1
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Fan C, Kim D, An H, Park Y. Identifying an oligodendrocyte enhancer that regulates Olig2 expression. Hum Mol Genet 2023; 32:835-846. [PMID: 36193754 PMCID: PMC9941837 DOI: 10.1093/hmg/ddac249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/14/2022] Open
Abstract
Olig2 is a basic helix-loop-helix transcription factor that plays a critical role in the central nervous system. It directs the specification of motor neurons and oligodendrocyte precursor cells (OPCs) from neural progenitors and the subsequent maturation of OPCs into myelin-forming oligodendrocytes (OLs). It is also required for the development of astrocytes. Despite a decade-long search, enhancers that regulate the expression of Olig2 remain elusive. We have recently developed an innovative method that maps promoter-distal enhancers to genes in a principled manner. Here, we applied it to Olig2 in the context of OL lineage cells, uncovering an OL enhancer for it (termed Olig2-E1). Silencing Olig2-E1 by CRISPRi epigenome editing significantly downregulated Olig2 expression. Luciferase assay and ATAC-seq and ChIP-seq data show that Olig2-E1 is an OL-specific enhancer that is conserved across human, mouse and rat. Hi-C data reveal that Olig2-E1 physically interacts with OLIG2 and suggest that this interaction is specific to OL lineage cells. In sum, Olig2-E1 is an evolutionarily conserved OL-specific enhancer that drives the expression of Olig2.
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Affiliation(s)
- Chuandong Fan
- Institute for Myelin and Glia Exploration, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Dongkyeong Kim
- Institute for Myelin and Glia Exploration, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Yungki Park
- Institute for Myelin and Glia Exploration, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
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2
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Golbourn BJ, Halbert ME, Halligan K, Varadharajan S, Krug B, Mbah NE, Kabir N, Stanton ACJ, Locke AL, Casillo SM, Zhao Y, Sanders LM, Cheney A, Mullett SJ, Chen A, Wassell M, Andren A, Perez J, Jane EP, Premkumar DRD, Koncar RF, Mirhadi S, McCarl LH, Chang YF, Wu YL, Gatesman TA, Cruz AF, Zapotocky M, Hu B, Kohanbash G, Wang X, Vartanian A, Moran MF, Lieberman F, Amankulor NM, Wendell SG, Vaske OM, Panigrahy A, Felker J, Bertrand KC, Kleinman CL, Rich JN, Friedlander RM, Broniscer A, Lyssiotis C, Jabado N, Pollack IF, Mack SC, Agnihotri S. Loss of MAT2A compromises methionine metabolism and represents a vulnerability in H3K27M mutant glioma by modulating the epigenome. NATURE CANCER 2022; 3:629-648. [PMID: 35422502 PMCID: PMC9551679 DOI: 10.1038/s43018-022-00348-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/18/2022] [Indexed: 12/31/2022]
Abstract
Diffuse midline gliomas (DMGs) bearing driver mutations of histone 3 lysine 27 (H3K27M) are incurable brain tumors with unique epigenomes. Here, we generated a syngeneic H3K27M mouse model to study the amino acid metabolic dependencies of these tumors. H3K27M mutant cells were highly dependent on methionine. Interrogating the methionine cycle dependency through a short-interfering RNA screen identified the enzyme methionine adenosyltransferase 2A (MAT2A) as a critical vulnerability in these tumors. This vulnerability was not mediated through the canonical mechanism of MTAP deletion; instead, DMG cells have lower levels of MAT2A protein, which is mediated by negative feedback induced by the metabolite decarboxylated S-adenosyl methionine. Depletion of residual MAT2A induces global depletion of H3K36me3, a chromatin mark of transcriptional elongation perturbing oncogenic and developmental transcriptional programs. Moreover, methionine-restricted diets extended survival in multiple models of DMG in vivo. Collectively, our results suggest that MAT2A presents an exploitable therapeutic vulnerability in H3K27M gliomas.
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Affiliation(s)
- Brian J Golbourn
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew E Halbert
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Katharine Halligan
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pediatrics, Division of Hematology-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Srinidhi Varadharajan
- Baylor College of Medicine, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, TX, USA
| | - Brian Krug
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, McGill University, The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Nneka E Mbah
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nisha Kabir
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ann-Catherine J Stanton
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Abigail L Locke
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stephanie M Casillo
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Yanhua Zhao
- Baylor College of Medicine, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, TX, USA
| | - Lauren M Sanders
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Allison Cheney
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, USA
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Steven J Mullett
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Apeng Chen
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, PR China
| | - Michelle Wassell
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Anthony Andren
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jennifer Perez
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Esther P Jane
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel R David Premkumar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Robert F Koncar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Shideh Mirhadi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lauren H McCarl
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Yue-Fang Chang
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yijen L Wu
- Department of Developmental Biology, University of Pittsburgh and Rangos Research Center Animal Imaging Core, Pittsburgh, PA, USA
| | - Taylor A Gatesman
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Andrea F Cruz
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Michal Zapotocky
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Gary Kohanbash
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Xiuxing Wang
- Department of Cell Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | | | - Michael F Moran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Lieberman
- Department of Neurology, Adult Neurooncology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Nduka M Amankulor
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stacy G Wendell
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Olena M Vaske
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, USA
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Ashok Panigrahy
- Department of Radiology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - James Felker
- Pediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Kelsey C Bertrand
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jeremy N Rich
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert M Friedlander
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alberto Broniscer
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Pediatrics, Division of Hematology-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Costas Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, McGill University, The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen C Mack
- Baylor College of Medicine, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, TX, USA.
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA.
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3
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King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen BA. Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells. eLife 2020; 9:41279. [PMID: 32043966 PMCID: PMC7077988 DOI: 10.7554/elife.41279] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
In embryonic stem cells (ESCs), a core transcription factor (TF) network establishes the gene expression program necessary for pluripotency. To address how interactions between four key TFs contribute to cis-regulation in mouse ESCs, we assayed two massively parallel reporter assay (MPRA) libraries composed of binding sites for SOX2, POU5F1 (OCT4), KLF4, and ESRRB. Comparisons between synthetic cis-regulatory elements and genomic sequences with comparable binding site configurations revealed some aspects of a regulatory grammar. The expression of synthetic elements is influenced by both the number and arrangement of binding sites. This grammar plays only a small role for genomic sequences, as the relative activities of genomic sequences are best explained by the predicted occupancy of binding sites, regardless of binding site identity and positioning. Our results suggest that the effects of transcription factor binding sites (TFBS) are influenced by the order and orientation of sites, but that in the genome the overall occupancy of TFs is the primary determinant of activity. Transcription factors are proteins that flip genetic switches; their role is to control when and where genes are active. They do this by binding to short stretches of DNA called cis-regulatory sequences. Each sequence can have several binding sites for different transcription factors, but it is largely unclear whether the transcription factors binding to the same regulatory sequence actually work together. It is possible that each transcription factor may work independently and there only needs to be critical mass of transcription factors bound to throw the genetic switch. If this is the case, the most important features of a cis-regulatory sequence should be the number of binding sites it contains, and how tightly the transcription factors bind to those sites. The more transcription factors and the more strongly they bind, the more active the gene should be. An alternative option is that certain transcription factors may work better together, enhancing each other's effects such that the total effect is more than the sum of its parts. If this is true, the order, orientation and spacing of the binding sites within a sequence should matter more than the number. One way to investigate to distinguish between these possibilities is to study mouse embryonic stem cells, which have a core set of four transcription factors. Looking directly at a real genome, however, can be confusing and it is difficult to measure the effects of different cis-regulatory sequences because genes differ in so many other ways. To tackle this problem, King et al. created a synthetic set of cis-regulatory sequences based on the four core transcription factors found in mouse stem cells. The synthetic set had every combination of two, three or four of the binding sites, with each site either facing forwards or backwards along the DNA strand. King et al. attached each of the synthetic cis-regulatory sequences to a reporter gene to find out how well each sequence performed. This revealed that the cis-regulatory sequences with the most binding sites and the tightest binding affinities work best, suggesting that transcription factors mainly work independently. There was evidence of some interaction between some transcription factors, because, of the synthetic sequences with four binding sites, some worked better than others, and there were patterns in the most effective binding site combinations. However, these effects were small and when King et al. went on to test sequences from the real mouse genome, the most important factor by far was the number of binding sites. Synthetic libraries of DNA sequences allow researchers to examine gene regulation more clearly than is possible in real genomes. Yet this approach does have its limitations and it is impossible to capture every type of cis-regulatory sequence in one library. The next step to extend this work is to combine the two approaches, taking sequences from the real genome and manipulating them one by one. This could help to unravel the rules that govern how cis-regulatory sequences work in real cells.
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Affiliation(s)
- Dana M King
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Clarice Kit Yee Hong
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - James L Shepherdson
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - David M Granas
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Brett B Maricque
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Barak A Cohen
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
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4
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Rauff A, LaBelle SA, Strobel HA, Hoying JB, Weiss JA. Imaging the Dynamic Interaction Between Sprouting Microvessels and the Extracellular Matrix. Front Physiol 2019; 10:1011. [PMID: 31507428 PMCID: PMC6713949 DOI: 10.3389/fphys.2019.01011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Thorough understanding of growth and evolution of tissue vasculature is fundamental to many fields of medicine including cancer therapy, wound healing, and tissue engineering. Angiogenesis, the growth of new vessels from existing ones, is dynamically influenced by a variety of environmental factors, including mechanical and biophysical factors, chemotactic factors, proteolysis, and interaction with stromal cells. Yet, dynamic interactions between neovessels and their environment are difficult to study with traditional fixed time imaging techniques. Advancements in imaging technologies permit time-series and volumetric imaging, affording the ability to visualize microvessel growth over 3D space and time. Time-lapse imaging has led to more informative investigations of angiogenesis. The environmental factors implicated in angiogenesis span a wide range of signals. Neovessels advance through stromal matrices by forming attachments and pulling and pushing on their microenvironment, reorganizing matrix fibers, and inducing large deformations of the surrounding stroma. Concurrently, neovessels secrete proteolytic enzymes to degrade their basement membrane, create space for new vessels to grow, and release matrix-bound cytokines. Growing neovessels also respond to a host of soluble and matrix-bound growth factors, and display preferential growth along a cytokine gradient. Lastly, stromal cells such as macrophages and mesenchymal stem cells (MSCs) interact directly with neovessels and their surrounding matrix to facilitate sprouting, vessel fusion, and tissue remodeling. This review highlights how time-lapse imaging techniques advanced our understanding of the interaction of blood vessels with their environment during sprouting angiogenesis. The technology provides means to characterize the evolution of microvessel behavior, providing new insights and holding great promise for further research on the process of angiogenesis.
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Affiliation(s)
- Adam Rauff
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States
| | - Steven A. LaBelle
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States
| | - Hannah A. Strobel
- Innovations Laboratory, Advanced Solutions Life Sciences, Manchester, NH, United States
| | - James B. Hoying
- Innovations Laboratory, Advanced Solutions Life Sciences, Manchester, NH, United States
| | - Jeffrey A. Weiss
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States
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5
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Gessler DJ, Tai PWL, Li J, Gao G. Intravenous Infusion of AAV for Widespread Gene Delivery to the Nervous System. Methods Mol Biol 2019; 1950:143-163. [PMID: 30783972 PMCID: PMC7339923 DOI: 10.1007/978-1-4939-9139-6_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The central nervous system (CNS) is a fascinating and intricate set of biological structures that we have yet to fully understand. Studying the in vivo function of the CNS and finding novel methods for treating neurological disorders have been particularly challenging. One difficulty is correcting genetic disorders afflicting the CNS in a targeted manner. Recombinant adeno-associated viruses (rAAVs) have emerged as promising therapeutic tools for treating genetic defects of the CNS, due to their excellent safety profile and ability to cross the blood-brain barrier (BBB). While stereotactic injection of AAV is promising for localized gene delivery, it is less desirable for some applications because of the technique's invasiveness and limited intraparenchymal spread. Alternatively, intravascular administration can achieve widespread delivery of rAAV to the CNS. In this chapter, we will discuss the prevalent routes of administration to deliver rAAV to the CNS via intravenous (IV) injection in mice. We will highlight key considerations for using rAAV, and the advantages and disadvantages of each administration method. We will also briefly discuss intravenous delivery in larger animal models, factors that may impact experimental interpretations, and outlooks for clinical translation.
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Affiliation(s)
- Dominic J Gessler
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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6
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Sundaram V, Choudhary MNK, Pehrsson E, Xing X, Fiore C, Pandey M, Maricque B, Udawatta M, Ngo D, Chen Y, Paguntalan A, Ray T, Hughes A, Cohen BA, Wang T. Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. Nat Commun 2017; 8:14550. [PMID: 28348391 PMCID: PMC5379053 DOI: 10.1038/ncomms14550] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 01/11/2017] [Indexed: 01/30/2023] Open
Abstract
Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate the effects of each TF to control gene expression in specific cellular contexts. Transposable elements (TEs) are uniquely equipped to deposit their regulatory sequences across a genome, which could also contain cis-regulatory modules that coordinate the control of multiple genes with the same regulatory logic. We provide the first evidence of mouse-specific TEs that encode a module of TF-binding sites in mouse embryonic stem cells (ESCs). The majority (77%) of the individual TEs tested exhibited enhancer activity in mouse ESCs. By mutating individual TF-binding sites within the TE, we identified a module of TF-binding motifs that cooperatively enhanced gene expression. Interestingly, we also observed the same motif module in the in silico constructed ancestral TE that also acted cooperatively to enhance gene expression. Our results suggest that ancestral TE insertions might have brought in cis-regulatory modules into the mouse genome.
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Affiliation(s)
- Vasavi Sundaram
- Division of Biological and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Mayank N. K. Choudhary
- Division of Biological and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Erica Pehrsson
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Christopher Fiore
- Division of Biological and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Manishi Pandey
- Division of Biological and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Brett Maricque
- Division of Biological and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Methma Udawatta
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Duc Ngo
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Yujie Chen
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Asia Paguntalan
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Tammy Ray
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Ava Hughes
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Barak A. Cohen
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, St. Louis, Missouri 63110, USA
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7
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Hwang SM, Uhm TG, Lee SK, Kong SK, Jung KH, Binas B, Chai YG, Park SW, Chung IY. Olig2 is expressed late in human eosinophil development and controls Siglec-8 expression. J Leukoc Biol 2016; 100:711-723. [DOI: 10.1189/jlb.1a0715-314rrr] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 03/12/2016] [Indexed: 01/01/2023] Open
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8
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Fiore C, Cohen BA. Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. Genome Res 2016; 26:778-86. [PMID: 27197208 PMCID: PMC4889965 DOI: 10.1101/gr.200733.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/13/2016] [Indexed: 01/06/2023]
Abstract
We investigated how interactions between pluripotency transcription factors (TFs) affect cis-regulation. We created hundreds of synthetic cis-regulatory elements (CREs) comprised of combinations of binding sites for pluripotency TFs and measured their expression in mouse embryonic stem (ES) cells. A thermodynamic model that incorporates interactions between TFs explains a large portion (72%) of the variance in expression of these CREs. These interactions include three favorable heterotypic interactions between TFs. The model also predicts an unfavorable homotypic interaction between TFs, helping to explain the observation that homotypic chains of binding sites express at low levels. We further investigated the expression driven by CREs comprised of homotypic chains of KLF4 binding sites. Our results suggest that KLF homologs make unique contributions to regulation by these CREs. We conclude that a specific set of interactions between pluripotency TFs plays a large role in setting the levels of expression driven by CREs in ES cells.
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Affiliation(s)
- Chris Fiore
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Barak A Cohen
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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9
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Katayama S, Moriguchi T, Ohtsu N, Kondo T. A Powerful CRISPR/Cas9-Based Method for Targeted Transcriptional Activation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Shota Katayama
- Graduate School of Medicine; Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University; Sapporo Hokkaido 060-0815 Japan
| | - Tetsuo Moriguchi
- Graduate School of Medicine; Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University; Sapporo Hokkaido 060-0815 Japan
| | - Naoki Ohtsu
- Graduate School of Medicine; Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University; Sapporo Hokkaido 060-0815 Japan
| | - Toru Kondo
- Graduate School of Medicine; Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University; Sapporo Hokkaido 060-0815 Japan
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10
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Katayama S, Moriguchi T, Ohtsu N, Kondo T. A Powerful CRISPR/Cas9-Based Method for Targeted Transcriptional Activation. Angew Chem Int Ed Engl 2016; 55:6452-6. [PMID: 27079176 DOI: 10.1002/anie.201601708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 12/26/2022]
Abstract
Targeted transcriptional activation of endogenous genes is important for understanding physiological transcriptional networks, synthesizing genetic circuits, and inducing cellular phenotype changes. The CRISPR/Cas9 system has great potential to achieve this purpose, however, it has not yet been successfully used to efficiently activate endogenous genes and induce changes in cellular phenotype. A powerful method for transcriptional activation by using CRISPR/Cas9 was developed. Replacement of a methylated promoter with an unmethylated one by CRISPR/Cas9 was sufficient to activate the expression of the neural cell gene OLIG2 and the embryonic stem cell gene NANOG in HEK293T cells. Moreover, CRISPR/Cas9-based OLIG2 activation induced the embryonic carcinoma cell line NTERA-2 to express the neuronal marker βIII-tubulin.
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Affiliation(s)
- Shota Katayama
- Graduate School of Medicine, Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0815, Japan.
| | - Tetsuo Moriguchi
- Graduate School of Medicine, Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0815, Japan
| | - Naoki Ohtsu
- Graduate School of Medicine, Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0815, Japan
| | - Toru Kondo
- Graduate School of Medicine, Hokkaido University, Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0815, Japan.
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11
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Abstract
Specification of spinal cord neurons depends on gene regulation networks that impose distinct fates in neural progenitor cells (NPCs). Olig2 is a key transcription factor in these networks by inducing motor neuron (MN) specification and inhibiting interneuron identity. Despite the critical role of Olig2 in nervous system development and cancer progression, the upstream molecular mechanisms that control Olig2 gene transcription are not well understood. Here we demonstrate that Prox1, a transcription repressor and downstream target of proneural genes, suppresses Olig2 expression and therefore controls ventral spinal cord patterning. In particular, Prox1 is strongly expressed in V2 interneuron progenitors and largely excluded from Olig2+ MN progenitors (pMN). Gain- and loss-of-function studies in mouse NPCs and chick neural tube show that Prox1 is sufficient and necessary for the suppression of Olig2 expression and proper control of MN versus V2 interneuron identity. Mechanistically, Prox1 interacts with the regulatory elements of Olig2 gene locus in vivo and it is critical for proper Olig2 transcription regulation. Specifically, chromatin immunoprecipitation analysis in the mouse neural tube showed that endogenous Prox1 directly binds to the proximal promoter of the Olig2 gene locus, as well as to the K23 enhancer, which drives Olig2 expression in the pMN domain. Moreover, plasmid-based transcriptional assays in mouse NPCs suggest that Prox1 suppresses the activity of Olig2 gene promoter and K23 enhancer. These observations indicate that Prox1 controls binary fate decisions between MNs and V2 interneurons in NPCs via direct repression of Olig2 gene regulatory elements.
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12
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Fulton DL, Denarier E, Friedman HC, Wasserman WW, Peterson AC. Towards resolving the transcription factor network controlling myelin gene expression. Nucleic Acids Res 2011; 39:7974-91. [PMID: 21729871 PMCID: PMC3185407 DOI: 10.1093/nar/gkr326] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In the central nervous system (CNS), myelin is produced from spirally-wrapped oligodendrocyte plasma membrane and, as exemplified by the debilitating effects of inherited or acquired myelin abnormalities in diseases such as multiple sclerosis, it plays a critical role in nervous system function. Myelin sheath production coincides with rapid up-regulation of numerous genes. The complexity of their subsequent expression patterns, along with recently recognized heterogeneity within the oligodendrocyte lineage, suggest that the regulatory networks controlling such genes drive multiple context-specific transcriptional programs. Conferring this nuanced level of control likely involves a large repertoire of interacting transcription factors (TFs). Here, we combined novel strategies of computational sequence analyses with in vivo functional analysis to establish a TF network model of coordinate myelin-associated gene transcription. Notably, the network model captures regulatory DNA elements and TFs known to regulate oligodendrocyte myelin gene transcription and/or oligodendrocyte development, thereby validating our approach. Further, it links to numerous TFs with previously unsuspected roles in CNS myelination and suggests collaborative relationships amongst both known and novel TFs, thus providing deeper insight into the myelin gene transcriptional network.
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Affiliation(s)
- Debra L Fulton
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, V5Z 4H4, Canada
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13
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Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE. Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One 2011; 6:e17634. [PMID: 21408183 PMCID: PMC3049788 DOI: 10.1371/journal.pone.0017634] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 02/04/2011] [Indexed: 02/02/2023] Open
Abstract
Comparative analyses of various mammalian genomes have identified numerous conserved non-coding (CNC) DNA elements that display striking conservation among species, suggesting that they have maintained specific functions throughout evolution. CNC function remains poorly understood, although recent studies have identified a role in gene regulation. We hypothesized that the identification of genomic loci that interact physically with CNCs would provide information on their functions. We have used circular chromosome conformation capture (4C) to characterize interactions of 10 CNCs from human chromosome 21 in K562 cells. The data provide evidence that CNCs are capable of interacting with loci that are enriched for CNCs. The number of trans interactions varies among CNCs; some show interactions with many loci, while others interact with few. Some of the tested CNCs are capable of driving the expression of a reporter gene in the mouse embryo, and associate with the oligodendrocyte genes OLIG1 and OLIG2. Our results underscore the power of chromosome conformation capture for the identification of targets of functional DNA elements and raise the possibility that CNCs exert their functions by physical association with defined genomic regions enriched in CNCs. These CNC-CNC interactions may in part explain their stringent conservation as a group of regulatory sequences.
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Affiliation(s)
- Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
- * E-mail: (SEA); (DR)
| | - Marc Friedli
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Mélanie Arcangeli
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Marilyn Marin
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | | | - Isabelle Barde
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sonia Verp
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
- * E-mail: (SEA); (DR)
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14
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A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One 2010; 5:e15741. [PMID: 21206754 PMCID: PMC3012086 DOI: 10.1371/journal.pone.0015741] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/23/2010] [Indexed: 01/22/2023] Open
Abstract
Finding sequences that control expression of genes is central to understanding genome function. Previous studies have used evolutionary conservation as an indicator of regulatory potential. Here, we present a method for the unbiased in vivo screen of putative enhancers in large DNA regions, using the mouse as a model. We cloned a library of 142 overlapping fragments from a 200 kb-long murine BAC in a lentiviral vector expressing LacZ from a minimal promoter, and used the resulting vectors to infect fertilized murine oocytes. LacZ staining of E11 embryos obtained by first using the vectors in pools and then testing individual candidates led to the identification of 3 enhancers, only one of which shows significant evolutionary conservation. In situ hybridization and 3C/4C experiments suggest that this enhancer, which is active in the neural tube and posterior diencephalon, influences the expression of the Olig1 and/or Olig2 genes. This work provides a new approach for the large-scale in vivo screening of transcriptional regulatory sequences, and further demonstrates that evolutionary conservation alone seems too limiting a criterion for the identification of enhancers.
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