1
|
Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A, Halbritter F. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. Nat Commun 2024; 15:3745. [PMID: 38702304 PMCID: PMC11068915 DOI: 10.1038/s41467-024-47945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
Collapse
Affiliation(s)
- Ingrid M Saldana-Guerrero
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | | | - Katy Boswell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Rebecca A Lea
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Sara Wernig-Zorc
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irfete S Fetahu
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Medical University of Vienna, Department of Neurology, Division of Neuropathology and Neurochemistry, Vienna, Austria
| | - Peter Zoescher
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik GmbH, Vienna, Austria
| | | | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Celine Souilhol
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Sophia Tarelli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Polyxeni Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Magdalena Rados
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Maria Guarini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter W Andrews
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Helen E Bryant
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | | | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK.
- Neuroscience Institute, The University of Sheffield, Sheffield, UK.
| | | |
Collapse
|
2
|
Andrews PW. The origins of human pluripotent stem cells: the road from a cancer to regenerative medicine. In Vitro Cell Dev Biol Anim 2024; 60:514-520. [PMID: 38396072 PMCID: PMC11126438 DOI: 10.1007/s11626-024-00865-8] [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: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
The notion of using pluripotent stem cells (PSCs) as a source of differentiated cell types for replacement of disease or damaged tissues in regenerative medicine is now an active area of research, with approaches to treating eye diseases such as age-related macular degeneration or Parkinson's disease now on the horizon. But the foundations for this research lie in a quite different area of science, namely the role of genetics of cancer. In this review, we trace the evolution of ideas starting with the discovery that strain 129 mice are particularly subject to develop germ cell tumors, through the identification of embryonal carcinoma (EC) cells as the stem cells of the teratocarcinoma manifestation of these tumors, to the recognition of their relationship to pluripotent cells of the early embryo, and eventually their role in the derivation of embryonic stem cells, first from mouse embryos and then from primates including humans. This is a story that illustrates how science commonly develops through the interests and insights of individual investigators, often with unexpected and unintended outcomes.
Collapse
Affiliation(s)
- Peter W Andrews
- The Centre for Stem Cell Biology, The School of Biosciences, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| |
Collapse
|
3
|
Beltran-Rendon C, Price CJ, Glen K, Stacey A, Barbaric I, Thomas RJ. Modeling the selective growth advantage of genetically variant human pluripotent stem cells to identify opportunities for manufacturing process control. Cytotherapy 2024; 26:383-392. [PMID: 38349312 DOI: 10.1016/j.jcyt.2024.01.010] [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: 05/24/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND AIMS The appearance of genetically variant populations in human pluripotent stem cell (hPSC) cultures represents a concern for research and clinical applications. Genetic variations may alter hPSC differentiation potential or cause phenotype variation in differentiated cells. Further, variants may have properties such as proliferative rate, or response to the culture environment, that differ from wild-type cells. As such, understanding the behavior of these variants in culture, and any potential operational impact on manufacturing processes, will be necessary to control quality of putative hPSC-based products that include a proportion of variant threshold in their quality specification. METHODS Here we show a computational model that mathematically describes the growth dynamics between commonly occurring genetically variant hPSCs and their counterpart wild-type cells in culture. RESULTS We show that our model is capable of representing the growth behaviors of both wild-type and variant hPSCs in individual and co-culture systems. CONCLUSIONS This representation allows us to identify three critical process parameters that drive critical quality attributes when genetically variant cells are present within the system: total culture density, proportion of variant cells within the culture system and variant cell overgrowth. Lastly, we used our model to predict how the variability of these parameters affects the prevalence of both populations in culture.
Collapse
Affiliation(s)
| | - Christopher J Price
- School of Biological Sciences, The University of Sheffield, Western Bank, Sheffield, UK; The Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, UK; INSIGNEO Institute, University of Sheffield, Sheffield, UK
| | - Katie Glen
- Centre for Biological Engineering, Loughborough University, Loughborough, UK
| | - Adrian Stacey
- Centre for Biological Engineering, Loughborough University, Loughborough, UK
| | - Ivana Barbaric
- School of Biological Sciences, The University of Sheffield, Western Bank, Sheffield, UK; The Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, UK; INSIGNEO Institute, University of Sheffield, Sheffield, UK.
| | - Robert J Thomas
- Centre for Biological Engineering, Loughborough University, Loughborough, UK.
| |
Collapse
|
4
|
Krishnan S, Paul PK, Rodriguez TA. Cell competition and the regulation of protein homeostasis. Curr Opin Cell Biol 2024; 87:102323. [PMID: 38301378 DOI: 10.1016/j.ceb.2024.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024]
Abstract
The process of embryonic development involves remarkable cellular plasticity, which governs the coordination between cells necessary to build an organism. One role of this plasticity is to ensure that when aberrant cells are eliminated, growth adjustment occurs so that the size of the tissue is maintained. An important regulator of cellular plasticity that ensures cellular cooperation is a fitness-sensing mechanism termed cell competition. During cell competition, cells with defects that lower fitness but do not affect viability, such as those that cause impaired signal transduction, slower cellular growth, mitochondrial dysregulation or impaired protein homeostasis, are killed when surrounded by fitter cells. This is accompanied by the compensatory proliferation of the surviving cells. The underlying factors and mechanisms that demarcate certain cells as less fit than their neighbouring cells and losers of cell competition are still relatively unknown. Recent evidence has pointed to mitochondrial defects and proteotoxic stress as important hallmarks of these loser cells. Here, we review recent advances in this area, focussing on the role of mitochondrial activity and protein homeostasis as major mechanisms determining competitive cell fitness during development and the importance of cell proteostasis in determining cell fitness.
Collapse
Affiliation(s)
| | - Pranab K Paul
- National Heart and Lung Institute, Imperial College London, UK
| | | |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Lezmi E, Jung J, Benvenisty N. High prevalence of acquired cancer-related mutations in 146 human pluripotent stem cell lines and their differentiated derivatives. Nat Biotechnol 2024:10.1038/s41587-023-02090-2. [PMID: 38195986 DOI: 10.1038/s41587-023-02090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
To survey cancer-related mutations in human pluripotent stem cells and their derivatives, we analyzed >2,200 transcriptomes from 146 independent lines in the NCBI's Sequence Read Archive. Twenty-two per cent of samples had at least one cancer-related mutation; of these, 64% had TP53 mutations, which conferred a pronounced selective advantage, perturbed target gene expression and altered cellular differentiation. These findings underscore the need for robust surveillance of cancer-related mutations in pluripotent cells, especially in clinical applications.
Collapse
Affiliation(s)
- Elyad Lezmi
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Jonathan Jung
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Camões dos Santos J, Appleton C, Cazaux Mateus F, Covas R, Bekman EP, da Rocha ST. Stem cell models of Angelman syndrome. Front Cell Dev Biol 2023; 11:1274040. [PMID: 37928900 PMCID: PMC10620611 DOI: 10.3389/fcell.2023.1274040] [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: 08/07/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Angelman syndrome (AS) is an imprinted neurodevelopmental disorder that lacks a cure, characterized by developmental delay, intellectual impairment, seizures, ataxia, and paroxysmal laughter. The condition arises due to the loss of the maternally inherited copy of the UBE3A gene in neurons. The paternally inherited UBE3A allele is unable to compensate because it is silenced by the expression of an antisense transcript (UBE3A-ATS) on the paternal chromosome. UBE3A, encoding enigmatic E3 ubiquitin ligase variants, regulates target proteins by either modifying their properties/functions or leading them to degradation through the proteasome. Over time, animal models, particularly the Ube3a mat-/pat+ Knock-Out (KO) mice, have significantly contributed to our understanding of the molecular mechanisms underlying AS. However, a shift toward human pluripotent stem cell models (PSCs), such as human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), has gained momentum. These stem cell models accurately capture human genetic and cellular characteristics, offering an alternative or a complement to animal experimentation. Human stem cells possess the remarkable ability to recapitulate neurogenesis and generate "brain-in-a-dish" models, making them valuable tools for studying neurodevelopmental disorders like AS. In this review, we provide an overview of the current state-of-the-art human stem cell models of AS and explore their potential to become the preclinical models of choice for drug screening and development, thus propelling AS therapeutic advancements and improving the lives of affected individuals.
Collapse
Affiliation(s)
- João Camões dos Santos
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carolina Appleton
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Francisca Cazaux Mateus
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Covas
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Evguenia Pavlovna Bekman
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- The Egas Moniz Center for Interdisciplinary Research (CiiEM), Caparica, Portugal
| | - Simão Teixeira da Rocha
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Ludwig TE, Andrews PW, Barbaric I, Benvenisty N, Bhattacharyya A, Crook JM, Daheron LM, Draper JS, Healy LE, Huch M, Inamdar MS, Jensen KB, Kurtz A, Lancaster MA, Liberali P, Lutolf MP, Mummery CL, Pera MF, Sato Y, Shimasaki N, Smith AG, Song J, Spits C, Stacey G, Wells CA, Zhao T, Mosher JT. ISSCR standards for the use of human stem cells in basic research. Stem Cell Reports 2023; 18:1744-1752. [PMID: 37703820 PMCID: PMC10545481 DOI: 10.1016/j.stemcr.2023.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
The laboratory culture of human stem cells seeks to capture a cellular state as an in vitro surrogate of a biological system. For the results and outputs from this research to be accurate, meaningful, and durable, standards that ensure reproducibility and reliability of the data should be applied. Although such standards have been previously proposed for repositories and distribution centers, no widely accepted best practices exist for laboratory research with human pluripotent and tissue stem cells. To fill that void, the International Society for Stem Cell Research has developed a set of recommendations, including reporting criteria, for scientists in basic research laboratories. These criteria are designed to be technically and financially feasible and, when implemented, enhance the reproducibility and rigor of stem cell research.
Collapse
Affiliation(s)
| | | | | | | | | | - Jeremy M Crook
- The University of Sydney, Camperdown, NSW Australia; Chris O'Brien Lifehouse, Camperdown, NSW, Australia; The University of Wollongong, Wollongong, NSW, Australia
| | | | | | | | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Maneesha S Inamdar
- Jawaharlal Nehru Centre for Advanced Scientific Research, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
| | - Kim B Jensen
- Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Kurtz
- Fraunhofer Institute for Biomedical Engineering, Sulzbach, Germany; Berlin Institute of Health at Charité, Berlin, Germany
| | | | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basal, Switzerland
| | | | | | | | - Yoji Sato
- National Institute of Health Sciences, Kawasaki, Japan
| | - Noriko Shimasaki
- Center for iPS Research and Application, Kyoto, Japan; Prefectural University of Medicine, Nagoya University, Nagoya, Japan; National University of Singapore, Singapore, Singapore
| | | | - Jihwan Song
- CHA University, Seoul, Korea; iPS Bio, Inc, Seoul, Korea
| | | | - Glyn Stacey
- International Stem Cell Banking Initiative, Barley, Herts, UK
| | | | - Tongbiao Zhao
- Institute of Zoology Chinese Academy of Sciences, Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jack T Mosher
- International Society for Stem Cell Research, Evanston, IL, USA
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Vitillo L, Anjum F, Hewitt Z, Stavish D, Laing O, Baker D, Barbaric I, Coffey P. The isochromosome 20q abnormality of pluripotent cells interrupts germ layer differentiation. Stem Cell Reports 2023; 18:782-797. [PMID: 36801002 PMCID: PMC10031278 DOI: 10.1016/j.stemcr.2023.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/18/2023] Open
Abstract
Chromosome 20 abnormalities are some of the most frequent genomic changes acquired by human pluripotent stem cell (hPSC) cultures worldwide. Yet their effects on differentiation remain largely unexplored. We investigated a recurrent abnormality also found on amniocentesis, the isochromosome 20q (iso20q), during a clinical retinal pigment epithelium differentiation. Here we show that the iso20q abnormality interrupts spontaneous embryonic lineage specification. Isogenic lines revealed that under conditions that promote the spontaneous differentiation of wild-type hPSCs, the iso20q variants fail to differentiate into primitive germ layers and to downregulate pluripotency networks, resulting in apoptosis. Instead, iso20q cells are highly biased for extra-embryonic/amnion differentiation following inhibition of DNMT3B methylation or BMP2 treatment. Finally, directed differentiation protocols can overcome the iso20q block. Our findings reveal in iso20q a chromosomal abnormality that impairs the developmental competency of hPSCs toward germ layers but not amnion, which models embryonic developmental bottlenecks in the presence of aberrations.
Collapse
Affiliation(s)
- Loriana Vitillo
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK.
| | - Fabiha Anjum
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - Zoe Hewitt
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Owen Laing
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Pete Coffey
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK; Centre for Stem Cell Biology and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA; NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, UK
| |
Collapse
|
14
|
Czerminski JT, King OD, Lawrence JB. Large-scale organoid study suggests effects of trisomy 21 on early fetal neurodevelopment are more subtle than variability between isogenic lines and experiments. Front Neurosci 2023; 16:972201. [PMID: 36817096 PMCID: PMC9935940 DOI: 10.3389/fnins.2022.972201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/08/2022] [Indexed: 02/05/2023] Open
Abstract
This study examines cortical organoids generated from a panel of isogenic trisomic and disomic iPSC lines (subclones) as a model of early fetal brain development in Down syndrome (DS). An initial experiment comparing organoids from one trisomic and one disomic line showed many genome-wide transcriptomic differences and modest differences in cell-type proportions, suggesting there may be a neurodevelopmental phenotype that is due to trisomy of chr21. To better control for multiple sources of variation, we undertook a highly robust study of ∼1,200 organoids using an expanded panel of six all-isogenic lines, three disomic, and three trisomic. The power of this experimental design was indicated by strong detection of the ∼1.5-fold difference in chr21 genes. However, the numerous expression differences in non-chr21 genes seen in the smaller experiment fell away, and the differences in cell-type representation between lines did not correlate with trisomy 21. Results suggest that the initial smaller experiment picked up differences between small organoid samples and individual isogenic lines, which "averaged out" in the larger panel of isogenic lines. Our results indicate that even when organoid and batch variability are better controlled for, variation between isogenic cell lines (even subclones) may obscure, or be conflated with, subtle neurodevelopmental phenotypes that may be present in ∼2nd trimester DS brain development. Interestingly, despite this variability between organoid batches and lines, and the "fetal stage" of these organoids, an increase in secreted Aβ40 peptide levels-an Alzheimer-related cellular phenotype-was more strongly associated with trisomy 21 status than were neurodevelopmental shifts in cell-type composition.
Collapse
Affiliation(s)
- Jan T. Czerminski
- Medical Scientist Training Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Oliver D. King
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States,Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States,*Correspondence: Jeanne B. Lawrence,
| |
Collapse
|
15
|
Kim YJ, Go YH, Jeong HC, Kwon EJ, Kim SM, Cheong HS, Kim W, Shin HD, Lee H, Cha HJ. TPX2 prompts mitotic survival via the induction of BCL2L1 through YAP1 protein stabilization in human embryonic stem cells. Exp Mol Med 2023; 55:32-42. [PMID: 36596852 PMCID: PMC9898288 DOI: 10.1038/s12276-022-00907-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/07/2022] [Accepted: 10/31/2022] [Indexed: 01/05/2023] Open
Abstract
Genetic alterations have been reported for decades in most human embryonic stem cells (hESCs). Survival advantage, a typical trait acquired during long-term in vitro culture, results from the induction of BCL2L1 upon frequent copy number variation (CNV) at locus 20q11.21 and is one of the strongest candidates associated with genetic alterations that occur via escape from mitotic stress. However, the underlying mechanisms for BCL2L1 induction remain unknown. Furthermore, abnormal mitosis and the survival advantage that frequently occur in late passage are associated with the expression of BCL2L1, which is in locus 20q11.21. In this study, we demonstrated that the expression of TPX2, a gene located in 20q11.21, led to BCL2L1 induction and consequent survival traits under mitotic stress in isogenic pairs of hESCs and human induced pluripotent stem cells (iPSCs) with normal and 20q11.21 CNVs. High Aurora A kinase activity by TPX2 stabilized the YAP1 protein to induce YAP1-dependent BCL2L1 expression. A chemical inhibitor of Aurora A kinase and knockdown of YAP/TAZ significantly abrogated the high tolerance to mitotic stress through BCL2L1 suppression. These results suggest that the collective expression of TPX2 and BCL2L1 from CNV at loci 20q11.21 and a consequent increase in YAP1 signaling promote genome instability during long-term in vitro hESC culture.
Collapse
Affiliation(s)
- Yun-Jeong Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Young-Hyun Go
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Ho-Chang Jeong
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Eun-Ji Kwon
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Seong-Min Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Hyun Sub Cheong
- grid.412670.60000 0001 0729 3748Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| | - Wantae Kim
- grid.254230.20000 0001 0722 6377Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hyoung Doo Shin
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Haeseung Lee
- grid.262229.f0000 0001 0719 8572College of Pharmacy, Pusan National University, Busan, 46241 Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
16
|
Guo X, Su F, Gao Y, Tang L, Yu X, Zi J, Zhou Y, Wang H, Xue J, Wang X. Effects of dietary restriction on genome stability are sex and feeding regimen dependent. Food Funct 2023; 14:471-488. [PMID: 36519635 DOI: 10.1039/d2fo03138h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Preserving genome stability is essential to prevent aging and cancer. Dietary restriction (DR) is the most reproducible non-pharmacological way to improve health and extend lifespan in various species. Whether DR helps to preserve genome stability and whether this effect is altered by experimental variables remain unclear. Moreover, DR research relies heavily on experimental animals, making the development of reliable in vitro mimetics of great interest. Therefore, we tested the effects of sex and feeding regimen (time-restricted eating, alternate day fasting and calorie restriction) on genome stability in CF-1 mice and whether these effects can be recapitulated by cell culture paradigms. Here, we show that calorie restriction significantly decreases the spontaneous micronuclei (MN), a biomarker of genome instability, in bone marrow cells of females instead of males. Alternate day fasting significantly decreases cisplatin-induced MN in females instead of males. Unexpectedly, daily time-restricted eating significantly exacerbates cisplatin-induced MN in males but not in females. Additionally, we design several culture paradigms that are able to faithfully recapitulate the key effects of these DR regimens on genome stability. In particular, 30% reduction of serum, a mimetic of calorie restriction, exhibits a strong ability to decrease spontaneous and cisplatin-induced MN in immortalized human umbilical vein endothelial cells. We conclude that the effects of different DR regimens on genome stability are not universal and females from each diet regimen sustain a more stable genome than males. Our results provide novel insight into the understanding of how DR influences genome stability in a sex and regimen dependent way, and suggest that our in vitro DR mimetics could be adopted to study the underlying molecular mechanisms.
Collapse
Affiliation(s)
- Xihan Guo
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China. .,Yunnan Environmental Mutagen Society, Kunming 650500, Yunnan, China
| | - Fuping Su
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Yue Gao
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Liyan Tang
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Xixi Yu
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Jiangli Zi
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Yingshui Zhou
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Han Wang
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China. .,Yunnan Environmental Mutagen Society, Kunming 650500, Yunnan, China
| | - Jinglun Xue
- Yeda Institute of Gene and Cell Therapy, Taizhou 318000, Zhejiang, China
| | - Xu Wang
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China. .,Yunnan Environmental Mutagen Society, Kunming 650500, Yunnan, China.,Yeda Institute of Gene and Cell Therapy, Taizhou 318000, Zhejiang, China
| |
Collapse
|
17
|
Cha Y, Park TY, Leblanc P, Kim KS. Current Status and Future Perspectives on Stem Cell-Based Therapies for Parkinson's Disease. J Mov Disord 2023; 16:22-41. [PMID: 36628428 PMCID: PMC9978267 DOI: 10.14802/jmd.22141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 01/12/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, affecting 1%-2% of the population over the age of 65. As the population ages, it is anticipated that the burden on society will significantly escalate. Although symptom reduction by currently available pharmacological and/or surgical treatments improves the quality of life of many PD patients, there are no treatments that can slow down, halt, or reverse disease progression. Because the loss of a specific cell type, midbrain dopamine neurons in the substantia nigra, is the main cause of motor dysfunction in PD, it is considered a promising target for cell replacement therapy. Indeed, numerous preclinical and clinical studies using fetal cell transplantation have provided proof of concept that cell replacement therapy may be a viable therapeutic approach for PD. However, the use of human fetal cells remains fraught with controversy due to fundamental ethical, practical, and clinical limitations. Groundbreaking work on human pluripotent stem cells (hPSCs), including human embryonic stem cells and human induced pluripotent stem cells, coupled with extensive basic research in the stem cell field offers promising potential for hPSC-based cell replacement to become a realistic treatment regimen for PD once several major issues can be successfully addressed. In this review, we will discuss the prospects and challenges of hPSC-based cell therapy for PD.
Collapse
Affiliation(s)
- Young Cha
- Department of Psychiatry and Molecular Neurobiology Laboratory, McLean Hospital and Program in Neuroscience, Harvard Medical School, Belmont, MA, USA
| | - Tae-Yoon Park
- Department of Psychiatry and Molecular Neurobiology Laboratory, McLean Hospital and Program in Neuroscience, Harvard Medical School, Belmont, MA, USA
| | - Pierre Leblanc
- Department of Psychiatry and Molecular Neurobiology Laboratory, McLean Hospital and Program in Neuroscience, Harvard Medical School, Belmont, MA, USA
| | - Kwang-Soo Kim
- Department of Psychiatry and Molecular Neurobiology Laboratory, McLean Hospital and Program in Neuroscience, Harvard Medical School, Belmont, MA, USA
| |
Collapse
|
18
|
Jiang J, Qiu T, Yang C, Yuan Y, Qin L, Zhang P. Atypical cell cycle profile of mouse embryonic stem cell is regulated by classic oncogenic and tumor suppressive genes in vitro. Heliyon 2022; 8:e11979. [PMID: 36578422 PMCID: PMC9791322 DOI: 10.1016/j.heliyon.2022.e11979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/17/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Embryonic stem cells (ESCs) exhibit an unusual cell cycle profile containing a short G1 phase. Whether this feature is required to maintain pluripotency is a matter of debate. Here, we report that the short G1 phase is a consequence of MEK1/2 kinase-mediated promotion of G1/S transition, but not necessarily coupled with pluripotency maintenance. We find that compared to primed ESCs, naïve ESCs exhibit a significantly longer G1 phase due to the inhibition of MEK1/2 kinases. MEK1/2 inhibition increases intracellular level of reactive oxygen species (ROS), leading to the stabilization of p53 protein. The genetic ablation of p53 largely converts the cell cycle profile of naïve ESCs to that of primed ESCs. These results demonstrate that pluripotency and proliferation are separable cellular events, and the short G1 phase of primed ESCs is a manifestation of the intricate interplay between classical oncogenes MEK1/2 and tumor suppressor gene TP53 to promote G1/S transition.
Collapse
Affiliation(s)
- Jinfeng Jiang
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Frontiers Science Center for Disease-related Molecular Network, West China Hospital
| | - Tong Qiu
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Frontiers Science Center for Disease-related Molecular Network, West China Hospital
| | - Chao Yang
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Frontiers Science Center for Disease-related Molecular Network, West China Hospital
| | - Yuan Yuan
- Division of Bioinformatics, Sichuan Cunde Therapeutics, Chengdu 610093, China
| | - Ling Qin
- Department of Gastroenterology, First Affiliated Hospital of Chengdu Medical College,Corresponding authors.
| | - Peixuan Zhang
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Corresponding authors.
| |
Collapse
|
19
|
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: 15] [Impact Index Per Article: 7.5] [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.
Collapse
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.
| |
Collapse
|
20
|
Pantazis CB, Yang A, Lara E, McDonough JA, Blauwendraat C, Peng L, Oguro H, Kanaujiya J, Zou J, Sebesta D, Pratt G, Cross E, Blockwick J, Buxton P, Kinner-Bibeau L, Medura C, Tompkins C, Hughes S, Santiana M, Faghri F, Nalls MA, Vitale D, Ballard S, Qi YA, Ramos DM, Anderson KM, Stadler J, Narayan P, Papademetriou J, Reilly L, Nelson MP, Aggarwal S, Rosen LU, Kirwan P, Pisupati V, Coon SL, Scholz SW, Priebe T, Öttl M, Dong J, Meijer M, Janssen LJM, Lourenco VS, van der Kant R, Crusius D, Paquet D, Raulin AC, Bu G, Held A, Wainger BJ, Gabriele RMC, Casey JM, Wray S, Abu-Bonsrah D, Parish CL, Beccari MS, Cleveland DW, Li E, Rose IVL, Kampmann M, Calatayud Aristoy C, Verstreken P, Heinrich L, Chen MY, Schüle B, Dou D, Holzbaur ELF, Zanellati MC, Basundra R, Deshmukh M, Cohen S, Khanna R, Raman M, Nevin ZS, Matia M, Van Lent J, Timmerman V, Conklin BR, Johnson Chase K, Zhang K, Funes S, Bosco DA, Erlebach L, Welzer M, Kronenberg-Versteeg D, Lyu G, Arenas E, Coccia E, Sarrafha L, Ahfeldt T, Marioni JC, Skarnes WC, Cookson MR, Ward ME, Merkle FT. A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell Stem Cell 2022; 29:1685-1702.e22. [PMID: 36459969 PMCID: PMC9782786 DOI: 10.1016/j.stem.2022.11.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.
Collapse
Affiliation(s)
- Caroline B Pantazis
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Andrian Yang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Erika Lara
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lirong Peng
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA; Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Hideyuki Oguro
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jitendra Kanaujiya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | | | - Marianita Santiana
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Daniel Vitale
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Shannon Ballard
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kailyn M Anderson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julia Stadler
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Priyanka Narayan
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Genetics and Biochemistry Branch, NIDDK, NINDS, National Institutes of Health, Bethesda, MD 20814, USA
| | - Jason Papademetriou
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Luke Reilly
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sanya Aggarwal
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Leah U Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Kirwan
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Venkat Pisupati
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Steven L Coon
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Theresa Priebe
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Miriam Öttl
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Jian Dong
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Marieke Meijer
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Lara J M Janssen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Vanessa S Lourenco
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Rik van der Kant
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, the Netherlands
| | - Dennis Crusius
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | | | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian J Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rebecca M C Gabriele
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jackie M Casey
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Dad Abu-Bonsrah
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Emmy Li
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Carles Calatayud Aristoy
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Laurin Heinrich
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Max Y Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dan Dou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria Clara Zanellati
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Basundra
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mohanish Deshmukh
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Khanna
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | | | | | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | | | | | - Ke Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Salome Funes
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Daryl A Bosco
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Lena Erlebach
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Marc Welzer
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Deborah Kronenberg-Versteeg
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Guochang Lyu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ernest Arenas
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elena Coccia
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Mark R Cookson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Michael E Ward
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Florian T Merkle
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| |
Collapse
|
21
|
Medina-Cano D, Corrigan EK, Glenn RA, Islam MT, Lin Y, Kim J, Cho H, Vierbuchen T. Rapid and robust directed differentiation of mouse epiblast stem cells into definitive endoderm and forebrain organoids. Development 2022; 149:dev200561. [PMID: 35899604 PMCID: PMC10655922 DOI: 10.1242/dev.200561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022]
Abstract
Directed differentiation of pluripotent stem cells (PSCs) is a powerful model system for deconstructing embryonic development. Although mice are the most advanced mammalian model system for genetic studies of embryonic development, state-of-the-art protocols for directed differentiation of mouse PSCs into defined lineages require additional steps and generates target cell types with lower purity than analogous protocols for human PSCs, limiting their application as models for mechanistic studies of development. Here, we examine the potential of mouse epiblast stem cells cultured in media containing Wnt pathway inhibitors as a starting point for directed differentiation. As a proof of concept, we focused our efforts on two specific cell/tissue types that have proven difficult to generate efficiently and reproducibly from mouse embryonic stem cells: definitive endoderm and neural organoids. We present new protocols for rapid generation of nearly pure definitive endoderm and forebrain-patterned neural organoids that model the development of prethalamic and hippocampal neurons. These differentiation models present new possibilities for combining mouse genetic tools with in vitro differentiation to characterize molecular and cellular mechanisms of embryonic development.
Collapse
Affiliation(s)
- Daniel Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Emily K. Corrigan
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Rachel A. Glenn
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Mohammed T. Islam
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Yuan Lin
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Juliet Kim
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Hyunwoo Cho
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| |
Collapse
|
22
|
DuBose CO, Daum JR, Sansam CL, Gorbsky GJ. Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells. Genes (Basel) 2022; 13:genes13071157. [PMID: 35885940 PMCID: PMC9318709 DOI: 10.3390/genes13071157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great potential for regenerative medicine. By reprogramming a patient′s own cells, immunological rejection can be avoided during transplantation. For expansion and gene editing, iPSCs are grown in artificial culture for extended times. Culture affords potential danger for the accumulation of genetic aberrations. To study these, two induced pluripotent stem (iPS) cell lines were cultured and periodically analyzed using advanced optical mapping to detect and classify chromosome numerical and segmental changes that included deletions, insertions, balanced translocations and inversions. In one of the lines, a population trisomic for chromosome 12 gained dominance over a small number of passages. This appearance and dominance of the culture by chromosome 12 trisomic cells was tracked through intermediate passages by the analysis of chromosome spreads. Mathematical modeling suggested that the proliferation rates of diploid versus trisomic cells could not account for the rapid dominance of the trisomic population. In addition, optical mapping revealed hundreds of structural variations distinct from those generally found within the human population. Many of these structural variants were detected in samples obtained early in the culturing process and were maintained in late passage samples, while others were acquired over the course of culturing.
Collapse
Affiliation(s)
- Casey O. DuBose
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
| | - John R. Daum
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
| | - Christopher L. Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Gary J. Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
| |
Collapse
|
23
|
Molina-Ruiz FJ, Introna C, Bombau G, Galofre M, Canals JM. Standardization of Cell Culture Conditions and Routine Genomic Screening under a Quality Management System Leads to Reduced Genomic Instability in hPSCs. Cells 2022; 11:cells11131984. [PMID: 35805069 PMCID: PMC9265327 DOI: 10.3390/cells11131984] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 01/27/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) have generated unprecedented interest in the scientific community, given their potential applications in regenerative medicine, disease modeling, toxicology and drug screening. However, hPSCs are prone to acquire genomic alterations in vitro, mainly due to suboptimal culture conditions and inappropriate routines to monitor genome integrity. This poses a challenge to both the safety of clinical applications and the reliability of basic and translational hPSC research. In this study, we aim to investigate if the implementation of a Quality Management System (QMS) such as ISO9001:2015 to ensure reproducible and standardized cell culture conditions and genomic screening strategies can decrease the prevalence of genomic alterations affecting hPSCs used for research applications. To this aim, we performed a retrospective analysis of G-banding karyotype and Comparative Genomic Hybridization array (aCGH) data generated by our group over a 5-year span of different hESC and hiPSC cultures. This work demonstrates that application of a QMS to standardize cell culture conditions and genomic monitoring routines leads to a striking improvement of genomic stability in hPSCs cultured in vitro, as evidenced by a reduced probability of potentially pathogenic chromosomal aberrations and subchromosomal genomic alterations. These results support the need to implement QMS in academic laboratories performing hPSC research.
Collapse
Affiliation(s)
- Francisco J. Molina-Ruiz
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Clelia Introna
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Georgina Bombau
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Mireia Galofre
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Josep M. Canals
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-934-035-288
| |
Collapse
|
24
|
Quality criteria for in vitro human pluripotent stem cell-derived models of tissue-based cells. Reprod Toxicol 2022; 112:36-50. [PMID: 35697279 DOI: 10.1016/j.reprotox.2022.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 12/21/2022]
Abstract
The advent of the technology to isolate or generate human pluripotent stem cells provided the potential to develop a wide range of human models that could enhance understanding of mechanisms underlying human development and disease. These systems are now beginning to mature and provide the basis for the development of in vitro assays suitable to understand the biological processes involved in the multi-organ systems of the human body, and will improve strategies for diagnosis, prevention, therapies and precision medicine. Induced pluripotent stem cell lines are prone to phenotypic and genotypic changes and donor/clone dependent variability, which means that it is important to identify the most appropriate characterization markers and quality control measures when sourcing new cell lines and assessing differentiated cell and tissue culture preparations for experimental work. This paper considers those core quality control measures for human pluripotent stem cell lines and evaluates the state of play in the development of key functional markers for their differentiated cell derivatives to promote assurance of reproducibility of scientific data derived from pluripotent stem cell-based systems.
Collapse
|
25
|
Lezmi E, Benvenisty N. The Tumorigenic Potential of Human Pluripotent Stem Cells. Stem Cells Transl Med 2022; 11:791-796. [PMID: 35679163 PMCID: PMC9397652 DOI: 10.1093/stcltm/szac039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/24/2022] [Indexed: 11/23/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are currently evaluated for clinical applications due to their proliferation and differentiation capacities, raising the need to both assess and enhance, the safety of hPSC-based treatments. Distinct molecular features contribute to the tumorigenicity of hPSCs, manifested in the formation of teratoma tumors upon transplantation in vivo. Prolonged in vitro culturing of hPSCs can enhance selection for specific genetic aberrations, either at the chromosome or gene level. Some of these aberrations are tightly linked to human tumor pathology and increase the tumorigenic aggressiveness of the abnormal cells. In this perspective, we describe major tumor-associated risk factors entailed in hPSC-based therapy, and present precautionary and safety measures relevant for the development and application of such therapies.
Collapse
Affiliation(s)
- Elyad Lezmi
- 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, Israel
| | - 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, Israel
| |
Collapse
|
26
|
Basile G, Qadir MMF, Mauvais-Jarvis F, Vetere A, Shoba V, Modell AE, Pastori RL, Russ HA, Wagner BK, Dominguez-Bendala J. Emerging diabetes therapies: Bringing back the β-cells. Mol Metab 2022; 60:101477. [PMID: 35331962 PMCID: PMC8987999 DOI: 10.1016/j.molmet.2022.101477] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Stem cell therapies are finally coming of age as a viable alternative to pancreatic islet transplantation for the treatment of insulin-dependent diabetes. Several clinical trials using human embryonic stem cell (hESC)-derived β-like cells are currently underway, with encouraging preliminary results. Remaining challenges notwithstanding, these strategies are widely expected to reduce our reliance on human isolated islets for transplantation procedures, making cell therapies available to millions of diabetic patients. At the same time, advances in our understanding of pancreatic cell plasticity and the molecular mechanisms behind β-cell replication and regeneration have spawned a multitude of translational efforts aimed at inducing β-cell replenishment in situ through pharmacological means, thus circumventing the need for transplantation. SCOPE OF REVIEW We discuss here the current state of the art in hESC transplantation, as well as the parallel quest to discover agents capable of either preserving the residual mass of β-cells or inducing their proliferation, transdifferentiation or differentiation from progenitor cells. MAJOR CONCLUSIONS Stem cell-based replacement therapies in the mold of islet transplantation are already around the corner, but a permanent cure for type 1 diabetes will likely require the endogenous regeneration of β-cells aided by interventions to restore the immune balance. The promise of current research avenues and a strong pipeline of clinical trials designed to tackle these challenges bode well for the realization of this goal.
Collapse
Affiliation(s)
- G Basile
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - M M F Qadir
- Tulane University School of Medicine, New Orleans, LA, USA; Southeast Louisiana Veterans Affairs Medical Center, New Orleans, LA, USA
| | - F Mauvais-Jarvis
- Tulane University School of Medicine, New Orleans, LA, USA; Southeast Louisiana Veterans Affairs Medical Center, New Orleans, LA, USA
| | - A Vetere
- Broad Institute, Cambridge, MA, USA
| | - V Shoba
- Broad Institute, Cambridge, MA, USA
| | | | - R L Pastori
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - H A Russ
- Barbara Davis Center for Diabetes, Colorado University Anschutz Medical Campus, Aurora, CO, USA.
| | | | - J Dominguez-Bendala
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA.
| |
Collapse
|
27
|
A real-time pluripotency reporter for the long-term and real-time monitoring of pluripotency changes in induced pluripotent stem cells. Aging (Albany NY) 2022; 14:4445-4458. [PMID: 35575836 PMCID: PMC9186763 DOI: 10.18632/aging.204083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/15/2022] [Indexed: 11/30/2022]
Abstract
To master the technology of reprogramming mouse somatic cells to induced pluripotent stem cells (iPSCs), which will lay a good foundation for setting up a technology platform on reprogramming human cancer cells into iPSCs. Mouse iPSCs (i.e., Oct4-GFP miPSCs) was successfully generated from mouse embryonic fibroblasts (MEFs) harboring Oct4-EGFP transgene by introducing four factors, Oct4, Sox2, c-Myc and Klf4, under mESC (Murine embryonic stem cells) culture conditions. Oct4-GFP miPSCs were similar to mESCs in morphology, proliferation, mESC-specific surface antigens and gene expression. Additionally, Oct4-GFP miPSCs could be cultured in suspension to form embryoid bodies (EBs) and differentiate into cell types of the three germ layers in vitro. Moreover, Oct4-GFP miPSCs could develop to teratoma and chimera in vivo. Unlike cell cycle distribution of MEFs, Oct4-GFP miPSCs are similar to mESCs in the cell cycle structure which consists of higher S phase and lower G1 phase. More importantly, our data demonstrated that MEFs harboring Oct4-EGFP transgene did not express GFP, until they were reprogrammed to the pluripotent stage (iPSCs), while the GFP expression was progressively lost when these pluripotent Oct4-GFP miPSCs exposed to EB-mediated differentiation conditions, suggesting the pluripotency of Oct4-GFP miPSCs can be real-time monitored over long periods of time via GFP assay. Altogether, our findings demonstrate that Oct4-GFP miPSC line is successfully established, which will lay a solid foundation for setting up a technology platform on reprogramming cancer cells into iPSCs. Furthermore, this pluripotency reporter system permits the long-term real-time monitoring of pluripotency changes in a live single-cell, and its progeny.
Collapse
|
28
|
Price CJ, Barbaric I. Assessing Cell Competition in Human Pluripotent Stem Cell (hPSC) Cultures. Curr Protoc 2022; 2:e435. [PMID: 35621694 PMCID: PMC9325404 DOI: 10.1002/cpz1.435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cell-cell interactions are required for development and homeostasis in multicellular organisms from insects to mammals. A critical process governed by these interactions is cell competition, which functions throughout development to control tissue composition by eliminating cells that possess a lower fitness status than their neighbors. Human pluripotent stem cells (hPSCs) are a key biological tool in modeling human development and offer further potential as a source of clinically relevant cell populations for regenerative medicine applications. Recently, cell competition has been demonstrated in hPSC cultures and during induced pluripotent stem cell reprogramming. In turn, these findings suggest that hPSCs can be used as a tool to study and model cell-cell interactions during different stages of development and disease. Here, we provide a panel of protocols optimized for hPSCs to investigate the potential role that cell competition may have in determining the fate and composition of cell populations during culture. The protocols entail assessment of the competitive phenotype and the mode through which cell competition may lead to elimination of less-fit cells from mosaic cultures with fitter counterparts. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Electroporation of hPSCs to establish a fluorescent reference cell line Support Protocol 1: Single-cell dissociation of hPSCs Support Protocol 2: Single-cell cloning of fluorescently labeled hPSCs Basic Protocol 2: Separate culture and co-culture proliferation assays Basic Protocol 3: Assessing levels of apoptosis in hPSC cultures using flow cytometry Basic Protocol 4: Transwell assay Support Protocol 3: Immunohistochemistry and image quantification of cleaved caspase-3 Basic Protocol 5: Cell confrontation assay Basic Protocol 6: Cell compression assay Basic Protocol 7: Time-lapse imaging to assess mechanical extrusion.
Collapse
Affiliation(s)
- Christopher J. Price
- School of BioscienceThe University of SheffieldWestern BankSheffieldUnited Kingdom,Neuroscience InstituteThe University of SheffieldWestern BankSheffieldUnited Kingdom
| | - Ivana Barbaric
- School of BioscienceThe University of SheffieldWestern BankSheffieldUnited Kingdom,Neuroscience InstituteThe University of SheffieldWestern BankSheffieldUnited Kingdom
| |
Collapse
|
29
|
Merkle FT, Ghosh S, Genovese G, Handsaker RE, Kashin S, Meyer D, Karczewski KJ, O'Dushlaine C, Pato C, Pato M, MacArthur DG, McCarroll SA, Eggan K. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Cell Stem Cell 2022; 29:472-486.e7. [PMID: 35176222 PMCID: PMC8900618 DOI: 10.1016/j.stem.2022.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.
Collapse
Affiliation(s)
- Florian T Merkle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome - MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Colm O'Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Michele Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Daniel G MacArthur
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
30
|
A call for consensus guidelines on monitoring the integrity of nuclear and mitochondrial genomes in human pluripotent stem cells. Stem Cell Reports 2022; 17:707-710. [PMID: 35245442 PMCID: PMC9023764 DOI: 10.1016/j.stemcr.2022.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/17/2022] Open
Abstract
Despite the widespread use of human pluripotent stem cells (hPSCs), there is no general consensus with respect to monitoring the integrity of nuclear and mitochondrial genome of hPSCs. We argue that clear guidelines should be in place, and we have identified frequently asked questions that can be used to develop a practical guide for hPSCs users.
Collapse
|
31
|
Baker D, Barbaric I. Characterizing the Genetic Stability of Human Naïve and Primed Pluripotent Stem Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2416:267-284. [PMID: 34870842 DOI: 10.1007/978-1-0716-1908-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of genetic changes in human pluripotent stem cells (hPSCs) can affect their behavior and impact on the utility of hPSC-based applications in research and clinic. The spectrum of spontaneously arising genetic abnormalities in hPSCs is wide and ranges from numerical and structural chromosomal anomalies down to point mutations. The detection of genetic changes in hPSCs is confounded by the fact that no single method detects all types of abnormalities with the same accuracy and sensitivity, therefore necessitating the use of a combination of different methods. Here, we provide detailed protocols for two methods commonly utilized for the detection of genetic changes in naïve and primed hPSCs: karyotyping by G-banding and fluorescent in situ hybridization (FISH).
Collapse
Affiliation(s)
- Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK.
| |
Collapse
|
32
|
Knock E, Julian LM. Building on a Solid Foundation: Adding Relevance and Reproducibility to Neurological Modeling Using Human Pluripotent Stem Cells. Front Cell Neurosci 2021; 15:767457. [PMID: 34867204 PMCID: PMC8637745 DOI: 10.3389/fncel.2021.767457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022] Open
Abstract
The brain is our most complex and least understood organ. Animal models have long been the most versatile tools available to dissect brain form and function; however, the human brain is highly distinct from that of standard model organisms. In addition to existing models, access to human brain cells and tissues is essential to reach new frontiers in our understanding of the human brain and how to intervene therapeutically in the face of disease or injury. In this review, we discuss current and developing culture models of human neural tissue, outlining advantages over animal models and key challenges that remain to be overcome. Our principal focus is on advances in engineering neural cells and tissue constructs from human pluripotent stem cells (PSCs), though primary human cell and slice culture are also discussed. By highlighting studies that combine animal models and human neural cell culture techniques, we endeavor to demonstrate that clever use of these orthogonal model systems produces more reproducible, physiological, and clinically relevant data than either approach alone. We provide examples across a range of topics in neuroscience research including brain development, injury, and cancer, neurodegenerative diseases, and psychiatric conditions. Finally, as testing of PSC-derived neurons for cell replacement therapy progresses, we touch on the advancements that are needed to make this a clinical mainstay.
Collapse
Affiliation(s)
- Erin Knock
- Research and Development, STEMCELL Technologies Inc., Vancouver, BC, Canada.,Department of Biological Sciences, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Lisa M Julian
- Department of Biological Sciences, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| |
Collapse
|
33
|
Keller A, Spits C. The Impact of Acquired Genetic Abnormalities on the Clinical Translation of Human Pluripotent Stem Cells. Cells 2021; 10:cells10113246. [PMID: 34831467 PMCID: PMC8625075 DOI: 10.3390/cells10113246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/07/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
Human pluripotent stem cells (hPSC) are known to acquire chromosomal abnormalities, which range from point mutations to large copy number changes, including full chromosome aneuploidy. These aberrations have a wide-ranging influence on the state of cells, in both the undifferentiated and differentiated state. Currently, very little is known on how these abnormalities will impact the clinical translation of hPSC, and particularly their potential to prime cells for oncogenic transformation. A further complication is that many of these abnormalities exist in a mosaic state in culture, which complicates their detection with conventional karyotyping methods. In this review we discuss current knowledge on how these aberrations influence the cell state and how this may impact the future of research and the cells’ clinical potential.
Collapse
|
34
|
Keshet G, Benvenisty N. Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling. Stem Cell Reports 2021; 16:2520-2533. [PMID: 34597600 PMCID: PMC8514966 DOI: 10.1016/j.stemcr.2021.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is a parent-of-origin dependent monoallelic expression of genes. Previous studies showed that conversion of primed human pluripotent stem cells (hPSCs) into naive pluripotency is accompanied by genome-wide loss of methylation that includes imprinted loci. However, the extent of aberrant biallelic expression of imprinted genes is still unknown. Here, we analyze loss of imprinting (LOI) in a large cohort of both bulk and single-cell RNA sequencing samples of naive and primed hPSCs. We show that naive hPSCs exhibit high levels of non-random LOI, with bias toward paternally methylated imprinting control regions. Importantly, we show that different protocols used for the primed to naive conversion led to different extents of LOI, tightly correlated to FGF signaling. This analysis sheds light on the process of LOI occurring during the conversion to naive pluripotency and highlights the importance of these events when modeling disease and development or when utilizing the cells for therapy.
Collapse
Affiliation(s)
- 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, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, 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, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
| |
Collapse
|
35
|
Tissue of Origin, but Not XCI State, Influences Germ Cell Differentiation from Human Pluripotent Stem Cells. Cells 2021; 10:cells10092400. [PMID: 34572048 PMCID: PMC8466594 DOI: 10.3390/cells10092400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are not only a promising tool to investigate differentiation to many cell types, including the germline, but are also a potential source of cells to use for regenerative medicine purposes in the future. However, current in vitro models to generate human primordial germ cell-like cells (hPGCLCs) have revealed high variability regarding differentiation efficiency depending on the hPSC lines used. Here, we investigated whether differences in X chromosome inactivation (XCI) in female hPSCs could contribute to the variability of hPGCLC differentiation efficiency during embryoid body (EB) formation. For this, we first characterized the XCI state in different hPSC lines by investigating the expression of XIST and H3K27me3, followed by differentiation and quantification of hPGCLCs. We observed that the XCI state did not influence the efficiency to differentiate to hPGCLCs; rather, hPSCs derived from cells isolated from urine showed an increased trend towards hPGCLCs differentiation compared to skin-derived hPSCs. In addition, we also characterized the XCI state in the generated hPGCLCs. Interestingly, we observed that independent of the XCI state of the hPSCs used, both hPGCLCs and soma cells in the EBs acquired XIST expression, indicative of an inactive X chromosome. In fact, culture conditions for EB formation seemed to promote XIST expression. Together, our results contribute to understanding how epigenetic properties of hPSCs influence differentiation and to optimize differentiation methods to obtain higher numbers of hPGCLCs, the first step to achieve human in vitro gametogenesis.
Collapse
|
36
|
Price CJ, Stavish D, Gokhale PJ, Stevenson BA, Sargeant S, Lacey J, Rodriguez TA, Barbaric I. Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition. Dev Cell 2021; 56:2455-2470.e10. [PMID: 34407428 PMCID: PMC8443275 DOI: 10.1016/j.devcel.2021.07.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/09/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
The appearance of genetic changes in human pluripotent stem cells (hPSCs) presents a concern for their use in research and regenerative medicine. Variant hPSCs that harbor recurrent culture-acquired aneuploidies display growth advantages over wild-type diploid cells, but the mechanisms that yield a drift from predominantly wild-type to variant cell populations remain poorly understood. Here, we show that the dominance of variant clones in mosaic cultures is enhanced through competitive interactions that result in the elimination of wild-type cells. This elimination occurs through corralling and mechanical compression by faster-growing variants, causing a redistribution of F-actin and sequestration of yes-associated protein (YAP) in the cytoplasm that induces apoptosis in wild-type cells. YAP overexpression or promotion of YAP nuclear localization in wild-type cells alleviates their "loser" phenotype. Our results demonstrate that hPSC fate is coupled to mechanical cues imposed by neighboring cells and reveal that hijacking this mechanism allows variants to achieve clonal dominance in cultures.
Collapse
Affiliation(s)
- Christopher J Price
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Dylan Stavish
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Paul J Gokhale
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ben A Stevenson
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Samantha Sargeant
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Department of Automatic Control and Systems Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Joanne Lacey
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Tristan A Rodriguez
- National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Ivana Barbaric
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| |
Collapse
|
37
|
De Boeck J, Verfaillie C. Doxycycline inducible overexpression systems: how to induce your gene of interest without inducing misinterpretations. Mol Biol Cell 2021; 32:1517-1522. [PMID: 34383558 PMCID: PMC8351744 DOI: 10.1091/mbc.e21-04-0177] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The doxycycline inducible overexpression system is a highly flexible and widely used tool for both in vitro and in vivo studies. However, during the past decade, a handful of reports have explicitly called for caution when using this system. The raised concerns are based on the notion that doxycycline can impair mitochondrial function of mammalian cells and can alter properties such as cell proliferation. As such, experimental outcomes can be confounded with the side effects of doxycycline and valid interpretation can be seriously threatened. Today, no consensus seems to exist about how these problems should be prevented. Moreover, some of the strategies that have been used to cope with these difficulties can actually introduce additional problems that are related to genomic instability and genetic modification of the cells. Here, we elaborate on the above statements and clarify them by some basic examples taken from our personal wet-lab experience. As such, we provide a nuanced overview of the doxycycline inducible overexpression system, some of its limitations and how to deal with them.
Collapse
Affiliation(s)
- Jolan De Boeck
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium
| |
Collapse
|
38
|
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.
Collapse
|
39
|
Wu J, Barbaric I. Fitness selection in human pluripotent stem cells and interspecies chimeras: Implications for human development and regenerative medicine. Dev Biol 2021; 476:209-217. [PMID: 33891964 PMCID: PMC8209287 DOI: 10.1016/j.ydbio.2021.03.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A small number of pluripotent cells within early embryo gives rise to all cells in the adult body, including germ cells. Hence, any mutations occurring in the pluripotent cell population are at risk of being propagated to their daughter cells and could lead to congenital defects or embryonic lethality and pose a risk of being transmitted to future generations. The observation that genetic errors are relatively common in preimplantation embryos, but their levels reduce as development progresses, suggests the existence of mechanisms for clearance of aberrant, unfit or damaged cells. Although early human embryogenesis is largely experimentally inaccessible, pluripotent stem cell (PSC) lines can be derived either from the inner cell mass (ICM) of a blastocyst or by reprogramming somatic cells into an embryonic stem cell-like state. PSCs retain the ability to differentiate into any cell type in vitro and, hence, they represent a unique and powerful tool for studying otherwise intractable stages of human development. The advent of PSCs has also opened up a possibility of developing regenerative medicine therapies, either through PSC differentiation in vitro or by creating interspecies chimeras for organ replacement. Here, we discuss the emerging evidence of cell selection in human PSC populations in vivo and in vitro and we highlight the implications of understanding this phenomenon for human development and regenerative medicine.
Collapse
Affiliation(s)
- Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom; Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom.
| |
Collapse
|
40
|
González-Martínez J, Malumbres M. Expanding the Differentiation Potential of Already-Established Pluripotent Stem Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2454:95-107. [PMID: 34128208 DOI: 10.1007/7651_2021_408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Pluripotent stem cells (PSCs) have proven to be an essential tool in many research fields including basic cell biology, development, or human disease. In addition, we are only starting to see their potential in regenerative medicine. Manipulation and culture of PSCs, however, imposes limitations in the quality of these cells and their ability to differentiate into functional cells with physiological function. Here we propose a novel and simple technique based on the transient expression of a single microRNA molecule to expand the differentiation potency of a wide range of PSCs including induced PSCs (iPSCs) as well as embryonic stem cells (ESCs). This method requires no genetic modification of PSCs and achieves stable improvement of the differentiation potential of these cells through several cell passages both in vitro and in vivo.
Collapse
Affiliation(s)
- José González-Martínez
- Cell Division and Cancer group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marcos Malumbres
- Cell Division and Cancer group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
| |
Collapse
|
41
|
von Willebrand disease: what does the future hold? Blood 2021; 137:2299-2306. [PMID: 33662989 DOI: 10.1182/blood.2020008501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
von Willebrand disease (VWD) is characterized by its heterogeneous clinical manifestation, which complicates its diagnosis and management. The clinical management of VWD has remained essentially unchanged over the last 30 years or so, using von Willebrand factor (VWF) concentrates, desmopressin, and anti-fibrinolytic agents as main tools to control bleeding. This is in contrast to hemophilia A, for which a continuous innovative path has led to novel treatment modalities. Despite current VWD management being considered effective, quality-of-life studies consistently reveal a higher than anticipated burden of VWD on patients, which is particularly true for women. Apparently, despite our perceived notion of current therapeutic efficiency, there is space for innovation with the goal of reaching superior efficacy. Developing innovative treatments for VWD is complex, especially given the heterogeneity of the disease and the multifunctional nature of VWF. In this perspective article, we describe several potential strategies that could provide the basis for future VWD treatments. These include genetic approaches, such as gene therapy using dual-vector adenoassociated virus and transcriptional silencing of mutant alleles. Furthermore, protein-based approaches to increase factor FVIII levels in VWD-type 3 or 2N patients are discussed. Finally, antibody-based options to interfere with VWF degradation (for congenital VWD-type 2A or acquired von Willebrand syndrome-type 2A) or increase endogenous VWF levels (for VWD-type 1) are presented. By highlighting these potential strategies, we hope to initiate an innovative path, which ultimately would allow us to better serve VWD patients and their specific needs.
Collapse
|
42
|
Affiliation(s)
- Peter W Andrews
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| |
Collapse
|
43
|
Understanding and Treating Niemann-Pick Type C Disease: Models Matter. Int J Mol Sci 2020; 21:ijms21238979. [PMID: 33256121 PMCID: PMC7730076 DOI: 10.3390/ijms21238979] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Biomedical research aims to understand the molecular mechanisms causing human diseases and to develop curative therapies. So far, these goals have been achieved for a small fraction of diseases, limiting factors being the availability, validity, and use of experimental models. Niemann–Pick type C (NPC) is a prime example for a disease that lacks a curative therapy despite substantial breakthroughs. This rare, fatal, and autosomal-recessive disorder is caused by defects in NPC1 or NPC2. These ubiquitously expressed proteins help cholesterol exit from the endosomal–lysosomal system. The dysfunction of either causes an aberrant accumulation of lipids with patients presenting a large range of disease onset, neurovisceral symptoms, and life span. Here, we note general aspects of experimental models, we describe the line-up used for NPC-related research and therapy development, and we provide an outlook on future topics.
Collapse
|