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Liang KX. The application of brain organoid for drug discovery in mitochondrial diseases. Int J Biochem Cell Biol 2024; 170:106556. [PMID: 38423381 DOI: 10.1016/j.biocel.2024.106556] [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: 08/11/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Mitochondrial diseases are difficult to treat due to the complexity and multifaceted nature of mitochondrial dysfunction. Brain organoids are three-dimensional (3D) structures derived from human pluripotent stem cells designed to mimic brain-like development and function. Brain organoids have received a lot of attention in recent years as powerful tools for modeling human diseases, brain development, and drug screening. Screening compounds for mitochondrial diseases using brain organoids could provide a more physiologically relevant platform for drug discovery. Brain organoids offer the possibility of personalized medicine because they can be derived from patient-specific cells, allowing testing of drugs tailored to specific genetic mutations. In this article, we highlight how brain organoids offer a promising avenue for screening compounds for mitochondrial diseases and address the challenges and limitations associated with their use. We hope this review will provide new insights into the further progress of brain organoids for mitochondrial screening studies.
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Sheikhlary S, Lopez DH, Moghimi S, Sun B. Recent Findings on Therapeutic Cancer Vaccines: An Updated Review. Biomolecules 2024; 14:503. [PMID: 38672519 PMCID: PMC11048403 DOI: 10.3390/biom14040503] [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: 02/23/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer remains one of the global leading causes of death and various vaccines have been developed over the years against it, including cell-based, nucleic acid-based, and viral-based cancer vaccines. Although many vaccines have been effective in in vivo and clinical studies and some have been FDA-approved, there are major limitations to overcome: (1) developing one universal vaccine for a specific cancer is difficult, as tumors with different antigens are different for different individuals, (2) the tumor antigens may be similar to the body's own antigens, and (3) there is the possibility of cancer recurrence. Therefore, developing personalized cancer vaccines with the ability to distinguish between the tumor and the body's antigens is indispensable. This paper provides a comprehensive review of different types of cancer vaccines and highlights important factors necessary for developing efficient cancer vaccines. Moreover, the application of other technologies in cancer therapy is discussed. Finally, several insights and conclusions are presented, such as the possibility of using cold plasma and cancer stem cells in developing future cancer vaccines, to tackle the major limitations in the cancer vaccine developmental process.
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Affiliation(s)
- Sara Sheikhlary
- Department of Biomedical Engineering, College of Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | - David Humberto Lopez
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
| | - Sophia Moghimi
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
| | - Bo Sun
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
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3
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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [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: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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4
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Niemsiri V, Rosenthal SB, Nievergelt CM, Maihofer AX, Marchetto MC, Santos R, Shekhtman T, Alliey-Rodriguez N, Anand A, Balaraman Y, Berrettini WH, Bertram H, Burdick KE, Calabrese JR, Calkin CV, Conroy C, Coryell WH, DeModena A, Eyler LT, Feeder S, Fisher C, Frazier N, Frye MA, Gao K, Garnham J, Gershon ES, Goes FS, Goto T, Harrington GJ, Jakobsen P, Kamali M, Kelly M, Leckband SG, Lohoff FW, McCarthy MJ, McInnis MG, Craig D, Millett CE, Mondimore F, Morken G, Nurnberger JI, Donovan CO, Øedegaard KJ, Ryan K, Schinagle M, Shilling PD, Slaney C, Stapp EK, Stautland A, Tarwater B, Zandi PP, Alda M, Fisch KM, Gage FH, Kelsoe JR. Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis. Mol Psychiatry 2024; 29:6-19. [PMID: 36991131 PMCID: PMC11078741 DOI: 10.1038/s41380-022-01909-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 11/14/2022] [Accepted: 12/02/2022] [Indexed: 03/31/2023]
Abstract
Lithium (Li) is one of the most effective drugs for treating bipolar disorder (BD), however, there is presently no way to predict response to guide treatment. The aim of this study is to identify functional genes and pathways that distinguish BD Li responders (LR) from BD Li non-responders (NR). An initial Pharmacogenomics of Bipolar Disorder study (PGBD) GWAS of lithium response did not provide any significant results. As a result, we then employed network-based integrative analysis of transcriptomic and genomic data. In transcriptomic study of iPSC-derived neurons, 41 significantly differentially expressed (DE) genes were identified in LR vs NR regardless of lithium exposure. In the PGBD, post-GWAS gene prioritization using the GWA-boosting (GWAB) approach identified 1119 candidate genes. Following DE-derived network propagation, there was a highly significant overlap of genes between the top 500- and top 2000-proximal gene networks and the GWAB gene list (Phypergeometric = 1.28E-09 and 4.10E-18, respectively). Functional enrichment analyses of the top 500 proximal network genes identified focal adhesion and the extracellular matrix (ECM) as the most significant functions. Our findings suggest that the difference between LR and NR was a much greater effect than that of lithium. The direct impact of dysregulation of focal adhesion on axon guidance and neuronal circuits could underpin mechanisms of response to lithium, as well as underlying BD. It also highlights the power of integrative multi-omics analysis of transcriptomic and genomic profiling to gain molecular insights into lithium response in BD.
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Grants
- R01 MH095741 NIMH NIH HHS
- UL1 TR001442 NCATS NIH HHS
- U19 MH106434 NIMH NIH HHS
- U01 MH092758 NIMH NIH HHS
- T32 MH018399 NIMH NIH HHS
- U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)
- Department of Veterans Affairs | Veterans Affairs San Diego Healthcare System (VA San Diego Healthcare System)
- The Halifax group (MA, CVC, JG, CO, and CS) is supported by grants from Canadian Institutes of Health Research (#166098), ERA PerMed project PLOT-BD, Research Nova Scotia, Genome Atlantic, Nova Scotia Health Authority and Dalhousie Medical Research Foundation (Lindsay Family Fund).
- U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- U19MH106434, part of the National Cooperative Reprogrammed Cell Research Groups (NCRCRG) to Study Mental Illness. AHA-Allen Initiative in Brain Health and Cognitive Impairment Award (19PABH134610000). The JPB Foundation, Bob and Mary Jane Engman, Annette C Merle-Smith, R01 MH095741, and Lynn and Edward Streim.
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Affiliation(s)
- Vipavee Niemsiri
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | | | - Adam X Maihofer
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Maria C Marchetto
- Department of Anthropology, University of California, San Diego, La Jolla, CA, USA
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Renata Santos
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA
- University of Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1261266, Laboratory of Dynamics of Neuronal Structure in Health and Disease, Paris, France
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Ney Alliey-Rodriguez
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
- Department of Psychiatry and Behavioral Neuroscience, Northwestern University, Chicago, IL, USA
| | - Amit Anand
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yokesh Balaraman
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wade H Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Holli Bertram
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Katherine E Burdick
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph R Calabrese
- Mood Disorders Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Mood Disorders Program, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Cynthia V Calkin
- Department of Psychiatry and Medical Neuroscience, Dalhousie University, Halifax, NS, Canada
| | - Carla Conroy
- Mood Disorders Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Mood Disorders Program, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | | | - Anna DeModena
- Psychiatry Service, VA San Diego Healthcare System, San Diego, CA, USA
| | - Lisa T Eyler
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Scott Feeder
- Department of Psychiatry, The Mayo Clinic, Rochester, MN, USA
| | - Carrie Fisher
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nicole Frazier
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Mark A Frye
- Department of Psychiatry, The Mayo Clinic, Rochester, MN, USA
| | - Keming Gao
- Mood Disorders Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Mood Disorders Program, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Julie Garnham
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Toyomi Goto
- Mood Disorders Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Petter Jakobsen
- Norment, Division of Psychiatry, Haukeland University Hospital and Department of Clinical medicine, University of Bergen, Bergen, Norway
| | - Masoud Kamali
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Marisa Kelly
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Susan G Leckband
- Psychiatry Service, VA San Diego Healthcare System, San Diego, CA, USA
| | - Falk W Lohoff
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J McCarthy
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - David Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Caitlin E Millett
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Francis Mondimore
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Gunnar Morken
- Division of Mental Health Care, St Olavs University Hospital, and Department of Mental Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
- Medical and Molecular Genetics, Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Ketil J Øedegaard
- Norment, Division of Psychiatry, Haukeland University Hospital and Department of Clinical medicine, University of Bergen, Bergen, Norway
| | - Kelly Ryan
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Martha Schinagle
- Mood Disorders Program, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Paul D Shilling
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Claire Slaney
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Emma K Stapp
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Andrea Stautland
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Bruce Tarwater
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Martin Alda
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
- National Institute of Mental Health, Klecany, Czech Republic
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - John R Kelsoe
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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5
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Marzoog BA. Transcription Factors in Brain Regeneration: A Potential Novel Therapeutic Target. Curr Drug Targets 2024; 25:46-61. [PMID: 38444255 DOI: 10.2174/0113894501279977231210170231] [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: 08/30/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 03/07/2024]
Abstract
Transcription factors play a crucial role in providing identity to each cell population. To maintain cell identity, it is essential to balance the expression of activator and inhibitor transcription factors. Cell plasticity and reprogramming offer great potential for future therapeutic applications, as they can regenerate damaged tissue. Specific niche factors can modify gene expression and differentiate or transdifferentiate the target cell to the required fate. Ongoing research is being carried out on the possibilities of transcription factors in regenerating neurons, with neural stem cells (NSCs) being considered the preferred cells for generating new neurons due to their epigenomic and transcriptome memory. NEUROD1/ASCL1, BRN2, MYTL1, and other transcription factors can induce direct reprogramming of somatic cells, such as fibroblasts, into neurons. However, the molecular biology of transcription factors in reprogramming and differentiation still needs to be fully understood.
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Affiliation(s)
- Basheer Abdullah Marzoog
- World-Class Research Center, Digital Biodesign and Personalized Healthcare», I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
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Nath SC, Menendez L, Friedrich Ben-Nun I. Overcoming the Variability of iPSCs in the Manufacturing of Cell-Based Therapies. Int J Mol Sci 2023; 24:16929. [PMID: 38069252 PMCID: PMC10706975 DOI: 10.3390/ijms242316929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Various factors are known to contribute to the diversity of human induced pluripotent stem cells (hiPSCs). Among these are the donor's genetic background and family history, the somatic cell source, the iPSC reprogramming method, and the culture system of choice. Moreover, variability is seen even in iPSC clones, generated in a single reprogramming event, where the donor, somatic cell type, and reprogramming platform are the same. The diversity seen in iPSC lines often translates to epigenetic differences, as well as to differences in the expansion rate, iPSC line culture robustness, and their ability to differentiate into specific cell types. As such, the diversity of iPSCs presents a hurdle to standardizing iPSC-based cell therapy manufacturing. In this review, we will expand on the various factors that impact iPSC diversity and the strategies and tools that could be taken by the industry to overcome the differences amongst various iPSC lines, therefore enabling robust and reproducible iPSC-based cell therapy manufacturing processes.
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Affiliation(s)
- Suman C. Nath
- Cell Therapy Process Department, Lonza Inc., Houston, TX 77047, USA; (S.C.N.); (L.M.)
| | - Laura Menendez
- Cell Therapy Process Department, Lonza Inc., Houston, TX 77047, USA; (S.C.N.); (L.M.)
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7
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Challenges with Cell-based Therapies for Type 1 Diabetes Mellitus. Stem Cell Rev Rep 2022; 19:601-624. [PMID: 36434300 DOI: 10.1007/s12015-022-10482-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2022] [Indexed: 11/27/2022]
Abstract
Type 1 diabetes (T1D) is a chronic, lifelong metabolic disease. It is characterised by the autoimmune-mediated loss of insulin-producing pancreatic β cells in the islets of Langerhans (β-islets), resulting in disrupted glucose homeostasis. Administration of exogenous insulin is the most common management method for T1D, but this requires lifelong reliance on insulin injections and invasive blood glucose monitoring. Replacement therapies with beta cells are being developed as an advanced curative treatment for T1D. Unfortunately, this approach is limited by the lack of donated pancreatic tissue, the difficulties in beta cell isolation and viability maintenance, the longevity of the transplanted cells in vivo, and consequently high costs. Emerging approaches to address these limitations are under intensive investigations, including the production of insulin-producing beta cells from various stem cells, and the development of bioengineered devices including nanotechnologies for improving islet transplantation efficacy without the need for recipients taking toxic anti-rejection drugs. These emerging approaches present promising prospects, while the challenges with the new techniques need to be tackled for ultimately clinical treatment of T1D. This review discussed the benefits and limitations of the cell-based therapies for beta cell replacement as potential curative treatment for T1D, and the applications of bioengineered devices including nanotechnology to overcome the challenges associated with beta cell transplantation.
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8
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Schaffner SL, Wassouf Z, Lazaro DF, Xylaki M, Gladish N, Lin DTS, MacIsaac J, Ramadori K, Hentrich T, Schulze-Hentrich JM, Outeiro TF, Kobor MS. Alpha-synuclein overexpression induces epigenomic dysregulation of glutamate signaling and locomotor pathways. Hum Mol Genet 2022; 31:3694-3714. [PMID: 35567546 PMCID: PMC9616577 DOI: 10.1093/hmg/ddac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/15/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Parkinson’s disease (PD) is a neurological disorder with complex interindividual etiology that is becoming increasingly prevalent worldwide. Elevated alpha-synuclein levels can increase risk of PD and may influence epigenetic regulation of PD pathways. Here, we report genome-wide DNA methylation and hydroxymethylation alterations associated with overexpression of two PD-linked alpha-synuclein variants (wild-type and A30P) in LUHMES cells differentiated to dopaminergic neurons. Alpha-synuclein altered DNA methylation at thousands of CpGs and DNA hydroxymethylation at hundreds of CpGs in both genotypes, primarily in locomotor behavior and glutamate signaling pathway genes. In some cases, epigenetic changes were associated with transcription. SMITE network analysis incorporating H3K4me1 ChIP-seq to score DNA methylation and hydroxymethylation changes across promoters, enhancers, and gene bodies confirmed epigenetic and transcriptional deregulation of glutamate signaling modules in both genotypes. Our results identify distinct and shared impacts of alpha-synuclein variants on the epigenome, and associate alpha-synuclein with the epigenetic etiology of PD.
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Affiliation(s)
- Samantha L Schaffner
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Zinah Wassouf
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Diana F Lazaro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mary Xylaki
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Nicole Gladish
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - David T S Lin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Julia MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Katia Ramadori
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Julia M Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
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Wang S, Bryan C, Xie J, Zhao H, Lin L, Tai JAC, Horzmann KA, Sanchez O, Zhang M, Freeman JL, Yuan C. Atrazine exposure in zebrafish induces aberrant genome-wide methylation. Neurotoxicol Teratol 2022; 92:107091. [DOI: 10.1016/j.ntt.2022.107091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/30/2022] [Accepted: 04/18/2022] [Indexed: 01/19/2023]
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10
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Koskuvi M, Lehtonen Š, Trontti K, Keuters M, Wu YC, Koivisto H, Ludwig A, Plotnikova L, Virtanen PLJ, Räsänen N, Kaipainen S, Hyötyläinen I, Dhungana H, Giniatullina R, Ojansuu I, Vaurio O, Cannon TD, Lönnqvist J, Therman S, Suvisaari J, Kaprio J, Lähteenvuo M, Tohka J, Giniatullin R, Rivera C, Hovatta I, Tanila H, Tiihonen J, Koistinaho J. Contribution of astrocytes to familial risk and clinical manifestation of schizophrenia. Glia 2021; 70:650-660. [PMID: 34936134 PMCID: PMC9306586 DOI: 10.1002/glia.24131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/28/2022]
Abstract
Previous studies have implicated several brain cell types in schizophrenia (SCZ), but the genetic impact of astrocytes is unknown. Considering their high complexity in humans, astrocytes are likely key determinants of neurodevelopmental diseases, such as SCZ. Human induced pluripotent stem cell (hiPSC)‐derived astrocytes differentiated from five monozygotic twin pairs discordant for SCZ and five healthy subjects were studied for alterations related to high genetic risk and clinical manifestation of SCZ in astrocyte transcriptomics, neuron‐astrocyte co‐cultures, and in humanized mice. We found gene expression and signaling pathway alterations related to synaptic dysfunction, inflammation, and extracellular matrix components in SCZ astrocytes, and demyelination in SCZ astrocyte transplanted mice. While Ingenuity Pathway Analysis identified SCZ disease and synaptic transmission pathway changes in SCZ astrocytes, the most consistent findings were related to collagen and cell adhesion associated pathways. Neuronal responses to glutamate and GABA differed between astrocytes from control persons, affected twins, and their unaffected co‐twins and were normalized by clozapine treatment. SCZ astrocyte cell transplantation to the mouse forebrain caused gene expression changes in synaptic dysfunction and inflammation pathways of mouse brain cells and resulted in behavioral changes in cognitive and olfactory functions. Differentially expressed transcriptomes and signaling pathways related to synaptic functions, inflammation, and especially collagen and glycoprotein 6 pathways indicate abnormal extracellular matrix composition in the brain as one of the key characteristics in the etiology of SCZ.
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Affiliation(s)
- Marja Koskuvi
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Šárka Lehtonen
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kalevi Trontti
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Meike Keuters
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ying-Chieh Wu
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Hennariikka Koivisto
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Lidiia Plotnikova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Noora Räsänen
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Satu Kaipainen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ida Hyötyläinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Hiramani Dhungana
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Raisa Giniatullina
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilkka Ojansuu
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
| | - Olli Vaurio
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
| | - Tyrone D Cannon
- Department of Psychology and Psychiatry, Yale University, New Haven, Connecticut, USA
| | - Jouko Lönnqvist
- Mental Health Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland.,Department of Psychiatry, University of Helsinki, Helsinki, Finland
| | - Sebastian Therman
- Mental Health Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jaana Suvisaari
- Mental Health Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Markku Lähteenvuo
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
| | - Jussi Tohka
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Rashid Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Claudio Rivera
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,INSERM, Institute of Mediterranean Neurobiology, Aix-Marseille University, Marseille, France
| | - Iiris Hovatta
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Heikki Tanila
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jari Tiihonen
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland.,Department of Clinical Neuroscience, Karolinska Institutet, and Center for Psychiatric Research, Stockholm City Council, Stockholm, Sweden
| | - Jari Koistinaho
- Neuroscience Center, University of Helsinki, Helsinki, Finland.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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11
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Samoilova EM, Belopasov VV, Ekusheva EV, Zhang C, Troitskiy AV, Baklaushev VP. Epigenetic Clock and Circadian Rhythms in Stem Cell Aging and Rejuvenation. J Pers Med 2021; 11:1050. [PMID: 34834402 PMCID: PMC8620936 DOI: 10.3390/jpm11111050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
This review summarizes the current understanding of the interaction between circadian rhythms of gene expression and epigenetic clocks characterized by the specific profile of DNA methylation in CpG-islands which mirror the senescence of all somatic cells and stem cells in particular. Basic mechanisms of regulation for circadian genes CLOCK-BMAL1 as well as downstream clock-controlled genes (ССG) are also discussed here. It has been shown that circadian rhythms operate by the finely tuned regulation of transcription and rely on various epigenetic mechanisms including the activation of enhancers/suppressors, acetylation/deacetylation of histones and other proteins as well as DNA methylation. Overall, up to 20% of all genes expressed by the cell are subject to expression oscillations associated with circadian rhythms. Additionally included in the review is a brief list of genes involved in the regulation of circadian rhythms, along with genes important for cell aging, and oncogenesis. Eliminating some of them (for example, Sirt1) accelerates the aging process, while the overexpression of Sirt1, on the contrary, protects against age-related changes. Circadian regulators control a number of genes that activate the cell cycle (Wee1, c-Myc, p20, p21, and Cyclin D1) and regulate histone modification and DNA methylation. Approaches for determining the epigenetic age from methylation profiles across CpG islands in individual cells are described. DNA methylation, which characterizes the function of the epigenetic clock, appears to link together such key biological processes as regeneration and functioning of stem cells, aging and malignant transformation. Finally, the main features of adult stem cell aging in stem cell niches and current possibilities for modulating the epigenetic clock and stem cells rejuvenation as part of antiaging therapy are discussed.
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Affiliation(s)
- Ekaterina M. Samoilova
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | | | - Evgenia V. Ekusheva
- Academy of Postgraduate Education of the Federal Scientific and Clinical Center for Specialized Types of Medical Care and Medical Technologies, FMBA of Russia, 125371 Moscow, Russia;
| | - Chao Zhang
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China;
| | - Alexander V. Troitskiy
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | - Vladimir P. Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
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12
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De Serres-Bérard T, Pierre M, Chahine M, Puymirat J. Deciphering the mechanisms underlying brain alterations and cognitive impairment in congenital myotonic dystrophy. Neurobiol Dis 2021; 160:105532. [PMID: 34655747 DOI: 10.1016/j.nbd.2021.105532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic and heterogeneous disorder caused by the expansion of CTG repeats in the 3' UTR of the myotonic dystrophy protein kinase (DMPK) gene. There is a congenital form (CDM1) of the disease characterized by severe hypotonia, respiratory insufficiency as well as developmental delays and intellectual disabilities. CDM1 infants manifest important brain structure abnormalities present from birth while, in contrast, older patients with adult-onset DM1 often present neurodegenerative features and milder progressive cognitive deficits. Promising therapies targeting central molecular mechanisms contributing to the symptoms of adult-onset DM1 are currently in development, but their relevance for treating cognitive impairment in CDM1, which seems to be a partially distinct neurodevelopmental disorder, remain to be elucidated. Here, we provide an update on the clinical presentation of CDM1 and review recent in vitro and in vivo models that have provided meaningful insights on its consequences in development, with a particular focus on the brain. We discuss how enhanced toxic gain-of-function of the mutated DMPK transcripts with larger CUG repeats and the resulting dysregulation of RNA-binding proteins may affect the developing cortex in utero. Because the methylation of CpG islets flanking the trinucleotide repeats has emerged as a strong biomarker of CDM1, we highlight the need to investigate the tissue-specific impacts of these chromatin modifications in the brain. Finally, we outline promising potential therapeutic treatments for CDM1 and propose future in vitro and in vivo models with great potential to shed light on this disease.
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Affiliation(s)
- Thiéry De Serres-Bérard
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, Canada; CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada
| | - Marion Pierre
- CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada
| | - Mohamed Chahine
- CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada.
| | - Jack Puymirat
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
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13
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Couch ACM, Berger T, Hanger B, Matuleviciute R, Srivastava DP, Thuret S, Vernon AC. Maternal immune activation primes deficiencies in adult hippocampal neurogenesis. Brain Behav Immun 2021; 97:410-422. [PMID: 34352366 PMCID: PMC8478664 DOI: 10.1016/j.bbi.2021.07.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/25/2021] [Accepted: 07/28/2021] [Indexed: 12/19/2022] Open
Abstract
Neurogenesis, the process in which new neurons are generated, occurs throughout life in the mammalian hippocampus. Decreased adult hippocampal neurogenesis (AHN) is a common feature across psychiatric disorders, including schizophrenia, depression- and anxiety-related behaviours, and is highly regulated by environmental influences. Epidemiological studies have consistently implicated maternal immune activation (MIA) during neurodevelopment as a risk factor for psychiatric disorders in adulthood. The extent to which the reduction of hippocampal neurogenesis in adulthood may be driven by early life exposures, such as MIA, is however unclear. We therefore reviewed the literature for evidence of the involvement of MIA in disrupting AHN. Consistent with our hypothesis, data from both in vivo murine and in vitro human models of AHN provide evidence for key roles of specific cytokines induced by MIA in the foetal brain in disrupting hippocampal neural progenitor cell proliferation and differentiation early in development. The precise molecular mechanisms however remain unclear. Nonetheless, these data suggest a potential latent vulnerability mechanism, whereby MIA primes dysfunction in the unique hippocampal pool of neural stem/progenitor cells. This renders offspring potentially more susceptible to additional environmental exposures later in life, such as chronic stress, resulting in the unmasking of psychopathology. We highlight the need for studies to test this hypothesis using validated animal models of MIA, but also to test the relevance of such data for human pathology at a molecular basis through the use of patient-derived induced pluripotent stem cells (hiPSC) differentiated into hippocampal progenitor cells.
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Affiliation(s)
- Amalie C M Couch
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Thomas Berger
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Bjørn Hanger
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | | | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Sandrine Thuret
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Anthony C Vernon
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
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14
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Haase FD, Coorey B, Riley L, Cantrill LC, Tam PPL, Gold WA. Pre-clinical Investigation of Rett Syndrome Using Human Stem Cell-Based Disease Models. Front Neurosci 2021; 15:698812. [PMID: 34512241 PMCID: PMC8423999 DOI: 10.3389/fnins.2021.698812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/19/2021] [Indexed: 01/02/2023] Open
Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder, mostly caused by mutations in MECP2. The disorder mainly affects girls and it is associated with severe cognitive and physical disabilities. Modeling RTT in neural and glial cell cultures and brain organoids derived from patient- or mutation-specific human induced pluripotent stem cells (iPSCs) has advanced our understanding of the pathogenesis of RTT, such as disease-causing mechanisms, disease progression, and cellular and molecular pathology enabling the identification of actionable therapeutic targets. Brain organoid models that recapitulate much of the tissue architecture and the complexity of cell types in the developing brain, offer further unprecedented opportunity for elucidating human neural development, without resorting to conventional animal models and the limited resource of human neural tissues. This review focuses on the new knowledge of RTT that has been gleaned from the iPSC-based models as well as limitations of the models and strategies to refine organoid technology in the quest for clinically relevant disease models for RTT and the broader spectrum of neurodevelopmental disorders.
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Affiliation(s)
- Florencia D. Haase
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead, NSW, Australia
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Hospital at Westmead, and Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Bronte Coorey
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead, NSW, Australia
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Hospital at Westmead, and Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Lisa Riley
- Rare Diseases Functional Genomics Laboratory, Kids Research, Children’s Hospital at Westmead, and Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Laurence C. Cantrill
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Kids Research, Children’s Hospital at Westmead, Westmead, NSW, Australia
| | - Patrick P. L. Tam
- Embryology Research Unit, Children’s Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Wendy A. Gold
- Kids Neuroscience Centre, Kids Research, Children’s Hospital at Westmead, Westmead, NSW, Australia
- Molecular Neurobiology Research Laboratory, Kids Research, Children’s Hospital at Westmead, and Children’s Medical Research Institute, Westmead, NSW, Australia
- Rare Diseases Functional Genomics Laboratory, Kids Research, Children’s Hospital at Westmead, and Children’s Medical Research Institute, Westmead, NSW, Australia
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15
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Retention of Somatic Memory Associated with Cell Identity, Age and Metabolism in Induced Pluripotent Stem (iPS) Cells Reprogramming. Stem Cell Rev Rep 2021; 16:251-261. [PMID: 32016780 DOI: 10.1007/s12015-020-09956-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The discovery of induced pluripotent stem (iPS) cells in 2006 marked a major breakthrough in regenerative medicine, enabling reversal of terminally differentiated somatic cells into pluripotent stem cells. The embryonic stem (ES) cells-like pluripotency and unlimited self-renewal capability of iPS cells have granted them enormous potential in many applications, particularly regenerative therapy. Unlike ES cells, however, iPS cells exhibit somatic memories which were carried over from the tissue of origin thus limited its translation in clinical applications. This review provides an updated overview of the retention of various somatic memories associated with the cellular identity, age and metabolism of tissue of origin in iPS cells. The influence of cell types, stage of maturation, age and various other factors on the retention of somatic memory has been discussed. Recent evidence of somatic memory in the form of epigenetic, transcriptomic, metabolic signatures and its functional manifestations in both in vitro and in vivo settings also have been reviewed. The increasing number of studies which had adopted isogenic cell lines for comparisons in recent years had facilitated the identification of genuine somatic memories. These memories functionally affect iPS cells and its derivatives and are potentially tumorigenic thus, raising concerns on their safety in clinical application. Various approaches for memory erasure had since being reported and their efficacies were highlighted in this review.
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16
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Khurana P, Kolundzic N, Flohr C, Ilic D. Human pluripotent stem cells: An alternative for 3D in vitro modelling of skin disease. Exp Dermatol 2021; 30:1572-1587. [PMID: 33864704 DOI: 10.1111/exd.14358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/15/2021] [Accepted: 04/05/2021] [Indexed: 01/05/2023]
Abstract
To effectively study the skin and its pathology, various platforms have been used to date, with in vitro 3D skin models being considered the future gold standard. These models have generally been engineered from primary cell lines. However, their short life span leading to the use of various donors, imposes issues with genetic variation. Human pluripotent stem cell (hPSC)-technology holds great prospects as an alternative to the use of primary cell lines to study the pathophysiology of human skin diseases. This is due to their potential to generate an unlimited number of genetically identical skin models that closely mimic the complexity of in vivo human skin. During the past decade, researchers have therefore started to use human embryonic and induced pluripotent stem cells (hESC/iPSC) to derive skin resident-like cells and components. These have subsequently been used to engineer hPSC-derived 3D skin models. In this review, we focus on the advantages, recent developments, and future perspectives in using hPSCs as an alternative cell source for modelling human skin diseases in vitro.
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Affiliation(s)
- Preeti Khurana
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Assisted Conception Unit, Guy's Hospital, London, UK
| | - Nikola Kolundzic
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Assisted Conception Unit, Guy's Hospital, London, UK
| | - Carsten Flohr
- St John's Institute of Dermatology, King's College London and Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dusko Ilic
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Assisted Conception Unit, Guy's Hospital, London, UK
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17
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Samoylova EM, Baklaushev VP. Cell Reprogramming Preserving Epigenetic Age: Advantages and Limitations. BIOCHEMISTRY (MOSCOW) 2021; 85:1035-1047. [PMID: 33050850 DOI: 10.1134/s0006297920090047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Our understanding of cell aging advanced significantly since the discovery of this phenomenon by Hayflick and Moorhead in 1961. In addition to the well-known shortening of telomeric regions of chromosomes, cell aging is closely associated with changes of the DNA methylation profile. Establishing, maintaining, or reversing epigenetic age of a cell is central to the technology of cell reprogramming. Two distinct approaches - iPSC- and transdifferentiation-based cell reprogramming - affect differently epigenetic age of the cells. The iPSC-based reprogramming protocols are generally believed to result in the reversion of DNA methylation profiles towards less differentiated states, while the original methylation profiles are preserved in the direct trans-differentiation protocols. Clearly, in order to develop adequate model of CNS pathologies, one has to have thorough understanding of the biological roles of DNA methylation in the development, maintenance of functional activity, tissue and cell diversity, restructuring of neural networks during learning, as well as in aging-associated neuronal decline. Direct cell reprogramming is an excellent alternative and a valuable supplement to the iPSC-based technologies both as a source of mature cells for modeling of neurodegenerative diseases, and as a novel powerful strategy for in vivo cell replacement therapy. Further advancement of the regenerative and personalized medicine will strongly depend on optimization of the production of patient-specific autologous cells involving alternative approaches of direct and indirect cell reprogramming that take into account epigenetic age of the starting cell material.
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Affiliation(s)
- E M Samoylova
- Federal Research Clinical Center, FMBA of Russia, Moscow, 115682, Russia.
| | - V P Baklaushev
- Federal Research Clinical Center, FMBA of Russia, Moscow, 115682, Russia
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18
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Scarfone RA, Pena SM, Russell KA, Betts DH, Koch TG. The use of induced pluripotent stem cells in domestic animals: a narrative review. BMC Vet Res 2020; 16:477. [PMID: 33292200 PMCID: PMC7722595 DOI: 10.1186/s12917-020-02696-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) are undifferentiated stem cells characterized by the ability to differentiate into any cell type in the body. iPSCs are a relatively new and rapidly developing technology in many fields of biology, including developmental anatomy and physiology, pathology, and toxicology. These cells have great potential in research as they are self-renewing and pluripotent with minimal ethical concerns. Protocols for their production have been developed for many domestic animal species, which have since been used to further our knowledge in the progression and treatment of diseases. This research is valuable both for veterinary medicine as well as for the prospect of translation to human medicine. Safety, cost, and feasibility are potential barriers for this technology that must be considered before widespread clinical adoption. This review will analyze the literature pertaining to iPSCs derived from various domestic species with a focus on iPSC production and characterization, applications for tissue and disease research, and applications for disease treatment.
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Affiliation(s)
- Rachel A Scarfone
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Samantha M Pena
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Keith A Russell
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Dean H Betts
- Department of Physiology and Pharmacology, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Thomas G Koch
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
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19
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Choi WY, Hwang JH, Cho AN, Lee AJ, Lee J, Jung I, Cho SW, Kim LK, Kim YJ. DNA Methylation of Intragenic CpG Islands are Required for Differentiation from iPSC to NPC. Stem Cell Rev Rep 2020; 16:1316-1327. [PMID: 32975781 DOI: 10.1007/s12015-020-10041-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/30/2022]
Abstract
The effects of gene body DNA methylation on gene regulation still remains highly controversial. In this study, we generated whole genome bisulfite sequencing (WGBS) data with high sequencing depth in induced pluripotent stem cell (iPSC) and neuronal progentior cell (NPC), and investigated the relationship between DNA methylation changes in CpG islands (CGIs) and corresponding gene expression during NPC differentiation. Interestingly, differentially methylated CGIs were more abundant in intragenic regions compared to promoters and these methylated intragenic CGIs (iCGIs) were associated with neuronal development-related genes. When we compared gene expression level of methylated and unmethylated CGIs in intragenic regions, DNA methylation of iCGI was positively correlated with gene expression in contrast with promoter CGIs (pCGIs). To gain insight into regulatory mechanism mediated by iCGI DNA methylation, we executed motif searching in hypermethylated iCGIs and found NEUROD1 as a hypermethylated iCGI binding transcription factor. This study highlights give rise to possibility of activating role of hypermethylation in iCGIs and involvement of neuronal development related TFs. Graphical Abstract The relationship between iCGI DNA methylation and expression of associated genes in neuronal developmental process. During iPSC to NPCdifferentiation, iCGI containing neural developmental genes show iCGI's DNA hypermethylation which is accompanied by gene activation and NEUROD1which is one of the core neuronal TFs interacts with hypermethylated iCGI regions.
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Affiliation(s)
- Won-Young Choi
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, The Graduate School, Yonsei University, Seoul, 03722, Republic of Korea
| | - Ji-Hyun Hwang
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, The Graduate School, Yonsei University, Seoul, 03722, Republic of Korea
| | - Ann-Na Cho
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Andrew J Lee
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Jungwoo Lee
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, The Graduate School, Yonsei University, Seoul, 03722, Republic of Korea
| | - Inkyung Jung
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Lark Kyun Kim
- Severance Biomedical Science Institute and BK21 PLUS Project for Medical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06230, Republic of Korea.
| | - Young-Joon Kim
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, The Graduate School, Yonsei University, Seoul, 03722, Republic of Korea. .,Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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20
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"Betwixt Mine Eye and Heart a League Is Took": The Progress of Induced Pluripotent Stem-Cell-Based Models of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2020; 21:ijms21196997. [PMID: 32977524 PMCID: PMC7582534 DOI: 10.3390/ijms21196997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
The ultimate goal of precision disease modeling is to artificially recreate the disease of affected people in a highly controllable and adaptable external environment. This field has rapidly advanced which is evident from the application of patient-specific pluripotent stem-cell-derived precision therapies in numerous clinical trials aimed at a diverse set of diseases such as macular degeneration, heart disease, spinal cord injury, graft-versus-host disease, and muscular dystrophy. Despite the existence of semi-adequate treatments for tempering skeletal muscle degeneration in dystrophic patients, nonischemic cardiomyopathy remains one of the primary causes of death. Therefore, cardiovascular cells derived from muscular dystrophy patients' induced pluripotent stem cells are well suited to mimic dystrophin-associated cardiomyopathy and hold great promise for the development of future fully effective therapies. The purpose of this article is to convey the realities of employing precision disease models of dystrophin-associated cardiomyopathy. This is achieved by discussing, as suggested in the title echoing William Shakespeare's words, the settlements (or "leagues") made by researchers to manage the constraints ("betwixt mine eye and heart") distancing them from achieving a perfect precision disease model.
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21
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Eintracht J, Toms M, Moosajee M. The Use of Induced Pluripotent Stem Cells as a Model for Developmental Eye Disorders. Front Cell Neurosci 2020; 14:265. [PMID: 32973457 PMCID: PMC7468397 DOI: 10.3389/fncel.2020.00265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Approximately one-third of childhood blindness is attributed to developmental eye disorders, of which 80% have a genetic cause. Eye morphogenesis is tightly regulated by a highly conserved network of transcription factors when disrupted by genetic mutations can result in severe ocular malformation. Human-induced pluripotent stem cells (hiPSCs) are an attractive tool to study early eye development as they are more physiologically relevant than animal models, can be patient-specific and their use does not elicit the ethical concerns associated with human embryonic stem cells. The generation of self-organizing hiPSC-derived optic cups is a major advancement to understanding mechanisms of ocular development and disease. Their development in vitro has been found to mirror that of the human eye and these early organoids have been used to effectively model microphthalmia caused by a VSX2 variant. hiPSC-derived optic cups, retina, and cornea organoids are powerful tools for future modeling of disease phenotypes and will enable a greater understanding of the pathophysiology of many other developmental eye disorders. These models will also provide an effective platform for identifying molecular therapeutic targets and for future clinical applications.
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Affiliation(s)
| | - Maria Toms
- UCL Institute of Ophthalmology, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom.,Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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22
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Lee D, Choi YH, Seo J, Kim JK, Lee SB. Discovery of new epigenomics-based biomarkers and the early diagnosis of neurodegenerative diseases. Ageing Res Rev 2020; 61:101069. [PMID: 32416267 DOI: 10.1016/j.arr.2020.101069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/02/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Treatment options for many neurodegenerative diseases are limited due to the lack of early diagnostic procedures that allow timely delivery of therapeutic agents to affected neurons prior to cell death. While notable advances have been made in neurodegenerative disease biomarkers, whether or not the biomarkers discovered to date are useful for early diagnosis remains an open question. Additionally, the reliability of these biomarkers has been disappointing, due in part to the large dissimilarities between the tissues traditionally used to source biomarkers and primarily diseased neurons. In this article, we review the potential viability of atypical epigenetic and/or consequent transcriptional alterations (ETAs) as biomarkers of early-stage neurodegenerative disease, and present our perspectives on the discovery and practical use of such biomarkers in patient-derived neural samples using single-cell level analyses, thereby greatly enhancing the reliability of biomarker application.
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23
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Krach F, Bogiongko ME, Winner B. Decoding Parkinson's disease - iPSC-derived models in the OMICs era. Mol Cell Neurosci 2020; 106:103501. [PMID: 32439399 DOI: 10.1016/j.mcn.2020.103501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/15/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain. In recent years, researchers have started studying PD using induced pluripotent stem cell (iPSC) models of the disease. Surprisingly, few studies have combined iPSC-technology with the so-called powerful 'omics' approaches. Here, we review the current state of omics applications used in combination with iPSC-derived models to study PD. Our focus is on studies investigating transcriptional changes and publications using proteomics applications. Lastly, we discuss current caveats in the field and identify potential future directions to obtain novel insights into PD pathology.
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Affiliation(s)
- Florian Krach
- Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuernberg (FAU), Glückstraße 6, 91054 Erlangen, Germany
| | - Marios-Evangelos Bogiongko
- Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuernberg (FAU), Glückstraße 6, 91054 Erlangen, Germany
| | - Beate Winner
- Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuernberg (FAU), Glückstraße 6, 91054 Erlangen, Germany.
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24
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Gordon A, Geschwind DH. Human in vitro models for understanding mechanisms of autism spectrum disorder. Mol Autism 2020; 11:26. [PMID: 32299488 PMCID: PMC7164291 DOI: 10.1186/s13229-020-00332-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
Early brain development is a critical epoch for the development of autism spectrum disorder (ASD). In vivo animal models have, until recently, been the principal tool used to study early brain development and the changes occurring in neurodevelopmental disorders such as ASD. In vitro models of brain development represent a significant advance in the field. Here, we review the main methods available to study human brain development in vitro and the applications of these models for studying ASD and other psychiatric disorders. We discuss the main findings from stem cell models to date focusing on cell cycle and proliferation, cell death, cell differentiation and maturation, and neuronal signaling and synaptic stimuli. To be able to generalize the results from these studies, we propose a framework of experimental design and power considerations for using in vitro models to study ASD. These include both technical issues such as reproducibility and power analysis and conceptual issues such as the brain region and cell types being modeled.
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Affiliation(s)
- Aaron Gordon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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25
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Li HT, Liu Y, Liu H, Sun X. Effect for Human Genomic Variation During the BMP4-Induced Conversion From Pluripotent Stem Cells to Trophoblast. Front Genet 2020; 11:230. [PMID: 32318089 PMCID: PMC7154154 DOI: 10.3389/fgene.2020.00230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022] Open
Abstract
The role of genomic variation in differentiation is currently not well understood. Here, the genomic variations were determined with the whole-genome sequencing for three pairs of pluripotent stem cell lines and their corresponding BMP4-induced trophoblast cell lines. We identified ∼3,500 single nucleotide variations and ∼4,500 indels by comparing the genome sequenced data between the stem cell lines and the matched BMP4-induced trophoblast cell lines and annotated them by integrating the epigenomic and transcriptomic datasets. Relatively, introns enrich more variations. We found ∼45% (42 genes) of the differentially expressed genes in trophoblasts that associate genomic variations. Six variations, located at transcription factor binding sites where H3K4me3 and H3K27ac are enriched in both H1 and H1_BMP4, were identified. The epigenetic status around the genomic variations in H1 was similar to that in H1_BMP4. This means that the variation-associated gene’s expression change can not be attributed to epigenetic alteration. The genes associated with the six variations were upregulated in differentiation. We inferred that during the differentiation, an increased in the expression level of the MEF2C gene is due to a genomic variation in chromosomes 5: 88179358 A > G, which is at a binding site of TFs KLF16, NR2C2, and ZNF740 to MEF2C. Allele G shows a higher affinity to the TFs in the induced cells. The increased expression of MEF2C leads to an increased expression of TF MEF2C’s target genes, subsequently affecting the differentiation. Although genomic variation should not be a dominant factor in differentiation, we believe that genomic variation could indeed play a role in the differentiation from stem cells into trophoblast.
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Affiliation(s)
- Hai-Tao Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yajun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences of Zhengzhou University Translational Medicine Platform, Zhengzhou University, Zhengzhou, China
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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26
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Volpato V, Webber C. Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility. Dis Model Mech 2020; 13:dmm042317. [PMID: 31953356 PMCID: PMC6994963 DOI: 10.1242/dmm.042317] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem cell (iPSC) technologies have provided in vitro models of inaccessible human cell types, yielding new insights into disease mechanisms especially for neurological disorders. However, without due consideration, the thousands of new human iPSC lines generated in the past decade will inevitably affect the reproducibility of iPSC-based experiments. Differences between donor individuals, genetic stability and experimental variability contribute to iPSC model variation by impacting differentiation potency, cellular heterogeneity, morphology, and transcript and protein abundance. Such effects will confound reproducible disease modelling in the absence of appropriate strategies. In this Review, we explore the causes and effects of iPSC heterogeneity, and propose approaches to detect and account for experimental variation between studies, or even exploit it for deeper biological insight.
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Affiliation(s)
- Viola Volpato
- UK Dementia Research Institute at Cardiff University, Division of Psychological Medicine and Clinical Neuroscience, Haydn Ellis Building, Maindy Rd, Cardiff CF24 4HQ, UK
| | - Caleb Webber
- UK Dementia Research Institute at Cardiff University, Division of Psychological Medicine and Clinical Neuroscience, Haydn Ellis Building, Maindy Rd, Cardiff CF24 4HQ, UK
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27
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Nielsen JJJ, Lillethorup TP, Glud AN, Sørensen JCH, Orlowski D. The application of iPSCs in Parkinson’s disease. Acta Neurobiol Exp (Wars) 2020. [DOI: 10.21307/ane-2020-024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Gao JY, Zhang W, Hu SQ, Zhang L, Chen TY, Tang B, Zhang ZJ, Hu JB. In vitro and in vivo induction of human embryonic stem cells differentiated into rosette neural stem cells and further generation of neuron-like cells. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1808082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Jian-Yi Gao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
- Translational Medicine Laboratory, Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Wei Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
- Department of Microbiology and Immunology, the Affiliated 3201 Hospital of Medical School, Xi’an Jiaotong University, Hanzhong, People’s Republic of China
| | - San-Qiang Hu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Lei Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
- Translational Medical Center, Department of Laboratory Medicine, the Affiliated Wuxi No. 2 People’s Hospital of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Tian-Yan Chen
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Bin Tang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Zhi-jian Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Jia-Bo Hu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
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29
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Ankam S, Rovini A, Baheti S, Hrstka R, Wu Y, Schmidt K, Wang H, Madigan N, Koenig LS, Stelzig K, Resch Z, Klein CJ, Sun Z, Staff NP. DNA methylation patterns in human iPSC-derived sensory neuronal differentiation. Epigenetics 2019; 14:927-937. [PMID: 31148524 PMCID: PMC6691994 DOI: 10.1080/15592294.2019.1625672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/19/2019] [Accepted: 05/23/2019] [Indexed: 12/18/2022] Open
Abstract
Sensory neurons of the peripheral nervous system are critical in health and disease. Sensory neurons derived from induced pluripotent stem (iPS) cells are now being used increasingly for in vitro models of neuropathy, pain, and neurotoxicity. DNA methylation is critical for neurodevelopment and has been implicated in many neuronal diseases, but has not been examined in iPS-derived sensory neurons. In order to better characterize the iPS-derived sensory neuron model, we have undertaken a genome-wide DNA methylation study on the cells from human iPS to iPS-derived sensory neurons during differentiation through reduced representation and bisulfite sequencing. We report decreasing DNA methylation with iPS-derived sensory neuronal differentiation that is reflected in increasing numbers and proportions of hypomethylated individual CpGs and regions, as well as lowered DNMT3b expression. Furthermore, genes with changes in DNA methylation near their TSS suggest key pathways that may be involved in iPS-derived sensory neuronal differentiation. These findings provide insights into sensory neuronal differentiation and can be used for further in vitro modelling of disease states.
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Affiliation(s)
- Soneela Ankam
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | - Saurabh Baheti
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Ron Hrstka
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Yanhong Wu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kiley Schmidt
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Hailong Wang
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Kimberly Stelzig
- Center for Regenerative Medicine Biotrust, Mayo Clinic, Rochester, MN, USA
| | - Zachary Resch
- Center for Regenerative Medicine Biotrust, Mayo Clinic, Rochester, MN, USA
| | | | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
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30
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Hack LM, Fries GR, Eyre HA, Bousman CA, Singh AB, Quevedo J, John VP, Baune BT, Dunlop BW. Moving pharmacoepigenetics tools for depression toward clinical use. J Affect Disord 2019; 249:336-346. [PMID: 30802699 PMCID: PMC6763314 DOI: 10.1016/j.jad.2019.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) is a leading cause of disability worldwide, and over half of patients do not achieve symptom remission following an initial antidepressant course. Despite evidence implicating a strong genetic basis for the pathophysiology of MDD, there are no adequately validated biomarkers of treatment response routinely used in clinical practice. Pharmacoepigenetics is an emerging field that has the potential to combine both genetic and environmental information into treatment selection and further the goal of precision psychiatry. However, this field is in its infancy compared to the more established pharmacogenetics approaches. METHODS We prepared a narrative review using literature searches of studies in English pertaining to pharmacoepigenetics and treatment of depressive disorders conducted in PubMed, Google Scholar, PsychINFO, and Ovid Medicine from inception through January 2019. We reviewed studies of DNA methylation and histone modifications in both humans and animal models of depression. RESULTS Emerging evidence from human and animal work suggests a key role for epigenetic marks, including DNA methylation and histone modifications, in the prediction of antidepressant response. The challenges of heterogeneity of patient characteristics and loci studied as well as lack of replication that have impacted the field of pharmacogenetics also pose challenges to the development of pharmacoepigenetic tools. Additionally, given the tissue specific nature of epigenetic marks as well as their susceptibility to change in response to environmental factors and aging, pharmacoepigenetic tools face additional challenges to their development. LIMITATIONS This is a narrative and not systematic review of the literature on the pharmacoepigenetics of antidepressant response. We highlight key studies pertaining to pharmacoepigenetics and treatment of depressive disorders in humans and depressive-like behaviors in animal models, regardless of sample size or methodology. While we discuss DNA methylation and histone modifications, we do not cover microRNAs, which have been reviewed elsewhere recently. CONCLUSIONS Utilization of genome-wide approaches and reproducible epigenetic assays, careful selection of the tissue assessed, and integration of genetic and clinical information into pharmacoepigenetic tools will improve the likelihood of developing clinically useful tests.
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Affiliation(s)
- Laura M Hack
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 401 Quarry Road, Palo Alto, CA 94305, USA; Sierra Pacific Mental Illness Research Education and Clinical Centers, VA Palo Alto Health Care System, Palo Alto, CA, USA.
| | - Gabriel R Fries
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Harris A Eyre
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 401 Quarry Road, Palo Alto, CA 94305, USA; Innovation Institute, Texas Medical Center, Houston, TX, USA; IMPACT SRC, School of Medicine, Deakin University, Geelong, Victoria, Australia; Department of Psychiatry, University of Melbourne, Melbourne, Victoria, Australia
| | - Chad A Bousman
- Departments of Medical Genetics, Psychiatry, Physiology & Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Ajeet B Singh
- IMPACT SRC, School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Joao Quevedo
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Vineeth P John
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Bernhard T Baune
- Department of Psychiatry, University of Melbourne, Melbourne, Victoria, Australia
| | - Boadie W Dunlop
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA, USA
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31
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de Boni L, Wüllner U. Epigenetic Analysis in Human Neurons: Considerations for Disease Modeling in PD. Front Neurosci 2019; 13:276. [PMID: 31024227 PMCID: PMC6460245 DOI: 10.3389/fnins.2019.00276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/08/2019] [Indexed: 12/28/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder next to Alzheimer’s disease. Most PD cases are considered to be sporadic and despite considerable scientific effort, the underlying cause(s) still remain(s) enigmatic. In particular, it is unknown to which extent epigenetic alterations contribute to the pathophysiology of this devastating disorder. This is partly due to the fact that appropriate PD models are not yet available. Moreover, epigenetic patterns and mechanisms are species specific and murine systems reflect only a few of the idiosyncrasies of human neurons. For several years now, patient-specific stem cell-derived neural and non-neural cells have been employed to overcome this limitation allowing the analysis and establishment of humanized disease models for PD. Thus, several studies tried to dissect epigenetic alterations such as aberrant DNA methylation or microRNA patterns using lund human mesencephalic cell lines or neurons derived from (patient-specific) induced pluripotent stem cells. These studies demonstrate that human neurons have the potential to be used as model systems for the study of epigenetic modifications in PD such as characterizing epigenetic changes, correlating epigenetic changes to gene expression alterations and hopefully using these insights for the development of novel therapeutics. However, more research is required to define the epigenetic (age-associated) landscape of human in vitro neurons and compare these to native neurons before they can be established as suitable models for epigenetic studies in PD. In this review, we summarize the knowledge about epigenetic studies performed on human neuronal PD models, and we discuss advantages and current limitations of these (stem cell-derived) neuronal models for the study of epigenetic alterations in PD.
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Affiliation(s)
- Laura de Boni
- Dementia Research Institute, University College London, London, United Kingdom
| | - Ullrich Wüllner
- Department of Neurology, University Hospital Bonn, German Center for Neurologic Diseases, Bonn, Germany
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32
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Ziff OJ, Patani R. Harnessing cellular aging in human stem cell models of amyotrophic lateral sclerosis. Aging Cell 2019; 18:e12862. [PMID: 30565851 PMCID: PMC6351881 DOI: 10.1111/acel.12862] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive neurodegenerative condition that is invariably fatal, usually within 3 to 5 years of diagnosis. The etiology of ALS remains unresolved and no effective treatments exist. There is therefore a desperate and unmet need for discovery of disease mechanisms to guide novel therapeutic strategies. The single major risk factor for ALS is aging, yet the molecular consequences of cell type‐specific aging remain understudied in this context. Induced pluripotent stem cells (iPSCs) have transformed the standard approach of examining human disease, generating unlimited numbers of disease‐relevant cells from patients, enabling analysis of disease mechanisms and drug screening. However, reprogramming patient cells to iPSCs reverses key hallmarks of cellular age. Therefore, although iPSC models recapitulate some disease hallmarks, a crucial challenge is to address the disparity between the advanced age of onset of neurodegenerative diseases and the fetal‐equivalent maturational state of iPSC‐derivatives. Increasing recognition of cell type‐specific aging paradigms underscores the importance of heterogeneity in ultimately tipping the balance from a state of compensated dysfunction (clinically pre‐symptomatic) to decompensation and progression (irreversible loss of neurological functions). In order to realize the true promise of iPSC technology in ALS, efforts need to prioritize faithfully recapitulating the clinical pathophysiological state, with proportionate emphasis on capturing the molecular sequelae of both cellular age and non‐cell‐autonomous disease mechanisms within this context.
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Affiliation(s)
- Oliver J. Ziff
- The Institute of Neurology; University College London; London UK
- The Francis Crick Institute; London UK
| | - Rickie Patani
- The Institute of Neurology; University College London; London UK
- The Francis Crick Institute; London UK
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33
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Lebedeva OS, Lagarkova MA. Pluripotent Stem Cells for Modelling and Cell Therapy of Parkinson's Disease. BIOCHEMISTRY (MOSCOW) 2018; 83:1046-1056. [PMID: 30472943 DOI: 10.1134/s0006297918090067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Studying pathogenesis of neurodegenerative diseases, including Parkinson's disease (PD), requires adequate disease models. The available patient's material is limited to biological fluids and post mortem brain samples. Disease modeling and drug screening can be done in animal models, although this approach has its own limitations, since laboratory animals do not suffer from many neurodegenerative diseases, including PD. The use of neurons obtained by targeted differentiation from induced pluripotent stem cells (iPSCs) with known genetic mutations, as well as from carriers of sporadic forms of the disease, will allow to elucidate new components of the molecular mechanisms of neurodegeneration. Such neuronal cultures can also serve as unique models for testing neuroprotective compounds and monitoring neurodegenerative changes against a background of various therapeutic interventions. In the future, dopaminergic neurons differentiated from iPSCs can be used for cell therapy of PD.
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Affiliation(s)
- O S Lebedeva
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
| | - M A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia.
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