urology, Cabrini Institute, Cabrini Health, Melbourne, VIC, Australia
| | - Mitchell G Lawrence
- Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Renea A Taylor
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. .,Prostate Cancer Research Group, Monash Biomedicine Discovery Institute, Cancer Program, Department of Physiology, Monash University, Clayton, VIC, Australia.
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8
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Ouyang JF, Kamaraj US, Cao EY, Rackham OJL. ShinyCell: Simple and sharable visualisation of single-cell gene expression data. Bioinformatics 2021; 37:3374-3376. [PMID: 33774659 DOI: 10.1093/bioinformatics/btab209] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/21/2021] [Accepted: 03/26/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION As the generation of complex single-cell RNA sequencing datasets becomes more commonplace it is the responsibility of researchers to provide access to these data in a way that can be easily explored and shared. Whilst it is often the case that data is deposited for future bioinformatic analysis many studies do not release their data in a way that is easy to explore by non-computational researchers. RESULTS In order to help address this we have developed ShinyCell, an R package that converts single-cell RNA sequencing datasets into explorable and shareable interactive interfaces. These interfaces can be easily customised in order to maximise their usability and can be easily uploaded to online platforms to facilitate wider access to published data. AVAILABILITY ShinyCell is available at https://github.com/SGDDNB/ShinyCell and https://figshare.com/projects/ShinyCell/100439.
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Affiliation(s)
- John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Uma S Kamaraj
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Elaine Y Cao
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
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9
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Choo XY, Lim YM, Katwadi K, Yap L, Tryggvason K, Sun AX, Li S, Handoko L, Ouyang JF, Rackham OJL. Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments. ACS Synth Biol 2021; 10:640-645. [PMID: 33625849 DOI: 10.1021/acssynbio.0c00499] [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] [Indexed: 11/30/2022]
Abstract
The combination of single-cell RNA sequencing with CRISPR inhibition/activation provides a high-throughput approach to simultaneously study the effects of hundreds if not thousands of gene perturbations in a single experiment. One recent development in CRISPR-based single-cell techniques introduces a feature barcoding technology that allows for the simultaneous capture of mRNA and guide RNA (gRNA) from the same cell. This is achieved by introducing a capture sequence, whose complement can be incorporated into each gRNA and that can be used to amplify these features prior to sequencing. However, because the technology is in its infancy, there is little information available on how such experimental parameters can be optimized. To overcome this, we varied the capture sequence, capture sequence position, and gRNA backbone to identify an optimal gRNA scaffold for CRISPR activation gene perturbation studies. We provide a report on our screening approach along with our observations and recommendations for future use.
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Affiliation(s)
- Xin Yi Choo
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Yu Ming Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Khairunnisa Katwadi
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Lynn Yap
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Alfred Xuyang Sun
- National Neuroscience Institute, Singapore 308433
- Genome Institute of Singapore, Singapore 138672
| | - Shang Li
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857
| | - Lusy Handoko
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
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10
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Liu X, Tan JP, Schröder J, Aberkane A, Ouyang JF, Mohenska M, Lim SM, Sun YBY, Chen J, Sun G, Zhou Y, Poppe D, Lister R, Clark AT, Rackham OJL, Zenker J, Polo JM. Modelling human blastocysts by reprogramming fibroblasts into iBlastoids. Nature 2021; 591:627-632. [PMID: 33731926 DOI: 10.1038/s41586-021-03372-y] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [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: 08/24/2020] [Accepted: 02/18/2021] [Indexed: 02/08/2023]
Abstract
Human pluripotent and trophoblast stem cells have been essential alternatives to blastocysts for understanding early human development1-4. However, these simple culture systems lack the complexity to adequately model the spatiotemporal cellular and molecular dynamics that occur during early embryonic development. Here we describe the reprogramming of fibroblasts into in vitro three-dimensional models of the human blastocyst, termed iBlastoids. Characterization of iBlastoids shows that they model the overall architecture of blastocysts, presenting an inner cell mass-like structure, with epiblast- and primitive endoderm-like cells, a blastocoel-like cavity and a trophectoderm-like outer layer of cells. Single-cell transcriptomics further confirmed the presence of epiblast-, primitive endoderm-, and trophectoderm-like cells. Moreover, iBlastoids can give rise to pluripotent and trophoblast stem cells and are capable of modelling, in vitro, several aspects of the early stage of implantation. In summary, we have developed a scalable and tractable system to model human blastocyst biology; we envision that this will facilitate the study of early human development and the effects of gene mutations and toxins during early embryogenesis, as well as aiding in the development of new therapies associated with in vitro fertilization.
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Affiliation(s)
- Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Jia Ping Tan
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Jan Schröder
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Asma Aberkane
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Monika Mohenska
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Sue Mei Lim
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Yu B Y Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Yichen Zhou
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Jennifer Zenker
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
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11
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Kamaraj US, Chen J, Katwadi K, Ouyang JF, Yang Sun YB, Lim YM, Liu X, Handoko L, Polo JM, Petretto E, Rackham OJ. EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance. Cell Syst 2020; 11:509-522.e10. [DOI: 10.1016/j.cels.2020.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 04/30/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022]
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12
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJ, Rackham OJ, Rizzu P, Martinez DFS, Sandelin A, Sanjana P, Semple CA, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest AR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJ, Shin JW, Carninci P. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020. [DOI: 10.1101/gr.270330.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Chothani S, Adami E, Ouyang JF, Viswanathan S, Hubner N, Cook SA, Schafer S, Rackham OJL. deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo-seq and RNA-seq Data. ACTA ACUST UNITED AC 2020; 129:e108. [PMID: 31763789 PMCID: PMC9285699 DOI: 10.1002/cpmb.108] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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] [Indexed: 11/22/2022]
Abstract
Ribosome profiling quantifies the genome‐wide ribosome occupancy of transcripts. With the integration of matched RNA sequencing data, the translation efficiency (TE) of genes can be calculated to reveal translational regulation. This layer of gene‐expression regulation is otherwise difficult to assess on a global scale and generally not well understood in the context of human disease. Current statistical methods to calculate differences in TE have low accuracy, cannot accommodate complex experimental designs or confounding factors, and do not categorize genes into buffered, intensified, or exclusively translationally regulated genes. This article outlines a method [referred to as deltaTE (ΔTE), standing for change in TE] to identify translationally regulated genes, which addresses the shortcomings of previous methods. In an extensive benchmarking analysis, ΔTE outperforms all methods tested. Furthermore, applying ΔTE on data from human primary cells allows detection of substantially more translationally regulated genes, providing a clearer understanding of translational regulation in pathogenic processes. In this article, we describe protocols for data preparation, normalization, analysis, and visualization, starting from raw sequencing files. © 2019 The Authors. Basic Protocol: One‐step detection and classification of differential translation efficiency genes using DTEG.R Alternate Protocol: Step‐wise detection and classification of differential translation efficiency genes using R Support Protocol: Workflow from raw data to read counts
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin, Berlin, Germany
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore.,National Heart Centre Singapore, Singapore.,National Heart and Lung Institute, Imperial College London, London, U.K.,MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London, U.K
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore.,National Heart Centre Singapore, Singapore
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
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14
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020; 30:1060-1072. [PMID: 32718982 PMCID: PMC7397864 DOI: 10.1101/gr.254219.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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Affiliation(s)
- Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Leonie Roos
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Christopher JF Cameron
- School of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden 01062, Germany.,Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Bioengineering, Tsinghua University, Beijing 100084, China
| | - Ryan Cardenas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Howard Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland
| | - Alexander Favorov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Diego Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lusy Handoko
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Hasegawa
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Norihito Hayatsu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Eddie L Imada
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Bogumil Kaczkowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Aditi Kanhere
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Emily Kawabata
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Tsugumi Kawashima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - S Thomas Kelly
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Anton Kratz
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mariola Kurowska-Stolarska
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom
| | - Andrew Tae Jun Kwon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jeffrey Leek
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fernando López-Redondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shiori Maeda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Vsevolod J Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuhiro R Nitta
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihiko Noro
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Denis Paquette
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Callum J C Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Patrizia Rizzu
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | | | - Albin Sandelin
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Pillay Sanjana
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Colin A M Semple
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Malte Thodberg
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Vidisha Tripathi
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roberto Verardo
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ilya E Vorontsov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chinatsu Yamamoto
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain
| | | | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen N-5008, Norway
| | - Claudio Schneider
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.,Department of Medicine and Consorzio Interuniversitario Biotecnologie p.zle Kolbe 1 University of Udine, Udine 33100, Italy
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
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15
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Cao EY, Ouyang JF, Rackham OJL. GeneSwitches: ordering gene expression and functional events in single-cell experiments. Bioinformatics 2020; 36:3273-3275. [DOI: 10.1093/bioinformatics/btaa099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/22/2020] [Accepted: 02/10/2020] [Indexed: 11/13/2022] Open
Abstract
Abstract
Summary
Emerging single-cell RNA-sequencing data technologies has made it possible to capture and assess the gene expression of individual cells. Based on the similarity of gene expression profiles, many tools have been developed to generate an in silico ordering of cells in the form of pseudo-time trajectories. However, these tools do not provide a means to find the ordering of critical gene expression changes over pseudo-time. We present GeneSwitches, a tool that takes any single-cell pseudo-time trajectory and determines the precise order of gene expression and functional-event changes over time. GeneSwitches uses a statistical framework based on logistic regression to identify the order in which genes are either switched on or off along pseudo-time. With this information, users can identify the order in which surface markers appear, investigate how functional ontologies are gained or lost over time and compare the ordering of switching genes from two related pseudo-temporal processes.
Availability
GeneSwitches is available at https://geneswitches.ddnetbio.com.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elaine Y Cao
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 169857, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 169857, Singapore
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 169857, Singapore
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16
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Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJL, Petretto E, Polo JM. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat Neurosci 2019; 22:2087-2097. [PMID: 31768052 DOI: 10.1038/s41593-019-0539-4] [Citation(s) in RCA: 434] [Impact Index Per Article: 86.8] [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] [Indexed: 12/12/2022]
Abstract
There is currently little information available about how individual cell types contribute to Alzheimer's disease. Here we applied single-nucleus RNA sequencing to entorhinal cortex samples from control and Alzheimer's disease brains (n = 6 per group), yielding a total of 13,214 high-quality nuclei. We detail cell-type-specific gene expression patterns, unveiling how transcriptional changes in specific cell subpopulations are associated with Alzheimer's disease. We report that the Alzheimer's disease risk gene APOE is specifically repressed in Alzheimer's disease oligodendrocyte progenitor cells and astrocyte subpopulations and upregulated in an Alzheimer's disease-specific microglial subopulation. Integrating transcription factor regulatory modules with Alzheimer's disease risk loci revealed drivers of cell-type-specific state transitions towards Alzheimer's disease. For example, transcription factor EB, a master regulator of lysosomal function, regulates multiple disease genes in a specific Alzheimer's disease astrocyte subpopulation. These results provide insights into the coordinated control of Alzheimer's disease risk genes and their cell-type-specific contribution to disease susceptibility. These results are available at http://adsn.ddnetbio.com.
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Affiliation(s)
- Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Gabriel Chew
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Xin Yi Choo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catriona McLean
- Victorian Brain Bank, Florey Institute of Neurosciences, Parkville, Victoria, Australia
| | - Rebecca K Simmons
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Sam Buckberry
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landin
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Daniel Poppe
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
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17
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Abstract
The process of identifying sets of transcription factors that can induce a cell conversion can be time-consuming and expensive. To help alleviate this, a number of computational tools have been developed which integrate gene expression data with molecular interaction networks in order to predict these factors. One such approach is Mogrify, an algorithm which ranks transcriptions factors based on their regulatory influence in different cell types and tissues. These ranks are then used to identify a nonredundant set of transcription factors to promote cell conversion between any two cell types/tissues. Here we summarize the important concepts and data sources that were used in the implementation of this approach. Furthermore, we describe how the associated web resource ( www.mogrify.net ) can be used to tailor predictions to specific experimental scenarios, for instance, limiting the set of possible transcription factors and including domain knowledge. Finally, we describe important considerations for the effective selection of reprogramming factors. We envision that such data-driven approaches will become commonplace in the field, rapidly accelerating the progress in stem cell biology.
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Affiliation(s)
- John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Uma S Kamaraj
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - Julian Gough
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
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Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
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Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
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Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Milan W. Cvitkovic
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
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Le HA, Tan HJ, Ouyang JF, Bettens RPA. Combined Fragmentation Method: A Simple Method for Fragmentation of Large Molecules. J Chem Theory Comput 2012; 8:469-78. [DOI: 10.1021/ct200783n] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Anh Le
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Hwee-Jia Tan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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