1
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Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Mol Biol Evol 2024; 41:msae036. [PMID: 38376487 PMCID: PMC10919930 DOI: 10.1093/molbev/msae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | | | | | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maylie Gonzales
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cara Argus
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jennifer Bolin
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mark E Berres
- University of Wisconsin Biotechnology Center, Bioinformatics Resource Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - John Steill
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott A Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Bogdan M Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Alexander Ionkov
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Kalpana Raja
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Aimee Lang
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Magnus Wolf
- Institute for Evolution and Biodiversity (IEB), University of Muenster, 48149, Muenster, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
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2
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Bukhman YV, Meyer S, Chu LF, Abueg L, Antosiewicz-Bourget J, Balacco J, Brecht M, Dinatale E, Fedrigo O, Formenti G, Fungtammasan A, Giri SJ, Hiller M, Howe K, Kihara D, Mamott D, Mountcastle J, Pelan S, Rabbani K, Sims Y, Tracey A, Wood JMD, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Sci Data 2024; 11:176. [PMID: 38326333 PMCID: PMC10850158 DOI: 10.1038/s41597-024-03011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/26/2024] [Indexed: 02/09/2024] Open
Abstract
Suncus etruscus is one of the world's smallest mammals, with an average body mass of about 2 grams. The Etruscan shrew's small body is accompanied by a very high energy demand and numerous metabolic adaptations. Here we report a chromosome-level genome assembly using PacBio long read sequencing, 10X Genomics linked short reads, optical mapping, and Hi-C linked reads. The assembly is partially phased, with the 2.472 Gbp primary pseudohaplotype and 1.515 Gbp alternate. We manually curated the primary assembly and identified 22 chromosomes, including X and Y sex chromosomes. The NCBI genome annotation pipeline identified 39,091 genes, 19,819 of them protein-coding. We also identified segmental duplications, inferred GO term annotations, and computed orthologs of human and mouse genes. This reference-quality genome will be an important resource for research on mammalian development, metabolism, and body size control.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
| | - Susanne Meyer
- Neuroscience Research Institute, University of California - Santa Barbara, 494 UCEN Rd, Isla Vista, CA, 93117, USA
| | - Li-Fang Chu
- Department of Comparative Biology and Experimental Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Linelle Abueg
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | | | - Jennifer Balacco
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Michael Brecht
- BCCN/Humboldt University Berlin, Philippstr, 13 House 6, 10115, Berlin, Germany
| | - Erica Dinatale
- Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA
| | | | - Swagarika Jaharlal Giri
- Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Purdue University, 249 S. Martin Jischke Dr., West Lafayette, IN, 47907, USA
| | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA
| | - Jacquelyn Mountcastle
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Keon Rabbani
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way RRI 408, Los Angeles, CA, 90089, USA
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | | | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way RRI 408, Los Angeles, CA, 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA
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3
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Conrad JV, Meyer S, Ramesh PS, Neira JA, Rusteika M, Mamott D, Duffin B, Bautista M, Zhang J, Hiles E, Higgins EM, Steill J, Freeman J, Ni Z, Liu S, Ungrin M, Rancourt D, Clegg DO, Stewart R, Thomson JA, Chu LF. Efficient derivation of transgene-free porcine induced pluripotent stem cells enables in vitro modeling of species-specific developmental timing. Stem Cell Reports 2023; 18:2328-2343. [PMID: 37949072 PMCID: PMC10724057 DOI: 10.1016/j.stemcr.2023.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Sus scrofa domesticus (pig) has served as a superb large mammalian model for biomedical studies because of its comparable physiology and organ size to humans. The derivation of transgene-free porcine induced pluripotent stem cells (PiPSCs) will, therefore, benefit the development of porcine-specific models for regenerative biology and its medical applications. In the past, this effort has been hampered by a lack of understanding of the signaling milieu that stabilizes the porcine pluripotent state in vitro. Here, we report that transgene-free PiPSCs can be efficiently derived from porcine fibroblasts by episomal vectors along with microRNA-302/367 using optimized protocols tailored for this species. PiPSCs can be differentiated into derivatives representing the primary germ layers in vitro and can form teratomas in immunocompromised mice. Furthermore, the transgene-free PiPSCs preserve intrinsic species-specific developmental timing in culture, known as developmental allochrony. This is demonstrated by establishing a porcine in vitro segmentation clock model that, for the first time, displays a specific periodicity at ∼3.7 h, a timescale recapitulating in vivo porcine somitogenesis. We conclude that the transgene-free PiPSCs can serve as a powerful tool for modeling development and disease and developing transplantation strategies. We also anticipate that they will provide insights into conserved and unique features on the regulations of mammalian pluripotency and developmental timing mechanisms.
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Affiliation(s)
- J Vanessa Conrad
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Pranav S Ramesh
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jaime A Neira
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Margaret Rusteika
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Daniel Mamott
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Bret Duffin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Monica Bautista
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jue Zhang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Emily Hiles
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Eve M Higgins
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - John Steill
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jack Freeman
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Zijian Ni
- Department of Statistics, University of Wisconsin, Madison, WI 53706, USA
| | - Shiying Liu
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mark Ungrin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Derrick Rancourt
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Dennis O Clegg
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Li-Fang Chu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
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4
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Anderson BJ, Curtis AM, Jen A, Thomson JA, Clegg DO, Jiang P, Coon JJ, Overmyer KA, Toh H. Plasma metabolomics supports non-fasted sampling for metabolic profiling across a spectrum of glucose tolerance in the Nile rat model for type 2 diabetes. Lab Anim (NY) 2023; 52:269-277. [PMID: 37857753 PMCID: PMC10611569 DOI: 10.1038/s41684-023-01268-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 09/12/2023] [Indexed: 10/21/2023]
Abstract
Type 2 diabetes is a challenge in modern healthcare, and animal models are necessary to identify underlying mechanisms. The Nile rat (Arvicanthis niloticus) develops diet-induced diabetes rapidly on a conventional rodent chow diet without genetic or chemical manipulation. Unlike common laboratory models, the outbred Nile rat model is diurnal and has a wide range of overt diabetes onset and diabetes progression patterns in both sexes, better mimicking the heterogeneous diabetic phenotype in humans. While fasted blood glucose has historically been used to monitor diabetic progression, postprandial blood glucose is more sensitive to the initial stages of diabetes. However, there is a long-held assumption that ad libitum feeding in rodent models leads to increased variance, thus masking diabetes-related metabolic changes in the plasma. Here we compared repeatability within triplicates of non-fasted or fasted plasma samples and assessed metabolic changes relevant to glucose tolerance in fasted and non-fasted plasma of 8-10-week-old male Nile rats. We used liquid chromatography-mass spectrometry lipidomics and polar metabolomics to measure relative metabolite abundances in the plasma samples. We found that, compared to fasted metabolites, non-fasted plasma metabolites are not only more strongly associated with glucose tolerance on the basis of unsupervised clustering and elastic net regression model, but also have a lower replicate variance. Between the two sampling groups, we detected 66 non-fasted metabolites and 32 fasted metabolites that were associated with glucose tolerance using a combined approach with multivariable elastic net and individual metabolite linear models. Further, to test if metabolite replicate variance is affected by age and sex, we measured non-fasted replicate variance in a cohort of mature 30-week-old male and female Nile rats. Our results support using non-fasted plasma metabolomics to study glucose tolerance in Nile rats across the progression of diabetes.
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Affiliation(s)
- Benton J Anderson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Curtis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - James A Thomson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Dennis O Clegg
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Peng Jiang
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA.
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5
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Toh H, Smolentsev A, Sadjadi R, Clegg D, Yan J, Stewart R, Thomson JA, Jiang P. Transcriptomic clock predicts vascular changes of prodromal diabetic retinopathy. Sci Rep 2023; 13:12968. [PMID: 37563287 PMCID: PMC10415264 DOI: 10.1038/s41598-023-40328-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/08/2023] [Indexed: 08/12/2023] Open
Abstract
Diabetic retinopathy is a common complication of long-term diabetes and that could lead to vision loss. Unfortunately, early diabetic retinopathy remains poorly understood. There is no effective way to prevent or treat early diabetic retinopathy until patients develop later stages of diabetic retinopathy. Elevated acellular capillary density is considered a reliable quantitative trait present in the early development of retinopathy. Hence, in this study, we interrogated whole retinal vascular transcriptomic changes via a Nile rat model to better understand the early pathogenesis of diabetic retinopathy. We uncovered the complexity of associations between acellular capillary density and the joint factors of blood glucose, diet, and sex, which was modeled through a Bayesian network. Using segmented regressions, we have identified different gene expression patterns and enriched Gene Ontology (GO) terms associated with acellular capillary density increasing. We developed a random forest regression model based on expression patterns of 14 genes to predict the acellular capillary density. Since acellular capillary density is a reliable quantitative trait in early diabetic retinopathy, and thus our model can be used as a transcriptomic clock to measure the severity of the progression of early retinopathy. We also identified NVP-TAE684, geldanamycin, and NVP-AUY922 as the top three potential drugs which can potentially attenuate the early DR. Although we need more in vivo studies in the future to support our re-purposed drugs, we have provided a data-driven approach to drug discovery.
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Affiliation(s)
- Huishi Toh
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Alexander Smolentsev
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Ryan Sadjadi
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Dennis Clegg
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Jingqi Yan
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, 44115, USA
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, 44115, USA
| | - Ron Stewart
- Morgridge Institute For Research, Madison, WI, 53706, USA
| | - James A Thomson
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
- Morgridge Institute For Research, Madison, WI, 53706, USA
| | - Peng Jiang
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, 44115, USA.
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, 44115, USA.
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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6
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Jung HS, Suknuntha K, Kim YH, Liu P, Dettle ST, Sedzro DM, Smith PR, Thomson JA, Ong IM, Slukvin II. SOX18-enforced expression diverts hemogenic endothelium-derived progenitors from T towards NK lymphoid pathways. iScience 2023; 26:106621. [PMID: 37250328 PMCID: PMC10214392 DOI: 10.1016/j.isci.2023.106621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/18/2022] [Accepted: 04/01/2023] [Indexed: 05/31/2023] Open
Abstract
Hemogenic endothelium (HE) is the main source of blood cells in the embryo. To improve blood manufacturing from human pluripotent stem cells (hPSCs), it is essential to define the molecular determinants that enhance HE specification and promote development of the desired blood lineage from HE. Here, using SOX18-inducible hPSCs, we revealed that SOX18 forced expression at the mesodermal stage, in contrast to its homolog SOX17, has minimal effects on arterial specification of HE, expression of HOXA genes and lymphoid differentiation. However, forced expression of SOX18 in HE during endothelial-to-hematopoietic transition (EHT) greatly increases NK versus T cell lineage commitment of hematopoietic progenitors (HPs) arising from HE predominantly expanding CD34+CD43+CD235a/CD41a-CD45- multipotent HPs and altering the expression of genes related to T cell and Toll-like receptor signaling. These studies improve our understanding of lymphoid cell specification during EHT and provide a new tool for enhancing NK cell production from hPSCs for immunotherapies.
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Affiliation(s)
- Ho Sun Jung
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Kran Suknuntha
- Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand
| | - Yun Hee Kim
- Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA
| | - Peng Liu
- Departments of Statistics and of Biostatistics and Medical Informatics, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel T. Dettle
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Divine Mensah Sedzro
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Portia R. Smith
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - James A. Thomson
- Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Irene M. Ong
- Departments of Statistics and of Biostatistics and Medical Informatics, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Igor I. Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
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7
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Zhang J, Webster S, Duffin B, Bernstein MN, Steill J, Swanson S, Forsberg MH, Bolin J, Brown ME, Majumder A, Capitini CM, Stewart R, Thomson JA, Slukvin II. Generation of anti-GD2 CAR macrophages from human pluripotent stem cells for cancer immunotherapies. Stem Cell Reports 2023; 18:585-596. [PMID: 36638788 PMCID: PMC9968983 DOI: 10.1016/j.stemcr.2022.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
Macrophages armed with chimeric antigen receptors (CARs) provide a potent new option for treating solid tumors. However, genetic engineering and scalable production of somatic macrophages remains significant challenges. Here, we used CRISPR-Cas9 gene editing methods to integrate an anti-GD2 CAR into the AAVS1 locus of human pluripotent stem cells (hPSCs). We then established a serum- and feeder-free differentiation protocol for generating CAR macrophages (CAR-Ms) through arterial endothelial-to-hematopoietic transition (EHT). CAR-M produced by this method displayed a potent cytotoxic activity against GD2-expressing neuroblastoma and melanoma in vitro and neuroblastoma in vivo. This study provides a new platform for the efficient generation of off-the-shelf CAR-Ms for antitumor immunotherapy.
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Affiliation(s)
- Jue Zhang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Sarah Webster
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Bret Duffin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | | | - John Steill
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Matthew H Forsberg
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Jennifer Bolin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Matthew E Brown
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Aditi Majumder
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Christian M Capitini
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53792, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison 53705, WI, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | | | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.
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8
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Toh H, Bagheri A, Dewey C, Stewart R, Yan L, Clegg D, Thomson JA, Jiang P. A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP). Comput Biol Chem 2023; 102:107795. [PMID: 36436489 DOI: 10.1016/j.compbiolchem.2022.107795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
RNA sequencing (RNA-seq) has been a widely used high-throughput method to characterize transcriptomic dynamics spatiotemporally. However, RNA-seq data analysis pipelines typically depend on either a sequenced genome and/or corresponding reference transcripts. This limitation is a challenge for species lacking sequenced genomes and corresponding reference transcripts. The Nile rat (Arvicanthis niloticus) has two key features - it is daytime active, and it is prone to diet-induced diabetes, which makes it more similar to humans than regular laboratory rodents. However, at the time of this study, neither a Nile rat genome nor a reference transcript set were available, making it technically challenging to perform large-scale RNA-seq based transcriptomic studies. This genome-independent work progressed concurrently with our generation of a Nile rat genome. A well-annotated genome requires several iterations of manually reviewing curated transcripts and takes years to achieve. Here, we developed a Comparative RNA-Seq Pipeline (CRSP), integrating a comparative species strategy independent of a specific sequenced genome or species-matched reference transcripts. We performed benchmarking to validate that our CRSP tool can accurately quantify gene expression levels. In this study, we generated the first ultra-deep (2.3 billion × 2 paired-end) Nile rat RNA-seq data from 59 biopsy samples representing 22 major organs, providing a unique resource and spatial gene expression reference for Nile rat researchers. Importantly, CRSP is not limited to the Nile rat species and can be applied to any species without prior genomic knowledge. To facilitate a general use of CRSP, we also characterized the number of RNA-seq reads required for accurate estimation via simulation studies. CRSP and documents are available at: https://github.com/pjiang1105/CRSP.
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Affiliation(s)
- Huishi Toh
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Atefeh Bagheri
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA; Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA
| | - Colin Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Computer Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53706, USA
| | - Lili Yan
- Department of Psychology and Neuroscience Program, Michigan State University, East Lansing, MI, USA
| | - Dennis Clegg
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53706, USA; Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Peng Jiang
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA; Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA; Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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9
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Lou X, Tang Y, Ye L, Pretorius D, Fast VG, Kahn-Krell AM, Zhang J, Zhang J, Qiao A, Qin G, Kamp T, Thomson JA, Zhang J. Cardiac muscle patches containing four types of cardiac cells derived from human pluripotent stem cells improve recovery from cardiac injury in mice. Cardiovasc Res 2023; 119:1062-1076. [PMID: 36647784 PMCID: PMC10153642 DOI: 10.1093/cvr/cvad004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/24/2022] [Accepted: 11/04/2022] [Indexed: 01/18/2023] Open
Abstract
AIMS We have shown that human cardiac muscle patches (hCMPs) containing three different types of cardiac cells-cardiomyocytes (CMs), smooth-muscle cells (SMCs), and endothelial cells (ECs), all of which were differentiated from human pluripotent stem cells (hPSCs)-significantly improved cardiac function, infarct size, and hypertrophy in a pig model of myocardial infarction (MI). However, hPSC-CMs are phenotypically immature, which may lead to arrythymogenic concerns; thus, since hPSC-derived cardiac fibroblasts (hPSC-CFs) appear to enhance the maturity of hPSC-CMs, we compared hCMPs containing hPSC-CMs, -SMCs, -ECs, and -CFs (4TCC-hCMPs) with a second hCMP construct that lacked hPSC-CFs but was otherwise identical (3TCC-hCMPs). METHODS hCMPs were generated in a fibrin scaffold. MI was induced in SCID mice through permanent coronary artery (LAD) ligation, followed by treatment with cardiac muscle patches. Animal groups included: MI heart treated with 3TCC-hCMP; with 4TCC-hCMP; MI heart treated with no patch (MI group) and sham group. Cardiac function was evaluated via echocardiography, and cell engraftment rate while infarct size was evaluated histologically at four weeks after patch transplantation. RESULTS The results from experiments in cultured hCMPs demonstrate that the inclusion of CF in 4TCC-hCMPs had: 1) better organized sarcomeres; 2) abundant structural, metabolic, and ion- channel markers of CM maturation; and 3) greater conduction velocities (31 ± 3.23 cm/s, p<0.005) and action-potential durations (APD50 = 365 ms ± 2.649, P<0.0001; APD = 408 ms ± 2.757, P<0.0001) than those (velocity and AP duration time) in 3TCC-hCMPs. Furthermore, when 4TCC- hCMPs transplantation resulted in better cardiac function (EF = 49.18% ± 0.86, p<0.05), reduced infarct size (22.72% ± 0.98, p<0.05), and better engraftment (15.99% ± 1.56, p<0.05) as compared with 3TCC-hCMPs (EF = 41.55 ± 0.92%, infarct size = 39.23 ± 4.28%, and engraftment = 8.56 ± 1.79%, respectively). CONCLUSION Collectively, these observations suggest that the inclusion of hPSC-CFs during hCMP manufacture promotes hPSC-CM maturation and increases the potency of implanted hCMPs for improving cardiac recovery in mice model of MI. TRANSLATIONAL PERSPECTIVE Heart transplantation surgery remains the only established treatment for end-stage heart disease, and the supply of donated hearts is far lower than the number of patients in need of treatment. Thus, the goal of cardiac tissue engineering is to replace the scarred region of an injured heart with functional cardiac muscle. The results presented in this report suggest that engineered human cardiac-muscle patches may be more effective for the treatment of heart disease when they are constructed with cardiomyocytes, smooth-muscle cells, endothelial cells, and cardiac fibroblasts than when the cardiac fibroblasts are omitted.
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Affiliation(s)
- Xi Lou
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yawen Tang
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lei Ye
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Danielle Pretorius
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Vladimir G Fast
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Asher M Kahn-Krell
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jue Zhang
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Jianhua Zhang
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aijun Qiao
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gangjian Qin
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Timothy Kamp
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jianyi Zhang
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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10
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Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. BMC Biol 2022; 20:245. [DOI: 10.1186/s12915-022-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.
Results
We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.
Conclusions
Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.
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11
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Seirup M, Sengupta S, Swanson S, McIntosh BE, Collins M, Chu LF, Cheng Z, Gorkin DU, Duffin B, Bolin JM, Argus C, Stewart R, Thomson JA. Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro. Genomics 2022; 114:110330. [PMID: 35278615 DOI: 10.1016/j.ygeno.2022.110330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/22/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
Abstract
Primary hepatocytes are widely used in the pharmaceutical industry to screen drug candidates for hepatotoxicity, but hepatocytes quickly dedifferentiate and lose their mature metabolic function in culture. Attempts have been made to better recapitulate the in vivo liver environment in culture, but the full spectrum of signals required to maintain hepatocyte function ex vivo remains elusive. To elucidate molecular changes that accompany, and may contribute to dedifferentiation of hepatocytes ex vivo, we performed lineage tracing and comprehensive profiling of alterations in their gene expression profiles and chromatin landscape during culture. First, using genetically tagged hepatocytes we demonstrate that expression of the fetal gene alpha-fetoprotein in cultured hepatocytes comes from cells that previously expressed the mature gene albumin, and not from a population of albumin-negative precursor cells, proving mature hepatocytes undergo true dedifferentiation in culture. Next we studied the dedifferentiation process in detail through bulk RNA-sequencing of hepatocytes cultured over an extended period. We identified three distinct phases of dedifferentiation: an early phase, where mature hepatocyte genes are rapidly downregulated in a matter of hours; a middle phase, where fetal genes are activated; and a late phase, where initially rare contaminating non-parenchymal cells proliferate, taking over the culture. Lastly, to better understand the signaling events that result in the rapid downregulation of mature genes in hepatocytes, we examined changes in chromatin accessibility in these cells during the first 24 h of culture using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). We find that drastic and rapid changes in chromatin accessibility occur immediately upon the start of culture. Using binding motif analysis of the areas of open chromatin sharing similar temporal profiles, we identify several candidate transcription factors potentially involved in the dedifferentiation of primary hepatocytes in culture.
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Affiliation(s)
- Morten Seirup
- Molecular and Environmental Toxicology Program, University of Wisconsin Madison, Madison, WI, United States of America; Morgridge Institute for Research, Madison, WI, United States of America; Endsulin, Madison, WI, United States of America.
| | - Srikumar Sengupta
- Morgridge Institute for Research, Madison, WI, United States of America; Upside Foods, Madison, WI, United States of America
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Brian E McIntosh
- Morgridge Institute for Research, Madison, WI, United States of America; Labcorp Drug Development, Madison, WI, United States of America
| | - Mike Collins
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Zhang Cheng
- The Center for Epigenomics, University of California San Diego School of Medicine, United States of America
| | - David U Gorkin
- The Center for Epigenomics, University of California San Diego School of Medicine, United States of America
| | - Bret Duffin
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Jennifer M Bolin
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Cara Argus
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, United States of America
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI, United States of America; Department of Cell & Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America; Department of Molecular, Cellular, & Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States of America
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12
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D'Souza SS, Kumar A, Weinfurter J, Park MA, Maufort J, Tao L, Kang H, Dettle ST, Golos T, Thomson JA, Reynolds MR, Slukvin I. Generation of SIV-resistant T cells and macrophages from nonhuman primate induced pluripotent stem cells with edited CCR5 locus. Stem Cell Reports 2022; 17:953-963. [PMID: 35364011 PMCID: PMC9023799 DOI: 10.1016/j.stemcr.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Adoptive therapies with genetically modified somatic T cells rendered HIV resistance have shown promise for AIDS therapy. A renewable source of HIV-resistant human T cells from induced pluripotent stem cells (iPSCs) would further facilitate and broaden the applicability of these therapies. Here, we report successful targeting of the CCR5 locus in iPSCs generated from T cells (T-iPSCs) or fibroblasts (fib-iPSCs) from Mauritian cynomolgus macaques (MCM), using CRISPR-Cas9 technology. We found that CCR5 editing does not affect hematopoietic and T cell differentiation potentials of fib-iPSCs. However, T-iPSCs with edited CCR5 lost their capacity to differentiate into CD4+CD8+ T cells while maintaining myeloid differentiation potential. T cells and macrophages produced from CCR5-edited MCM iPSCs did not support replication of the CCR5-tropic simian immunodeficiency viruses SIVmac239 (T cell tropic) and SIVmac316 (macrophage-tropic). Overall, these studies provide a platform for further exploration of AIDS therapies based on gene-edited iPSCs in a nonhuman primate model.
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Affiliation(s)
- Saritha S D'Souza
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Akhilesh Kumar
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jason Weinfurter
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Mi Ae Park
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | | | - Lihong Tao
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - HyunJun Kang
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Samuel T Dettle
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Thaddeus Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, USA; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Matthew R Reynolds
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Igor Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53792, USA.
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13
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Yu C, Yang H, Wang L, Thomson JA, Turng LS, Guan G. Surface modification of polytetrafluoroethylene (PTFE) with a heparin-immobilized extracellular matrix (ECM) coating for small-diameter vascular grafts applications. Mater Sci Eng C Mater Biol Appl 2021; 128:112301. [PMID: 34474852 PMCID: PMC8417426 DOI: 10.1016/j.msec.2021.112301] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/08/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022]
Abstract
Intimal hyperplasia, thrombosis formation, and delayed endothelium regeneration are the main causes that restrict the clinical applications of PTFE small-diameter vascular grafts (inner diameter < 6 mm). An ideal strategy to solve such problems is to facilitate in situ endothelialization. Since the natural vascular endothelium adheres onto the basement membrane, which is a specialized form of extracellular matrix (ECM) secreted by endothelial cells (ECs) and smooth muscle cells (SMCs), functionalizing PTFE with an ECM coating was proposed. However, besides ECs, the ECM-modified PTFE improved SMC growth as well, thereby increasing the risk of intimal hyperplasia. In the present study, heparin was immobilized on the ECM coating at different densities (4.89 ± 1.02 μg/cm2, 7.24 ± 1.56 μg/cm2, 15.63 ± 2.45 μg/cm2, and 26.59 ± 3.48 μg/cm2), aiming to develop a bio-favorable environment that possessed excellent hemocompatibility and selectively inhibited SMC growth while promoting endothelialization. The results indicated that a low heparin density (4.89 ± 1.02 μg/cm2) was not enough to restrict platelet adhesion, whereas a high heparin density (26.59 ± 3.48 μg/cm2) resulted in decreased EC growth and enhanced SMC proliferation. Therefore, a heparin density at 7.24 ± 1.56 μg/cm2 was the optimal level in terms of antithrombogenicity, endothelialization, and SMC inhibition. Collectively, this study proposed a heparin-immobilized ECM coating to modify PTFE, offering a promising means to functionalize biomaterials for developing small-diameter vascular grafts.
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Affiliation(s)
- Chenglong Yu
- Key Laboratory of Textile Industry for Biomedical Textile Materials and Technology, College of Textiles, Donghua University, Shanghai 201620, China; Engineering Research Center of Technical Textiles of Ministry of Education, College of Textiles, Donghua University, Shanghai 201620, China; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Huaguang Yang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Lu Wang
- Key Laboratory of Textile Industry for Biomedical Textile Materials and Technology, College of Textiles, Donghua University, Shanghai 201620, China; Engineering Research Center of Technical Textiles of Ministry of Education, College of Textiles, Donghua University, Shanghai 201620, China
| | - James A Thomson
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, United States
| | - Lih-Sheng Turng
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States.
| | - Guoping Guan
- Key Laboratory of Textile Industry for Biomedical Textile Materials and Technology, College of Textiles, Donghua University, Shanghai 201620, China; Engineering Research Center of Technical Textiles of Ministry of Education, College of Textiles, Donghua University, Shanghai 201620, China.
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14
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Brown J, Barry C, Schmitz MT, Argus C, Bolin JM, Schwartz MP, Van Aartsen A, Steill J, Swanson S, Stewart R, Thomson JA, Kendziorski C. Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PLoS Comput Biol 2021; 17:e1008778. [PMID: 33647016 PMCID: PMC7951976 DOI: 10.1371/journal.pcbi.1008778] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/11/2021] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Human pluripotent stem cells hold significant promise for regenerative medicine. However, long differentiation protocols and immature characteristics of stem cell-derived cell types remain challenges to the development of many therapeutic applications. In contrast to the slow differentiation of human stem cells in vitro that mirrors a nine-month gestation period, mouse stem cells develop according to a much faster three-week gestation timeline. Here, we tested if co-differentiation with mouse pluripotent stem cells could accelerate the differentiation speed of human embryonic stem cells. Following a six-week RNA-sequencing time course of neural differentiation, we identified 929 human genes that were upregulated earlier and 535 genes that exhibited earlier peaked expression profiles in chimeric cell cultures than in human cell cultures alone. Genes with accelerated upregulation were significantly enriched in Gene Ontology terms associated with neurogenesis, neuron differentiation and maturation, and synapse signaling. Moreover, chimeric mixed samples correlated with in utero human embryonic samples earlier than human cells alone, and acceleration was dose-dependent on human-mouse co-culture ratios. The altered gene expression patterns and developmental rates described in this report have implications for accelerating human stem cell differentiation and the use of interspecies chimeric embryos in developing human organs for transplantation.
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Affiliation(s)
- Jared Brown
- Department of Statistics, University of Wisconsin-Madison, Wisconsin, United States of America
- * E-mail: (JB); (CK)
| | - Christopher Barry
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Matthew T. Schmitz
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Cara Argus
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Jennifer M. Bolin
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Michael P. Schwartz
- NSF Center for Sustainable Nanotechnology, Department of Chemistry, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Amy Van Aartsen
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - John Steill
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Scott Swanson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - James A. Thomson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Wisconsin, United States of America
- * E-mail: (JB); (CK)
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15
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Jung HS, Uenishi G, Park MA, Liu P, Suknuntha K, Raymond M, Choi YJ, Thomson JA, Ong IM, Slukvin II. SOX17 integrates HOXA and arterial programs in hemogenic endothelium to drive definitive lympho-myeloid hematopoiesis. Cell Rep 2021; 34:108758. [PMID: 33596423 PMCID: PMC7988717 DOI: 10.1016/j.celrep.2021.108758] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/12/2020] [Accepted: 01/26/2021] [Indexed: 12/30/2022] Open
Abstract
SOX17 has been implicated in arterial specification and the maintenance of hematopoietic stem cells (HSCs) in the murine embryo. However, knowledge about molecular pathways and stage-specific effects of SOX17 in humans remains limited. Here, using SOX17-knockout and SOX17-inducible human pluripotent stem cells (hPSCs), paired with molecular profiling studies, we reveal that SOX17 is a master regulator of HOXA and arterial programs in hemogenic endothelium (HE) and is required for the specification of HE with robust lympho-myeloid potential and DLL4+CXCR4+ phenotype resembling arterial HE at the sites of HSC emergence. Along with the activation of NOTCH signaling, SOX17 directly activates CDX2 expression, leading to the upregulation of the HOXA cluster genes. Since deficiencies in HOXA and NOTCH signaling contribute to the impaired in vivo engraftment of hPSC-derived hematopoietic cells, the identification of SOX17 as a key regulator linking arterial and HOXA programs in HE may help to program HSC fate from hPSCs.
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Affiliation(s)
- Ho Sun Jung
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Gene Uenishi
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Mi Ae Park
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Peng Liu
- Departments of Statistics and of Biostatistics and Medical Informatics, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Kran Suknuntha
- Chakri Naruebodindra Medical Institute, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand; Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA
| | - Matthew Raymond
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Yoon Jung Choi
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Irene M Ong
- Departments of Statistics and of Biostatistics and Medical Informatics, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA.
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16
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Jiang P, Chamberlain CS, Vanderby R, Thomson JA, Stewart R. TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes. Nucleic Acids Res 2020; 48:e51. [PMID: 32123905 PMCID: PMC7229845 DOI: 10.1093/nar/gkaa142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/03/2020] [Accepted: 02/26/2020] [Indexed: 01/02/2023] Open
Abstract
Comparative time series transcriptome analysis is a powerful tool to study development, evolution, aging, disease progression and cancer prognosis. We develop TimeMeter, a statistical method and tool to assess temporal gene expression similarity, and identify differentially progressing genes where one pattern is more temporally advanced than the other. We apply TimeMeter to several datasets, and show that TimeMeter is capable of characterizing complicated temporal gene expression associations. Interestingly, we find: (i) the measurement of differential progression provides a novel feature in addition to pattern similarity that can characterize early developmental divergence between two species; (ii) genes exhibiting similar temporal patterns between human and mouse during neural differentiation are under strong negative (purifying) selection during evolution; (iii) analysis of genes with similar temporal patterns in mouse digit regeneration and axolotl blastema differentiation reveals common gene groups for appendage regeneration with potential implications in regenerative medicine.
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Affiliation(s)
- Peng Jiang
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI 53707, USA
| | - Connie S Chamberlain
- Department of Orthopedics and Rehabilitation, University of Wisconsin, Madison, WI 53706, USA
| | - Ray Vanderby
- Department of Orthopedics and Rehabilitation, University of Wisconsin, Madison, WI 53706, USA.,Department of Biomedical Engineering, University of Wisconsin, Madison, WI 53706, USA
| | - James A Thomson
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI 53707, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Ron Stewart
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI 53707, USA
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17
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Sengupta S, Johnson B, Seirup M, Ardalani H, Duffin B, Barrett-Wilt GA, Stewart R, Thomson JA. Co-culture with mouse embryonic fibroblasts improves maintenance of metabolic function of human small hepatocyte progenitor cells. Curr Res Toxicol 2020; 1:70-84. [PMID: 34345838 PMCID: PMC8320630 DOI: 10.1016/j.crtox.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Derivation and culture of small hepatocyte progenitor cells (SHPCs) capable of proliferating in vitro has been described in rodents and recently in humans. These cells are capable of engrafting in injured livers, however, they display de-differentiated morphology and reduced xenobiotic metabolism activity in culture over passages. Here we report that SHPCs derived from adult primary human hepatocytes (PHHs) and cultured on mouse embryonic fibroblasts (MEFs) not only display differentiated morphology and exhibit gene expression profiles similar to adult PHHs, but importantly, they retain their phenotype over several passages. Further, unlike previous reports, where extensive manipulations of culture conditions are required to convert SHPCs to metabolically functional hepatocytes, SHPCs in our co-culture system maintain expression of xenobiotic metabolism-associated genes. We show that SHPCs in co-culture are able to perform xenobiotic metabolism at rates equal to their parent PHHs as evidenced by the metabolism of acetaminophen to all of its major metabolites. In summary, we present an improved co-culture system that allows generation of SHPCs from adult PHHs that maintain their differentiated phenotype over multiple passages. Our findings would be useful for expansion of limited PHHs for use in studies of drug metabolism and toxicity testing.
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Affiliation(s)
- Srikumar Sengupta
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Brian Johnson
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States of America.,Institute for Quantitative Health Science and Engineering, Departments of Pharmacology & Toxicology and Biomedical Engineering, Michigan State University, East Lansing, MI, United States of America
| | - Morten Seirup
- Morgridge Institute for Research, Madison, WI, United States of America.,Dianomi Therapeutics, Madison, WI, United States of America
| | - Hamisha Ardalani
- Morgridge Institute for Research, Madison, WI, United States of America.,Beckman Coulter Life Sciences, San Jose, CA, United States of America
| | - Bret Duffin
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Gregory A Barrett-Wilt
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, United States of America
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI, United States of America.,Department of Cell & Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America.,Department of Molecular, Cellular, & Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States of America
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18
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Wang D, Xu Y, Lin YJ, Yilmaz G, Zhang J, Schmidt G, Li Q, Thomson JA, Turng LS. Biologically Functionalized Expanded Polytetrafluoroethylene Blood Vessel Grafts. Biomacromolecules 2020; 21:3807-3816. [DOI: 10.1021/acs.biomac.0c00897] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dongfang Wang
- School of Mechanics and Engineering Science, Zhengzhou University, Zhengzhou 450001, P. R. China
- National Center for International Research of Micro−Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
- Department of Mechanical Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin−Madison, Madison, Wisconsin 53715, United States
| | - Yiyang Xu
- Department of Mechanical Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin−Madison, Madison, Wisconsin 53715, United States
| | - Yu-Jyun Lin
- Department of Mechanical Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin−Madison, Madison, Wisconsin 53715, United States
| | - Galip Yilmaz
- Department of Mechanical Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin−Madison, Madison, Wisconsin 53715, United States
| | - Jue Zhang
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - George Schmidt
- Department of Mechanical Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin−Madison, Madison, Wisconsin 53715, United States
| | - Qian Li
- School of Mechanics and Engineering Science, Zhengzhou University, Zhengzhou 450001, P. R. China
- National Center for International Research of Micro−Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - James A. Thomson
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Lih-Sheng Turng
- Department of Mechanical Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin−Madison, Madison, Wisconsin 53715, United States
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19
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Kaushik G, Gupta K, Harms V, Torr E, Evans J, Johnson HJ, Soref C, Acevedo‐Acevedo S, Antosiewicz‐Bourget J, Mamott D, Uhl P, Johnson BP, Palecek SP, Beebe DJ, Thomson JA, Daly WT, Murphy WL. Engineered Perineural Vascular Plexus for Modeling Developmental Toxicity. Adv Healthc Mater 2020; 9:e2000825. [PMID: 32613760 DOI: 10.1002/adhm.202000825] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Indexed: 12/19/2022]
Abstract
There is a vital need to develop in vitro models of the developing human brain to recapitulate the biological effects that toxic compounds have on the brain. To model perineural vascular plexus (PNVP) in vitro, which is a key stage in embryonic development, human embryonic stem cells (hESC)-derived endothelial cells (ECs), neural progenitor cells, and microglia (MG) with primary pericytes (PCs) in synthetic hydrogels in a custom-designed microfluidics device are cocultured. The formation of a vascular plexus that includes networks of ECs (CD31+, VE-cadherin+), MG (IBA1+), and PCs (PDGFRβ+), and an overlying neuronal layer that includes differentiated neuronal cells (βIII Tubulin+, GFAP+) and radial glia (Nestin+, Notch2NL+), are characterized. Increased brain-derived neurotrophic factor secretion and differential metabolite secretion by the vascular plexus and the neuronal cells over time are consistent with PNVP functionality. Multiple concentrations of developmental toxicants (teratogens, microglial disruptor, and vascular network disruptors) significantly reduce the migration of ECs and MG toward the neuronal layer, inhibit formation of the vascular network, and decrease vascular endothelial growth factor A (VEGFA) secretion. By quantifying 3D cell migration, metabolic activity, vascular network disruption, and cytotoxicity, the PNVP model may be a useful tool to make physiologically relevant predictions of developmental toxicity.
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Affiliation(s)
- Gaurav Kaushik
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐Madison 1111 Highland Ave., WIMR 5418 Madison WI 53705 USA
| | - Kartik Gupta
- Department of SurgeryUniversity of Wisconsin‐Madison 1111 Highland Ave. Madison WI 53705 USA
| | - Victoria Harms
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐Madison 1111 Highland Ave., WIMR 5418 Madison WI 53705 USA
| | - Elizabeth Torr
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐Madison 1111 Highland Ave., WIMR 5418 Madison WI 53705 USA
| | - Jonathan Evans
- Department of Biomedical EngineeringUniversity of Wisconsin‐Madison 1415 Engineering Drive Madison WI 53706 USA
| | - Hunter J. Johnson
- Department of Biomedical EngineeringUniversity of Wisconsin‐Madison 1415 Engineering Drive Madison WI 53706 USA
| | - Cheryl Soref
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐Madison 1111 Highland Ave., WIMR 5418 Madison WI 53705 USA
| | - Suehelay Acevedo‐Acevedo
- Department of Biomedical EngineeringUniversity of Wisconsin‐Madison 1415 Engineering Drive Madison WI 53706 USA
| | | | - Daniel Mamott
- Morgridge Institute for Research 330 N Orchard St Madison WI 53715 USA
| | - Peyton Uhl
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐Madison 1111 Highland Ave., WIMR 5418 Madison WI 53705 USA
| | - Brian P. Johnson
- Department of Biomedical EngineeringUniversity of Wisconsin‐Madison 1415 Engineering Drive Madison WI 53706 USA
| | - Sean P. Palecek
- Department of Chemical and Biological EngineeringUniversity of Wisconsin‐Madison 1415 Engineering Drive Madison WI 53706 USA
| | - David J. Beebe
- Department of Biomedical EngineeringUniversity of Wisconsin‐Madison 1415 Engineering Drive Madison WI 53706 USA
- Department of Pathology and Laboratory MedicineUniversity of Wisconsin‐Madison 1685 Highland Ave. Madison WI 53705 USA
- University of Wisconsin Carbone Center Research 600 Highland Ave. Madison WI 53792 USA
| | - James A. Thomson
- Morgridge Institute for Research 330 N Orchard St Madison WI 53715 USA
| | - William T. Daly
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐Madison 1111 Highland Ave., WIMR 5418 Madison WI 53705 USA
| | - William L. Murphy
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐Madison 1111 Highland Ave., WIMR 5418 Madison WI 53705 USA
- Department of Biomedical EngineeringUniversity of Wisconsin‐Madison 1415 Engineering Drive Madison WI 53706 USA
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20
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Wang D, Xu Y, Wang L, Wang X, Ren C, Zhang B, Li Q, Thomson JA, Turng LS. Expanded Poly(tetrafluoroethylene) Blood Vessel Grafts with Embedded Reactive Oxygen Species (ROS)-Responsive Antithrombogenic Drug for Elimination of Thrombosis. ACS Appl Mater Interfaces 2020; 12:29844-29853. [PMID: 32496045 DOI: 10.1021/acsami.0c07868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Treatment of cardiovascular diseases suffers from the lack of transplantable small-diameter blood vessel (SDBV) grafts that can prohibit/eliminate thrombosis. Although expanded poly(tetrafluoroethylene) (ePTFE) has the potential to be used for SDBV grafts, recurrence of thrombus remains the biggest challenge. In this study, a reactive oxygen species (ROS)-responsive antithrombogenic drug synthesis and a bulk coating process were employed to fabricate functional ePTFE grafts capable of prohibiting/eliminating blood clots. The synthesized drug that would release antiplatelet ethyl salicylate (ESA), in responding to ROS, was dissolved in a polycaprolactone (PCL) solution, followed by a bulk coating of the as-fabricated ePTFE grafts with the PCL/drug solution. Nuclear magnetic resonance (NMR) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and atomic force microscopy (AFM) were employed to investigate and confirm the synthesis and presence of the ROS-responsive drug in the ePTFE grafts. The ESA release functions were demonstrated via the drug-release profile and dynamic anticoagulation tests. The biocompatibility of the ROS-responsive ePTFE grafts was demonstrated via lactate dehydrogenase (LDH) cytotoxicity assays, live and dead cell assays, cell morphology, and cell-graft interactions. The ROS-responsive, antithrombogenic ePTFE grafts provide a feasible way for maintaining long-term patency, potentially solving a critical challenge in SDBV applications.
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Affiliation(s)
- Dongfang Wang
- School of Mechanics and Engineering Science, Zhengzhou University, Zhengzhou 450001, P. R. China
- National Center for International Research of Micro-Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Yiyang Xu
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Lixia Wang
- School of Mechanics and Engineering Science, Zhengzhou University, Zhengzhou 450001, P. R. China
- National Center for International Research of Micro-Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Xiaofeng Wang
- School of Mechanics and Engineering Science, Zhengzhou University, Zhengzhou 450001, P. R. China
- National Center for International Research of Micro-Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Cuihong Ren
- School of Mechanics and Engineering Science, Zhengzhou University, Zhengzhou 450001, P. R. China
- National Center for International Research of Micro-Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Bo Zhang
- School of Mechanics and Engineering Science, Zhengzhou University, Zhengzhou 450001, P. R. China
- National Center for International Research of Micro-Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Qian Li
- National Center for International Research of Micro-Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - James A Thomson
- Morgridge Institute for Research, University of Wisconsin-Madison, Wisconsin 53715, United States
| | - Lih-Sheng Turng
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
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21
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Park MA, Kumar A, Jung HS, Uenishi G, Moskvin OV, Thomson JA, Slukvin II. Activation of the Arterial Program Drives Development of Definitive Hemogenic Endothelium with Lymphoid Potential. Cell Rep 2019; 23:2467-2481. [PMID: 29791856 DOI: 10.1016/j.celrep.2018.04.092] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/01/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
Abstract
Understanding the pathways guiding the development of definitive hematopoiesis with lymphoid potential is essential for advancing human pluripotent stem cell (hPSC) technologies for the treatment of blood diseases and immunotherapies. In the embryo, lymphoid progenitors and hematopoietic stem cells (HSCs) arise from hemogenic endothelium (HE) lining arteries but not veins. Here, we show that activation of the arterial program through ETS1 overexpression or by modulating MAPK/ERK signaling pathways at the mesodermal stage of development dramatically enhanced the formation of arterial-type HE expressing DLL4 and CXCR4. Blood cells generated from arterial HE were more than 100-fold enriched in T cell precursor frequency and possessed the capacity to produce B lymphocytes and red blood cells expressing high levels of BCL11a and β-globin. Together, these findings provide an innovative strategy to aid in the generation of definitive lymphomyeloid progenitors and lymphoid cells from hPSCs for immunotherapy through enhancing arterial programming of HE.
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Affiliation(s)
- Mi Ae Park
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Akhilesh Kumar
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Ho Sun Jung
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Gene Uenishi
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Oleg V Moskvin
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Igor I Slukvin
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA.
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22
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Barry C, Schmitz MT, Argus C, Bolin JM, Probasco MD, Leng N, Duffin BM, Steill J, Swanson S, McIntosh BE, Stewart R, Kendziorski C, Thomson JA, Bacher R. Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. PLoS Comput Biol 2019; 15:e1007543. [PMID: 31815944 PMCID: PMC6922475 DOI: 10.1371/journal.pcbi.1007543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/19/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Pluripotent stem cells retain the developmental timing of their species of origin in vitro, an observation that suggests the existence of a cell-intrinsic developmental clock, yet the nature and machinery of the clock remain a mystery. We hypothesize that one possible component may lie in species-specific differences in the kinetics of transcriptional responses to differentiation signals. Using a liquid-handling robot, mouse and human pluripotent stem cells were exposed to identical neural differentiation conditions and sampled for RNA-sequencing at high frequency, every 4 or 10 minutes, for the first 10 hours of differentiation to test for differences in transcriptomic response rates. The majority of initial transcriptional responses occurred within a rapid window in the first minutes of differentiation for both human and mouse stem cells. Despite similarly early onsets of gene expression changes, we observed shortened and condensed gene expression patterns in mouse pluripotent stem cells compared to protracted trends in human pluripotent stem cells. Moreover, the speed at which individual genes were upregulated, as measured by the slopes of gene expression changes over time, was significantly faster in mouse compared to human cells. These results suggest that downstream transcriptomic response kinetics to signaling cues are faster in mouse versus human cells, and may offer a partial account for the vast differences in developmental rates across species.
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Affiliation(s)
- Christopher Barry
- Morgridge Institute for Research, Madison, WI, United States of America
| | | | - Cara Argus
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Jennifer M. Bolin
- Morgridge Institute for Research, Madison, WI, United States of America
| | | | - Ning Leng
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Bret M. Duffin
- Morgridge Institute for Research, Madison, WI, United States of America
| | - John Steill
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Brian E. McIntosh
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - James A. Thomson
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, United States of America
| | - Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, FL, United States of America
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23
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Toh H, Smolentsev A, Bozadjian RV, Keeley PW, Lockwood MD, Sadjadi R, Clegg DO, Blodi BA, Coffey PJ, Reese BE, Thomson JA. Vascular changes in diabetic retinopathy-a longitudinal study in the Nile rat. J Transl Med 2019; 99:1547-1560. [PMID: 31101854 PMCID: PMC6788790 DOI: 10.1038/s41374-019-0264-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 03/11/2019] [Accepted: 03/24/2019] [Indexed: 12/15/2022] Open
Abstract
Diabetic retinopathy is the most common microvascular complication of diabetes and is a major cause of blindness, but an understanding of the pathogenesis of the disease has been hampered by a lack of accurate animal models. Here, we explore the dynamics of retinal cellular changes in the Nile rat (Arvicanthis niloticus), a carbohydrate-sensitive model for type 2 diabetes. The early retinal changes in diabetic Nile rats included increased acellular capillaries and loss of pericytes that correlated linearly with the duration of diabetes. These vascular changes occurred in the presence of microglial infiltration but in the absence of retinal ganglion cell loss. After a prolonged duration of diabetes, the Nile rat also exhibits a spectrum of retinal lesions commonly seen in the human condition including vascular leakage, capillary non-perfusion, and neovascularization. Our longitudinal study documents a range and progression of retinal lesions in the diabetic Nile rat remarkably similar to those observed in human diabetic retinopathy, and suggests that this model will be valuable in identifying new therapeutic strategies.
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Affiliation(s)
- Huishi Toh
- Center for Stem Cell Biology and Engineering, University of California at Santa Barbara, Santa Barbara, CA, USA. .,Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA, USA.
| | - Alexander Smolentsev
- Center for Stem Cell Biology and Engineering, University of California at Santa Barbara, Santa Barbara, California, USA,Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA
| | - Rachel V. Bozadjian
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA
| | - Patrick W. Keeley
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA
| | - Madison D. Lockwood
- Center for Stem Cell Biology and Engineering, University of California at Santa Barbara, Santa Barbara, California, USA,Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA
| | - Ryan Sadjadi
- Center for Stem Cell Biology and Engineering, University of California at Santa Barbara, Santa Barbara, California, USA,Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA
| | - Dennis O. Clegg
- Center for Stem Cell Biology and Engineering, University of California at Santa Barbara, Santa Barbara, California, USA,Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Barbara A. Blodi
- University of Wisconsin Fundus Photograph Reading Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Peter J. Coffey
- Center for Stem Cell Biology and Engineering, University of California at Santa Barbara, Santa Barbara, California, USA,Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA,NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, UK,The London Project to Cure Blindness, ORBIT, Institute of Ophthalmology, University College London (UCL), London, UK
| | - Benjamin E. Reese
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA,Department of Psychological and Brain Sciences, University of California at Santa Barbara, Santa Barbara, California, USA
| | - James A. Thomson
- Center for Stem Cell Biology and Engineering, University of California at Santa Barbara, Santa Barbara, California, USA,Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA,Morgridge Institute for Research, Madison, Wisconsin, USA,Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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Ardalani H, Sengupta S, Harms V, Vickerman V, Thomson JA, Murphy WL. 3-D culture and endothelial cells improve maturity of human pluripotent stem cell-derived hepatocytes. Acta Biomater 2019; 95:371-381. [PMID: 31362140 DOI: 10.1016/j.actbio.2019.07.047] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/18/2022]
Abstract
Human-induced pluripotent stem cell (hiPSC)-derived hepatocytes (iHEP) offer an attractive alternative to primary human hepatocytes (PHH) for drug toxicity studies, as PHHs are limited in supply, vary in their metabolic activity between donors, and rapidly lose their functionality in vitro. However, one of the major drawbacks with iHEP cells in drug safety studies is their decreased phenotypic maturity, with lower liver specific enzyme activity compared with that of PHH. Here we evaluated the effects of 3D culture and non-parenchymal cells on the maturation of iHEPs. We describe a serum-free, chemically defined 3D in vitro model using iHEP cells, which is compatible with automation and conventional assay plates. The iHEP cells cultured in this model form polarized aggregates with functional bile canaliculi and strongly increased expression of albumin, urea and genes encoding phase I and II drug metabolism enzymes and bile transporters. Cytochrome P450-mediated metabolism is significantly higher in 3D iHEP aggregates compared to 2D iHEP culture. Furthermore, addition of human liver sinusoidal endothelial cells (sECs) and iPS-derived endothelial cells (iECs) improved mature hepatocyte function and CYP450 enzyme activity. Also, ECs formed endothelial networks within the hepatic 3D cultures, mimicking aspects of an in vivo architecture. Collectively, these results suggest that the iHEP/EC aggregates described here may have the potential to be used for many applications, including as an in vitro model to study liver diseases associated with sinusoidal endothelial cells. STATEMENT OF SIGNIFICANCE: iPS-derived hepatocytes provide an inexhaustible source of cells for drug screening, toxicology studies and cell-based therapies, but lack mature phenotype of adult primary human hepatocytes (PHH). Herein, we show that 3D culture of iPS-derived hepatocytes and their co-culture with human sinusoidal endothelial cells (sECs) to improve their maturity.
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Affiliation(s)
- Hamisha Ardalani
- Department of Biomedical Engineering, University of Wisconsin-Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA
| | | | - Victoria Harms
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, WI, USA
| | | | - James A Thomson
- Morgridge Institute for Research, Madison, WI, USA; Cell and Regenerative Biology, University of Wisconsin-Madison, WI, USA; Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, CA, USA
| | - William L Murphy
- Department of Biomedical Engineering, University of Wisconsin-Madison, WI, USA; Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, WI, USA.
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25
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Maufort JP, Israel JS, Brown ME, Kempton SJ, Albano NJ, Zeng W, Kelnhofer LE, Reynolds MR, Perrin ES, Sanchez RJ, Sluvkin II, Thomson JA, Poore SO. Major Histocompatibility Complex-Matched Arteries Have Similar Patency to Autologous Arteries in a Mauritian Cynomolgus Macaque Major Histocompatibility Complex-Defined Transplant Model. J Am Heart Assoc 2019; 8:e012135. [PMID: 31313646 PMCID: PMC6761673 DOI: 10.1161/jaha.119.012135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background Arterial bypass and interposition grafts are used routinely across multiple surgical subspecialties. Current options include both autologous and synthetic materials; however, each graft presents specific limitations. Engineering artificial small‐diameter arteries with vascular cells derived from induced pluripotent stem cells could provide a useful therapeutic solution. Banking induced pluripotent stem cells from rare individuals who are homozygous for human leukocyte antigen alleles has been proposed as a strategy to facilitate economy of scale while reducing the potential for rejection of induced pluripotent stem cell–derived transplanted tissues. Currently, there is no standardized model to study transplantation of small‐diameter arteries in major histocompatibility complex–defined backgrounds. Methods and Results In this study, we developed a limb‐sparing nonhuman primate model to study arterial allotransplantation in the absence of immunosuppression. Our model was used to compare degrees of major histocompatibility complex matching between arterial grafts and recipient animals with long‐term maintenance of patency and function. Unexpectedly, we (1) found that major histocompatibility complex partial haplomatched allografts perform as well as autologous control grafts; (2) detected little long‐term immune response in even completely major histocompatibility complex mismatched allografts; and (3) observed that arterial grafts become almost completely replaced over time with recipient cells. Conclusions Given these findings, induced pluripotent stem cell–derived tissue‐engineered blood vessels may prove to be promising and customizable grafts for future use by cardiac, vascular, and plastic surgeons.
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Affiliation(s)
- John P Maufort
- Department of Regenerative Biology Morgridge Institute for Research Madison WI.,Wisconsin National Primate Research Center University of Wisconsin-Madison WI
| | - Jacqueline S Israel
- Department of Surgery Division of Plastic Surgery School of Medicine and Public Health University of Wisconsin Madison WI
| | - Matthew E Brown
- Department of Regenerative Biology Morgridge Institute for Research Madison WI.,Department of Surgery School of Medicine and Public Health University of Wisconsin-Madison Madison WI
| | - Steve J Kempton
- Department of Surgery Division of Plastic Surgery School of Medicine and Public Health University of Wisconsin Madison WI
| | - Nicholas J Albano
- Department of Surgery Division of Plastic Surgery School of Medicine and Public Health University of Wisconsin Madison WI
| | - Weifeng Zeng
- Department of Surgery Division of Plastic Surgery School of Medicine and Public Health University of Wisconsin Madison WI
| | - Laurel E Kelnhofer
- Wisconsin National Primate Research Center University of Wisconsin-Madison WI
| | - Matthew R Reynolds
- Wisconsin National Primate Research Center University of Wisconsin-Madison WI
| | - Elizabeth S Perrin
- Department of Regenerative Biology Morgridge Institute for Research Madison WI.,Wisconsin National Primate Research Center University of Wisconsin-Madison WI
| | - Ruston J Sanchez
- Department of Surgery Division of Plastic Surgery School of Medicine and Public Health University of Wisconsin Madison WI
| | - Igor I Sluvkin
- Wisconsin National Primate Research Center University of Wisconsin-Madison WI
| | - James A Thomson
- Department of Regenerative Biology Morgridge Institute for Research Madison WI.,Wisconsin National Primate Research Center University of Wisconsin-Madison WI.,Department of Molecular, Cellular, and Developmental Biology University of California Santa Barbara CA
| | - Samuel O Poore
- Department of Surgery Division of Plastic Surgery School of Medicine and Public Health University of Wisconsin Madison WI
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Chasman D, Iyer N, Fotuhi Siahpirani A, Estevez Silva M, Lippmann E, McIntosh B, Probasco MD, Jiang P, Stewart R, Thomson JA, Ashton RS, Roy S. Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. Cell Syst 2019; 9:167-186.e12. [PMID: 31302154 DOI: 10.1016/j.cels.2019.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 05/05/2019] [Accepted: 05/30/2019] [Indexed: 12/19/2022]
Abstract
Neuroepithelial stem cells (NSC) from different anatomical regions of the embryonic neural tube's rostrocaudal axis can differentiate into diverse central nervous system tissues, but the transcriptional regulatory networks governing these processes are incompletely understood. Here, we measure region-specific NSC gene expression along the rostrocaudal axis in a human pluripotent stem cell model of early central nervous system development over a 72-h time course, spanning the hindbrain to cervical spinal cord. We introduce Escarole, a probabilistic clustering algorithm for non-stationary time series, and combine it with prior-based regulatory network inference to identify genes that are regulated dynamically and predict their upstream regulators. We identify known regulators of patterning and neural development, including the HOX genes, and predict a direct regulatory connection between the transcription factor POU3F2 and target gene STMN2. We demonstrate that POU3F2 is required for expression of STMN2, suggesting that this regulatory connection is important for region specificity of NSCs.
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Affiliation(s)
- Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Nisha Iyer
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alireza Fotuhi Siahpirani
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Maria Estevez Silva
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ethan Lippmann
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian McIntosh
- Regenerative Biology Theme, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mitchell D Probasco
- Regenerative Biology Theme, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Regenerative Biology Theme, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ron Stewart
- Regenerative Biology Theme, Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Regenerative Biology Theme, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Randolph S Ashton
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA.
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Mina SG, Alaybeyoglu B, Murphy WL, Thomson JA, Stokes CL, Cirit M. Assessment of Drug-Induced Toxicity Biomarkers in the Brain Microphysiological System (MPS) Using Targeted and Untargeted Molecular Profiling. Front Big Data 2019; 2:23. [PMID: 33693346 PMCID: PMC7931859 DOI: 10.3389/fdata.2019.00023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/05/2019] [Indexed: 12/19/2022] Open
Abstract
Early assessment of adverse drug effects in humans is critical to avoid long-lasting harm. However, current approaches for early detection of adverse effects still lack predictive and organ-specific biomarkers to evaluate undesired responses in humans. Microphysiological systems (MPSs) are in vitro representations of human tissues and provide organ-specific translational insights for physiological processes. In this study, a brain MPS was utilized to assess molecular signatures of neurotoxic and non-neurotoxic compounds using targeted and untargeted molecular approaches. The brain MPS comprising of human embryonic stem (ES) cell-derived neural progenitor cells seeded on three-dimensional (3D), chemically defined, polyethylene glycol hydrogels was treated with the neurotoxic drug, bortezomib and the non-neurotoxic drug, tamoxifen over 14-days. Possible toxic effects were monitored with human N-acetylaspartic acid (NAA) kinetics, which correlates the neuronal function/health and DJ-1/PARK7, an oxidative stress biomarker. Changes in NAA levels were observed as early as 2-days post-bortezomib treatment, while onset detection of oxidative stress (DJ-1) was delayed until 4-days post-treatment. Separately, the untargeted extracellular metabolomics approach revealed distinct fingerprints 2-days post-bortezomib treatment as perturbations in cysteine and glycerophospholipid metabolic pathways. These results suggest accumulation of reactive oxygen species associated with oxidative stress, and disruption of membrane structure and integrity. The NAA response was strongly correlated with changes in a subset of the detected metabolites at the same time point 2-days post-treatment. Moreover, these metabolite changes correlated strongly with DJ-1 levels measured at the later time point (4-days post-treatment). This suggests that early cellular metabolic dysfunction leads to later DJ-1 leakage and cell death, and that early measurement of this subset of metabolites could predict the later occurrence of cell death. While the approach demonstrated here provides an individual case study for proof of concept, we suggest that this approach can be extended for preclinical toxicity screening and biomarker discovery studies.
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Affiliation(s)
- Sara G. Mina
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Begum Alaybeyoglu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - William L. Murphy
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - James A. Thomson
- Regenerative Biology, The Morgridge Institute for Research, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, United States
| | | | - Murat Cirit
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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Zhang J, Tao R, Campbell KF, Carvalho JL, Ruiz EC, Kim GC, Schmuck EG, Raval AN, da Rocha AM, Herron TJ, Jalife J, Thomson JA, Kamp TJ. Functional cardiac fibroblasts derived from human pluripotent stem cells via second heart field progenitors. Nat Commun 2019; 10:2238. [PMID: 31110246 PMCID: PMC6527555 DOI: 10.1038/s41467-019-09831-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 04/02/2019] [Indexed: 01/17/2023] Open
Abstract
Cardiac fibroblasts (CFs) play critical roles in heart development, homeostasis, and disease. The limited availability of human CFs from native heart impedes investigations of CF biology and their role in disease. Human pluripotent stem cells (hPSCs) provide a highly renewable and genetically defined cell source, but efficient methods to generate CFs from hPSCs have not been described. Here, we show differentiation of hPSCs using sequential modulation of Wnt and FGF signaling to generate second heart field progenitors that efficiently give rise to hPSC-CFs. The hPSC-CFs resemble native heart CFs in cell morphology, proliferation, gene expression, fibroblast marker expression, production of extracellular matrix and myofibroblast transformation induced by TGFβ1 and angiotensin II. Furthermore, hPSC-CFs exhibit a more embryonic phenotype when compared to fetal and adult primary human CFs. Co-culture of hPSC-CFs with hPSC-derived cardiomyocytes distinctly alters the electrophysiological properties of the cardiomyocytes compared to co-culture with dermal fibroblasts. The hPSC-CFs provide a powerful cell source for research, drug discovery, precision medicine, and therapeutic applications in cardiac regeneration. Cardiac fibroblasts (CFs) play critical roles in heart development, homeostasis, and disease. Here the authors efficiently differentiate human pluripotent stem cells through second heart field progenitors to CFs that exhibit features and functional properties similar to native CFs.
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Affiliation(s)
- Jianhua Zhang
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA. .,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| | - Ran Tao
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Katherine F Campbell
- Center for Arrhythmia Research, Department of Internal Medicine, Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Frankel Cardiovascular Regeneration Core Laboratory, Ann Arbor, MI, 48109, USA
| | - Juliana L Carvalho
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasilia, 70790, Distrito Federal, Brazil
| | - Edward C Ruiz
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Gina C Kim
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Eric G Schmuck
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Amish N Raval
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - André Monteiro da Rocha
- Center for Arrhythmia Research, Department of Internal Medicine, Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Frankel Cardiovascular Regeneration Core Laboratory, Ann Arbor, MI, 48109, USA
| | - Todd J Herron
- Center for Arrhythmia Research, Department of Internal Medicine, Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Frankel Cardiovascular Regeneration Core Laboratory, Ann Arbor, MI, 48109, USA
| | - José Jalife
- Center for Arrhythmia Research, Department of Internal Medicine, Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Fundación Nacional Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Melchor Fernández Almagro, 328029, Madrid, Spain
| | - James A Thomson
- Regenerative Biology Division, Morgridge Institute for Research, Madison, WI, 53715, USA.,Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Timothy J Kamp
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA. .,Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, WI, 53705, USA. .,Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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Zhang J, McIntosh BE, Wang B, Brown ME, Probasco MD, Webster S, Duffin B, Zhou Y, Guo LW, Burlingham WJ, Kent C, Ferris M, Thomson JA. A Human Pluripotent Stem Cell-Based Screen for Smooth Muscle Cell Differentiation and Maturation Identifies Inhibitors of Intimal Hyperplasia. Stem Cell Reports 2019; 12:1269-1281. [PMID: 31080110 PMCID: PMC6565755 DOI: 10.1016/j.stemcr.2019.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 02/04/2023] Open
Abstract
Contractile to synthetic phenotypic switching of smooth muscle cells (SMCs) contributes to stenosis in vascular disease and vascular transplants. To generate more contractile SMCs, we performed a high-throughput differentiation screen using a MYH11-NLuc-tdTomato human embryonic stem cell reporter cell line. We identified RepSox as a factor that promotes differentiation of MYH11-positive cells by promoting NOTCH signaling. RepSox induces SMCs to exhibit a more contractile phenotype than SMCs generated using PDGF-BB and TGF-β1, two factors previously used for SMC differentiation but which also cause intimal hyperplasia. In addition, RepSox inhibited intimal hyperplasia caused by contractile to synthetic phenotypic switching of SMCs in a rat balloon injury model. Thus, in addition to providing more contractile SMCs that could prove useful for constructing artificial blood vessels, this study suggests a strategy for identifying drugs for inhibiting intimal hyperplasia that act by driving contractile differentiation rather than inhibiting proliferation non-specifically. Fully defined differentiation of contractile (95% MYH11+) smooth muscle cells (SMCs) RepSox-NOTCH signal promotes SMC differentiation and inhibits intimal hyperplasia RepSox-SMCs could reduce the risk of intimal hyperplasia compared with PDGF/TGF-SMCs Applying SMC differentiation for high-throughput screening of anti-restenosis drugs
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Affiliation(s)
- Jue Zhang
- Regenerative Biology, Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA.
| | - Brian E McIntosh
- Regenerative Biology, Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA
| | - Bowen Wang
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA; College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew E Brown
- Regenerative Biology, Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA; Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Mitchell D Probasco
- Regenerative Biology, Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA
| | - Sarah Webster
- Regenerative Biology, Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA
| | - Bret Duffin
- Regenerative Biology, Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA
| | - Ying Zhou
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Lian-Wang Guo
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA; College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | | | - Craig Kent
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA; College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Michael Ferris
- College of Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Computer Sciences, Industrial & Systems Engineering, Mathematics, Optimization, Wisconsin Institute for Discovery, Madison, WI 53715, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA; Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA 93117, USA.
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Joseph DB, Chandrashekar AS, Abler LL, Chu LF, Thomson JA, Vezina CM. Epithelial DNA methyltransferase-1 regulates cell survival, growth and maturation in developing prostatic buds. Dev Biol 2019; 447:157-169. [PMID: 30659795 DOI: 10.1016/j.ydbio.2019.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/17/2018] [Accepted: 01/14/2019] [Indexed: 02/07/2023]
Abstract
DNA methyltransferase 1 (DNMT1) is required for embryogenesis but roles in late forming organ systems including the prostate, which emerges from the urethral epithelium, have not been fully examined. We used a targeted genetic approach involving a Shhcre recombinase to demonstrate requirement of epithelial DNA methyltransferase-1 (Dnmt1) in mouse prostate morphogenesis. Dnmt1 mutant urethral cells exhibit DNA hypomethylation, DNA damage, p53 accumulation and undergo cell cycle arrest and apoptosis. Urethral epithelial cells are disorganized in Dnmt1 mutants, leading to impaired prostate growth and maturation and failed glandular development. We evaluated oriented cell division as a mechanism of bud elongation and widening by demonstrating that mitotic spindle axes typically form parallel or perpendicular to prostatic bud elongation axes. We then deployed a ShhcreERT allele to delete Dnmt1 from a subset of urethral epithelial cells, creating mosaic mutants with which to interrogate the requirement for cell division in specific prostatic bud epithelial populations. DNMT1- cell distribution within prostatic buds is not random as would be expected in a process where DNMT1 was not required. Instead, replication competent DNMT1 + cells primarily accumulate in prostatic bud margins and tips while replication impeded DNMT1- cells accumulate in prostatic bud cores. Together, these results highlight the role of DNMT1 in regulating epithelial bud formation by maintaining cell cycle progression and survival of rapidly dividing urethral epithelial cells, which can be extended to the study of other developing epithelial organs. In addition, our results show that prostatic buds consist of two epithelial cell populations with distinct molecular and functional characteristics that could potentially contribute to specialized lineages in the adult prostate.
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Affiliation(s)
- Diya B Joseph
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anoop S Chandrashekar
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lisa L Abler
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
| | - Chad M Vezina
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Joseph DB, Chandrashekar AS, Chu LF, Thomson JA, Vezina CM. A folic acid-enriched diet attenuates prostate involution in response to androgen deprivation. Prostate 2019; 79:183-194. [PMID: 30298636 PMCID: PMC6420320 DOI: 10.1002/pros.23723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/19/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Serum folate concentrations in the United States have risen since dietary folic acid fortification was first mandated in 1998. Although maternal folic acid offers protection against neural tube defects in conceptuses, its impact on other organ systems and life stages have not been fully examined. Here, we used a mouse model to investigate the impact of a Folic acid (FA) enriched diet on prostate homeostasis and response to androgen deprivation. METHODS Male mice were fed a control diet (4 mg FA/kg feed) or a folic acid supplemented diet (24 mg FA/kg feed) beginning at conception and continuing through early adulthood, when mice were castrated. RESULTS We made the surprising observation that dietary FA supplementation confers partial resistance to castration-mediated prostate involution. At 3, 10, and 14 days post-castration, FA enriched diet fed mice had larger prostates as assessed by wet weight, taller prostatic luminal epithelial cells, and more abundant RNAs encoding prostate secretory proteins than castrated control diet fed mice. Diet did not significantly affect prostate weights of intact mice or serum testosterone concentrations of castrated mice. RNA-Seq analysis revealed that the FA enriched diet was associated with a unique prostate gene expression signature, affecting several signaling and metabolic pathways. CONCLUSIONS Continuous exposure to a FA enriched diet slows prostate involution in response to androgen deprivation. Prostates from FA diet mice have increased secretory gene expression and increased luminal cell heights. The influence of dietary FA supplementation on the prostate response to androgen deprivation raises a future need to consider how dietary folic acid supplementation affects efficacy of androgen-reducing therapies for treating prostate disease.
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Affiliation(s)
- Diya B Joseph
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anoop S Chandrashekar
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
| | - Chad M Vezina
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
- Corresponding author Correspondence: Chad M Vezina, Room 201 Hanson Labs, 1656 Linden Drive, Madison, WI 53706, USA. Phone: 608-890-3235,
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Magli A, Baik J, Mills LJ, Kwak IY, Dillon BS, Mondragon Gonzalez R, Stafford DA, Swanson SA, Stewart R, Thomson JA, Garry DJ, Dynlacht BD, Perlingeiro RCR. Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm. PLoS Biol 2019; 17:e3000153. [PMID: 30807574 PMCID: PMC6390996 DOI: 10.1371/journal.pbio.3000153] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 02/01/2019] [Indexed: 12/26/2022] Open
Abstract
The transcriptional mechanisms driving lineage specification during development are still largely unknown, as the interplay of multiple transcription factors makes it difficult to dissect these molecular events. Using a cell-based differentiation platform to probe transcription function, we investigated the role of the key paraxial mesoderm and skeletal myogenic commitment factors-mesogenin 1 (Msgn1), T-box 6 (Tbx6), forkhead box C1 (Foxc1), paired box 3 (Pax3), Paraxis, mesenchyme homeobox 1 (Meox1), sine oculis-related homeobox 1 (Six1), and myogenic factor 5 (Myf5)-in paraxial mesoderm and skeletal myogenesis. From this study, we define a genetic hierarchy, with Pax3 emerging as the gatekeeper between the presomitic mesoderm and the myogenic lineage. By assaying chromatin accessibility, genomic binding and transcription profiling in mesodermal cells from mouse and human Pax3-induced embryonic stem cells and Pax3-null embryonic day (E)9.5 mouse embryos, we identified conserved Pax3 functions in the activation of the skeletal myogenic lineage through modulation of Hedgehog, Notch, and bone morphogenetic protein (BMP) signaling pathways. In addition, we demonstrate that Pax3 molecular function involves chromatin remodeling of its bound elements through an increase in chromatin accessibility and cooperation with sine oculis-related homeobox 4 (Six4) and TEA domain family member 2 (Tead2) factors. To our knowledge, these data provide the first integrated analysis of Pax3 function, demonstrating its ability to remodel chromatin in mesodermal cells from developing embryos and proving a mechanistic footing for the transcriptional hierarchy driving myogenesis.
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Affiliation(s)
- Alessandro Magli
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - June Baik
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lauren J. Mills
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Il-Youp Kwak
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Bridget S. Dillon
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ricardo Mondragon Gonzalez
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David A. Stafford
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Scott A. Swanson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - James A. Thomson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Daniel J. Garry
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian D. Dynlacht
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, New York, United States of America
| | - Rita C. R. Perlingeiro
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
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Mi H, Jing X, Li Z, Lin Y, Thomson JA, Turng L. Fabrication and modification of wavy multicomponent vascular grafts with biomimetic mechanical properties, antithrombogenicity, and enhanced endothelial cell affinity. J Biomed Mater Res B Appl Biomater 2019; 107:2397-2408. [DOI: 10.1002/jbm.b.34333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 12/31/2018] [Accepted: 01/05/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Hao‐Yang Mi
- Wisconsin Institute for DiscoveryUniversity of Wisconsin–Madison Madison Wisconsin 53715 USA
- Department of Mechanical EngineeringUniversity of Wisconsin–Madison Madison Wisconsin, 53706 USA
| | - Xin Jing
- Wisconsin Institute for DiscoveryUniversity of Wisconsin–Madison Madison Wisconsin 53715 USA
- Department of Mechanical EngineeringUniversity of Wisconsin–Madison Madison Wisconsin, 53706 USA
- School of Packaging and Materials EngineeringHunan University of Technology Zhuzhou, 412007 China
| | - Zhu‐Tong Li
- Wisconsin Institute for DiscoveryUniversity of Wisconsin–Madison Madison Wisconsin 53715 USA
- Department of Mechanical EngineeringUniversity of Wisconsin–Madison Madison Wisconsin, 53706 USA
| | - Yu‐Jyun Lin
- Wisconsin Institute for DiscoveryUniversity of Wisconsin–Madison Madison Wisconsin 53715 USA
| | - James A. Thomson
- Morgridge Institute for ResearchUniversity of Wisconsin–Madison Madison Wisconsin, 53715 USA
| | - Lih‐Sheng Turng
- Wisconsin Institute for DiscoveryUniversity of Wisconsin–Madison Madison Wisconsin 53715 USA
- Department of Mechanical EngineeringUniversity of Wisconsin–Madison Madison Wisconsin, 53706 USA
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Kaushik G, Gil DA, Torr E, Berge ES, Soref C, Uhl P, Fontana G, Antosiewicz-Bourget J, Edington C, Schwartz MP, Griffith LG, Thomson JA, Skala MC, Daly WT, Murphy WL. Vascular Networks: Quantitative Label-Free Imaging of 3D Vascular Networks Self-Assembled in Synthetic Hydrogels (Adv. Healthcare Mater. 2/2019). Adv Healthc Mater 2019. [DOI: 10.1002/adhm.201970004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gaurav Kaushik
- Department of Orthopedics and Rehabilitation; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
| | - Daniel A. Gil
- Morgridge Institute for Research; 330 North Orchard Street Madison WI 53715 USA
- Department of Biomedical Engineering; University of Wisconsin-Madison; 1415 Engineering Drive Madison WI 53706 USA
| | - Elizabeth Torr
- Department of Orthopedics and Rehabilitation; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
| | - Elizabeth S. Berge
- Morgridge Institute for Research; 330 North Orchard Street Madison WI 53715 USA
- Department of Biomedical Engineering; University of Wisconsin-Madison; 1415 Engineering Drive Madison WI 53706 USA
| | - Cheryl Soref
- Department of Orthopedics and Rehabilitation; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
| | - Peyton Uhl
- Department of Orthopedics and Rehabilitation; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
| | - Gianluca Fontana
- Department of Orthopedics and Rehabilitation; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
| | - Jessica Antosiewicz-Bourget
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Morgridge Institute for Research; 330 North Orchard Street Madison WI 53715 USA
| | - Collin Edington
- Department of Biological Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Michael P. Schwartz
- Department of Biomedical Engineering; University of Wisconsin-Madison; 1415 Engineering Drive Madison WI 53706 USA
| | - Linda G. Griffith
- Department of Biological Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - James A. Thomson
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Morgridge Institute for Research; 330 North Orchard Street Madison WI 53715 USA
| | - Melissa C. Skala
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Morgridge Institute for Research; 330 North Orchard Street Madison WI 53715 USA
- Department of Biological Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - William T. Daly
- Department of Orthopedics and Rehabilitation; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
| | - William L. Murphy
- Department of Orthopedics and Rehabilitation; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Human Models for Analysis of Pathways (HMAPs) Center; University of Wisconsin-Madison; 1111 Highland Avenue, WIMR 5418 Madison WI 53705 USA
- Department of Biomedical Engineering; University of Wisconsin-Madison; 1415 Engineering Drive Madison WI 53706 USA
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Kaushik G, Gil DA, Torr E, Berge ES, Soref C, Uhl P, Fontana G, Antosiewicz-Bourget J, Edington C, Schwartz MP, Griffith LG, Thomson JA, Skala MC, Daly WT, Murphy WL. Quantitative Label-Free Imaging of 3D Vascular Networks Self-Assembled in Synthetic Hydrogels. Adv Healthc Mater 2019; 8:e1801186. [PMID: 30565891 DOI: 10.1002/adhm.201801186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/22/2018] [Indexed: 12/17/2022]
Abstract
Vascularization is an important strategy to overcome diffusion limits and enable the formation of complex, physiologically relevant engineered tissues and organoids. Self-assembly is a technique to generate in vitro vascular networks, but engineering the necessary network morphology and function remains challenging. Here, autofluorescence multiphoton microscopy (aMPM), a label-free imaging technique, is used to quantitatively evaluate in vitro vascular network morphology. Vascular networks are generated using human embryonic stem cell-derived endothelial cells and primary human pericytes encapsulated in synthetic poly(ethylene glycol)-based hydrogels. Two custom-built bioreactors are used to generate distinct fluid flow patterns during vascular network formation: recirculating flow or continuous flow. aMPM is used to image these 3D vascular networks without the need for fixation, labels, or dyes. Image processing and analysis algorithms are developed to extract quantitative morphological parameters from these label-free images. It is observed with aMPM that both bioreactors promote formation of vascular networks with lower network anisotropy compared to static conditions, and the continuous flow bioreactor induces more branch points compared to static conditions. Importantly, these results agree with trends observed with immunocytochemistry. These studies demonstrate that aMPM allows label-free monitoring of vascular network morphology to streamline optimization of growth conditions and provide quality control of engineered tissues.
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Affiliation(s)
- Gaurav Kaushik
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
| | - Daniel A Gil
- Morgridge Institute for Research, 330 North Orchard Street, Madison, WI, 53715, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Elizabeth Torr
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
| | - Elizabeth S Berge
- Morgridge Institute for Research, 330 North Orchard Street, Madison, WI, 53715, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Cheryl Soref
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
| | - Peyton Uhl
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
| | - Gianluca Fontana
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
| | - Jessica Antosiewicz-Bourget
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Morgridge Institute for Research, 330 North Orchard Street, Madison, WI, 53715, USA
| | - Collin Edington
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Michael P Schwartz
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - James A Thomson
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Morgridge Institute for Research, 330 North Orchard Street, Madison, WI, 53715, USA
| | - Melissa C Skala
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Morgridge Institute for Research, 330 North Orchard Street, Madison, WI, 53715, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - William T Daly
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
| | - William L Murphy
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Human Models for Analysis of Pathways (HMAPs) Center, University of Wisconsin-Madison, 1111 Highland Avenue, WIMR 5418, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
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Bacher R, Leng N, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart R. Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments. BMC Bioinformatics 2018; 19:380. [PMID: 30326833 PMCID: PMC6192113 DOI: 10.1186/s12859-018-2405-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/01/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND High-throughput expression profiling experiments with ordered conditions (e.g. time-course or spatial-course) are becoming more common for studying detailed differentiation processes or spatial patterns. Identifying dynamic changes at both the individual gene and whole transcriptome level can provide important insights about genes, pathways, and critical time points. RESULTS We present an R package, Trendy, which utilizes segmented regression models to simultaneously characterize each gene's expression pattern and summarize overall dynamic activity in ordered condition experiments. For each gene, Trendy finds the optimal segmented regression model and provides the location and direction of dynamic changes in expression. We demonstrate the utility of Trendy to provide biologically relevant results on both microarray and RNA-sequencing (RNA-seq) datasets. CONCLUSIONS Trendy is a flexible R package which characterizes gene-specific expression patterns and summarizes changes of global dynamics over ordered conditions. Trendy is freely available on Bioconductor with a full vignette at https://bioconductor.org/packages/release/bioc/html/Trendy.html .
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Affiliation(s)
- Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.
| | - Ning Leng
- Morgridge Institute for Research, Madison, WI, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI, USA
| | - Zijian Ni
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, USA.
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Kang H, Mesquitta WT, Jung HS, Moskvin OV, Thomson JA, Slukvin II. GATA2 Is Dispensable for Specification of Hemogenic Endothelium but Promotes Endothelial-to-Hematopoietic Transition. Stem Cell Reports 2018; 11:197-211. [PMID: 29861167 PMCID: PMC6066910 DOI: 10.1016/j.stemcr.2018.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 01/05/2023] Open
Abstract
The transcriptional factor GATA2 is required for blood and hematopoietic stem cell formation during the hemogenic endothelium (HE) stage of development in the embryo. However, it is unclear if GATA2 controls HE lineage specification or if it solely regulates endothelial-to-hematopoietic transition (EHT). To address this problem, we innovated a unique system, which involved generating GATA2 knockout human embryonic stem cell (hESC) lines with conditional GATA2 expression (iG2-/- hESCs). We demonstrated that GATA2 activity is not required for VE-cadherin+CD43-CD73+ non-HE or VE-cadherin+CD43-CD73- HE generation and subsequent HE diversification into DLL4+ arterial and DLL4- non-arterial lineages. However, GATA2 is primarily needed for HE to undergo EHT. Forced expression of GATA2 in non-HE failed to induce blood formation. The lack of GATA2 requirement for generation of HE and non-HE indicates the critical role of GATA2-independent pathways in specification of these two distinct endothelial lineages.
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Affiliation(s)
- HyunJun Kang
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Walatta-Tseyon Mesquitta
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Ho Sun Jung
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - Oleg V Moskvin
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA.
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Uenishi GI, Jung HS, Kumar A, Park MA, Hadland BK, McLeod E, Raymond M, Moskvin O, Zimmerman CE, Theisen DJ, Swanson S, J Tamplin O, Zon LI, Thomson JA, Bernstein ID, Slukvin II. NOTCH signaling specifies arterial-type definitive hemogenic endothelium from human pluripotent stem cells. Nat Commun 2018; 9:1828. [PMID: 29739946 PMCID: PMC5940870 DOI: 10.1038/s41467-018-04134-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/06/2018] [Indexed: 02/06/2023] Open
Abstract
NOTCH signaling is required for the arterial specification and formation of hematopoietic stem cells (HSCs) and lympho-myeloid progenitors in the embryonic aorta-gonad-mesonephros region and extraembryonic vasculature from a distinct lineage of vascular endothelial cells with hemogenic potential. However, the role of NOTCH signaling in hemogenic endothelium (HE) specification from human pluripotent stem cell (hPSC) has not been studied. Here, using a chemically defined hPSC differentiation system combined with the use of DLL1-Fc and DAPT to manipulate NOTCH, we discover that NOTCH activation in hPSC-derived immature HE progenitors leads to formation of CD144+CD43−CD73−DLL4+Runx1 + 23-GFP+ arterial-type HE, which requires NOTCH signaling to undergo endothelial-to-hematopoietic transition and produce definitive lympho-myeloid and erythroid cells. These findings demonstrate that NOTCH-mediated arterialization of HE is an essential prerequisite for establishing definitive lympho-myeloid program and suggest that exploring molecular pathways that lead to arterial specification may aid in vitro approaches to enhance definitive hematopoiesis from hPSCs. It is unclear whether arterial specification is required for hematopoietic stem cell formation. Here, the authors use a chemically defined human pluripotent stem cell (hPSC) differentiation system to show the role of NOTCH signaling in forming arterial-type hemogenic endothelial cells.
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Affiliation(s)
- Gene I Uenishi
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA.,Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA
| | - Ho Sun Jung
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA
| | - Akhilesh Kumar
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA
| | - Mi Ae Park
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA
| | - Brandon K Hadland
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Ethan McLeod
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA
| | - Matthew Raymond
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA.,Department of Biomedical Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Oleg Moskvin
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA
| | - Catherine E Zimmerman
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA
| | - Derek J Theisen
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Owen J Tamplin
- Department of Pharmacology, University of Illinois, Chicago, IL, 60612, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI, 53715, USA.,Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53707, USA.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Irwin D Bernstein
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53715, USA. .,Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA. .,Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53707, USA.
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Magli A, Incitti T, Kiley J, Swanson SA, Darabi R, Rinaldi F, Selvaraj S, Yamamoto A, Tolar J, Yuan C, Stewart R, Thomson JA, Perlingeiro RCR. PAX7 Targets, CD54, Integrin α9β1, and SDC2, Allow Isolation of Human ESC/iPSC-Derived Myogenic Progenitors. Cell Rep 2018; 19:2867-2877. [PMID: 28658631 DOI: 10.1016/j.celrep.2017.06.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/02/2017] [Accepted: 05/29/2017] [Indexed: 10/19/2022] Open
Abstract
Pluripotent stem (PS)-cell-derived cell types hold promise for treating degenerative diseases. However, PS cell differentiation is intrinsically heterogeneous; therefore, clinical translation requires the development of practical methods for isolating progenitors from unwanted and potentially teratogenic cells. Muscle-regenerating progenitors can be derived through transient PAX7 expression. To better understand the biology, and to discover potential markers for these cells, here we investigate PAX7 genomic targets and transcriptional changes in human cells undergoing PAX7-mediated myogenic commitment. We identify CD54, integrin α9β1, and Syndecan2 (SDC2) as surface markers on PAX7-induced myogenic progenitors. We show that these markers allow for the isolation of myogenic progenitors using both fluorescent- and CGMP-compatible magnetic-based sorting technologies and that CD54+α9β1+SDC2+ cells contribute to long-term muscle regeneration in vivo. These findings represent a critical step toward enabling the translation of PS-cell-based therapies for muscle diseases.
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Affiliation(s)
- Alessandro Magli
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tania Incitti
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - James Kiley
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine, Department of Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fabrizio Rinaldi
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sridhar Selvaraj
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ami Yamamoto
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA; Minnesota Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ce Yuan
- Minnesota Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | | | - Rita C R Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
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Vermillion KL, Bacher R, Tannenbaum AP, Swanson S, Jiang P, Chu LF, Stewart R, Thomson JA, Vereide DT. Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Dev Biol 2018; 439:30-41. [PMID: 29678445 DOI: 10.1016/j.ydbio.2018.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 01/07/2023]
Abstract
During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos. The single-cell transcriptomes were then ordered by the statistical method Wave-Crest to deduce both the relative position along the AP axis and the prospective lineage of single cells. The ordered transcriptomes reveal intricate patterns of gene expression along the primitive streak.
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Affiliation(s)
| | - Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA
| | | | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell&Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Molecular, Cellular,&Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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Yu E, Mi HY, Zhang J, Thomson JA, Turng LS. Development of biomimetic thermoplastic polyurethane/fibroin small-diameter vascular grafts via a novel electrospinning approach. J Biomed Mater Res A 2018; 106:985-996. [PMID: 29143442 PMCID: PMC5826852 DOI: 10.1002/jbm.a.36297] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/28/2017] [Accepted: 11/10/2017] [Indexed: 12/18/2022]
Abstract
A new electrospinning approach for fabricating vascular grafts with a layered, circumferentially aligned, and micro-wavy fibrous structure similar to natural elastic tissues has been developed. The customized electrospinning collector was able to generate wavy fibers using the dynamic "jump rope" collecting process, which also solved the sample removal problem for mandrel-type collectors. In this study, natural silk fibroin and synthetic thermoplastic polyurethane (TPU) were combined at different weight ratios to produce hybrid small-diameter vascular grafts. The purpose of combining these two materials was to leverage the bioactivity and tunable mechanical properties of these natural and synthetic materials. Results showed that the electrospun fiber morphology was highly influenced by the material compositions and solvents employed. All of the TPU/fibroin hybrid grafts had mechanical properties comparable to natural blood vessels. The circumferentially aligned and wavy biomimetic configuration provided the grafts with a sufficient toe region and the capacity for long-term usage under repeated dilatation and contraction. Cell culture tests with human endothelial cells (EC) also revealed high cell viability and good biocompatibility for these grafts. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 985-996, 2018.
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Affiliation(s)
- Emily Yu
- Department of Mechanical Engineering, University of Wisconsin–Madison, WI, USA, 53706
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, WI, USA, 53715
| | - Hao-Yang Mi
- Department of Mechanical Engineering, University of Wisconsin–Madison, WI, USA, 53706
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, WI, USA, 53715
- Department of Industrial Equipment and Control Engineering, South China University of Technology, Guangzhou, China
| | - Jue Zhang
- Morgridge Institute for Research, WI, USA, 53715
| | | | - Lih-Sheng Turng
- Department of Mechanical Engineering, University of Wisconsin–Madison, WI, USA, 53706
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, WI, USA, 53715
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Brown ME, Zhou Y, McIntosh BE, Norman IG, Lou HE, Biermann M, Sullivan JA, Kamp TJ, Thomson JA, Anagnostopoulos PV, Burlingham WJ. A Humanized Mouse Model Generated Using Surplus Neonatal Tissue. Stem Cell Reports 2018; 10:1175-1183. [PMID: 29576539 PMCID: PMC5998340 DOI: 10.1016/j.stemcr.2018.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 02/20/2018] [Accepted: 02/23/2018] [Indexed: 12/30/2022] Open
Abstract
Here, we describe the NeoThy humanized mouse model created using non-fetal human tissue sources, cryopreserved neonatal thymus and umbilical cord blood hematopoietic stem cells (HSCs). Conventional humanized mouse models are made by engrafting human fetal thymus and HSCs into immunocompromised mice. These mice harbor functional human T cells that have matured in the presence of human self-peptides and human leukocyte antigen molecules. Neonatal thymus tissue is more abundant and developmentally mature and allows for creation of up to ∼50-fold more mice per donor compared with fetal tissue models. The NeoThy has equivalent frequencies of engrafted human immune cells compared with fetal tissue humanized mice and exhibits T cell function in assays of ex vivo cell proliferation, interferon γ secretion, and in vivo graft infiltration. The NeoThy model may provide significant advantages for induced pluripotent stem cell immunogenicity studies, while bypassing the requirement for fetal tissue. Neonatal tissue is a viable alternative to fetal for mouse humanization Over 1,000 NeoThy mice can be made from one neonatal thymus donor The NeoThy enables robust pre-clinical immunogenicity studies of iPSC therapies
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Affiliation(s)
- Matthew E Brown
- Division of Transplantation/Department of Surgery, University of Wisconsin, Madison, WI 53792, USA; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ying Zhou
- Division of Transplantation/Department of Surgery, University of Wisconsin, Madison, WI 53792, USA
| | | | - Ian G Norman
- Division of Transplantation/Department of Surgery, University of Wisconsin, Madison, WI 53792, USA
| | - Hannah E Lou
- Division of Transplantation/Department of Surgery, University of Wisconsin, Madison, WI 53792, USA
| | - Mitch Biermann
- Department of Medicine, University of Wisconsin, Madison, WI 53792, USA
| | - Jeremy A Sullivan
- Division of Transplantation/Department of Surgery, University of Wisconsin, Madison, WI 53792, USA
| | - Timothy J Kamp
- Department of Medicine, University of Wisconsin, Madison, WI 53792, USA; Department of Cell & Regenerative Biology, University of Wisconsin, Madison, WI 53792, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell & Regenerative Biology, University of Wisconsin, Madison, WI 53792, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Petros V Anagnostopoulos
- Division of Cardiothoracic Surgery/Department of Surgery, University of Wisconsin, Madison, WI 53792, USA
| | - William J Burlingham
- Division of Transplantation/Department of Surgery, University of Wisconsin, Madison, WI 53792, USA.
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Kumar A, D'Souza SS, Moskvin OV, Toh H, Wang B, Zhang J, Swanson S, Guo LW, Thomson JA, Slukvin II. Specification and Diversification of Pericytes and Smooth Muscle Cells from Mesenchymoangioblasts. Cell Rep 2018; 19:1902-1916. [PMID: 28564607 PMCID: PMC6428685 DOI: 10.1016/j.celrep.2017.05.019] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/25/2017] [Accepted: 05/04/2017] [Indexed: 02/06/2023] Open
Abstract
Elucidating the pathways that lead to vasculogenic cells, and being able to identify their progenitors and lineage-restricted cells, is critical to the establishment of human pluripotent stem cell (hPSC) models for vascular diseases and development of vascular therapies. Here, we find that mesoderm-derived pericytes (PCs) and smooth muscle cells (SMCs) originate from a clonal mesenchymal progenitor mesenchymoangioblast (MB). In clonogenic cultures, MBs differentiate into primitive PDGFRβ+ CD271+CD73− mesenchymal progenitors, which give rise to proliferative PCs, SMCs, and mesenchymal stem/stromal cells. MB-derived PCs can be further specified to CD274+ capillary and DLK1+ arteriolar PCs with a proinflammatory and contractile phenotype, respectively. SMC maturation was induced using a MEK inhibitor. Establishing the vasculogenic lineage tree, along with identification of stage- and lineage-specific markers, provides a platform for interrogating the molecular mechanisms that regulate vasculogenic cell specification and diversification and manufacturing well-defined mural cell populations for vascular engineering and cellular therapies from hPSCs. Kumar et al. find that mesodermal pericytes and smooth muscle cells in human pluripotent stem cell cultures originate from a common endothelial and mesenchymal cell precursor, the mesenchymoangioblast. They show how different lineages of mural cells are specified from mesenchymoangioblasts and define stage- and lineage-specific markers for vasculogenic cells.
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Affiliation(s)
- Akhilesh Kumar
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Saritha Sandra D'Souza
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Oleg V Moskvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703, USA
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Bowen Wang
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Jue Zhang
- Morgridge Institute for Research, Madison, WI 53707, USA
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53707, USA
| | - Lian-Wang Guo
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53707, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53707, USA; Department of Molecular, Cellular & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53707, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53792, USA.
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Phillips MJ, Jiang P, Howden S, Barney P, Min J, York NW, Chu LF, Capowski EE, Cash A, Jain S, Barlow K, Tabassum T, Stewart R, Pattnaik BR, Thomson JA, Gamm DM. A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types. Stem Cells 2017; 36:313-324. [PMID: 29230913 DOI: 10.1002/stem.2755] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/31/2017] [Accepted: 11/29/2017] [Indexed: 11/07/2022]
Abstract
Cell type-specific investigations commonly use gene reporters or single-cell analytical techniques. However, reporter line development is arduous and generally limited to a single gene of interest, while single-cell RNA (scRNA)-sequencing (seq) frequently yields equivocal results that preclude definitive cell identification. To examine gene expression profiles of multiple retinal cell types derived from human pluripotent stem cells (hPSCs), we performed scRNA-seq on optic vesicle (OV)-like structures cultured under cGMP-compatible conditions. However, efforts to apply traditional scRNA-seq analytical methods based on unbiased algorithms were unrevealing. Therefore, we developed a simple, versatile, and universally applicable approach that generates gene expression data akin to those obtained from reporter lines. This method ranks single cells by expression level of a bait gene and searches the transcriptome for genes whose cell-to-cell rank order expression most closely matches that of the bait. Moreover, multiple bait genes can be combined to refine datasets. Using this approach, we provide further evidence for the authenticity of hPSC-derived retinal cell types. Stem Cells 2018;36:313-324.
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Affiliation(s)
| | - Peng Jiang
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Sara Howden
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | | | | | | | - Li-Fang Chu
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | | | | | | | | | | | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Bikash R Pattnaik
- McPherson Eye Research Institute
- Department of Pediatrics
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - David M Gamm
- Waisman Center
- McPherson Eye Research Institute
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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45
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Barry C, Schmitz MT, Propson NE, Hou Z, Zhang J, Nguyen BK, Bolin JM, Jiang P, McIntosh BE, Probasco MD, Swanson S, Stewart R, Thomson JA, Schwartz MP, Murphy WL. Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques. Exp Biol Med (Maywood) 2017; 242:1679-1689. [PMID: 28599598 PMCID: PMC5786368 DOI: 10.1177/1535370217715028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The aim of the present study was to test sample reproducibility for model neural tissues formed on synthetic hydrogels. Human embryonic stem (ES) cell-derived precursor cells were cultured on synthetic poly(ethylene glycol) (PEG) hydrogels to promote differentiation and self-organization into model neural tissue constructs. Neural progenitor, vascular, and microglial precursor cells were combined on PEG hydrogels to mimic developmental timing, which produced multicomponent neural constructs with 3D neuronal and glial organization, organized vascular networks, and microglia with ramified morphologies. Spearman's rank correlation analysis of global gene expression profiles and a comparison of coefficient of variation for expressed genes demonstrated that replicate neural constructs were highly uniform to at least day 21 for samples from independent experiments. We also demonstrate that model neural tissues formed on PEG hydrogels using a simplified neural differentiation protocol correlated more strongly to in vivo brain development than samples cultured on tissue culture polystyrene surfaces alone. These results provide a proof-of-concept demonstration that 3D cellular models that mimic aspects of human brain development can be produced from human pluripotent stem cells with high sample uniformity between experiments by using standard culture techniques, cryopreserved cell stocks, and a synthetic extracellular matrix. Impact statement Pluripotent stem (PS) cells have been characterized by an inherent ability to self-organize into 3D "organoids" resembling stomach, intestine, liver, kidney, and brain tissues, offering a potentially powerful tool for modeling human development and disease. However, organoid formation must be quantitatively reproducible for applications such as drug and toxicity screening. Here, we report a strategy to produce uniform neural tissue constructs with reproducible global gene expression profiles for replicate samples from multiple experiments.
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Affiliation(s)
| | | | | | - Zhonggang Hou
- Morgridge Institute for Research, Madison, WI 53705, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA (current address)
| | - Jue Zhang
- Morgridge Institute for Research, Madison, WI 53705, USA
| | - Bao K Nguyen
- Morgridge Institute for Research, Madison, WI 53705, USA
| | | | - Peng Jiang
- Morgridge Institute for Research, Madison, WI 53705, USA
| | | | | | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53705, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53705, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53705, USA
- Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Michael P Schwartz
- Center for Sustainable Nanotechnology, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William L Murphy
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705, USA
- Materials Science Program, University of Wisconsin-Madison, WI 53705, USA
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI 53705, USA
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46
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Jiang P, Hou Z, Bolin JM, Thomson JA, Stewart R. RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations. Toxicol Sci 2017; 159:251-265. [PMID: 28903495 PMCID: PMC6372217 DOI: 10.1093/toxsci/kfx129] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lead (Pb) is a well-known toxicant, especially for the developing nervous system, albeit the mechanism is largely unknown. In this study, we use time series RNA-seq to conduct a genome-wide survey of the transcriptome response of human embryonic stem cell-derived neural progenitor cells to lead treatment. Using a dynamic time warping algorithm coupled with statistical tests, we find that lead can either accelerate or decelerate the expression of specific genes during the time series. We further show that lead disrupts a neuron- and brain-specific splicing factor NOVA1 regulated splicing network. Using lead induced transcriptome change signatures, we predict several known and novel disease risks under lead exposure. The findings in this study will allow a better understanding of the mechanism of lead toxicity, facilitate the development of diagnostic biomarkers and treatment for lead exposure, and comprise a highly valuable resource for environmental toxicology. Our study also demonstrates that a human (embryonic stem) cell-derived system can be used for studying the mechanism of toxicants, which can be useful for drug or compound toxicity screens and safety assessment.
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Affiliation(s)
- Peng Jiang
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
| | - Zhonggang Hou
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
| | - Jennifer M. Bolin
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
| | - James A. Thomson
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin 53706
- Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106
| | - Ron Stewart
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
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Vermilyea SC, Guthrie S, Meyer M, Smuga-Otto K, Braun K, Howden S, Thomson JA, Zhang SC, Emborg ME, Golos TG. Induced Pluripotent Stem Cell-Derived Dopaminergic Neurons from Adult Common Marmoset Fibroblasts. Stem Cells Dev 2017. [PMID: 28635509 DOI: 10.1089/scd.2017.0069] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The common marmoset monkey (Callithrix jacchus; Cj) is an advantageous nonhuman primate species for modeling age-related disorders, including Parkinson's disease, due to their shorter life span compared to macaques. Cj-derived induced pluripotent stem cells (Cj-iPSCs) from somatic cells are needed for in vitro disease modeling and testing regenerative medicine approaches. Here we report the development of a novel Cj-iPSC line derived from adult marmoset fibroblasts. The Cj-iPSCs showed potent pluripotency properties, including the development of mesodermal lineages in tumors after injection to immunocompromised mice, as well as ectoderm and endoderm lineages after in vitro differentiation regimens, demonstrating differentiated derivatives of all three embryonic layers. In addition, expression of key pluripotency genes (ZFP42, PODXL, DNMT3B, C-MYC, LIN28, KLF4, NANOG, SOX2, and OCT4) was observed. We then tested the neural differentiation capacity and gene expression profiles of Cj-iPSCs and a marmoset embryonic stem cell line (Cj-ESC) after dual-SMAD inhibition. Exposure to CHIR99021 and sonic hedgehog (SHH) for 12 and 16 days, respectively, patterned the cells toward a ventralized midbrain dopaminergic phenotype, confirmed by expression of FOXA2, OTX2, EN-1, and tyrosine hydroxylase. These results demonstrate that common marmoset stem cells will be able to serve as a platform for investigating regenerative medicine approaches targeting the dopaminergic system.
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Affiliation(s)
- Scott C Vermilyea
- 1 Neuroscience Training Program, University of Wisconsin-Madison , Madison, Wisconsin.,2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin
| | - Scott Guthrie
- 2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin
| | - Michael Meyer
- 2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin
| | - Kim Smuga-Otto
- 2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin.,3 Morgridge Institute for Research, University of Wisconsin-Madison , Madison, Wisconsin
| | - Katarina Braun
- 2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin
| | - Sara Howden
- 3 Morgridge Institute for Research, University of Wisconsin-Madison , Madison, Wisconsin
| | - James A Thomson
- 2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin.,3 Morgridge Institute for Research, University of Wisconsin-Madison , Madison, Wisconsin.,4 Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin
| | - Su-Chun Zhang
- 5 Department of Neuroscience, University of Wisconsin-Madison , Madison, Wisconsin
| | - Marina E Emborg
- 1 Neuroscience Training Program, University of Wisconsin-Madison , Madison, Wisconsin.,2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin.,6 Department of Medical Physics, University of Wisconsin-Madison , Madison, Wisconsin
| | - Thaddeus G Golos
- 2 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin.,7 Department of Comparative Biosciences and Obstetrics and Gynecology, University of Wisconsin-Madison , Madison, Wisconsin
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48
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Zhang J, Schwartz MP, Hou Z, Bai Y, Ardalani H, Swanson S, Steill J, Ruotti V, Elwell A, Nguyen BK, Bolin J, Stewart R, Thomson JA, Murphy WL. A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture. Stem Cell Reports 2017; 8:907-918. [PMID: 28343999 PMCID: PMC5390115 DOI: 10.1016/j.stemcr.2017.02.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 02/07/2023] Open
Abstract
A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type. Endothelial cells cultured on tissue-culture polystyrene adopted a proliferative phenotype compared with cells cultured on or encapsulated in PEG hydrogels. The proliferative phenotype correlated to increased FAK-ERK activity, and knockdown or inhibition of ERK signaling reduced proliferation and expression for cell-cycle genes while increasing expression for “3D-like” vasculature development genes. Our results provide insight into the influence of 2D and 3D culture formats on global biological processes that regulate cell function. Defined, high-efficiency differentiation of human PSCs to endothelial cell Comprehensive genome-wide comparisons of 2D and 3D cell-culture formats Gene expression profiles for endothelial cells and pericytes in 3D cell culture Highly proliferative phenotypes on tissue-culture polystyrene surfaces
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Affiliation(s)
- Jue Zhang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Michael P Schwartz
- Department of Biomedical Engineering, University of Wisconsin-Madison, Wisconsin Institute for Medical Research, Room 5405, Madison, WI 53706, USA.
| | - Zhonggang Hou
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Yongsheng Bai
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Hamisha Ardalani
- Department of Biomedical Engineering, University of Wisconsin-Madison, Wisconsin Institute for Medical Research, Room 5405, Madison, WI 53706, USA
| | - Scott Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - John Steill
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Victor Ruotti
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Angela Elwell
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Bao Kim Nguyen
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jennifer Bolin
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA 93117, USA
| | - William L Murphy
- Department of Biomedical Engineering, University of Wisconsin-Madison, Wisconsin Institute for Medical Research, Room 5405, Madison, WI 53706, USA; Materials Science Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI 53705, USA.
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49
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Barry C, Schmitz MT, Jiang P, Schwartz MP, Duffin BM, Swanson S, Bacher R, Bolin JM, Elwell AL, McIntosh BE, Stewart R, Thomson JA. Species-specific developmental timing is maintained by pluripotent stem cells ex utero. Dev Biol 2017; 423:101-110. [PMID: 28179190 DOI: 10.1016/j.ydbio.2017.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/27/2017] [Accepted: 02/04/2017] [Indexed: 12/24/2022]
Abstract
How species-specific developmental timing is controlled is largely unknown. By following human embryonic stem (ES) cell and mouse epiblast stem (EpiS) cell differentiation through detailed RNA-sequencing time courses, here we show that pluripotent stem cells closely retain in vivo species-specific developmental timing in vitro. In identical neural differentiation conditions in vitro, gene expression profiles are accelerated in mouse EpiS cells compared to human ES cells with relative rates of differentiation closely reflecting the rates of progression through the Carnegie stages in utero. Dynamic Time Warping analysis identified 3389 genes that were regulated more quickly in mouse EpiS cells and identified none that were regulated more quickly in human ES cells. Interestingly, we also find that human ES cells differentiated in teratomas maintain the same rate of differentiation observed in vitro in spite of being grown in a mouse host. These results suggest the existence of a cell autonomous, species-specific developmental clock that pluripotent stem cells maintain even out of context of an intact embryo.
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Affiliation(s)
| | | | - Peng Jiang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Michael P Schwartz
- Center for Sustainable Nanotechnology, Department of Chemistry, University of Wisconsin-Madison, WI 53706, USA
| | - Bret M Duffin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Rhonda Bacher
- Department of Statistics, University of Wisconsin-Madison, WI 53706, USA
| | | | | | | | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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Yu E, Zhang J, Thomson JA, Turng LS. Fabrication and Characterization of Electrospun Thermoplastic Polyurethane/Fibroin Small-Diameter Vascular Grafts for Vascular Tissue Engineering. ACTA ACUST UNITED AC 2016; 31:638-646. [PMID: 29033499 DOI: 10.3139/217.3247] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The demand for small-diameter blood vessel substitutes has been increasing due to a shortage of autograft vessels and problems with thrombosis and intimal hyperplasia with synthetic grafts. In this study, hybrid small-diameter vascular grafts made of thermoplastic polyurethane (TPU) and silk fibroin, which possessed a hybrid fibrous structure of an aligned inner layer and a random outer layer, were fabricated by the electrospinning technique using a customized striated collector that generated both aligned and random fibers simultaneously. A methanol post-treatment process induced the transition of fibroin protein conformation from the water-soluble, amorphous, and less ordered structures to the water-insoluble β-sheet structures that possessed robust mechanical properties and relatively slow proteolytic degradation. The methanol post-treatment also created crimped fibers that mimicked the wavy structure of collagen fibers in natural blood vessels. Ultrafine nanofibers and nanowebs were found on the electrospun TPU/fibroin samples, which effectively increased the surface area for cell adhesion and migration. Cyclic circumferential tensile test results showed compatible mechanical properties for grafts made of a soft TPU/fibroin blend compared to human coronary arteries. In addition, cell culture tests with endothelial cells after 6 and 60 days of culture exhibited high cell viability and good biocompatibility of TPU/fibroin grafts, suggesting the potential of applying electrospun TPU/fibroin grafts in vascular tissue engineering.
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Affiliation(s)
- E Yu
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, USA.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - J Zhang
- Morgridge Institute for Research, Madison, WI, USA
| | - J A Thomson
- Morgridge Institute for Research, Madison, WI, USA
| | - L-S Turng
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, USA.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
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