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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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2
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Daniszewski M, Nguyen Q, Chy HS, Singh V, Crombie DE, Kulkarni T, Liang HH, Sivakumaran P, Lidgerwood GE, Hernández D, Conquest A, Rooney LA, Chevalier S, Andersen SB, Senabouth A, Vickers JC, Mackey DA, Craig JE, Laslett AL, Hewitt AW, Powell JE, Pébay A. Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media. iScience 2018; 7:30-39. [PMID: 30267684 PMCID: PMC6135898 DOI: 10.1016/j.isci.2018.08.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 02/08/2023] Open
Abstract
We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium.
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Affiliation(s)
- Maciej Daniszewski
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hun S Chy
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Vikrant Singh
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Duncan E Crombie
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Tejal Kulkarni
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Priyadharshini Sivakumaran
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Grace E Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Damián Hernández
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Alison Conquest
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Louise A Rooney
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Sophie Chevalier
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Stacey B Andersen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne Senabouth
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA 6009, Australia
| | | | - Andrew L Laslett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Joseph E Powell
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia.
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3
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O'Brien CM, Chy HS, Zhou Q, Blumenfeld S, Lambshead JW, Liu X, Kie J, Capaldo BD, Chung TL, Adams TE, Phan T, Bentley JD, McKinstry WJ, Oliva K, McMurrick PJ, Wang YC, Rossello FJ, Lindeman GJ, Chen D, Jarde T, Clark AT, Abud HE, Visvader JE, Nefzger CM, Polo JM, Loring JF, Laslett AL. New Monoclonal Antibodies to Defined Cell Surface Proteins on Human Pluripotent Stem Cells. Stem Cells 2017; 35:626-640. [PMID: 28009074 PMCID: PMC5412944 DOI: 10.1002/stem.2558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/31/2016] [Accepted: 11/18/2016] [Indexed: 01/28/2023]
Abstract
The study and application of human pluripotent stem cells (hPSCs) will be enhanced by the availability of well‐characterized monoclonal antibodies (mAbs) detecting cell‐surface epitopes. Here, we report generation of seven new mAbs that detect cell surface proteins present on live and fixed human ES cells (hESCs) and human iPS cells (hiPSCs), confirming our previous prediction that these proteins were present on the cell surface of hPSCs. The mAbs all show a high correlation with POU5F1 (OCT4) expression and other hPSC surface markers (TRA‐160 and SSEA‐4) in hPSC cultures and detect rare OCT4 positive cells in differentiated cell cultures. These mAbs are immunoreactive to cell surface protein epitopes on both primed and naive state hPSCs, providing useful research tools to investigate the cellular mechanisms underlying human pluripotency and states of cellular reprogramming. In addition, we report that subsets of the seven new mAbs are also immunoreactive to human bone marrow‐derived mesenchymal stem cells (MSCs), normal human breast subsets and both normal and tumorigenic colorectal cell populations. The mAbs reported here should accelerate the investigation of the nature of pluripotency, and enable development of robust cell separation and tracing technologies to enrich or deplete for hPSCs and other human stem and somatic cell types. Stem Cells2017;35:626–640
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Affiliation(s)
- Carmel M O'Brien
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Hun S Chy
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Qi Zhou
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | | | - Jack W Lambshead
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Xiaodong Liu
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Joshua Kie
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Bianca D Capaldo
- The Walter and Eliza Hall Institute (WEHI), Parkville, Victoria, Australia.,Department of Medical Biology
| | - Tung-Liang Chung
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Timothy E Adams
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia
| | - Tram Phan
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia
| | - John D Bentley
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia
| | | | - Karen Oliva
- Department of Surgery, Cabrini Monash University, Malvern, Victoria, Australia
| | - Paul J McMurrick
- Department of Surgery, Cabrini Monash University, Malvern, Victoria, Australia
| | - Yu-Chieh Wang
- Department of Chemical Physiology.,Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Fernando J Rossello
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Geoffrey J Lindeman
- The Walter and Eliza Hall Institute (WEHI), Parkville, Victoria, Australia.,Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia.,Department of Medical Oncology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Di Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | - Thierry Jarde
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Cancer Program, Monash Biomedicine Discovery Institute.,Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | - Helen E Abud
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Cancer Program, Monash Biomedicine Discovery Institute
| | - Jane E Visvader
- The Walter and Eliza Hall Institute (WEHI), Parkville, Victoria, Australia.,Department of Medical Biology
| | - Christian M Nefzger
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Jose M Polo
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Jeanne F Loring
- Department of Chemical Physiology.,Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew L Laslett
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
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Kolle G, Shepherd JL, Gardiner B, Kassahn KS, Cloonan N, Wood DLA, Nourbakhsh E, Taylor DF, Wani S, Chy HS, Zhou Q, McKernan K, Kuersten S, Laslett AL, Grimmond SM. Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells. Genome Res 2011; 21:2014-25. [PMID: 22042643 DOI: 10.1101/gr.119321.110] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem cells (hESCs). We have shown that human embryonic stem (ES) cells display a high degree of transcriptional diversity, with more than half of active genes generating RNAs that differ from conventional gene models. We found evidence that more than 1000 genes express long 5' and/or extended 3'UTRs, which was confirmed by "virtual Northern" analysis. Exhaustive sequencing of the membrane-polysome and cytosolic/untranslated fractions of hESCs was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. The impact of this newly defined complexity on known gene-centric network models such as the Plurinet and the cell surface signaling machinery in human ES cells revealed a significant expansion of known transcript isoforms at play, many predicting possible alternative functions based on sequence alterations within key functional domains.
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Affiliation(s)
- Gabriel Kolle
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Queensland 4072, Australia
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5
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Kolle G, Ho M, Zhou Q, Chy HS, Krishnan K, Cloonan N, Bertoncello I, Laslett AL, Grimmond SM. Identification of human embryonic stem cell surface markers by combined membrane-polysome translation state array analysis and immunotranscriptional profiling. Stem Cells 2010; 27:2446-56. [PMID: 19650036 DOI: 10.1002/stem.182] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Surface marker expression forms the basis for characterization and isolation of human embryonic stem cells (hESCs). Currently, there are few well-defined protein epitopes that definitively mark hESCs. Here we combine immunotranscriptional profiling of hESC lines with membrane-polysome translation state array analysis (TSAA) to determine the full set of genes encoding potential hESC surface marker proteins. Three independently isolated hESC lines (HES2, H9, and MEL1) grown under feeder and feeder-free conditions were sorted into subpopulations by fluorescence-activated cell sorting based on coimmunoreactivity to the hESC surface markers GCTM-2 and CD9. Colony-forming assays confirmed that cells displaying high coimmunoreactivity to GCTM-2 and CD9 constitute an enriched subpopulation displaying multiple stem cell properties. Following microarray profiling, 820 genes were identified that were common to the GCTM-2(high)/CD9(high) stem cell-like subpopulation. Membrane-polysome TSAA analysis of hESCs identified 1,492 mRNAs encoding actively translated plasma membrane and secreted proteins. Combining these data sets, 88 genes encode proteins that mark the pluripotent subpopulation, of which only four had been previously reported. Cell surface immunoreactivity was confirmed for two of these markers: TACSTD1/EPCAM and CDH3/P-Cadherin, with antibodies for EPCAM able to enrich for pluripotent hESCs. This comprehensive listing of both hESCs and spontaneous differentiation-associated transcripts and survey of translated membrane-bound and secreted proteins provides a valuable resource for future study into the role of the extracellular environment in both the maintenance of pluripotency and directed differentiation.
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Affiliation(s)
- Gabriel Kolle
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
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McManamny P, Chy HS, Finkelstein DI, Craythorn RG, Crack PJ, Kola I, Cheema SS, Horne MK, Wreford NG, O'Bryan MK, De Kretser DM, Morrison JR. A mouse model of spinal and bulbar muscular atrophy. Hum Mol Genet 2002; 11:2103-11. [PMID: 12189162 DOI: 10.1093/hmg/11.18.2103] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Spinal and bulbar muscular atrophy (SBMA) is an adult-onset motor neuron disease, caused by the expansion of a trinucleotide repeat (TNR) in exon 1 of the androgen receptor (AR) gene. This disorder is characterized by degeneration of motor and sensory neurons, proximal muscular atrophy, and endocrine abnormalities, such as gynecomastia and reduced fertility. We describe the development of a transgenic model of SBMA expressing a full-length human AR (hAR) cDNA carrying 65 (AR(65)) or 120 CAG repeats (AR(120)), with widespread expression driven by the cytomegalovirus promoter. Mice carrying the AR(120) transgene displayed behavioral and motor dysfunction, while mice carrying 65 CAG repeats showed a mild phenotype. Progressive muscle weakness and atrophy was observed in AR(120) mice and was associated with the loss of alpha-motor neurons in the spinal cord. There was no evidence of neurodegeneration in other brain structures. Motor dysfunction was observed in both male and female animals, showing that in SBMA the polyglutamine repeat expansion causes a dominant gain-of-function mutation in the AR. The male mice displayed a progressive reduction in sperm production consistent with testis defects reported in human patients. These mice represent the first model to reproduce the key features of SBMA, making them a useful resource for characterizing disease progression, and for testing therapeutic strategies for both polyglutamine and motor neuron diseases.
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Affiliation(s)
- Patrick McManamny
- Monash Institute of Reproduction and Development, Monash University, 27-31 Wright Street, Clayton, Melbourne, Victoria, 3168, Australia
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