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Lei Y, Al Delbany D, Krivec N, Regin M, Couvreu de Deckersberg E, Janssens C, Ghosh M, Sermon K, Spits C. SALL3 mediates the loss of neuroectodermal differentiation potential in human embryonic stem cells with chromosome 18q loss. Stem Cell Reports 2024; 19:562-578. [PMID: 38552632 PMCID: PMC11096619 DOI: 10.1016/j.stemcr.2024.03.001] [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: 09/28/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/12/2024] Open
Abstract
Human pluripotent stem cell (hPSC) cultures are prone to genetic drift, because cells that have acquired specific genetic abnormalities experience a selective advantage in vitro. These abnormalities are highly recurrent in hPSC lines worldwide, but their functional consequences in differentiating cells are scarcely described. In this work, we show that the loss of chromosome 18q impairs neuroectoderm commitment and that downregulation of SALL3, a gene located in the common 18q loss region, is responsible for this failed neuroectodermal differentiation. Knockdown of SALL3 in control lines impaired differentiation in a manner similar to the loss of 18q, and transgenic overexpression of SALL3 in hESCs with 18q loss rescued the differentiation capacity of the cells. Finally, we show that loss of 18q and downregulation of SALL3 leads to changes in the expression of genes involved in pathways regulating pluripotency and differentiation, suggesting that these cells are in an altered state of pluripotency.
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Affiliation(s)
- Yingnan Lei
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Diana Al Delbany
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Nuša Krivec
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Charlotte Janssens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Manjusha Ghosh
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium.
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2
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Maussion G, Rocha C, Ramoz N. iPSC-derived models for anorexia nervosa research. Trends Mol Med 2024; 30:339-349. [PMID: 38472034 DOI: 10.1016/j.molmed.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
Anorexia nervosa (AN) is a complex neuropsychiatric disorder with genetic and epigenetic components that results in reduced food intake combined with alterations in the reward-processing network. While studies of patient cohorts and mouse models have uncovered genes and epigenetic changes associated with the disease, neuronal networks and brain areas preferentially activated and metabolic changes associated with reduced food intake, the underlying molecular and cellular mechanisms remain unknown. The use of both 2D in vitro cultures and 3D models, namely organoids and spheroids, derived from either human embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs), would allow identification of cell type-specific changes associated with AN and comorbid diseases, to study preferential connections between brain areas and organs, and the development of therapeutic strategies.
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Affiliation(s)
- Gilles Maussion
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, Quebec H3A 2B4, Canada.
| | - Cecilia Rocha
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Nicolas Ramoz
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris 75014, France; GHU Paris Psychiatrie et Neurosciences, CMME, Hôpital Sainte-Anne, Paris F-75014, France
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3
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Frost ER, Gilchrist RB. Making human eggs in a dish: are we close? Trends Biotechnol 2024; 42:168-178. [PMID: 37625913 DOI: 10.1016/j.tibtech.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/05/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023]
Abstract
In the space of 50 years, we have seen incredible achievements in human reproductive medicine. With these leaps forward, it is no wonder that there is a major interest in women's reproductive health research, including extension of reproductive lifespan. Substantial effort is currently being made to address this challenge, including from the commercial sector. In vitro gametogenesis (IVG) in mice is a spectacular breakthrough and has the potential to offer hope to women with intractable infertility. However, with such lofty goals, some reflection may be called for: mastering all of the techniques required for complete and safe IVG in women is likely to be extraordinarily difficult.
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Affiliation(s)
- Emily R Frost
- Fertility & Research Centre, Discipline of Women's Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Robert B Gilchrist
- Fertility & Research Centre, Discipline of Women's Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
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4
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Kim J, Kwon EJ, Kim YJ, Kim D, Shin YZ, Gil D, Kim JH, Shin HD, Kim LH, Lee MO, Go YH, Cha HJ. Epigenetic repression of CHCHD2 enhances survival from single cell dissociation through attenuated Rho A kinase activity. Cell Mol Life Sci 2024; 81:38. [PMID: 38214772 PMCID: PMC10787008 DOI: 10.1007/s00018-023-05060-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/18/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024]
Abstract
During in vitro culture, human pluripotent stem cells (hPSCs) often acquire survival advantages characterized by decreased susceptibility to mitochondrial cell death, known as "culture adaptation." This adaptation is associated with genetic and epigenetic abnormalities, including TP53 mutations, copy number variations, trisomy, and methylation changes. Understanding the molecular mechanisms underlying this acquired survival advantage is crucial for safe hPSC-based cell therapies. Through transcriptome and methylome analysis, we discovered that the epigenetic repression of CHCHD2, a mitochondrial protein, is a common occurrence during in vitro culture using enzymatic dissociation. We confirmed this finding through genetic perturbation and reconstitution experiments in normal human embryonic stem cells (hESCs). Loss of CHCHD2 expression conferred resistance to single cell dissociation-induced cell death, a common stress encountered during in vitro culture. Importantly, we found that the downregulation of CHCHD2 significantly attenuates the activity of Rho-associated protein kinase (ROCK), which is responsible for inducing single cell death in hESCs. This suggests that hESCs may survive routine enzyme-based cell dissociation by downregulating CHCHD2 and thereby attenuating ROCK activity. These findings provide insights into the mechanisms by which hPSCs acquire survival advantages and adapt to in vitro culture conditions.
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Affiliation(s)
- Jumee Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eun-Ji Kwon
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yun-Jeong Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yoon-Ze Shin
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Gil
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Jung-Hyun Kim
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Young-Hyun Go
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
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5
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Krivec N, Ghosh MS, Spits C. Gains of 20q11.21 in human pluripotent stem cells: Insights from cancer research. Stem Cell Reports 2024; 19:11-27. [PMID: 38157850 PMCID: PMC10828824 DOI: 10.1016/j.stemcr.2023.11.013] [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: 09/08/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
The genetic abnormalities observed in hPSC cultures worldwide have been suggested to pose an important hurdle in their safe use in regenerative medicine due to the possibility of oncogenic transformation by mutant cells in the patient posttransplantation. One of the best-characterized genetic lesions in hPSCs is the gain of 20q11.21, found in 20% of hPSC lines worldwide, and strikingly, also amplified in 20% of human cancers. In this review, we have curated the existing knowledge on the incidence of this mutation in hPSCs and cancer, explored the significance of chromosome 20q11.21 amplification in cancer progression, and reviewed the oncogenic role of the genes in the smallest common region of gain, to shed light on the significance of this mutation in hPSC-based cell therapy. Lastly, we discuss the state-of-the-art strategies devised to detect aneuploidies in hPSC cultures, avoid genetic changes in vitro cultures of hPSCs, and strategies to eliminate genetically abnormal cells from culture.
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Affiliation(s)
- Nuša Krivec
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Manjusha S Ghosh
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium.
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6
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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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7
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Horisawa K, Miura S, Araki H, Miura F, Ito T, Suzuki A. Transcription factor-mediated direct cellular reprogramming yields cell-type specific DNA methylation signature. Sci Rep 2023; 13:22317. [PMID: 38102164 PMCID: PMC10724236 DOI: 10.1038/s41598-023-49546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023] Open
Abstract
Direct reprogramming, inducing the conversion of one type of somatic cell into another by the forced expression of defined transcription factors, is a technology with anticipated medical applications. However, due to the many unresolved aspects of the induction mechanisms, it is essential to thoroughly analyze the epigenomic state of the generated cells. Here, we performed comparative genome-wide DNA methylation analyses of mouse embryonic fibroblasts (MEFs) and cells composing organoids formed by intestinal stem cells (ISCs) or induced ISCs (iISCs) that were directly induced from MEFs. We found that the CpG methylation state was similar between cells forming ISC organoids and iISC organoids, while they differed widely from those in MEFs. Moreover, genomic regions that were differentially methylated between ISC organoid- and iISC organoid-forming cells did not significantly affect gene expression. These results demonstrate the accuracy and safety of iISC induction, leading to the medical applications of this technology.
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Affiliation(s)
- Kenichi Horisawa
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shizuka Miura
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hiromitsu Araki
- Insect Science and Creative Entomology Center, Kyushu University Graduate School of Agriculture, Fukuoka, 819-0395, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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8
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Contreras-Jurado C, Montero-Pedrazuela A, Pérez RF, Alemany S, Fraga MF, Aranda A. The thyroid hormone enhances mouse embryonic fibroblasts reprogramming to pluripotent stem cells: role of the nuclear receptor corepressor 1. Front Endocrinol (Lausanne) 2023; 14:1235614. [PMID: 38107517 PMCID: PMC10722291 DOI: 10.3389/fendo.2023.1235614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction Pluripotent stem cells can be generated from somatic cells by the Yamanaka factors Oct4, Sox2, Klf4 and c-Myc. Methods Mouse embryonic fibroblasts (MEFs) were transduced with the Yamanaka factors and generation of induced pluripotent stem cells (iPSCs) was assessed by formation of alkaline phosphatase positive colonies, pluripotency gene expression and embryod bodies formation. Results The thyroid hormone triiodothyronine (T3) enhances MEFs reprogramming. T3-induced iPSCs resemble embryonic stem cells in terms of the expression profile and DNA methylation pattern of pluripotency genes, and of their potential for embryod body formation and differentiation into the three major germ layers. T3 induces reprogramming even though it increases expression of the cyclin kinase inhibitors p21 and p27, which are known to oppose acquisition of pluripotency. The actions of T3 on reprogramming are mainly mediated by the thyroid hormone receptor beta and T3 can enhance iPSC generation in the absence of c-Myc. The hormone cannot replace Oct4 on reprogramming, but in the presence of T3 is possible to obtain iPSCs, although with low efficiency, without exogenous Klf4. Furthermore, depletion of the corepressor NCoR (or Nuclear Receptor Corepressor 1) reduces MEFs reprogramming in the absence of the hormone and strongly decreases iPSC generation by T3 and also by 9cis-retinoic acid, a well-known inducer of reprogramming. NCoR depletion also markedly antagonizes induction of pluripotency gene expression by both ligands. Conclusions Inclusion of T3 on reprogramming strategies has a potential use in enhancing the generation of functional iPSCs for studies of cell plasticity, disease and regenerative medicine.
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Affiliation(s)
- Constanza Contreras-Jurado
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Departamento de Bioquímica, Facultad de Medicina, Universidad Alfonso X El Sabio, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Montero-Pedrazuela
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Raúl F. Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología (CINN), CSIC-UNIOVI-Principado de Asturias, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
- CIBER of Rare Diseases (CIBERER), Oviedo, Spain
| | - Susana Alemany
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Mario F. Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología (CINN), CSIC-UNIOVI-Principado de Asturias, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
- CIBER of Rare Diseases (CIBERER), Oviedo, Spain
| | - Ana Aranda
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
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9
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Sarel-Gallily R, Keshet G, Kinreich S, Haim-Abadi G, Benvenisty N. EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq. Nat Protoc 2023; 18:3881-3917. [PMID: 37914783 DOI: 10.1038/s41596-023-00898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/28/2023] [Indexed: 11/03/2023]
Abstract
Human pluripotent stem cells (hPSCs) hold a central role in studying human development, in disease modeling and in regenerative medicine. These cells not only acquire genetic modifications when kept in culture, but they may also harbor epigenetic aberrations, mainly involving parental imprinting and X-chromosome inactivation. Here we present a detailed bioinformatic protocol for detecting such aberrations using RNA sequencing data. We provide a pipeline designed to process and analyze RNA sequencing data for the identification of abnormal biallelic expression of imprinted genes, and thus detect loss of imprinting. Furthermore, we show how to differentiate among X-chromosome inactivation, full activation and aberrant erosion of X chromosome in female hPSCs. In addition to providing bioinformatic tools, we discuss the impact of such epigenetic variations in hPSCs on their utility for various purposes. This pipeline can be used by any user with basic understanding of the Linux command line. It is available on GitHub as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d.
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Affiliation(s)
- Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Shay Kinreich
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Guy Haim-Abadi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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10
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Verma A, Poondi Krishnan V, Cecere F, D’Angelo E, Lullo V, Strazzullo M, Selig S, Angelini C, Matarazzo MR, Riccio A. ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming. Biomolecules 2023; 13:1717. [PMID: 38136588 PMCID: PMC10741953 DOI: 10.3390/biom13121717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parent-of-origin-dependent gene expression of a few hundred human genes is achieved by differential DNA methylation of both parental alleles. This imprinting is required for normal development, and defects in this process lead to human disease. Induced pluripotent stem cells (iPSCs) serve as a valuable tool for in vitro disease modeling. However, a wave of de novo DNA methylation during reprogramming of iPSCs affects DNA methylation, thus limiting their use. The DNA methyltransferase 3B (DNMT3B) gene is highly expressed in human iPSCs; however, whether the hypermethylation of imprinted loci depends on DNMT3B activity has been poorly investigated. To explore the role of DNMT3B in mediating de novo DNA methylation at imprinted DMRs, we utilized iPSCs generated from patients with immunodeficiency, centromeric instability, facial anomalies type I (ICF1) syndrome that harbor biallelic hypomorphic DNMT3B mutations. Using a whole-genome array-based approach, we observed a gain of methylation at several imprinted loci in control iPSCs but not in ICF1 iPSCs compared to their parental fibroblasts. Moreover, in corrected ICF1 iPSCs, which restore DNMT3B enzymatic activity, imprinted DMRs did not acquire control DNA methylation levels, in contrast to the majority of the hypomethylated CpGs in the genome that were rescued in the corrected iPSC clones. Overall, our study indicates that DNMT3B is responsible for de novo methylation of a subset of imprinted DMRs during iPSC reprogramming and suggests that imprinting is unstable during a specific time window of this process, after which the epigenetic state at these regions becomes resistant to perturbation.
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Affiliation(s)
- Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Emilia D’Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Vincenzo Lullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel;
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy;
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
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11
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Poulet A, Kratkiewicz AJ, Li D, van Wolfswinkel JC. Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy. SCIENCE ADVANCES 2023; 9:eadh4887. [PMID: 37801496 PMCID: PMC10558129 DOI: 10.1126/sciadv.adh4887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/05/2023] [Indexed: 10/08/2023]
Abstract
Many highly regenerative organisms maintain adult pluripotent stem cells throughout their life, but how the long-term maintenance of pluripotency is accomplished is unclear. To decipher the regulatory logic of adult pluripotent stem cells, we analyzed the chromatin organization of stem cell genes in the planarian Schmidtea mediterranea. We identify a special chromatin state of stem cell genes, which is distinct from that of tissue-specific genes and resembles constitutive genes. Where tissue-specific promoters have detectable transcription factor binding sites, the promoters of stem cell-specific genes instead have sequence features that broadly decrease nucleosome binding affinity. This genic organization makes pluripotency-related gene expression the default state in these cells, which is maintained by the activity of chromatin remodelers ISWI and SNF2 in the stem cells.
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Affiliation(s)
- Axel Poulet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Arcadia J. Kratkiewicz
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Danyan Li
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Josien C. van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Yale Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06511, USA
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12
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Pera MF. Seven days in the life cycle of Homo sapiens. Cell 2023; 186:3755-3757. [PMID: 37657417 DOI: 10.1016/j.cell.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 09/03/2023]
Abstract
The second week of embryonic development is a critical phase of the human life cycle and one that has been largely inaccessible to scientific investigation. Recent studies of human embryo models built from stem cells promise to yield dramatic insights into the key events of cell specification and morphogenesis that occur during this brief window of embryogenesis.
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13
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Patterson B, Yang B, Tanaka Y, Kim KY, Cakir B, Xiang Y, Kim J, Wang S, Park IH. Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. SCIENCE ADVANCES 2023; 9:eadf2245. [PMID: 37540754 PMCID: PMC10403202 DOI: 10.1126/sciadv.adf2245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/06/2023] [Indexed: 08/06/2023]
Abstract
Three-dimensional (3D) genomics shows immense promise for studying X chromosome inactivation (XCI) by interrogating changes to the X chromosomes' 3D states. Here, we sought to characterize the 3D state of the X chromosome in naïve and primed human pluripotent stem cells (hPSCs). Using chromatin tracing, we analyzed X chromosome folding conformations in these cells with megabase genomic resolution. X chromosomes in female naïve hPSCs exhibit folding conformations similar to the active X chromosome (Xa) and the inactive X chromosome (Xi) in somatic cells. However, naïve X chromosomes do not exhibit the chromatin compaction typically associated with these somatic X chromosome states. In H7 naïve human embryonic stem cells, XIST accumulation observed on damaged X chromosomes demonstrates the potential for naïve hPSCs to activate XCI-related mechanisms. Overall, our findings provide insight into the X chromosome status of naïve hPSCs with a single-chromosome resolution and are critical in understanding the unique epigenetic regulation in early embryonic cells.
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Affiliation(s)
- Benjamin Patterson
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bing Yang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yangfei Xiang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Siyuan Wang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
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14
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Jiang F, Wang L, Dong Y, Nie W, Zhou H, Gao J, Zheng P. DPPA5A suppresses the mutagenic TLS and MMEJ pathways by modulating the cryptic splicing of Rev1 and Polq in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2023; 120:e2305187120. [PMID: 37459543 PMCID: PMC10372678 DOI: 10.1073/pnas.2305187120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Genetic alterations are often acquired during prolonged propagation of pluripotent stem cells (PSCs). This ruins the stem cell quality and hampers their full applications. Understanding how PSCs maintain genomic integrity would provide the clues to overcome the hurdle. It has been known that embryonic stem cells (ESCs) utilize high-fidelity pathways to ensure genomic stability, but the underlying mechanisms remain largely elusive. Here, we show that many DNA damage response and repair genes display differential alternative splicing in mouse ESCs compared to differentiated cells. Particularly, Rev1 and Polq, two key genes for mutagenic translesion DNA synthesis (TLS) and microhomology-mediated end joining (MMEJ) repair pathways, respectively, display a significantly higher rate of cryptic exon (CE) inclusion in ESCs. The frequent CE inclusion disrupts the normal protein expressions of REV1 and POLθ, thereby suppressing the mutagenic TLS and MMEJ. Further, we identify an ESC-specific RNA binding protein DPPA5A which stimulates the CE inclusion in Rev1 and Polq. Depletion of DPPA5A in mouse ESCs decreased the CE inclusion of Rev1 and Polq, induced the protein expression, and stimulated the TLS and MMEJ activity. Enforced expression of DPPA5A in NIH3T3 cells displayed reverse effects. Mechanistically, we found that DPPA5A directly regulated CE splicing of Rev1. DPPA5A associates with U2 small nuclear ribonucleoprotein of the spliceosome and binds to the GA-rich motif in the CE of Rev1 to promote CE inclusion. Thus, our study uncovers a mechanism to suppress mutagenic TLS and MMEJ pathways in ESCs.
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Affiliation(s)
- Fangjie Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- University of Chinese Academy of Sciences, Beijing101408, China
- Department of Reproductive Medicine, The Second Affiliated Hospital of Kunming Medical University,Kunming650101, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Yuping Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- University of Chinese Academy of Sciences, Beijing101408, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Hu Zhou
- Department of Analytical Chemistry and Key Laboratory of Receptor Research of Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Jing Gao
- Department of Analytical Chemistry and Key Laboratory of Receptor Research of Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- The Chinese University of Hong Kong and Kunming Institute of Zoology Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
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15
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Rosner M, Horer S, Feichtinger M, Hengstschläger M. Multipotent fetal stem cells in reproductive biology research. Stem Cell Res Ther 2023; 14:157. [PMID: 37287077 DOI: 10.1186/s13287-023-03379-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/16/2023] [Indexed: 06/09/2023] Open
Abstract
Due to the limited accessibility of the in vivo situation, the scarcity of the human tissue, legal constraints, and ethical considerations, the underlying molecular mechanisms of disorders, such as preeclampsia, the pathological consequences of fetomaternal microchimerism, or infertility, are still not fully understood. And although substantial progress has already been made, the therapeutic strategies for reproductive system diseases are still facing limitations. In the recent years, it became more and more evident that stem cells are powerful tools for basic research in human reproduction and stem cell-based approaches moved into the center of endeavors to establish new clinical concepts. Multipotent fetal stem cells derived from the amniotic fluid, amniotic membrane, chorion leave, Wharton´s jelly, or placenta came to the fore because they are easy to acquire, are not associated with ethical concerns or covered by strict legal restrictions, and can be banked for autologous utilization later in life. Compared to adult stem cells, they exhibit a significantly higher differentiation potential and are much easier to propagate in vitro. Compared to pluripotent stem cells, they harbor less mutations, are not tumorigenic, and exhibit low immunogenicity. Studies on multipotent fetal stem cells can be invaluable to gain knowledge on the development of dysfunctional fetal cell types, to characterize the fetal stem cells migrating into the body of a pregnant woman in the context of fetomaternal microchimerism, and to obtain a more comprehensive picture of germ cell development in the course of in vitro differentiation experiments. The in vivo transplantation of fetal stem cells or their paracrine factors can mediate therapeutic effects in preeclampsia and can restore reproductive organ functions. Together with the use of fetal stem cell-derived gametes, such strategies could once help individuals, who do not develop functional gametes, to conceive genetically related children. Although there is still a long way to go, these developments regarding the usage of multipotent fetal stem cells in the clinic should continuously be accompanied by a wide and detailed ethical discussion.
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Affiliation(s)
- Margit Rosner
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria
| | - Stefanie Horer
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria
| | | | - Markus Hengstschläger
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria.
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16
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Blair JD, Hartman A, Zenk F, Dalgarno C, Treutlein B, Satija R. Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534442. [PMID: 37034703 PMCID: PMC10081255 DOI: 10.1101/2023.03.27.534442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Cell signaling plays a critical role in regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. Here we present Phospho-seq, an integrated approach that aims to quantify phosphorylated intracellular and intranuclear proteins, and to connect their activity with cis-regulatory elements and transcriptional targets. We utilize a simplified benchtop antibody conjugation method to create large custom antibody panels for simultaneous protein and scATAC-seq profiling on whole cells, and integrate this information with scRNA-seq datasets via bridge integration. We apply our workflow to cell lines, induced pluripotent stem cells, and 3-month-old brain organoids to demonstrate its broad applicability. We demonstrate that Phospho-seq can define cellular states and trajectories, reconstruct gene regulatory relationships, and characterize the causes and consequences of heterogeneous cell signaling in neurodevelopment.
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Affiliation(s)
- John D. Blair
- New York Genome Center, New York, NY
- New York University, Center for Genomics and Systems Biology, New York, NY
| | | | | | | | | | - Rahul Satija
- New York Genome Center, New York, NY
- New York University, Center for Genomics and Systems Biology, New York, NY
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17
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Du H, Huo Z, Chen Y, Zhao Z, Meng F, Wang X, Liu S, Zhang H, Zhou F, Liu J, Zhang L, Zhou S, Guan Y, Wang X. Induced Pluripotent Stem Cells and Their Applications in Amyotrophic Lateral Sclerosis. Cells 2023; 12:cells12060971. [PMID: 36980310 PMCID: PMC10047679 DOI: 10.3390/cells12060971] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that results in the loss of motor function in the central nervous system (CNS) and ultimately death. The mechanisms underlying ALS pathogenesis have not yet been fully elucidated, and ALS cannot be treated effectively. Most studies have applied animal or single-gene intervention cell lines as ALS disease models, but they cannot accurately reflect the pathological characteristics of ALS. Induced pluripotent stem cells (iPSCs) can be reprogrammed from somatic cells, possessing the ability to self-renew and differentiate into a variety of cells. iPSCs can be obtained from ALS patients with different genotypes and phenotypes, and the genetic background of the donor cells remains unchanged during reprogramming. iPSCs can differentiate into neurons and glial cells related to ALS. Therefore, iPSCs provide an excellent method to evaluate the impact of diseases on ALS patients. Moreover, patient-derived iPSCs are obtained from their own somatic cells, avoiding ethical concerns and posing only a low risk of immune rejection. The iPSC technology creates new hope for ALS treatment. Here, we review recent studies on iPSCs and their applications in disease modeling, drug screening and cell therapy in ALS, with a particular focus on the potential for ALS treatment.
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Affiliation(s)
- Hongmei Du
- Department of Histology and Embryology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
| | - Zijun Huo
- Department of Histology and Embryology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
| | - Yanchun Chen
- Department of Histology and Embryology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
| | - Zhenhan Zhao
- Department of Histology and Embryology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
| | - Fandi Meng
- Department of Histology and Embryology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
| | - Xuemei Wang
- Department of Histology and Embryology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
| | - Shiyue Liu
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
| | - Haoyun Zhang
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
| | - Fenghua Zhou
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
- Department of Pathology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
| | - Jinmeng Liu
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
| | - Lingyun Zhang
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
| | - Shuanhu Zhou
- Harvard Medical School and Harvard Stem Cell Institute, Harvard University, Boston, MA 02115, USA
| | - Yingjun Guan
- Department of Histology and Embryology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
- Neurologic Disorders and Regenerative Repair Laboratory, Weifang Medical University, Weifang 261053, China
| | - Xin Wang
- Harvard Medical School and Harvard Stem Cell Institute, Harvard University, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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18
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Rubio K, Hernández-Cruz EY, Rogel-Ayala DG, Sarvari P, Isidoro C, Barreto G, Pedraza-Chaverri J. Nutriepigenomics in Environmental-Associated Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12030771. [PMID: 36979019 PMCID: PMC10045733 DOI: 10.3390/antiox12030771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Complex molecular mechanisms define our responses to environmental stimuli. Beyond the DNA sequence itself, epigenetic machinery orchestrates changes in gene expression induced by diet, physical activity, stress and pollution, among others. Importantly, nutrition has a strong impact on epigenetic players and, consequently, sustains a promising role in the regulation of cellular responses such as oxidative stress. As oxidative stress is a natural physiological process where the presence of reactive oxygen-derived species and nitrogen-derived species overcomes the uptake strategy of antioxidant defenses, it plays an essential role in epigenetic changes induced by environmental pollutants and culminates in signaling the disruption of redox control. In this review, we present an update on epigenetic mechanisms induced by environmental factors that lead to oxidative stress and potentially to pathogenesis and disease progression in humans. In addition, we introduce the microenvironment factors (physical contacts, nutrients, extracellular vesicle-mediated communication) that influence the epigenetic regulation of cellular responses. Understanding the mechanisms by which nutrients influence the epigenome, and thus global transcription, is crucial for future early diagnostic and therapeutic efforts in the field of environmental medicine.
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Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Estefani Y Hernández-Cruz
- Postgraduate in Biological Sciences, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
| | - Diana G Rogel-Ayala
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | | | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale, Via Paolo Solaroli 17, 28100 Novara, Italy
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
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19
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Silva-Pedrosa R, Salgado AJ, Ferreira PE. Revolutionizing Disease Modeling: The Emergence of Organoids in Cellular Systems. Cells 2023; 12:cells12060930. [PMID: 36980271 PMCID: PMC10047824 DOI: 10.3390/cells12060930] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cellular models have created opportunities to explore the characteristics of human diseases through well-established protocols, while avoiding the ethical restrictions associated with post-mortem studies and the costs associated with researching animal models. The capability of cell reprogramming, such as induced pluripotent stem cells (iPSCs) technology, solved the complications associated with human embryonic stem cells (hESC) usage. Moreover, iPSCs made significant contributions for human medicine, such as in diagnosis, therapeutic and regenerative medicine. The two-dimensional (2D) models allowed for monolayer cellular culture in vitro; however, they were surpassed by the three-dimensional (3D) cell culture system. The 3D cell culture provides higher cell-cell contact and a multi-layered cell culture, which more closely respects cellular morphology and polarity. It is more tightly able to resemble conditions in vivo and a closer approach to the architecture of human tissues, such as human organoids. Organoids are 3D cellular structures that mimic the architecture and function of native tissues. They are generated in vitro from stem cells or differentiated cells, such as epithelial or neural cells, and are used to study organ development, disease modeling, and drug discovery. Organoids have become a powerful tool for understanding the cellular and molecular mechanisms underlying human physiology, providing new insights into the pathogenesis of cancer, metabolic diseases, and brain disorders. Although organoid technology is up-and-coming, it also has some limitations that require improvements.
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Affiliation(s)
- Rita Silva-Pedrosa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga, Portugal
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - António José Salgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Pedro Eduardo Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga, Portugal
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20
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Stojkovic M, Ortuño Guzmán FM, Han D, Stojkovic P, Dopazo J, Stankovic KM. Polystyrene nanoplastics affect transcriptomic and epigenomic signatures of human fibroblasts and derived induced pluripotent stem cells: Implications for human health. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 320:120849. [PMID: 36509347 DOI: 10.1016/j.envpol.2022.120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Plastic pollution is increasing at an alarming rate yet the impact of this pollution on human health is poorly understood. Because human induced pluripotent stem cells (hiPSC) are frequently derived from dermal fibroblasts, these cells offer a powerful platform for the identification of molecular biomarkers of environmental pollution in human cells. Here, we describe a novel proof-of-concept for deriving hiPSC from human dermal fibroblasts deliberately exposed to polystyrene (PS) nanoplastic particles; unexposed hiPSC served as controls. In parallel, unexposed hiPSC were exposed to low and high concentrations of PS nanoparticles. Transcriptomic and epigenomic signatures of all fibroblasts and hiPSCs were defined using RNA-seq and whole genome methyl-seq, respectively. Both PS-treated fibroblasts and derived hiPSC showed alterations in expression of ESRRB and HNF1A genes and circuits involved in the pluripotency of stem cells, as well as in pathways involved in cancer, inflammatory disorders, gluconeogenesis, carbohydrate metabolism, innate immunity, and dopaminergic synapse. Similarly, the expression levels of identified key transcriptional and DNA methylation changes (DNMT3A, ESSRB, FAM133CP, HNF1A, SEPTIN7P8, and TTC34) were significantly affected in both PS-exposed fibroblasts and hiPSC. This study illustrates the power of human cellular models of environmental pollution to narrow down and prioritize the list of candidate molecular biomarkers of environmental pollution. This knowledge will facilitate the deciphering of the origins of environmental diseases.
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Affiliation(s)
| | | | - Dongjun Han
- Otolaryngology - Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Joaquin Dopazo
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain; Bioinformatics in Rare Diseases (BiER), Centro de Investigaciones Biomédicas en Reden Enfermedades Raras (CIBERER), Seville, Spain; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen Del Rocío, Seville, Spain
| | - Konstantina M Stankovic
- Otolaryngology - Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA.
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21
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Takahashi Y, Morales Valencia M, Yu Y, Ouchi Y, Takahashi K, Shokhirev MN, Lande K, Williams AE, Fresia C, Kurita M, Hishida T, Shojima K, Hatanaka F, Nuñez-Delicado E, Esteban CR, Izpisua Belmonte JC. Transgenerational inheritance of acquired epigenetic signatures at CpG islands in mice. Cell 2023; 186:715-731.e19. [PMID: 36754048 DOI: 10.1016/j.cell.2022.12.047] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/19/2022] [Accepted: 12/29/2022] [Indexed: 02/10/2023]
Abstract
Transgenerational epigenetic inheritance in mammals remains a debated subject. Here, we demonstrate that DNA methylation of promoter-associated CpG islands (CGIs) can be transmitted from parents to their offspring in mice. We generated DNA methylation-edited mouse embryonic stem cells (ESCs), in which CGIs of two metabolism-related genes, the Ankyrin repeat domain 26 and the low-density lipoprotein receptor, were specifically methylated and silenced. DNA methylation-edited mice generated by microinjection of the methylated ESCs exhibited abnormal metabolic phenotypes. Acquired methylation of the targeted CGI and the phenotypic traits were maintained and transmitted across multiple generations. The heritable CGI methylation was subjected to reprogramming in parental PGCs and subsequently reestablished in the next generation at post-implantation stages. These observations provide a concrete step toward demonstrating transgenerational epigenetic inheritance in mammals, which may have implications in our understanding of evolutionary biology as well as the etiology, diagnosis, and prevention of non-genetically inherited human diseases.
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Affiliation(s)
- Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Mariana Morales Valencia
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Yang Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yasuo Ouchi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuou-ku, Chiba 260-8670, Japan
| | - Kazuki Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Maxim Nikolaievich Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kathryn Lande
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - April E Williams
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chiara Fresia
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Masakazu Kurita
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Plastic, Reconstructive and Aesthetic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shitibancho, Wakayama, Wakayama, Japan
| | - Kensaku Shojima
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fumiyuki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Estrella Nuñez-Delicado
- Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, no. 135 Guadalupe 30107, Murcia, Spain
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA.
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22
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Transition from Animal-Based to Human Induced Pluripotent Stem Cells (iPSCs)-Based Models of Neurodevelopmental Disorders: Opportunities and Challenges. Cells 2023; 12:cells12040538. [PMID: 36831205 PMCID: PMC9954744 DOI: 10.3390/cells12040538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) arise from the disruption of highly coordinated mechanisms underlying brain development, which results in impaired sensory, motor and/or cognitive functions. Although rodent models have offered very relevant insights to the field, the translation of findings to clinics, particularly regarding therapeutic approaches for these diseases, remains challenging. Part of the explanation for this failure may be the genetic differences-some targets not being conserved between species-and, most importantly, the differences in regulation of gene expression. This prompts the use of human-derived models to study NDDS. The generation of human induced pluripotent stem cells (hIPSCs) added a new suitable alternative to overcome species limitations, allowing for the study of human neuronal development while maintaining the genetic background of the donor patient. Several hIPSC models of NDDs already proved their worth by mimicking several pathological phenotypes found in humans. In this review, we highlight the utility of hIPSCs to pave new paths for NDD research and development of new therapeutic tools, summarize the challenges and advances of hIPSC-culture and neuronal differentiation protocols and discuss the best way to take advantage of these models, illustrating this with examples of success for some NDDs.
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23
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Maintenance of methylation profile in imprinting control regions in human induced pluripotent stem cells. Clin Epigenetics 2022; 14:190. [PMID: 36578048 PMCID: PMC9798676 DOI: 10.1186/s13148-022-01410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/14/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Parental imprinting is an epigenetic mechanism that leads to monoallelic expression of a subset of genes depending on their parental origin. Imprinting disorders (IDs), caused by disturbances of imprinted genes, are a set of rare congenital diseases that mainly affect growth, metabolism and development. To date, there is no accurate model to study the physiopathology of IDs or test therapeutic strategies. Human induced pluripotent stem cells (iPSCs) are a promising cellular approach to model human diseases and complex genetic disorders. However, aberrant hypermethylation of imprinting control regions (ICRs) may appear during the reprogramming process and subsequent culture of iPSCs. Therefore, we tested various conditions of reprogramming and culture of iPSCs and performed an extensive analysis of methylation marks at the ICRs to develop a cellular model that can be used to study IDs. RESULTS We assessed the methylation levels at seven imprinted loci in iPSCs before differentiation, at various passages of cell culture, and during chondrogenic differentiation. Abnormal methylation levels were found, with hypermethylation at 11p15 H19/IGF2:IG-DMR and 14q32 MEG3/DLK1:IG-DMR, independently of the reprogramming method and cells of origin. Hypermethylation at these two loci led to the loss of parental imprinting (LOI), with biallelic expression of the imprinted genes IGF2 and DLK1, respectively. The epiPS™ culture medium combined with culturing of the cells under hypoxic conditions prevented hypermethylation at H19/IGF2:IG-DMR (ICR1) and MEG3/DLK1:IG-DMR, as well as at other imprinted loci, while preserving the proliferation and pluripotency qualities of these iPSCs. CONCLUSIONS An extensive and quantitative analysis of methylation levels of ICRs in iPSCs showed hypermethylation of certain ICRs in human iPSCs, especially paternally methylated ICRs, and subsequent LOI of certain imprinted genes. The epiPS™ culture medium and culturing of the cells under hypoxic conditions prevented hypermethylation of ICRs in iPSCs. We demonstrated that the reprogramming and culture in epiPS™ medium allow the generation of control iPSCs lines with a balanced methylation and ID patient iPSCs lines with unbalanced methylation. Human iPSCs are therefore a promising cellular model to study the physiopathology of IDs and test therapies in tissues of interest.
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24
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Jin Y, Kim H, Min S, Choi YS, Seo SJ, Jeong E, Kim SK, Lee HA, Jo SH, Park JH, Park BW, Sim WS, Kim JJ, Ban K, Kim YG, Park HJ, Cho SW. Three-dimensional heart extracellular matrix enhances chemically induced direct cardiac reprogramming. SCIENCE ADVANCES 2022; 8:eabn5768. [PMID: 36516259 PMCID: PMC9750148 DOI: 10.1126/sciadv.abn5768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 11/12/2022] [Indexed: 06/17/2023]
Abstract
Direct cardiac reprogramming has emerged as a promising therapeutic approach for cardiac regeneration. Full chemical reprogramming with small molecules to generate cardiomyocytes may be more amenable than genetic reprogramming for clinical applications as it avoids safety concerns associated with genetic manipulations. However, challenges remain regarding low conversion efficiency and incomplete cardiomyocyte maturation. Furthermore, the therapeutic potential of chemically induced cardiomyocytes (CiCMs) has not been investigated. Here, we report that a three-dimensional microenvironment reconstituted with decellularized heart extracellular matrix can enhance chemical reprogramming and cardiac maturation of fibroblasts to cardiomyocytes. The resultant CiCMs exhibit elevated cardiac marker expression, sarcomeric organization, and improved electrophysiological features and drug responses. We investigated the therapeutic potential of CiCMs reprogrammed in three-dimensional heart extracellular matrix in a rat model of myocardial infarction. Our platform can facilitate the use of CiCMs for regenerative medicine, disease modeling, and drug screening.
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Affiliation(s)
- Yoonhee Jin
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Department of Physiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyeok Kim
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sungjin Min
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yi Sun Choi
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Seung Ju Seo
- Department of Physiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Eunseon Jeong
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Su Kyeom Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyang-Ae Lee
- Korea Institute of Toxicology, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea
| | - Jae-Hyun Park
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Bong-Woo Park
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Woo-Sup Sim
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jin-Ju Kim
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Kiwon Ban
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon 999077, Hong Kong
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea
| | - Hun-Jun Park
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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25
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Andrews PW, Barbaric I, Benvenisty N, Draper JS, Ludwig T, Merkle FT, Sato Y, Spits C, Stacey GN, Wang H, Pera MF. The consequences of recurrent genetic and epigenetic variants in human pluripotent stem cells. Cell Stem Cell 2022; 29:1624-1636. [PMID: 36459966 DOI: 10.1016/j.stem.2022.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
It is well established that human pluripotent stem cells (hPSCs) can acquire genetic and epigenetic changes during culture in vitro. Given the increasing use of hPSCs in research and therapy and the vast expansion in the number of hPSC lines available for researchers, the International Society for Stem Cell Research has recognized the need to reassess quality control standards for ensuring the genetic integrity of hPSCs. Here, we summarize current knowledge of the nature of recurrent genetic and epigenetic variants in hPSC culture, the methods for their detection, and what is known concerning their effects on cell behavior in vitro or in vivo. We argue that the potential consequences of low-level contamination of cell therapy products with cells bearing oncogenic variants are essentially unknown at present. We highlight the key challenges facing the field with particular reference to safety assessment of hPSC-derived cellular therapeutics.
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Affiliation(s)
- Peter W Andrews
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; Steering Committee, International Stem Cell Initiative
| | - Jonathan S Draper
- Stem Cell Network, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Steering Committee, International Stem Cell Initiative
| | - Tenneille Ludwig
- WiCell Research Institute, Madison, WI, USA; University of Wisconsin-Madison, Madison, WI 53719, USA; Steering Committee, International Stem Cell Initiative
| | - Florian T Merkle
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0QQ, UK; Steering Committee, International Stem Cell Initiative
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki Ward, Kawasaki City, Kanagawa 210-9501, Japan; Steering Committee, International Stem Cell Initiative
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; Steering Committee, International Stem Cell Initiative
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High Street, Barley, UK; National Stem Cell Resource Centre, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100190, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China; Steering Committee, International Stem Cell Initiative
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China; Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China; Steering Committee, International Stem Cell Initiative
| | - Martin F Pera
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; Steering Committee, International Stem Cell Initiative.
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26
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Epigenetic Regulation of Methylation in Determining the Fate of Dental Mesenchymal Stem Cells. Stem Cells Int 2022; 2022:5015856. [PMID: 36187229 PMCID: PMC9522499 DOI: 10.1155/2022/5015856] [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: 04/10/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Dental mesenchymal stem cells (DMSCs) are crucial in tooth development and periodontal health, and their multipotential differentiation and self-renewal ability play a critical role in tissue engineering and regenerative medicine. Methylation modifications could promote the appropriate biological behavior by postsynthetic modification of DNA or protein and make the organism adapt to developmental and environmental prompts by regulating gene expression without changing the DNA sequence. Methylation modifications involved in DMSC fate include DNA methylation, RNA methylation, and histone modifications, which have been proven to exert a significant effect on the regulation of the fate of DMSCs, such as proliferation, self-renewal, and differentiation potential. Understanding the regulation of methylation modifications on the behavior and the immunoinflammatory responses involved in DMSCs contributes to further study of the mechanism of methylation on tissue regeneration and inflammation. In this review, we briefly summarize the key functions of histone methylation, RNA methylation, and DNA methylation in the differentiation potential and self-renewal of DMSCs as well as the opportunities and challenges for their application in tissue regeneration and disease therapy.
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27
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Liu Y, Xu Z, Shi J, Zhang Y, Yang S, Chen Q, Song C, Geng S, Li Q, Li J, Xu GL, Xie W, Lin H, Li X. DNA methyltransferases are complementary in maintaining DNA methylation in embryonic stem cells. iScience 2022; 25:105003. [PMID: 36117996 PMCID: PMC9478929 DOI: 10.1016/j.isci.2022.105003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Abstract
ZFP57 and ZFP445 maintain genomic imprinting in mouse embryos. We found DNA methylation was lost at most examined imprinting control regions (ICRs) in mouse Zfp57 mutant ES cells, which could not be prevented by the elimination of three TET proteins. To elucidate methylation maintenance mechanisms, we generated mutant ES clones lacking three major DNA methyltransferases (DNMTs). Intriguingly, DNMT3A and DNMT3B were essential for DNA methylation at a subset of ICRs in mouse ES cells although DNMT1 maintained DNA methylation at most known ICRs. These were similarly observed after extended culture. Germline-derived DNA methylation was lost at the examined ICRs lacking DNMTs according to allelic analysis. Similar to DNMT1, DNMT3A and DNMT3B were required for maintaining DNA methylation at repeats, genic regions, and other genomic sequences. Therefore, three DNA methyltransferases play complementary roles in maintaining DNA methylation in mouse ES cells including DNA methylation at the ICRs primarily mediated through the ZFP57-dependent pathway. ZFP57 maintains DNA methylation at the ICR of most imprinted regions in ES cells TET proteins may not be essential for maintaining most ICR DNA methylation in ES cells DNMT3 is required for the maintenance of DNA methylation at a subset of ICRs in ES cells Maintenance functions of DNMT1 and DNMT3 are complementary at repeats and genic regions
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Affiliation(s)
- Yuhan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiajia Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200032, China
| | - Shuting Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qian Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chenglin Song
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuhui Geng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qing Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinsong Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Liang Xu
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haodong Lin
- Department of Orthopedic Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Shanghai 200080, China
| | - Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Genome Editing Center, ShanghaiTech University, Shanghai 201210, China
- Corresponding author
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Kaye J, Reisine T, Finkbeiner S. Huntington's disease iPSC models-using human patient cells to understand the pathology caused by expanded CAG repeats. Fac Rev 2022; 11:16. [PMID: 35865413 PMCID: PMC9264339 DOI: 10.12703/r/11-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A major advance in the study of Huntington's disease (HD) has been the development of human disease models employing induced pluripotent stem cells (iPSCs) derived from patients with HD. Because iPSCs provide an unlimited source of cells and can be obtained from large numbers of HD patients, they are a uniquely valuable tool for investigating disease mechanisms and for discovering potential disease-modifying therapeutics. Here, we summarize some of the important findings in HD pathophysiology that have emerged from studies of patient-derived iPSC lines. Because they retain the genome and actual disease mutations of the patient, they provide a cell source to investigate genetic contributions to the disease. iPSCs provide advantages over other disease models. While iPSC-based technology erases some epigenetic marks, newly developed transdifferentiation methods now let us investigate epigenetic factors that control expression of mutant huntingtin (mHTT). Human HD iPSC lines allow us to investigate how endogenous levels of mHTT affect cell health, in contrast to other models that often rely on overexpressing the protein. iPSCs can be differentiated into neurons and other disease-related cells such as astrocytes from different brain regions to study brain regional differences in the disease process, as well as the cell-cell dependencies involved in HD-associated neurodegeneration. They also serve as a tissue source to investigate factors that impact CAG repeat instability, which is involved in regional differences in neurodegeneration in the HD brain. Human iPSC models can serve as a powerful model system to identify genetic modifiers that may impact disease onset, progression, and symptomatology, providing novel molecular targets for drug discovery.
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Affiliation(s)
- Julia Kaye
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Terry Reisine
- Independent Scientific Consultant, Santa Cruz, CA, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology and Physiology, University of California, San Francisco, CA, USA
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Carotenuto F, Politi S, Ul Haq A, De Matteis F, Tamburri E, Terranova ML, Teodori L, Pasquo A, Di Nardo P. From Soft to Hard Biomimetic Materials: Tuning Micro/Nano-Architecture of Scaffolds for Tissue Regeneration. MICROMACHINES 2022; 13:mi13050780. [PMID: 35630247 PMCID: PMC9144100 DOI: 10.3390/mi13050780] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 03/30/2022] [Accepted: 05/13/2022] [Indexed: 11/23/2022]
Abstract
Failure of tissues and organs resulting from degenerative diseases or trauma has caused huge economic and health concerns around the world. Tissue engineering represents the only possibility to revert this scenario owing to its potential to regenerate or replace damaged tissues and organs. In a regeneration strategy, biomaterials play a key role promoting new tissue formation by providing adequate space for cell accommodation and appropriate biochemical and biophysical cues to support cell proliferation and differentiation. Among other physical cues, the architectural features of the biomaterial as a kind of instructive stimuli can influence cellular behaviors and guide cells towards a specific tissue organization. Thus, the optimization of biomaterial micro/nano architecture, through different manufacturing techniques, is a crucial strategy for a successful regenerative therapy. Over the last decades, many micro/nanostructured biomaterials have been developed to mimic the defined structure of ECM of various soft and hard tissues. This review intends to provide an overview of the relevant studies on micro/nanostructured scaffolds created for soft and hard tissue regeneration and highlights their biological effects, with a particular focus on striated muscle, cartilage, and bone tissue engineering applications.
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Affiliation(s)
- Felicia Carotenuto
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy;
- Department of Fusion and Technologies for Nuclear Safety and Security, Diagnostic and Metrology (FSN-TECFIS-DIM), ENEA, CR Frascati, 00044 Rome, Italy; (S.P.); (L.T.); (A.P.)
- Centro di Ricerca Interdipartimentale di Medicina Rigenerativa (CIMER), Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (F.D.M.); (E.T.); (M.L.T.)
- Correspondence: (F.C.); (P.D.N.)
| | - Sara Politi
- Department of Fusion and Technologies for Nuclear Safety and Security, Diagnostic and Metrology (FSN-TECFIS-DIM), ENEA, CR Frascati, 00044 Rome, Italy; (S.P.); (L.T.); (A.P.)
- Dipartimento di Scienze e Tecnologie Chimiche, Università Degli Studi di Roma “Tor Vergata”, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Arsalan Ul Haq
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy;
- Centro di Ricerca Interdipartimentale di Medicina Rigenerativa (CIMER), Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (F.D.M.); (E.T.); (M.L.T.)
| | - Fabio De Matteis
- Centro di Ricerca Interdipartimentale di Medicina Rigenerativa (CIMER), Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (F.D.M.); (E.T.); (M.L.T.)
- Dipartimento Ingegneria Industriale, Università Degli Studi di Roma “Tor Vergata”, Via del Politecnico, 00133 Roma, Italy
| | - Emanuela Tamburri
- Centro di Ricerca Interdipartimentale di Medicina Rigenerativa (CIMER), Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (F.D.M.); (E.T.); (M.L.T.)
- Dipartimento di Scienze e Tecnologie Chimiche, Università Degli Studi di Roma “Tor Vergata”, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Maria Letizia Terranova
- Centro di Ricerca Interdipartimentale di Medicina Rigenerativa (CIMER), Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (F.D.M.); (E.T.); (M.L.T.)
- Dipartimento di Scienze e Tecnologie Chimiche, Università Degli Studi di Roma “Tor Vergata”, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Laura Teodori
- Department of Fusion and Technologies for Nuclear Safety and Security, Diagnostic and Metrology (FSN-TECFIS-DIM), ENEA, CR Frascati, 00044 Rome, Italy; (S.P.); (L.T.); (A.P.)
- Centro di Ricerca Interdipartimentale di Medicina Rigenerativa (CIMER), Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (F.D.M.); (E.T.); (M.L.T.)
| | - Alessandra Pasquo
- Department of Fusion and Technologies for Nuclear Safety and Security, Diagnostic and Metrology (FSN-TECFIS-DIM), ENEA, CR Frascati, 00044 Rome, Italy; (S.P.); (L.T.); (A.P.)
| | - Paolo Di Nardo
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy;
- Centro di Ricerca Interdipartimentale di Medicina Rigenerativa (CIMER), Università Degli Studi di Roma “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (F.D.M.); (E.T.); (M.L.T.)
- Correspondence: (F.C.); (P.D.N.)
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Cloutier M, Kumar S, Buttigieg E, Keller L, Lee B, Williams A, Mojica-Perez S, Erliandri I, Rocha AMD, Cadigan K, Smith GD, Kalantry S. Preventing erosion of X-chromosome inactivation in human embryonic stem cells. Nat Commun 2022; 13:2516. [PMID: 35523820 PMCID: PMC9076865 DOI: 10.1038/s41467-022-30259-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
X-chromosome inactivation is a paradigm of epigenetic transcriptional regulation. Female human embryonic stem cells (hESCs) often undergo erosion of X-inactivation upon prolonged culture. Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines. We find that culture media composition dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation. hESCs cultured in a defined xenofree medium stably maintained XIST RNA expression and coating, whereas hESCs cultured in the widely used mTeSR1 medium lost XIST RNA expression. We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss. The addition of lithium chloride or inhibitors of GSK-3 proteins that are targeted by lithium to the defined hESC culture medium impeded XIST RNA expression. GSK-3 inhibition in differentiating female mouse embryonic stem cells and epiblast stem cells also resulted in a loss of XIST RNA expression. Together, these data may reconcile observed variations in X-inactivation in hESCs and inform the faithful culture of pluripotent stem cells.
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Affiliation(s)
- Marissa Cloutier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laura Keller
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brandon Lee
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Aaron Williams
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sandra Mojica-Perez
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Indri Erliandri
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Andre Monteiro Da Rocha
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine & Cardiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Cadigan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Gary D Smith
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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31
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Giabicani E, Pham A, Sélénou C, Sobrier ML, Andrique C, Lesieur J, Linglart A, Poliard A, Chaussain C, Netchine I. Dental pulp stem cells as a promising model to study imprinting diseases. Int J Oral Sci 2022; 14:19. [PMID: 35368018 PMCID: PMC8976849 DOI: 10.1038/s41368-022-00169-1] [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: 11/12/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Parental imprinting is an epigenetic process leading to monoallelic expression of certain genes depending on their parental origin. Imprinting diseases are characterized by growth and metabolic issues starting from birth to adulthood. They are mainly due to methylation defects in imprinting control region that drive the abnormal expression of imprinted genes. We currently lack relevant animal or cellular models to unravel the pathophysiology of growth failure in these diseases. We aimed to characterize the methylation of imprinting regions in dental pulp stem cells and during their differentiation in osteogenic cells (involved in growth regulation) to assess the interest of this cells in modeling imprinting diseases. We collected dental pulp stem cells from five controls and four patients (three with Silver-Russell syndrome and one with Beckwith-Wiedemann syndrome). Methylation analysis of imprinting control regions involved in these syndromes showed a normal profile in controls and the imprinting defect in patients. These results were maintained in dental pulp stem cells cultured under osteogenic conditions. Furthermore, we confirmed the same pattern in six other loci involved in imprinting diseases in humans. We also confirmed monoallelic expression of H19 (an imprinted gene) in controls and its biallelic expression in one patient. Extensive imprinting control regions methylation analysis shows the strong potential of dental pulp stem cells in modeling imprinting diseases, in which imprinting regions are preserved in culture and during osteogenic differentiation. This will allow to perform in vitro functional and therapeutic tests in cells derived from dental pulp stem cells and generate other cell-types.
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Artificial Oocyte: Development and Potential Application. Cells 2022; 11:cells11071135. [PMID: 35406698 PMCID: PMC8998074 DOI: 10.3390/cells11071135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 02/07/2023] Open
Abstract
Millions of people around the world suffer from infertility, with the number of infertile couples and individuals increasing every year. Assisted reproductive technologies (ART) have been widely developed in recent years; however, some patients are unable to benefit from these technologies due to their lack of functional germ cells. Therefore, the development of alternative methods seems necessary. One of these methods is to create artificial oocytes. Oocytes can be generated in vitro from the ovary, fetal gonad, germline stem cells (GSCs), ovarian stem cells, or pluripotent stem cells (PSCs). This approach has raised new hopes in both basic research and medical applications. In this article, we looked at the principle of oocyte development, the landmark studies that enhanced our understanding of the cellular and molecular mechanisms that govern oogenesis in vivo, as well as the mechanisms underlying in vitro generation of functional oocytes from different sources of mouse and human stem cells. In addition, we introduced next-generation ART using somatic cells with artificial oocytes. Finally, we provided an overview of the reproductive application of in vitro oogenesis and its use in human fertility.
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Xu Z, Shi J, Zhang Y, Liu Y, Zhao J, Chen Q, Song C, Geng S, Xie W, Wu F, Bai Y, Yang Y, Li X. Zfp57 Exerts Maternal and Sexually Dimorphic Effects on Genomic Imprinting. Front Cell Dev Biol 2022; 10:784128. [PMID: 35252168 PMCID: PMC8895500 DOI: 10.3389/fcell.2022.784128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/04/2022] [Indexed: 12/05/2022] Open
Abstract
Zfp57 has both maternal and zygotic functions in mouse. It maintains genomic imprinting at most known imprinted regions and controls allelic expression of the target imprinted genes in mouse embryos. The DNA methylation imprint at many imprinting control regions (ICRs) is lost when both maternal and zygotic Zfp57 are absent in Zfp57 maternal–zygotic mutant mouse embryos. Interestingly, we found that DNA methylation at a few ICRs was partially lost without maternal Zfp57 in Zfp57 heterozygous mouse embryos derived from Zfp57 homozygous female mice. This suggests that maternal Zfp57 is essential for the maintenance of DNA methylation at a small subset of imprinted regions in mouse embryos. This maternal effect of Zfp57 was applied to allelic expression switch as well as expression levels of the corresponding imprinted genes. It is rather surprising that DNA methylation imprint was affected differently at Rasgrf1 and AK008011 imprinted regions in the female or male Zfp57 maternal–zygotic mutant embryos, with more significant loss of DNA methylation observed in the male mutant embryos. Loss of ZFP57 resulted in gender-specific differences in allelic expression switch and expression level changes of some imprinted genes in female or male mutant embryos. These results indicate maternal and sexually dimorphic effects of ZFP57 on genomic imprinting in mouse.
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Affiliation(s)
- Zhen Xu
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Jiajia Shi
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuhan Liu
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Junzheng Zhao
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Qian Chen
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Chenglin Song
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Shuhui Geng
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Feizhen Wu
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Yang Yang
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
- *Correspondence: Xiajun Li,
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Li Y, Darabi R. Role of epigenetics in cellular reprogramming; from iPSCs to disease modeling and cell therapy. J Cell Biochem 2022; 123:147-154. [PMID: 34668236 PMCID: PMC8860854 DOI: 10.1002/jcb.30164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023]
Abstract
Epigenetics play a fundamental role in induced pluripotent stem cell (iPSC) technology due to their effect on iPSC's reprogramming efficiency and their subsequent role in iPSC differentiation toward a specific lineage. Epigenetics can skew the differentiation course of iPSCs toward a specific lineage based on the epigenetic memory of the source cells, or even lead to acquisition of new cell phenotypes, due to its aberrations during reprogramming. This viewpoint discusses key features of the epigenetic process during iPSC reprogramming/differentiation and outlines important epigenetic factors that need to be considered for successful generation and differentiation of iPSCs for downstream applications.
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Affiliation(s)
- Yong Li
- Department of Orthopaedic Surgery, BioMedical Engineering, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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Spathopoulou A, Edenhofer F, Fellner L. Targeting α-Synuclein in Parkinson's Disease by Induced Pluripotent Stem Cell Models. Front Neurol 2022; 12:786835. [PMID: 35145469 PMCID: PMC8821105 DOI: 10.3389/fneur.2021.786835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/24/2021] [Indexed: 11/22/2022] Open
Abstract
Parkinson's disease (PD) is a progressive, neurodegenerative disorder characterized by motor and non-motor symptoms. To date, no specific treatment to halt disease progression is available, only medication to alleviate symptoms can be prescribed. The main pathological hallmark of PD is the development of neuronal inclusions, positive for α-synuclein (α-syn), which are termed Lewy bodies (LBs) or Lewy neurites. However, the cause of the inclusion formation and the loss of neurons remain largely elusive. Various genetic determinants were reported to be involved in PD etiology, including SNCA, DJ-1, PRKN, PINK1, LRRK2, and GBA. Comprehensive insights into pathophysiology of PD critically depend on appropriate models. However, conventional model organisms fall short to faithfully recapitulate some features of this complex disease and as a matter-of-fact access to physiological tissue is limiting. The development of disease models replicating PD that are close to human physiology and dynamic enough to analyze the underlying molecular mechanisms of disease initiation and progression, as well as the generation of new treatment options, is an important and overdue step. Recently, the establishment of induced pluripotent stem cell (iPSC)-derived neural models, particularly from genetic PD-variants, developed into a promising strategy to investigate the molecular mechanisms regarding formation of inclusions and neurodegeneration. As these iPSC-derived neurons can be generated from accessible biopsied samples of PD patients, they carry pathological alterations and enable the possibility to analyze the differences compared to healthy neurons. This review focuses on iPSC models carrying genetic PD-variants of α-syn that will be especially helpful in elucidating the pathophysiological mechanisms of PD. Furthermore, we discuss how iPSC models can be instrumental in identifying cellular targets, potentially leading to the development of new therapeutic treatments. We will outline the enormous potential, but also discuss the limitations of iPSC-based α-syn models.
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Ashmore-Harris C, Fruhwirth GO. Generation of In Vivo Traceable Hepatocyte-Like Cells from Human iPSCs. Methods Mol Biol 2022; 2544:15-49. [PMID: 36125708 DOI: 10.1007/978-1-0716-2557-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this chapter, we describe a protocol for differentiation of human-induced pluripotent stem cells (iPSCs) into hepatocyte-like cells (HLCs) and their transduction with a lentivirus for gene transfer. Here, we engineer them to express the human sodium iodide symporter, which can be exploited as a radionuclide reporter gene, thereby enabling these cells to be tracked in vivo by single-photon emission computed tomography (SPECT) or positron emission tomography (PET) imaging. Differentiation of HLCs from iPSCs involves three steps: induction of iPSCs to definitive endoderm, differentiation to a hepatic progenitor cell population, and maturation of immature HLCs. Once proliferation of hepatic progenitors has ceased and an immature HLC population is generated, lentiviral transduction can be performed. The immature hepatic gene expression profile/morphology at the stage of transduction will be compatible with further maturation following transgene expression either in vitro or in vivo, with expression of the transgene retained. We detail how transgenic cells can be imaged in vivo. While we provide a protocol for the NIS reporter gene, the cell engineering aspects of this protocol are transferable for use with other (reporter) genes if desired.
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Affiliation(s)
- Candice Ashmore-Harris
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, UK
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Gilbert O Fruhwirth
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, UK.
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Somatic Reprogramming-Above and Beyond Pluripotency. Cells 2021; 10:cells10112888. [PMID: 34831113 PMCID: PMC8616127 DOI: 10.3390/cells10112888] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells, having long been considered the fountain of youth, have caught the attention of many researchers from diverse backgrounds due to their capacity for unlimited self-renewal and potential to differentiate into all cell types. Over the past 15 years, the advanced development of induced pluripotent stem cells (iPSCs) has displayed an unparalleled potential for regenerative medicine, cell-based therapies, modeling human diseases in culture, and drug discovery. The transcription factor quartet (Oct4, Sox2, Klf4, and c-Myc) reprograms highly differentiated somatic cells back to a pluripotent state recapitulated embryonic stem cells (ESCs) in different aspects, including gene expression profile, epigenetic signature, and functional pluripotency. With the prior fruitful studies in SCNT and cell fusion experiments, iPSC finds its place and implicates that the differentiated somatic epigenome retains plasticity for re-gaining the pluripotency and further stretchability to reach a totipotency-like state. These achievements have revolutionized the concept and created a new avenue in biomedical sciences for clinical applications. With the advent of 15 years’ progress-making after iPSC discovery, this review is focused on how the current concept is established by revisiting those essential landmark studies and summarizing its current biomedical applications status to facilitate the new era entry of regenerative therapy.
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Horánszky A, Becker JL, Zana M, Ferguson-Smith AC, Dinnyés A. Epigenetic Mechanisms of ART-Related Imprinting Disorders: Lessons From iPSC and Mouse Models. Genes (Basel) 2021; 12:genes12111704. [PMID: 34828310 PMCID: PMC8620286 DOI: 10.3390/genes12111704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
The rising frequency of ART-conceived births is accompanied by the need for an improved understanding of the implications of ART on gametes and embryos. Increasing evidence from mouse models and human epidemiological data suggests that ART procedures may play a role in the pathophysiology of certain imprinting disorders (IDs), including Beckwith-Wiedemann syndrome, Silver-Russell syndrome, Prader-Willi syndrome, and Angelman syndrome. The underlying molecular basis of this association, however, requires further elucidation. In this review, we discuss the epigenetic and imprinting alterations of in vivo mouse models and human iPSC models of ART. Mouse models have demonstrated aberrant regulation of imprinted genes involved with ART-related IDs. In the past decade, iPSC technology has provided a platform for patient-specific cellular models of culture-associated perturbed imprinting. However, despite ongoing efforts, a deeper understanding of the susceptibility of iPSCs to epigenetic perturbation is required if they are to be reliably used for modelling ART-associated IDs. Comparing the patterns of susceptibility of imprinted genes in mouse models and IPSCs in culture improves the current understanding of the underlying mechanisms of ART-linked IDs with implications for our understanding of the influence of environmental factors such as culture and hormone treatments on epigenetically important regions of the genome such as imprints.
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Affiliation(s)
- Alex Horánszky
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
| | - Jessica L. Becker
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; (J.L.B.); (A.C.F.-S.)
| | - Melinda Zana
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
| | - Anne C. Ferguson-Smith
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; (J.L.B.); (A.C.F.-S.)
| | - András Dinnyés
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
- HCEMM-USZ Stem Cell Research Group, Hungarian Centre of Excellence for Molecular Medicine, H-6723 Szeged, Hungary
- Department of Cell Biology and Molecular Medicine, University of Szeged, H-6720 Szeged, Hungary
- Correspondence: ; Tel.: +36-20-510-9632; Fax: +36-28-526-151
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39
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Abstract
[Figure: see text].
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Affiliation(s)
- Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.,Department of Germline Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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Miloradovic D, Pavlovic D, Jankovic MG, Nikolic S, Papic M, Milivojevic N, Stojkovic M, Ljujic B. Human Embryos, Induced Pluripotent Stem Cells, and Organoids: Models to Assess the Effects of Environmental Plastic Pollution. Front Cell Dev Biol 2021; 9:709183. [PMID: 34540831 PMCID: PMC8446652 DOI: 10.3389/fcell.2021.709183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/19/2021] [Indexed: 02/03/2023] Open
Abstract
For a long time, animal models were used to mimic human biology and diseases. However, animal models are not an ideal solution due to numerous interspecies differences between humans and animals. New technologies, such as human-induced pluripotent stem cells and three-dimensional (3D) cultures such as organoids, represent promising solutions for replacing, refining, and reducing animal models. The capacity of organoids to differentiate, self-organize, and form specific, complex, biologically suitable structures makes them excellent in vitro models of development and disease pathogenesis, as well as drug-screening platforms. Despite significant potential health advantages, further studies and considerable nuances are necessary before their clinical use. This article summarizes the definition of embryoids, gastruloids, and organoids and clarifies their appliance as models for early development, diseases, environmental pollution, drug screening, and bioinformatics.
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Affiliation(s)
- Dragana Miloradovic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Dragica Pavlovic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Marina Gazdic Jankovic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Sandra Nikolic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Milos Papic
- Department of Dentistry, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Nevena Milivojevic
- Laboratory for Bioengineering, Department of Science, Institute for Information Technologies, University of Kragujevac, Kragujevac, Serbia
| | - Miodrag Stojkovic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
- SPEBO Medical Fertility Hospital, Leskovac, Serbia
| | - Biljana Ljujic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
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41
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Kim MH, Kino-Oka M. Mechanobiological conceptual framework for assessing stem cell bioprocess effectiveness. Biotechnol Bioeng 2021; 118:4537-4549. [PMID: 34460101 DOI: 10.1002/bit.27929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022]
Abstract
Fully realizing the enormous potential of stem cells requires developing efficient bioprocesses and optimizations founded in mechanobiological considerations. Here, we emphasize the importance of mechanotransduction as one of the governing principles of stem cell bioprocesses, underscoring the need to further explore the behavioral mechanisms involved in sensing mechanical cues and coordinating transcriptional responses. We identify the sources of intrinsic, extrinsic, and external noise in bioprocesses requiring further study, and discuss the criteria and indicators that may be used to assess and predict cell-to-cell variability resulting from environmental fluctuations. Specifically, we propose a conceptual framework to explain the impact of mechanical forces within the cellular environment, identify key cell state determinants in bioprocesses, and discuss downstream implementation challenges.
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Affiliation(s)
- Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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42
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Florkowska A, Meszka I, Nowacka J, Granica M, Jablonska Z, Zawada M, Truszkowski L, Ciemerych MA, Grabowska I. PAX7 Balances the Cell Cycle Progression via Regulating Expression of Dnmt3b and Apobec2 in Differentiating PSCs. Cells 2021; 10:2205. [PMID: 34571854 PMCID: PMC8472244 DOI: 10.3390/cells10092205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
PAX7 transcription factor plays a crucial role in embryonic myogenesis and in adult muscles in which it secures proper function of satellite cells, including regulation of their self renewal. PAX7 downregulation is necessary for the myogenic differentiation of satellite cells induced after muscle damage, what is prerequisite step for regeneration. Using differentiating pluripotent stem cells we documented that the absence of functional PAX7 facilitates proliferation. Such action is executed by the modulation of the expression of two proteins involved in the DNA methylation, i.e., Dnmt3b and Apobec2. Increase in Dnmt3b expression led to the downregulation of the CDK inhibitors and facilitated cell cycle progression. Changes in Apobec2 expression, on the other hand, differently impacted proliferation/differentiation balance, depending on the experimental model used.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Iwona Grabowska
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (A.F.); (I.M.); (J.N.); (M.G.); (Z.J.); (M.Z.); (L.T.); (M.A.C.)
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43
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Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis. Nat Protoc 2021; 16:4522-4537. [PMID: 34363070 DOI: 10.1038/s41596-021-00591-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/16/2021] [Indexed: 01/10/2023]
Abstract
Human pluripotent stem cells (hPSCs) are known to acquire genetic aberrations during in vitro propagation. In addition to recurrent chromosomal aberrations, it has recently been shown that these cells also gain point mutations in cancer-related genes, predominantly in TP53. The need for routine quality control of hPSCs is critical for both basic research and clinical applications. Here we discuss the relevance of detecting mutations for various hPSCs applications, and present a detailed protocol to identify cancer-related point mutations using data from RNA sequencing, an assay commonly performed during the growth and differentiation of hPSCs. In this protocol, we describe how to process and align the sequencing data, analyze it and conservatively interpret the results in order to generate an accurate estimation of mutations in tumor-related genes. This pipeline is designed to work in high throughput and is available as a software container at https://github.com/elyadlezmi/RNA2CM . The protocol requires minimal command-line skills and can be carried out in 1-2 d.
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44
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Franek M, Kilar A, Fojtík P, Olšinová M, Benda A, Rotrekl V, Dvořáčková M, Fajkus J. Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations. J Cell Sci 2021; 134:jcs258374. [PMID: 34350964 DOI: 10.1242/jcs.258374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. Although uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques that involve averaging of cell populations or analysis of clusters of tandem repeats in a single-cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context, and thus constitutes an important tool for gaining a complete understanding of the epigenetic organization of genomes. We report that using an optimized fiber extension protocol is essential in order to obtain more reproducible data and to minimize the clustering of fibers. We also demonstrate that the use of super-resolution microscopy is important for reliable evaluation of the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script for the analysis of methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.
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Affiliation(s)
- Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
| | - Petr Fojtík
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Marie Olšinová
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Aleš Benda
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Vladimír Rotrekl
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jíří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
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45
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Abstract
ZFP57 is a master regulator of genomic imprinting. It has both maternal and zygotic functions that are partially redundant in maintaining DNA methylation at some imprinting control regions (ICRs). In this study, we found that DNA methylation was lost at most known ICRs in Zfp57 mutant embryos. Furthermore, loss of ZFP57 caused loss of parent-of-origin-dependent monoallelic expression of the target imprinted genes. The allelic expression switch occurred in the ZFP57 target imprinted genes upon loss of differential DNA methylation at the ICRs in Zfp57 mutant embryos. Specifically, upon loss of ZFP57, the alleles of the imprinted genes located on the same chromosome with the originally methylated ICR switched their expression to mimic their counterparts on the other chromosome with unmethylated ICR. Consistent with our previous study, ZFP57 could regulate the NOTCH signaling pathway in mouse embryos by impacting allelic expression of a few regulators in the NOTCH pathway. In addition, the imprinted Dlk1 gene that has been implicated in the NOTCH pathway was significantly down-regulated in Zfp57 mutant embryos. Our allelic expression switch models apply to the examined target imprinted genes controlled by either maternally or paternally methylated ICRs. Our results support the view that ZFP57 controls imprinted expression of its target imprinted genes primarily through maintaining differential DNA methylation at the ICRs.
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46
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Bansal P, Ahern DT, Kondaveeti Y, Qiu CW, Pinter SF. Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation. Cell Rep 2021; 35:109215. [PMID: 34107261 PMCID: PMC8267460 DOI: 10.1016/j.celrep.2021.109215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/18/2020] [Accepted: 05/13/2021] [Indexed: 01/21/2023] Open
Abstract
Female human pluripotent stem cells (hPSCs) routinely undergo inactive X (Xi) erosion. This progressive loss of key repressive features follows the loss of XIST expression, the long non-coding RNA driving X inactivation, and causes reactivation of silenced genes across the eroding X (Xe). To date, the sporadic and progressive nature of erosion has obscured its scale, dynamics, and key transition events. To address this problem, we perform an integrated analysis of DNA methylation (DNAme), chromatin accessibility, and gene expression across hundreds of hPSC samples. Differential DNAme orders female hPSCs across a trajectory from initiation to terminal Xi erosion. Our results identify a cis-regulatory element crucial for XIST expression, trace contiguously growing reactivated domains to a few euchromatic origins, and indicate that the late-stage Xe impairs DNAme genome-wide. Surprisingly, from this altered regulatory landscape emerge select features of naive pluripotency, suggesting that its link to X dosage may be partially conserved in human embryonic development. Reactivation of the silenced X in human female iPSC/ESCs compromises their utility. Bansal et al. perform an integrated genomics analysis to reveal a prevalent X erosion trajectory that they validate in long-term culture. Starting with XIST loss, this trajectory indicates that reactivation may spread contiguously from escapees to silenced genes.
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Affiliation(s)
- Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Darcy T Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Catherine W Qiu
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Stefan F Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
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47
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Histone Deacetylase Inhibitors Ameliorate Morphological Defects and Hypoexcitability of iPSC-Neurons from Rubinstein-Taybi Patients. Int J Mol Sci 2021; 22:ijms22115777. [PMID: 34071322 PMCID: PMC8197986 DOI: 10.3390/ijms22115777] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 12/13/2022] Open
Abstract
Rubinstein-Taybi syndrome (RSTS) is a rare neurodevelopmental disorder caused by mutations in CREBBP or EP300 genes encoding CBP/p300 lysine acetyltransferases. We investigated the efficacy of the histone deacetylase inhibitor (HDACi) Trichostatin A (TSA) in ameliorating morphological abnormalities of iPSC-derived young neurons from P149 and P34 CREBBP-mutated patients and hypoexcitability of mature neurons from P149. Neural progenitors from both patients’ iPSC lines were cultured one week with TSA 20 nM and, only P149, for 6 weeks with TSA 0.2 nM, in parallel to neural progenitors from controls. Immunofluorescence of MAP2/TUJ1 positive cells using the Skeletonize Image J plugin evidenced that TSA partially rescued reduced nuclear area, and decreased branch length and abnormal end points number of both 45 days patients’ neurons, but did not influence the diminished percentage of their neurons with respect to controls. Patch clamp recordings of TSA-treated post-mitotic P149 neurons showed complete/partial rescue of sodium/potassium currents and significant enhancement of neuron excitability compared to untreated replicas. Correction of abnormalities of P149 young neurons was also affected by valproic acid 1 mM for 72 h, with some variation, with respect to TSA, on the morphological parameter. These findings hold promise for development of an epigenetic therapy to attenuate RSTS patients cognitive impairment.
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48
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Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm. Sci Rep 2021; 11:8242. [PMID: 33859268 PMCID: PMC8050086 DOI: 10.1038/s41598-021-87547-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
We identified a human embryonic stem cell subline that fails to respond to the differentiation cues needed to obtain endoderm derivatives, differentiating instead into extra-embryonic mesoderm. RNA-sequencing analysis showed that the subline has hyperactivation of the WNT and BMP4 signalling. Modulation of these pathways with small molecules confirmed them as the cause of the differentiation impairment. While activation of WNT and BMP4 in control cells resulted in a loss of endoderm differentiation and induction of extra-embryonic mesoderm markers, inhibition of these pathways in the subline restored its ability to differentiate. Karyotyping and exome sequencing analysis did not identify any changes in the genome that could account for the pathway deregulation. These findings add to the increasing evidence that different responses of stem cell lines to differentiation protocols are based on genetic and epigenetic factors, inherent to the line or acquired during cell culture.
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49
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Swanzey E, McNamara TF, Apostolou E, Tahiliani M, Stadtfeld M. A Susceptibility Locus on Chromosome 13 Profoundly Impacts the Stability of Genomic Imprinting in Mouse Pluripotent Stem Cells. Cell Rep 2021; 30:3597-3604.e3. [PMID: 32187532 DOI: 10.1016/j.celrep.2020.02.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 01/28/2023] Open
Abstract
Cultured pluripotent cells accumulate detrimental chromatin alterations, including DNA methylation changes at imprinted genes known as loss of imprinting (LOI). Although the occurrence of LOI is considered a stochastic phenomenon, here we document a genetic determinant that segregates mouse pluripotent cells into stable and unstable cell lines. Unstable lines exhibit hypermethylation at Dlk1-Dio3 and other imprinted loci, in addition to impaired developmental potential. Stimulation of demethylases by ascorbic acid prevents LOI and loss of developmental potential. Susceptibility to LOI greatly differs between commonly used mouse strains, which we use to map a causal region on chromosome 13 with quantitative trait locus (QTL) analysis. Our observations identify a strong genetic determinant of locus-specific chromatin abnormalities in pluripotent cells and provide a non-invasive way to suppress them. This highlights the importance of considering genetics in conjunction with culture conditions for assuring the quality of pluripotent cells for biomedical applications.
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Affiliation(s)
- Emily Swanzey
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Thomas F McNamara
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Mamta Tahiliani
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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50
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Thomas D, Shenoy S, Sayed N. Building Multi-Dimensional Induced Pluripotent Stem Cells-Based Model Platforms to Assess Cardiotoxicity in Cancer Therapies. Front Pharmacol 2021; 12:607364. [PMID: 33679396 PMCID: PMC7930625 DOI: 10.3389/fphar.2021.607364] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease (CVD) complications have contributed significantly toward poor survival of cancer patients worldwide. These complications that result in myocardial and vascular damage lead to long-term multisystemic disorders. In some patient cohorts, the progression from acute to symptomatic CVD state may be accelerated due to exacerbation of underlying comorbidities such as obesity, diabetes and hypertension. In such situations, cardio-oncologists are often left with a clinical predicament in finding the optimal therapeutic balance to minimize cardiovascular risks and maximize the benefits in treating cancer. Hence, prognostically there is an urgent need for cost-effective, rapid, sensitive and patient-specific screening platform to allow risk-adapted decision making to prevent cancer therapy related cardiotoxicity. In recent years, momentous progress has been made toward the successful derivation of human cardiovascular cells from induced pluripotent stem cells (iPSCs). This technology has not only provided deeper mechanistic insights into basic cardiovascular biology but has also seamlessly integrated within the drug screening and discovery programs for early efficacy and safety evaluation. In this review, we discuss how iPSC-derived cardiovascular cells have been utilized for testing oncotherapeutics to pre-determine patient predisposition to cardiovascular toxicity. Lastly, we highlight the convergence of tissue engineering technologies and precision medicine that can enable patient-specific cardiotoxicity prognosis and treatment on a multi-organ level.
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Affiliation(s)
- Dilip Thomas
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States
| | - Sushma Shenoy
- Stanford Cardiovascular Institute, Stanford, CA, United States
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States.,Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
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