1
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Vo QD, Saito Y, Ida T, Nakamura K, Yuasa S. The use of artificial intelligence in induced pluripotent stem cell-based technology over 10-year period: A systematic scoping review. PLoS One 2024; 19:e0302537. [PMID: 38771829 PMCID: PMC11108174 DOI: 10.1371/journal.pone.0302537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/09/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Stem cell research, particularly in the domain of induced pluripotent stem cell (iPSC) technology, has shown significant progress. The integration of artificial intelligence (AI), especially machine learning (ML) and deep learning (DL), has played a pivotal role in refining iPSC classification, monitoring cell functionality, and conducting genetic analysis. These enhancements are broadening the applications of iPSC technology in disease modelling, drug screening, and regenerative medicine. This review aims to explore the role of AI in the advancement of iPSC research. METHODS In December 2023, data were collected from three electronic databases (PubMed, Web of Science, and Science Direct) to investigate the application of AI technology in iPSC processing. RESULTS This systematic scoping review encompassed 79 studies that met the inclusion criteria. The number of research studies in this area has increased over time, with the United States emerging as a leading contributor in this field. AI technologies have been diversely applied in iPSC technology, encompassing the classification of cell types, assessment of disease-specific phenotypes in iPSC-derived cells, and the facilitation of drug screening using iPSC. The precision of AI methodologies has improved significantly in recent years, creating a foundation for future advancements in iPSC-based technologies. CONCLUSIONS Our review offers insights into the role of AI in regenerative and personalized medicine, highlighting both challenges and opportunities. Although still in its early stages, AI technologies show significant promise in advancing our understanding of disease progression and development, paving the way for future clinical applications.
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Affiliation(s)
- Quan Duy Vo
- Faculty of Medicine, Department of Cardiovascular Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
- Faculty of Medicine, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Yukihiro Saito
- Department of Cardiovascular Medicine, Okayama University Hospital, Okayama, Japan
| | - Toshihiro Ida
- Faculty of Medicine, Department of Cardiovascular Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kazufumi Nakamura
- Faculty of Medicine, Department of Cardiovascular Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shinsuke Yuasa
- Faculty of Medicine, Department of Cardiovascular Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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2
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Krontira AC, Cruceanu C, Dony L, Kyrousi C, Link MH, Rek N, Pöhlchen D, Raimundo C, Penner-Goeke S, Schowe A, Czamara D, Lahti-Pulkkinen M, Sammallahti S, Wolford E, Heinonen K, Roeh S, Sportelli V, Wölfel B, Ködel M, Sauer S, Rex-Haffner M, Räikkönen K, Labeur M, Cappello S, Binder EB. Human cortical neurogenesis is altered via glucocorticoid-mediated regulation of ZBTB16 expression. Neuron 2024; 112:1426-1443.e11. [PMID: 38442714 DOI: 10.1016/j.neuron.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 08/15/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
Glucocorticoids are important for proper organ maturation, and their levels are tightly regulated during development. Here, we use human cerebral organoids and mice to study the cell-type-specific effects of glucocorticoids on neurogenesis. We show that glucocorticoids increase a specific type of basal progenitors (co-expressing PAX6 and EOMES) that has been shown to contribute to cortical expansion in gyrified species. This effect is mediated via the transcription factor ZBTB16 and leads to increased production of neurons. A phenome-wide Mendelian randomization analysis of an enhancer variant that moderates glucocorticoid-induced ZBTB16 levels reveals causal relationships with higher educational attainment and altered brain structure. The relationship with postnatal cognition is also supported by data from a prospective pregnancy cohort study. This work provides a cellular and molecular pathway for the effects of glucocorticoids on human neurogenesis that relates to lasting postnatal phenotypes.
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Affiliation(s)
- Anthi C Krontira
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany.
| | - Cristiana Cruceanu
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Leander Dony
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany; Department for Computational Health, Helmholtz Munich, Neuherberg 85764, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising 85354, Germany
| | - Christina Kyrousi
- Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich 80804, Germany; First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, Athens 15784, Greece; University Mental Health, Neurosciences and Precision Medicine Research Institute "Costas Stefanis", Athens 15601, Greece
| | - Marie-Helen Link
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Nils Rek
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany
| | - Dorothee Pöhlchen
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany
| | - Catarina Raimundo
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Signe Penner-Goeke
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Alicia Schowe
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University, Munich 82152, Germany
| | - Darina Czamara
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Marius Lahti-Pulkkinen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland; Finnish Institute for Health and Welfare, Helsinki 00271, Finland; Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Sara Sammallahti
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki 00014, Finland
| | - Elina Wolford
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Kati Heinonen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland; Psychology/Welfare, Faculty of Social Sciences, University of Tampere, Tampere 33014, Finland; Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, ON M5T 1P8, Canada
| | - Simone Roeh
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Vincenza Sportelli
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Wölfel
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Maik Ködel
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Susann Sauer
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Monika Rex-Haffner
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Marta Labeur
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Silvia Cappello
- Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich 80804, Germany; Physiological Genomics, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU), Munich 82152, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany.
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3
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KIMURA K, NAGAKURA H, TSUKAMOTO M, YOSHIDA T, SUGISAKI H, SHISHIDA K, TACHI Y, SHIMASAKI S, SUGIURA K, HATOYA S. Canine induced pluripotent stem cells can be successfully maintained in weekend-free culture systems. J Vet Med Sci 2024; 86:247-257. [PMID: 38171744 PMCID: PMC10963097 DOI: 10.1292/jvms.23-0422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024] Open
Abstract
Canine induced pluripotent stem cells (ciPSCs) can provide useful insights into novel therapies in both veterinary and medical fields. However, limited accessibility to the present culture medium and requirement of considerable time, effort, and cost for routine ciPSC maintenance restrict advancement in ciPSC research. In addition, it is unknown whether ciPSC culture conditions influence differentiation propensity. We investigated the availability of the common human pluripotent stem cells (hPSCs) culture systems for ciPSC maintenance and the differentiation propensities of the ciPSCs maintained in these culture systems. StemFlex and mTeSR Plus supported PSC-like colony formation and pluripotency markers expression in ciPSCs even after five passages. Additionally, ciPSCs were maintained under weekend-free culture conditions with a stable growth rate, pluripotency marker expression, and differentiation abilities using vitronectin (VTN-N) and Geltrex. Following maintenance of spontaneously differentiated ciPSCs under various conditions by embryoid body formation, there were few differences in the differentiation propensities of ciPSCs among the tested culture conditions. Thus, ciPSCs were successfully cultured under weekend-free conditions for ciPSC maintenance using StemFlex or mTeSR Plus with VTN-N or Geltrex. The present study offers simpler and more effort-, time-, and cost-saving options for ciPSC culture systems, which may lead to further development in research using ciPSCs.
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Affiliation(s)
- Kazuto KIMURA
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Hiroya NAGAKURA
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Masaya TSUKAMOTO
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Takumi YOSHIDA
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Hiroko SUGISAKI
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Kohei SHISHIDA
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Yuta TACHI
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Shoko SHIMASAKI
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Kikuya SUGIURA
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
| | - Shingo HATOYA
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
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4
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Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Rep 2024; 43:113664. [PMID: 38194345 PMCID: PMC11231959 DOI: 10.1016/j.celrep.2023.113664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sakshi Bhatele
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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5
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Andrews PW, Gokhale PJ. A short history of pluripotent stem cells markers. Stem Cell Reports 2024; 19:1-10. [PMID: 38157849 PMCID: PMC10828816 DOI: 10.1016/j.stemcr.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
The expression of one or more of a small number of molecules, typically cell surface-associated antigens, or transcription factors, is widely used for identifying pluripotent stem cells (PSCs) or for monitoring their differentiation. However, none of these marker molecules are uniquely expressed by PSCs and all are expressed by stem cells that have lost the ability to differentiate. Consequently, none are indicators of pluripotency, per se. Here we summarize the nature and characteristics of several markers that are in wide use, including the cell surface antigens, stage-specific embryonic antigen (SSEA)-1, SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, GCTM2, and the transcription factors POUF5/OCT4, NANOG, and SOX2, highlighting issues that must be considered when interpreting data about their expression on putative PSCs.
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Affiliation(s)
- Peter W Andrews
- The School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Paul J Gokhale
- The School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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6
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Li CY, Liang Z, Liu L, Kuang Y. Intracellular Molecules Induced Extracellular Peptide Self-Assembly for Efficient and Effective In Situ Cell Purification. Angew Chem Int Ed Engl 2023; 62:e202306533. [PMID: 37483172 DOI: 10.1002/anie.202306533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/25/2023]
Abstract
Synthetic messenger RNA (mRNA) switches are powerful tools for in situ cell purification, especially for cells derived from stem cells. However, the retention effectiveness of the target cells is limited by the leaky expression of toxic protein. The elimination efficiency of non-target cells is also constrained due to the lack of signal amplification. In this study, we designed a novel approach that uses synthetic mRNA switch to convey intracellular marker molecule information into spatially controlled extracellular toxic assembly formation. The approach bypasses the use of toxic protein to ensure high target cell recovery effectiveness. Meanwhile, the marker molecule information is amplified at multiple levels to ensure high non-target cell elimination effectiveness. Our approach can be tailored to meet various in situ cell purification needs, promising high-quality in situ cell purification for a wide range of biomedical applications.
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Affiliation(s)
- Cheuk Yin Li
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, Hong Kong
| | - Zhenghua Liang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, Hong Kong
| | - Lejian Liu
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, Hong Kong
| | - Yi Kuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, Hong Kong
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7
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Sun T, Xu Y, Xiang Y, Ou J, Soderblom EJ, Diao Y. Crosstalk between RNA m 6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells. Nat Genet 2023; 55:1324-1335. [PMID: 37474847 PMCID: PMC10766344 DOI: 10.1038/s41588-023-01452-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Transposable elements (TEs) are parasitic DNA sequences accounting for over half of the human genome. Tight control of the repression and activation states of TEs is critical for genome integrity, development, immunity and diseases, including cancer. However, precisely how this regulation is achieved remains unclear. Here we develop a targeted proteomic proximity labeling approach to capture TE-associated proteins in human embryonic stem cells (hESCs). We find that the RNA N6-methyladenosine (m6A) reader, YTHDC2, occupies genomic loci of the primate-specific TE, LTR7/HERV-H, specifically through its interaction with m6A-modified HERV-H RNAs. Unexpectedly, YTHDC2 recruits the DNA 5-methylcytosine (5mC)-demethylase, TET1, to remove 5mC from LTR7/HERV-H and prevent epigenetic silencing. Functionally, the YTHDC2/LTR7 axis inhibits neural differentiation of hESCs. Our results reveal both an underappreciated crosstalk between RNA m6A and DNA 5mC, the most abundant regulatory modifications of RNA and DNA in eukaryotes, and the fact that in hESCs this interplay controls TE activity and cell fate.
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Affiliation(s)
- Tongyu Sun
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Yueyuan Xu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Erik J Soderblom
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.
- Department of Orthopaedics Surgery, Duke University Medical Center, Durham, NC, USA.
- Department of Pathology, Duke University Medical Center, Durham, NC, USA.
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8
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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: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [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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Noh KM, Park SJ, Moon SH, Jung SY. Extracellular matrix cues regulate the differentiation of pluripotent stem cell-derived endothelial cells. Front Cardiovasc Med 2023; 10:1169331. [PMID: 37435057 PMCID: PMC10330705 DOI: 10.3389/fcvm.2023.1169331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023] Open
Abstract
The generation of endothelial cells (ECs) from human pluripotent stem cells (PSCs) has been a promising approach for treating cardiovascular diseases for several years. Human PSCs, particularly induced pluripotent stem cells (iPSCs), are an attractive source of ECs for cell therapy. Although there is a diversity of methods for endothelial cell differentiation using biochemical factors, such as small molecules and cytokines, the efficiency of EC production varies depending on the type and dose of biochemical factors. Moreover, the protocols in which most EC differentiation studies have been performed were in very unphysiological conditions that do not reflect the microenvironment of native tissue. The microenvironment surrounding stem cells exerts variable biochemical and biomechanical stimuli that can affect stem cell differentiation and behavior. The stiffness and components of the extracellular microenvironment are critical inducers of stem cell behavior and fate specification by sensing the extracellular matrix (ECM) cues, adjusting the cytoskeleton tension, and delivering external signals to the nucleus. Differentiation of stem cells into ECs using a cocktail of biochemical factors has been performed for decades. However, the effects of mechanical stimuli on endothelial cell differentiation remain poorly understood. This review provides an overview of the methods used to differentiate ECs from stem cells by chemical and mechanical stimuli. We also propose the possibility of a novel EC differentiation strategy using a synthetic and natural extracellular matrix.
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Affiliation(s)
- Kyung Mu Noh
- Stem Cell Research Institute, T&R Biofab Co. Ltd., Seongnam-si, Republic of Korea
| | - Soon-Jung Park
- Stem Cell Research Institute, T&R Biofab Co. Ltd., Seongnam-si, Republic of Korea
| | - Sung-Hwan Moon
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong-si, Republic of Korea
| | - Seok Yun Jung
- Stem Cell Research Institute, T&R Biofab Co. Ltd., Seongnam-si, Republic of Korea
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10
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Cooke JA, Voigt AP, Collingwood MA, Stone NE, Whitmore SS, DeLuca AP, Burnight ER, Anfinson KR, Vakulskas CA, Reutzel AJ, Daggett HT, Andorf JL, Stone EM, Mullins RF, Tucker BA. Propensity of Patient-Derived iPSCs for Retinal Differentiation: Implications for Autologous Cell Replacement. Stem Cells Transl Med 2023; 12:365-378. [PMID: 37221451 PMCID: PMC10267581 DOI: 10.1093/stcltm/szad028] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/26/2023] [Indexed: 05/25/2023] Open
Abstract
Prior to use, newly generated induced pluripotent stem cells (iPSC) should be thoroughly validated. While excellent validation and release testing assays designed to evaluate potency, genetic integrity, and sterility exist, they do not have the ability to predict cell type-specific differentiation capacity. Selection of iPSC lines that have limited capacity to produce high-quality transplantable cells, places significant strain on valuable clinical manufacturing resources. The purpose of this study was to determine the degree and root cause of variability in retinal differentiation capacity between cGMP-derived patient iPSC lines. In turn, our goal was to develop a release testing assay that could be used to augment the widely used ScoreCard panel. IPSCs were generated from 15 patients (14-76 years old), differentiated into retinal organoids, and scored based on their retinal differentiation capacity. Despite significant differences in retinal differentiation propensity, RNA-sequencing revealed remarkable similarity between patient-derived iPSC lines prior to differentiation. At 7 days of differentiation, significant differences in gene expression could be detected. Ingenuity pathway analysis revealed perturbations in pathways associated with pluripotency and early cell fate commitment. For example, good and poor producers had noticeably different expressions of OCT4 and SOX2 effector genes. QPCR assays targeting genes identified via RNA sequencing were developed and validated in a masked fashion using iPSCs from 8 independent patients. A subset of 14 genes, which include the retinal cell fate markers RAX, LHX2, VSX2, and SIX6 (all elevated in the good producers), were found to be predictive of retinal differentiation propensity.
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Affiliation(s)
- Jessica A Cooke
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Andrew P Voigt
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | | | - Nicholas E Stone
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - S Scott Whitmore
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Adam P DeLuca
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Erin R Burnight
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Kristin R Anfinson
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | | | - Austin J Reutzel
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Heather T Daggett
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jeaneen L Andorf
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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11
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Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544654. [PMID: 37398435 PMCID: PMC10312660 DOI: 10.1101/2023.06.12.544654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.
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Affiliation(s)
- Matthew M. Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Dashiell J. Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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12
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Isoda M, Sanosaka T, Tomooka R, Mabuchi Y, Shinozaki M, Andoh-Noda T, Banno S, Mizota N, Yamaguchi R, Okano H, Kohyama J. Mesenchymal properties of iPSC-derived neural progenitors that generate undesired grafts after transplantation. Commun Biol 2023; 6:611. [PMID: 37286713 DOI: 10.1038/s42003-023-04995-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
Although neural stem/progenitor cells derived from human induced pluripotent stem cells (hiPSC-NS/PCs) are expected to be a cell source for cell-based therapy, tumorigenesis of hiPSC-NS/PCs is a potential problem for clinical applications. Therefore, to understand the mechanisms of tumorigenicity in NS/PCs, we clarified the cell populations of NS/PCs. We established single cell-derived NS/PC clones (scNS/PCs) from hiPSC-NS/PCs that generated undesired grafts. Additionally, we performed bioassays on scNS/PCs, which classified cell types within parental hiPSC-NS/PCs. Interestingly, we found unique subsets of scNS/PCs, which exhibited the transcriptome signature of mesenchymal lineages. Furthermore, these scNS/PCs expressed both neural (PSA-NCAM) and mesenchymal (CD73 and CD105) markers, and had an osteogenic differentiation capacity. Notably, eliminating CD73+ CD105+ cells from among parental hiPSC-NS/PCs ensured the quality of hiPSC-NS/PCs. Taken together, the existence of unexpected cell populations among NS/PCs may explain their tumorigenicity leading to potential safety issues of hiPSC-NS/PCs for future regenerative medicine.
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Affiliation(s)
- Miho Isoda
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
- Regenerative & Cellular Medicine Kobe Center, Sumitomo Pharma Co., Ltd., Kobe, Hyogo, 650-0047, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ryo Tomooka
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yo Mabuchi
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
- Intractable Disease Research Centre, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
- Department of Clinical Regenerative Medicine, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Munehisa Shinozaki
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Tomoko Andoh-Noda
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Satoe Banno
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Noriko Mizota
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ryo Yamaguchi
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
- Regenerative & Cellular Medicine Kobe Center, Sumitomo Pharma Co., Ltd., Kobe, Hyogo, 650-0047, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Jun Kohyama
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.
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Li YR, Dunn ZS, Yu Y, Li M, Wang P, Yang L. Advancing cell-based cancer immunotherapy through stem cell engineering. Cell Stem Cell 2023; 30:592-610. [PMID: 36948187 PMCID: PMC10164150 DOI: 10.1016/j.stem.2023.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/04/2023] [Accepted: 02/22/2023] [Indexed: 03/24/2023]
Abstract
Advances in cell-based therapy, particularly CAR-T cell therapy, have transformed the treatment of hematological malignancies. Although an important step forward for the field, autologous CAR-T therapies are hindered by high costs, manufacturing challenges, and limited efficacy against solid tumors. With ongoing progress in gene editing and culture techniques, engineered stem cells and their application in cell therapy are poised to address some of these challenges. Here, we review stem cell-based immunotherapy approaches, stem cell sources, gene engineering and manufacturing strategies, therapeutic platforms, and clinical trials, as well as challenges and future directions for the field.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zachary Spencer Dunn
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Yanqi Yu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Miao Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pin Wang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA; Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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14
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Stricker E, Peckham-Gregory EC, Scheurer ME. HERVs and Cancer-A Comprehensive Review of the Relationship of Human Endogenous Retroviruses and Human Cancers. Biomedicines 2023; 11:936. [PMID: 36979914 PMCID: PMC10046157 DOI: 10.3390/biomedicines11030936] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Genomic instability and genetic mutations can lead to exhibition of several cancer hallmarks in affected cells such as sustained proliferative signaling, evasion of growth suppression, activated invasion, deregulation of cellular energetics, and avoidance of immune destruction. Similar biological changes have been observed to be a result of pathogenic viruses and, in some cases, have been linked to virus-induced cancers. Human endogenous retroviruses (HERVs), once external pathogens, now occupy more than 8% of the human genome, representing the merge of genomic and external factors. In this review, we outline all reported effects of HERVs on cancer development and discuss the HERV targets most suitable for cancer treatments as well as ongoing clinical trials for HERV-targeting drugs. We reviewed all currently available reports of the effects of HERVs on human cancers including solid tumors, lymphomas, and leukemias. Our review highlights the central roles of HERV genes, such as gag, env, pol, np9, and rec in immune regulation, checkpoint blockade, cell differentiation, cell fusion, proliferation, metastasis, and cell transformation. In addition, we summarize the involvement of HERV long terminal repeat (LTR) regions in transcriptional regulation, creation of fusion proteins, expression of long non-coding RNAs (lncRNAs), and promotion of genome instability through recombination.
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Affiliation(s)
- Erik Stricker
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
| | | | - Michael E. Scheurer
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
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15
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Czerminski JT, King OD, Lawrence JB. Large-scale organoid study suggests effects of trisomy 21 on early fetal neurodevelopment are more subtle than variability between isogenic lines and experiments. Front Neurosci 2023; 16:972201. [PMID: 36817096 PMCID: PMC9935940 DOI: 10.3389/fnins.2022.972201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/08/2022] [Indexed: 02/05/2023] Open
Abstract
This study examines cortical organoids generated from a panel of isogenic trisomic and disomic iPSC lines (subclones) as a model of early fetal brain development in Down syndrome (DS). An initial experiment comparing organoids from one trisomic and one disomic line showed many genome-wide transcriptomic differences and modest differences in cell-type proportions, suggesting there may be a neurodevelopmental phenotype that is due to trisomy of chr21. To better control for multiple sources of variation, we undertook a highly robust study of ∼1,200 organoids using an expanded panel of six all-isogenic lines, three disomic, and three trisomic. The power of this experimental design was indicated by strong detection of the ∼1.5-fold difference in chr21 genes. However, the numerous expression differences in non-chr21 genes seen in the smaller experiment fell away, and the differences in cell-type representation between lines did not correlate with trisomy 21. Results suggest that the initial smaller experiment picked up differences between small organoid samples and individual isogenic lines, which "averaged out" in the larger panel of isogenic lines. Our results indicate that even when organoid and batch variability are better controlled for, variation between isogenic cell lines (even subclones) may obscure, or be conflated with, subtle neurodevelopmental phenotypes that may be present in ∼2nd trimester DS brain development. Interestingly, despite this variability between organoid batches and lines, and the "fetal stage" of these organoids, an increase in secreted Aβ40 peptide levels-an Alzheimer-related cellular phenotype-was more strongly associated with trisomy 21 status than were neurodevelopmental shifts in cell-type composition.
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Affiliation(s)
- Jan T. Czerminski
- Medical Scientist Training Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Oliver D. King
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States,Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States,*Correspondence: Jeanne B. Lawrence,
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16
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Suresh Babu S, Duvvuru H, Baker J, Switalski S, Shafa M, Panchalingam KM, Dadgar S, Beller J, Ahmadian Baghbaderani B. Characterization of human induced pluripotent stems cells: Current approaches, challenges, and future solutions. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 37:e00784. [PMID: 36818379 PMCID: PMC9929203 DOI: 10.1016/j.btre.2023.e00784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023]
Abstract
Human induced pluripotent stem cells (iPSC) have demonstrated massive potentials for use in regenerative and personalized medicine due to their ability to expand in culture and differentiate into specialized cells with therapeutic benefits. However, in order to industrialize iPSC-derived therapies, it is necessary to address the existing challenges surrounding the analytics implemented in the manufacturing process to evaluate and monitor cell expansion, differentiation, and quality of the final products. Here, we review some of the key analytical methods used as part of identity, potency, or safety for in-process or final product release testing and highlighted the challenges and potential solutions for consideration in the Chemistry, Manufacturing and Controls (CMC) strategy for iPSC-based therapies. Some of the challenges associated with characterization and testing of iPSC-based products are related to the choice of analytical technology (to ensure fit-for-purpose), assay reliability and robustness. Automation of analytical methods may be required to reduce hands on time, and improve reliability of the methods through reducing assay variability. Indeed, we have shown that automation of analytical methods is feasible (evaluated using an ELISA based assay) and would result in more precise measurements (demonstrated by lower co-efficient of Variation and standard deviation), less hands-on time, and swift compared to a manually run assay. Therefore, in order to support commercialization of iPSC-based therapies we suggest a well-designed testing strategy to be established in the development phase while incorporating robust, reproducible, reliable, and potentially automated analytics in the manufacturing process.
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Yoshida S, Kato TM, Sato Y, Umekage M, Ichisaka T, Tsukahara M, Takasu N, Yamanaka S. A clinical-grade HLA haplobank of human induced pluripotent stem cells matching approximately 40% of the Japanese population. MED 2023; 4:51-66.e10. [PMID: 36395757 DOI: 10.1016/j.medj.2022.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/02/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Human induced pluripotent stem cells (iPSCs) are expected to be useful for regenerative medicine for many diseases. Many researchers have focused on and enabled the generation of differentiated cells or tissue-like structures, including organoids, which help to ameliorate target diseases. To promote such cell therapies, we established a clinically applicable iPSC haplobank matching as many people as possible in Japan. METHODS Through cooperation with several organizations, we recruited donors whose human leukocyte antigens (HLAs) involved in immunorejection were homozygous. The peripheral or umbilical cord blood collected from the donors was used for iPSC production by electroporation of episomal vectors. These iPSC lines were then subjected to testing, including genome analyses and sterility, to maximize safety. FINDINGS We constructed a clinical-grade haplobank of 27 iPSC lines from 7 donors according to good manufacturing practice regulations. However, reasons to avoid using iPSC lines include the presence of residual episomal vectors or genetic mutations in cancer-related genes. CONCLUSIONS This haplobank provides HLA-matched iPSC lines for approximately 40% of the Japanese population. Since the haplobank's release in 2015, these iPSC lines have been used in more than 10 clinical trials. The establishment of this haplobank is an important step toward the clinical application of iPSCs in cell therapies. FUNDING This study was supported by a research center network for the realization of regenerative medicine of the Japan Agency for Medical Research and Development (AMED) under grant number JP20bm0104001h0108.
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Affiliation(s)
- Shinsuke Yoshida
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Tomoaki M Kato
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Yoshiko Sato
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masafumi Umekage
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Tomoko Ichisaka
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | | | - Naoko Takasu
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Shinya Yamanaka
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan; Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
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18
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Galiakberova AA, Brovkina OI, Kondratyev NV, Artyuhov AS, Momotyuk ED, Kulmukhametova ON, Lagunin AA, Shilov BV, Zadorozhny AD, Zakharov IS, Okorokova LS, Golimbet VE, Dashinimaev EB. Different iPSC-derived neural stem cells shows various spectrums of spontaneous differentiation during long term cultivation. Front Mol Neurosci 2023; 16:1037902. [PMID: 37201156 PMCID: PMC10186475 DOI: 10.3389/fnmol.2023.1037902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/23/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction Culturing of human neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSC) is a promising area of research, as these cells have the potential to treat a wide range of neurological, neurodegenerative and psychiatric diseases. However, the development of optimal protocols for the production and long-term culturing of NSCs remains a challenge. One of the most important aspects of this problem is to determine the stability of NSCs during long-term in vitro passaging. To address this problem, our study was aimed at investigating the spontaneous differentiation profile in different iPSC-derived human NSCs cultures during long-term cultivation using. Methods Four different IPSC lines were used to generate NSC and spontaneously differentiated neural cultures using DUAL SMAD inhibition. These cells were analyzed at different passages using immunocytochemistry, qPCR, bulk transcriptomes and scRNA-seq. Results We found that various NSC lines generate significantly different spectrums of differentiated neural cells, which can also change significantly during long-term cultivation in vitro. Discussion Our results indicate that both internal (genetic and epigenetic) and external (conditions and duration of cultivation) factors influence the stability of NSCs. These results have important implications for the development of optimal NSCs culturing protocols and highlight the need to further investigate the factors influencing the stability of these cells in vitro.
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Affiliation(s)
- Adelya Albertovna Galiakberova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Igorevna Brovkina
- Federal Research and Clinical Center, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | | | - Alexander Sergeevich Artyuhov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina Dmitrievna Momotyuk
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Alexey Aleksandrovich Lagunin
- Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - Igor Sergeevitch Zakharov
- Department of Bioinformatics, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Erdem Bairovich Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Bioinformatics, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- *Correspondence: Erdem Bairovich Dashinimaev,
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Byers C, Spruce C, Fortin HJ, Hartig EI, Czechanski A, Munger SC, Reinholdt LG, Skelly DA, Baker CL. Genetic control of the pluripotency epigenome determines differentiation bias in mouse embryonic stem cells. EMBO J 2022; 41:e109445. [PMID: 34931323 PMCID: PMC8762565 DOI: 10.15252/embj.2021109445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023] Open
Abstract
Genetically diverse pluripotent stem cells display varied, heritable responses to differentiation cues. Here, we harnessed these disparities through derivation of mouse embryonic stem cells from the BXD genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, to identify loci regulating cell state transitions. Upon transition to formative pluripotency, B6 stem cells quickly dissolved naïve networks adopting gene expression modules indicative of neuroectoderm lineages, whereas D2 retained aspects of naïve pluripotency. Spontaneous formation of embryoid bodies identified divergent differentiation where B6 showed a propensity toward neuroectoderm and D2 toward definitive endoderm. Genetic mapping identified major trans-acting loci co-regulating chromatin accessibility and gene expression in both naïve and formative pluripotency. These loci distally modulated occupancy of pluripotency factors at hundreds of regulatory elements. One trans-acting locus on Chr 12 primarily impacted chromatin accessibility in embryonic stem cells, while in epiblast-like cells, the same locus subsequently influenced expression of genes enriched for neurogenesis, suggesting early chromatin priming. These results demonstrate genetically determined biases in lineage commitment and identify major regulators of the pluripotency epigenome.
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Affiliation(s)
- Candice Byers
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | - Haley J Fortin
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | - Ellen I Hartig
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | - Steven C Munger
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | | | - Christopher L Baker
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
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20
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Yamatani Y, Nakai K. Comprehensive comparison of gene expression diversity among a variety of human stem cells. NAR Genom Bioinform 2022; 4:lqac087. [PMCID: PMC9706419 DOI: 10.1093/nargab/lqac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/26/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022] Open
Abstract
Several factors, including tissue origins and culture conditions, affect the gene expression of undifferentiated stem cells. However, understanding the basic identity across different stem cells has not been pursued well despite its importance in stem cell biology. Thus, we aimed to rank the relative importance of multiple factors to gene expression profile among undifferentiated human stem cells by analyzing publicly available RNA-seq datasets. We first conducted batch effect correction to avoid undefined variance in the dataset as possible. Then, we highlighted the relative impact of biological and technical factors among undifferentiated stem cell types: a more influence on tissue origins in induced pluripotent stem cells than in other stem cell types; a stronger impact of culture condition in embryonic stem cells and somatic stem cell types, including mesenchymal stem cells and hematopoietic stem cells. In addition, we found that a characteristic gene module, enriched in histones, exhibits higher expression across different stem cell types that were annotated by specific culture conditions. This tendency was also observed in mouse stem cell RNA-seq data. Our findings would help to obtain general insights into stem cell quality, such as the balance of differentiation potentials that undifferentiated stem cells possess.
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Affiliation(s)
- Yukiyo Yamatani
- Department of Computational Biology and Medical Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Kenta Nakai
- To whom correspondence should be addressed. Tel: +81 3 5449 5131; Fax: +81 3 5449 5133;
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21
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Thanuthanakhun N, Kim MH, Kino-oka M. Cell Behavioral Dynamics as a Cue in Optimizing Culture Stabilization in the Bioprocessing of Pluripotent Stem Cells. Bioengineering (Basel) 2022; 9:669. [PMID: 36354580 PMCID: PMC9687444 DOI: 10.3390/bioengineering9110669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/28/2022] [Accepted: 11/05/2022] [Indexed: 04/23/2024] Open
Abstract
Pluripotent stem cells (PSCs) are important for future regenerative medicine therapies. However, in the production of PSCs and derivatives, the control of culture-induced fluctuations in the outcome of cell quality remains challenging. A detailed mechanistic understanding of how PSC behaviors are altered in response to biomechanical microenvironments within a culture is necessary for rational bioprocessing optimization. In this review, we discuss recent insights into the role of cell behavioral and mechanical homeostasis in modulating the states and functions of PSCs during culture processes. We delineate promising ways to manipulate the culture variability through regulating cell behaviors using currently developed tools. Furthermore, we anticipate their potential implementation for designing a culture strategy based on the concept of Waddington's epigenetic landscape that may provide a feasible solution for tuning the culture quality and stability in the bioprocessing space.
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Affiliation(s)
- Naruchit Thanuthanakhun
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Masahiro Kino-oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
- Research Base for Cell Manufacturability, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
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22
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Miyazaki T, Hanamatsu H, Onodera T, Furukawa JI, Xu L, Homan K, Baba R, Kawasaki T, Iwasaki N. Establishment of the removal method of undifferentiated induced pluripotent stem cells coexisting with chondrocytes using R-17F antibody. Regen Med 2022; 17:793-803. [PMID: 36154668 DOI: 10.2217/rme-2022-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Tumorigenicity of residual undifferentiated induced pluripotent stem cells (iPSCs) is a major concern. The purpose of this study was to investigate the optimal conditions for removal of iPSCs using R-17F antibody, which recognizes specific glycosphingolipids glycans on undifferentiated iPSCs and exhibits selective cytotoxicity to iPSCs. Materials & methods: After adding of R-17F and secondary antibody to co-cultured iPSCs and chondrocytes, residual iPSCs were quantitatively evaluated by iPS specific glycome analysis. Results: Undifferentiated iPSCs were sufficiently removed using R-17F in combination with an equal amount of a secondary antibody. Furthermore, teratomas were not observed upon transplantation of co-cultured cells pretreated under the same conditions into testes of immunodeficient mice. Conclusion: This removal method incorporating R-17F may be useful for regenerative medicine using iPSCs.
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Affiliation(s)
- Takuji Miyazaki
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060 8638, Japan
| | - Hisatoshi Hanamatsu
- Department of Advanced Clinical Glycobiology, Faculty of Medicine & Graduate School of Medicine, Hokkaido, Kita 21, Nishi 11, Kita-ku, Sapporo, Hokkaido, 001 0021, Japan
| | - Tomohiro Onodera
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060 8638, Japan.,Department of Advanced Clinical Glycobiology, Faculty of Medicine & Graduate School of Medicine, Hokkaido, Kita 21, Nishi 11, Kita-ku, Sapporo, Hokkaido, 001 0021, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research & Education (GSS, GI-CoRE), Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, Hokkaido, 001 0021, Japan
| | - Jun-Ichi Furukawa
- Department of Advanced Clinical Glycobiology, Faculty of Medicine & Graduate School of Medicine, Hokkaido, Kita 21, Nishi 11, Kita-ku, Sapporo, Hokkaido, 001 0021, Japan
| | - Liang Xu
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060 8638, Japan
| | - Kentaro Homan
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060 8638, Japan
| | - Rikiya Baba
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060 8638, Japan
| | - Toshisuke Kawasaki
- Research Center for Glycobiotechnology, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525 8577, Japan
| | - Norimasa Iwasaki
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060 8638, Japan.,Department of Advanced Clinical Glycobiology, Faculty of Medicine & Graduate School of Medicine, Hokkaido, Kita 21, Nishi 11, Kita-ku, Sapporo, Hokkaido, 001 0021, Japan
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23
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Cantor EL, Shen F, Jiang G, Tan Z, Cunningham GM, Wu X, Philips S, Schneider BP. Passage number affects differentiation of sensory neurons from human induced pluripotent stem cells. Sci Rep 2022; 12:15869. [PMID: 36151116 PMCID: PMC9508090 DOI: 10.1038/s41598-022-19018-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are a valuable resource for neurological disease-modeling and drug discovery due to their ability to differentiate into neurons reflecting the genetics of the patient from which they are derived. iPSC-derived cultures, however, are highly variable due to heterogeneity in culture conditions. We investigated the effect of passage number on iPSC differentiation to optimize the generation of sensory neurons (iPSC-dSNs). Three iPSC lines reprogrammed from the peripheral blood of three donors were differentiated into iPSC-dSNs at passage numbers within each of the following ranges: low (5-10), intermediate (20-26), and high (30-38). Morphology and pluripotency of the parent iPSCs were assessed prior to differentiation. iPSC-dSNs were evaluated based on electrophysiological properties and expression of key neuronal markers. All iPSC lines displayed similar morphology and were similarly pluripotent across passage numbers. However, the expression levels of neuronal markers and sodium channel function analyses indicated that iPSC-dSNs differentiated from low passage numbers better recapitulated the sensory neuron phenotype than those differentiated from intermediate or high passage numbers. Our results demonstrate that lower passage numbers may be better suited for differentiation into peripheral sensory neurons.
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Affiliation(s)
- Erica L Cantor
- Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fei Shen
- Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Guanglong Jiang
- Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhiyong Tan
- Pharmacology & Toxicology, Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Geneva M Cunningham
- Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xi Wu
- Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Santosh Philips
- Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bryan P Schneider
- Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN, USA.
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24
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Arez M, Eckersley-Maslin M, Klobučar T, von Gilsa Lopes J, Krueger F, Mupo A, Raposo AC, Oxley D, Mancino S, Gendrel AV, Bernardes de Jesus B, da Rocha ST. Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation. Nat Commun 2022; 13:5432. [PMID: 36114205 PMCID: PMC9481624 DOI: 10.1038/s41467-022-33013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalised approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. Epigenetic fidelity can be tracked by genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unknown reasons. To try to understand the causes underlying these defects, we conducted a thorough imprinting analysis using IMPLICON, a high-throughput method measuring DNA methylation levels, in multiple female and male murine iPSC lines generated under different experimental conditions. Our results show that imprinting defects are remarkably common in iPSCs, but their nature depends on the sex of donor cells and their response to culture conditions. Imprints in female iPSCs resist the initial genome-wide DNA demethylation wave during reprogramming, but ultimately cells accumulate hypomethylation defects irrespective of culture medium formulations. In contrast, imprinting defects on male iPSCs depends on the experimental conditions and arise during reprogramming, being mitigated by the addition of vitamin C (VitC). Our findings are fundamental to further optimise reprogramming strategies and generate iPSCs with a stable epigenome.
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Affiliation(s)
- Maria Arez
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Melanie Eckersley-Maslin
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, United Kingdom
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Victoria, 3010, Australia
| | - Tajda Klobučar
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- National Institute of Chemistry, Ljubljana, Slovenia
| | - João von Gilsa Lopes
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge, CB22 3AT, United Kingdom
- Altos Labs, Cambridge, United Kingdom
| | - Annalisa Mupo
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, United Kingdom
- Altos Labs, Cambridge, United Kingdom
| | - Ana Cláudia Raposo
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, United Kingdom
| | - Samantha Mancino
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Genetics and Developmental Biology Unit, Institut Curie, INSERM U934, CNRS UMR3215, PSL University, Paris, France
| | - Bruno Bernardes de Jesus
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Simão Teixeira da Rocha
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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25
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Mehta C, Shah R, Yanamala N, Sengupta PP. Cardiovascular Imaging Databases: Building Machine Learning Algorithms for Regenerative Medicine. CURRENT STEM CELL REPORTS 2022. [DOI: 10.1007/s40778-022-00216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Moon JE, Lawrence JB. Chromosome silencing in vitro reveals trisomy 21 causes cell-autonomous deficits in angiogenesis and early dysregulation in Notch signaling. Cell Rep 2022; 40:111174. [PMID: 35947952 PMCID: PMC9505374 DOI: 10.1016/j.celrep.2022.111174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 12/24/2021] [Accepted: 07/18/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the prevalence of Down syndrome (DS), little is known regarding the specific cell pathologies that underlie this multi-system disorder. To understand which cell types and pathways are more directly affected by trisomy 21 (T21), we used an inducible-XIST system to silence one chromosome 21 in vitro. T21 caused the dysregulation of Notch signaling in iPSCs, potentially affecting cell-type programming. Further analyses identified dysregulation of pathways important for two cell types: neurogenesis and angiogenesis. Angiogenesis is essential to many bodily systems, yet is understudied in DS; therefore, we focused next on whether T21 affects endothelial cells. An in vitro assay for microvasculature formation revealed a cellular pathology involving delayed tube formation in response to angiogenic signals. Parallel transcriptomic analysis of endothelia further showed deficits in angiogenesis regulators. Results indicate a direct cell-autonomous impact of T21 on endothelial function, highlighting the importance of angiogenesis, with wide-reaching implications for development and disease progression. Moon and Lawrence examine the immediate effects of trisomy 21 silencing and find angiogenesis and neurogenesis pathways, including Notch signaling, affected as early as pluripotency. In endothelial cells, functional analyses show that trisomy delays the angiogenic response for microvessel formation and transcriptomics show a parallel impact on angiogenic regulators and signal-response and cytoskeleton processes.
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Affiliation(s)
- Jennifer E Moon
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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27
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Chen Y, Wen R, Yang Z, Chen Z. Genome editing using CRISPR/Cas9 to treat hereditary hematological disorders. Gene Ther 2022; 29:207-216. [PMID: 33750926 DOI: 10.1038/s41434-021-00247-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023]
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system is a versatile and convenient genome-editing tool with prospects in gene therapy. This technique is based on customized site-specific nucleases with programmable guiding RNAs that cleave and introduce double-strand breaks (DSBs) at the target locus and achieve precise genome modification by triggering DNA repair mechanisms. Human hematopoietic stem/progenitor cells (HSPCs) are conventional cell targets for gene therapy in hematological diseases and have been widely used in most studies. Induced pluripotent stem cells (iPSCs) can be generated from a variety of somatic cells and hold great promise for personalized cell-based therapies. CRISPR/Cas9-mediated genome editing in autologous HSPCs and iPSCs is an ideal therapeutic solution for treating hereditary hematological disorders. Here, we review and summarize the latest studies about CRISPR/Cas9-mediated genome editing in patient-derived HSPCs and iPSCs to treat hereditary hematological disorders. Current challenges and prospects are also discussed.
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Affiliation(s)
- Yan Chen
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
| | - Ruiting Wen
- Department of Hematology, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
| | - Zhigang Yang
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
- Department of Hematology, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
| | - Zhanghui Chen
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China.
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28
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Cruceanu C, Dony L, Krontira AC, Fischer DS, Roeh S, Di Giaimo R, Kyrousi C, Kaspar L, Arloth J, Czamara D, Gerstner N, Martinelli S, Wehner S, Breen MS, Koedel M, Sauer S, Sportelli V, Rex-Haffner M, Cappello S, Theis FJ, Binder EB. Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study. Am J Psychiatry 2022; 179:375-387. [PMID: 34698522 DOI: 10.1176/appi.ajp.2021.21010095] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE A fine-tuned balance of glucocorticoid receptor (GR) activation is essential for organ formation, with disturbances influencing many health outcomes. In utero, glucocorticoids have been linked to brain-related negative outcomes, with unclear underlying mechanisms, especially regarding cell-type-specific effects. An in vitro model of fetal human brain development, induced human pluripotent stem cell (hiPSC)-derived cerebral organoids, was used to test whether cerebral organoids are suitable for studying the impact of prenatal glucocorticoid exposure on the developing brain. METHODS The GR was activated with the synthetic glucocorticoid dexamethasone, and the effects were mapped using single-cell transcriptomics across development. RESULTS The GR was expressed in all cell types, with increasing expression levels through development. Not only did its activation elicit translocation to the nucleus and the expected effects on known GR-regulated pathways, but also neurons and progenitor cells showed targeted regulation of differentiation- and maturation-related transcripts. Uniquely in neurons, differentially expressed transcripts were significantly enriched for genes associated with behavior-related phenotypes and disorders. This human neuronal glucocorticoid response profile was validated across organoids from three independent hiPSC lines reprogrammed from different source tissues from both male and female donors. CONCLUSIONS These findings suggest that excessive glucocorticoid exposure could interfere with neuronal maturation in utero, leading to increased disease susceptibility through neurodevelopmental processes at the interface of genetic susceptibility and environmental exposure. Cerebral organoids are a valuable translational resource for exploring the effects of glucocorticoids on early human brain development.
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Affiliation(s)
- Cristiana Cruceanu
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Leander Dony
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Anthi C Krontira
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - David S Fischer
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Simone Roeh
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Rossella Di Giaimo
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Christina Kyrousi
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Lea Kaspar
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Janine Arloth
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Darina Czamara
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Nathalie Gerstner
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Silvia Martinelli
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Stefanie Wehner
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Michael S Breen
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Maik Koedel
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Susann Sauer
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Vincenza Sportelli
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Monika Rex-Haffner
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Silvia Cappello
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Fabian J Theis
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
| | - Elisabeth B Binder
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany (Cruceanu, Dony, Krontira, Roeh, Kaspar, Arloth, Czamara, Gerstner, Martinelli, Wehner, Koedel, Sauer, Sportelli, Rex-Haffner, Binder);International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich (Dony, Krontira, Kaspar, Gerstner);Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany (Dony, Fischer, Arloth, Theis);TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany (Fischer);Max Planck Institute of Psychiatry, Munich (Di Giaimo, Kyrousi, Cappello);Department of Biology, University of Naples Federico II, Naples, Italy (Di Giaimo);First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, and University Mental Health, Neurosciences, and Precision Medicine Research Institute "Costas Stefanis," Athens, Greece (Kyrousi);Department of Psychiatry, Department of Genetics and Genomic Sciences, Seaver Autism Center for Research and Treatment, and Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York (Breen);School of Life Sciences Weihenstephan and Department of Mathematics, Technical University of Munich, Munich (Theis);Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta (Binder)
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Multi-omics approach reveals posttranscriptionally regulated genes are essential for human pluripotent stem cells. iScience 2022; 25:104289. [PMID: 35573189 PMCID: PMC9097716 DOI: 10.1016/j.isci.2022.104289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/01/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
The effects of transcription factors on the maintenance and differentiation of human-induced or embryonic pluripotent stem cells (iPSCs/ESCs) have been well studied. However, the importance of posttranscriptional regulatory mechanisms, which cause the quantitative dissociation of mRNA and protein expression, has not been explored in detail. Here, by combining transcriptome and proteome profiling, we identified 228 posttranscriptionally regulated genes with strict upregulation of the protein level in iPSCs/ESCs. Among them, we found 84 genes were vital for the survival of iPSCs and HDFs, including 20 genes that were specifically necessary for iPSC survival. These 20 proteins were upregulated only in iPSCs/ESCs and not in differentiated cells derived from the three germ layers. Although there are still unknown mechanisms that downregulate protein levels in HDFs, these results reveal that posttranscriptionally regulated genes have a crucial role in iPSC survival. The posttranscriptionally regulated 20 genes are necessary for iPSC survival The proteins of HSPA8, EIF3D, and NCBP2 are quickly degraded in HDFs mRNA localization affects the protein amounts in most of the 20 genes Translation is repressed in HDFs despite mRNA binding to ribosomes
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Romero-Morales AI, Gama V. Revealing the Impact of Mitochondrial Fitness During Early Neural Development Using Human Brain Organoids. Front Mol Neurosci 2022; 15:840265. [PMID: 35571368 PMCID: PMC9102998 DOI: 10.3389/fnmol.2022.840265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial homeostasis -including function, morphology, and inter-organelle communication- provides guidance to the intrinsic developmental programs of corticogenesis, while also being responsive to environmental and intercellular signals. Two- and three-dimensional platforms have become useful tools to interrogate the capacity of cells to generate neuronal and glia progeny in a background of metabolic dysregulation, but the mechanistic underpinnings underlying the role of mitochondria during human neurogenesis remain unexplored. Here we provide a concise overview of cortical development and the use of pluripotent stem cell models that have contributed to our understanding of mitochondrial and metabolic regulation of early human brain development. We finally discuss the effects of mitochondrial fitness dysregulation seen under stress conditions such as metabolic dysregulation, absence of developmental apoptosis, and hypoxia; and the avenues of research that can be explored with the use of brain organoids.
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Affiliation(s)
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, United States
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Takahashi K, Okubo C, Nakamura M, Iwasaki M, Kawahara Y, Tabata T, Miyamoto Y, Woltjen K, Yamanaka S. A stress-reduced passaging technique improves the viability of human pluripotent cells. CELL REPORTS METHODS 2022; 2:100155. [PMID: 35474962 PMCID: PMC9017214 DOI: 10.1016/j.crmeth.2021.100155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/13/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Xeno-free culture systems have expanded the clinical and industrial application of human pluripotent stem cells (PSCs). However, reproducibility issues, often arising from variability during passaging steps, remain. Here, we describe an improved method for the subculture of human PSCs. The revised method significantly enhances the viability of human PSCs by lowering DNA damage and apoptosis, resulting in more efficient and reproducible downstream applications such as gene editing and directed differentiation. Furthermore, the method does not alter PSC characteristics after long-term culture and attenuates the growth advantage of abnormal subpopulations. This robust passaging method minimizes experimental error and reduces the rate of PSCs failing quality control of human PSC research and application.
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Affiliation(s)
- Kazutoshi Takahashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Chikako Okubo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Michiko Nakamura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Mio Iwasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yuka Kawahara
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Tsuyoshi Tabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yousuke Miyamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
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32
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Lawing AM, McCoy M, Reinke BA, Sarkar SK, Smith FA, Wright D. A Framework for Investigating Rules of Life by Establishing Zones of Influence. Integr Comp Biol 2022; 61:2095-2108. [PMID: 34297089 PMCID: PMC8825771 DOI: 10.1093/icb/icab169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/26/2021] [Accepted: 07/20/2021] [Indexed: 12/18/2022] Open
Abstract
The incredible complexity of biological processes across temporal and spatial scales hampers defining common underlying mechanisms driving the patterns of life. However, recent advances in sequencing, big data analysis, machine learning, and molecular dynamics simulation have renewed the hope and urgency of finding potential hidden rules of life. There currently exists no framework to develop such synoptic investigations. Some efforts aim to identify unifying rules of life across hierarchical levels of time, space, and biological organization, but not all phenomena occur across all the levels of these hierarchies. Instead of identifying the same parameters and rules across levels, we posit that each level of a temporal and spatial scale and each level of biological organization has unique parameters and rules that may or may not predict outcomes in neighboring levels. We define this neighborhood, or the set of levels, across which a rule functions as the zone of influence. Here, we introduce the zone of influence framework and explain using three examples: (a) randomness in biology, where we use a Poisson process to describe processes from protein dynamics to DNA mutations to gene expressions, (b) island biogeography, and (c) animal coloration. The zone of influence framework may enable researchers to identify which levels are worth investigating for a particular phenomenon and reframe the narrative of searching for a unifying rule of life to the investigation of how, when, and where various rules of life operate.
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Affiliation(s)
- A Michelle Lawing
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Michael McCoy
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Beth A Reinke
- Department of Biology, Northeastern Illinois University, IL 60625, USA
| | | | - Felisa A Smith
- Department of Biology, University of New Mexico, NM 87131, USA
| | - Derek Wright
- Department of Physics, Colorado School of Mines, CO 80401, USA
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MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains. Sci Rep 2021; 11:24254. [PMID: 34930932 PMCID: PMC8688507 DOI: 10.1038/s41598-021-03260-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 11/08/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) can differentiate into cells of the three germ layers and are promising cell sources for regenerative medicine therapies. However, current protocols generate hiPSCs with low efficiency, and the generated iPSCs have variable differentiation capacity among different clones. Our previous study reported that MYC proteins (c-MYC and MYCL) are essential for reprogramming and germline transmission but that MYCL can generate hiPSC colonies more efficiently than c-MYC. The molecular underpinnings for the different reprogramming efficiencies between c-MYC and MYCL, however, are unknown. In this study, we found that MYC Box 0 (MB0) and MB2, two functional domains conserved in the MYC protein family, contribute to the phenotypic differences and promote hiPSC generation in MYCL-induced reprogramming. Proteome analyses suggested that in MYCL-induced reprogramming, cell adhesion-related cytoskeletal proteins are regulated by the MB0 domain, while the MB2 domain regulates RNA processes. These findings provide a molecular explanation for why MYCL has higher reprogramming efficiency than c-MYC.
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34
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Moving Towards Induced Pluripotent Stem Cell-based Therapies with Artificial Intelligence and Machine Learning. Stem Cell Rev Rep 2021; 18:559-569. [PMID: 34843066 PMCID: PMC8930923 DOI: 10.1007/s12015-021-10302-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2021] [Indexed: 10/28/2022]
Abstract
The advent of induced pluripotent stem cell (iPSC) technology, which allows to transform one cell type into another, holds the promise to produce therapeutic cells and organs on demand. Realization of this objective is contingent on the ability to demonstrate quality and safety of the cellular product for its intended use. Bottlenecks and backlogs to the clinical use of iPSCs have been fully outlined and a need has emerged for safer and standardized protocols to trigger cell reprogramming and functional differentiation. Amidst great challenges, in particular associated with lengthy culture time and laborious cell characterization, a demand for faster and more accurate methods for the validation of cell identity and function at different stages of the iPSC manufacturing process has risen. Artificial intelligence-based methods are proving helpful for these complex tasks and might revolutionize the way iPSCs are managed to create surrogate cells and organs. Here, we briefly review recent progress in artificial intelligence approaches for evaluation of iPSCs and their derivatives in experimental studies.
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35
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Nicaise AM, D'Angelo A, Ionescu RB, Krzak G, Willis CM, Pluchino S. The role of neural stem cells in regulating glial scar formation and repair. Cell Tissue Res 2021; 387:399-414. [PMID: 34820704 PMCID: PMC8975756 DOI: 10.1007/s00441-021-03554-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/10/2021] [Indexed: 02/06/2023]
Abstract
Glial scars are a common pathological occurrence in a variety of central nervous system (CNS) diseases and injuries. They are caused after severe damage and consist of reactive glia that form a barrier around the damaged tissue that leads to a non-permissive microenvironment which prevents proper endogenous regeneration. While there are a number of therapies that are able to address some components of disease, there are none that provide regenerative properties. Within the past decade, neural stem cells (NSCs) have been heavily studied due to their potent anti-inflammatory and reparative capabilities in disease and injury. Exogenously applied NSCs have been found to aid in glial scar healing by reducing inflammation and providing cell replacement. However, endogenous NSCs have also been found to contribute to the reactive environment by different means. Further understanding how NSCs can be leveraged to aid in the resolution of the glial scar is imperative in the use of these cells as regenerative therapies. To do so, humanised 3D model systems have been developed to study the development and maintenance of the glial scar. Herein, we explore the current work on endogenous and exogenous NSCs in the glial scar as well as the novel 3D stem cell–based technologies being used to model this pathology in a dish.
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Affiliation(s)
- Alexandra M Nicaise
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, UK.
| | - Andrea D'Angelo
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Rosana-Bristena Ionescu
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Grzegorz Krzak
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Cory M Willis
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Stefano Pluchino
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, UK.
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36
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Krog RT, de Miranda NFCC, Vahrmeijer AL, Kooreman NG. The Potential of Induced Pluripotent Stem Cells to Advance the Treatment of Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13225789. [PMID: 34830945 PMCID: PMC8616212 DOI: 10.3390/cancers13225789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Despite improvements in the treatment of several cancer types, the extremely poor prognosis of pancreatic cancer patients has remained unchanged over the last decades. Therefore, new therapeutic regimens for pancreatic cancer are highly needed. In this review, we will discuss the potential of induced pluripotent stem cells (iPSCs) to generate representative pancreatic cancer models that can aid the development of novel diagnostics and therapeutic strategies. Furthermore, the potential of iPSCs as pancreatic cancer vaccines or as a basis for cellular therapies will be discussed. With promising preclinical results and ongoing clinical trials, the potential of iPSCs to further the treatment of pancreatic cancer is being explored and, in turn, will hopefully provide additional therapies to increase the poor survival rates of this patient population. Abstract Advances in the treatment of pancreatic ductal adenocarcinoma (PDAC) using neoadjuvant chemoradiotherapy, chemotherapy, and immunotherapy have had minimal impact on the overall survival of patients. A general lack of immunogenic features and a complex tumor microenvironment (TME) are likely culprits for therapy refractoriness in PDAC. Induced pluripotent stem cells (iPSCs) should be explored as a means to advance the treatment options for PDAC, by providing representative in vitro models of pancreatic cancer development. In addition, iPSCs could be used for tailor-made cellular immunotherapies or as a source of tumor-associated antigens in the context of vaccination.
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Affiliation(s)
- Ricki T. Krog
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.T.K.); (A.L.V.)
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
| | | | - Alexander L. Vahrmeijer
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.T.K.); (A.L.V.)
| | - Nigel G. Kooreman
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.T.K.); (A.L.V.)
- Correspondence:
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37
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Armitage LH, Stimpson SE, Santostefano KE, Sui L, Ogundare S, Newby BN, Castro-Gutierrez R, Huber MK, Taylor JP, Sharma P, Radichev IA, Perry DJ, Fredette NC, Savinov AY, Wallet MA, Terada N, Brusko TM, Russ HA, Chen J, Egli D, Mathews CE. Use of Induced Pluripotent Stem Cells to Build Isogenic Systems and Investigate Type 1 Diabetes. Front Endocrinol (Lausanne) 2021; 12:737276. [PMID: 34858326 PMCID: PMC8630743 DOI: 10.3389/fendo.2021.737276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Type 1 diabetes (T1D) is a disease that arises due to complex immunogenetic mechanisms. Key cell-cell interactions involved in the pathogenesis of T1D are activation of autoreactive T cells by dendritic cells (DC), migration of T cells across endothelial cells (EC) lining capillary walls into the islets of Langerhans, interaction of T cells with macrophages in the islets, and killing of β-cells by autoreactive CD8+ T cells. Overall, pathogenic cell-cell interactions are likely regulated by the individual's collection of genetic T1D-risk variants. To accurately model the role of genetics, it is essential to build systems to interrogate single candidate genes in isolation during the interactions of cells that are essential for disease development. However, obtaining single-donor matched cells relevant to T1D is a challenge. Sourcing these genetic variants from human induced pluripotent stem cells (iPSC) avoids this limitation. Herein, we have differentiated iPSC from one donor into DC, macrophages, EC, and β-cells. Additionally, we also engineered T cell avatars from the same donor to provide an in vitro platform to study genetic influences on these critical cellular interactions. This proof of concept demonstrates the ability to derive an isogenic system from a single donor to study these relevant cell-cell interactions. Our system constitutes an interdisciplinary approach with a controlled environment that provides a proof-of-concept for future studies to determine the role of disease alleles (e.g. IFIH1, PTPN22, SH2B3, TYK2) in regulating cell-cell interactions and cell-specific contributions to the pathogenesis of T1D.
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Affiliation(s)
- Lucas H. Armitage
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Scott E. Stimpson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Katherine E. Santostefano
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
- Century Therapeutics, iPSC Biology, Philadelphia, PA, United States
| | - Lina Sui
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, United States
| | - Similoluwa Ogundare
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Brittney N. Newby
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Roberto Castro-Gutierrez
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Mollie K. Huber
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Jared P. Taylor
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Prerana Sharma
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Ilian A. Radichev
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Daniel J. Perry
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Natalie C. Fredette
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Alexei Y. Savinov
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Mark A. Wallet
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
- Century Therapeutics, Immunology, Philadelphia, PA, United States
| | - Naohiro Terada
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Todd M. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Holger A. Russ
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jing Chen
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Dieter Egli
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
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38
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Vickers A, Tewary M, Laddach A, Poletti M, Salameti V, Fraternali F, Danovi D, Watt FM. Plating human iPSC lines on micropatterned substrates reveals role for ITGB1 nsSNV in endoderm formation. Stem Cell Reports 2021; 16:2628-2641. [PMID: 34678211 PMCID: PMC8581167 DOI: 10.1016/j.stemcr.2021.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
Quantitative analysis of human induced pluripotent stem cell (iPSC) lines from healthy donors is a powerful tool for uncovering the relationship between genetic variants and cellular behavior. We previously identified rare, deleterious non-synonymous single nucleotide variants (nsSNVs) in cell adhesion genes that are associated with outlier iPSC phenotypes in the pluripotent state. Here, we generated micropatterned colonies of iPSCs to test whether nsSNVs influence patterning of radially ordered germ layers. Using a custom-built image analysis pipeline, we quantified the differentiation phenotypes of 13 iPSC lines that harbor nsSNVs in genes related to cell adhesion or germ layer development. All iPSC lines differentiated into the three germ layers; however, there was donor-specific variation in germ layer patterning. We identified one line that presented an outlier phenotype of expanded endodermal differentiation, which was associated with a nsSNV in ITGB1. Our study establishes a platform for investigating the impact of nsSNVs on differentiation.
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Affiliation(s)
- Alice Vickers
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK
| | - Mukul Tewary
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK
| | - Anna Laddach
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Great Maze Pond, London SE1 9RT, UK; Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Martina Poletti
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; Quadram Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Vasiliki Salameti
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Great Maze Pond, London SE1 9RT, UK
| | - Davide Danovi
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK; bit.bio, Babraham Research Campus, The Dorothy Hodgkin Building, Cambridge CB22 3FH, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK.
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39
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Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells. Cell Rep 2021; 37:109909. [PMID: 34731633 DOI: 10.1016/j.celrep.2021.109909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/24/2021] [Accepted: 10/08/2021] [Indexed: 01/13/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. Nearly a quarter of autosomal regions bear potentially differential chromatin modifications, with promoters/CpG islands for H3K27me3/H2AK119ub1 and evolutionarily young retrotransposons for H3K4me3. We identify 145 large autosomal blocks (≥100 kb) with differential H3K9me3 enrichment, many of which are lamina-associated domains (LADs) in somatic but not in embryonic stem cells. A majority of these epigenomic heterogeneities are independent of genetic variations. We identify an X chromosome state with chromosome-wide H3K9me3 that stably prevents X chromosome erosion. Importantly, the germline potential of female hiPSCs correlates with X chromosome inactivation. We propose that inherent genomic properties, including CpG density, transposons, and LADs, engender epigenomic heterogeneity in hiPSCs.
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40
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Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet 2021; 22:691-711. [PMID: 34354263 DOI: 10.1038/s41576-021-00385-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.
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Affiliation(s)
- Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
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41
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Tadokoro S, Tokuyama-Toda R, Tatehara S, Ide S, Umeki H, Miyoshi K, Noma T, Satomura K. A New Induction Method for the Controlled Differentiation of Human-Induced Pluripotent Stem Cells Using Frozen Sections. Cells 2021; 10:2827. [PMID: 34831050 PMCID: PMC8616214 DOI: 10.3390/cells10112827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 02/04/2023] Open
Abstract
Considering that every tissue/organ has the most suitable microenvironment for its functional cells, controlling induced pluripotent stem cell (iPSC) differentiation by culture on frozen sections having a suitable microenvironment is possible. Induced PSCs were cultured on frozen sections of the liver, the brain, the spinal cord, and cover glasses (control) for 9 days. The iPSCs cultured on the sections of the liver resembled hepatocytes, whereas those on sections of the brain and the spinal cord resembled neuronal cells. The percentage of hepatocytic marker-positive cells in the iPSCs cultured on the sections of the liver was statistically higher than that of those in the iPSCs cultured on the sections of the brain and the spinal cord or on cover glasses. In contrast, the iPSCs cultured on the sections of the brain and the spinal cord revealed a high percentage of neural marker-positive cells. Thus, iPSCs can be differentiated into a specific cell lineage in response to specific factors within frozen sections of tissues/organs. Differentiation efficacy of the frozen sections markedly differed between the iPSC clones. Therefore, our induction method could be simple and effective for evaluating the iPSC quality.
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Affiliation(s)
- Susumu Tadokoro
- Department of Oral Medicine and Stomatology, Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan; (S.T.); (R.T.-T.); (S.T.); (S.I.); (H.U.)
| | - Reiko Tokuyama-Toda
- Department of Oral Medicine and Stomatology, Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan; (S.T.); (R.T.-T.); (S.T.); (S.I.); (H.U.)
| | - Seiko Tatehara
- Department of Oral Medicine and Stomatology, Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan; (S.T.); (R.T.-T.); (S.T.); (S.I.); (H.U.)
| | - Shinji Ide
- Department of Oral Medicine and Stomatology, Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan; (S.T.); (R.T.-T.); (S.T.); (S.I.); (H.U.)
| | - Hirochika Umeki
- Department of Oral Medicine and Stomatology, Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan; (S.T.); (R.T.-T.); (S.T.); (S.I.); (H.U.)
| | - Keiko Miyoshi
- Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, 3-18-15, Kuramoto, Tokushima 770-8504, Japan;
| | - Takafumi Noma
- Department of Nutrition and Health Promotion, Hiroshima Jogakuin University, 4-13-1, Ushitahigashi, Higashiku, Hiroshima 732-0063, Japan;
| | - Kazuhito Satomura
- Department of Oral Medicine and Stomatology, Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan; (S.T.); (R.T.-T.); (S.T.); (S.I.); (H.U.)
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42
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Alvarez-Palomo AB, Requena-Osete J, Delgado-Morales R, Moreno-Manzano V, Grau-Bove C, Tejera AM, Otero MJ, Barrot C, Santos-Barriopedro I, Vaquero A, Mezquita-Pla J, Moran S, Naya CH, Garcia-Martínez I, Pérez FV, Blasco MA, Esteller M, Edel MJ. A synthetic mRNA cell reprogramming method using CYCLIN D1 promotes DNA repair, generating improved genetically stable human induced pluripotent stem cells. Stem Cells 2021; 39:866-881. [PMID: 33621399 DOI: 10.1002/stem.3358] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
A key challenge for clinical application of induced pluripotent stem cells (iPSC) to accurately model and treat human pathologies depends on developing a method to generate genetically stable cells to reduce long-term risks of cell transplant therapy. Here, we hypothesized that CYCLIN D1 repairs DNA by highly efficient homologous recombination (HR) during reprogramming to iPSC that reduces genetic instability and threat of neoplastic growth. We adopted a synthetic mRNA transfection method using clinically compatible conditions with CYCLIN D1 plus base factors (OCT3/4, SOX2, KLF4, LIN28) and compared with methods that use C-MYC. We demonstrate that CYCLIN D1 made iPSC have (a) lower multitelomeric signal, (b) reduced double-strand DNA breaks, (c) correct nuclear localization of RAD51 protein expression, and (d) reduced single-nucleotide polymorphism (SNP) changes per chromosome, compared with the classical reprogramming method using C-MYC. CYCLIN D1 iPSC have reduced teratoma Ki67 cell growth kinetics and derived neural stem cells successfully engraft in a hostile spinal cord injury (SCI) microenvironment with efficient survival, differentiation. We demonstrate that CYCLIN D1 promotes double-stranded DNA damage repair predominantly through HR during cell reprogramming to efficiently produce iPSC. CYCLIN D1 reduces general cell stress associated with significantly lower SIRT1 gene expression and can rescue Sirt1 null mouse cell reprogramming. In conclusion, we show synthetic mRNA transfection of CYCLIN D1 repairs DNA during reprogramming resulting in significantly improved genetically stable footprint in human iPSC, enabling a new cell reprogramming method for more accurate and reliable generation of human iPSC for disease modeling and future clinical applications.
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Affiliation(s)
- Ana Belén Alvarez-Palomo
- Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, Institute of Neuroscience, Faculty of Medicine, University of Barcelona, Hospital Clinic, Barcelona, Catalonia, Spain
- Cell Therapy Service, Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Jordi Requena-Osete
- Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, Institute of Neuroscience, Faculty of Medicine, University of Barcelona, Hospital Clinic, Barcelona, Catalonia, Spain
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, NORMENT, Centre for Mental Disorders Research, Oslo, Norway
| | - Raul Delgado-Morales
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Victoria Moreno-Manzano
- Neuronal and Tissue Regeneration Laboratory, Príncipe Felipe Research Center, Valencia, Spain
| | - Carme Grau-Bove
- Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, Institute of Neuroscience, Faculty of Medicine, University of Barcelona, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Agueda M Tejera
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Manel Juan Otero
- Hospital Clinic, Department of Clinical Immunology, Biomedical Diagnostic Center (CDB), Villarroel, Catalonia, Spain
| | - Carme Barrot
- Forensic Genetics Laboratory, Legal Medicine Department, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Irene Santos-Barriopedro
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Alejandro Vaquero
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Jovita Mezquita-Pla
- Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, Institute of Neuroscience, Faculty of Medicine, University of Barcelona, Hospital Clinic, Barcelona, Catalonia, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Sebastian Moran
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Carlos Hobeich Naya
- Congenital Coagulopathies Department, Banc de Sang i Teixits (BST), Barcelona, Spain
- Transfusional Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Iris Garcia-Martínez
- Congenital Coagulopathies Department, Banc de Sang i Teixits (BST), Barcelona, Spain
- Transfusional Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Francisco Vidal Pérez
- Congenital Coagulopathies Department, Banc de Sang i Teixits (BST), Barcelona, Spain
- Transfusional Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - María A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Michael J Edel
- Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, Institute of Neuroscience, Faculty of Medicine, University of Barcelona, Hospital Clinic, Barcelona, Catalonia, Spain
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- University of Western Australia, School of Medicine and Pharmacology, Harry Perkins Research Institute, Centre for Cell Therapy and Regenerative Medicine (CCTRM), Perth, Western Australia, Australia
- Centro de Oftalmología Barraquer, Institut Universitari Barraquer, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Human Pluripotent Stem Cells for High-Throughput Drug Screening and Characterization of Small Molecules. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2454:811-827. [PMID: 34128205 DOI: 10.1007/7651_2021_394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Human pluripotent stem cells (hPSCs), such as induced pluripotent stem cells (iPSCs), hold great promise for drug discovery, toxicology studies, and regenerative medicine. Here, we describe standardized protocols and experimental procedures that combine automated cell culture for scalable production of hPSCs with quantitative high-throughput screening (qHTS) in miniaturized 384-well plates. As a proof of principle, we established dose-response assessments and determined optimal concentrations of 12 small molecule compounds that are commonly used in the stem cell field. Multi-parametric analysis of readouts from diverse assays including cell viability, mitochondrial membrane potential, plasma membrane integrity, and ATP production was used to distinguish normal biological responses from cellular stress induced by small molecule treatment. Collectively, the establishment of integrated workflows for cell manufacturing, qHTS, high-content imaging, and data analysis provides an end-to-end platform for industrial-scale projects and should leverage the drug discovery process using hPSC-derived cell types.
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The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency. PLoS Genet 2021; 17:e1009587. [PMID: 34033652 PMCID: PMC8184003 DOI: 10.1371/journal.pgen.1009587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/07/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022] Open
Abstract
Human pluripotent stem cells (PSCs) express human endogenous retrovirus type-H (HERV-H), which exists as more than a thousand copies on the human genome and frequently produces chimeric transcripts as long-non-coding RNAs (lncRNAs) fused with downstream neighbor genes. Previous studies showed that HERV-H expression is required for the maintenance of PSC identity, and aberrant HERV-H expression attenuates neural differentiation potentials, however, little is known about the actual of function of HERV-H. In this study, we focused on ESRG, which is known as a PSC-related HERV-H-driven lncRNA. The global transcriptome data of various tissues and cell lines and quantitative expression analysis of PSCs showed that ESRG expression is much higher than other HERV-Hs and tightly silenced after differentiation. However, the loss of function by the complete excision of the entire ESRG gene body using a CRISPR/Cas9 platform revealed that ESRG is dispensable for the maintenance of the primed and naïve pluripotent states. The loss of ESRG hardly affected the global gene expression of PSCs or the differentiation potential toward trilineage. Differentiated cells derived from ESRG-deficient PSCs retained the potential to be reprogrammed into induced PSCs (iPSCs) by the forced expression of OCT3/4, SOX2, and KLF4. In conclusion, ESRG is dispensable for the maintenance and recapturing of human pluripotency. We have been interested in the role of human endogenous retrovirus (HERVs) in human pluripotent stem cells (PSCs). Although we and others have demonstrated that HERV expression is crucial for somatic cell reprogramming to a pluripotent state and the characteristics of PSCs. Little is known which one of more than 1,000 copies of HERVs is important. Thus, in this study, we focused on a HERV-related gene, ESRG which is expressed strongly and specifically in human PSCs but not in differentiated cells. Using a CRISPR/Cas9 platform, we generated complete knockout cell lines by deleting the entire gene body of ESRG. Our results demonstrate that ESRG is dispensable for the PSC characters such as gene expression, self-renewing capacity, and differentiation potential. In addition, ESRG does not contribute to the reprogramming of differentiated cells to a pluripotent state. Altogether, we concluded that ESRG is an excellent marker of pluripotency but dispensable for the PSC identity.
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Abstract
Human pluripotent stem cells such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) provide unprecedented opportunities for cell therapies against intractable diseases and injuries. Both ESCs and iPSCs are already being used in clinical trials. However, we continue to encounter practical issues that limit their use, including their inherent properties of tumorigenicity, immunogenicity, and heterogeneity. Here, I review two decades of research aimed at overcoming these three difficulties.
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46
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Dannemann M, Gallego Romero I. Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J 2021; 289:2992-3010. [PMID: 33876573 DOI: 10.1111/febs.15885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
The study of human evolution, long constrained by a lack of experimental model systems, has been transformed by the emergence of the induced pluripotent stem cell (iPSC) field. iPSCs can be readily established from noninvasive tissue sources, from both humans and other primates; they can be maintained in the laboratory indefinitely, and they can be differentiated into other tissue types. These qualities mean that iPSCs are rapidly becoming established as viable and powerful model systems with which it is possible to address questions in human evolution that were until now logistically and ethically intractable, especially in the quest to understand humans' place among the great apes, and the genetic basis of human uniqueness. In this review, we discuss the key lessons and takeaways of this nascent field; from the types of research, iPSCs make possible to lingering challenges and likely future directions. We provide a comprehensive overview of how the seemingly unlikely combination of iPSCs and explicit evolutionary frameworks is transforming what is possible in our understanding of humanity's past and present.
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Affiliation(s)
| | - Irene Gallego Romero
- Institute of Genomics, University of Tartu, Estonia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Australia.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Centre for Stem Cell Systems, The University of Melbourne, Parkville, Australia
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47
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Sutcliffe DJ, Dinasarapu AR, Visser JE, Hoed JD, Seifar F, Joshi P, Ceballos-Picot I, Sardar T, Hess EJ, Sun YV, Wen Z, Zwick ME, Jinnah HA. Induced pluripotent stem cells from subjects with Lesch-Nyhan disease. Sci Rep 2021; 11:8523. [PMID: 33875724 PMCID: PMC8055678 DOI: 10.1038/s41598-021-87955-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/24/2021] [Indexed: 12/18/2022] Open
Abstract
Lesch-Nyhan disease (LND) is an inherited disorder caused by pathogenic variants in the HPRT1 gene, which encodes the purine recycling enzyme hypoxanthine-guanine phosphoribosyltransferase (HGprt). We generated 6 induced pluripotent stem cell (iPSC) lines from 3 individuals with LND, along with 6 control lines from 3 normal individuals. All 12 lines had the characteristics of pluripotent stem cells, as assessed by immunostaining for pluripotency markers, expression of pluripotency genes, and differentiation into the 3 primary germ cell layers. Gene expression profiling with RNAseq demonstrated significant heterogeneity among the lines. Despite this heterogeneity, several anticipated abnormalities were readily detectable across all LND lines, including reduced HPRT1 mRNA. Several unexpected abnormalities were also consistently detectable across the LND lines, including decreases in FAR2P1 and increases in RNF39. Shotgun proteomics also demonstrated several expected abnormalities in the LND lines, such as absence of HGprt protein. The proteomics study also revealed several unexpected abnormalities across the LND lines, including increases in GNAO1 decreases in NSE4A. There was a good but partial correlation between abnormalities revealed by the RNAseq and proteomics methods. Finally, functional studies demonstrated LND lines had no HGprt enzyme activity and resistance to the toxic pro-drug 6-thioguanine. Intracellular purines in the LND lines were normal, but they did not recycle hypoxanthine. These cells provide a novel resource to reveal insights into the relevance of heterogeneity among iPSC lines and applications for modeling LND.
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Affiliation(s)
- Diane J Sutcliffe
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Ashok R Dinasarapu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jasper E Visser
- Department of Neurology, Cognition and Behavior, Donders Institute for Brain, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neurology, Amphia Hospital, Breda, The Netherlands
| | - Joery den Hoed
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Fatemeh Seifar
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
- Neurosciences Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, 30322, USA
| | - Piyush Joshi
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Irene Ceballos-Picot
- Laboratoire de Biochimie Métabolomique Et Protéomique, Hôpital Universitaire Necker, Paris, France
| | - Tejas Sardar
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Ellen J Hess
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
- Neurosciences Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, 30322, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA. 30322, USA
| | - Zhexing Wen
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
- Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - H A Jinnah
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Neurosciences Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, 30322, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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48
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Glinsky GV. Genomics-Guided Drawing of Molecular and Pathophysiological Components of Malignant Regulatory Signatures Reveals a Pivotal Role in Human Diseases of Stem Cell-Associated Retroviral Sequences and Functionally-Active hESC Enhancers. Front Oncol 2021; 11:638363. [PMID: 33869024 PMCID: PMC8044830 DOI: 10.3389/fonc.2021.638363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/10/2021] [Indexed: 12/31/2022] Open
Abstract
Repetitive DNA sequences (repeats) colonized two-third of human genome and a majority of repeats comprised of transposable genetic elements (TE). Evolutionary distinct categories of TE represent nucleic acid sequences that are repeatedly copied from and pasted into chromosomes at multiple genomic locations and acquired a multitude of regulatory functions. Here, genomics-guided maps of stemness regulatory signatures were drawn to dissect the contribution of TE to clinical manifestations of malignant phenotypes of human cancers. From patients’ and physicians’ perspectives, the clinical definition of a tumor’s malignant phenotype could be restricted to the early diagnosis of sub-types of malignancies with the increased risk of existing therapy failure and high likelihood of death from cancer. It is the viewpoint from which the understanding of stemness and malignant regulatory signatures is considered in this contribution. Genomics-guided analyses of experimental and clinical observations revealed the pivotal role of human stem cell-associated retroviral sequences (SCARS) in the origin and pathophysiology of clinically-lethal malignancies. SCARS were defined as the evolutionary- and biologically-related family of genomic regulatory sequences, the principal physiological function of which is to create and maintain the stemness phenotype during human preimplantation embryogenesis. For cell differentiation to occur, SCARS expression must be silenced and SCARS activity remains repressed in most terminally-differentiated human cells which are destined to perform specialized functions in the human body. Epigenetic reprogramming, de-repression, and sustained activity of SCARS results in various differentiation-defective phenotypes. One of the most prominent tissue- and organ-specific clinical manifestations of sustained SCARS activities is diagnosed as a pathological condition defined by a consensus of morphological, molecular, and genetic examinations as the malignant growth. Here, contemporary evidence are acquired, analyzed, and reported defining both novel diagnostic tools and druggable molecular targets readily amenable for diagnosis and efficient therapeutic management of clinically-lethal malignancies. These diagnostic and therapeutic approaches are based on monitoring of high-fidelity molecular signals of continuing SCARS activities in conjunction with genomic regulatory networks of thousands’ functionally-active embryonic enhancers affecting down-stream phenotype-altering genetic loci. Collectively, reported herein observations support a model of SCARS-activation triggered singular source code facilitating the intracellular propagation and intercellular (systemic) dissemination of disease states in the human body.
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Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States.,Department of Functional & Translational Genomics, OncoSCAR, Inc., Portland, OR, United States
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49
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Wind M, Gogolou A, Manipur I, Granata I, Butler L, Andrews PW, Barbaric I, Ning K, Guarracino MR, Placzek M, Tsakiridis A. Defining the signalling determinants of a posterior ventral spinal cord identity in human neuromesodermal progenitor derivatives. Development 2021; 148:dev194415. [PMID: 33658223 PMCID: PMC8015249 DOI: 10.1242/dev.194415] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/23/2021] [Indexed: 12/14/2022]
Abstract
The anteroposterior axial identity of motor neurons (MNs) determines their functionality and vulnerability to neurodegeneration. Thus, it is a crucial parameter in the design of strategies aiming to produce MNs from human pluripotent stem cells (hPSCs) for regenerative medicine/disease modelling applications. However, the in vitro generation of posterior MNs corresponding to the thoracic/lumbosacral spinal cord has been challenging. Although the induction of cells resembling neuromesodermal progenitors (NMPs), the bona fide precursors of the spinal cord, offers a promising solution, the progressive specification of posterior MNs from these cells is not well defined. Here, we determine the signals guiding the transition of human NMP-like cells toward thoracic ventral spinal cord neurectoderm. We show that combined WNT-FGF activities drive a posterior dorsal pre-/early neural state, whereas suppression of TGFβ-BMP signalling pathways promotes a ventral identity and neural commitment. Based on these results, we define an optimised protocol for the generation of thoracic MNs that can efficiently integrate within the neural tube of chick embryos. We expect that our findings will facilitate the comparison of hPSC-derived spinal cord cells of distinct axial identities.
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Affiliation(s)
- Matthew Wind
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield S10 2TN, UK
- Department of Neuroscience, Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Antigoni Gogolou
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield S10 2TN, UK
- Department of Neuroscience, Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ichcha Manipur
- Computational and Data Science Laboratory, High Performance Computing and Networking Institute, National Research Council of Italy, Napoli 80131, Italy
| | - Ilaria Granata
- Computational and Data Science Laboratory, High Performance Computing and Networking Institute, National Research Council of Italy, Napoli 80131, Italy
| | - Larissa Butler
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Peter W Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Ke Ning
- Department of Neuroscience, Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | | | - Marysia Placzek
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield S10 2TN, UK
- Department of Neuroscience, Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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50
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Ito A, Ye K, Onda M, Morimoto N, Osakada F. Efficient and robust induction of retinal pigment epithelium cells by tankyrase inhibition regardless of the differentiation propensity of human induced pluripotent stem cells. Biochem Biophys Res Commun 2021; 552:66-72. [PMID: 33743349 DOI: 10.1016/j.bbrc.2021.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/29/2022]
Abstract
Transplantation of retinal pigment epithelium (RPE) cells derived from human embryonic stem cells (hESCs) or induced pluripotent stem cells (hiPSCs) hold great promise as a new therapeutic modality for age-related macular degeneration and Stargardt disease. The development of hESC/hiPSC-derived RPE cells as cell-based therapeutic products requires a robust, scalable production for every hiPSC line congruent for patients. However, individual hESC/hiPSC lines show bias in differentiation. Here we report an efficient, robust method that induces RPE cells regardless of the differentiation propensity of the hiPSC lines. Application of the tankyrase inhibitor IWR-1-endo, which potentially inhibits Wnt signaling, promoted retinal differentiation in dissociated hiPSCs under feeder-free, two-dimensional culture conditions. The other tankyrase inhibitor, XAV939, also promoted retinal differentiation. However, Wnt signaling inhibitors, IWP-2 and iCRT3, that target porcupine and β-catenin/TCF, respectively, did not. Further treatment with the GSK3β inhibitor CHIR99021 and FGF receptor inhibitor SU5402 induced hexagonal pigmented cells with phagocytotic ability. Notably, the IWR-1-endo-based differentiation method induced RPE cells even in an hiPSC line that expresses a lower level of the differentiation propensity marker SALL3, which is indicative of resistance to ectoderm differentiation. The present study demonstrated that tankyrase inhibitors cause efficient and robust RPE differentiation, irrespective of the SALL3 expression levels in hiPSC lines. This differentiation method will resolve line-to-line variations of hiPSCs in RPE production and facilitate clinical application and industrialization of RPE cell products for regenerative medicine.
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Affiliation(s)
- Arisa Ito
- Laboratory of Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Ke Ye
- Laboratory of Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Masanari Onda
- Laboratory of Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Nao Morimoto
- Laboratory of Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan; Laboratory of Neural Information Processing, Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Fumitaka Osakada
- Laboratory of Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan; Laboratory of Neural Information Processing, Institute for Advanced Research, Nagoya University, Nagoya, Japan.
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