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Thompson SH, Anselmi C, Ishizuka KJ, Palmeri KJ, Voskoboynik A. Contributions from both the brain and the vascular network guide behavior in the colonial tunicate Botryllus schlosseri. J Exp Biol 2022; 225:279340. [PMID: 36314197 PMCID: PMC9720745 DOI: 10.1242/jeb.244491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/01/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
We studied the function, development and aging of the adult nervous system in the colonial tunicate Botryllus schlosseri. Adults, termed zooids, are filter-feeding individuals. Sister zooids group together to form modules, and modules, in turn, are linked by a shared vascular network to form a well-integrated colony. Zooids undergo a weekly cycle of regression and renewal during which mature zooids are replaced by developing buds. The zooid brain matures and degenerates on this 7-day cycle. We used focal extracellular recording and video imaging to explore brain activity in the context of development and degeneration and to examine the contributions of the nervous system and vascular network to behavior. Recordings from the brain revealed complex firing patterns arising both spontaneously and in response to stimulation. Neural activity increases as the brain matures and declines thereafter. Motor behavior follows the identical time course. The behavior of each zooid is guided predominantly by its individual brain, but sister zooids can also exhibit synchronous motor behavior. The vascular network also generates action potentials that are largely independent of neural activity. In addition, the entire vascular network undergoes slow rhythmic contractions that appear to arise from processes endogenous to vascular epithelial cells. We found that neurons in the brain and cells of the vascular network both express multiple genes for voltage-gated Na+ and Ca2+ ion channels homologous (based on sequence) to mammalian ion channel genes.
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Affiliation(s)
- Stuart H. Thompson
- Department of Biology and Hopkins Marine Station, Stanford University, Stanford, CA 93950, USA,Author for correspondence ()
| | - Chiara Anselmi
- Department of Biology and Hopkins Marine Station, Stanford University, Stanford, CA 93950, USA,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katherine J. Ishizuka
- Department of Biology and Hopkins Marine Station, Stanford University, Stanford, CA 93950, USA,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karla J. Palmeri
- Department of Biology and Hopkins Marine Station, Stanford University, Stanford, CA 93950, USA,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ayelet Voskoboynik
- Department of Biology and Hopkins Marine Station, Stanford University, Stanford, CA 93950, USA,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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2
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Anselmi C, Kowarsky M, Gasparini F, Caicci F, Ishizuka KJ, Palmeri KJ, Raveh T, Sinha R, Neff N, Quake SR, Weissman IL, Voskoboynik A, Manni L. Two distinct evolutionary conserved neural degeneration pathways characterized in a colonial chordate. Proc Natl Acad Sci U S A 2022; 119:e2203032119. [PMID: 35858312 PMCID: PMC9303981 DOI: 10.1073/pnas.2203032119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/26/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022] Open
Abstract
Colonial tunicates are marine organisms that possess multiple brains simultaneously during their colonial phase. While the cyclical processes of neurogenesis and neurodegeneration characterizing their life cycle have been documented previously, the cellular and molecular changes associated with such processes and their relationship with variation in brain morphology and individual (zooid) behavior throughout adult life remains unknown. Here, we introduce Botryllus schlosseri as an invertebrate model for neurogenesis, neural degeneration, and evolutionary neuroscience. Our analysis reveals that during the weekly colony budding (i.e., asexual reproduction), prior to programmed cell death and removal by phagocytes, decreases in the number of neurons in the adult brain are associated with reduced behavioral response and significant change in the expression of 73 mammalian homologous genes associated with neurodegenerative disease. Similarly, when comparing young colonies (1 to 2 y of age) to those reared in a laboratory for ∼20 y, we found that older colonies contained significantly fewer neurons and exhibited reduced behavioral response alongside changes in the expression of 148 such genes (35 of which were differentially expressed across both timescales). The existence of two distinct yet apparently related neurodegenerative pathways represents a novel platform to study the gene products governing the relationship between aging, neural regeneration and degeneration, and loss of nervous system function. Indeed, as a member of an evolutionary clade considered to be a sister group of vertebrates, this organism may be a fundamental resource in understanding how evolution has shaped these processes across phylogeny and obtaining mechanistic insight.
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Affiliation(s)
- Chiara Anselmi
- Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Mark Kowarsky
- Department of Physics, Stanford University, Stanford, CA 94305
| | - Fabio Gasparini
- Dipartimento di Biologia, Università degli Studi di Padova, 35131, Padova, Italy
| | - Federico Caicci
- Dipartimento di Biologia, Università degli Studi di Padova, 35131, Padova, Italy
| | | | - Karla J. Palmeri
- Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950
| | - Tal Raveh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco CA 94158
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco CA 94158
- Departments of Applied Physics and Bioengineering, Stanford University, Stanford, CA 94305
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco CA 94158
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950
| | - Ayelet Voskoboynik
- Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco CA 94158
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950
| | - Lucia Manni
- Dipartimento di Biologia, Università degli Studi di Padova, 35131, Padova, Italy
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Kowarsky M, Anselmi C, Hotta K, Burighel P, Zaniolo G, Caicci F, Rosental B, Neff NF, Ishizuka KJ, Palmeri KJ, Okamoto J, Gordon T, Weissman IL, Quake SR, Manni L, Voskoboynik A. Sexual and asexual development: two distinct programs producing the same tunicate. Cell Rep 2021; 34:108681. [PMID: 33503429 PMCID: PMC7949349 DOI: 10.1016/j.celrep.2020.108681] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 11/02/2019] [Revised: 08/24/2020] [Accepted: 12/30/2020] [Indexed: 01/04/2023] Open
Abstract
Colonial tunicates are the only chordate that possess two distinct developmental pathways to produce an adult body: either sexually through embryogenesis or asexually through a stem cell-mediated renewal termed blastogenesis. Using the colonial tunicate Botryllus schlosseri, we combine transcriptomics and microscopy to build an atlas of the molecular and morphological signatures at each developmental stage for both pathways. The general molecular profiles of these processes are largely distinct. However, the relative timing of organogenesis and ordering of tissue-specific gene expression are conserved. By comparing the developmental pathways of B. schlosseri with other chordates, we identify hundreds of putative transcription factors with conserved temporal expression. Our findings demonstrate that convergent morphology need not imply convergent molecular mechanisms but that it showcases the importance that tissue-specific stem cells and transcription factors play in producing the same mature body through different pathways.
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Affiliation(s)
- Mark Kowarsky
- Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Chiara Anselmi
- Dipartimento di Biologia, Università degli Studi di Padova, 35122 Padova, Italy; Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Kohji Hotta
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
| | - Paolo Burighel
- Dipartimento di Biologia, Università degli Studi di Padova, 35122 Padova, Italy
| | - Giovanna Zaniolo
- Dipartimento di Biologia, Università degli Studi di Padova, 35122 Padova, Italy
| | - Federico Caicci
- Dipartimento di Biologia, Università degli Studi di Padova, 35122 Padova, Italy
| | - Benyamin Rosental
- Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA; The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Regenerative Medicine and Stem Cells, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Katherine J Ishizuka
- Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Karla J Palmeri
- Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | | | - Tal Gordon
- Zoology Department, Tel Aviv University, Tel Aviv 69978, Israel
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Departments of Applied Physics and Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lucia Manni
- Dipartimento di Biologia, Università degli Studi di Padova, 35122 Padova, Italy.
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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4
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Rosental B, Kowarsky M, Seita J, Corey DM, Ishizuka KJ, Palmeri KJ, Chen SY, Sinha R, Okamoto J, Mantalas G, Manni L, Raveh T, Clarke DN, Tsai JM, Newman AM, Neff NF, Nolan GP, Quake SR, Weissman IL, Voskoboynik A. Complex mammalian-like haematopoietic system found in a colonial chordate. Nature 2018; 564:425-429. [PMID: 30518860 PMCID: PMC6347970 DOI: 10.1038/s41586-018-0783-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [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: 12/01/2017] [Accepted: 10/15/2018] [Indexed: 12/11/2022]
Abstract
Haematopoiesis is an essential process that evolved in multicellular animals. At the heart of this process are haematopoietic stem cells (HSCs), which are multipotent and self-renewing, and generate the entire repertoire of blood and immune cells throughout an animal's life1. Although there have been comprehensive studies on self-renewal, differentiation, physiological regulation and niche occupation in vertebrate HSCs, relatively little is known about the evolutionary origin and niches of these cells. Here we describe the haematopoietic system of Botryllus schlosseri, a colonial tunicate that has a vasculature and circulating blood cells, and interesting stem-cell biology and immunity characteristics2-8. Self-recognition between genetically compatible B. schlosseri colonies leads to the formation of natural parabionts with shared circulation, whereas incompatible colonies reject each other3,4,7. Using flow cytometry, whole-transcriptome sequencing of defined cell populations and diverse functional assays, we identify HSCs, progenitors, immune effector cells and an HSC niche, and demonstrate that self-recognition inhibits allospecific cytotoxic reactions. Our results show that HSC and myeloid lineage immune cells emerged in a common ancestor of tunicates and vertebrates, and also suggest that haematopoietic bone marrow and the B. schlosseri endostyle niche evolved from a common origin.
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Affiliation(s)
- Benyamin Rosental
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA.
| | - Mark Kowarsky
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Jun Seita
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- AI based Healthcare and Medical Data Analysis Standardization Unit, Medical Sciences Innovation Hub Program, RIKEN, Tokyo, Japan
| | - Daniel M Corey
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine J Ishizuka
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA
| | - Karla J Palmeri
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA
| | - Shih-Yu Chen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Gary Mantalas
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Molecular Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lucia Manni
- Dipartimento di Biologia, Università degli Studi di Padova, Padova, Italy
| | - Tal Raveh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - D Nathaniel Clarke
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA
| | - Jonathan M Tsai
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA.
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA.
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5
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Rosental B, Kowarsky MA, Corey DM, Ishizuka KJ, Palmeri KJ, Chen SY, Sinha R, Voskoboynik A, Weissman IL. Finding the evolutionary precursor of vertebrate hematopoietic lineage: Functional and molecular characterization of B. schlosseri immune system. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.216.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
We are characterizing the immune system and cell populations of the tunicate model Botryllus schlosseri on functional and molecular levels. The chordate B. schlosseri belongs to a group that is considered the closest living invertebrate relative of vertebrates. Using FACS analysis we can isolate 12 populations of B. schlosseri cells by size, granularity and auto fluorescence. In order to increase the number of isolated cell populations, we used Cytof to scan large numbers of antibodies. Antibodies that differentially bind to B. schlosseri cells were validated by flow cytometry. Serum against the Botryllus Histocompatibility Factor, and lectins and fluorescent reagents activated by enzymatic activity were also used to differentiate live B. schlosseri cell types. Using these markers we isolated 34 cell populations and created RNA libraries for deep sequencing. Additionally, we developed immunological assays for cytotoxicity, phagocytosis and stem cell tracking. Using gene expression analysis we found hematopoietic stem cells and progenitors; in transplantation assays we showed their capability to induce chimerism of pigmentation and differentiation to other cell types, as well as localization to the stem cell niches. We characterized 3 different phagocytic cell types including a previously undescribed myeloid derived cell population. We describe the B. schlosseri cytotoxic cell population that originates as a large granular lymphocyte-like cell type that become morula cells upon allogeneic challenge activation. Altogether, it seems that the common ancestor of tunicates and vertebrates had a true hematopoietic myeloid lineage, while the cytotoxic cells are a convergent evolutionary system.
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Voskoboynik A, Newman AM, Corey DM, Sahoo D, Pushkarev D, Neff NF, Passarelli B, Koh W, Ishizuka KJ, Palmeri KJ, Dimov IK, Keasar C, Fan HC, Mantalas GL, Sinha R, Penland L, Quake SR, Weissman IL. Identification of a colonial chordate histocompatibility gene. Science 2013; 341:384-7. [PMID: 23888037 PMCID: PMC3810301 DOI: 10.1126/science.1238036] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Histocompatibility is the basis by which multicellular organisms of the same species distinguish self from nonself. Relatively little is known about the mechanisms underlying histocompatibility reactions in lower organisms. Botryllus schlosseri is a colonial urochordate, a sister group of vertebrates, that exhibits a genetically determined natural transplantation reaction, whereby self-recognition between colonies leads to formation of parabionts with a common vasculature, whereas rejection occurs between incompatible colonies. Using genetically defined lines, whole-transcriptome sequencing, and genomics, we identified a single gene that encodes self-nonself and determines "graft" outcomes in this organism. This gene is significantly up-regulated in colonies poised to undergo fusion and/or rejection, is highly expressed in the vasculature, and is functionally linked to histocompatibility outcomes. These findings establish a platform for advancing the science of allorecognition.
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Affiliation(s)
- Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel M. Corey
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Debashis Sahoo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dmitry Pushkarev
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Norma F. Neff
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Benedetto Passarelli
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Winston Koh
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Katherine J. Ishizuka
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Karla J. Palmeri
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Ivan K. Dimov
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chen Keasar
- Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - H. Christina Fan
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Gary L. Mantalas
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lolita Penland
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Stephen R. Quake
- Departments of Applied Physics and Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, Passarelli B, Fan HC, Mantalas GL, Palmeri KJ, Ishizuka KJ, Gissi C, Griggio F, Ben-Shlomo R, Corey DM, Penland L, White RA, Weissman IL, Quake SR. The genome sequence of the colonial chordate, Botryllus schlosseri. eLife 2013; 2:e00569. [PMID: 23840927 PMCID: PMC3699833 DOI: 10.7554/elife.00569] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [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: 01/22/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022] Open
Abstract
Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated budding program during subsequent rounds of asexual reproduction. As urochordates are considered to be the closest living invertebrate relatives of vertebrates, they are ideal subjects for whole genome sequence analyses. Using a novel method for high-throughput sequencing of eukaryotic genomes, we sequenced and assembled 580 Mbp of the B. schlosseri genome. The genome assembly is comprised of nearly 14,000 intron-containing predicted genes, and 13,500 intron-less predicted genes, 40% of which could be confidently parceled into 13 (of 16 haploid) chromosomes. A comparison of homologous genes between B. schlosseri and other diverse taxonomic groups revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity. The B. schlosseri genome is a community resource for studying alternative modes of reproduction, natural transplantation reactions, and stem cell-mediated regeneration. DOI:http://dx.doi.org/10.7554/eLife.00569.001.
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Affiliation(s)
- Ayelet Voskoboynik
- Department of Pathology , Institute for Stem Cell Biology and Regenerative Medicine, Stanford University , Stanford , United States ; Hopkins Marine Station , Stanford University , Pacific Grove , United States
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Rinkevich Y, Voskoboynik A, Rosner A, Rabinowitz C, Paz G, Oren M, Douek J, Alfassi G, Moiseeva E, Ishizuka KJ, Palmeri KJ, Weissman IL, Rinkevich B. Repeated, long-term cycling of putative stem cells between niches in a basal chordate. Dev Cell 2012; 24:76-88. [PMID: 23260626 DOI: 10.1016/j.devcel.2012.11.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 09/07/2012] [Accepted: 11/15/2012] [Indexed: 11/30/2022]
Abstract
The mechanisms that sustain stem cells are fundamental to tissue maintenance. Here, we identify "cell islands" (CIs) as a niche for putative germ and somatic stem cells in Botryllus schlosseri, a colonial chordate that undergoes weekly cycles of death and regeneration. Cells within CIs express markers associated with germ and somatic stem cells and gene products that implicate CIs as signaling centers for stem cells. Transplantation of CIs induced long-term germline and somatic chimerism, demonstrating self-renewal and pluripotency of CI cells. Cell labeling and in vivo time-lapse imaging of CI cells reveal waves of migrations from degrading CIs into developing buds, contributing to soma and germline development. Knockdown of cadherin, which is highly expressed within CIs, elicited the migration of CI cells to circulation. Piwi knockdown resulted in regeneration arrest. We suggest that repeated trafficking of stem cells allows them to escape constraints imposed by the niche, enabling self-preservation throughout life.
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Affiliation(s)
- Yuval Rinkevich
- Institute of Stem Cell Biology and Regenerative Medicine, Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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9
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Carpenter MA, Powell JH, Ishizuka KJ, Palmeri KJ, Rendulic S, De Tomaso AW. Growth and long-term somatic and germline chimerism following fusion of juvenile Botryllus schlosseri. Biol Bull 2011; 220:57-70. [PMID: 21385958 PMCID: PMC4265767 DOI: 10.1086/bblv220n1p57] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The colonial ascidian Botryllus schlosseri undergoes a histocompatibility reaction that can result in vascular fusion of distinct genotypes, creating a chimera. Chimerism has both potential benefits, such as an immediate increase in size that may enhance growth rates, and costs. For the latter, the presence of multiple genotypes in a chimera can lead to competition between genetically distinct stem cell lineages, resulting in complete replacement of somatic and germline tissues by a single genotype. Although fusion can occur at any point after metamorphosis, previous studies have focused on chimeras created from sexually mature adults, where no benefit to chimerism has been documented. Here we focus on the costs and benefits of fusion between juveniles, characterizing growth rates and patterns of somatic and germline chimerism after natural and controlled fusion events. We also compared outcomes between low- and high-density growth conditions, the latter more likely representative of what occurs in natural populations. We found that growth rates were density-dependent, and that only chimeras grew under high-density conditions. We also observed a positional component to a post-fusion event called resorption, indicating that extrinsic factors were important in this process. Patterns of germline and somatic chimerism and dominance in chimeras made from fused juveniles were equivalent to those after fusion of sexually mature adults, and there were no age-related differences in these processes. Finally, by using genetic markers that could retrospectively assign genotypes, we also found that the majority of individual testes in a chimera were clonally derived.
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Affiliation(s)
| | - John H. Powell
- Department of Ecology, Montana State University, Bozeman, Montana 59717
| | | | - Karla J. Palmeri
- Stanford University, Hopkins Marine Station, Pacific Grove, California 93950
| | - Snjezana Rendulic
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106
| | - Anthony W. De Tomaso
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106
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Voskoboynik A, Soen Y, Rinkevich Y, Rosner A, Ueno H, Reshef R, Ishizuka KJ, Palmeri KJ, Moiseeva E, Rinkevich B, Weissman IL. Identification of the endostyle as a stem cell niche in a colonial chordate. Cell Stem Cell 2008; 3:456-64. [PMID: 18940736 DOI: 10.1016/j.stem.2008.07.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 06/10/2008] [Accepted: 07/24/2008] [Indexed: 10/21/2022]
Abstract
Stem cell populations exist in "niches" that hold them and regulate their fate decisions. Identification and characterization of these niches is essential for understanding stem cell maintenance and tissue regeneration. Here we report on the identification of a novel stem cell niche in Botryllus schlosseri, a colonial urochordate with high stem cell-mediated developmental activities. Using in vivo cell labeling, engraftment, confocal microscopy, and time-lapse imaging, we have identified cells with stemness capabilities in the anterior ventral region of the Botryllus' endostyle. These cells proliferate and migrate to regenerating organs in developing buds and buds of chimeric partners but do not contribute to the germ line. When cells are transplanted from the endostyle region, they contribute to tissue development and induce long-term chimerism in allogeneic tissues. In contrast, cells from other Botryllus' regions do not show comparable stemness capabilities. Cumulatively, these results define the Botryllus' endostyle region as an adult somatic stem cell niche.
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Affiliation(s)
- Ayelet Voskoboynik
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Voskoboynik A, Simon-Blecher N, Soen Y, Rinkevich B, De Tomaso AW, Ishizuka KJ, Weissman IL. Striving for normality: whole body regeneration through a series of abnormal generations. FASEB J 2007; 21:1335-44. [PMID: 17289924 DOI: 10.1096/fj.06-7337com] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Embryogenesis and asexual reproduction are commonly considered to be coordinated developmental processes, which depend on accurate progression through a defined sequence of developmental stages. Here we report a peculiar developmental scenario in a simple chordate, Botryllus schlosseri, wherein a normal colony of individuals (zooids and buds) is regenerated from the vasculature (vascular budding) through a sequence of morphologically abnormal developmental stages. Vascular budding was induced by surgically removing buds and zooids from B. schlosseri colonies, leaving only the vasculature and the tunic that connects them. In vivo imaging and histological sections showed that the timing and morphology of developing structures during vascular budding deviated significantly from other asexual reproduction modes (the regular asexual reproduction mode in this organism and vascular budding in other botryllid species). Subsequent asexual reproduction cycles exhibited gradual regaining of normal developmental patterns, eventually leading to regeneration of a normal colony. The conversion into a normal body form suggests the activation of an alternative pathway of asexual reproduction, which involves gradual regaining of normal positional information. It presents a powerful model for studying the specification of the same body plan by different developmental programs.
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Affiliation(s)
- Ayelet Voskoboynik
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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De Tomaso AW, Nyholm SV, Palmeri KJ, Ishizuka KJ, Ludington WB, Mitchel K, Weissman IL. MHC-Independent Allorecognition of Invertebrates—A Link between Invertebrate Histocompatibility and Vertebrate Adaptive Immunity? J Am Soc Nephrol 2006; 17:595-599. [PMID: 37000956 DOI: 10.1681/01.asn.0000926784.72431.9d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023] Open
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De Tomaso AW, Nyholm SV, Palmeri KJ, Ishizuka KJ, Ludington WB, Mitchel K, Weissman IL. Isolation and characterization of a protochordate histocompatibility locus. Nature 2005; 438:454-9. [PMID: 16306984 PMCID: PMC1401502 DOI: 10.1038/nature04150] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Accepted: 08/18/2005] [Indexed: 11/08/2022]
Abstract
Histocompatibility--the ability of an organism to distinguish its own cells and tissue from those of another--is a universal phenomenon in the Metazoa. In vertebrates, histocompatibility is a function of the immune system controlled by a highly polymorphic major histocompatibility complex (MHC), which encodes proteins that target foreign molecules for immune cell recognition. The association of the MHC and immune function suggests an evolutionary relationship between metazoan histocompatibility and the origins of vertebrate immunity. However, the MHC of vertebrates is the only functionally characterized histocompatibility system; the mechanisms underlying this process in non-vertebrates are unknown. A primitive chordate, the ascidian Botryllus schlosseri, also undergoes a histocompatibility reaction controlled by a highly polymorphic locus. Here we describe the isolation of a candidate gene encoding an immunoglobulin superfamily member that, by itself, predicts the outcome of histocompatibility reactions. This is the first non-vertebrate histocompatibility gene described, and may provide insights into the evolution of vertebrate adaptive immunity.
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Affiliation(s)
- Anthony W De Tomaso
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA.
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Lauzon RJ, Ishizuka KJ, Weissman IL. Cyclical generation and degeneration of organs in a colonial urochordate involves crosstalk between old and new: a model for development and regeneration. Dev Biol 2002; 249:333-48. [PMID: 12221010 DOI: 10.1006/dbio.2002.0772] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Botryllus schlosseri is a colonial marine urochordate in which all adult organisms (called zooids) in a colony die synchronously by apoptosis (programmed cell death) in cyclical fashion. During this death phase called takeover, cell corpses within the dying organism are engulfed by circulating phagocytic cells. The "old" zooids and their organs are resorbed within 24-36 h (programmed cell removal). This process coincides temporally with the growth of asexually derived primary buds, that harbor a small number of undifferentiated cells, into mature zooids containing functional organs and tissues with the same body plan as adult zooids from which they budded. Within these colonies, all zooids share a ramifying network of extracorporeal blood vessels embedded in a gelatinous tunic. The underlying mechanisms regulating programmed cell death and programmed cell removal in this organism are unknown. In this study, we extirpated buds or zooids from B. schlosseri colonies in order to investigate the interplay that exists between buds, zooids, and the vascular system during takeover. Our findings indicate that, in the complete absence of buds (budectomy), organs from adult zooids underwent programmed cell death but were markedly impaired in their ability to be resorbed despite engulfment of zooid-derived cell corpses by phagocytes. However, when buds were removed from only half of the flower-shaped systems of zooids in a colony (hemibudectomy), the budectomized zooids were completely resorbed within 36-48 h following onset of programmed cell death. Furthermore, if hemibudectomies were carried out by using small colonies, leaving only a single functional bud, zooids from the old generation were also resorbed, albeit delayed to 48-60 h following onset of programmed cell death. This bud eventually reached functional maturity, but grew significantly larger in size than any control zooid, and exhibited hyperplasia. This finding strongly suggested that components of the dying zooid viscera could be reutilized by the developing buds, possibly as part of a colony-wide recycling mechanism. In order to test this hypothesis, zooids were surgically removed (zooidectomy) at the onset of takeover, and bud growth was quantitatively determined. In these zooidectomized colonies, bud growth was severely curtailed. In most solitary, long-lived animals, organs and tissues are maintained by processes of continual death and removal of aging cells counterbalanced by regeneration with stem and progenitor cells. In the colonial tunicate B. schlosseri, the same kinds of processes ensure the longevity of the colony (an animal) by cycles of death and regeneration of its constituent zooids (also animals).
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Affiliation(s)
- Robert J Lauzon
- Department of Biological Sciences, Union College, Schenectady, NY 12308, USA.
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De Tomaso AW, Saito Y, Ishizuka KJ, Palmeri KJ, Weissman IL. Mapping the genome of a model protochordate. I. A low resolution genetic map encompassing the fusion/histocompatibility (Fu/HC) locus of Botryllus schlosseri. Genetics 1998; 149:277-87. [PMID: 9584102 PMCID: PMC1460123 DOI: 10.1093/genetics/149.1.277] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The colonial protochordate, Botryllus schlosseri, undergoes a genetically defined, natural transplantation reaction when the edges of two growing colonies interact. Peripheral blood vessels of each colony touch and will either fuse together to form a common vasculature between the colonies, or reject each other in an active blood-based inflammatory process in which the interacting vessels are cut off and the two colonies no longer interact. Previous studies have demonstrated that allorecognition in Botryllus is principally controlled by a single Mendelian locus named the fusion/histocompatibility (Fu/HC) locus, with multiple codominantly expressed alleles. However, identification and cloning of this locus has been difficult. We are taking a genomic approach in isolating this locus by creating a detailed genetic linkage map of the 725 Mbp Botryllus genome using DNA polymorphisms (primarily identified as AFLPs) as molecular genetic markers. DNA polymorphisms are identified in inbred laboratory strains of Fu/HC defined Botryllus, and their segregation and linkage is analyzed in a series of defined crosses. Using bulk segregant analysis, we have focused our mapping efforts on the Fu/HC region of the genome, and have generated an initial map which delineates the Fu/HC locus to a 5.5 cM region.
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Affiliation(s)
- A W De Tomaso
- Hopkins Marine Station, Pacific Grove, California 93950, USA.
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Abstract
Botryllus schlosseri is a colonial ascidian whose asexually derived, clonally modular systems of zooids exhibit developmental synchrony. The blastogenic cycle culminates in a phase of programmed cell and zooid death called takeover, in which all functional zooids die over a 30 hr period, and are replaced by a new generation of individuals. Because of the weekly recurrence and magnitude of visceral death in this model organism, we have begun to characterize the mechanisms that govern takeover. Here we describe a monoclonal antibody (B3F12.9) that recognizes a novel 57 Kd polypeptide (under reducing conditions) localized to the perivisceral extracellular matrix (PVEM) of buds and zooids, as well as blood cells of Botryllus by immunofluorescence and immunogold labeling of tissue sections. During their active feeding phase, zooids exhibited a uniform labeling pattern of PVEM along their anteroposterior (A-P) axis. At the onset of takeover (T = 3 hr), B3F12.9 immunostaining became diffuse or absent at the anterior end, which paralleled the axis of contraction of the dying zooid, whereas the posterior end retained its labeling integrity. During mid (T = 15 hr) to late (T = 28 hr) takeover, issue damage was extensive, large blood macrophages and other B3F12.9 immunoreactive blood cells invaded the peribranchial cavity, whereas PVEM labeling gradually disappeared along the entire A-P axis. These findings indicate that takeover is a dynamic process in which extracellular matrix breakdown proceeds in a polarized fashion, beginning at the anterior end of each zooid and gradually propagating toward the posterior end.
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Affiliation(s)
- R J Lauzon
- Department of Pediatrics, Albany Medical College, New York 12208
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