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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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Teske KA, Corona C, Wilkinson J, Mamott D, Good DA, Zambrano D, Lazar DF, Cali JJ, Robers MB, O'Brien MA. Interrogating direct NLRP3 engagement and functional inflammasome inhibition using cellular assays. Cell Chem Biol 2024; 31:349-360.e6. [PMID: 37858335 DOI: 10.1016/j.chembiol.2023.09.016] [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: 03/17/2023] [Revised: 07/20/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
As a key regulator of the innate immune system, the NLRP3 inflammasome responds to a variety of environmental insults through activation of caspase-1 and release of the proinflammatory cytokines IL-1β and IL-18. Aberrant NLRP3 inflammasome function is implicated in numerous inflammatory diseases, spurring drug discovery efforts at NLRP3 as a therapeutic target. A diverse array of small molecules is undergoing preclinical/clinical evaluation with a reported mode of action involving direct modulation of the NLRP3 pathway. However, for a subset of these ligands the functional link between live-cell target engagement and pathway inhibition has yet to be fully established. Herein we present a cohort of mechanistic assays to both query direct NLRP3 engagement in cells, and functionally interrogate different nodes of NLRP3 pathway activity. This system enabled the stratification of potency for five confirmed NLRP3 inhibitors, and identification of two reported NLRP3 inhibitors that failed to demonstrate direct pathway antagonism.
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Affiliation(s)
- Kelly A Teske
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - Cesear Corona
- Promega Corporation, Research & Development, San Luis Obispo, CA 93401, USA
| | | | - Daniel Mamott
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - David A Good
- Promega Corporation, Research & Development, San Luis Obispo, CA 93401, USA
| | - Delia Zambrano
- Promega Corporation, Research & Development, San Luis Obispo, CA 93401, USA
| | - Dan F Lazar
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - James J Cali
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - Matthew B Robers
- Promega Corporation, Research & Development, Madison, WI 53711, USA.
| | - Martha A O'Brien
- Promega Corporation, Research & Development, Madison, WI 53711, USA.
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3
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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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4
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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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5
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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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6
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Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA. Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Genome Biol 2016; 17:173. [PMID: 27534536 PMCID: PMC4989499 DOI: 10.1186/s13059-016-1033-x] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [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: 04/09/2016] [Accepted: 07/27/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human pluripotent stem cells offer the best available model to study the underlying cellular and molecular mechanisms of human embryonic lineage specification. However, it is not fully understood how individual stem cells exit the pluripotent state and transition towards their respective progenitor states. RESULTS Here, we analyze the transcriptomes of human embryonic stem cell-derived lineage-specific progenitors by single-cell RNA-sequencing (scRNA-seq). We identify a definitive endoderm (DE) transcriptomic signature that leads us to pinpoint a critical time window when DE differentiation is enhanced by hypoxia. The molecular mechanisms governing the emergence of DE are further examined by time course scRNA-seq experiments, employing two new statistical tools to identify stage-specific genes over time (SCPattern) and to reconstruct the differentiation trajectory from the pluripotent state through mesendoderm to DE (Wave-Crest). Importantly, presumptive DE cells can be detected during the transitory phase from Brachyury (T) (+) mesendoderm toward a CXCR4 (+) DE state. Novel regulators are identified within this time window and are functionally validated on a screening platform with a T-2A-EGFP knock-in reporter engineered by CRISPR/Cas9. Through loss-of-function and gain-of-function experiments, we demonstrate that KLF8 plays a pivotal role modulating mesendoderm to DE differentiation. CONCLUSIONS We report the analysis of 1776 cells by scRNA-seq covering distinct human embryonic stem cell-derived progenitor states. By reconstructing a differentiation trajectory at single-cell resolution, novel regulators of the mesendoderm transition to DE are elucidated and validated. Our strategy of combining single-cell analysis and genetic approaches can be applied to uncover novel regulators governing cell fate decisions in a variety of systems.
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Affiliation(s)
- Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.
| | - Ning Leng
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.,Present address: Genentech, Inc., South San Francisco, CA, USA
| | - Jue Zhang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Zhonggang Hou
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.,Present address: Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - David T Vereide
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Jeea Choi
- Department of Statistics, University of Wisconsin, Madison, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, 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, USA. .,Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA, USA.
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