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Abstract
Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression. The mechanisms of heterochromatin establishment and of heterochromatin maintenance are separable and involve the ability of sequence-specific factors bound to nascent transcripts to recruit chromatin-modifying enzymes. Heterochromatin can spread along the chromatin from nucleation sites. The propensity of heterochromatin to promote its own spreading and inheritance is counteracted by inhibitory factors. Because of its importance for chromosome function, heterochromatin has key roles in the pathogenesis of various human diseases. In this Review, we discuss conserved principles of heterochromatin formation and function using selected examples from studies of a range of eukaryotes, from yeast to human, with an emphasis on insights obtained from unicellular model organisms.
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102
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Gonzales PK, Roberts CM, Fonte V, Jacobsen C, Stein GH, Link CD. Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21. PLoS One 2018; 13:e0194581. [PMID: 29584757 PMCID: PMC5870938 DOI: 10.1371/journal.pone.0194581] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/06/2018] [Indexed: 12/03/2022] Open
Abstract
Trisomy of chromosome 21, the genetic cause of Down syndrome, has the potential to alter expression of genes on chromosome 21, as well as other locations throughout the genome. These transcriptome changes are likely to underlie the Down syndrome clinical phenotypes. We have employed RNA-seq to undertake an in-depth analysis of transcriptome changes resulting from trisomy of chromosome 21, using induced pluripotent stem cells (iPSCs) derived from a single individual with Down syndrome. These cells were originally derived by Li et al, who genetically targeted chromosome 21 in trisomic iPSCs, allowing selection of disomic sibling iPSC clones. Analyses were conducted on trisomic/disomic cell pairs maintained as iPSCs or differentiated into cortical neuronal cultures. In addition to characterization of gene expression levels, we have also investigated patterns of RNA adenosine-to-inosine editing, alternative splicing, and repetitive element expression, aspects of the transcriptome that have not been significantly characterized in the context of Down syndrome. We identified significant changes in transcript accumulation associated with chromosome 21 trisomy, as well as changes in alternative splicing and repetitive element transcripts. Unexpectedly, the trisomic iPSCs we characterized expressed higher levels of neuronal transcripts than control disomic iPSCs, and readily differentiated into cortical neurons, in contrast to another reported study. Comparison of our transcriptome data with similar studies of trisomic iPSCs suggests that trisomy of chromosome 21 may not intrinsically limit neuronal differentiation, but instead may interfere with the maintenance of pluripotency.
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Affiliation(s)
- Patrick K. Gonzales
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, Colorado, United States of America
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Christine M. Roberts
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, Colorado, United States of America
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Virginia Fonte
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, Colorado, United States of America
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Connor Jacobsen
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Gretchen H. Stein
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, Colorado, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Christopher D. Link
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, Colorado, United States of America
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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103
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Urnov FD. Genome Editing B.C. (Before CRISPR): Lasting Lessons from the “Old Testament”. CRISPR J 2018; 1:34-46. [DOI: 10.1089/crispr.2018.29007.fyu] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Fyodor D. Urnov
- Altius Institute for Biomedical Sciences, Seattle, Washington
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104
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Zuo E, Huo X, Yao X, Hu X, Sun Y, Yin J, He B, Wang X, Shi L, Ping J, Wei Y, Ying W, Wei W, Liu W, Tang C, Li Y, Hu J, Yang H. CRISPR/Cas9-mediated targeted chromosome elimination. Genome Biol 2017; 18:224. [PMID: 29178945 PMCID: PMC5701507 DOI: 10.1186/s13059-017-1354-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/26/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The CRISPR/Cas9 system has become an efficient gene editing method for generating cells carrying precise gene mutations, including the rearrangement and deletion of chromosomal segments. However, whether an entire chromosome could be eliminated by this technology is still unknown. RESULTS Here we demonstrate the use of the CRISPR/Cas9 system to eliminate targeted chromosomes. Using either multiple cleavages induced by a single-guide RNA (sgRNA) that targets multiple chromosome-specific sites or a cocktail of multiple sgRNAs, each targeting one specific site, we found that a sex chromosome could be selectively eliminated in cultured cells, embryos, and tissues in vivo. Furthermore, this approach was able to produce a targeted autosome loss in aneuploid mouse embryonic stem cells with an extra human chromosome and human induced pluripotent stem cells with trisomy 21, as well as cancer cells. CONCLUSIONS CRISPR/Cas9-mediated targeted chromosome elimination offers a new approach to develop animal models with chromosome deletions, and a potential therapeutic strategy for human aneuploidy diseases involving additional chromosomes.
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Affiliation(s)
- Erwei Zuo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaona Huo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xuan Yao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xinde Hu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yidi Sun
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jianhang Yin
- State Key Laboratory of Membrane Biology and Minstry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Bingbing He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xing Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Linyu Shi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jie Ping
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232, USA
| | - Yu Wei
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai University, Shanghai, 200444, China
| | - Wenqin Ying
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wei Wei
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Wenjia Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Tang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jiazhi Hu
- State Key Laboratory of Membrane Biology and Minstry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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105
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Ransohoff JD, Wei Y, Khavari PA. The functions and unique features of long intergenic non-coding RNA. Nat Rev Mol Cell Biol 2017; 19:143-157. [PMID: 29138516 DOI: 10.1038/nrm.2017.104] [Citation(s) in RCA: 856] [Impact Index Per Article: 122.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome.
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Affiliation(s)
- Julia D Ransohoff
- Program in Epithelial Biology, Stanford University School of Medicine, California 94305, USA
| | - Yuning Wei
- Program in Epithelial Biology, Stanford University School of Medicine, California 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, California 94305, USA.,Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA
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106
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Creamer KM, Lawrence JB. XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160360. [PMID: 28947659 PMCID: PMC5627162 DOI: 10.1098/rstb.2016.0360] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2017] [Indexed: 12/31/2022] Open
Abstract
XIST RNA triggers the transformation of an active X chromosome into a condensed, inactive Barr body and therefore provides a unique window into transitions of higher-order chromosome architecture. Despite recent progress, how XIST RNA localizes and interacts with the X chromosome remains poorly understood. Genetic engineering of XIST into a trisomic autosome demonstrates remarkable capacity of XIST RNA to localize and comprehensively silence that autosome. Thus, XIST does not require X chromosome-specific sequences but operates on mechanisms available genome-wide. Prior results suggested XIST localization is controlled by attachment to the insoluble nuclear scaffold. Our recent work affirms that scaffold attachment factor A (SAF-A) is involved in anchoring XIST, but argues against the view that SAF-A provides a unimolecular bridge between RNA and the chromosome. Rather, we suggest that a complex meshwork of architectural proteins interact with XIST RNA. Parallel work studying the territory of actively transcribed chromosomes suggests that repeat-rich RNA 'coats' euchromatin and may impact chromosome architecture in a manner opposite of XIST A model is discussed whereby RNA may not just recruit histone modifications, but more directly impact higher-order chromatin condensation via interaction with architectural proteins of the nucleus.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- K M Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - J B Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
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107
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Li T, Zhao H, Han X, Yao J, Zhang L, Guo Y, Shao Z, Jin Y, Lai D. The spontaneous differentiation and chromosome loss in iPSCs of human trisomy 18 syndrome. Cell Death Dis 2017; 8:e3149. [PMID: 29072700 PMCID: PMC5680928 DOI: 10.1038/cddis.2017.565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/04/2017] [Accepted: 09/25/2017] [Indexed: 01/18/2023]
Abstract
Aneuploidy including trisomy results in developmental disabilities and is the leading cause of miscarriages in humans. Unlike trisomy 21, pathogenic mechanisms of trisomy 18 remain unclear. Here, we successfully generated induced pluripotent stem cells (iPSCs) from human amniotic fluid cells (AFCs) with trisomy 18 pregnancies. We found that trisomy 18 iPSCs (18T-iPSCs) were prone to differentiate spontaneously. Intriguingly, 18T-iPSCs lost their extra 18 chromosomes and converted to diploid cells after 10 generations. fluorescence in situ hybridization analysis showed chromosome loss was a random event that might happen in any trisomic cells. Selection undifferentiated cells for passage accelerated the recovery of euploid cells. Overall, our findings indicate the genomic instability of trisomy 18 iPSCs bearing an extra chromosome 18.
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Affiliation(s)
- Ting Li
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Hanzhi Zhao
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200032, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Jiaying Yao
- Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lingling Zhang
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200032, China
| | - Ying Guo
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Zhen Shao
- Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying Jin
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200032, China
| | - Dongmei Lai
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
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108
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Hirota T, Ohta H, Powell BE, Mahadevaiah SK, Ojarikre OA, Saitou M, Turner JMA. Fertile offspring from sterile sex chromosome trisomic mice. Science 2017; 357:932-935. [PMID: 28818972 PMCID: PMC5581950 DOI: 10.1126/science.aam9046] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/04/2017] [Indexed: 12/24/2022]
Abstract
Having the correct number of chromosomes is vital for normal development and health. Sex chromosome trisomy affects 0.1% of the human population and is associated with infertility. We show that during reprogramming to induced pluripotent stem cells (iPSCs), fibroblasts from sterile trisomic XXY and XYY mice lose the extra sex chromosome through a phenomenon we term trisomy-biased chromosome loss (TCL). Resulting euploid XY iPSCs can be differentiated into the male germ cell lineage and functional sperm that can be used in intracytoplasmic sperm injection to produce chromosomally normal, fertile offspring. Sex chromosome loss is comparatively infrequent during mouse XX and XY iPSC generation. TCL also applies to other chromosomes, generating euploid iPSCs from cells of a Down syndrome mouse model. It can also create euploid iPSCs from human trisomic patient fibroblasts. The findings have relevance to overcoming infertility and other trisomic phenotypes.
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Affiliation(s)
- Takayuki Hirota
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Hiroshi Ohta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
- Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Kyoto, 606-8501, Japan
| | - Benjamin E Powell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Obah A Ojarikre
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
- Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Kyoto, 606-8501, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, 606-8501, Japan
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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109
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Chandrasekaran AP, Song M, Ramakrishna S. Genome editing: a robust technology for human stem cells. Cell Mol Life Sci 2017; 74:3335-3346. [PMID: 28405721 PMCID: PMC11107609 DOI: 10.1007/s00018-017-2522-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/20/2022]
Abstract
Human pluripotent stem cells comprise induced pluripotent and embryonic stem cells, which have tremendous potential for biological and therapeutic applications. The development of efficient technologies for the targeted genome alteration of stem cells in disease models is a prerequisite for utilizing stem cells to their full potential. Genome editing of stem cells is possible with the help of synthetic nucleases that facilitate site-specific modification of a gene of interest. Recent advances in genome editing techniques have improved the efficiency and speed of the development of stem cells for human disease models. Zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system are powerful tools for editing DNA at specific loci. Here, we discuss recent technological advances in genome editing with site-specific nucleases in human stem cells.
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Affiliation(s)
| | - Minjung Song
- Division of Bioindustry, Department of Food Biotechnology, College of Medical and Life Science, Silla University, Seoul, Republic of Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Republic of Korea.
- College of Medicine, Hanyang University, Seoul, Republic of Korea.
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110
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Torkamani A, Andersen KG, Steinhubl SR, Topol EJ. High-Definition Medicine. Cell 2017; 170:828-843. [PMID: 28841416 DOI: 10.1016/j.cell.2017.08.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/10/2017] [Accepted: 08/04/2017] [Indexed: 12/13/2022]
Abstract
The foundation for a new era of data-driven medicine has been set by recent technological advances that enable the assessment and management of human health at an unprecedented level of resolution-what we refer to as high-definition medicine. Our ability to assess human health in high definition is enabled, in part, by advances in DNA sequencing, physiological and environmental monitoring, advanced imaging, and behavioral tracking. Our ability to understand and act upon these observations at equally high precision is driven by advances in genome editing, cellular reprogramming, tissue engineering, and information technologies, especially artificial intelligence. In this review, we will examine the core disciplines that enable high-definition medicine and project how these technologies will alter the future of medicine.
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Affiliation(s)
- Ali Torkamani
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Kristian G Andersen
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven R Steinhubl
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric J Topol
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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111
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Capalbo A, Hoffmann ER, Cimadomo D, Maria Ubaldi F, Rienzi L. Human female meiosis revised: new insights into the mechanisms of chromosome segregation and aneuploidies from advanced genomics and time-lapse imaging. Hum Reprod Update 2017; 23:706-722. [DOI: 10.1093/humupd/dmx026] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/11/2017] [Indexed: 12/14/2022] Open
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112
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Mussolino C, Alzubi J, Pennucci V, Turchiano G, Cathomen T. Genome and Epigenome Editing to Treat Disorders of the Hematopoietic System. Hum Gene Ther 2017; 28:1105-1115. [PMID: 28806883 DOI: 10.1089/hum.2017.149] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The possibility of editing complex genomes in a targeted fashion has revolutionized basic research as well as biomedical and biotechnological applications in the last 5 years. The targeted introduction of genetic changes has allowed researchers to create smart model systems for basic research, bio-engineers to modify crops and farm animals, and translational scientists to develop novel treatment approaches for inherited and acquired disorders for which curative treatment options are not yet available. With the rapid development of genome editing tools, in particular zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the CRISPR-Cas system, a wide range of therapeutic options have been-and will be-developed at an unprecedented speed, which will change the clinical routine of various disciplines in a revolutionary way. This review summarizes the fundamentals of genome editing and the current state of research. It particularly focuses on the advances made in employing engineered nucleases in hematopoietic stem cells for the treatment of primary immunodeficiencies and hemoglobinopathies, provides a perspective of combining gene editing with the chimeric antigen receptor T cell technology, and concludes by presenting targeted epigenome editing as a novel potential treatment option.
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Affiliation(s)
- Claudio Mussolino
- 1 Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Germany .,2 Center for Chronic Immunodeficiency, Medical Center - University of Freiburg , Germany
| | - Jamal Alzubi
- 1 Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Germany .,2 Center for Chronic Immunodeficiency, Medical Center - University of Freiburg , Germany
| | - Valentina Pennucci
- 1 Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Germany .,2 Center for Chronic Immunodeficiency, Medical Center - University of Freiburg , Germany
| | - Giandomenico Turchiano
- 1 Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Germany .,2 Center for Chronic Immunodeficiency, Medical Center - University of Freiburg , Germany
| | - Toni Cathomen
- 1 Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Germany .,2 Center for Chronic Immunodeficiency, Medical Center - University of Freiburg , Germany .,3 Faculty of Medicine, University of Freiburg , Freiburg, Germany
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113
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Tang J, Yu Y, Yang W. Long noncoding RNA and its contribution to autism spectrum disorders. CNS Neurosci Ther 2017; 23:645-656. [PMID: 28635106 PMCID: PMC6492731 DOI: 10.1111/cns.12710] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022] Open
Abstract
Recent studies have indicated that long noncoding RNAs (lncRNAs) play important roles in multiple processes, such as epigenetic regulation, gene expression regulation, development, nutrition-related and other diseases, toxic response, and response to drugs. Although the functional roles and mechanisms of several lncRNAs have been discovered, a better understanding of the vast majority of lncRNAs remains elusive. To understand the functional roles and mechanisms of lncRNAs is critical because these transcripts represent the majority of the transcriptional output of the mammalian genome. Recent studies have also suggested that lncRNAs are more abundant in the human brain and are involved in neurodevelopment and neurodevelopmental disorders, including autism spectrum disorders (ASDs). In this study, we review several known functions of lncRNAs and the potential contribution of lncRNAs to ASDs and to other genetic syndromes that have a similar clinical presentation to ASDs, such as fragile X syndrome and Rett syndrome.
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Affiliation(s)
- Jie Tang
- The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Preventive MedicineSchool of Public HealthGuangzhou Medical UniversityXinzaoPanyu DistrictGuangzhouChina
| | - Yizhen Yu
- Department of Child and Women Health CareSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wei Yang
- Department of Nutrition and Food HygieneHubei Key Laboratory of Food Nutrition and SafetyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Nutrition and Food HygieneMOE Key Lab of Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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114
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115
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Abstract
It is extremely rare for a single experiment to be so impactful and timely that it shapes and forecasts the experiments of the next decade. Here, we review how two such experiments-the generation of human induced pluripotent stem cells (iPSCs) and the development of CRISPR/Cas9 technology-have fundamentally reshaped our approach to biomedical research, stem cell biology, and human genetics. We will also highlight the previous knowledge that iPSC and CRISPR/Cas9 technologies were built on as this groundwork demonstrated the need for solutions and the benefits that these technologies provided and set the stage for their success.
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Affiliation(s)
- Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research and Department of Biology, MIT, Cambridge, MA 02142, USA
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116
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Minami T. Pathophysiology Derived from Down Syndrome Related Genes on the 21st Chromosome. YAKUGAKU ZASSHI 2017; 137:791-793. [PMID: 28674288 DOI: 10.1248/yakushi.16-00236-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takashi Minami
- Division of Vascular Biology, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo
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117
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Abstract
Human genetic studies have been the driving force in bringing to light the underlying biology of psychiatric conditions. As these studies fill in the gaps in our knowledge of the mechanisms at play, we will be better equipped to design therapies in rational and targeted ways, or repurpose existing therapies in previously unanticipated ways. This review is intended for those unfamiliar with psychiatric genetics as a field and provides a primer on different modes of genetic variation, the technologies currently used to probe them, and concepts that provide context for interpreting the gene-phenotype relationship. Like other subfields in human genetics, psychiatric genetics is moving from microarray technology to sequencing-based approaches as barriers of cost and expertise are removed, and the ramifications of this transition are discussed here. A summary is then given of recent genetic discoveries in a number of neuropsychiatric conditions, with particular emphasis on neurodevelopmental conditions. The general impact of genetics on drug development has been to underscore the extensive etiological heterogeneity in seemingly cohesive diagnostic categories. Consequently, the path forward is not in therapies hoping to reach large swaths of patients sharing a clinically defined diagnosis, but rather in targeting patients belonging to specific "biotypes" defined through a combination of objective, quantifiable data, including genotype.
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Affiliation(s)
- Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
- Department of Biomedical Engineering, University of Iowa College of Engineering, Iowa City, IA, USA.
- Department of Communication Sciences and Disorders, University of Iowa College of Liberal Arts and Sciences, Iowa City, IA, USA.
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA.
- Genetics Cluster Initiative, University of Iowa, Iowa City, IA, USA.
- The DeLTA Center, University of Iowa, Iowa City, IA, USA.
- University of Iowa Informatics Initiative, University of Iowa, Iowa City, IA, USA.
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118
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Quan Z, Zheng D, Qing H. Regulatory Roles of Long Non-Coding RNAs in the Central Nervous System and Associated Neurodegenerative Diseases. Front Cell Neurosci 2017; 11:175. [PMID: 28713244 PMCID: PMC5491930 DOI: 10.3389/fncel.2017.00175] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Accumulating studies have revealed that the human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), which participate in multiple biological networks modulating gene expression via transcriptional, post-transcriptional and epigenetic regulation. Strikingly, a large fraction of tissue-specific lncRNAs are expressed in the Central Nervous System (CNS) with precisely regulated temporal and spatial expression patterns. These brain-specific lncRNAs are also featured with the cell-type specificity, the highest signals of evolutionary conservation, and their preferential location adjacent to brain-expressed protein-coding genes. Mounting evidence has indicated dysregulation or mutations in lncRNA gene loci are associated with a variety of CNS-associated neurodegenerative disorders, such as Alzheimer's, Parkinson's, Huntington's diseases, Amyotrophic Lateral Sclerosis and others. However, how lncRNAs contribute to these disorders remains to be further explored and studied. In this review article, we systematically and comprehensively summarize the current studies of lncRNAs, demonstrate the specificity of lncRNAs expressed in the brain, their functions during neural development and expression profiles in major cell types of the CNS, highlight the regulatory mechanisms of several studied lncRNAs that may play essential roles in the pathophysiology of neurodegenerative diseases, and discuss the current challenges and future perspectives of lncRNA studies involved in neurodegenerative and other diseases.
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Affiliation(s)
- Zhenzhen Quan
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Da Zheng
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Hong Qing
- School of Life Science, Beijing Institute of TechnologyBeijing, China
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119
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Belling K, Russo F, Jensen AB, Dalgaard MD, Westergaard D, Rajpert-De Meyts E, Skakkebæk NE, Juul A, Brunak S. Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity. Hum Mol Genet 2017; 26:1219-1229. [PMID: 28369266 PMCID: PMC5390676 DOI: 10.1093/hmg/ddx014] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/21/2016] [Indexed: 01/10/2023] Open
Abstract
Klinefelter syndrome (KS) (47,XXY) is the most common male sex chromosome aneuploidy. Diagnosis and clinical supervision remain a challenge due to varying phenotypic presentation and insufficient characterization of the syndrome. Here we combine health data-driven epidemiology and molecular level systems biology to improve the understanding of KS and the molecular interplay influencing its comorbidities. In total, 78 overrepresented KS comorbidities were identified using in- and out-patient registry data from the entire Danish population covering 6.8 million individuals. The comorbidities extracted included both clinically well-known (e.g. infertility and osteoporosis) and still less established KS comorbidities (e.g. pituitary gland hypofunction and dental caries). Several systems biology approaches were applied to identify key molecular players underlying KS comorbidities: Identification of co-expressed modules as well as central hubs and gene dosage perturbed protein complexes in a KS comorbidity network build from known disease proteins and their protein–protein interactions. The systems biology approaches together pointed to novel aspects of KS disease phenotypes including perturbed Jak-STAT pathway, dysregulated genes important for disturbed immune system (IL4), energy balance (POMC and LEP) and erythropoietin signalling in KS. We present an extended epidemiological study that links KS comorbidities to the molecular level and identify potential causal players in the disease biology underlying the identified comorbidities.
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Affiliation(s)
- Kirstine Belling
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Russo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders B Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marlene D Dalgaard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Research and Research Training Centre in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Niels E Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Research and Research Training Centre in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Research and Research Training Centre in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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120
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Lamas-Toranzo I, Pericuesta E, Bermejo-Álvarez P. Memories of an X-chromosome. Stem Cell Investig 2017; 4:27. [PMID: 28447042 DOI: 10.21037/sci.2017.03.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 03/07/2017] [Indexed: 11/06/2022]
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121
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A Pair of Maternal Chromosomes Derived from Meiotic Nondisjunction in Trisomy 21 Affects Nuclear Architecture and Transcriptional Regulation. Sci Rep 2017; 7:764. [PMID: 28396582 PMCID: PMC5429678 DOI: 10.1038/s41598-017-00714-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/10/2017] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes are organised into complex higher-order structures within the nucleus, and the three-dimensional arrangement of chromosomes is functionally important for global gene regulation. The existence of supernumerary chromosome 21 in Down syndrome may perturb the nuclear architecture at different levels, which is normally optimised to maintain the physiological balance of gene expression. However, it has not been clearly elucidated whether and how aberrant configuration of chromosomes affects gene activities. To investigate the effects of trisomy 21 on nuclear organisation and gene expression, we performed three-dimensional fluorescent imaging analysis of chromosome-edited human induced pluripotent stem cells (iPSCs), which enabled identification of the parental origin of the three copies of chromosome 21. We found that two copies of maternal chromosomes resulting from meiotic nondisjunction had a higher tendency to form an adjacent pair and were located relatively distant from the nuclear membrane, suggesting the conserved interaction between these homologous chromosomes. Transcriptional profiling of parental-origin-specific corrected disomy 21 iPSC lines indicated upregulated expression of the maternal alleles for a group of genes, which was accompanied by a fluctuating expression pattern. These results suggest the unique effects of a pair of maternal chromosomes in trisomy 21, which may contribute to the pathological phenotype.
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122
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M Lee Y, Zampieri BL, Scott-McKean JJ, Johnson MW, Costa ACS. Generation of Integration-Free Induced Pluripotent Stem Cells from Urine-Derived Cells Isolated from Individuals with Down Syndrome. Stem Cells Transl Med 2017; 6:1465-1476. [PMID: 28371411 PMCID: PMC5689751 DOI: 10.1002/sctm.16-0128] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 02/20/2017] [Indexed: 01/19/2023] Open
Abstract
Down syndrome (DS) is a genetic disorder caused by trisomy 21 (T21). Over the past two decades, the use of mouse models has led to significant advances in the understanding of mechanisms underlying various phenotypic features and comorbidities secondary to T21 and even informed the design of clinical trials aimed at enhancing the cognitive abilities of persons with DS. In spite of its success, this approach has been plagued by all the typical limitations of rodent modeling of human disorders and diseases. Recently, several laboratories have succeeded in producing T21 human induced pluripotent stem cells (T21-iPSCs) from individuals with DS, which is emerging as a promising complementary tool for the study of DS. Here, we describe the method by which we generated 10 T21-iPSC lines from epithelial cells in urine samples, presumably from kidney epithelial origin, using nonintegrating episomal vectors. We also show that these iPSCs maintain chromosomal stability for well over 20 passages and are more sensitive to proteotoxic stress than euploid iPSCs. Furthermore, these iPSC lines can be differentiated into glutamatergic neurons and cardiomyocytes. By culturing urine-derived cells and maximizing the efficiency of episomal vector transfection, we have been able to generate iPSCs noninvasively and effectively from participants with DS in an ongoing clinical trial, and thus address most shortcomings of previously generated T21-iPSC lines. These techniques should extend the application of iPSCs in modeling DS and other neurodevelopmental and neurodegenerative disorders, and may lead to future human cell-based platforms for high-throughput drug screening. Stem Cells Translational Medicine 2017;6:1465-1476.
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Affiliation(s)
- Young M Lee
- Division of Pediatric Neurology, Department of Pediatrics
| | | | | | - Mark W Johnson
- Division of Pediatric Neurology, Department of Pediatrics
| | - Alberto C S Costa
- Division of Pediatric Neurology, Department of Pediatrics.,Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, USA
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123
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Robert C, Pasquier L, Cohen D, Fradin M, Canitano R, Damaj L, Odent S, Tordjman S. Role of Genetics in the Etiology of Autistic Spectrum Disorder: Towards a Hierarchical Diagnostic Strategy. Int J Mol Sci 2017; 18:E618. [PMID: 28287497 PMCID: PMC5372633 DOI: 10.3390/ijms18030618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 12/27/2022] Open
Abstract
Progress in epidemiological, molecular and clinical genetics with the development of new techniques has improved knowledge on genetic syndromes associated with autism spectrum disorder (ASD). The objective of this article is to show the diversity of genetic disorders associated with ASD (based on an extensive review of single-gene disorders, copy number variants, and other chromosomal disorders), and consequently to propose a hierarchical diagnostic strategy with a stepwise evaluation, helping general practitioners/pediatricians and child psychiatrists to collaborate with geneticists and neuropediatricians, in order to search for genetic disorders associated with ASD. The first step is a clinical investigation involving: (i) a child psychiatric and psychological evaluation confirming autism diagnosis from different observational sources and assessing autism severity; (ii) a neuropediatric evaluation examining neurological symptoms and developmental milestones; and (iii) a genetic evaluation searching for dysmorphic features and malformations. The second step involves laboratory and if necessary neuroimaging and EEG studies oriented by clinical results based on clinical genetic and neuropediatric examinations. The identification of genetic disorders associated with ASD has practical implications for diagnostic strategies, early detection or prevention of co-morbidity, specific treatment and follow up, and genetic counseling.
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Affiliation(s)
- Cyrille Robert
- Pôle Hospitalo-Universitaire de Psychiatrie de l'Enfant et de l'Adolescent (PHUPEA), University of Rennes 1 and Centre Hospitalier Guillaume Régnier, 35200 Rennes, France.
- Service de Génétique Clinique, Centre de Référence Maladies Rares Anomalies du Développement (Centre Labellisé pour les Anomalies du Développement de l'Ouest: CLAD Ouest), Hôpital Sud, Centre Hospitalier Universitaire de Rennes, 35200 Rennes, France.
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre de Référence Maladies Rares Anomalies du Développement (Centre Labellisé pour les Anomalies du Développement de l'Ouest: CLAD Ouest), Hôpital Sud, Centre Hospitalier Universitaire de Rennes, 35200 Rennes, France.
| | - David Cohen
- Hospital-University Department of Child and Adolescent Psychiatry, Pitié-Salpétrière Hospital, Paris 6 University, 75013 Paris, France.
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Maladies Rares Anomalies du Développement (Centre Labellisé pour les Anomalies du Développement de l'Ouest: CLAD Ouest), Hôpital Sud, Centre Hospitalier Universitaire de Rennes, 35200 Rennes, France.
| | - Roberto Canitano
- Division of Child and Adolescent Neuropsychiatry, University Hospital of Siena, 53100 Siena, Italy.
| | - Léna Damaj
- Service de Génétique Clinique, Centre de Référence Maladies Rares Anomalies du Développement (Centre Labellisé pour les Anomalies du Développement de l'Ouest: CLAD Ouest), Hôpital Sud, Centre Hospitalier Universitaire de Rennes, 35200 Rennes, France.
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence Maladies Rares Anomalies du Développement (Centre Labellisé pour les Anomalies du Développement de l'Ouest: CLAD Ouest), Hôpital Sud, Centre Hospitalier Universitaire de Rennes, 35200 Rennes, France.
| | - Sylvie Tordjman
- Pôle Hospitalo-Universitaire de Psychiatrie de l'Enfant et de l'Adolescent (PHUPEA), University of Rennes 1 and Centre Hospitalier Guillaume Régnier, 35200 Rennes, France.
- Laboratory of Psychology of Perception, University Paris Descartes, 75270 Paris, France.
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124
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de Wert G, Dondorp W, Bianchi DW. Fetal therapy for Down syndrome: an ethical exploration. Prenat Diagn 2017; 37:222-228. [PMID: 28004394 PMCID: PMC10066512 DOI: 10.1002/pd.4995] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/11/2016] [Accepted: 12/15/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Parallel to recent advances in prenatal screening for Down syndrome (DS), therapies for different aspects of the condition have become available. As intellectual disability is a key aspect, this is an active area for research. Several groups have hypothesized that prenatal interventions will give better chances at improving cognitive functioning in persons with DS than postnatal treatment. Clinical trials are being developed. METHOD We first discuss the ethical pros and cons of trying to improve cognitive functioning in persons with DS to see if there are categorical objections to the general idea, and then move on to explore ethically relevant aspects of the prospect of developing fetal therapy for DS (FTDS). RESULTS Only on the basis of a one-dimensional emphasis on the social model of disability would (fetal) therapy aimed at cognitive improvement be inherently problematic. CONCLUSIONS Inviting pregnant women to participate in FTDS-research should be based on adequate pre-clinical trials, as well as information aimed at avoiding the so-called 'therapeutic misconception'. Should FTDS be proven to be effective and safe, women carrying a fetus with trisomy 21 who have decided to continue the pregnancy may have a moral obligation to make use of this option. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Guido de Wert
- Department of Health, Ethics & Society, School for Oncology and Developmental Biology (GROW), School for Public Health and Primary Care (CAPHRI); Maastricht University; Maastricht The Netherlands
| | - Wybo Dondorp
- Department of Health, Ethics & Society, School for Oncology and Developmental Biology (GROW), School for Public Health and Primary Care (CAPHRI); Maastricht University; Maastricht The Netherlands
| | - Diana W. Bianchi
- Mother Infant Research Institute; Tufts Medical Center and Tufts University School of Medicine; Boston MA US
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125
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Tordjman S, Cohen D, Coulon N, Anderson GM, Botbol M, Canitano R, Roubertoux PL. Reframing autism as a behavioral syndrome and not a specific mental disorder: Implications of genetic and phenotypic heterogeneity. Neurosci Biobehav Rev 2017; 80:210. [PMID: 28153685 DOI: 10.1016/j.neubiorev.2017.01.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/18/2016] [Accepted: 01/23/2017] [Indexed: 12/13/2022]
Abstract
Clinical and molecular genetics have advanced current knowledge on genetic disorders associated with autism. A review of diverse genetic disorders associated with autism is presented and for the first time discussed extensively with regard to possible common underlying mechanisms leading to a similar cognitive-behavioral phenotype of autism. The possible role of interactions between genetic and environmental factors, including epigenetic mechanisms, is in particular examined. Finally, the pertinence of distinguishing non-syndromic autism (isolated autism) from syndromic autism (autism associated with genetic disorders) will be reconsidered. Given the high genetic and etiological heterogeneity of autism, autism can be viewed as a behavioral syndrome related to known genetic disorders (syndromic autism) or currently unknown disorders (apparent non-syndromic autism), rather than a specific categorical mental disorder. It highlights the need to study autism phenotype and developmental trajectory through a multidimensional, non-categorical approach with multivariate analyses within autism spectrum disorder but also across mental disorders, and to conduct systematically clinical genetic examination searching for genetic disorders in all individuals (children but also adults) with autism.
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Affiliation(s)
- S Tordjman
- Pôle Hospitalo-Universitaire de Psychiatrie de l'Enfant et de l'Adolescent, Université de Rennes 1 and Centre Hospitalier Guillaume Régnier, 154 rue de Châtillon, 35200 Rennes, France; Laboratoire Psychologie de la Perception, Université Paris Descartes and CNRS UMR 8158, Paris, France.
| | - D Cohen
- Department of Child and Adolescent Psychiatry, AP-HP, GH Pitié-Salpétrière, CNRS FRE 2987, Université Pierre et Marie Curie, Paris, France
| | - N Coulon
- Laboratoire Psychologie de la Perception, Université Paris Descartes and CNRS UMR 8158, Paris, France
| | - G M Anderson
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - M Botbol
- Departement Hospitalo-Universitaire de Psychiatrie de l'Enfant et de l'Adolescent, Université de Bretagne Occidentale, Brest, France
| | - R Canitano
- Division of Child and Adolescent Neuropsychiatry, University Hospital of Siena, Siena, Italy
| | - P L Roubertoux
- Aix Marseille Université, GMGF, Inserm, UMR_S 910, 13385, Marseille, France
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126
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Yang T, Yildirim E. Epigenetic and LncRNA-Mediated Regulation of X Chromosome Inactivation and Its Impact on Pathogenesis. CURRENT PATHOBIOLOGY REPORTS 2017. [DOI: 10.1007/s40139-017-0120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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127
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DeWitt JJ, Hecht PM, Grepo N, Wilkinson B, Evgrafov OV, Morris KV, Knowles JA, Campbell DB. Transcriptional Gene Silencing of the Autism-Associated Long Noncoding RNA MSNP1AS in Human Neural Progenitor Cells. Dev Neurosci 2016; 38:375-383. [PMID: 28030860 DOI: 10.1159/000453258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/08/2016] [Indexed: 12/21/2022] Open
Abstract
The long noncoding RNA MSNP1AS (moesin pseudogene 1, antisense) is a functional element that was previously associated with autism spectrum disorder (ASD) with genome-wide significance. Expression of MSNP1AS was increased 12-fold in the cerebral cortex of individuals with ASD and 22-fold in individuals with a genome-wide significantly associated ASD genetic marker on chromosome 5p14.1. Overexpression of MSNP1AS in human neuronal cells caused decreased expression of moesin protein, which is involved in neuronal process stability. In this study, we hypothesize that MSNP1AS knockdown impacts global transcriptome levels. We transfected the human neural progenitor cell line SK- N-SH with constructs that caused a 50% suppression of MSNP1AS expression. After 24 h, cells were harvested for total RNA isolation. Strand-specific RNA sequencing analysis indicated altered expression of 1,352 genes, including altered expression of 318 genes following correction for multiple comparisons. Expression of the OAS2 gene was increased >150-fold, a result that was validated by quantitative PCR. Gene ontology analysis of the 318 genes with altered expression following correction for multiple comparisons indicated that upregulated genes were significantly enriched for genes involved in immune response, and downregulated genes were significantly enriched for genes involved in chromatin remodeling. These data indicate multiple transcriptional and translational functions of MSNP1AS that impact ASD-relevant biological processes. Chromatin remodeling and immune response are biological processes implicated by genes with rare mutations associated with ASD. Our data suggest that the functional elements implicated by association of common genetic variants impact the same biological processes, suggesting a possible shared common molecular pathway of ASD.
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Affiliation(s)
- Jessica J DeWitt
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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128
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Abstract
Down syndrome (also known as trisomy 21) is the model human phenotype for all genomic gain dosage imbalances, including microduplications. The functional genomic exploration of the post-sequencing years of chromosome 21, and the generation of numerous cellular and mouse models, have provided an unprecedented opportunity to decipher the molecular consequences of genome dosage imbalance. Studies of Down syndrome could provide knowledge far beyond the well-known characteristics of intellectual disability and dysmorphic features, as several other important features, including congenital heart defects, early ageing, Alzheimer disease and childhood leukaemia, are also part of the Down syndrome phenotypic spectrum. The elucidation of the molecular mechanisms that cause or modify the risk for different Down syndrome phenotypes could lead to the introduction of previously unimaginable therapeutic options.
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129
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Generation of Cholinergic and Dopaminergic Interneurons from Human Pluripotent Stem Cells as a Relevant Tool for In Vitro Modeling of Neurological Disorders Pathology and Therapy. Stem Cells Int 2016; 2016:5838934. [PMID: 28105055 PMCID: PMC5220531 DOI: 10.1155/2016/5838934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/24/2023] Open
Abstract
The cellular and molecular bases of neurological diseases have been studied for decades; however, the underlying mechanisms are not yet fully elucidated. Compared with other disorders, diseases of the nervous system have been very difficult to study mainly due to the inaccessibility of the human brain and live neurons in vivo or in vitro and difficulties in examination of human postmortem brain tissue. Despite the availability of various genetically engineered animal models, these systems are still not adequate enough due to species variation and differences in genetic background. Human induced pluripotent stem cells (hiPSCs) reprogrammed from patient somatic cells possess the potential to differentiate into any cell type, including neural progenitor cells and postmitotic neurons; thus, they open a new area to in vitro modeling of neurological diseases and their potential treatment. Currently, many protocols for generation of various neuronal subtypes are being developed; however, most of them still require further optimization. Here, we highlight accomplishments made in the generation of dopaminergic and cholinergic neurons, the two subtypes most affected in Alzheimer's and Parkinson's diseases and indirectly affected in Huntington's disease. Furthermore, we discuss the potential role of hiPSC-derived neurons in the modeling and treatment of neurological diseases related to dopaminergic and cholinergic system dysfunction.
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130
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Patel S, Bonora G, Sahakyan A, Kim R, Chronis C, Langerman J, Fitz-Gibbon S, Rubbi L, Skelton RJP, Ardehali R, Pellegrini M, Lowry WE, Clark AT, Plath K. Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation. Cell Rep 2016; 18:54-67. [PMID: 27989715 DOI: 10.1016/j.celrep.2016.11.054] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/09/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022] Open
Abstract
Applications of embryonic stem cells (ESCs) require faithful chromatin changes during differentiation, but the fate of the X chromosome state in differentiating ESCs is unclear. Female human ESC lines either carry two active X chromosomes (XaXa), an Xa and inactive X chromosome with or without XIST RNA coating (XiXIST+Xa;XiXa), or an Xa and an eroded Xi (XeXa) where the Xi no longer expresses XIST RNA and has partially reactivated. Here, we established XiXa, XeXa, and XaXa ESC lines and followed their X chromosome state during differentiation. Surprisingly, we found that the X state pre-existing in primed ESCs is maintained in differentiated cells. Consequently, differentiated XeXa and XaXa cells lacked XIST, did not induce X inactivation, and displayed higher X-linked gene expression than XiXa cells. These results demonstrate that X chromosome dosage compensation is not required for ESC differentiation. Our data imply that XiXIST+Xa ESCs are most suited for downstream applications and show that all other X states are abnormal byproducts of our ESC derivation and propagation method.
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Affiliation(s)
- Sanjeet Patel
- Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giancarlo Bonora
- Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rachel Kim
- Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Justin Langerman
- Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sorel Fitz-Gibbon
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rhys J P Skelton
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Reza Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William E Lowry
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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131
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Epigenomic engineering for Down syndrome. Neurosci Biobehav Rev 2016; 71:323-327. [DOI: 10.1016/j.neubiorev.2016.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/11/2016] [Accepted: 09/15/2016] [Indexed: 12/27/2022]
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132
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Brigida AL, Siniscalco D. Induced pluripotent stem cells as a cellular model for studying Down Syndrome. J Stem Cells Regen Med 2016; 12:54-60. [PMID: 28096629 PMCID: PMC5227104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/27/2016] [Indexed: 05/22/2024]
Abstract
Down Syndrome (DS), or Trisomy 21 Syndrome, is one of the most common genetic diseases. It is a chromosomal abnormality caused by a duplication of chromosome 21. DS patients show the presence of a third copy (or a partial third copy) of chromosome 21 (trisomy), as result of meiotic errors. These patients suffer of many health problems, such as intellectual disability, congenital heart disease, duodenal stenosis, Alzheimer's disease, leukemia, immune system deficiencies, muscle hypotonia and motor disorders. About one in 1000 babies born each year are affected by DS. Alterations in the dosage of genes located on chromosome 21 (also called HSA21) are responsible for the DS phenotype. However, the molecular pathogenic mechanisms of DS triggering are still not understood; newest evidences suggest the involvement of epigenetic mechanisms. For obvious ethical reasons, studies performed on DS patients, as well as on human trisomic tissues are limited. Some authors have proposed mouse models of this syndrome. However, not all the features of the syndrome are represented. Stem cells are considered the future of molecular and regenerative medicine. Several types of stem cells could provide a valid approach to offer a potential treatment for some untreatable human diseases. Stem cells also represent a valid system to develop new cell-based drugs and/or a model to study molecular disease pathways. Among stem cell types, patient-derived induced pluripotent stem (iPS) cells offer some advantages for cell and tissue replacement, engineering and studying: self-renewal capacity, pluripotency and ease of accessibility to donor tissues. These cells can be reprogrammed into completely different cellular types. They are derived from adult somatic cells via reprogramming with ectopic expression of four transcription factors (Oct3/4, Sox2, c-Myc and Klf4; or, Oct3/4, Sox2, Nanog, and Lin28). By reprogramming cells from DS patients, it is possible to obtain new tissue with the same genetic background, offering a valuable tool for studying this genetic disease and to design customized patient-specific stem cell therapies.
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Affiliation(s)
- Anna Lisa Brigida
- Department of Experimental Medicine, Second University of Naples, 80138 Napoli, Italy.
| | - Dario Siniscalco
- Department of Experimental Medicine, Second University of Naples, 80138 Napoli, Italy.
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133
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Brigida AL, Siniscalco D. Induced pluripotent stem cells as a cellular model for studying Down Syndrome. J Stem Cells Regen Med 2016. [PMID: 28096629 PMCID: PMC5227104 DOI: 10.46582/jsrm.1202009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Down Syndrome (DS), or Trisomy 21 Syndrome, is one of the most common genetic diseases. It is a chromosomal abnormality caused by a duplication of chromosome 21. DS patients show the presence of a third copy (or a partial third copy) of chromosome 21 (trisomy), as result of meiotic errors. These patients suffer of many health problems, such as intellectual disability, congenital heart disease, duodenal stenosis, Alzheimer’s disease, leukemia, immune system deficiencies, muscle hypotonia and motor disorders. About one in 1000 babies born each year are affected by DS. Alterations in the dosage of genes located on chromosome 21 (also called HSA21) are responsible for the DS phenotype. However, the molecular pathogenic mechanisms of DS triggering are still not understood; newest evidences suggest the involvement of epigenetic mechanisms. For obvious ethical reasons, studies performed on DS patients, as well as on human trisomic tissues are limited. Some authors have proposed mouse models of this syndrome. However, not all the features of the syndrome are represented. Stem cells are considered the future of molecular and regenerative medicine. Several types of stem cells could provide a valid approach to offer a potential treatment for some untreatable human diseases. Stem cells also represent a valid system to develop new cell-based drugs and/or a model to study molecular disease pathways. Among stem cell types, patient-derived induced pluripotent stem (iPS) cells offer some advantages for cell and tissue replacement, engineering and studying: self-renewal capacity, pluripotency and ease of accessibility to donor tissues. These cells can be reprogrammed into completely different cellular types. They are derived from adult somatic cells via reprogramming with ectopic expression of four transcription factors (Oct3/4, Sox2, c-Myc and Klf4; or, Oct3/4, Sox2, Nanog, and Lin28). By reprogramming cells from DS patients, it is possible to obtain new tissue with the same genetic background, offering a valuable tool for studying this genetic disease and to design customized patient-specific stem cell therapies.
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Affiliation(s)
- Anna Lisa Brigida
- Department of Experimental Medicine, Second University of Naples, 80138 Napoli, Italy
| | - Dario Siniscalco
- Department of Experimental Medicine, Second University of Naples, 80138 Napoli, Italy
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134
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Kim T, Plona K, Wynshaw-Boris A. A novel system for correcting large-scale chromosomal aberrations: ring chromosome correction via reprogramming into induced pluripotent stem cell (iPSC). Chromosoma 2016; 126:457-463. [PMID: 27882407 DOI: 10.1007/s00412-016-0621-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/13/2016] [Accepted: 11/15/2016] [Indexed: 01/20/2023]
Abstract
Approximately 1 in 500 newborns are born with chromosomal abnormalities that include trisomies, translocations, large deletions, and duplications. There is currently no therapeutic approach for correcting such chromosomal aberrations in vivo or in vitro. When we attempted to produce induced pluripotent stem cell (iPSC) models from patient-derived fibroblasts that contained ring chromosomes, we found that the ring chromosomes were eliminated and replaced by duplicated normal copies of chromosomes through a mechanism of uniparental isodisomy (Bershteyn et al. 2014, Nature 507:99). The discovery of this previously unforeseen system for aberrant chromosome correction during reprogramming enables us for the first time to model and understand this process of cell-autonomous correction of ring chromosomes during human patient somatic cell reprograming to iPSCs. This knowledge could lead to a potential therapeutic strategy to correct common large-scale chromosomal aberrations, termed "chromosome therapy".
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Affiliation(s)
- Taehyun Kim
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Kathleen Plona
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anthony Wynshaw-Boris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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135
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Plona K, Kim T, Halloran K, Wynshaw-Boris A. Chromosome therapy: Potential strategies for the correction of severe chromosome aberrations. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:422-430. [PMID: 27813255 DOI: 10.1002/ajmg.c.31530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Large chromosomal aberrations occur commonly during development, resulting in complex and multisystem diseases. In spite of this high frequency, there are currently no means for correcting these disorders due to their complexity and involvement of multiple genes. Recently, several new approaches have been devised that target whole chromosomes in vitro, which are collectively referred to as "Chromosome Therapies." These include silencing and selection for loss of the extra chromosome in trisomies, promotion of euploidy in an aneuploid culture, and forced loss and replacement of a chromosome. Here, we provide a review of Chromosome Therapy, and discuss potential directions for these methods clinically, as well as research applications and cellular models that can be made using these technologies. © 2016 Wiley Periodicals, Inc.
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136
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Abstract
X-chromosome inactivation, which was discovered by Mary Lyon in 1961 results in random silencing of one X chromosome in female mammals. This review is dedicated to Mary Lyon, who passed away last year. She predicted many of the features of X inactivation, for e.g., the existence of an X inactivation center, the role of L1 elements in spreading of silencing and the existence of genes that escape X inactivation. Starting from her published work here we summarize advances in the field.
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137
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Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis. BMC Bioinformatics 2016; 17:374. [PMID: 27628041 PMCID: PMC5024470 DOI: 10.1186/s12859-016-1234-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 09/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene Expression Data (GED) analysis poses a great challenge to the scientific community that can be framed into the Knowledge Discovery in Databases (KDD) and Data Mining (DM) paradigm. Biclustering has emerged as the machine learning method of choice to solve this task, but its unsupervised nature makes result assessment problematic. This is often addressed by means of Gene Set Enrichment Analysis (GSEA). RESULTS We put forward a framework in which GED analysis is understood as an Exploratory Data Analysis (EDA) process where we provide support for continuous human interaction with data aiming at improving the step of hypothesis abduction and assessment. We focus on the adaptation to human cognition of data interpretation and visualization of the output of EDA. First, we give a proper theoretical background to bi-clustering using Lattice Theory and provide a set of analysis tools revolving around [Formula: see text]-Formal Concept Analysis ([Formula: see text]-FCA), a lattice-theoretic unsupervised learning technique for real-valued matrices. By using different kinds of cost structures to quantify expression we obtain different sequences of hierarchical bi-clusterings for gene under- and over-expression using thresholds. Consequently, we provide a method with interleaved analysis steps and visualization devices so that the sequences of lattices for a particular experiment summarize the researcher's vision of the data. This also allows us to define measures of persistence and robustness of biclusters to assess them. Second, the resulting biclusters are used to index external omics databases-for instance, Gene Ontology (GO)-thus offering a new way of accessing publicly available resources. This provides different flavors of gene set enrichment against which to assess the biclusters, by obtaining their p-values according to the terminology of those resources. We illustrate the exploration procedure on a real data example confirming results previously published. CONCLUSIONS The GED analysis problem gets transformed into the exploration of a sequence of lattices enabling the visualization of the hierarchical structure of the biclusters with a certain degree of granularity. The ability of FCA-based bi-clustering methods to index external databases such as GO allows us to obtain a quality measure of the biclusters, to observe the evolution of a gene throughout the different biclusters it appears in, to look for relevant biclusters-by observing their genes and what their persistence is-to infer, for instance, hypotheses on their function.
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138
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Kaufmann WE, Stallworth JL, Everman DB, Skinner SA. Neurobiologically-based treatments in Rett syndrome: opportunities and challenges. Expert Opin Orphan Drugs 2016; 4:1043-1055. [PMID: 28163986 PMCID: PMC5214376 DOI: 10.1080/21678707.2016.1229181] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022]
Abstract
Introduction: Rett syndrome (RTT) is an X-linked neurodevelopmental disorder that primarily affects females, typically resulting in a period of developmental regression in early childhood followed by stabilization and severe chronic cognitive, behavioral, and physical disability. No known treatment exists beyond symptomatic management, and while insights into the genetic cause, pathophysiology, neurobiology, and natural history of RTT have been gained, many challenges remain. Areas covered: Based on a comprehensive survey of the primary literature on RTT, this article describes and comments upon the general and unique features of the disorder, genetic and neurobiological bases of drug development, and the history of clinical trials in RTT, with an emphasis on drug trial design, outcome measures, and implementation. Expert opinion: Neurobiologically based drug trials are the ultimate goal in RTT, and due to the complexity and global nature of the disorder, drugs targeting both general mechanisms (e.g., growth factors) and specific systems (e.g., glutamate modulators) could be effective. Trial design should optimize data on safety and efficacy, but selection of outcome measures with adequate measurement properties, as well as innovative strategies, such as those enhancing synaptic plasticity and use of biomarkers, are essential for progress in RTT and other neurodevelopmental disorders.
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Affiliation(s)
- Walter E Kaufmann
- Center for Translational Research, Greenwood Genetic Center, Greenwood, SC, USA; Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | | | - David B Everman
- Center for Translational Research, Greenwood Genetic Center , Greenwood , SC , USA
| | - Steven A Skinner
- Center for Translational Research, Greenwood Genetic Center , Greenwood , SC , USA
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139
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Guedj F, Pennings JLA, Massingham LJ, Wick HC, Siegel AE, Tantravahi U, Bianchi DW. An Integrated Human/Murine Transcriptome and Pathway Approach To Identify Prenatal Treatments For Down Syndrome. Sci Rep 2016; 6:32353. [PMID: 27586445 PMCID: PMC5009456 DOI: 10.1038/srep32353] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/27/2016] [Indexed: 01/23/2023] Open
Abstract
Anatomical and functional brain abnormalities begin during fetal life in Down syndrome (DS). We hypothesize that novel prenatal treatments can be identified by targeting signaling pathways that are consistently perturbed in cell types/tissues obtained from human fetuses with DS and mouse embryos. We analyzed transcriptome data from fetuses with trisomy 21, age and sex-matched euploid controls, and embryonic day 15.5 forebrains from Ts1Cje, Ts65Dn, and Dp16 mice. The new datasets were compared to other publicly available datasets from humans with DS. We used the human Connectivity Map (CMap) database and created a murine adaptation to identify FDA-approved drugs that can rescue affected pathways. USP16 and TTC3 were dysregulated in all affected human cells and two mouse models. DS-associated pathway abnormalities were either the result of gene dosage specific effects or the consequence of a global cell stress response with activation of compensatory mechanisms. CMap analyses identified 56 molecules with high predictive scores to rescue abnormal gene expression in both species. Our novel integrated human/murine systems biology approach identified commonly dysregulated genes and pathways. This can help to prioritize therapeutic molecules on which to further test safety and efficacy. Additional studies in human cells are ongoing prior to pre-clinical prenatal treatment in mice.
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Affiliation(s)
- Faycal Guedj
- Mother Infant Research Institute, Tufts Medical Center and the Floating Hospital for Children, Boston, MA, United States
| | - Jeroen LA Pennings
- Center for Health Protection (GZB), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Lauren J Massingham
- Mother Infant Research Institute, Tufts Medical Center and the Floating Hospital for Children, Boston, MA, United States
| | - Heather C Wick
- Department of Computer Science, Tufts University, Medford, MA, United States
| | - Ashley E Siegel
- Mother Infant Research Institute, Tufts Medical Center and the Floating Hospital for Children, Boston, MA, United States
| | - Umadevi Tantravahi
- Department of Pathology, Women and Infants' Hospital, Providence, RI, United States
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center and the Floating Hospital for Children, Boston, MA, United States
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140
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Teixeira FG, Vasconcelos NL, Gomes ED, Marques F, Sousa JC, Sousa N, Silva NA, Assunção-Silva R, Lima R, Salgado AJ. Bioengineered cell culture systems of central nervous system injury and disease. Drug Discov Today 2016; 21:1456-1463. [DOI: 10.1016/j.drudis.2016.04.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/02/2016] [Accepted: 04/21/2016] [Indexed: 01/10/2023]
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141
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Zhao J, Zhang Z, Ren S, Zong Y, Kong X. Co-expression network analysis of Down's syndrome based on microarray data. Exp Ther Med 2016; 12:1503-1508. [PMID: 27588071 DOI: 10.3892/etm.2016.3462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/11/2016] [Indexed: 12/17/2022] Open
Abstract
Down's syndrome (DS) is a type of chromosome disease. The present study aimed to explore the underlying molecular mechanisms of DS. GSE5390 microarray data downloaded from the gene expression omnibus database was used to identify differentially expressed genes (DEGs) in DS. Pathway enrichment analysis of the DEGs was performed, followed by co-expression network construction. Significant differential modules were mined by mutual information, followed by functional analysis. The accuracy of sample classification for the significant differential modules of DEGs was evaluated by leave-one-out cross-validation. A total of 997 DEGs, including 638 upregulated and 359 downregulated genes, were identified. Upregulated DEGs were enriched in 15 pathways, such as cell adhesion molecules, whereas downregulated DEGs were enriched in maturity onset diabetes of the young. Three significant differential modules with the highest discriminative scores (mutual information>0.35) were selected from a co-expression network. The classification accuracy of GSE16677 expression profile samples was 54.55% and 72.73% when characterized by 12 DEGs and 3 significant differential modules, respectively. Genes in significant differential modules were significantly enriched in 5 functions, including the endoplasmic reticulum (P=0.018) and regulation of apoptosis (P=0.061). The identified DEGs, in particular the 12 DEGs in the significant differential modules, such as B-cell lymphoma 2-associated transcription factor 1, heat shock protein 90 kDa beta member 1, UBX domain-containing protein 2 and transmembrane protein 50B, may serve important roles in the pathogenesis of DS.
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Affiliation(s)
- Jianping Zhao
- Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, Henan 450012, P.R. China
| | - Zhengguo Zhang
- Clinical Laboratory, Henan Provincial Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Shumin Ren
- Center of Prenatal Diagnosis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yanan Zong
- Center of Prenatal Diagnosis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Xiangdong Kong
- Center of Prenatal Diagnosis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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142
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Pelleri MC, Cicchini E, Locatelli C, Vitale L, Caracausi M, Piovesan A, Rocca A, Poletti G, Seri M, Strippoli P, Cocchi G. Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype. Hum Mol Genet 2016; 25:2525-2538. [PMID: 27106104 PMCID: PMC5181629 DOI: 10.1093/hmg/ddw116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/12/2016] [Accepted: 04/12/2016] [Indexed: 01/13/2023] Open
Abstract
A 'Down Syndrome critical region' (DSCR) sufficient to induce the most constant phenotypes of Down syndrome (DS) had been identified by studying partial (segmental) trisomy 21 (PT21) as an interval of 0.6-8.3 Mb within human chromosome 21 (Hsa21), although its existence was later questioned. We propose an innovative, systematic reanalysis of all described PT21 cases (from 1973 to 2015). In particular, we built an integrated, comparative map from 125 cases with or without DS fulfilling stringent cytogenetic and clinical criteria. The map allowed to define or exclude as candidates for DS fine Hsa21 sequence intervals, also integrating duplication copy number variants (CNVs) data. A highly restricted DSCR (HR-DSCR) of only 34 kb on distal 21q22.13 has been identified as the minimal region whose duplication is shared by all DS subjects and is absent in all non-DS subjects. Also being spared by any duplication CNV in healthy subjects, HR-DSCR is proposed as a candidate for the typical DS features, the intellectual disability and some facial phenotypes. HR-DSCR contains no known gene and has relevant homology only to the chimpanzee genome. Searching for HR-DSCR functional loci might become a priority for understanding the fundamental genotype-phenotype relationships in DS.
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Affiliation(s)
- Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Elena Cicchini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Alessandro Rocca
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy
| | - Giulia Poletti
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy
| | | | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138 Bologna, BO, Italy
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143
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Ballantyne RL, Zhang X, Nuñez S, Xue C, Zhao W, Reed E, Salaheen D, Foulkes AS, Li M, Reilly MP. Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits. Hum Mol Genet 2016; 25:3125-3141. [PMID: 27288454 DOI: 10.1093/hmg/ddw154] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/26/2016] [Accepted: 05/18/2016] [Indexed: 02/07/2023] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) play important roles in disease, but the vast majority of these transcripts remain uncharacterized. We defined a set of 54 944 human lincRNAs by drawing on four publicly available lincRNA datasets, and annotated ∼2.5 million single nucleotide polymorphisms (SNPs) from each of 15 cardiometabolic genome-wide association study datasets into these lincRNAs. We identified hundreds of lincRNAs with at least one trait-associated SNP: 898 SNPs in 343 unique lincRNAs at 5% false discovery rate, and 469 SNPs in 146 unique lincRNAs meeting Bonferroni-corrected P < 0.05. An additional 64 trait-associated lincRNAs were identified using a class-level testing strategy at Bonferroni-corrected P < 0.05. To better understand the genomic context and prioritize trait-associated lincRNAs, we examined the pattern of linkage disequilibrium between SNPs in the lincRNAs and SNPs that met genome-wide-significance in the region (±500 kb of lincRNAs). A subset of the lincRNA-trait association findings was replicated in independent Genome-wide association studies data from the Pakistan Risk of Myocardial Infarction Study study. For trait-associated lincRNAs, we also investigated synteny and conservation relative to mouse, expression patterns in five cardiometabolic-relevant tissues, and allele-specific expression in RNA sequencing data for adipose tissue and leukocytes. Finally, we revealed a functional role in human adipocytes for linc-NFE2L3-1, which is expressed in adipose and is associated with waist-hip ratio adjusted for BMI. This comprehensive profile of trait-associated lincRNAs provides novel insights into disease mechanism and serves as a launching point for interrogation of the biology of specific lincRNAs in cardiometabolic disease.
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Affiliation(s)
| | - Xuan Zhang
- Department of Medicine, Division of Cardiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Sara Nuñez
- Department of Mathematics and Statistics, Mount Holyoke College, MA 01075, USA
| | - Chenyi Xue
- Department of Medicine, Division of Cardiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Wei Zhao
- Division of Translational Medicine and Human Genetics
| | - Eric Reed
- Department of Mathematics and Statistics, Mount Holyoke College, MA 01075, USA
| | - Danish Salaheen
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Andrea S Foulkes
- Department of Mathematics and Statistics, Mount Holyoke College, MA 01075, USA
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Muredach P Reilly
- Department of Medicine, Division of Cardiology, Columbia University Medical Center, New York, NY 10032, USA
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144
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Hall LL, Lawrence JB. RNA as a fundamental component of interphase chromosomes: could repeats prove key? Curr Opin Genet Dev 2016; 37:137-147. [PMID: 27218204 DOI: 10.1016/j.gde.2016.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 11/29/2022]
Abstract
Beginning with the precedent of XIST RNA as a 'chromosomal RNA' (cRNA), there is growing interest in the possibility that a diversity of non-coding RNAs may function in chromatin. We review findings which lead us to suggest that RNA is essentially a widespread component of interphase chromosomes. Further, RNA likely contributes to architecture and regulation, with repeat-rich 'junk' RNA in euchromatin (ecRNA) promoting a more open chromatin state. Thousands of low-abundance nuclear RNAs have been reported, however it remains a challenge to determine which of these may function in chromatin. Recent findings indicate that repetitive sequences are enriched in chromosome-associated non-coding RNAs, and repeat-rich RNA shows unusual properties, including localization and stability, with similarities to XIST RNA. We suggest two frontiers in genome biology are emerging and may intersect: the broad contribution of RNA to interphase chromosomes and the distinctive properties of repeat-rich intronic or intergenic junk sequences that may play a role in chromosome structure and regulation.
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Affiliation(s)
- Lisa L Hall
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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145
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Disteche CM. Dosage compensation of the sex chromosomes and autosomes. Semin Cell Dev Biol 2016; 56:9-18. [PMID: 27112542 DOI: 10.1016/j.semcdb.2016.04.013] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/16/2022]
Abstract
Males are XY and females are XX in most mammalian species. Other species such as birds have a different sex chromosome make-up: ZZ in males and ZW in females. In both types of organisms one of the sex chromosomes, Y or W, has degenerated due to lack of recombination with its respective homolog X or Z. Since autosomes are present in two copies in diploid organisms the heterogametic sex has become a natural "aneuploid" with haploinsufficiency for X- or Z-linked genes. Specific mechanisms have evolved to restore a balance between critical gene products throughout the genome and between males and females. Some of these mechanisms were co-opted from and/or added to compensatory processes that alleviate autosomal aneuploidy. Surprisingly, several modes of dosage compensation have evolved. In this review we will consider the evidence for dosage compensation and the molecular mechanisms implicated.
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Affiliation(s)
- Christine M Disteche
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA; Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA.
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146
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Pandya-Jones A, Plath K. The "lnc" between 3D chromatin structure and X chromosome inactivation. Semin Cell Dev Biol 2016; 56:35-47. [PMID: 27062886 DOI: 10.1016/j.semcdb.2016.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/01/2022]
Abstract
The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions.
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Affiliation(s)
- Amy Pandya-Jones
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA.
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147
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Abstract
The terms 'haploid' and 'diploid' that describe single (n) and double (2n) chromosome sets in cells were coined by the Polish-German botanist Eduard Strasburger and originate from the Greek terms haplóos meaning 'single' and diplóos meaning 'double'. The term 'ploidy' was subsequently derived to describe the total chromosome content of cells. Consequently, the term 'euploid' refers to a chromosome complement that is an exact multiple of the haploid number. Therefore, haploids and diploids are both cases of normal euploidy. Euploid types that have more than two sets of chromosomes are 'polyploid' such as 'triploid' (3n), 'tetraploid' (4n), 'pentaploid' (5n), and so forth. There are various natural euploid states with some organisms existing as haploids (fungi), diploids (most mammals), and polyploids (plants).
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Affiliation(s)
- Bernardo Orr
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Kristina M Godek
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Duane Compton
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Norris Cotton Cancer Center, Lebanon, NH, USA.
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148
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Schneider K, Schiermeyer A, Dolls A, Koch N, Herwartz D, Kirchhoff J, Fischer R, Russell SM, Cao Z, Corbin DR, Sastry-Dent L, Ainley WM, Webb SR, Schinkel H, Schillberg S. Targeted gene exchange in plant cells mediated by a zinc finger nuclease double cut. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1151-60. [PMID: 26426390 DOI: 10.1111/pbi.12483] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/21/2015] [Accepted: 09/03/2015] [Indexed: 06/05/2023]
Abstract
Genome modification by homology-directed repair (HDR) is an attractive tool for the controlled genetic manipulation of plants. Here, we report the HDR-mediated gene exchange of expression cassettes in tobacco BY-2 cells using a designed zinc finger nuclease (ZFN). The target contained a 7-kb fragment flanked by two ZFN cutting sites. That fragment was replaced with a 4-kb donor cassette, which integrates gene markers for selection (kanamycin resistance) and for scoring targeting (red fluorescent protein, RFP). Candidates resulting from cassette exchange were identified by molecular analysis of calli generated by transformation via direct DNA delivery. The precision of HDR-mediated donor integration was evaluated by Southern blot analysis, sequencing of the integration locus and analysis of RFP fluorescence by flow cytometry. Screening of 1326 kanamycin-resistant calli yielded 18 HDR events, 16 of which had a perfect cassette exchange at the insert junction and 13 of which produced functional RFP. Our results demonstrate that ZFN-based HDR can be used for high frequency, precise, targeted exchange of fragments of sizes that are commercially relevant in plants.
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Affiliation(s)
- Katja Schneider
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Anja Dolls
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Natalie Koch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Denise Herwartz
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Janina Kirchhoff
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | | | - Zehui Cao
- Dow AgroSciences LLC, Indianapolis, IN, USA
| | | | | | | | | | - Helga Schinkel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
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149
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Vacca M, Della Ragione F, Scalabrì F, D'Esposito M. X inactivation and reactivation in X-linked diseases. Semin Cell Dev Biol 2016; 56:78-87. [PMID: 26994527 DOI: 10.1016/j.semcdb.2016.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/22/2022]
Abstract
X chromosome inactivation (XCI) is the phenomenon by which mammals compensate for dosage of X-linked genes in females (XX) versus males (XY). XCI patterns can be random or show extreme skewing, and can modify the mode of inheritance of X-driven phenotypes, which contributes to the variability of human pathologies. Recent findings have shown reversibility of the XCI process, which has opened new avenues in the approaches used for the treatment of X-linked diseases.
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Affiliation(s)
- Marcella Vacca
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy.
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
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150
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Murray A, Letourneau A, Canzonetta C, Stathaki E, Gimelli S, Sloan-Bena F, Abrehart R, Goh P, Lim S, Baldo C, Dagna-Bricarelli F, Hannan S, Mortensen M, Ballard D, Syndercombe Court D, Fusaki N, Hasegawa M, Smart TG, Bishop C, Antonarakis SE, Groet J, Nizetic D. Brief report: isogenic induced pluripotent stem cell lines from an adult with mosaic down syndrome model accelerated neuronal ageing and neurodegeneration. Stem Cells 2016; 33:2077-84. [PMID: 25694335 PMCID: PMC4737213 DOI: 10.1002/stem.1968] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/17/2015] [Indexed: 01/11/2023]
Abstract
Trisomy 21 (T21), Down Syndrome (DS) is the most common genetic cause of dementia and intellectual disability. Modeling DS is beginning to yield pharmaceutical therapeutic interventions for amelioration of intellectual disability, which are currently being tested in clinical trials. DS is also a unique genetic system for investigation of pathological and protective mechanisms for accelerated ageing, neurodegeneration, dementia, cancer, and other important common diseases. New drugs could be identified and disease mechanisms better understood by establishment of well-controlled cell model systems. We have developed a first nonintegration-reprogrammed isogenic human induced pluripotent stem cell (iPSC) model of DS by reprogramming the skin fibroblasts from an adult individual with constitutional mosaicism for DS and separately cloning multiple isogenic T21 and euploid (D21) iPSC lines. Our model shows a very low number of reprogramming rearrangements as assessed by a high-resolution whole genome CGH-array hybridization, and it reproduces several cellular pathologies seen in primary human DS cells, as assessed by automated high-content microscopic analysis. Early differentiation shows an imbalance of the lineage-specific stem/progenitor cell compartments: T21 causes slower proliferation of neural and faster expansion of hematopoietic lineage. T21 iPSC-derived neurons show increased production of amyloid peptide-containing material, a decrease in mitochondrial membrane potential, and an increased number and abnormal appearance of mitochondria. Finally, T21-derived neurons show significantly higher number of DNA double-strand breaks than isogenic D21 controls. Our fully isogenic system therefore opens possibilities for modeling mechanisms of developmental, accelerated ageing, and neurodegenerative pathologies caused by T21.
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Affiliation(s)
- Aoife Murray
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Claudia Canzonetta
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom
| | - Elisavet Stathaki
- Service of Genetic Medicine, University Geneva Hospitals, Geneva, Switzerland
| | - Stefania Gimelli
- Service of Genetic Medicine, University Geneva Hospitals, Geneva, Switzerland
| | | | - Robert Abrehart
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom
| | - Pollyanna Goh
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom
| | - Shuhui Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Chiara Baldo
- Human Genetics Laboratory, Galliera Hospital, Genoa, Italy
| | | | - Saad Hannan
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Martin Mortensen
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - David Ballard
- Department of Forensic and Analytical Science, King's College, London, United Kingdom
| | | | - Noemi Fusaki
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | | | - Trevor G Smart
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Cleo Bishop
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jürgen Groet
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,Stem Cell Laboratory, National Centre for Bowel Research and Surgical Innovation, Queen Mary University of London, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom
| | - Dean Nizetic
- The Blizard Institute, Barts and The London School of Medicine, London, United Kingdom.,The LonDownS Consortium, Wellcome Trust, London, United Kingdom.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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