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Hutchison V, Lynch A, Gutierrez-Gamez AM, Chen J. Inducible tricolor reporter mouse for parallel imaging of lysosomes, mitochondria, and microtubules. J Cell Biol 2024; 223:e202305086. [PMID: 37917008 PMCID: PMC10621751 DOI: 10.1083/jcb.202305086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/22/2023] [Revised: 09/06/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
Cell type-specific use of the same DNA blueprint generates diverse cell types. Such diversity must also be executed via differential deployment of the same subcellular machinery. However, our understanding of the size, distribution, and dynamics of subcellular machinery in native tissues and their connection to cellular diversity remains limited. We generate and characterize an inducible tricolor reporter mouse, dubbed "Kaleidoscope," for simultaneous imaging of lysosomes, mitochondria, and microtubules in any cell type and at a single-cell resolution. The expected subcellular compartments are labeled in culture and in tissues with no impact on cellular and organismal viability. Quantitative and live imaging of the tricolor reporter captures cell type-specific organelle features and kinetics in the lung, as well as their changes after Sendai virus infection. Yap/Taz mutant lung epithelial cells undergo accelerated lamellar body maturation, a subcellular manifestation of their molecular defects. A comprehensive toolbox of reporters for all subcellular structures is expected to transform our understanding of cell biology in tissues.
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Affiliation(s)
- Vera Hutchison
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Anne Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | | | - Jichao Chen
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Hutchison V, Lynch A, Gamez AMG, Chen J. An inducible tricolor reporter mouse for simultaneous imaging of lysosomes, mitochondria and microtubules. bioRxiv 2023:2023.05.22.541817. [PMID: 37293075 PMCID: PMC10245888 DOI: 10.1101/2023.05.22.541817] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cell-type-specific use of the same DNA blueprint generates diverse cell types. Such diversity must also be executed via differential deployment of the same subcellular machinery. However, our understanding of the size, distribution, and dynamics of subcellular machinery in native tissues, and their connection to cellular diversity, remain limited. We generate and characterize an inducible tricolor reporter mouse, dubbed "kaleidoscope", for simultaneous imaging of lysosomes, mitochondria and microtubules in any cell type and at a single cell resolution. The expected subcellular compartments are labeled in culture and in tissues with no impact on cellular and organismal viability. Quantitative and live imaging of the tricolor reporter captures cell-type-specific organelle features and kinetics in the lung, as well as their changes after Sendai virus infection. Yap/Taz mutant lung epithelial cells undergo accelerated lamellar body maturation, a subcellular manifestation of their molecular defects. A comprehensive toolbox of reporters for all subcellular structures is expected to transform our understanding of cell biology in tissues.
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Affiliation(s)
- Vera Hutchison
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Anne Lynch
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | - Jichao Chen
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Vila Ellis L, Cain MP, Hutchison V, Flodby P, Crandall ED, Borok Z, Zhou B, Ostrin EJ, Wythe JD, Chen J. Epithelial Vegfa Specifies a Distinct Endothelial Population in the Mouse Lung. Dev Cell 2020; 52:617-630.e6. [PMID: 32059772 PMCID: PMC7170573 DOI: 10.1016/j.devcel.2020.01.009] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 11/26/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
The lung microvasculature is essential for gas exchange and commonly considered homogeneous. We show that VEGFA from the epithelium is required for a distinct endothelial cell (EC) population in the mouse lung. Vegfa is predominantly expressed by alveolar type 1 (AT1) cells and locally required to specify a subset of ECs. Single-cell RNA sequencing (scRNA-seq) reveals that ∼15% of lung ECs are transcriptionally distinct-marked by Carbonic anhydrase 4 (Car4)-and arise from bulk ECs, as suggested by trajectory analysis. Car4 ECs have extensive cellular projections and are separated from AT1 cells by a limited basement membrane without intervening pericytes. Car4 ECs are specifically lost upon epithelial Vegfa deletion; without Car4 ECs, the alveolar space is aberrantly enlarged despite the normal appearance of myofibroblasts. Lung Car4 ECs and retina tip ECs have common and distinct features. These findings support a signaling role of AT1 cells and shed light on alveologenesis.
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Affiliation(s)
- Lisandra Vila Ellis
- Department of Pulmonary Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; Tecnológico de Monterrey - Escuela de Medicina, Monterrey 64710, Mexico
| | - Margo P Cain
- Department of Pulmonary Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas M D Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Vera Hutchison
- Department of Pulmonary Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Per Flodby
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine and Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Edward D Crandall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine and Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine and Hastings Center for Pulmonary Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Edwin J Ostrin
- Department of Pulmonary Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; Department of General Internal Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Joshua D Wythe
- Department of Molecular Physiology and Biophysics, Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
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Wang N, Yang Y, Moore MJ, Brockington SF, Walker JF, Brown JW, Liang B, Feng T, Edwards C, Mikenas J, Olivieri J, Hutchison V, Timoneda A, Stoughton T, Puente R, Majure LC, Eggli U, Smith SA. Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments. Mol Biol Evol 2019; 36:112-126. [PMID: 30371871 DOI: 10.1093/molbev/msy200] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.
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Affiliation(s)
- Ning Wang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Joseph W Brown
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Bin Liang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Caroline Edwards
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Jessica Mikenas
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Julia Olivieri
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Vera Hutchison
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Tommy Stoughton
- Center for the Environment, MSC 63, Plymouth State University, Plymouth, NH
| | - Raúl Puente
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich, Zürich, Switzerland
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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Walker JF, Yang Y, Feng T, Timoneda A, Mikenas J, Hutchison V, Edwards C, Wang N, Ahluwalia S, Olivieri J, Walker-Hale N, Majure LC, Puente R, Kadereit G, Lauterbach M, Eggli U, Flores-Olvera H, Ochoterena H, Brockington SF, Moore MJ, Smith SA. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales. Am J Bot 2018; 105:446-462. [PMID: 29738076 DOI: 10.1002/ajb2.1069] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/04/2018] [Indexed: 05/27/2023]
Abstract
PREMISE OF THE STUDY The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. METHODS We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. KEY RESULTS Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. CONCLUSIONS Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.
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Affiliation(s)
- Joseph F Walker
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jessica Mikenas
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Vera Hutchison
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Caroline Edwards
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Ning Wang
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Sonia Ahluwalia
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Julia Olivieri
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
- Institute of Computational and Mathematical Engineering (ICME), Stanford University, 475 Via Ortega, Suite B060, Stanford, CA, 94305-4042, USA
| | - Nathanael Walker-Hale
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, Wellington, 6012, New Zealand
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, 85008, USA
| | - Raúl Puente
- Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, 85008, USA
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
- Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
| | - Maximilian Lauterbach
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
- Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich / Grün Stadt Zürich, Mythenquai 88, CH-8002, Zürich, Switzerland
| | - Hilda Flores-Olvera
- Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, 04510, Mexico City, Mexico
| | - Helga Ochoterena
- Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, 04510, Mexico City, Mexico
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
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