1
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Kidder BL. Decoding the universal human chromatin landscape through teratoma-based profiling. Nucleic Acids Res 2024; 52:3589-3606. [PMID: 38281248 PMCID: PMC11039989 DOI: 10.1093/nar/gkae021] [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: 05/02/2023] [Revised: 12/15/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Teratoma formation is key for evaluating differentiation of human pluripotent stem cells into embryonic germ layers and serves as a model for understanding stem cell differentiation and developmental processes. Its potential for insights into epigenome and transcriptome profiling is significant. This study integrates the analysis of the epigenome and transcriptome of hESC-generated teratomas, comparing transcriptomes between hESCs and teratomas. It employs cell type-specific expression patterns from single-cell data to deconvolve RNA-Seq data and identify cell types within teratomas. Our results provide a catalog of activating and repressive histone modifications, while also elucidating distinctive features of chromatin states. Construction of an epigenetic signature matrix enabled the quantification of diverse cell populations in teratomas and enhanced the ability to unravel the epigenetic landscape in heterogeneous tissue contexts. This study also includes a single cell multiome atlas of expression (scRNA-Seq) and chromatin accessibility (scATAC-Seq) of human teratomas, further revealing the complexity of these tissues. A histology-based digital staining tool further complemented the annotation of cell types in teratomas, enhancing our understanding of their cellular composition. This research is a valuable resource for examining teratoma epigenomic and transcriptomic landscapes and serves as a model for epigenetic data comparison.
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Affiliation(s)
- Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
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2
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Liu D, Fu Y, Wang X, Wang X, Fang X, Zhou Y, Wang R, Zhang P, Jiang M, Jia D, Wang J, Chen H, Guo G, Han X. Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses. Stem Cell Reports 2023; 18:2464-2481. [PMID: 37995704 PMCID: PMC10724075 DOI: 10.1016/j.stemcr.2023.10.018] [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: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages, such as multilineage differentiation, angiogenesis, and close cell-cell interactions. To systematically investigate multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We identified 43 cell types, inferred 18 cell differentiation trajectories, and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. Additionally, we developed the developmental single-cell Basic Local Alignment Search Tool (dscBLAST), an R-based cell identification tool, to simplify the identification processes of developmental cells. Using dscBLAST, we aligned cells in multiple differentiation models to normally developing cells to further understand their differentiation states. Overall, our study offers new insights into stem cell differentiation and human embryonic development; dscBLAST shows favorable cell identification performance, providing a powerful identification tool for developmental cells.
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Affiliation(s)
- Daiyuan Liu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xueyi Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xing Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Yincong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Danmei Jia
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingjing Wang
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; M20 Genomics, Hangzhou, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China.
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3
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Torre D, Francoeur NJ, Kalma Y, Gross Carmel I, Melo BS, Deikus G, Allette K, Flohr R, Fridrikh M, Vlachos K, Madrid K, Shah H, Wang YC, Sridhar SH, Smith ML, Eliyahu E, Azem F, Amir H, Mayshar Y, Marazzi I, Guccione E, Schadt E, Ben-Yosef D, Sebra R. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun 2023; 14:6902. [PMID: 37903791 PMCID: PMC10616205 DOI: 10.1038/s41467-023-42558-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023] Open
Abstract
Human preimplantation development involves extensive remodeling of RNA expression and splicing. However, its transcriptome has been compiled using short-read sequencing data, which fails to capture most full-length mRNAs. Here, we generate an isoform-resolved transcriptome of early human development by performing long- and short-read RNA sequencing on 73 embryos spanning the zygote to blastocyst stages. We identify 110,212 unannotated isoforms transcribed from known genes, including highly conserved protein-coding loci and key developmental regulators. We further identify 17,964 isoforms from 5,239 unannotated genes, which are largely non-coding, primate-specific, and highly associated with transposable elements. These isoforms are widely supported by the integration of published multi-omics datasets, including single-cell 8CLC and blastoid studies. Alternative splicing and gene co-expression network analyses further reveal that embryonic genome activation is associated with splicing disruption and transient upregulation of gene modules. Together, these findings show that the human embryo transcriptome is far more complex than currently known, and will act as a valuable resource to empower future studies exploring development.
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Affiliation(s)
- Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Yael Kalma
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Ilana Gross Carmel
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Betsaida S Melo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ron Flohr
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel
| | - Maya Fridrikh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shwetha H Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Foad Azem
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Hadar Amir
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Yoav Mayshar
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Ivan Marazzi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT); Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalit Ben-Yosef
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel.
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel.
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel.
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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4
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Ali HRW, Suliman S, Osman TAH, Carrasco M, Bruland O, Costea DE, Ræder H, Mustafa K. Xeno-free generation of human induced pluripotent stem cells from donor-matched fibroblasts isolated from dermal and oral tissues. Stem Cell Res Ther 2023; 14:199. [PMID: 37559144 PMCID: PMC10410907 DOI: 10.1186/s13287-023-03403-7] [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: 10/20/2022] [Accepted: 06/15/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Induced pluripotent stem cells (iPS) can be generated from various somatic cells and can subsequently be differentiated to multiple cell types of the body. This makes them highly promising for cellular therapy in regenerative medicine. However, to facilitate their clinical use and to ensure safety, iPS culturing protocols must be compliant with good manufacturing practice guidelines and devoid of xenogenic products. Therefore, we aimed to compare the efficiency of using humanized culture conditions, specifically human platelet lysate to fetal bovine serum, for iPS generation from different sources, and to evaluate their stemness. METHODS iPS were generated via a platelet lysate or fetal bovine serum-based culturing protocol from matched dermal, buccal and gingival human fibroblasts, isolated from healthy donors (n = 2) after informed consent, via episomal plasmid transfection. Pluripotency, genotype and phenotype of iPS, generated by both protocols, were then assessed by various methods. RESULTS More attempts were generally required to successfully reprogram xeno-free fibroblasts to iPS, as compared to xenogenic cultured fibroblasts. Furthermore, oral fibroblasts generally required more attempts for successful iPS generation as opposed to dermal fibroblasts. Morphologically, all iPS generated from fibroblasts formed tight colonies surrounded by a reflective "whitish" outer rim, typical for iPS. They also expressed pluripotency markers at both gene (SOX2, OCT4, NANOG) and protein level (SOX2, OCT4). Upon stimulation, all iPS showed ability to differentiate into the three primary germ layers via expression of lineage-specific markers for mesoderm (MESP1, OSR1, HOPX), endoderm (GATA4) and ectoderm (PAX6, RAX). Genome analysis revealed several amplifications and deletions within the chromosomes of each iPS type. CONCLUSIONS The xeno-free protocol had a lower reprogramming efficiency compared to the standard xenogenic protocol. The oral fibroblasts generally proved to be more difficult to reprogram than dermal fibroblasts. Xeno-free dermal, buccal and gingival fibroblasts can successfully generate iPS with a comparable genotype/phenotype to their xenogenic counterparts.
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Affiliation(s)
- Hassan R W Ali
- Department of Clinical Dentistry, Centre for Translational Oral Research (TOR), University of Bergen, 5009, Bergen, Norway
| | - Salwa Suliman
- Department of Clinical Dentistry, Centre for Translational Oral Research (TOR), University of Bergen, 5009, Bergen, Norway
| | - Tarig Al-Hadi Osman
- Department of Clinical Dentistry, Centre for Translational Oral Research (TOR), University of Bergen, 5009, Bergen, Norway
| | - Manuel Carrasco
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Ove Bruland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Daniela-Elena Costea
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
- Gade Laboratory for Pathology, Haukeland University Hospital, Bergen, Norway
| | - Helge Ræder
- Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway.
| | - Kamal Mustafa
- Department of Clinical Dentistry, Centre for Translational Oral Research (TOR), University of Bergen, 5009, Bergen, Norway.
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5
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Li H, Xu W, Xiang S, Tao L, Fu W, Liu J, Liu W, Xiao Y, Peng L. Defining the Pluripotent Marker Genes for Identification of Teleost Fish Cell Pluripotency During Reprogramming. Front Genet 2022; 13:819682. [PMID: 35222539 PMCID: PMC8874021 DOI: 10.3389/fgene.2022.819682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Pluripotency is a transient state in early embryos, which is regulated by an interconnected network of pluripotency-related genes. The pluripotent state itself seems to be highly dynamic, which leads to significant differences in the description of induced pluripotent stem cells from different species at the molecular level. With the application of cell reprogramming technology in fish, the establishment of a set of molecular standards for defining pluripotency will be important for the research and potential application of induced pluripotent stem cells in fish. In this study, by BLAST search and expression pattern analysis, we screen out four pluripotent genes (Oct4, Nanog, Tdgf1, and Gdf3) in zebrafish (Danio rerio) and crucian carp (Carassius). These genes were highly expressed in the short period of early embryonic development, but significantly down-regulated after differentiation. Moreover, three genes (Oct4, Nanog and Tdgf1) have been verified that are suitable for identifying the pluripotency of induced pluripotent stem cells in zebrafish and crucian carp. Our study expands the understanding of the pluripotent markers of induced pluripotent stem cells in fish.
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Affiliation(s)
- Huajin Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenting Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Sijia Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Leiting Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wen Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Jinhui Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenbin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Yamei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Liangyue Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Liangyue Peng,
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6
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Novak G, Kyriakis D, Grzyb K, Bernini M, Rodius S, Dittmar G, Finkbeiner S, Skupin A. Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson's disease. Commun Biol 2022; 5:49. [PMID: 35027645 PMCID: PMC8758783 DOI: 10.1038/s42003-021-02973-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/14/2021] [Indexed: 01/02/2023] Open
Abstract
Parkinson's disease (PD) is the second-most prevalent neurodegenerative disorder, characterized by the loss of dopaminergic neurons (mDA) in the midbrain. The underlying mechanisms are only partly understood and there is no treatment to reverse PD progression. Here, we investigated the disease mechanism using mDA neurons differentiated from human induced pluripotent stem cells (hiPSCs) carrying the ILE368ASN mutation within the PINK1 gene, which is strongly associated with PD. Single-cell RNA sequencing (RNAseq) and gene expression analysis of a PINK1-ILE368ASN and a control cell line identified genes differentially expressed during mDA neuron differentiation. Network analysis revealed that these genes form a core network, members of which interact with all known 19 protein-coding Parkinson's disease-associated genes. This core network encompasses key PD-associated pathways, including ubiquitination, mitochondrial function, protein processing, RNA metabolism, and vesicular transport. Proteomics analysis showed a consistent alteration in proteins of dopamine metabolism, indicating a defect of dopaminergic metabolism in PINK1-ILE368ASN neurons. Our findings suggest the existence of a network onto which pathways associated with PD pathology converge, and offers an inclusive interpretation of the phenotypic heterogeneity of PD.
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Affiliation(s)
- Gabriela Novak
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg.
- Center for Systems and Therapeutics, the Gladstone Institutes and Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Dimitrios Kyriakis
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Michela Bernini
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sophie Rodius
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, the Gladstone Institutes and Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Alexander Skupin
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- University of California San Diego, La Jolla, CA, 92093, USA.
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7
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Isaja L, Ferriol-Laffouillere SL, Mucci S, Rodríguez-Varela MS, Romorini L. Embryoid Bodies-Based Multilineage Differentiation of Human Embryonic Stem Cells Grown on Feeder-Free Conditions. Methods Mol Biol 2022; 2520:189-198. [PMID: 34611823 DOI: 10.1007/7651_2021_440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Human embryonic stem cells (hESCs) can differentiate into any cell lineage (pluripotency potential) derived from the three germ layers: ectoderm, mesoderm, and endoderm. Pluripotency is usually demonstrated in vitro by spontaneous differentiation of hESCs grown on a monolayer of feeder-cells using an embryoid bodies (EBs)-based method. However, currently hESCs are grown mostly using fully defined media in the absence of a feeder layer. Here we describe a EBs-based protocol that allows multilineage differentiation of hESCs and human induced pluripotent stem cells (hiPSCs) grown on feeder-free conditions.
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Affiliation(s)
- Luciana Isaja
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (Fleni), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Sofía Luján Ferriol-Laffouillere
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (Fleni), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Sofía Mucci
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (Fleni), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - María Soledad Rodríguez-Varela
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (Fleni), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Leonardo Romorini
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (Fleni), Belén de Escobar, Provincia de Buenos Aires, Argentina.
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8
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Ghosh A, Som A. Transcriptomic Analysis of Human Naïve and Primed Pluripotent Stem Cells. Methods Mol Biol 2022; 2416:213-237. [PMID: 34870839 DOI: 10.1007/978-1-0716-1908-7_14] [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] [Indexed: 06/13/2023]
Abstract
Over the last decade, RNA-Sequencing (RNA-Seq) has revolutionized the field of transcriptomics due to its sheer advantage over previous technologies for studying gene expression. Even the domain of stem cell bioinformatics has benefited from these advancements. It has helped look deeper into how the process of pluripotency is maintained by stem cells and how it may be exploited for application in regenerative medicine. However, as it is still an evolving technology, there is no single accepted protocol for RNA-Seq data analysis. From a wide array of tools and/or algorithms available for the purpose, researchers tend to develop a pipeline that is best suited for their sample, experimental design, and computational power. In this tutorial, we describe a pipeline based on open-source tools to analyze RNA-Seq data from naïve and primed state human pluripotent stem cell samples. Precisely, we show how RNA-Seq data can be downloaded from databases, processed, and used to identify differentially expressed genes and construct a co-expression network. Further, we also show how the list of interesting genes obtained from differential expression testing or co-expression network be analyzed to gain biological insights.
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Affiliation(s)
- Arindam Ghosh
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, India
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, India.
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9
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Current State-of-the-Art and Unresolved Problems in Using Human Induced Pluripotent Stem Cell-Derived Dopamine Neurons for Parkinson's Disease Drug Development. Int J Mol Sci 2021; 22:ijms22073381. [PMID: 33806103 PMCID: PMC8037675 DOI: 10.3390/ijms22073381] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
Human induced pluripotent stem (iPS) cells have the potential to give rise to a new era in Parkinson's disease (PD) research. As a unique source of midbrain dopaminergic (DA) neurons, iPS cells provide unparalleled capabilities for investigating the pathogenesis of PD, the development of novel anti-parkinsonian drugs, and personalized therapy design. Significant progress in developmental biology of midbrain DA neurons laid the foundation for their efficient derivation from iPS cells. The introduction of 3D culture methods to mimic the brain microenvironment further expanded the vast opportunities of iPS cell-based research of the neurodegenerative diseases. However, while the benefits for basic and applied studies provided by iPS cells receive widespread coverage in the current literature, the drawbacks of this model in its current state, and in particular, the aspects of differentiation protocols requiring further refinement are commonly overlooked. This review summarizes the recent data on general and subtype-specific features of midbrain DA neurons and their development. Here, we review the current protocols for derivation of DA neurons from human iPS cells and outline their general weak spots. The associated gaps in the contemporary knowledge are considered and the possible directions for future research that may assist in improving the differentiation conditions and increase the efficiency of using iPS cell-derived neurons for PD drug development are discussed.
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10
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Miura K, Oiwa Y, Kawamura Y. Induced Pluripotent Stem Cells from Cancer-Resistant Naked Mole-Rats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1319:329-339. [PMID: 34424523 DOI: 10.1007/978-3-030-65943-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Stem cells play essential roles in the development and tissue homeostasis of animals and are closely associated with carcinogenesis and aging. Also, the somatic cell reprogramming process to induced pluripotent stem (iPS) cells shares several characteristics with carcinogenesis. In this chapter, we focus on iPS cells and the reprogramming process of somatic cells in the naked mole-rat (NMR), the longest-living rodent with remarkable cancer resistance capabilities. NMR somatic cells show resistance to reprogramming induction, and generated NMR-iPS cells have a unique tumor-resistant phenotype. This phenotype is regulated by expressional activation of the tumor suppressor ARF gene and loss-of-function mutation in oncogene ERAS. Notably, it was also found that NMR somatic cells undergo senescence when ARF is suppressed during reprogramming, which would contribute to the resistance to both reprogramming and cancer in NMR somatic cells. Further studies on reprogramming resistance in NMR somatic cells and their concomitant tumor resistance in NMR-iPS cells would contribute to a better understanding of both cancer resistance and delayed aging in NMRs. In addition, NMR-iPS cells can be used as a new and important cell source for advancing research concerning several extraordinary physiological characteristics of NMR. Furthermore, study of NMR-iPS cells could lead to the development of safer regenerative therapies in the future.
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Affiliation(s)
- Kyoko Miura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan. .,Biomedical Animal Research Laboratory, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
| | - Yuki Oiwa
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Biomedical Animal Research Laboratory, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshimi Kawamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Biomedical Animal Research Laboratory, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
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11
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McDonald D, Wu Y, Dailamy A, Tat J, Parekh U, Zhao D, Hu M, Tipps A, Zhang K, Mali P. Defining the Teratoma as a Model for Multi-lineage Human Development. Cell 2020; 183:1402-1419.e18. [PMID: 33152263 PMCID: PMC7704916 DOI: 10.1016/j.cell.2020.10.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 06/06/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022]
Abstract
We propose that the teratoma, a recognized standard for validating pluripotency in stem cells, could be a promising platform for studying human developmental processes. Performing single-cell RNA sequencing (RNA-seq) of 179,632 cells across 23 teratomas from 4 cell lines, we found that teratomas reproducibly contain approximately 20 cell types across all 3 germ layers, that inter-teratoma cell type heterogeneity is comparable with organoid systems, and teratoma gut and brain cell types correspond well to similar fetal cell types. Furthermore, cellular barcoding confirmed that injected stem cells robustly engraft and contribute to all lineages. Using pooled CRISPR-Cas9 knockout screens, we showed that teratomas can enable simultaneous assaying of the effects of genetic perturbations across all germ layers. Additionally, we demonstrated that teratomas can be sculpted molecularly via microRNA (miRNA)-regulated suicide gene expression to enrich for specific tissues. Taken together, teratomas are a promising platform for modeling multi-lineage development, pan-tissue functional genetic screening, and tissue engineering.
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Affiliation(s)
- Daniella McDonald
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA 92093, USA
| | - Yan Wu
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Amir Dailamy
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Justin Tat
- Department of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Udit Parekh
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Dongxin Zhao
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Michael Hu
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Ann Tipps
- School of Medicine, University of California, San Diego, San Diego, CA 92103, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA 92093, USA.
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA 92093, USA.
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12
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Veiga A, Aran B, Raya A, Messinis I, Mahmood T. EBCOG position statement: ethics of stem cell research. Eur J Obstet Gynecol Reprod Biol 2020; 247:244-245. [PMID: 32007341 DOI: 10.1016/j.ejogrb.2020.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 01/10/2020] [Indexed: 01/08/2023]
Abstract
Over the past 10 years' significant research developments have taken place on human pluripotent stem cells and human embryonic stem cells to exploit the future potential in gene therapy and other focused treatments. There remains concerns around ethics of research and the fate of the human embryo used in such studies. European Board and College of Obstetrics and Gynaecology urge upon all scientists and the research bodies to adhere to the highest ethical principles of confidentiality and their actions should meet the criteria as set out by the international society for stem cell research.
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Affiliation(s)
- Anna Veiga
- Reproductive MedicineDexeus Women's Health, Barcelona Stem Cell Bank, Centre for Regenerative Medicine in Barcelona (CMRB), Facultat de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra (UPF), Spain
| | - Begoña Aran
- Barcelona Stem Cell Bank, Centre for Regenerative Medicine in Barcelona (CMRB), Spain
| | - Angel Raya
- Centre for Regenerative Medicine inBarcelona (CMRB), Spain
| | - Ioannis Messinis
- Chairman EBCOG Standing Committee on Examinations and Member of Executive Board, EBCOG.
| | - Tahir Mahmood
- Chairman EBCOG Standards of Care and Position Statements Working Group
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13
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Kaneko Y, Lee JY, Tajiri N, Tuazon JP, Lippert T, Russo E, Yu SJ, Bonsack B, Corey S, Coats AB, Kingsbury C, Chase TN, Koga M, Borlongan CV. Translating intracarotid artery transplantation of bone marrow-derived NCS-01 cells for ischemic stroke: Behavioral and histological readouts and mechanistic insights into stem cell therapy. Stem Cells Transl Med 2019; 9:203-220. [PMID: 31738023 PMCID: PMC6988762 DOI: 10.1002/sctm.19-0229] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
The present study used in vitro and in vivo stroke models to demonstrate the safety, efficacy, and mechanism of action of adult human bone marrow‐derived NCS‐01 cells. Coculture with NCS‐01 cells protected primary rat cortical cells or human neural progenitor cells from oxygen glucose deprivation. Adult rats that were subjected to middle cerebral artery occlusion, transiently or permanently, and subsequently received intracarotid artery or intravenous transplants of NCS‐01 cells displayed dose‐dependent improvements in motor and neurological behaviors, and reductions in infarct area and peri‐infarct cell loss, much better than intravenous administration. The optimal dose was 7.5 × 106 cells/mL when delivered via the intracarotid artery within 3 days poststroke, although therapeutic effects persisted even when administered at 1 week after stroke. Compared with other mesenchymal stem cells, NCS‐01 cells ameliorated both the structural and functional deficits after stroke through a broad therapeutic window. NCS‐01 cells secreted therapeutic molecules, such as basic fibroblast growth factor and interleukin‐6, but equally importantly we observed for the first time the formation of filopodia by NCS‐01 cells under stroke conditions, characterized by cadherin‐positive processes extending from the stem cells toward the ischemic cells. Collectively, the present efficacy readouts and the novel filopodia‐mediated mechanism of action provide solid lab‐to‐clinic evidence supporting the use of NCS‐01 cells for treatment of stroke in the clinical setting.
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Affiliation(s)
- Yuji Kaneko
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Jea-Young Lee
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Naoki Tajiri
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Julian P Tuazon
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Trenton Lippert
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Eleonora Russo
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Seong-Jin Yu
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Brooke Bonsack
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Sydney Corey
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Alexandreya B Coats
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Chase Kingsbury
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
| | - Thomas N Chase
- KM Pharmaceutical Consulting LLC, Washington, District of Columbia
| | - Minako Koga
- KM Pharmaceutical Consulting LLC, Washington, District of Columbia
| | - Cesar V Borlongan
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, Tampa, Florida
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14
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Yoo DH, Im YS, Jo EH, Kim BY, Jo HY, Park MH, Koo SK, Kim YO. Simple differentiation method using FBS identifies DUSP6 as a marker for fine-tuning of FGF-ERK signaling activity in human pluripotent stem cells. Biochem Biophys Res Commun 2019; 521:375-382. [PMID: 31668921 DOI: 10.1016/j.bbrc.2019.10.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/09/2019] [Indexed: 10/25/2022]
Abstract
Assessment of differentiation potential is a basic requirement to obtain qualified human pluripotent stem cells (hPSCs). Here, we report a simple differentiation method using fetal bovine serum (FBS) to estimate differentiation potential and propensity of hPSCs. PluriTest using RNA-sequencing showed that cells differentiated after treatment with 5% FBS. Expression patterns of three germ layer markers revealed that cells cultured in Knockout Serum Replacement-containing medium (KSR) with mouse feeder cells had higher differentiation potential than cells cultured in a chemically defined medium (E8) with recombinant matrix proteins, especially into the mesoderm and endoderm lineages. Analysis of differentially expressed genes between KSR and E8 identified DUSP6 as a marker for where cells had been cultured. Expression of DUSP6 correlated with FGF-ERK signaling activity. Fine-tuning of FGF-ERK signaling activity to a range that can shut down DUSP6 transcription but sustain NANOG transcription partially increased the differentiation potential. Our data suggest that differentiation with 5% FBS is good to estimate differentiation potential and propensity at the early stage, and that DUSP6 is an excellent marker to monitor ERK signaling activity.
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Affiliation(s)
- Dae Hoon Yoo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Young Sam Im
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Eun Hee Jo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Bo Young Kim
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Hye-Yeong Jo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Mi-Hyun Park
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Soo Kyung Koo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Yong-Ou Kim
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, Republic of Korea.
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15
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Zhang C, Skamagki M, Liu Z, Ananthanarayanan A, Zhao R, Li H, Kim K. Biological Significance of the Suppression of Oxidative Phosphorylation in Induced Pluripotent Stem Cells. Cell Rep 2018; 21:2058-2065. [PMID: 29166598 PMCID: PMC5841608 DOI: 10.1016/j.celrep.2017.10.098] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/31/2017] [Accepted: 10/25/2017] [Indexed: 12/15/2022] Open
Abstract
We discovered that induced pluripotent stem cell (iPSC) clones generated from aged tissue donors (A-iPSCs) fail to suppress oxidative phosphorylation. Compared to embryonic stem cells (ESCs) and iPSCs generated from young donors (Y-iPSCs), A-iPSCs show poor expression of the pluripotent stem cell-specific glucose transporter 3 (GLUT3) and impaired glucose uptake, making them unable to support the high glucose demands of glycolysis. Persistent oxidative phosphorylation in A-iPSCs generates higher levels of reactive oxygen species (ROS), which leads to excessive elevation of glutathione (a ROS-scavenging metabolite) and a blunted DNA damage response. These phenotypes were recapitulated in Y-iPSCs by inhibiting pyruvate dehydrogenase kinase (PDK) or supplying citrate to activate oxidative phosphorylation. In addition, oxidative phosphorylation in A-iPSC clones depletes citrate, a nuclear source of acetyl group donors for histone acetylation; this consequently alters histone acetylation status. Expression of GLUT3 in A-iPSCs recovers the metabolic defect, DNA damage response, and histone acetylation status.
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Affiliation(s)
- Cheng Zhang
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Maria Skamagki
- Cancer Biology and Genetics Program, The Center for Cell Engineering, The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Zhong Liu
- Department of Biochemistry and Molecular Genetics, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aparna Ananthanarayanan
- Cancer Biology and Genetics Program, The Center for Cell Engineering, The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Hu Li
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
| | - Kitai Kim
- Cancer Biology and Genetics Program, The Center for Cell Engineering, The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA.
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16
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Manipulating cell fate while confronting reproducibility concerns. Biochem Pharmacol 2018; 151:144-156. [DOI: 10.1016/j.bcp.2018.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
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17
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Hammad M, Rao W, Smith JGW, Anderson DG, Langer R, Young LE, Barrett DA, Davies MC, Denning C, Alexander MR. Identification of polymer surface adsorbed proteins implicated in pluripotent human embryonic stem cell expansion. Biomater Sci 2018; 4:1381-91. [PMID: 27466628 PMCID: PMC5038343 DOI: 10.1039/c6bm00214e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The discovery of heat shock proteins as candidates for human pluripotent stem cell culture using high throughput screening.
Improved biomaterials are required for application in regenerative medicine, biosensing, and as medical devices. The response of cells to the chemistry of polymers cultured in media is generally regarded as being dominated by proteins adsorbed to the surface. Here we use mass spectrometry to identify proteins adsorbed from a complex mouse embryonic fibroblast (MEF) conditioned medium found to support pluripotent human embryonic stem cell (hESC) expansion on a plasma etched tissue culture polystyrene surface. A total of 71 proteins were identified, of which 14 uniquely correlated with the surface on which pluripotent stem cell expansion was achieved. We have developed a microarray combinatorial protein spotting approach to test the potential of these 14 proteins to support expansion of a hESC cell line (HUES-7) and a human induced pluripotent stem cell line (ReBl-PAT) on a novel polymer (N-(4-Hydroxyphenyl) methacrylamide). These proteins were spotted to form a primary array yielding several protein mixture ‘hits’ that enhanced cell attachment to the polymer. A second array was generated to test the function of a refined set of protein mixtures. We found that a combination of heat shock protein 90 and heat shock protein-1 encourage elevated adherence of pluripotent stem cells at a level comparable to fibronectin pre-treatment.
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Affiliation(s)
- Moamen Hammad
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK. morgan.alexander.nottingham.ac.uk
| | - Wei Rao
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James G W Smith
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), University of Nottingham, Nottingham NG7 2RD, UK
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lorraine E Young
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), University of Nottingham, Nottingham NG7 2RD, UK
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Martyn C Davies
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK. morgan.alexander.nottingham.ac.uk
| | - Chris Denning
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), University of Nottingham, Nottingham NG7 2RD, UK
| | - Morgan R Alexander
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK. morgan.alexander.nottingham.ac.uk
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18
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Shukla V, Rao M, Zhang H, Beers J, Wangsa D, Wangsa D, Buishand FO, Wang Y, Yu Z, Stevenson HS, Reardon ES, McLoughlin KC, Kaufman AS, Payabyab EC, Hong JA, Zhang M, Davis S, Edelman D, Chen G, Miettinen MM, Restifo NP, Ried T, Meltzer PA, Schrump DS. ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer. Cancer Res 2017; 77:6267-6281. [PMID: 28935813 DOI: 10.1158/0008-5472.can-17-0570] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/28/2017] [Accepted: 09/07/2017] [Indexed: 01/16/2023]
Abstract
In this study, we generated induced pluripotent stem cells (iPSC) from normal human small airway epithelial cells (SAEC) to investigate epigenetic mechanisms of stemness and pluripotency in lung cancers. We documented key hallmarks of reprogramming in lung iPSCs (Lu-iPSC) that coincided with modulation of more than 15,000 genes relative to parental SAECs. Of particular novelty, we identified the PRC2-associated protein, ASXL3, which was markedly upregulated in Lu-iPSCs and small cell lung cancer (SCLC) lines and clinical specimens. ASXL3 overexpression correlated with increased genomic copy number in SCLC lines. ASXL3 silencing inhibited proliferation, clonogenicity, and teratoma formation by Lu-iPSCs, and diminished clonogenicity and malignant growth of SCLC cells in vivo Collectively, our studies validate the utility of the Lu-iPSC model for elucidating epigenetic mechanisms contributing to pulmonary carcinogenesis and highlight ASXL3 as a novel candidate target for SCLC therapy. Cancer Res; 77(22); 6267-81. ©2017 AACR.
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Affiliation(s)
- Vivek Shukla
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Mahadev Rao
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Hongen Zhang
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Danny Wangsa
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Yonghong Wang
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Zhiya Yu
- Laboratory of Pathology, Center for Cancer Research, NCI, Rockville, Maryland
| | - Holly S Stevenson
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Emily S Reardon
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Kaitlin C McLoughlin
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Andrew S Kaufman
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Eden C Payabyab
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Julie A Hong
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Mary Zhang
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Sean Davis
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Daniel Edelman
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Markku M Miettinen
- Laboratory of Pathology, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Thomas Ried
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Paul A Meltzer
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland.
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19
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Park S, Sung Y, Jeong J, Choi M, Lee J, Kwon W, Jang S, Park SJ, Kim JY, Kim SH, Yoon D, Ryoo ZY, Kim MO. Critical roles of hMAGEA2 in induced pluripotent stem cell pluripotency, proliferation, and differentiation. Cell Biochem Funct 2017; 35:392-400. [PMID: 28895148 DOI: 10.1002/cbf.3286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/30/2017] [Accepted: 07/07/2017] [Indexed: 12/20/2022]
Abstract
Induced pluripotent stem (iPS) cells are important for clinical application and stem cell research. Although human melanoma-associated antigen A2 (hMAGEA2) expression is known to affect differentiation in embryonic stem cells, its specific role in iPS cells remains unclear. To evaluate the function of hMAGEA2 and its characteristics in iPS cells, we produced hMAGEA2-overexpressing iPS cells from hMAGEA2-overexpressing transgenic mice. Although the iPS cells with overexpressed hMAGEA2 did not differ in morphology, their pluripotency, and self-renewal related genes (Nanog, Oct3/4, Sox2, and Stat3), expression level was significantly upregulated. Moreover, hMAGEA2 contributed to the promotion of cell cycle progression, thereby accelerating cell proliferation. Through embryoid body formation in vitro and teratoma formation in vivo, we demonstrated that hMAGEA2 critically decreases the differentiation ability of iPS cells. These data indicate that hMAGEA2 intensifies the self-renewal, pluripotency, and degree of proliferation of iPS cells, while significantly repressing their differentiation efficiency. Therefore, our findings prove that hMAGEA2 plays key roles in iPS cells.
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Affiliation(s)
- Song Park
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea.,Core Protein Resources Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Yonghun Sung
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jain Jeong
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minjee Choi
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jinhee Lee
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Wookbong Kwon
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Soyoung Jang
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Si Jun Park
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae Young Kim
- Department of Biochemistry, School of Dentistry, IHBR, Kyungpook National University, Daegu, South Korea
| | - Sung Hyun Kim
- China-US (Henan) Hormel Cancer Institute, No.127 Dongming Road, Zhengzhou, Henan 450008, China
| | - Duhak Yoon
- The School of Animal BT Science, Kyungpook National University, Sangju-si, Gyeongsangbuk-do, South Korea
| | - Zae Young Ryoo
- School of Life Science, BK21 plus KNU Creative Bio Research Group, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Myoung Ok Kim
- The School of Animal BT Science, Kyungpook National University, Sangju-si, Gyeongsangbuk-do, South Korea
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20
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Skamagki M, Correia C, Yeung P, Baslan T, Beck S, Zhang C, Ross CA, Dang L, Liu Z, Giunta S, Chang TP, Wang J, Ananthanarayanan A, Bohndorf M, Bosbach B, Adjaye J, Funabiki H, Kim J, Lowe S, Collins JJ, Lu CW, Li H, Zhao R, Kim K. ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nat Cell Biol 2017; 19:1037-1048. [PMID: 28846095 PMCID: PMC5843481 DOI: 10.1038/ncb3598] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023]
Abstract
Induced pluripotent stem cells (iPSCs), which are used to produce transplantable tissues, may particularly benefit older patients, who are more likely to suffer from degenerative diseases. However, iPSCs generated from aged donors (A-iPSCs) exhibit higher genomic instability, defects in apoptosis and a blunted DNA damage response compared with iPSCs generated from younger donors. We demonstrated that A-iPSCs exhibit excessive glutathione-mediated reactive oxygen species (ROS) scavenging activity, which blocks the DNA damage response and apoptosis and permits survival of cells with genomic instability. We found that the pluripotency factor ZSCAN10 is poorly expressed in A-iPSCs and addition of ZSCAN10 to the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) during A-iPSC reprogramming normalizes ROS-glutathione homeostasis and the DNA damage response, and recovers genomic stability. Correcting the genomic instability of A-iPSCs will ultimately enhance our ability to produce histocompatible functional tissues from older patients' own cells that are safe for transplantation.
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Affiliation(s)
- Maria Skamagki
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55904, USA
| | - Percy Yeung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Child Health Institute of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Timour Baslan
- Howard Hughes Medical Institute, Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA
| | - Samuel Beck
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55904, USA
| | - Christian A. Ross
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55904, USA
| | - Lam Dang
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Zhong Liu
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York 10065, USA
| | - Tzu-Pei Chang
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Joye Wang
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Aparna Ananthanarayanan
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Martina Bohndorf
- Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Benedikt Bosbach
- Howard Hughes Medical Institute, Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York 10065, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Scott Lowe
- Howard Hughes Medical Institute, Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology, Broad Institute of MIT and Harvard, and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02118, USA
| | - Chi-Wei Lu
- Department of Obstetrics, Gynecology and Reproductive Sciences, Child Health Institute of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55904, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Kitai Kim
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, USA
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21
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Paterson YZ, Kafarnik C, Guest DJ. Characterization of companion animal pluripotent stem cells. Cytometry A 2017; 93:137-148. [PMID: 28678404 DOI: 10.1002/cyto.a.23163] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/19/2017] [Accepted: 06/10/2017] [Indexed: 02/06/2023]
Abstract
Pluripotent stem cells have the capacity to grow indefinitely in culture and differentiate into derivatives of the three germ layers. These properties underpin their potential to be used in regenerative medicine. Originally derived from early embryos, pluripotent stem cells can now be derived by reprogramming an adult cell back to a pluripotent state. Companion animals such as horses, dogs, and cats suffer from many injuries and diseases for which regenerative medicine may offer new treatments. As many of the injuries and diseases are similar to conditions in humans the use of companion animals for the experimental and clinical testing of stem cell and regenerative medicine products would provide relevant animal models for the translation of therapies to the human field. In order to fully utilize companion animal pluripotent stem cells robust, standardized methods of characterization must be developed to ensure that safe and effective treatments can be delivered. In this review we discuss the methods that are available for characterizing pluripotent stem cells and the techniques that have been applied in cells from companion animals. We describe characteristics which have been described consistently across reports as well as highlighting discrepant results. Significant steps have been made to define the in vitro culture requirements and drive lineage specific differentiation of pluripotent stem cells in companion animal species. However, additional basic research to compare pluripotent stem cell types and define characteristics of pluripotency in companion animal species is still required. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Y Z Paterson
- Centre for Preventive Medicine, Animal Health Trust, Newmarket, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - C Kafarnik
- Centre for Preventive Medicine, Animal Health Trust, Newmarket, UK.,Institute of Ophthalmology, University College London, London, UK
| | - D J Guest
- Centre for Preventive Medicine, Animal Health Trust, Newmarket, UK
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22
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Culture of iPSCs Derived Pancreatic β-Like Cells In Vitro Using Decellularized Pancreatic Scaffolds: A Preliminary Trial. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4276928. [PMID: 28480220 PMCID: PMC5396430 DOI: 10.1155/2017/4276928] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/30/2016] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
Abstract
Diabetes mellitus is a disease which has affected 415 million patients in 2015. In an effort to replace the significant demands on transplantation and morbidity associated with transplantation, the production of β-like cells differentiated from induced pluripotent stem cells (iPSCs) was evaluated. This approach is associated with promising decellularized scaffolds with natural extracellular matrix (ECM) and ideal cubic environment that will promote cell growth in vivo. Our efforts focused on combining decellularized rat pancreatic scaffolds with mouse GFP+-iPSCs-derived pancreatic β-like cells, to evaluate whether decellularized scaffolds could facilitate the growth and function of β-like cells. β-like cells were differentiated from GFP+-iPSCs and evaluated via cultivating in the dynamic circulation perfusion device. Our results demonstrated that decellularized pancreatic scaffolds display favorable biochemical properties. Furthermore, not only could the scaffolds support the survival of β-like cells, but they also accelerated the expression of the insulin as compared to plate-based cell culture. In conclusion, these results suggest that decellularized pancreatic scaffolds could provide a suitable platform for cellular activities of β-like cells including survival and insulin secretion. This study provides preliminary support for regenerating insulin-secreting organs from the decellularized scaffolds combined with iPSCs derived β-like cells as a potential clinical application.
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23
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Bibliography. Stem Cell Res 2017. [DOI: 10.1201/9781315152943-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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24
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Rezvanfar MA, Hodjat M, Abdollahi M. Growing knowledge of using embryonic stem cells as a novel tool in developmental risk assessment of environmental toxicants. Life Sci 2016; 158:137-60. [DOI: 10.1016/j.lfs.2016.05.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/27/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022]
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25
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Heesen L, Peitz M, Torres-Benito L, Hölker I, Hupperich K, Dobrindt K, Jungverdorben J, Ritzenhofen S, Weykopf B, Eckert D, Hosseini-Barkooie SM, Storbeck M, Fusaki N, Lonigro R, Heller R, Kye MJ, Brüstle O, Wirth B. Plastin 3 is upregulated in iPSC-derived motoneurons from asymptomatic SMN1-deleted individuals. Cell Mol Life Sci 2016; 73:2089-104. [PMID: 26573968 PMCID: PMC11108513 DOI: 10.1007/s00018-015-2084-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/02/2015] [Accepted: 10/26/2015] [Indexed: 11/26/2022]
Abstract
Spinal muscular atrophy (SMA) is a devastating motoneuron (MN) disorder caused by homozygous loss of SMN1. Rarely, SMN1-deleted individuals are fully asymptomatic despite carrying identical SMN2 copies as their SMA III-affected siblings suggesting protection by genetic modifiers other than SMN2. High plastin 3 (PLS3) expression has previously been found in lymphoblastoid cells but not in fibroblasts of asymptomatic compared to symptomatic siblings. To find out whether PLS3 is also upregulated in MNs of asymptomatic individuals and thus a convincing SMA protective modifier, we generated induced pluripotent stem cells (iPSCs) from fibroblasts of three asymptomatic and three SMA III-affected siblings from two families and compared these to iPSCs from a SMA I patient and control individuals. MNs were differentiated from iPSC-derived small molecule neural precursor cells (smNPCs). All four genotype classes showed similar capacity to differentiate into MNs at day 8. However, SMA I-derived MN survival was significantly decreased while SMA III- and asymptomatic-derived MN survival was moderately reduced compared to controls at day 27. SMN expression levels and concomitant gem numbers broadly matched SMN2 copy number distribution; SMA I presented the lowest levels, whereas SMA III and asymptomatic showed similar levels. In contrast, PLS3 was significantly upregulated in mixed MN cultures from asymptomatic individuals pinpointing a tissue-specific regulation. Evidence for strong PLS3 accumulation in shaft and rim of growth cones in MN cultures from asymptomatic individuals implies an important role in neuromuscular synapse formation and maintenance. These findings provide strong evidence that PLS3 is a genuine SMA protective modifier.
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Affiliation(s)
- Ludwig Heesen
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Laura Torres-Benito
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Irmgard Hölker
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Kristina Hupperich
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Kristina Dobrindt
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Johannes Jungverdorben
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Swetlana Ritzenhofen
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Beatrice Weykopf
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Daniela Eckert
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Seyyed Mohsen Hosseini-Barkooie
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Markus Storbeck
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Noemi Fusaki
- Keio University School of Medicine and JST PRESTO, Tokyo, Japan
| | - Renata Lonigro
- Department of Biological and Medical Sciences, University of Udine, Udine, Italy
- Institute of Clinical Pathology, A. O. U, Udine, Italy
| | - Raoul Heller
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Min Jeong Kye
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany.
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany.
| | - Brunhilde Wirth
- Institute of Human Genetics, Institute of Genetics and Center for Molecular Medicine Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany.
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26
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Highly efficient delivery of functional cargoes by the synergistic effect of GAG binding motifs and cell-penetrating peptides. Proc Natl Acad Sci U S A 2016; 113:E291-9. [PMID: 26733682 DOI: 10.1073/pnas.1518634113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protein transduction domains (PTDs) are powerful nongenetic tools that allow intracellular delivery of conjugated cargoes to modify cell behavior. Their use in biomedicine has been hampered by inefficient delivery to nuclear and cytoplasmic targets. Here we overcame this deficiency by developing a series of novel fusion proteins that couple a membrane-docking peptide to heparan sulfate glycosaminoglycans (GAGs) with a PTD. We showed that this GET (GAG-binding enhanced transduction) system could deliver enzymes (Cre, neomycin phosphotransferase), transcription factors (NANOG, MYOD), antibodies, native proteins (cytochrome C), magnetic nanoparticles (MNPs), and nucleic acids [plasmid (p)DNA, modified (mod)RNA, and small inhibitory RNA] at efficiencies of up to two orders of magnitude higher than previously reported in cell types considered hard to transduce, such as mouse embryonic stem cells (mESCs), human ESCs (hESCs), and induced pluripotent stem cells (hiPSCs). This technology represents an efficient strategy for controlling cell labeling and directing cell fate or behavior that has broad applicability for basic research, disease modeling, and clinical application.
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27
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Pluripotent Stem Cells: Current Understanding and Future Directions. Stem Cells Int 2015; 2016:9451492. [PMID: 26798367 PMCID: PMC4699068 DOI: 10.1155/2016/9451492] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/26/2015] [Indexed: 02/06/2023] Open
Abstract
Pluripotent stem cells have the ability to undergo self-renewal and to give rise to all cells of the tissues of the body. However, this definition has been recently complicated by the existence of distinct cellular states that display these features. Here, we provide a detailed overview of the family of pluripotent cell lines derived from early mouse and human embryos and compare them with induced pluripotent stem cells. Shared and distinct features of these cells are reported as additional hallmark of pluripotency, offering a comprehensive scenario of pluripotent stem cells.
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28
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Ohshima S, Mori S, Shigenari A, Miyamoto A, Takasu M, Imaeda N, Nunomura S, Okayama Y, Tanaka M, Kitagawa H, Kulski JK, Inoko H, Ando A, Kametani Y. Differentiation ability of multipotent hematopoietic stem/progenitor cells detected by a porcine specific anti-CD117 monoclonal antibody. Biosci Trends 2015; 8:308-15. [PMID: 25641176 DOI: 10.5582/bst.2014.01084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
CD117 is a cytokine receptor expressed on the surface of hematopoietic stem cells with a likely role in cell survival, proliferation and differentiation. In order to study the differentiation activity of porcine CD117 hematopoietic cells in vitro and in vivo we prepared an anti-swine CD117 Mab (2A1) with high specificity for flow-cytometrical analysis. The 2A1 Mab did not recognize mouse or human mast cells suggesting that 2A1 is species-specific. Swine bone marrow (BM) CD117+ cells differentiated in vitro mainly into erythroid and monocyte lineages in the methylcellulose-based colony assay. When the swine BM CD117+ cells were transplanted in vivo into immunodeficient NOG (NOD/SCID/IL-2gc-null) mice, a significant amount of swine CD45+ leukocytes, including CD3 positive T cells, were developed in the mice. These results revealed that the swine BM CD117+ cells possess hematopoietic stem/progenitor activity and when monitored in immunodeficient mice or in vitro they can develop into lymphoid, erythroid, and myeloid cells efficiently with the new monoclonal antibody.
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Affiliation(s)
- Shino Ohshima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine
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29
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Schuster J, Halvardson J, Pilar Lorenzo L, Ameur A, Sobol M, Raykova D, Annerén G, Feuk L, Dahl N. Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling. Cell Reprogram 2015; 17:327-37. [PMID: 26348590 DOI: 10.1089/cell.2015.0009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Induced pluripotent stem cell (iPSC) technology has become an important tool for disease modeling. Insufficient data on the variability among iPSC lines derived from a single somatic parental cell line have in practice led to generation and analysis of several, usually three, iPSC sister lines from each parental cell line. We established iPSC lines from a human fibroblast line (HDF-K1) and used transcriptome sequencing to investigate the variation among three sister lines (iPSC-K1A, B, and C). For comparison, we analyzed the transcriptome of an iPSC line (iPSC-K5B) derived from a different fibroblast line (HDF-K5), a human embryonic stem cell (ESC) line (ESC-HS181), as well as the two parental fibroblast lines. All iPSC lines fulfilled stringent criteria for pluripotency. In an unbiased cluster analysis, all stem cell lines (four iPSCs and one ESC) clustered together as opposed to the parental fibroblasts. The transcriptome profiles of the three iPSC sister lines were indistinguishable from each other, and functional pathway analysis did not reveal any significant hits. In contrast, the expression profiles of the ESC line and the iPSC-K5B line were distinct from that of the sister lines iPSC-K1A, B, and C. Differentiation to embryoid bodies and subsequent analysis of germ layer markers in the five stem cell clones confirmed that the distribution of their expression profiles was retained. Taken together, our observations stress the importance of using iPSCs of different parental origin rather than several sister iPSC lines to distinguish disease-associated mechanisms from genetic background effects in disease modeling.
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Affiliation(s)
- Jens Schuster
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Laureanne Pilar Lorenzo
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Maria Sobol
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Doroteya Raykova
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala, Sweden
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30
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Sanal MG. Cell therapy from bench to bedside: Hepatocytes from fibroblasts - the truth and myth of transdifferentiation. World J Gastroenterol 2015; 21:6427-6433. [PMID: 26074681 PMCID: PMC4458753 DOI: 10.3748/wjg.v21.i21.6427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/24/2015] [Accepted: 05/07/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte transplantation is an alternative to liver transplantation in certain disorders such as inherited liver diseases and liver failure. It is a relatively less complicated surgical procedure, and has the advantage that it can be repeated several times if unsuccessful. Another advantage is that hepatocytes can be isolated from partly damaged livers which are not suitable for liver transplantation. Despite these advantages hepatocyte transplantation is less popular. Important issues are poor engraftment of the transplanted cells and the scarcity of donor hepatocytes. Generation of “hepatocyte like cells”/iHeps from embryonic stem cells (ES) and induced pluripotent stem cells (iPSCs) by directed differentiation is an emerging solution to the latter issue. Direct conversation or trans-differentiation of fibroblasts to “hepatocyte like cells” is another way which is, being explored. However this method has several inherent and technical disadvantages compared to the directed differentiation from ES or iPSC. There are several methods claiming to be “highly efficient” for generating “highly functional”“hepatocyte like cells”. Currently different groups are working independently and coming up with differentiation protocols and each group claiming an advantage for their protocol. Directed differentiation protocols need to be designed, compared, analyzed and tweaked systematically and logically than empirically. There is a need for a well-coordinated global initiative comparable to the Human Genome Project to achieve this goal in the near future.
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31
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Çağlayan ES, Güran Ş. Importance of Myc-related microRNAs in induced pluripotency. Cell Biol Int 2015; 39:987-94. [PMID: 25809132 DOI: 10.1002/cbin.10467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 03/14/2015] [Indexed: 01/23/2023]
Abstract
Pluripotent stem cells (PSCs) have the capacity to differentiate into any cell type of the body. Therefore, induced pluripotent stem cells (iPSCs) are seen as a promising solution for patient-specific cell therapies. However, the safety is major issue for in vitro methods that are used in induction of pluripotency and also in differentiation of PSCs toward specific cell types. In pioneer studies of iPSC generation, the role of c-Myc has been highlighted as a possible master regulator of pluripotency, but direct c-Myc overexpression is known to prompt drawbacks, especially in human cells. In recent studies, the role of non-protein coding RNA molecules such as microRNAs (miRNAs) has been shown in enhanced reprogramming efficiency. In addition, new reprogramming methods have been ultimately improved by adding miRNAs, in the absence of previous factors. Cross interaction between miRNAs and c-Myc has been also found in differentiation of iPSCs, as well as in reprogramming and self-renewing the pluripotent state. Thence, miRNAs are promising solution for efficiency and safety of iPSC derivation and differentiation methods. The purpose of the present review is to evaluate interaction mechanisms of miRNAs with c-Myc and in iPSC technology.
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Affiliation(s)
- E Sacide Çağlayan
- Nutrition and Dietetics Department, Yildirim Beyazıt University, Health Science Faculty, Ankara, Turkey
| | - Şefik Güran
- Medical Biology Department, Gulhane Military Medicine Academy, Ankara, Turkey
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Shoni M, Lui KO, Vavvas DG, Muto MG, Berkowitz RS, Vlahos N, Ng SW. Protein kinases and associated pathways in pluripotent state and lineage differentiation. Curr Stem Cell Res Ther 2015; 9:366-87. [PMID: 24998240 DOI: 10.2174/1574888x09666140616130217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 06/07/2014] [Accepted: 06/12/2014] [Indexed: 02/06/2023]
Abstract
Protein kinases (PKs) mediate the reversible conversion of substrate proteins to phosphorylated forms, a key process in controlling intracellular signaling transduction cascades. Pluripotency is, among others, characterized by specifically expressed PKs forming a highly interconnected regulatory network that culminates in a finely-balanced molecular switch. Current high-throughput phosphoproteomic approaches have shed light on the specific regulatory PKs and their function in controlling pluripotent states. Pluripotent cell-derived endothelial and hematopoietic developments represent an example of the importance of pluripotency in cancer therapeutics and organ regeneration. This review attempts to provide the hitherto known kinome profile and the individual characterization of PK-related pathways that regulate pluripotency. Elucidating the underlying intrinsic and extrinsic signals may improve our understanding of the different pluripotent states, the maintenance or induction of pluripotency, and the ability to tailor lineage differentiation, with a particular focus on endothelial cell differentiation for anti-cancer treatment, cell-based tissue engineering, and regenerative medicine strategies.
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Affiliation(s)
| | | | | | | | | | | | - Shu-Wing Ng
- 221 Longwood Avenue, BLI- 449A, Boston MA 02115, USA.
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33
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Lenz M, Goetzke R, Schenk A, Schubert C, Veeck J, Hemeda H, Koschmieder S, Zenke M, Schuppert A, Wagner W. Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells. Sci Rep 2015; 5:8973. [PMID: 25754700 PMCID: PMC4354028 DOI: 10.1038/srep08973] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/11/2015] [Indexed: 12/12/2022] Open
Abstract
Quality control of human induced pluripotent stem cells (iPSCs) can be performed by several methods. These methods are usually relatively labor-intensive, difficult to standardize, or they do not facilitate reliable quantification. Here, we describe a biomarker to distinguish between pluripotent and non-pluripotent cells based on DNA methylation (DNAm) levels at only three specific CpG sites. Two of these CpG sites were selected by their discriminatory power in 258 DNAm profiles – they were either methylated in pluripotent or non-pluripotent cells. The difference between these two β-values provides an Epi-Pluri-Score that was validated on independent DNAm-datasets (264 pluripotent and 1,951 non-pluripotent samples) with 99.9% specificity and 98.9% sensitivity. This score was complemented by a third CpG within the gene POU5F1 (OCT4), which better demarcates early differentiation events. We established pyrosequencing assays for the three relevant CpG sites and thereby correctly classified DNA of 12 pluripotent cell lines and 31 non-pluripotent cell lines. Furthermore, DNAm changes at these three CpGs were tracked in the course of differentiation of iPSCs towards mesenchymal stromal cells. The Epi-Pluri-Score does not give information on lineage-specific differentiation potential, but it provides a simple, reliable, and robust biomarker to support high-throughput classification into either pluripotent or non-pluripotent cells.
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Affiliation(s)
- Michael Lenz
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Arne Schenk
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Bayer Technology Services GmbH, Leverkusen, Germany
| | - Claudia Schubert
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Jürgen Veeck
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Hatim Hemeda
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Martin Zenke
- 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Andreas Schuppert
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Bayer Technology Services GmbH, Leverkusen, Germany
| | - Wolfgang Wagner
- 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
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34
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Fang YL, Chen XG, W T G. Gene delivery in tissue engineering and regenerative medicine. J Biomed Mater Res B Appl Biomater 2014; 103:1679-99. [PMID: 25557560 DOI: 10.1002/jbm.b.33354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 11/07/2014] [Accepted: 11/18/2014] [Indexed: 12/13/2022]
Abstract
As a promising strategy to aid or replace tissue/organ transplantation, gene delivery has been used for regenerative medicine applications to create or restore normal function at the cell and tissue levels. Gene delivery has been successfully performed ex vivo and in vivo in these applications. Excellent proliferation capabilities and differentiation potentials render certain cells as excellent candidates for ex vivo gene delivery for regenerative medicine applications, which is why multipotent and pluripotent cells have been intensely studied in this vein. In this review, gene delivery is discussed in detail, along with its applications to tissue engineering and regenerative medicine. A definition of a stem cell is compared to a definition of a stem property, and both provide the foundation for an in-depth look at gene delivery investigations from a germ lineage angle.
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Affiliation(s)
- Y L Fang
- Department of Chemical & Biomolecular Engineering, Laboratory for Gene Therapy and Cellular Engineering, Tulane University, 300 Lindy Boggs Center, New Orleans, Louisiana, 70118
| | - X G Chen
- Department of Chemical & Biomolecular Engineering, Laboratory for Gene Therapy and Cellular Engineering, Tulane University, 300 Lindy Boggs Center, New Orleans, Louisiana, 70118
| | - Godbey W T
- Department of Chemical & Biomolecular Engineering, Laboratory for Gene Therapy and Cellular Engineering, Tulane University, 300 Lindy Boggs Center, New Orleans, Louisiana, 70118
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35
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Ratajczak MZ, Marycz K, Poniewierska-Baran A, Fiedorowicz K, Zbucka-Kretowska M, Moniuszko M. Very small embryonic-like stem cells as a novel developmental concept and the hierarchy of the stem cell compartment. Adv Med Sci 2014; 59:273-80. [PMID: 25170822 DOI: 10.1016/j.advms.2014.08.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/06/2014] [Accepted: 08/04/2014] [Indexed: 01/14/2023]
Abstract
Our current understanding of stem cells suffers from a lack of precision, as the stem cell compartment is a broad continuum between early stages of development and adult postnatal tissues, and it is not fully understood how this transition occurs. The definition of stem cell pluripotency is adapted from embryology and excludes the possibility that some early-development stem cells with pluri- and/or multipotential differentiation potential may reside in postnatal tissues in a dormant state in which they are protected from uncontrolled proliferation and thus do not form teratomas or have the ability to complement blastocyst development. We will discuss the concept that a population of very small embryonic-like stem cells (VSELs) could be a link between early-development stages and adult stem cell compartments and reside in a quiescent state in adult tissues. The epigenetic mechanism identified that changes expression of certain genes involved in insulin/insulin-like growth factor signaling (IIS) in VSELs, on the one hand, keeps these cells quiescent in adult tissues and, on the other hand, provides a novel view of the stem cell compartment, IIS, tissue/organ rejuvenation, aging, and cancerogenesis.
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Affiliation(s)
- Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA; Department of Physiology, Pomeranian Medical University, Szczecin, Poland.
| | - Krzysztof Marycz
- University of Environmental and Life Sciences, Electron Microscopy Laboratory, Wroclaw, Poland; Wroclaw Research Centre EIT+, Wroclaw, Poland
| | - Agata Poniewierska-Baran
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA; Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | | | - Monika Zbucka-Kretowska
- Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland; Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
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36
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Kues WA, Nowak-Imialek M, Haridoss S, Niemann H. Strategies for the derivation of pluripotent cells from farm animals. Reprod Domest Anim 2014; 45 Suppl 3:25-31. [PMID: 24417196 DOI: 10.1111/j.1439-0531.2010.01663.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent experiments demonstrated that forced expression of few critical genes drives conversion of a somatic into a pluripotent cell state. These induced pluripotent cells (iPS) were first generated from murine fibroblasts by Shinya Yamanaka's laboratory in 2006. By using retroviral vectors to express combinations of stemness genes, they identified Oct4, Sox2, Krueppel-like factor 4 and c-Myc as essential factors for reprogramming of somatic cells. Subsequent experiments applied this technology to human and rat fibroblasts, as well as other cell types and several groups showed that iPS can be generated by an even smaller number of transcription factors. The efficiency of conversion and maintenance of a pluripotent state can be supported by small molecules, such as valproic acid and specific pharmacological inhibitors. This technology is a milestone for a basic understanding of cell potency, cell fate and pathogenesis, as well as for development of cell therapies and potential applications in animal breeding.
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Affiliation(s)
- W A Kues
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute, Mariensee, Neustadt Department of Reprogramming, Hannover Medical School, Hannover, Germany
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37
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Induced pluripotent stem cell technology in regenerative medicine and biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 123:127-41. [PMID: 20549468 DOI: 10.1007/10_2010_72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The potential of human embryonic stem cells (ESCs) for regenerative medicine is unquestionable, but practical and ethical considerations have hampered clinical application and research. In an attempt to overcome these issues, the conversion of somatic cells into pluripotent stem cells similar to ESCs, commonly termed nuclear reprogramming, has been a top objective of contemporary biology. More than 40 years ago, King, Briggs, and Gurdon pioneered somatic cell nuclear reprogramming in frogs, and in 1981 Evans successfully isolated mouse ESCs. In 1997 Wilmut and collaborators produced the first cloned mammal using nuclear transfer, and then Thomson obtained human ESCs from in vitro fertilized blastocysts in 1998. Over the last 2 decades we have also seen remarkable findings regarding how ESC behavior is controlled, the importance of which should not be underestimated. This knowledge allowed the laboratory of Shinya Yamanaka to overcome brilliantly conceptual and technical barriers in 2006 and generate induced pluripotent stem cells (iPSCs) from mouse fibroblasts by overexpressing defined combinations of ESC-enriched transcription factors. Here, we discuss some important implications of human iPSCs for biology and medicine and also point to possible future directions.
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38
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Suszynska M, Zuba-Surma EK, Maj M, Mierzejewska K, Ratajczak J, Kucia M, Ratajczak MZ. The proper criteria for identification and sorting of very small embryonic-like stem cells, and some nomenclature issues. Stem Cells Dev 2014; 23:702-13. [PMID: 24299281 DOI: 10.1089/scd.2013.0472] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Evidence has accumulated that both murine and human adult tissues contain early-development stem cells with a broader differentiation potential than other adult monopotent stem cells. These cells, being pluripotent or multipotent, exist at different levels of specification and most likely represent overlapping populations of cells that, depending on the isolation strategy, ex vivo expansion protocol, and markers employed for their identification, have been given different names. In this review, we will discuss a population of very small embryonic-like stem cells (VSELs) in the context of other stem cells that express pluripotent/multipotent markers isolated from adult tissues as well as review the most current, validated working criteria on how to properly identify and isolate these very rare cells. VSELs have been successfully purified in several laboratories; however, a few have failed to isolate them, which has raised some unnecessary controversy in the field. Therefore, in this short review, we will address the most important reasons that some investigators have experienced problems in isolating these very rare cells and discuss some still unresolved challenges which should be overcome before these cells can be widely employed in the clinic.
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Affiliation(s)
- Malwina Suszynska
- 1 Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky
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Mallon BS, Hamilton RS, Kozhich OA, Johnson KR, Fann YC, Rao MS, Robey PG. Comparison of the molecular profiles of human embryonic and induced pluripotent stem cells of isogenic origin. Stem Cell Res 2013; 12:376-86. [PMID: 24374290 PMCID: PMC4157340 DOI: 10.1016/j.scr.2013.11.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/21/2013] [Accepted: 11/22/2013] [Indexed: 11/17/2022] Open
Abstract
Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level.
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Affiliation(s)
- Barbara S Mallon
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Rebecca S Hamilton
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olga A Kozhich
- Laboratory of Molecular Biology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kory R Johnson
- Bioinformatics Section, Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yang C Fann
- Bioinformatics Section, Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mahendra S Rao
- NIH Center for Regenerative Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela G Robey
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Craniofacial and Skeletal Disease Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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40
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Thrombospondin-1 signaling through CD47 inhibits self-renewal by regulating c-Myc and other stem cell transcription factors. Sci Rep 2013; 3:1673. [PMID: 23591719 PMCID: PMC3628113 DOI: 10.1038/srep01673] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/02/2013] [Indexed: 12/11/2022] Open
Abstract
Signaling through the thrombospondin-1 receptor CD47 broadly limits cell and tissue survival of stress, but the molecular mechanisms are incompletely understood. We now show that loss of CD47 permits sustained proliferation of primary murine endothelial cells, increases asymmetric division, and enables these cells to spontaneously reprogram to form multipotent embryoid body-like clusters. c-Myc, Klf4, Oct4, and Sox2 expression is elevated in CD47-null endothelial cells, in several tissues of CD47- and thrombospondin-1-null mice, and in a human T cell line lacking CD47. CD47 knockdown acutely increases mRNA levels of c-Myc and other stem cell transcription factors in cells and in vivo, whereas CD47 ligation by thrombospondin-1 suppresses c-Myc expression. The inhibitory effects of increasing CD47 levels can be overcome by maintaining c-Myc expression and are absent in cells with dysregulated c-Myc. Thus, CD47 antagonists enable cell self-renewal and reprogramming by overcoming negative regulation of c-Myc and other stem cell transcription factors.
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Telomere reprogramming and maintenance in porcine iPS cells. PLoS One 2013; 8:e74202. [PMID: 24098638 PMCID: PMC3787036 DOI: 10.1371/journal.pone.0074202] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/29/2013] [Indexed: 01/12/2023] Open
Abstract
Telomere reprogramming and silencing of exogenous genes have been demonstrated in mouse and human induced pluripotent stem cells (iPS cells). Pigs have the potential to provide xenotransplant for humans, and to model and test human diseases. We investigated the telomere length and maintenance in porcine iPS cells generated and cultured under various conditions. Telomere lengths vary among different porcine iPS cell lines, some with telomere elongation and maintenance, and others telomere shortening. Porcine iPS cells with sufficient telomere length maintenance show the ability to differentiate in vivo by teratoma formation test. IPS cells with short or dysfunctional telomeres exhibit reduced ability to form teratomas. Moreover, insufficient telomerase and incomplete telomere reprogramming and/or maintenance link to sustained activation of exogenous genes in porcine iPS cells. In contrast, porcine iPS cells with reduced expression of exogenous genes or partial exogene silencing exhibit insufficient activation of endogenous pluripotent genes and telomerase genes, accompanied by telomere shortening with increasing passages. Moreover, telomere doublets, telomere sister chromatid exchanges and t-circles that presumably are involved in telomere lengthening by recombination also are found in porcine iPS cells. These data suggest that both telomerase-dependent and telomerase-independent mechanisms are involved in telomere reprogramming during induction and passages of porcine iPS cells, but these are insufficient, resulting in increased telomere damage and shortening, and chromosomal instability. Active exogenes might compensate for insufficient activation of endogenous genes and incomplete telomere reprogramming and maintenance of porcine iPS cells. Further understanding of telomere reprogramming and maintenance may help improve the quality of porcine iPS cells.
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Vossaert L, O'Leary T, Van Neste C, Heindryckx B, Vandesompele J, De Sutter P, Deforce D. Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells. BMC Mol Biol 2013; 14:21. [PMID: 24028740 PMCID: PMC3848990 DOI: 10.1186/1471-2199-14-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selecting stably expressed reference genes is essential for proper reverse transcription quantitative polymerase chain reaction gene expression analysis. However, this choice is not always straightforward. In the case of differentiating human embryonic stem (hES) cells, differentiation itself introduces changes whereby reference gene stability may be influenced. RESULTS In this study, we evaluated the stability of various references during retinoic acid-induced (2 microM) differentiation of hES cells. Out of 12 candidate references, beta-2-microglobulin, ribosomal protein L13A and Alu repeats are found to be the most stable for this experimental set-up. CONCLUSIONS Our results show that some of the commonly used reference genes are actually not amongst the most stable loci during hES cell differentiation promoted by retinoic acid. Moreover, a novel normalization strategy based on expressed Alu repeats is validated for use in hES cell experiments.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, Ghent 9000, Belgium.
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Folmes CD, Arrell DK, Zlatkovic-Lindor J, Martinez-Fernandez A, Perez-Terzic C, Nelson TJ, Terzic A. Metabolome and metaboproteome remodeling in nuclear reprogramming. Cell Cycle 2013; 12:2355-65. [PMID: 23839047 DOI: 10.4161/cc.25509] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nuclear reprogramming resets differentiated tissue to generate induced pluripotent stem (iPS) cells. While genomic attributes underlying reacquisition of the embryonic-like state have been delineated, less is known regarding the metabolic dynamics underscoring induction of pluripotency. Metabolomic profiling of fibroblasts vs. iPS cells demonstrated nuclear reprogramming-associated induction of glycolysis, realized through augmented utilization of glucose and accumulation of lactate. Real-time assessment unmasked downregulated mitochondrial reserve capacity and ATP turnover correlating with pluripotent induction. Reduction in oxygen consumption and acceleration of extracellular acidification rates represent high-throughput markers of the transition from oxidative to glycolytic metabolism, characterizing stemness acquisition. The bioenergetic transition was supported by proteome remodeling, whereby 441 proteins were altered between fibroblasts and derived iPS cells. Systems analysis revealed overrepresented canonical pathways and interactome-associated biological processes predicting differential metabolic behavior in response to reprogramming stimuli, including upregulation of glycolysis, purine, arginine, proline, ribonucleoside and ribonucleotide metabolism, and biopolymer and macromolecular catabolism, with concomitant downregulation of oxidative phosphorylation, phosphate metabolism regulation, and precursor biosynthesis processes, prioritizing the impact of energy metabolism within the hierarchy of nuclear reprogramming. Thus, metabolome and metaboproteome remodeling is integral for induction of pluripotency, expanding on the genetic and epigenetic requirements for cell fate manipulation.
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Affiliation(s)
- Clifford Dl Folmes
- Center for Regenerative Medicine and Marriott Heart Disease Research Program; Division of Cardiovascular Diseases; Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Medical Genetics; Mayo Clinic; Rochester, MN USA
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Sphingosine Phosphate Lyase Regulates Murine Embryonic Stem Cell Proliferation and Pluripotency through an S1P 2/STAT3 Signaling Pathway. Biomolecules 2013; 3:351-368. [PMID: 24619572 PMCID: PMC3947625 DOI: 10.3390/biom3030351] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Sphingosine-1-phosphate (S1P) is a bioactive sphingolipid that activates a family of G protein coupled-receptors (GPCRs) implicated in mammalian development, angiogenesis, immunity and tissue regeneration. S1P functions as a trophic factor for many cell types, including embryonic stem cells (ESCs). Sphingosine phosphate lyase (SPL) is an intracellular enzyme that catalyzes the irreversible degradation of S1P. We found SPL to be highly expressed in murine ESCs (mESCs). To investigate the role of SPL in mESC biology, we silenced SPL in mESCs via stable transfection with a lentiviral SPL-specific short hairpin RNA (shRNA) construct. SPL-knockdown (SPL-KD) mESCs showed a 5-fold increase in cellular S1P levels, increased proliferation rates and high expression of cell surface pluripotency markers SSEA1 and OCT4 compared to vector control cells. Compared to control mESCs, SPL-KD cells showed robust activation of STAT3 and a 10-fold increase in S1P2 expression. Inhibition of S1P2 or STAT3 reversed the proliferation and pluripotency phenotypes of SPL-KD mESCs. Further, inhibition of S1P2 attenuated, in a dose-dependent fashion, the high levels of OCT4 and STAT3 activation observed in SPL-KD mESCs. Finally, we showed that SPL-KD cells are capable of generating embryoid bodies from which muscle stem cells, called satellite cells, can be isolated. These findings demonstrate an important role for SPL in ESC homeostasis and suggest that SPL inhibition could facilitate ex vivo ESC expansion for therapeutic purposes.
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45
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Nowak-Imialek M, Niemann H. Pluripotent cells in farm animals: state of the art and future perspectives. Reprod Fertil Dev 2013; 25:103-28. [PMID: 23244833 DOI: 10.1071/rd12265] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pluripotent cells, such as embryonic stem (ES) cells, embryonic germ cells and embryonic carcinoma cells are a unique type of cell because they remain undifferentiated indefinitely in in vitro culture, show self-renewal and possess the ability to differentiate into derivatives of the three germ layers. These capabilities make them a unique in vitro model for studying development, differentiation and for targeted modification of the genome. True pluripotent ESCs have only been described in the laboratory mouse and rat. However, rodent physiology and anatomy differ substantially from that of humans, detracting from the value of the rodent model for studies of human diseases and the development of cellular therapies in regenerative medicine. Recently, progress in the isolation of pluripotent cells in farm animals has been made and new technologies for reprogramming of somatic cells into a pluripotent state have been developed. Prior to clinical application of therapeutic cells differentiated from pluripotent stem cells in human patients, their survival and the absence of tumourigenic potential must be assessed in suitable preclinical large animal models. The establishment of pluripotent cell lines in farm animals may provide new opportunities for the production of transgenic animals, would facilitate development and validation of large animal models for evaluating ESC-based therapies and would thus contribute to the improvement of human and animal health. This review summarises the recent progress in the derivation of pluripotent and reprogrammed cells from farm animals. We refer to our recent review on this area, to which this article is complementary.
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Affiliation(s)
- Monika Nowak-Imialek
- Institut of Farm Animal Genetics, Friedrich-Loefller-Institut (FLI), Biotechnology, Höltystrasse 10, Mariensee, 31535 Neustadt, Germany.
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46
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Kramer AS, Harvey AR, Plant GW, Hodgetts SI. Systematic Review of Induced Pluripotent Stem Cell Technology as a Potential Clinical Therapy for Spinal Cord Injury. Cell Transplant 2013; 22:571-617. [DOI: 10.3727/096368912x655208] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transplantation therapies aimed at repairing neurodegenerative and neuropathological conditions of the central nervous system (CNS) have utilized and tested a variety of cell candidates, each with its own unique set of advantages and disadvantages. The use and popularity of each cell type is guided by a number of factors including the nature of the experimental model, neuroprotection capacity, the ability to promote plasticity and guided axonal growth, and the cells' myelination capability. The promise of stem cells, with their reported ability to give rise to neuronal lineages to replace lost endogenous cells and myelin, integrate into host tissue, restore functional connectivity, and provide trophic support to enhance and direct intrinsic regenerative ability, has been seen as a most encouraging step forward. The advent of the induced pluripotent stem cell (iPSC), which represents the ability to “reprogram” somatic cells into a pluripotent state, hails the arrival of a new cell transplantation candidate for potential clinical application in therapies designed to promote repair and/or regeneration of the CNS. Since the initial development of iPSC technology, these cells have been extensively characterized in vitro and in a number of pathological conditions and were originally reported to be equivalent to embryonic stem cells (ESCs). This review highlights emerging evidence that suggests iPSCs are not necessarily indistinguishable from ESCs and may occupy a different “state” of pluripotency with differences in gene expression, methylation patterns, and genomic aberrations, which may reflect incomplete reprogramming and may therefore impact on the regenerative potential of these donor cells in therapies. It also highlights the limitations of current technologies used to generate these cells. Moreover, we provide a systematic review of the state of play with regard to the use of iPSCs in the treatment of neurodegenerative and neuropathological conditions. The importance of balancing the promise of this transplantation candidate in the light of these emerging properties is crucial as the potential application in the clinical setting approaches. The first of three sections in this review discusses (A) the pathophysiology of spinal cord injury (SCI) and how stem cell therapies can positively alter the pathology in experimental SCI. Part B summarizes (i) the available technologies to deliver transgenes to generate iPSCs and (ii) recent data comparing iPSCs to ESCs in terms of characteristics and molecular composition. Lastly, in (C) we evaluate iPSC-based therapies as a candidate to treat SCI on the basis of their neurite induction capability compared to embryonic stem cells and provide a summary of available in vivo data of iPSCs used in SCI and other disease models.
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Affiliation(s)
- Anne S. Kramer
- Spinal Cord Repair Laboratory, School of Anatomy, Physiology and Human Biology, The University of Western Australia, Perth, Western Australia
| | - Alan R. Harvey
- Spinal Cord Repair Laboratory, School of Anatomy, Physiology and Human Biology, The University of Western Australia, Perth, Western Australia
| | - Giles W. Plant
- Stanford Partnership for Spinal Cord Injury and Repair, Stanford Institute for Neuro-Innovation and Translational Neurosciences, Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Stuart I. Hodgetts
- Spinal Cord Repair Laboratory, School of Anatomy, Physiology and Human Biology, The University of Western Australia, Perth, Western Australia
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Ratajczak MZ, Mierzejewska K, Ratajczak J, Kucia M. CD133 Expression Strongly Correlates with the Phenotype of Very Small Embryonic-/Epiblast-Like Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 777:125-41. [PMID: 23161080 DOI: 10.1007/978-1-4614-5894-4_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CD133 antigen (prominin-1) is a useful cell surface marker of very small embryonic-like stem cells (VSELs). Antibodies against it, conjugated to paramagnetic beads or fluorochromes, are thus powerful biological tools for their isolation from human umbilical cord blood, mobilized peripheral blood, and bone marrow. VSELs are described with the following characteristics: (1) are slightly smaller than red blood cells; (2) display a distinct morphology, typified by a high nuclear/cytoplasmic ratio and an unorganized euchromatin; (3) become mobilized during stress situations into peripheral blood; (4) are enriched in the CD133(+)Lin(-)CD45(-) cell fraction in humans; and (5) express markers of pluripotent stem cells (e.g., Oct-4, Nanog, and stage-specific embryonic antigen-4). The most recent in vivo data from our and other laboratories demonstrated that human VSELs exhibit some characteristics of long-term repopulating hematopoietic stem cells and are at the top of the hierarchy in the mesenchymal lineage. However, still more labor is needed to characterize better at a molecular level these rare cells.
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Affiliation(s)
- Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, 500 S. Floyd Street, 40202 Rm. 107, Louisville, KY, USA,
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Kaltschmidt B, Kaltschmidt C, Widera D. Adult craniofacial stem cells: sources and relation to the neural crest. Stem Cell Rev Rep 2012; 8:658-71. [PMID: 22170630 DOI: 10.1007/s12015-011-9340-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the process of development, neural crest cells migrate out from their niche between the newly formed ectoderm and the neural tube. Thereafter, they give rise not only to ectodermal cell types, but also to mesodermal cell types. Cell types with neural crest ancestry consequently comprise a number of specialized varieties, such as ectodermal neurons, melanocytes and Schwann cells, as well as mesodermal osteoblasts, adipocytes and smooth muscle cells. Numerous recent studies suggest that stem cells with a neural crest origin persist into adulthood, especially within the mammalian craniofacial compartment. This review discusses the sources of adult neural crest-derived stem cells (NCSCs) derived from the cranium, as well as their differentiation potential and expression of key stem cell markers. Furthermore, the expression of marker genes associated with embryonic stem cells and the issue of multi- versus pluripotency of adult NCSCs is reviewed. Stringent tests are proposed, which, if performed, are anticipated to clarify the issue of adult NCSC potency. Finally, current pre-clinical and clinical data are discussed in light of the clinical impact of adult NCSCs.
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Affiliation(s)
- Barbara Kaltschmidt
- Molecular Neurobiology, University of Bielefeld, Universitätsstr. 25, 33501 Bielefeld, Germany
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Vêncio EF, Nelson AM, Cavanaugh C, Ware CB, Milller DG, Garcia JCO, Vêncio RZN, Loprieno MA, Liu AY. Reprogramming of prostate cancer-associated stromal cells to embryonic stem-like. Prostate 2012; 72:1453-63. [PMID: 22314551 DOI: 10.1002/pros.22497] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 01/11/2012] [Indexed: 02/06/2023]
Abstract
BACKGROUND CD90(+) prostate cancer-associated (CP) stromal cells represent a diseased cell type found only in tumor tissue. They differ from their normal counterpart in gene expression and inductive signaling. Genetic reprogramming by induced pluripotent stem (iPS) cell technology can effectively change adult cells into stem-like cells through wholesale alteration of the gene expression program. This technology might be used to 'erase' the abnormal gene expression of diseased cells. The resultant iPS cells would no longer express the disease phenotype, and behave like stem cells. METHODS CP stromal cells, isolated from tumor tissue of a surgically resected prostate by anti-CD90-mediated sorting and cultured in vitro, were transfected with in vitro packaged lentiviral expression vectors containing stem cell transcription factor genes POU5F1, LIN28, NANOG, and SOX2. RESULTS Alkaline phosphatase-positive iPS cells were obtained in about 3 weeks post-transfection at a frequency of 10(-4) . Their colony morphology was indistinguishable from that of human embryonic stem (ES) cells. Transcriptome analysis showed a virtually complete match in gene expression between the iPS and ES cells. CONCLUSIONS Genes of CP stromal cells could be fully inactivated by genetic reprogramming. As a consequence, the disease phenotype was 'cured'.
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Affiliation(s)
- Eneida F Vêncio
- Department of Urology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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Ratajczak MZ, Shin DM, Liu R, Mierzejewska K, Ratajczak J, Kucia M, Zuba-Surma EK. Very small embryonic/epiblast-like stem cells (VSELs) and their potential role in aging and organ rejuvenation--an update and comparison to other primitive small stem cells isolated from adult tissues. Aging (Albany NY) 2012; 4:235-46. [PMID: 22498452 PMCID: PMC3371759 DOI: 10.18632/aging.100449] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Very small embryonic-like stem cells (VSELs) are a population of developmentally early stem cells residing in adult tissues. These rare cells, which are slightly smaller than red blood cells, i) become mobilized during stress situations into peripheral blood, ii) are enriched in the Sca1+Lin−CD45− cell fraction in mice and the CD133+ Lin−CD45− cell fraction in humans, iii) express markers of pluripotent stem cells (e.g., Oct4, Nanog, and SSEA), and iv) display a distinct morphology characterized by a high nuclear/cytoplasmic ratio and undifferentiated chromatin. Recent evidence indicates that murine VSELs are kept quiescent in adult tissues and protected from teratoma formation by epigenetic modification of imprinted genes that regulate insulin/insulin like growth factor signaling (IIS). The successful reversal of these epigenetic changes in VSELs that render them quiescent will be crucial for efficient expansion of these cells. The most recent data in vivo from our and other laboratories demonstrated that both murine and human VSELs exhibit some characteristics of long-term repopulating hematopoietic stem cells (LT-HSCs), are at the top of the hierarchy in the mesenchymal lineage, and may differentiate into organ-specific cells (e.g., cardiomyocytes). Moreover, as recently demonstrated the number of these cells positively correlates in several murine models with longevity. Finally, while murine BM-derived VSELs have been extensively characterized more work is needed to better characterize these small cells at the molecular level in humans.
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Affiliation(s)
- Mariusz Z Ratajczak
- Stem Cell Biology Program at the James Graham Brown Cancer Center, University of Louisville, Louisville, KT, USA.
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