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Vales JP, Barbaric I. Culture-acquired genetic variation in human pluripotent stem cells: Twenty years on. Bioessays 2024:e2400062. [PMID: 38873900 DOI: 10.1002/bies.202400062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
Genetic changes arising in human pluripotent stem cells (hPSC) upon culture may bestow unwanted or detrimental phenotypes to cells, thus potentially impacting on the applications of hPSCs for clinical use and basic research. In the 20 years since the first report of culture-acquired genetic aberrations in hPSCs, a characteristic spectrum of recurrent aberrations has emerged. The preponderance of such aberrations implies that they provide a selective growth advantage to hPSCs upon expansion. However, understanding the consequences of culture-acquired variants for specific applications in cell therapy or research has been more elusive. The rapid progress of hPSC-based therapies to clinics is galvanizing the field to address this uncertainty and provide definitive ways both for risk assessment of variants and reducing their prevalence in culture. Here, we aim to provide a timely update on almost 20 years of research on this fascinating, but a still unresolved and concerning, phenomenon.
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Affiliation(s)
- John P Vales
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Neuroscience Institute, University of Sheffield, Sheffield, UK
- INSIGNEO Institute, University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Neuroscience Institute, University of Sheffield, Sheffield, UK
- INSIGNEO Institute, University of Sheffield, Sheffield, UK
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2
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Son B, Park S, Cho S, Kim JA, Baek SH, Yoo KH, Han D, Joo J, Park HH, Park TH. Improved Neural Inductivity of Size-Controlled 3D Human Embryonic Stem Cells Using Magnetic Nanoparticles. Biomater Res 2024; 28:0011. [PMID: 38500782 PMCID: PMC10944702 DOI: 10.34133/bmr.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/12/2024] [Indexed: 03/20/2024] Open
Abstract
Background: To improve the efficiency of neural development from human embryonic stem cells, human embryoid body (hEB) generation is vital through 3-dimensional formation. However, conventional approaches still have limitations: long-term cultivation and laborious steps for lineage determination. Methods: In this study, we controlled the size of hEBs for ectodermal lineage specification using cell-penetrating magnetic nanoparticles (MNPs), which resulted in reduced time required for initial neural induction. The magnetized cells were applied to concentrated magnetic force for magnet-derived multicellular organization. The uniformly sized hEBs were differentiated in neural induction medium (NIM) and suspended condition. This neurally induced MNP-hEBs were compared with other groups. Results: As a result, the uniformly sized MNP-hEBs in NIM showed significantly improved neural inductivity through morphological analysis and expression of neural markers. Signaling pathways of the accelerated neural induction were detected via expression of representative proteins; Wnt signaling, dopaminergic neuronal pathway, intercellular communications, and mechanotransduction. Consequently, we could shorten the time necessary for early neurogenesis, thereby enhancing the neural induction efficiency. Conclusion: Overall, this study suggests not only the importance of size regulation of hEBs at initial differentiation stage but also the efficacy of MNP-based neural induction method and stimulations for enhanced neural tissue regeneration.
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Affiliation(s)
- Boram Son
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Sora Park
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sungwoo Cho
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jeong Ah Kim
- Center for Scientific Instrumentation, Korea Basic Science Institute, Cheongju, Chungbuk 28119, Republic of Korea
| | - Seung-Ho Baek
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Korea
| | - Ki Hyun Yoo
- SIMPLE Planet Inc., 48 Achasan-ro 17-gil, Seongdong-gu, Seoul 04799, Korea
| | - Dongoh Han
- SIMPLE Planet Inc., 48 Achasan-ro 17-gil, Seongdong-gu, Seoul 04799, Korea
| | - Jinmyoung Joo
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hee Ho Park
- Department of Bioengineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Tai Hyun Park
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seodaemun-gu, Seoul 03760, Republic of Korea
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3
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Martinez JL, Piciw JG, Crockett M, Sorci IA, Makwana N, Sirois CL, Giffin-Rao Y, Bhattacharyya A. Transcriptional consequences of trisomy 21 on neural induction. Front Cell Neurosci 2024; 18:1341141. [PMID: 38357436 PMCID: PMC10865501 DOI: 10.3389/fncel.2024.1341141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Down syndrome, caused by trisomy 21, is a complex developmental disorder associated with intellectual disability and reduced growth of multiple organs. Structural pathologies are present at birth, reflecting embryonic origins. A fundamental unanswered question is how an extra copy of human chromosome 21 contributes to organ-specific pathologies that characterize individuals with Down syndrome, and, relevant to the hallmark intellectual disability in Down syndrome, how trisomy 21 affects neural development. We tested the hypothesis that trisomy 21 exerts effects on human neural development as early as neural induction. Methods Bulk RNA sequencing was performed on isogenic trisomy 21 and euploid human induced pluripotent stem cells (iPSCs) at successive stages of neural induction: embryoid bodies at Day 6, early neuroectoderm at Day 10, and differentiated neuroectoderm at Day 17. Results Gene expression analysis revealed over 1,300 differentially expressed genes in trisomy 21 cells along the differentiation pathway compared to euploid controls. Less than 5% of the gene expression changes included upregulated chromosome 21 encoded genes at every timepoint. Genes involved in specific growth factor signaling pathways (WNT and Notch), metabolism (including oxidative stress), and extracellular matrix were altered in trisomy 21 cells. Further analysis uncovered heterochronic expression of genes. Conclusion Trisomy 21 impacts discrete developmental pathways at the earliest stages of neural development. The results suggest that metabolic dysfunction arises early in embryogenesis in trisomy 21 and may affect development and function more broadly.
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Affiliation(s)
- José L. Martinez
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Jennifer G. Piciw
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, United States
- Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Madeline Crockett
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Isabella A. Sorci
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Nikunj Makwana
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Carissa L. Sirois
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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4
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Alibutud R, Hansali S, Cao X, Zhou A, Mahaganapathy V, Azaro M, Gwin C, Wilson S, Buyske S, Bartlett CW, Flax JF, Brzustowicz LM, Xing J. Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments. Int J Mol Sci 2023; 24:13248. [PMID: 37686052 PMCID: PMC10487745 DOI: 10.3390/ijms241713248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by restrictive interests and/or repetitive behaviors and deficits in social interaction and communication. ASD is a multifactorial disease with a complex polygenic genetic architecture. Its genetic contributing factors are not yet fully understood, especially large structural variations (SVs). In this study, we aimed to assess the contribution of SVs, including copy number variants (CNVs), insertions, deletions, duplications, and mobile element insertions, to ASD and related language impairments in the New Jersey Language and Autism Genetics Study (NJLAGS) cohort. Within the cohort, ~77% of the families contain SVs that followed expected segregation or de novo patterns and passed our filtering criteria. These SVs affected 344 brain-expressed genes and can potentially contribute to the genetic etiology of the disorders. Gene Ontology and protein-protein interaction network analysis suggested several clusters of genes in different functional categories, such as neuronal development and histone modification machinery. Genes and biological processes identified in this study contribute to the understanding of ASD and related neurodevelopment disorders.
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Affiliation(s)
- Rohan Alibutud
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sammy Hansali
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Xiaolong Cao
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Anbo Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Vaidhyanathan Mahaganapathy
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Marco Azaro
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Christine Gwin
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sherri Wilson
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Steven Buyske
- Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Christopher W. Bartlett
- The Steve Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Judy F. Flax
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Linda M. Brzustowicz
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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5
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Vitillo L, Anjum F, Hewitt Z, Stavish D, Laing O, Baker D, Barbaric I, Coffey P. The isochromosome 20q abnormality of pluripotent cells interrupts germ layer differentiation. Stem Cell Reports 2023; 18:782-797. [PMID: 36801002 PMCID: PMC10031278 DOI: 10.1016/j.stemcr.2023.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/18/2023] Open
Abstract
Chromosome 20 abnormalities are some of the most frequent genomic changes acquired by human pluripotent stem cell (hPSC) cultures worldwide. Yet their effects on differentiation remain largely unexplored. We investigated a recurrent abnormality also found on amniocentesis, the isochromosome 20q (iso20q), during a clinical retinal pigment epithelium differentiation. Here we show that the iso20q abnormality interrupts spontaneous embryonic lineage specification. Isogenic lines revealed that under conditions that promote the spontaneous differentiation of wild-type hPSCs, the iso20q variants fail to differentiate into primitive germ layers and to downregulate pluripotency networks, resulting in apoptosis. Instead, iso20q cells are highly biased for extra-embryonic/amnion differentiation following inhibition of DNMT3B methylation or BMP2 treatment. Finally, directed differentiation protocols can overcome the iso20q block. Our findings reveal in iso20q a chromosomal abnormality that impairs the developmental competency of hPSCs toward germ layers but not amnion, which models embryonic developmental bottlenecks in the presence of aberrations.
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Affiliation(s)
- Loriana Vitillo
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK.
| | - Fabiha Anjum
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - Zoe Hewitt
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Owen Laing
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Pete Coffey
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK; Centre for Stem Cell Biology and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA; NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, UK
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6
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Abstract
The possibility of reprogramming human somatic cells to pluripotency has opened unprecedented opportunities for creating genuinely human experimental models of disease. Inborn errors of metabolism (IEMs) constitute a greatly heterogeneous class of diseases that appear, in principle, especially suited to be modeled by iPSC-based technology. Indeed, dozens of IEMs have already been modeled to some extent using patient-specific iPSCs. Here, we review the advantages and disadvantages of iPSC-based disease modeling in the context of IEMs, as well as particular challenges associated to this approach, together with solutions researchers have proposed to tackle them. We have structured this review around six lessons that we have learnt from those previous modeling efforts, and that we believe should be carefully considered by researchers wishing to embark in future iPSC-based models of IEMs.
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Affiliation(s)
- Rubén Escribá
- Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Program for Clinical Translation of Regenerative Medicine in Catalonia - P-[CMRC], L'Hospitalet de Llobregat, Spain
- Center for Networked Biomedical Research On Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Raquel Ferrer-Lorente
- Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Program for Clinical Translation of Regenerative Medicine in Catalonia - P-[CMRC], L'Hospitalet de Llobregat, Spain
- Center for Networked Biomedical Research On Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Ángel Raya
- Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain.
- Program for Clinical Translation of Regenerative Medicine in Catalonia - P-[CMRC], L'Hospitalet de Llobregat, Spain.
- Center for Networked Biomedical Research On Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain.
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain.
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7
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Affiliation(s)
- Seungbok Yang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Yoonjae Cho
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Jiwon Jang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Institute of Convergence Science, Yonsei University, Seoul 03722, Korea
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8
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Halliwell J, Barbaric I, Andrews PW. Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat Rev Mol Cell Biol 2020; 21:715-728. [DOI: 10.1038/s41580-020-00292-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2020] [Indexed: 12/14/2022]
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9
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Gao J, Liao Y, Qiu M, Shen W. Wnt/β-Catenin Signaling in Neural Stem Cell Homeostasis and Neurological Diseases. Neuroscientist 2020; 27:58-72. [PMID: 32242761 DOI: 10.1177/1073858420914509] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neural stem/progenitor cells (NSCs) maintain the ability of self-renewal and differentiation and compose the complex nervous system. Wnt signaling is thought to control the balance of NSC proliferation and differentiation via the transcriptional coactivator β-catenin during brain development and adult tissue homeostasis. Disruption of Wnt signaling may result in developmental defects and neurological diseases. Here, we summarize recent findings of the roles of Wnt/β-catenin signaling components in NSC homeostasis for the regulation of functional brain circuits. We also suggest that the potential role of Wnt/β-catenin signaling might lead to new therapeutic strategies for neurological diseases, including, but not limited to, spinal cord injury, Alzheimer's disease, Parkinson's disease, and depression.
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Affiliation(s)
- Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China.,College of Life and Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuan Liao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Mengsheng Qiu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China.,College of Life and Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
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10
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Spirito G, Mangoni D, Sanges R, Gustincich S. Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data. BMC Bioinformatics 2019; 20:495. [PMID: 31757210 PMCID: PMC6873650 DOI: 10.1186/s12859-019-3113-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. RESULTS In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. CONCLUSION We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.
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Affiliation(s)
- Giovanni Spirito
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy.
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
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11
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Calatayud C, Carola G, Fernández-Carasa I, Valtorta M, Jiménez-Delgado S, Díaz M, Soriano-Fradera J, Cappelletti G, García-Sancho J, Raya Á, Consiglio A. CRISPR/Cas9-mediated generation of a tyrosine hydroxylase reporter iPSC line for live imaging and isolation of dopaminergic neurons. Sci Rep 2019; 9:6811. [PMID: 31048719 PMCID: PMC6497635 DOI: 10.1038/s41598-019-43080-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/10/2019] [Indexed: 01/03/2023] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) are a powerful tool to investigate the molecular mechanisms underlying Parkinson’s disease (PD), and might provide novel platforms for systematic drug screening. Several strategies have been developed to generate iPSC-derived tyrosine hydroxylase (TH)-positive dopaminergic neurons (DAn), the clinically relevant cell type in PD; however, they often result in mixed neuronal cultures containing only a small proportion of TH-positive DAn. To overcome this limitation, we used CRISPR/Cas9-based editing to generate a human iPSC line expressing a fluorescent protein (mOrange) knocked-in at the last exon of the TH locus. After differentiation of the TH-mOrange reporter iPSC line, we confirmed that mOrange expression faithfully mimicked endogenous TH expression in iPSC-derived DAn. We also employed calcium imaging techniques to determine the intrinsic functional differences between dopaminergic and non-dopaminergic ventral midbrain neurons. Crucially, the brightness of mOrange allowed direct visualization of TH-expressing cells in heterogeneous cultures, and enabled us to isolate live mOrange-positive cells through fluorescence-activated cell sorting, for further differentiation. This technique, coupled to refined imaging and data processing tools, could advance the investigation of PD pathogenesis and might offer a platform to test potential new therapeutics for PD and other neurodegenerative diseases.
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Affiliation(s)
- Carles Calatayud
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, 08908, Hospitalet de Llobregat, Spain.,Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028, Barcelona, Spain.,Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Giulia Carola
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, 08908, Hospitalet de Llobregat, Spain.,Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028, Barcelona, Spain
| | - Irene Fernández-Carasa
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, 08908, Hospitalet de Llobregat, Spain.,Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028, Barcelona, Spain
| | - Marco Valtorta
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, 08908, Hospitalet de Llobregat, Spain.,Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028, Barcelona, Spain.,Department of Bioscience, University of Milan, Via Festa del Perdono 7, Milan, 20122, Italy
| | - Senda Jiménez-Delgado
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, 08908, Barcelona, Spain.,Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Hospitalet de Llobregat, 08098, Barcelona, Spain
| | - Mònica Díaz
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, 08908, Barcelona, Spain.,Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Hospitalet de Llobregat, 08098, Barcelona, Spain
| | - Jordi Soriano-Fradera
- Department of Condensed Matter Physics, University of Barcelona, Avinguda de la Diagonal 645, 08028, Barcelona, Spain
| | - Graziella Cappelletti
- Department of Bioscience, University of Milan, Via Festa del Perdono 7, Milan, 20122, Italy
| | - Javier García-Sancho
- Instituto de Biología y Genética Molecular (IBGM), Universidad de Valladolid, Calle Sanz y Forés 3, 47003, Valladolid, Spain
| | - Ángel Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, 08908, Barcelona, Spain. .,Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Hospitalet de Llobregat, 08098, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
| | - Antonella Consiglio
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, 08908, Hospitalet de Llobregat, Spain. .,Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028, Barcelona, Spain. .,Department of Molecular and Translational Medicine, University of Brescia, Piazza del Mercato 15, 25121, Brescia, Italy.
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12
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Tsai SY, Bendriem RM, Lee CTD. The cellular basis of fetal endoplasmic reticulum stress and oxidative stress in drug-induced neurodevelopmental deficits. Neurobiol Stress 2019; 10:100145. [PMID: 30937351 PMCID: PMC6430408 DOI: 10.1016/j.ynstr.2018.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 12/02/2018] [Accepted: 12/26/2018] [Indexed: 11/30/2022] Open
Abstract
Prenatal substance exposure is a growing public health concern worldwide. Although the opioid crisis remains one of the most prevalent addiction problems in our society, abuse of cocaine, methamphetamines, and other illicit drugs, particularly amongst pregnant women, are nonetheless significant and widespread. Evidence demonstrates prenatal drug exposure can affect fetal brain development and thus can have long-lasting impact on neurobehavioral and cognitive performance later in life. In this review, we highlight research examining the most prevalent drugs of abuse and their effects on brain development with a focus on endoplasmic reticulum stress and oxidative stress signaling pathways. A thorough exploration of drug-induced cellular stress mechanisms during prenatal brain development may provide insight into therapeutic interventions to combat effects of prenatal drug exposure.
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Affiliation(s)
- S-Y.A. Tsai
- Integrative Neuroscience Branch, Division of Neuroscience and Behavior, National Institute on Drug Abuse, The National Institute of Health, Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Raphael M. Bendriem
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Chun-Ting D. Lee
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, USA
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13
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Keller A, Dziedzicka D, Zambelli F, Markouli C, Sermon K, Spits C, Geens M. Genetic and epigenetic factors which modulate differentiation propensity in human pluripotent stem cells. Hum Reprod Update 2018; 24:162-175. [PMID: 29377992 DOI: 10.1093/humupd/dmx042] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Accepted: 12/22/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Human pluripotent stem cell (hPSC) lines are known to have a bias in their differentiation. This gives individual cell lines a propensity to preferentially differentiate towards one germ layer or cell type over others. Chromosomal aberrations, mitochondrial mutations, genetic diversity and epigenetic variance are the main drivers of this phenomenon, and can lead to a wide range of phenotypes. OBJECTIVE AND RATIONALE Our aim is to provide a comprehensive overview of the different factors which influence differentiation propensity. Specifically, we sought to highlight known genetic variances and their mechanisms, in addition to more general observations from larger abnormalities. Furthermore, we wanted to provide an up-to-date list of a growing number of predictive indicators which are able to identify differentiation propensity before the initiation of differentiation. As differentiation propensity can lead to difficulties in both research as well as clinical translation, our thorough overview could be a useful tool. SEARCH METHODS Combinations of the following key words were applied as search criteria in the PubMed database: embryonic stem cells, induced pluripotent stem cells, differentiation propensity (also: potential, efficiency, capacity, bias, variability), epigenetics, chromosomal abnormalities, genetic aberrations, X chromosome inactivation, mitochondrial function, mitochondrial metabolism, genetic diversity, reprogramming, predictive marker, residual stem cell, clinic. Only studies in English were included, ranging from 2000 to 2017, with a majority ranging from 2010 to 1017. Further manuscripts were added from cross-references. OUTCOMES Differentiation propensity is affected by a wide variety of (epi)genetic factors. These factors clearly lead to a loss of differentiation capacity, preference towards certain cell types and oftentimes, phenotypes which begin to resemble cancer. Broad changes in (epi)genetics, such as aneuploidies or wide-ranging modifications to the epigenetic landscape tend to lead to extensive, less definite changes in differentiation capacity, whereas more specific abnormalities often have precise ramifications in which certain cell types become more preferential. Furthermore, there appears to be a greater, though often less considered, contribution to differentiation propensity by factors such as mitochondria and inherent genetic diversity. Varied differentiation capacity can also lead to potential consequences in the clinical translation of hPSC, including the occurrence of residual undifferentiated stem cells, and the transplantation of potentially transformed cells. WIDER IMPLICATIONS As hPSC continue to advance towards the clinic, our understanding of them progresses as well. As a result, the challenges faced become more numerous, but also more clear. If the transition to the clinic is to be achieved with a minimum number of potential setbacks, thorough evaluation of the cells will be an absolute necessity. Altered differentiation propensity represents at least one such hurdle, for which researchers and eventually clinicians will need to find solutions. Already, steps are being taken to tackle the issue, though further research will be required to evaluate any long-term risks it poses.
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Affiliation(s)
- Alexander Keller
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Dominika Dziedzicka
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Filippo Zambelli
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Christina Markouli
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Karen Sermon
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Claudia Spits
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Mieke Geens
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
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14
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Lee CT, Boeshore KL, Wu C, Becker KG, Errico SL, Mash DC, Freed WJ. Cocaine promotes primary human astrocyte proliferation via JNK-dependent up-regulation of cyclin A2. Restor Neurol Neurosci 2018; 34:965-976. [PMID: 27834787 DOI: 10.3233/rnn-160676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE Astrocytes perform a plethora of important functions in the central nervous system (CNS) and are involved in cocaine-evoked synaptic plasticity. Previously, we showed that while cocaine decreased cyclin A2 expression in primary human neural progenitor cells, it increased cyclin A2 expression in human astrocytes. Since cyclin A2 is an essential regulator of the cell cycle, the aim of the present study is to clarify the effect of cocaine on proliferation of human astrocytes and elucidate the underlying molecular mechanisms. METHODS Primary human astrocytes were treated with either 1, 10, or 100 μM cocaine for 48 hr, and cell proliferation was measured using the CyQUANT cell proliferation assay. To elucidate the molecular mechanisms through which cocaine affects the proliferation of astrocytes, we analyzed gene expression profiles in cocaine-treated primary human astrocytes using a human focused cDNA array. Gene ontology/pathway enrichment analysis, STRING protein-protein interaction analysis, RT-qPCR, and western blotting were used to identify signal transduction pathways that are involved in cocaine-induced astrocyte dysfunction. RESULTS Cocaine at 10 and 100 μM significantly increased human astrocyte proliferation. Gene expression profiling revealed the JNK MAP kinase pathway as a driver of cell proliferation affected by cocaine in human astrocytes. Further experiments showed that cocaine-induced JNK activation induced up-regulation of cyclin A2, leading to enhanced proliferation of human astrocytes. CONCLUSION Cocaine-induced abnormal increases in the number of astrocytes may cause disruption in neuron-glia signaling and contribute to synaptic impairment in the CNS. Understanding the mechanisms of cocaine's effects on human astrocytes may help to reveal the involvement of glial cells in addictive behaviors.
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Affiliation(s)
- Chun-Ting Lee
- Section on Development and Plasticity, Cellular Neurobiology Research Branch, Intramural Research Program (IRP), National Institute on Drug Abuse, National Institutes of Health (NIH), Baltimore, MD, USA.,Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Chun Wu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, Research Resources Branch, IRP, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Stacie L Errico
- Section on Development and Plasticity, Cellular Neurobiology Research Branch, Intramural Research Program (IRP), National Institute on Drug Abuse, National Institutes of Health (NIH), Baltimore, MD, USA
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William J Freed
- Section on Development and Plasticity, Cellular Neurobiology Research Branch, Intramural Research Program (IRP), National Institute on Drug Abuse, National Institutes of Health (NIH), Baltimore, MD, USA.,Department of Biology, Lebanon Valley College, Annville, PA, USA
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15
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Brafman D, Willert K. Wnt/β-catenin signaling during early vertebrate neural development. Dev Neurobiol 2017; 77:1239-1259. [PMID: 28799266 DOI: 10.1002/dneu.22517] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/24/2017] [Accepted: 08/09/2017] [Indexed: 12/29/2022]
Abstract
The vertebrate central nervous system (CNS) is comprised of vast number of distinct cell types arranged in a highly organized manner. This high degree of complexity is achieved by cellular communication, including direct cell-cell contact, cell-matrix interactions, and cell-growth factor signaling. Among the several developmental signals controlling the development of the CNS, Wnt proteins have emerged as particularly critical and, hence, have captivated the attention of many researchers. With Wnts' evolutionarily conserved function as primordial symmetry breaking signals, these proteins and their downstream effects are responsible for simultaneously establishing cellular diversity and tissue organization. With their expansive repertoire of secreted agonists and antagonists, cell surface receptors, signaling cascades and downstream biological effects, Wnts are ideally suited to control the complex processes underlying vertebrate neural development. In this review, we will describe the mechanisms by which Wnts exert their potent effects on cells and tissues and highlight the many roles of Wnt signaling during neural development, starting from the initial induction of the neural plate, the subsequent patterning along the embryonic axes, to the intricately organized structure of the CNS. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1239-1259, 2017.
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Affiliation(s)
- David Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, 85287
| | - Karl Willert
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, 92093-0695
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16
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Lee CT, Bendriem RM, Wu WW, Shen RF. 3D brain Organoids derived from pluripotent stem cells: promising experimental models for brain development and neurodegenerative disorders. J Biomed Sci 2017; 24:59. [PMID: 28822354 PMCID: PMC5563385 DOI: 10.1186/s12929-017-0362-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/09/2017] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional (3D) brain organoids derived from human pluripotent stem cells (hPSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), appear to recapitulate the brain's 3D cytoarchitectural arrangement and provide new opportunities to explore disease pathogenesis in the human brain. Human iPSC (hiPSC) reprogramming methods, combined with 3D brain organoid tools, may allow patient-derived organoids to serve as a preclinical platform to bridge the translational gap between animal models and human clinical trials. Studies using patient-derived brain organoids have already revealed novel insights into molecular and genetic mechanisms of certain complex human neurological disorders such as microcephaly, autism, and Alzheimer's disease. Furthermore, the combination of hiPSC technology and small-molecule high-throughput screening (HTS) facilitates the development of novel pharmacotherapeutic strategies, while transcriptome sequencing enables the transcriptional profiling of patient-derived brain organoids. Finally, the addition of CRISPR/Cas9 genome editing provides incredible potential for personalized cell replacement therapy with genetically corrected hiPSCs. This review describes the history and current state of 3D brain organoid differentiation strategies, a survey of applications of organoids towards studies of neurodevelopmental and neurodegenerative disorders, and the challenges associated with their use as in vitro models of neurological disorders.
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Affiliation(s)
- Chun-Ting Lee
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD 20993 USA
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Building 52, Rm 1121, 10903 New Hampshire Avenue, Silver Spring, MD 20993 USA
| | - Raphael M. Bendriem
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021 USA
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD 20993 USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD 20993 USA
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17
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Calatayud C, Carola G, Consiglio A, Raya A. Modeling the genetic complexity of Parkinson's disease by targeted genome edition in iPS cells. Curr Opin Genet Dev 2017; 46:123-131. [PMID: 28759872 DOI: 10.1016/j.gde.2017.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/27/2017] [Accepted: 06/08/2017] [Indexed: 02/08/2023]
Abstract
Patient-specific iPSC are being intensively exploited as experimental disease models. Even for late-onset diseases of complex genetic influence, such as Parkinson's disease (PD), the use of iPSC-based models is beginning to provide important insights into the genetic bases of PD heritability. Here, we present an update on recently reported genetic risk factors associated with PD. We discuss how iPSC technology, combined with targeted edition of the coding or noncoding genome, can be used to address clinical observations such as incomplete penetrance, and variability in phenoconversion or age-at-onset in familial PD. Finally, we also discuss the relevance of advanced iPSC/CRISPR/Cas9 disease models to ascertain causality in genotype-to-phenotype correlation studies of sporadic PD.
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Affiliation(s)
- Carles Calatayud
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, 3rd Floor, Av. Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain; Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028 Barcelona, Spain; Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, 08908 Barcelona, Spain
| | - Giulia Carola
- Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028 Barcelona, Spain; Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, 08908 Barcelona, Spain
| | - Antonella Consiglio
- Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08028 Barcelona, Spain; Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, 08908 Barcelona, Spain; Department of Molecular and Translational Medicine, University of Brescia and National Institute of Neuroscience, 25123 Brescia, Italy.
| | - Angel Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, 3rd Floor, Av. Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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18
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CYP3A5 Mediates Effects of Cocaine on Human Neocorticogenesis: Studies using an In Vitro 3D Self-Organized hPSC Model with a Single Cortex-Like Unit. Neuropsychopharmacology 2017; 42:774-784. [PMID: 27534267 PMCID: PMC5240177 DOI: 10.1038/npp.2016.156] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/26/2016] [Accepted: 08/10/2016] [Indexed: 12/31/2022]
Abstract
Because of unavoidable confounding variables in the direct study of human subjects, it has been difficult to unravel the effects of prenatal cocaine exposure on the human fetal brain, as well as the cellular and biochemical mechanisms involved. Here, we propose a novel approach using a human pluripotent stem cell (hPSC)-based 3D neocortical organoid model. This model retains essential features of human neocortical development by encompassing a single self-organized neocortical structure, without including an animal-derived gelatinous matrix. We reported previously that prenatal cocaine exposure to rats during the most active period of neural progenitor proliferation induces cytoarchitectural changes in the embryonic neocortex. We also identified a role of CYP450 and consequent oxidative ER stress signaling in these effects. However, because of differences between humans and rodents in neocorticogenesis and brain CYP metabolism, translation of the research findings from the rodent model to human brain development is uncertain. Using hPSC 3D neocortical organoids, we demonstrate that the effects of cocaine are mediated through CYP3A5-induced generation of reactive oxygen species, inhibition of neocortical progenitor cell proliferation, induction of premature neuronal differentiation, and interruption of neural tissue development. Furthermore, knockdown of CYP3A5 reversed these cocaine-induced pathological phenotypes, suggesting CYP3A5 as a therapeutic target to mitigate the deleterious neurodevelopmental effects of prenatal cocaine exposure in humans. Moreover, 3D organoid methodology provides an innovative platform for identifying adverse effects of abused psychostimulants and pharmaceutical agents, and can be adapted for use in neurodevelopmental disorders with genetic etiologies.
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19
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Adil MM, Rodrigues GMC, Kulkarni RU, Rao AT, Chernavsky NE, Miller EW, Schaffer DV. Efficient generation of hPSC-derived midbrain dopaminergic neurons in a fully defined, scalable, 3D biomaterial platform. Sci Rep 2017; 7:40573. [PMID: 28091566 PMCID: PMC5238378 DOI: 10.1038/srep40573] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023] Open
Abstract
Pluripotent stem cells (PSCs) have major potential as an unlimited source of functional cells for many biomedical applications; however, the development of cell manufacturing systems to enable this promise faces many challenges. For example, there have been major recent advances in the generation of midbrain dopaminergic (mDA) neurons from stem cells for Parkinson's Disease (PD) therapy; however, production of these cells typically involves undefined components and difficult to scale 2D culture formats. Here, we used a fully defined, 3D, thermoresponsive biomaterial platform to rapidly generate large numbers of action-potential firing mDA neurons after 25 days of differentiation (~40% tyrosine hydroxylase (TH) positive, maturing into 25% cells exhibiting mDA neuron-like spiking behavior). Importantly, mDA neurons generated in 3D exhibited a 30-fold increase in viability upon implantation into rat striatum compared to neurons generated on 2D, consistent with the elevated expression of survival markers FOXA2 and EN1 in 3D. A defined, scalable, and resource-efficient cell culture platform can thus rapidly generate high quality differentiated cells, both neurons and potentially other cell types, with strong potential to accelerate both basic and translational research.
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Affiliation(s)
- Maroof M. Adil
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Gonçalo M. C. Rodrigues
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | | | - Antara T. Rao
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Nicole E. Chernavsky
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Evan W. Miller
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - David V. Schaffer
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
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20
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Noelanders R, Vleminckx K. How Wnt Signaling Builds the Brain: Bridging Development and Disease. Neuroscientist 2016; 23:314-329. [DOI: 10.1177/1073858416667270] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Wnt/β-catenin signaling plays a crucial role throughout all stages of brain development and remains important in the adult brain. Accordingly, many neurological disorders have been linked to Wnt signaling. Defects in Wnt signaling during neural development can give rise to birth defects or lead to neurological dysfunction later in life. Developmental signaling events can also be hijacked in the adult and result in disease. Moreover, knowledge about the physiological role of Wnt signaling in the brain might lead to new therapeutic strategies for neurological diseases. Especially, the important role for Wnt signaling in neural differentiation of pluripotent stem cells has received much attention as this might provide a cure for neurodegenerative disorders. In this review, we summarize the versatile role of Wnt/β-catenin signaling during neural development and discuss some recent studies linking Wnt signaling to neurological disorders.
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Affiliation(s)
- Rivka Noelanders
- Unit of Developmental Biology, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kris Vleminckx
- Unit of Developmental Biology, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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21
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Neural Conversion and Patterning of Human Pluripotent Stem Cells: A Developmental Perspective. Stem Cells Int 2016; 2016:8291260. [PMID: 27069483 PMCID: PMC4812494 DOI: 10.1155/2016/8291260] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/24/2016] [Indexed: 01/19/2023] Open
Abstract
Since the reprogramming of adult human terminally differentiated somatic cells into induced pluripotent stem cells (hiPSCs) became a reality in 2007, only eight years have passed. Yet over this relatively short period, myriad experiments have revolutionized previous stem cell dogmata. The tremendous promise of hiPSC technology for regenerative medicine has fuelled rising expectations from both the public and scientific communities alike. In order to effectively harness hiPSCs to uncover fundamental mechanisms of disease, it is imperative to first understand the developmental neurobiology underpinning their lineage restriction choices in order to predictably manipulate cell fate to desired derivatives. Significant progress in developmental biology provides an invaluable resource for rationalising directed differentiation of hiPSCs to cellular derivatives of the nervous system. In this paper we begin by reviewing core developmental concepts underlying neural induction in order to provide context for how such insights have guided reductionist in vitro models of neural conversion from hiPSCs. We then discuss early factors relevant in neural patterning, again drawing upon crucial knowledge gained from developmental neurobiological studies. We conclude by discussing open questions relating to these concepts and how their resolution might serve to strengthen the promise of pluripotent stem cells in regenerative medicine.
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22
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Bengoa-Vergniory N, Kypta RM. Canonical and noncanonical Wnt signaling in neural stem/progenitor cells. Cell Mol Life Sci 2015; 72:4157-72. [PMID: 26306936 PMCID: PMC11113751 DOI: 10.1007/s00018-015-2028-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/17/2015] [Accepted: 08/18/2015] [Indexed: 02/07/2023]
Abstract
The first mammalian Wnt to be discovered, Wnt-1, was found to be essential for the development of a large part of the mouse brain over 25 years ago. We have since learned that Wnt family secreted glycolipoproteins, of which there are nineteen, which activate a diverse network of signals that are particularly important during embryonic development and tissue regeneration. Wnt signals in the developing and adult brain can drive neural stem cell self-renewal, expansion, asymmetric cell division, maturation and differentiation. The molecular events taking place after a Wnt binds to its cell-surface receptors are complex and, at times, controversial. A deeper understanding of these events is anticipated to lead to improvements in the treatment of neurodegenerative diseases and stem cell-based replacement therapies. Here, we review the roles played by Wnts in neural stem cells in the developing mouse brain, at neurogenic sites of the adult mouse and in neural stem cell culture models.
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Affiliation(s)
- Nora Bengoa-Vergniory
- Cell Biology and Stem Cells Unit, CIC bioGUNE, Bilbao, Spain.
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, UK.
| | - Robert M Kypta
- Cell Biology and Stem Cells Unit, CIC bioGUNE, Bilbao, Spain.
- Department of Surgery and Cancer, Imperial College London, London, UK.
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23
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Tanabe S. Signaling involved in stem cell reprogramming and differentiation. World J Stem Cells 2015; 7:992-8. [PMID: 26328015 PMCID: PMC4550631 DOI: 10.4252/wjsc.v7.i7.992] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/29/2015] [Accepted: 06/18/2015] [Indexed: 02/06/2023] Open
Abstract
Stem cell differentiation is regulated by multiple signaling events. Recent technical advances have revealed that differentiated cells can be reprogrammed into stem cells. The signals involved in stem cell programming are of major interest in stem cell research. The signaling mechanisms involved in regulating stem cell reprogramming and differentiation are the subject of intense study in the field of life sciences. In this review, the molecular interactions and signaling pathways related to stem cell differentiation are discussed.
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Affiliation(s)
- Shihori Tanabe
- Shihori Tanabe, National Institute of Health Sciences, Tokyo 158-8501, Japan
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24
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Lee CT, Freed WJ, Mash DC. CNVs in neurodevelopmental disorders. Oncotarget 2015; 6:18238-9. [PMID: 26285833 PMCID: PMC4621882 DOI: 10.18632/oncotarget.4853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/10/2015] [Indexed: 11/25/2022] Open
Affiliation(s)
- Chun-Ting Lee
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - William J Freed
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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