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Surette E, Donahue J, Robinson S, McKenna D, Martinez CS, Fitzgerald B, Karlstrom RO, Cumplido N, McMenamin SK. Adult caudal fin shape is imprinted in the embryonic fin fold. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603744. [PMID: 39071346 PMCID: PMC11275767 DOI: 10.1101/2024.07.16.603744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Appendage shape is formed during development (and re-formed during regeneration) according to spatial and temporal cues that orchestrate local cellular morphogenesis. The caudal fin is the primary appendage used for propulsion in most fish species, and exhibits a range of distinct morphologies adapted for different swimming strategies, however the molecular mechanisms responsible for generating these diverse shapes remain mostly unknown. In zebrafish, caudal fins display a forked shape, with longer supportive bony rays at the periphery and shortest rays at the center. Here, we show that a premature, transient pulse of sonic hedgehog a (shha) overexpression during late embryonic development results in excess proliferation and growth of the central rays, causing the adult caudal fin to grow into a triangular, truncate shape. Both global and regional ectopic shha overexpression are sufficient to alter fin shape, and forked shape may be rescued by subsequent treatment with an antagonist of the canonical Shh pathway. The induced truncate fins show a decreased fin ray number and fail to form the hypural diastema that normally separates the dorsal and ventral fin lobes. While forked fins regenerate their original forked morphology, truncate fins regenerate truncate, suggesting that positional memory of the fin rays can be permanently altered by a transient treatment during embryogenesis. Ray finned fish have evolved a wide spectrum of caudal fin morphologies, ranging from truncate to forked, and the current work offers insights into the developmental mechanisms that may underlie this shape diversity.
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VanWinkle PE, Lee E, Wynn B, Nawara TJ, Thomas H, Parant J, Alvarez C, Serra R, Sztul E. Disruption of the creb3l1 gene causes defects in caudal fin regeneration and patterning in zebrafish Danio rerio. Dev Dyn 2024. [PMID: 39003620 DOI: 10.1002/dvdy.726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 06/12/2024] [Accepted: 06/22/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND The gene cAMP-Responsive Element Binding protein 3-like-1 (CREB3L1) has been implicated in bone development in mice, with CREB3L1 knock-out mice exhibiting fragile bones, and in humans, with CREB3L1 mutations linked to osteogenesis imperfecta. However, the mechanism through which Creb3l1 regulates bone development is not fully understood. RESULTS To probe the role of Creb3l1 in organismal physiology, we used CRISPR-Cas9 genome editing to generate a Danio rerio (zebrafish) model of Creb3l1 deficiency. In contrast to mammalian phenotypes, the Creb3l1 deficient fish do not display abnormalities in osteogenesis, except for a decrease in the bifurcation pattern of caudal fin. Both, skeletal morphology and overall bone density appear normal in the mutant fish. However, the regeneration of caudal fin postamputation is significantly affected, with decreased overall regenerate and mineralized bone area. Moreover, the mutant fish exhibit a severe patterning defect during regeneration, with a significant decrease in bifurcation complexity of the fin rays and distalization of the bifurcation sites. Analysis of genes implicated in bone development showed aberrant patterning of shha and ptch2 in Creb3l1 deficient fish, linking Creb3l1 with Sonic Hedgehog signaling during fin regeneration. CONCLUSIONS Our results uncover a novel role for Creb3l1 in regulating tissue growth and patterning during regeneration.
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Affiliation(s)
- Peyton E VanWinkle
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eunjoo Lee
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bridge Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tomasz J Nawara
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Holly Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - John Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Cecilia Alvarez
- CIBICI-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosa Serra
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Autumn M, Hu Y, Zeng J, McMenamin SK. Growth patterns of caudal fin rays are informed by both external signals from the regenerating organ and remembered identity autonomous to the local tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586899. [PMID: 38585773 PMCID: PMC10996721 DOI: 10.1101/2024.03.29.586899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Regenerating tissues must remember or interpret their spatial position, using this information to restore original size and patterning. The external skeleton of the zebrafish caudal fin is composed of 18 rays; after any portion of the fin is amputated, position-dependent regenerative growth restores each ray to its original length. We tested for transcriptional differences during regeneration of proximal versus distal tissues and identified 489 genes that differed in proximodistal expression. Thyroid hormone directs multiple aspects of ray patterning along the proximodistal axis, and we identified 364 transcripts showing a proximodistal expression pattern that was dependent on thyroid hormone context. To test what aspects of ray positional identity are directed by extrinsic cues versus remembered identity autonomous to the tissue itself, we transplanted distal portions of rays to proximal environments and evaluated regeneration within the new location. While neighboring proximal tissue showed robust expression of scpp7, a transcript with thyroid-regulated proximal enrichment, regenerating rays originating from transplanted distal tissue showed reduced (distal-like) expression during outgrowth. These distal-to-proximal transplants regenerated far beyond the length of the graft itself, indicating that cues from the proximal environment promoted additional growth. Nonetheless, these transplants initially regenerated at a much slower rate compared to controls, suggesting memory of distal identity was retained by the transplanted tissue. This early growth retardation caused rays that originated from transplants to become noticeably shorter than their native neighboring rays. While several aspects of fin ray morphology (bifurcation, segment length) were found to be determined by the environment, regeneration speed and ray length are remembered autonomously by tissues, persisting across multiple rounds of amputation and regeneration.
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Affiliation(s)
- Melody Autumn
- Biology Department, Boston College, Chestnut Hill, MA 02467
| | - Yinan Hu
- Biology Department, Boston College, Chestnut Hill, MA 02467
| | - Jenny Zeng
- Biology Department, Boston College, Chestnut Hill, MA 02467
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Xu C, Hutchins ED, Eckalbar W, Pendarvis K, Benson DM, Lake DF, McCarthy FM, Kusumi K. Comparative proteomic analysis of tail regeneration in the green anole lizard, Anolis carolinensis. NATURAL SCIENCES (WEINHEIM, GERMANY) 2024; 4:e20210421. [PMID: 38505006 PMCID: PMC10947082 DOI: 10.1002/ntls.20210421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
As amniote vertebrates, lizards are the most closely related organisms to humans capable of appendage regeneration. Lizards can autotomize, or release their tails as a means of predator evasion, and subsequently regenerate a functional replacement. Green anoles (Anolis carolinensis) can regenerate their tails through a process that involves differential expression of hundreds of genes, which has previously been analyzed by transcriptomic and microRNA analysis. To investigate protein expression in regenerating tissue, we performed whole proteomic analysis of regenerating tail tip and base. This is the first proteomic data set available for any anole lizard. We identified a total of 2,646 proteins - 976 proteins only in the regenerating tail base, 796 only in the tail tip, and 874 in both tip and base. For over 90% of these proteins in these tissues, we were able to assign a clear orthology to gene models in either the Ensembl or NCBI databases. For 13 proteins in the tail base, 9 proteins in the tail tip, and 10 proteins in both regions, the gene model in Ensembl and NCBI matched an uncharacterized protein, confirming that these predictions are present in the proteome. Ontology and pathways analysis of proteins expressed in the regenerating tail base identified categories including actin filament-based process, ncRNA metabolism, regulation of phosphatase activity, small GTPase mediated signal transduction, and cellular component organization or biogenesis. Analysis of proteins expressed in the tail tip identified categories including regulation of organelle organization, regulation of protein localization, ubiquitin-dependent protein catabolism, small GTPase mediated signal transduction, morphogenesis of epithelium, and regulation of biological quality. These proteomic findings confirm pathways and gene families activated in tail regeneration in the green anole as well as identify uncharacterized proteins whose role in regrowth remains to be revealed. This study demonstrates the insights that are possible from the integration of proteomic and transcriptomic data in tail regrowth in the green anole, with potentially broader application to studies in other regenerative models.
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Affiliation(s)
- Cindy Xu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Elizabeth D. Hutchins
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Current addresses: Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Walter Eckalbar
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Current addresses: School of Medicine, University of California, San Francisco, California, USA
| | - Ken Pendarvis
- Department of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Derek M. Benson
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Douglas F. Lake
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Fiona M. McCarthy
- Department of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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Liu R, Ren X, Wang J, Chen T, Sun X, Lin T, Huang J, Guo Z, Luo L, Ren C, Luo P, Hu C, Cao X, Yan A, Yuan L. Transcriptomic analysis reveals the early body wall regeneration mechanism of the sea cucumber Holothuria leucospilota after artificially induced transverse fission. BMC Genomics 2023; 24:766. [PMID: 38087211 PMCID: PMC10714614 DOI: 10.1186/s12864-023-09808-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Sea cucumbers exhibit a remarkable ability to regenerate damaged or lost tissues and organs, making them an outstanding model system for investigating processes and mechanisms of regeneration. They can also reproduce asexually by transverse fission, whereby the anterior and posterior bodies can regenerate independently. Despite the recent focus on intestinal regeneration, the molecular mechanisms underlying body wall regeneration in sea cucumbers still remain unclear. RESULTS In this study, transverse fission was induced in the tropical sea cucumber, Holothuria leucospilota, through constrainment using rubber bands. Histological examination revealed the degradation and loosening of collagen fibers on day-3, followed by increased density but disorganization of the connective tissue on day-7 of regeneration. An Illumina transcriptome analysis was performed on the H. leucospilota at 0-, 3- and 7-days after artificially induced fission. The differential expression genes were classified and enriched by GO terms and KEGG database, respectively. An upregulation of genes associated with extracellular matrix remodeling was observed, while a downregulation of pluripotency factors Myc, Klf2 and Oct1 was detected, although Sox2 showed an upregulation in expression. In addition, this study also identified progressively declining expression of transcription factors in the Wnt, Hippo, TGF-β, and MAPK signaling pathways. Moreover, changes in genes related to development, stress response, apoptosis, and cytoskeleton formation were observed. The localization of the related genes was further confirmed through in situ hybridization. CONCLUSION The early regeneration of H. leucospilota body wall is associated with the degradation and subsequent reconstruction of the extracellular matrix. Pluripotency factors participate in the regenerative process. Multiple transcription factors involved in regulating cell proliferation were found to be gradually downregulated, indicating reduced cell proliferation. Moreover, genes related to development, stress response, apoptosis, and cell cytoskeleton formation were also involved in this process. Overall, this study provides new insights into the mechanisms of whole-body regeneration and uncover potential cross-species regenerative-related genes.
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Affiliation(s)
- Renhui Liu
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Xinyue Ren
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Junyan Wang
- School of Medicine, Foshan University, Foshan, 528000, People's Republic of China
| | - Ting Chen
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Xinyu Sun
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Tiehao Lin
- Guangdong Institute for Drug Control, Guangzhou, 510301, People's Republic of China
| | - Jiasheng Huang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Zhengyan Guo
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Ling Luo
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Chunhua Ren
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Peng Luo
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Chaoqun Hu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Xudong Cao
- Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, ON, 999040, Canada
| | - Aifen Yan
- School of Medicine, Foshan University, Foshan, 528000, People's Republic of China.
| | - Lihong Yuan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China.
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Paré L, Bideau L, Baduel L, Dalle C, Benchouaia M, Schneider SQ, Laplane L, Clément Y, Vervoort M, Gazave E. Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii. BMC Genomics 2023; 24:583. [PMID: 37784028 PMCID: PMC10546743 DOI: 10.1186/s12864-023-09602-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered. RESULTS We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process. CONCLUSIONS In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.
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Affiliation(s)
- Louis Paré
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loïc Bideau
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loeiza Baduel
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Caroline Dalle
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Médine Benchouaia
- Département de biologie, GenomiqueENS, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Stephan Q Schneider
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Lucie Laplane
- Université Paris I Panthéon-Sorbonne, CNRS UMR 8590 Institut d'Histoire et de Philosophie des Sciences et des Techniques (IHPST), Paris, France
- Gustave Roussy, UMR 1287, Villejuif, France
| | - Yves Clément
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France.
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Zhang S, Li X, Li X, Wang X, Ru S, Tian H. 17β-Trenbolone activates androgen receptor, upregulates transforming growth factor beta/bone morphogenetic protein and Wnt signaling pathways, and induces masculinization of caudal and anal fins in female guppies (Poecilia reticulata). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 263:106677. [PMID: 37677862 DOI: 10.1016/j.aquatox.2023.106677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 07/13/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Sexually mature female guppies (Poecilia reticulata) were exposed to environmentally relevant concentrations (20, 200, and 2000 ng/L) of 17β-trenbolone for four weeks. As evidenced by the increased caudal fin index and anal fins developing into gonopodium-like structures, exposed females displayed masculinized secondary sexual characteristics. Differential gene expression and subsequent pathway analysis of mRNA sequencing data revealed that the transcription of transforming growth factor beta/bone morphogenetic protein signaling pathway and Wnt signaling pathway were upregulated following 17β-trenbolone exposure. Enzyme-linked immunosorbent assays showed that the bone morphogenetic protein 7 protein content was elevated after 17β-trenbolone exposure. Finally, real-time PCR revealed that 17β-trenbolone treatment significantly increased androgen receptor mRNA levels, and molecular docking showed potent interaction between 17β-trenbolone and guppy androgen receptor. Furthermore, 17β-trenbolone-induced masculinization of caudal and anal fins in female guppies, concomitant to the upregulated expression of differentially expressed genes involved in the above-mentioned two signaling pathways, was significantly inhibited by flutamide (androgen receptor antagonist). These findings demonstrated that 17β-trenbolone masculinized fins of female guppies by activating the androgen receptor. This study revealed that 17β-trenbolone could upregulate signaling pathways related to fin growth and differentiation, and eventually cause caudal and anal fin masculinization in female guppies.
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Affiliation(s)
- Suqiu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Xinyu Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Xuefu Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China; College of Life Science, Langfang Normal University, Langfang 065000, Hebei province, China
| | - Xue Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Shaoguo Ru
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Hua Tian
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China.
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Chen F, Köhler M, Cucun G, Takamiya M, Kizil C, Cosacak MI, Rastegar S. sox1a:eGFP transgenic line and single-cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons. iScience 2023; 26:107342. [PMID: 37529101 PMCID: PMC10387610 DOI: 10.1016/j.isci.2023.107342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/03/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023] Open
Abstract
Sox transcription factors are crucial for vertebrate nervous system development. In zebrafish embryo, sox1 genes are expressed in neural progenitor cells and neurons of ventral spinal cord. Our recent study revealed that the loss of sox1a and sox1b function results in a significant decline of V2 subtype neurons (V2s). Using single-cell RNA sequencing, we analyzed the transcriptome of sox1a lineage progenitors and neurons in the zebrafish spinal cord at four time points during embryonic development, employing the Tg(sox1a:eGFP) line. In addition to previously characterized sox1a-expressing neurons, we discovered the expression of sox1a in late-developing intraspinal serotonergic neurons (ISNs). Developmental trajectory analysis suggests that ISNs arise from lateral floor plate (LFP) progenitor cells. Pharmacological inhibition of the Notch signaling pathway revealed its role in negatively regulating LFP progenitor cell differentiation into ISNs. Our findings highlight the zebrafish LFP as a progenitor domain for ISNs, alongside known Kolmer-Agduhr (KA) and V3 interneurons.
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Affiliation(s)
- Fushun Chen
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Melina Köhler
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gokhan Cucun
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032, USA
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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9
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Harper M, Hu Y, Donahue J, Acosta B, Dievenich Braes F, Nguyen S, Zeng J, Barbaro J, Lee H, Bui H, McMenamin SK. Thyroid hormone regulates proximodistal patterning in fin rays. Proc Natl Acad Sci U S A 2023; 120:e2219770120. [PMID: 37186843 PMCID: PMC10214145 DOI: 10.1073/pnas.2219770120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/26/2023] [Indexed: 05/17/2023] Open
Abstract
Processes that regulate size and patterning along an axis must be highly integrated to generate robust shapes; relative changes in these processes underlie both congenital disease and evolutionary change. Fin length mutants in zebrafish have provided considerable insight into the pathways regulating fin size, yet signals underlying patterning have remained less clear. The bony rays of the fins possess distinct patterning along the proximodistal axis, reflected in the location of ray bifurcations and the lengths of ray segments, which show progressive shortening along the axis. Here, we show that thyroid hormone (TH) regulates aspects of proximodistal patterning of the caudal fin rays, regardless of fin size. TH promotes distal gene expression patterns, coordinating ray bifurcations and segment shortening with skeletal outgrowth along the proximodistal axis. This distalizing role for TH is conserved between development and regeneration, in all fins (paired and medial), and between Danio species as well as distantly related medaka. During regenerative outgrowth, TH acutely induces Shh-mediated skeletal bifurcation. Zebrafish have multiple nuclear TH receptors, and we found that unliganded Thrab-but not Thraa or Thrb-inhibits the formation of distal features. Broadly, these results demonstrate that proximodistal morphology is regulated independently from size-instructive signals. Modulating proximodistal patterning relative to size-either through changes to TH metabolism or other hormone-independent pathways-can shift skeletal patterning in ways that recapitulate aspects of fin ray diversity found in nature.
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Affiliation(s)
- Melody Harper
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Yinan Hu
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Joan Donahue
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Benjamin Acosta
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Flora Dievenich Braes
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Stacy Nguyen
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Jenny Zeng
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Julianna Barbaro
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Hyungwoo Lee
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Hoa Bui
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
| | - Sarah K. McMenamin
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA02467
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10
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Jackson A, Lin SJ, Jones EA, Chandler KE, Orr D, Moss C, Haider Z, Ryan G, Holden S, Harrison M, Burrows N, Jones WD, Loveless M, Petree C, Stewart H, Low K, Donnelly D, Lovell S, Drosou K, Varshney GK, Banka S. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14. HGG ADVANCES 2023; 4:100186. [PMID: 37009414 PMCID: PMC10064225 DOI: 10.1016/j.xhgg.2023.100186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/27/2023] [Indexed: 06/11/2023] Open
Abstract
TSPEAR variants cause autosomal recessive ectodermal dysplasia (ARED) 14. The function of TSPEAR is unknown. The clinical features, the mutation spectrum, and the underlying mechanisms of ARED14 are poorly understood. Combining data from new and previously published individuals established that ARED14 is primarily characterized by dental anomalies such as conical tooth cusps and hypodontia, like those seen in individuals with WNT10A-related odontoonychodermal dysplasia. AlphaFold-predicted structure-based analysis showed that most of the pathogenic TSPEAR missense variants likely destabilize the β-propeller of the protein. Analysis of 100000 Genomes Project (100KGP) data revealed multiple founder TSPEAR variants across different populations. Mutational and recombination clock analyses demonstrated that non-Finnish European founder variants likely originated around the end of the last ice age, a period of major climatic transition. Analysis of gnomAD data showed that the non-Finnish European population TSPEAR gene-carrier rate is ∼1/140, making it one of the commonest AREDs. Phylogenetic and AlphaFold structural analyses showed that TSPEAR is an ortholog of drosophila Closca, an extracellular matrix-dependent signaling regulator. We, therefore, hypothesized that TSPEAR could have a role in enamel knot, a structure that coordinates patterning of developing tooth cusps. Analysis of mouse single-cell RNA sequencing (scRNA-seq) data revealed highly restricted expression of Tspear in clusters representing enamel knots. A tspeara -/-;tspearb -/- double-knockout zebrafish model recapitulated the clinical features of ARED14 and fin regeneration abnormalities of wnt10a knockout fish, thus suggesting interaction between tspear and wnt10a. In summary, we provide insights into the role of TSPEAR in ectodermal development and the evolutionary history, epidemiology, mechanisms, and consequences of its loss of function variants.
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Affiliation(s)
- Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Sheng-Jia Lin
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Elizabeth A. Jones
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Kate E. Chandler
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Orr
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Celia Moss
- Department of Dermatology, Birmingham Children’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Zahra Haider
- Department of Dermatology, Birmingham Children’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Simon Holden
- Clinical Genetics, Addenbrooke’s Hospital, Cambridge, UK
| | - Mike Harrison
- Department of Pediatric Dentistry, Guy’s and St Thomas' Dental Institute, London, UK
| | - Nigel Burrows
- Department of Dermatology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Wendy D. Jones
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, Great Ormond Street NHS Foundation Trust, London, UK
| | - Mary Loveless
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Cassidy Petree
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Karen Low
- Department of Clinical Genetics, St Michael’s Hospital, Bristol, UK
| | - Deirdre Donnelly
- Department of Genetic Medicine, Belfast HSC Trust, Lisburn Road, Belfast, UK
| | - Simon Lovell
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Konstantina Drosou
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, 99 Oxford Road, Manchester, UK
| | - Gaurav K. Varshney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
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11
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Samarasinghe S, Minh-Thai TN. A Comprehensive conceptual and computational dynamics framework for autonomous regeneration of form and function in biological organisms. PNAS NEXUS 2023; 2:pgac308. [PMID: 36845351 PMCID: PMC9944231 DOI: 10.1093/pnasnexus/pgac308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
In biology, regeneration is a mysterious phenomenon that has inspired self-repairing systems, robots, and biobots. It is a collective computational process whereby cells communicate to achieve an anatomical set point and restore original function in regenerated tissue or the whole organism. Despite decades of research, the mechanisms involved in this process are still poorly understood. Likewise, the current algorithms are insufficient to overcome this knowledge barrier and enable advances in regenerative medicine, synthetic biology, and living machines/biobots. We propose a comprehensive conceptual framework for the engine of regeneration with hypotheses for the mechanisms and algorithms of stem cell-mediated regeneration that enables a system like the planarian flatworm to fully restore anatomical (form) and bioelectric (function) homeostasis from any small- or large-scale damage. The framework extends the available regeneration knowledge with novel hypotheses to propose collective intelligent self-repair machines with multi-level feedback neural control systems driven by somatic and stem cells. We computationally implemented the framework to demonstrate the robust recovery of both form and function (anatomical and bioelectric homeostasis) in an in silico worm that, in a simple way, resembles the planarian. In the absence of complete regeneration knowledge, the framework contributes to understanding and generating hypotheses for stem cell mediated form and function regeneration, which may help advance regenerative medicine and synthetic biology. Further, as our framework is a bio-inspired and bio-computing self-repair machine, it may be useful for building self-repair robots/biobots and artificial self-repair systems.
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Affiliation(s)
| | - Tran Nguyen Minh-Thai
- Precision Agriculture Team, Lincoln Agritech Limited, PO Box 69133, Lincoln, New Zealand
- Department of Information Systems, College of Information and Communication Technology, Can Tho University, 3/2 Street, Ninh Kieu District, Can Tho, Vietnam
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12
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Bergen DJM, Maurizi A, Formosa MM, McDonald GLK, El-Gazzar A, Hassan N, Brandi ML, Riancho JA, Rivadeneira F, Ntzani E, Duncan EL, Gregson CL, Kiel DP, Zillikens MC, Sangiorgi L, Högler W, Duran I, Mäkitie O, Van Hul W, Hendrickx G. High Bone Mass Disorders: New Insights From Connecting the Clinic and the Bench. J Bone Miner Res 2023; 38:229-247. [PMID: 36161343 PMCID: PMC10092806 DOI: 10.1002/jbmr.4715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/05/2022] [Accepted: 09/22/2022] [Indexed: 02/04/2023]
Abstract
Monogenic high bone mass (HBM) disorders are characterized by an increased amount of bone in general, or at specific sites in the skeleton. Here, we describe 59 HBM disorders with 50 known disease-causing genes from the literature, and we provide an overview of the signaling pathways and mechanisms involved in the pathogenesis of these disorders. Based on this, we classify the known HBM genes into HBM (sub)groups according to uniform Gene Ontology (GO) terminology. This classification system may aid in hypothesis generation, for both wet lab experimental design and clinical genetic screening strategies. We discuss how functional genomics can shape discovery of novel HBM genes and/or mechanisms in the future, through implementation of omics assessments in existing and future model systems. Finally, we address strategies to improve gene identification in unsolved HBM cases and highlight the importance for cross-laboratory collaborations encompassing multidisciplinary efforts to transfer knowledge generated at the bench to the clinic. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Dylan J M Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, UK.,Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Antonio Maurizi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Melissa M Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta.,Center for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Georgina L K McDonald
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Ahmed El-Gazzar
- Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria
| | - Neelam Hassan
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | | | - José A Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evangelia Ntzani
- Department of Hygiene and Epidemiology, Medical School, University of Ioannina, Ioannina, Greece.,Center for Evidence Synthesis in Health, Policy and Practice, Center for Research Synthesis in Health, School of Public Health, Brown University, Providence, RI, USA.,Institute of Biosciences, University Research Center of loannina, University of Ioannina, Ioannina, Greece
| | - Emma L Duncan
- Department of Twin Research & Genetic Epidemiology, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Department of Endocrinology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Celia L Gregson
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Douglas P Kiel
- Marcus Institute for Aging Research, Hebrew SeniorLife and Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Luca Sangiorgi
- Department of Rare Skeletal Diseases, IRCCS Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Wolfgang Högler
- Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | | | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Centre, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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13
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Johnson GL, Glasser MB, Charles JF, Duryea J, Lehoczky JA. En1 and Lmx1b do not recapitulate embryonic dorsal-ventral limb patterning functions during mouse digit tip regeneration. Cell Rep 2022; 41:111701. [PMID: 36417876 PMCID: PMC9727699 DOI: 10.1016/j.celrep.2022.111701] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/09/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The mouse digit tip regenerates following amputation. How the regenerate is patterned is unknown, but a long-standing hypothesis proposes developmental patterning mechanisms are re-used during regeneration. The digit tip bone exhibits dorsal-ventral (DV) polarity, so we focus on En1 and Lmx1b, two factors necessary for DV patterning during limb development. We investigate whether they are re-expressed during regeneration in a developmental-like pattern and whether they direct DV morphology of the regenerate. We find that both En1 and Lmx1b are expressed in the regenerating digit tip epithelium and mesenchyme, respectively, but without DV polarity. Conditional genetics and quantitative analysis of digit tip bone morphology determine that genetic deletion of En1 or Lmx1b in adult digit tip regeneration modestly reduces bone regeneration but does not affect DV patterning. Collectively, our data suggest that, while En1 and Lmx1b are re-expressed during mouse digit tip regeneration, they do not define the DV axis during regeneration.
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Affiliation(s)
- Gemma L. Johnson
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Morgan B. Glasser
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Julia F. Charles
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jeffrey Duryea
- Department of Radiology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jessica A. Lehoczky
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Lead contact,Correspondence:
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14
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Patel JH, Ong DJ, Williams CR, Callies LK, Wills AE. Elevated pentose phosphate pathway flux supports appendage regeneration. Cell Rep 2022; 41:111552. [PMID: 36288713 PMCID: PMC10569227 DOI: 10.1016/j.celrep.2022.111552] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/01/2022] [Accepted: 10/03/2022] [Indexed: 11/18/2022] Open
Abstract
A fundamental step in regeneration is rapid growth to replace lost tissue. Cells must generate sufficient lipids, nucleotides, and proteins to fuel rapid cell division. To define metabolic pathways underlying regenerative growth, we undertake a multimodal investigation of metabolic reprogramming in Xenopus tropicalis appendage regeneration. Regenerating tissues have increased glucose uptake; however, inhibition of glycolysis does not decrease regeneration. Instead, glucose is funneled to the pentose phosphate pathway (PPP), which is essential for full tail regeneration. Liquid chromatography-mass spectrometry (LC-MS) metabolite profiling reveals increased nucleotide and nicotinamide intermediates required for cell division. Using single-cell RNA sequencing (scRNA-seq), we find that highly proliferative cells have increased transcription of PPP enzymes and not glycolytic enzymes. Further, PPP inhibition results in decreased cell division specifically in regenerating tissue. Our results inform a model wherein regenerating tissues direct glucose toward the PPP, yielding nucleotide precursors to drive regenerative cell proliferation.
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Affiliation(s)
- Jeet H Patel
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Program in Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, WA, USA
| | - Daniel J Ong
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Claire R Williams
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - LuLu K Callies
- Program in Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrea E Wills
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Program in Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
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15
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Liedtke D, Klopocki E. Microarray expression profiling of fndc3a zebrafish mutants. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000646. [PMID: 36254247 PMCID: PMC9568745 DOI: 10.17912/micropub.biology.000646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
The group of Fibronectin type III domain-containing (FNDC; InterPro IPR003961) protein super family splits into a large number of gene-orthologues and mediates a variety of cellular functions during development and disease. They act as anti-inflammatory factors, are linked to cell-cell-interactions, regulate cell signaling and are associated with different cancer types, like cervical and colorectal. One member of this gene family is FNDC3A , which influences different developmental processes in vertebrates, like Sertoli cell/spermatid adhesion in mice testis, bone traits in chicken, and fin development in zebrafish. To identify downstream molecular processes during vertebrate development we investigated gene expression profiles in the previously established fndc3a zebrafish mutants via microarray analyses on 22 hpf embryos (26-somite stage). Our analyses imply distinct transcriptional profiles between genotype groups and hint to altered cell binding and catalytic activity in fndc3a mutants.
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Affiliation(s)
- Daniel Liedtke
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany
,
Correspondence to: Daniel Liedtke (
)
| | - Eva Klopocki
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany
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16
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Ouyang T, Yin H, Yang J, Liu Y, Ma S. Tissue regeneration effect of betulin via inhibition of ROS/MAPKs/NF-ĸB axis using zebrafish model. Biomed Pharmacother 2022; 153:113420. [DOI: 10.1016/j.biopha.2022.113420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 11/02/2022] Open
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17
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Patel S, Ranadive I, Buch P, Khaire K, Balakrishnan S. De Novo Transcriptome Sequencing and Analysis of Differential Gene Expression among Various Stages of Tail Regeneration in Hemidactylus flaviviridis. J Dev Biol 2022; 10:jdb10020024. [PMID: 35735915 PMCID: PMC9225231 DOI: 10.3390/jdb10020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
Across the animal kingdom, lizards are the only amniotes capable of regenerating their lost tail through epimorphosis. Of the many reptiles, the northern house gecko, Hemidactylus flaviviridis, is an excellent model system that is used for understanding the mechanism of epimorphic regeneration. A stage-specific transcriptome profile was generated in the current study following an autotomized tail with the HiSeq2500 platform. The reads obtained from de novo sequencing were filtered and high-quality reads were considered for gene ontology (GO) annotation and pathway analysis. Millions of reads were recorded for each stage upon de novo assembly. Up and down-regulated transcripts were categorized for early blastema (EBL), blastema (BL) and differentiation (DF) stages compared to the normal tail (NT) by differential gene expression analysis. The transcripts from developmentally significant pathways such as FGF, Wnt, Shh and TGF-β/BMP were present during tail regeneration. Additionally, differential expression of transcripts was recorded from biological processes, namely inflammation, cell proliferation, apoptosis and cell migration. Overall, the study reveals the stage-wise transcriptome analysis in conjunction with cellular processes as well as molecular signaling pathways during lizard tail regeneration. The knowledge obtained from the data can be extrapolated to configure regenerative responses in other amniotes, including humans, upon loss of a complex organ.
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18
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Otsuki L, Tanaka EM. Positional Memory in Vertebrate Regeneration: A Century's Insights from the Salamander Limb. Cold Spring Harb Perspect Biol 2022; 14:a040899. [PMID: 34607829 PMCID: PMC9248832 DOI: 10.1101/cshperspect.a040899] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Salamanders, such as axolotls and newts, can regenerate complex tissues including entire limbs. But what mechanisms ensure that an amputated limb regenerates a limb, and not a tail or unpatterned tissue? An important concept in regeneration is positional memory-the notion that adult cells "remember" spatial identities assigned to them during embryogenesis (e.g., "head" or "hand") and use this information to restore the correct body parts after injury. Although positional memory is well documented at a phenomenological level, the underlying cellular and molecular bases are just beginning to be decoded. Herein, we review how major principles in positional memory were established in the salamander limb model, enabling the discovery of positional memory-encoding molecules, and advancing insights into their pattern-forming logic during regeneration. We explore findings in other amphibians, fish, reptiles, and mammals and speculate on conserved aspects of positional memory. We consider the possibility that manipulating positional memory in human cells could represent one route toward improved tissue repair or engineering of patterned tissues for therapeutic purposes.
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Affiliation(s)
- Leo Otsuki
- Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Elly M Tanaka
- Research Institute of Molecular Pathology, 1030 Vienna, Austria
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19
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Ulhaq ZS, Tse WKF. A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration. Biomolecules 2021; 12:biom12010035. [PMID: 35053182 PMCID: PMC8773715 DOI: 10.3390/biom12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Unlike mammals, zebrafish are capable to regenerate many of their organs, however, the response of tissue damage varies across tissues. Understanding the molecular mechanism behind the robust regenerative capacity in a model organism may help to identify and develop novel treatment strategies for mammals (including humans). Hence, we systematically analyzed the current literature on the proteome profile collected from different regenerated zebrafish tissues. Our analyses underlining that several proteins and protein families responsible as a component of cytoskeleton and structure, protein synthesis and degradation, cell cycle control, and energy metabolism were frequently identified. Moreover, target proteins responsible for the initiation of the regeneration process, such as inflammation and immune response were less frequently detected. This highlights the limitation of previous proteomic analysis and suggested a more sensitive modern proteomics analysis is needed to unfold the mechanism. This brief report provides a list of target proteins with predicted functions that could be useful for further biological studies.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University of Malang, Batu 65144, Indonesia;
- National Research and Innovation Agency, Central Jakarta 10340, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence:
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20
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Wandy J, Daly R. GraphOmics: an interactive platform to explore and integrate multi-omics data. BMC Bioinformatics 2021; 22:603. [PMID: 34922446 PMCID: PMC8684259 DOI: 10.1186/s12859-021-04500-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND An increasing number of studies now produce multiple omics measurements that require using sophisticated computational methods for analysis. While each omics data can be examined separately, jointly integrating multiple omics data allows for deeper understanding and insights to be gained from the study. In particular, data integration can be performed horizontally, where biological entities from multiple omics measurements are mapped to common reactions and pathways. However, data integration remains a challenge due to the complexity of the data and the difficulty in interpreting analysis results. RESULTS Here we present GraphOmics, a user-friendly platform to explore and integrate multiple omics datasets and support hypothesis generation. Users can upload transcriptomics, proteomics and metabolomics data to GraphOmics. Relevant entities are connected based on their biochemical relationships, and mapped to reactions and pathways from Reactome. From the Data Browser in GraphOmics, mapped entities and pathways can be ranked, sorted and filtered according to their statistical significance (p values) and fold changes. Context-sensitive panels provide information on the currently selected entities, while interactive heatmaps and clustering functionalities are also available. As a case study, we demonstrated how GraphOmics was used to interactively explore multi-omics data and support hypothesis generation using two complex datasets from existing Zebrafish regeneration and Covid-19 human studies. CONCLUSIONS GraphOmics is fully open-sourced and freely accessible from https://graphomics.glasgowcompbio.org/ . It can be used to integrate multiple omics data horizontally by mapping entities across omics to reactions and pathways. Our demonstration showed that by using interactive explorations from GraphOmics, interesting insights and biological hypotheses could be rapidly revealed.
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Affiliation(s)
- Joe Wandy
- Glasgow Polyomics, University of Glasgow, Glasgow, G61 1BD, UK
| | - Rónán Daly
- Glasgow Polyomics, University of Glasgow, Glasgow, G61 1BD, UK.
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21
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Khajavi M, Zhou Y, Schiffer AJ, Bazinet L, Birsner AE, Zon L, D'Amato RJ. Identification of Basp1 as a novel angiogenesis-regulating gene by multi-model system studies. FASEB J 2021; 35:e21404. [PMID: 33899275 DOI: 10.1096/fj.202001936rrr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 01/23/2023]
Abstract
We have previously used the genetic diversity available in common inbred mouse strains to identify quantitative trait loci (QTLs) responsible for the differences in angiogenic response using the corneal micropocket neovascularization (CoNV) assay. Employing a mouse genome-wide association study (GWAS) approach, the region on chromosome 15 containing Basp1 was identified as being significantly associated with angiogenesis in inbred strains. Here, we developed a unique strategy to determine and verify the role of BASP1 in angiogenic pathways. Basp1 expression in cornea had a strong correlation with a haplotype shared by mouse strains with varied angiogenic phenotypes. In addition, inhibition of BASP1 demonstrated a dosage-dependent effect in both primary mouse brain endothelial and human microvascular endothelial cell (HMVEC) migration. To investigate its role in vivo, we knocked out basp1 in transgenic kdrl:zsGreen zebrafish embryos using a widely adopted CRISPR-Cas9 system. These embryos had severely disrupted vessel formation compared to control siblings. We further show that basp1 promotes angiogenesis by upregulating β-catenin gene and the Dll4/Notch1 signaling pathway. These results, to the best of our knowledge, provide the first in vivo evidence to indicate the role of Basp1 as an angiogenesis-regulating gene and opens the potential therapeutic avenues for a wide variety of systemic angiogenesis-dependent diseases.
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Affiliation(s)
- Mehrdad Khajavi
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Zhou
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Alex J Schiffer
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren Bazinet
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy E Birsner
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonard Zon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - Robert J D'Amato
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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22
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Stewart S, Le Bleu HK, Yette GA, Henner AL, Robbins AE, Braunstein JA, Stankunas K. longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth. Development 2021; 148:dev199384. [PMID: 34061172 PMCID: PMC8217709 DOI: 10.1242/dev.199384] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
Organs stop growing to achieve a characteristic size and shape in scale with the body of an animal. Likewise, regenerating organs sense injury extents to instruct appropriate replacement growth. Fish fins exemplify both phenomena through their tremendous diversity of form and remarkably robust regeneration. The classic zebrafish mutant longfint2 develops and regenerates dramatically elongated fins and underlying ray skeleton. We show longfint2 chromosome 2 overexpresses the ether-a-go-go-related voltage-gated potassium channel kcnh2a. Genetic disruption of kcnh2a in cis rescues longfint2, indicating longfint2 is a regulatory kcnh2a allele. We find longfint2 fin overgrowth originates from prolonged outgrowth periods by showing Kcnh2a chemical inhibition during late stage regeneration fully suppresses overgrowth. Cell transplantations demonstrate longfint2-ectopic kcnh2a acts tissue autonomously within the fin intra-ray mesenchymal lineage. Temporal inhibition of the Ca2+-dependent phosphatase calcineurin indicates it likewise entirely acts late in regeneration to attenuate fin outgrowth. Epistasis experiments suggest longfint2-expressed Kcnh2a inhibits calcineurin output to supersede growth cessation signals. We conclude ion signaling within the growth-determining mesenchyme lineage controls fin size by tuning outgrowth periods rather than altering positional information or cell-level growth potency.
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Affiliation(s)
- Scott Stewart
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Heather K. Le Bleu
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Gabriel A. Yette
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Astra L. Henner
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Amy E. Robbins
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Joshua A. Braunstein
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
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23
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Meehan SD, Abdelrahman L, Arcuri J, Park KK, Samarah M, Bhattacharya SK. Proteomics and systems biology in optic nerve regeneration. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:249-270. [PMID: 34340769 DOI: 10.1016/bs.apcsb.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We present an overview of current state of proteomic approaches as applied to optic nerve regeneration in the historical context of nerve regeneration particularly central nervous system neuronal regeneration. We present outlook pertaining to the optic nerve regeneration proteomics that the latter can extrapolate information from multi-systems level investigations. We present an account of the current need of systems level standardization for comparison of proteome from various models and across different pharmacological or biophysical treatments that promote adult neuron regeneration. We briefly overview the need for deriving knowledge from proteomics and integrating with other omics to obtain greater biological insight into process of adult neuron regeneration in the optic nerve and its potential applicability to other central nervous system neuron regeneration.
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Affiliation(s)
- Sean D Meehan
- Molecular and Cellular Pharmacology Graduate Program, University of Miami, Miami, FL, United States; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, United States
| | - Leila Abdelrahman
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States; Department of Electrical and Computer Engineering, University of Miami, Miami, FL, United States
| | - Jennifer Arcuri
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States; Molecular and Cellular Pharmacology Graduate Program, University of Miami, Miami, FL, United States; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, United States
| | - Kevin K Park
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, United States; Miami Project to Cure Paralysis, University of Miami, Miami, FL, United States
| | | | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States; Molecular and Cellular Pharmacology Graduate Program, University of Miami, Miami, FL, United States; Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, United States.
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24
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Bioelectric signaling: Reprogrammable circuits underlying embryogenesis, regeneration, and cancer. Cell 2021; 184:1971-1989. [PMID: 33826908 DOI: 10.1016/j.cell.2021.02.034] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/08/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022]
Abstract
How are individual cell behaviors coordinated toward invariant large-scale anatomical outcomes in development and regeneration despite unpredictable perturbations? Endogenous distributions of membrane potentials, produced by ion channels and gap junctions, are present across all tissues. These bioelectrical networks process morphogenetic information that controls gene expression, enabling cell collectives to make decisions about large-scale growth and form. Recent progress in the analysis and computational modeling of developmental bioelectric circuits and channelopathies reveals how cellular collectives cooperate toward organ-level structural order. These advances suggest a roadmap for exploiting bioelectric signaling for interventions addressing developmental disorders, regenerative medicine, cancer reprogramming, and synthetic bioengineering.
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25
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Bideau L, Kerner P, Hui J, Vervoort M, Gazave E. Animal regeneration in the era of transcriptomics. Cell Mol Life Sci 2021; 78:3941-3956. [PMID: 33515282 PMCID: PMC11072743 DOI: 10.1007/s00018-021-03760-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 12/27/2022]
Abstract
Animal regeneration, the ability to restore a lost body part, is a process that has fascinated scientists for centuries. In this review, we first present what regeneration is and how it relates to development, as well as the widespread and diverse nature of regeneration in animals. Despite this diversity, animal regeneration includes three common mechanistic steps: initiation, induction and activation of progenitors, and morphogenesis. In this review article, we summarize and discuss, from an evolutionary perspective, the recent data obtained for a variety of regeneration models which have allowed to identify key shared mechanisms that control these main steps of animal regeneration. This review also synthesizes the wealth of high-throughput mRNA sequencing data (bulk mRNA-seq) concerning regeneration which have been obtained in recent years, highlighting the major advances in the regeneration field that these studies have revealed. We stress out that, through a comparative approach, these data provide opportunities to further shed light on the evolution of regeneration in animals. Finally, we point out how the use of single-cell mRNA-seq technology and integration with epigenomic approaches may further help researchers to decipher mechanisms controlling regeneration and their evolution in animals.
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Affiliation(s)
- Loïc Bideau
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Pierre Kerner
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
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26
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Kurup K, Matyi S, Giles CB, Wren JD, Jones K, Ericsson A, Raftery D, Wang L, Promislow D, Richardson A, Unnikrishnan A. Calorie restriction prevents age-related changes in the intestinal microbiota. Aging (Albany NY) 2021; 13:6298-6329. [PMID: 33744869 PMCID: PMC7993711 DOI: 10.18632/aging.202753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/19/2021] [Indexed: 12/14/2022]
Abstract
The effect of calorie restriction (CR) on the microbiome, fecal metabolome, and colon transcriptome of adult and old male mice was compared. Life-long CR increased microbial diversity and the Bacteroidetes/Firmicutes ratio and prevented the age-related changes in the microbiota, shifting it to a younger microbial and fecal metabolite profile in both C57BL/6JN and B6D2F1 mice. Old mice fed CR were enriched in the Rikenellaceae, S24-7 and Bacteroides families. The changes in the microbiome that occur with age and CR were initiated in the cecum and further modified in the colon. Short-term CR in adult mice had a minor effect on the microbiome but a major effect on the transcriptome of the colon mucosa. These data suggest that CR has a major impact on the physiological status of the gastrointestinal system, maintaining it in a more youthful state, which in turn could result in a more diverse and youthful microbiome.
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Affiliation(s)
- Kavitha Kurup
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Stephanie Matyi
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Cory B. Giles
- Genes and Human Diseases Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Genes and Human Diseases Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Oklahoma Center for Geoscience and Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kenneth Jones
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Harold Hamm Diabetes Center, Oklahoma City, OK 73104, USA
| | - Aaron Ericsson
- University of Missouri Metagenomics Center, University of Missouri, Columbia, MO 65211, USA
| | - Daniel Raftery
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Promislow
- Department of Lab Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Arlan Richardson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Oklahoma Center for Geoscience and Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Oklahoma City VA Medical Center, Oklahoma City, OK 73104, USA
| | - Archana Unnikrishnan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Oklahoma Center for Geoscience and Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Harold Hamm Diabetes Center, Oklahoma City, OK 73104, USA
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27
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Wang B, Farooq Z, Chu L, Liu J, Wang H, Guo J, Tu J, Ma C, Dai C, Wen J, Shen J, Fu T, Yi B. High-generation near-isogenic lines combined with multi-omics to study the mechanism of polima cytoplasmic male sterility. BMC PLANT BIOLOGY 2021; 21:130. [PMID: 33673810 PMCID: PMC7934456 DOI: 10.1186/s12870-021-02852-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/24/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS), which naturally exists in higher plants, is a useful mechanism for analyzing nuclear and mitochondrial genome functions and identifying the role of mitochondrial genes in the plant growth and development. Polima (pol) CMS is the most universally valued male sterility type in oil-seed rape. Previous studies have described the pol CMS restorer gene Rfp and the sterility-inducing gene orf224 in oil-seed rape, located in mitochondria. However, the mechanism of fertility restoration and infertility remains unknown. Moreover, it is still unknown how the fecundity restorer gene interferes with the sterility gene, provokes the sterility gene to lose its function, and leads to fertility restoration. RESULT In this study, we used multi-omics joint analysis to discover candidate genes that interact with the sterility gene orf224 and the restorer gene Rfp of pol CMS to provide theoretical support for the occurrence and restoration mechanisms of sterility. Via multi-omics analysis, we screened 24 differential genes encoding proteins related to RNA editing, respiratory electron transport chain, anther development, energy transport, tapetum development, and oxidative phosphorylation. Using a yeast two-hybrid assay, we obtained a total of seven Rfp interaction proteins, with orf224 protein covering five interaction proteins. CONCLUSIONS We propose that Rfp and its interacting protein cleave the transcript of atp6/orf224, causing the infertility gene to lose its function and restore fertility. When Rfp is not cleaved, orf224 poisons the tapetum cells and anther development-related proteins, resulting in pol CMS mitochondrial dysfunction and male infertility. The data from the joint analysis of multiple omics provided information on pol CMS's potential molecular mechanism and will help breed B. napus hybrids.
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Affiliation(s)
- Benqi Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Chu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Guo
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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28
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Daponte V, Tylzanowski P, Forlino A. Appendage Regeneration in Vertebrates: What Makes This Possible? Cells 2021; 10:cells10020242. [PMID: 33513779 PMCID: PMC7911911 DOI: 10.3390/cells10020242] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ability to regenerate amputated or injured tissues and organs is a fascinating property shared by several invertebrates and, interestingly, some vertebrates. The mechanism of evolutionary loss of regeneration in mammals is not understood, yet from the biomedical and clinical point of view, it would be very beneficial to be able, at least partially, to restore that capability. The current availability of new experimental tools, facilitating the comparative study of models with high regenerative ability, provides a powerful instrument to unveil what is needed for a successful regeneration. The present review provides an updated overview of multiple aspects of appendage regeneration in three vertebrates: lizard, salamander, and zebrafish. The deep investigation of this process points to common mechanisms, including the relevance of Wnt/β-catenin and FGF signaling for the restoration of a functional appendage. We discuss the formation and cellular origin of the blastema and the identification of epigenetic and cellular changes and molecular pathways shared by vertebrates capable of regeneration. Understanding the similarities, being aware of the differences of the processes, during lizard, salamander, and zebrafish regeneration can provide a useful guide for supporting effective regenerative strategies in mammals.
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Affiliation(s)
- Valentina Daponte
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
| | - Przemko Tylzanowski
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, University of Leuven, 3000 Leuven, Belgium;
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Antonella Forlino
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
- Correspondence: ; Tel.: +39-0382-987235
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29
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Meyer-Alert H, Wiseman S, Tang S, Hecker M, Hollert H. Identification of molecular toxicity pathways across early life-stages of zebrafish exposed to PCB126 using a whole transcriptomics approach. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111716. [PMID: 33396047 DOI: 10.1016/j.ecoenv.2020.111716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Although withdrawn from the market in the 1980s, polychlorinated biphenyls (PCBs) are still found ubiquitously in the aquatic environment and pose a serious risk to biota due to their teratogenic potential. In fish, early life-stages are often considered most sensitive with regard to their exposure to PCBs and other dioxin-like compounds. However, little is known about the molecular drivers of the frequently observed teratogenic effects. Therefore, the aims of our study were to: (1) characterize the baseline transcriptome profiles at different embryonic life-stages in zebrafish (Danio rerio); and (2) to identify the molecular response to PCB exposure and life-stage specific-effects of the chemical on associated processes. For both objectives, embryos were sampled at 12, 48, and 96 h post-fertilization (hpf) and subjected to Illumina sequence-by-synthesis and RNAseq analysis. Results revealed that with increasing age more genes and related pathways were upregulated both in terms of number and magnitude. Yet, other transcripts followed an opposite pattern with greater transcript abundance at the earlier time points. Additionally, embryos were exposed to PCB126, a potent agonist of the aryl hydrocarbon receptor (AHR). ClueGO network analysis revealed significant enrichment of genes associated with basic cell metabolism, communication, and homeostasis as well as eye development, muscle formation, and skeletal formation. We selected eight genes involved in the affected pathways for an in-depth characterization of their regulation throughout normal embryogenesis and after exposure to PCB126 by quantification of transcript abundances every 12 h until 118 hpf. Among these, fgf7 and c9 stood out because of their strong upregulation by PCB126 exposure at 48 and 96 hpf, respectively. Cyp2aa12 was upregulated from 84 hpf on. Fabp10ab, myhz1.1, col8a1a, sulf1, and opn1sw1 displayed specific regulation depending on the developmental stage. Overall, we demonstrate that (1) the developmental transcriptome of zebrafish is highly dynamic, and (2) dysregulation of gene expression by exposure to PCB126 was significant and in several cases not directly connected to AHR-signaling. Hence, this study improves the understanding of linkages between molecular events and apical outcomes that are of regulatory relevance.
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Affiliation(s)
- Henriette Meyer-Alert
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Steve Wiseman
- Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, Saskatchewan S7N 5B3, Canada; Department of Biological Sciences and Water Institute for Sustainable Environments (WISE), University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Song Tang
- Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, Saskatchewan S7N 5B3, Canada; National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166 Jiangsu, China
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Henner Hollert
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
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30
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The transcriptome of anterior regeneration in earthworm Eudrilus eugeniae. Mol Biol Rep 2020; 48:259-283. [PMID: 33306150 DOI: 10.1007/s11033-020-06044-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/28/2020] [Indexed: 12/25/2022]
Abstract
The oligochaete earthworm, Eudrilus eugeniae is capable of regenerating both anterior and posterior segments. The present study focuses on the transcriptome analysis of earthworm E. eugeniae to identify and functionally annotate the key genes supporting the anterior blastema formation and regulating the anterior regeneration of the worm. The Illumina sequencing generated a total of 91,593,182 raw reads which were assembled into 105,193 contigs using CLC genomics workbench. In total, 40,946 contigs were annotated against the NCBI nr and SwissProt database and among them, 15,702 contigs were assigned to 14,575 GO terms. Besides a total of 9389 contigs were mapped to 416 KEGG biological pathways. The RNA-Seq comparison study identified 10,868 differentially expressed genes (DEGs) and of them, 3986 genes were significantly upregulated in the anterior regenerated blastema tissue samples of the worm. The GO enrichment analysis showed angiogenesis and unfolded protein binding as the top enriched functions and the pathway enrichment analysis denoted TCA cycle as the most significantly enriched pathway associated with the upregulated gene dataset of the worm. The identified DEGs and their function and pathway information can be effectively utilized further to interpret the key cellular, genetic and molecular events associated with the regeneration of the worm.
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31
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Li G, Zhao H, Guo H, Wang Y, Cui X, Xu B, Guo X. Functional and transcriptomic analyses of the NF-Y family provide insights into the defense mechanisms of honeybees under adverse circumstances. Cell Mol Life Sci 2020; 77:4977-4995. [PMID: 32016487 PMCID: PMC11104996 DOI: 10.1007/s00018-019-03447-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 12/02/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
As predominant pollinators, honeybees are important for crop production and terrestrial ecosystems. Recently, various environmental stresses have led to large declines in honeybee populations in many regions. The ability of honeybees to respond to these stresses is critical for their survival. However, the details of the stress defense mechanisms of honeybees have remained elusive. Here, we found that the Nuclear Factor Y (NF-Y) family (containing NF-YA, NF-YB, and NF-YC) is a novel stress mediator family that regulates honeybee environmental stress resistance. NF-YA localized in the nucleus, NF-YB accumulated in the cytoplasm, and NF-YC presented in both the nucleus and cytoplasm. NF-YC interacted with NF-YA and NF-YB in vitro and in vivo, and the nuclear import of NF-YB relied on its interaction with NF-YC. We further found that the expression of NF-Y was induced under multiple stress conditions. In addition, NF-Y regulated many stress responses and antioxidant genes at the transcriptome-wide level, and knockdown of NF-Y repressed the expression of stress-inducible genes, particularly LOC108003540 and LOC107994062, under adverse circumstances. Silencing NF-Y lowered honeybee stress resistance by reducing total antioxidant capacity and enhancing oxidative impairment. Collectively, these results indicate that NF-Y plays important roles in stress responses. Our study sheds light on the underlying defense mechanisms of honeybees under environmental stress.
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Affiliation(s)
- Guilin Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Hang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Hongbin Guo
- Statistics Department, University of Auckland, 38 Princes Street, Auckland, New Zealand
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Xuepei Cui
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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32
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Gu L, Tian L, Gao G, Peng S, Zhang J, Wu D, Huang J, Hua Q, Lu T, Zhong L, Fu Z, Pan X, Qian H, Sun L. Inhibitory effects of polystyrene microplastics on caudal fin regeneration in zebrafish larvae. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:114664. [PMID: 32768670 DOI: 10.1016/j.envpol.2020.114664] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Microplastic pollution is pervasive in aquatic environments, but the potential effects of microplastics on aquatic organisms are still under debate. Given that tissue damage is unavoidable in fish and the available data mostly concentrate on healthy fish, there is a large chance that the ecotoxicological risk of microplastic pollution is underrated. Therefore, in this study, the effects of microplastics on the regenerative capacity of injured fish were investigated using a zebrafish caudal fin regeneration model. After fin amputation at 72 h post fertilization, the larvae were exposed to polystyrene microplastics (0.1-10 mg/L) with diameters of 50 or 500 nm. Microplastic exposure significantly inhibited fin regeneration, both morphologically and functionally. Furthermore, the signaling networks that regulate fin regeneration, as well as reactive oxygen species signaling and the immune response, both of which are essential for tissue repair and regeneration, were altered. Transcriptomic analyses of the regenerating fin confirmed that genes related to fin regeneration were transcriptionally modulated in response to microplastic exposure and that metabolic pathways were also extensively involved. In conclusion, this study demonstrated for the first time that microplastic exposure could disrupt the regenerative capacity of fish and might eventually impair their fitness in the wild.
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Affiliation(s)
- Linqi Gu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Li Tian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Gan Gao
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Shaohong Peng
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jieyu Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Di Wu
- Department of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, 211166, PR China
| | - Jing Huang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qing Hua
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Li Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Li G, Zhao H, Guo H, Wang Y, Cui X, Li H, Xu B, Guo X. Analyses of the function of DnaJ family proteins reveal an underlying regulatory mechanism of heat tolerance in honeybee. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:137036. [PMID: 32059293 DOI: 10.1016/j.scitotenv.2020.137036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
There is clear evidence of severe honeybee declines in recent years, and parallel declines of plant community and crop productivity that rely on them. Different stresses, including heat stress, are among the primary drivers of this decline. However, the mechanisms by which honeybees respond to heat stress are elusive. Though heat shock proteins (Hsps) play important roles in heat stress response, the function of DnaJs (a subfamily of Hsps) is unclear. Here, we aimed to determine the underlying regulatory mechanism of honeybees to heat stress mediated by DnaJs. We found that several DnaJ genes, including DnaJA1, DnaJB12 and DnaJC8, are key for honeybee heat tolerance. DnaJA1 and DnaJB12 are cytoplasmic proteins, and DnaJC8 is a nuclear protein. The expression of DnaJA1, DnaJB12 and DnaJC8 was induced at different levels under short-term and long-term heat stress. Phenotypic analysis indicated that DnaJA1, DnaJB12 and DnaJC8 knockdown attenuated honeybee heat resistance. In addition, DnaJA1 participated in the heat stress response by upregulating many heat-inducible genes at the transcriptome-wide level, especially LOC108002668 and LOC107995148. Importantly, the upregulation of LOC108002668 and LOC107995148 was significantly repressed under heat stress when DnaJA1 was knocked down. We also found that knockdown of DnaJA1, DnaJB12 and DnaJC8 decreased antioxidant defense ability and increased the degree of oxidative damage in the honeybee. Taken together, our results indicate that DnaJ genes play important roles under heat stress in the honeybee. Overexpression of DnaJ genes may protect honeybees from heat stress-induced injuries and increase their survival rate.
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Affiliation(s)
- Guilin Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Hang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Hongbin Guo
- Statistics Department, University of Auckland, 38 Princes Street, Auckland, New Zealand
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Xuepei Cui
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Han Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China.
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34
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Harris MP, Daane JM, Lanni J. Through veiled mirrors: Fish fins giving insight into size regulation. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e381. [PMID: 32323915 DOI: 10.1002/wdev.381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/13/2020] [Accepted: 03/19/2020] [Indexed: 12/25/2022]
Abstract
Faithful establishment and maintenance of proportion is seen across biological systems and provides a glimpse at fundamental rules of scaling that underlie development and evolution. Dysregulation of proportion is observed in a range of human diseases and growth disorders, indicating that proper scaling is an essential component of normal anatomy and physiology. However, when viewed through an evolutionary lens, shifts in the regulation of relative proportion are one of the most striking sources of morphological diversity among organisms. To date, the mechanisms via which relative proportion is specified and maintained remain unclear. Through the application of powerful experimental, genetic and molecular approaches, the teleost fin has provided an effective model to investigate the regulation of scaling, size, and relative growth in vertebrate organisms. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Comparative Development and Evolution > Regulation of Organ Diversity.
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Affiliation(s)
- Matthew P Harris
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jacob M Daane
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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35
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Li XY, Hou HT, Chen HX, Liu XC, Wang J, Yang Q, He GW. Preoperative plasma biomarkers associated with atrial fibrillation after coronary artery bypass surgery. J Thorac Cardiovasc Surg 2020; 162:851-863.e3. [PMID: 32197906 DOI: 10.1016/j.jtcvs.2020.01.079] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/15/2020] [Accepted: 01/29/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Postoperative atrial fibrillation (POAF) is a common complication in coronary artery bypass grafting (CABG) procedures. This prospective study aimed to investigate predisposition of proteins and metabolites correlated to POAF after CABG and related cellular pathways. METHODS Preoperative plasma samples from patients undergoing CABG procedures were prospectively collected. After CABG, the patients were grouped to POAF or sinus rhythm (N = 170; n = 90 in the discovery set and n = 80 in the validation set). The plasma samples were analyzed using proteomics, metabolomics, and bioinformatics to identify the differential proteins and differential metabolites. The correlation between differential proteins and POAF was also investigated by multivariable regression analysis and receiver operator characteristic analysis. RESULTS In the POAF(+) group, 29 differential proteins and 61 differential metabolites were identified compared with the POAF(-) group. The analysis of integrated omics revealed that preoperative alteration of peroxisome proliferators-activated receptor α and glutathione metabolism pathways increased the susceptibility of POAF after CABG. There was a correlation between plasma levels of apolipoprotein-C3, phospholipid transfer protein, glutathione peroxidase 3, cholesteryl ester transfer protein, and POAF. CONCLUSIONS The present study for first time at multi-omics levels explored the mechanism of POAF and validated the results in a new cohort of patients, suggesting preexisting differential proteins and differential metabolites in the plasma of patients prone to POAF after CABG. Dysregulation of peroxisome proliferators-activated receptor α and glutathione metabolism pathways related to metabolic remodeling and redox imbalance-associated electrical remodeling may play a key role in the pathogenesis of POAF. Lower plasma phospholipid transfer protein, apolipoprotein-C3, higher cholesteryl ester transfer protein and glutathione peroxidase 3 levels are linked with POAF. These proteins/metabolites may be developed as biomarkers to predict POAF.
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Affiliation(s)
- Xin-Ya Li
- Center for Basic Medical Research and Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Hai-Tao Hou
- Center for Basic Medical Research and Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Huan-Xin Chen
- Center for Basic Medical Research and Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiao-Cheng Liu
- Center for Basic Medical Research and Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jun Wang
- Center for Basic Medical Research and Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Qin Yang
- Center for Basic Medical Research and Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Guo-Wei He
- Center for Basic Medical Research and Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China; Department of Cardiac Surgery, The First Affiliated Hospital, Zhejiang University, Hangzhou, China; School of Pharmacy, Wannan Medical College, Wuhu, Anhui, China; Department of Surgery, Oregon Health and Science University, Portland, Ore.
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36
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Regrowth of zebrafish caudal fin regeneration is determined by the amputated length. Sci Rep 2020; 10:649. [PMID: 31959817 PMCID: PMC6971026 DOI: 10.1038/s41598-020-57533-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 01/03/2020] [Indexed: 11/08/2022] Open
Abstract
Fish have a high ability to regenerate fins, including the caudal fin. After caudal fin amputation, original bi-lobed morphology is reconstructed during its rapid regrowth. It is still controversial whether positional memory in the blastema cells regulates reconstruction of fin morphology as in amphibian limb regeneration, in which limb blastema cells located at the same proximal-distal level have the same positional identity. We investigated growth period and growth rate in zebrafish caudal fin regeneration. We found that both the growth period and growth rate differed for fin rays that were amputated at the same proximal-distal level, indicating that it takes different periods of time for fin rays to restore their original lengths after straight amputation. We also show that more proximal amputation takes longer period to reconstruct the original morphology/size than more distal amputation. Statistical analysis suggested that both the growth period/rate are determined by amputated length (depth) regardless of the fin ray identity along dorsal-ventral axis. In addition, we suggest the possibility that the structural/physical condition such as width of the fin ray at the amputation site (niche at the stump) may determine the growth period/rate.
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37
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Zhang T, Trauger SA, Vidoudez C, Doane KP, Pluimer BR, Peterson RT. Parallel Reaction Monitoring reveals structure-specific ceramide alterations in the zebrafish. Sci Rep 2019; 9:19939. [PMID: 31882772 PMCID: PMC6934720 DOI: 10.1038/s41598-019-56466-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 12/05/2019] [Indexed: 12/19/2022] Open
Abstract
Extensive characterisations of the zebrafish genome and proteome have established a foundation for the use of the zebrafish as a model organism; however, characterisation of the zebrafish lipidome has not been as comprehensive. In an effort to expand current knowledge of the zebrafish sphingolipidome, a Parallel Reaction Monitoring (PRM)-based liquid chromatography-mass spectrometry (LC-MS) method was developed to comprehensively quantify zebrafish ceramides. Comparison between zebrafish and a human cell line demonstrated remarkable overlap in ceramide composition, but also revealed a surprising lack of most sphingadiene-containing ceramides in the zebrafish. PRM analysis of zebrafish embryogenesis identified developmental stage-specific ceramide changes based on long chain base (LCB) length. A CRISPR-Cas9-generated zebrafish model of Farber disease exhibited reduced size, early mortality, and severe ceramide accumulation where the amplitude of ceramide change depended on both acyl chain and LCB lengths. Our method adds an additional level of detail to current understanding of the zebrafish lipidome, and could aid in the elucidation of structure-function associations in the context of lipid-related diseases.
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Affiliation(s)
- Tejia Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA
| | - Sunia A Trauger
- Small Molecule Mass Spectrometry, Harvard University, Cambridge, Massachusetts, USA
| | - Charles Vidoudez
- Small Molecule Mass Spectrometry, Harvard University, Cambridge, Massachusetts, USA
| | - Kim P Doane
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA
| | - Brock R Pluimer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA
| | - Randall T Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA.
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38
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Vieira WA, Wells KM, McCusker CD. Advancements to the Axolotl Model for Regeneration and Aging. Gerontology 2019; 66:212-222. [PMID: 31779024 PMCID: PMC7214127 DOI: 10.1159/000504294] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Loss of regenerative capacity is a normal part of aging. However, some organisms, such as the Mexican axolotl, retain striking regenerative capacity throughout their lives. Moreover, the development of age-related diseases is rare in this organism. In this review, we will explore how axolotls are used as a model system to study regenerative processes, the exciting new technological advancements now available for this model, and how we can apply the lessons we learn from studying regeneration in the axolotl to understand, and potentially treat, age-related decline in humans.
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Affiliation(s)
- Warren A Vieira
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA
| | - Kaylee M Wells
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA
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39
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Recent advancements in understanding fin regeneration in zebrafish. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 9:e367. [DOI: 10.1002/wdev.367] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 11/07/2022]
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40
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Cox BD, Yun MH, Poss KD. Can laboratory model systems instruct human limb regeneration? Development 2019; 146:146/20/dev181016. [PMID: 31578190 DOI: 10.1242/dev.181016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Regeneration has fascinated scientists since well before the 20th century revolutions in genetics and molecular biology. The field of regenerative biology has grown steadily over the past decade, incorporating advances in imaging, genomics and genome editing to identify key cell types and molecules involved across many model organisms. Yet for many or most tissues, it can be difficult to predict when and how findings from these studies will advance regenerative medicine. Establishing technologies to stimulate regrowth of a lost or amputated limb with a patterned replicate, as salamanders do routinely, is one of the most challenging directives of tissue regeneration research. Here, we speculate upon what research avenues the field must explore to move closer to this capstone achievement.
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Affiliation(s)
- Ben D Cox
- Regeneration Next, Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maximina H Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden 01307, Germany .,Max Planck Institute for Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Kenneth D Poss
- Regeneration Next, Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
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41
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Marques IJ, Lupi E, Mercader N. Model systems for regeneration: zebrafish. Development 2019; 146:146/18/dev167692. [DOI: 10.1242/dev.167692] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Tissue damage can resolve completely through healing and regeneration, or can produce permanent scarring and loss of function. The response to tissue damage varies across tissues and between species. Determining the natural mechanisms behind regeneration in model organisms that regenerate well can help us develop strategies for tissue recovery in species with poor regenerative capacity (such as humans). The zebrafish (Danio rerio) is one of the most accessible vertebrate models to study regeneration. In this Primer, we highlight the tools available to study regeneration in the zebrafish, provide an overview of the mechanisms underlying regeneration in this system and discuss future perspectives for the field.
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Affiliation(s)
- Ines J. Marques
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
| | - Eleonora Lupi
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Acquifer, Ditabis, Digital Biomedical Imaging Systems, Pforzheim, Germany
| | - Nadia Mercader
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Centro Nacional de Investigaciones Cardiovasculares CNIC, Madrid 2029, Spain
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42
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Suhail Y, Cain MP, Vanaja K, Kurywchak PA, Levchenko A, Kalluri R, Kshitiz. Systems Biology of Cancer Metastasis. Cell Syst 2019; 9:109-127. [PMID: 31465728 PMCID: PMC6716621 DOI: 10.1016/j.cels.2019.07.003] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/29/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon.
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Affiliation(s)
- Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, USA; Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT, USA
| | - Margo P Cain
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Kiran Vanaja
- Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT, USA
| | - Paul A Kurywchak
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Andre Levchenko
- Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT, USA
| | - Raghu Kalluri
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Kshitiz
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, USA; Cancer Systems Biology @ Yale (CaSB@Yale), Yale University, West Haven, CT, USA.
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43
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Bioelectrical controls of morphogenesis: from ancient mechanisms of cell coordination to biomedical opportunities. Curr Opin Genet Dev 2019; 57:61-69. [PMID: 31442749 DOI: 10.1016/j.gde.2019.06.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/06/2019] [Accepted: 06/18/2019] [Indexed: 11/21/2022]
Abstract
Cell-to-cell communication is a cornerstone of multicellular existence. The ancient mechanism of sharing information between cells using the conductance of ions across cell membranes and the propagation of electrical signals through tissue space is a powerful means of efficiently controlling cell decisions and behaviors. Our understanding of how cells use changes in 'bioelectrical' signals to elicit systems-level responses has dramatically improved in recent years. We are now in a position to not just describe these changes, but to also predictively alter them to learn more about their importance for developmental biology and regenerative medicine. Recent work is helping researchers construct a more integrative view of how these simple controls can orchestrate downstream changes in protein signaling pathways and gene regulatory networks. In this review, we highlight experiments and analyses that have led to new insights in bioelectrical controls, specifically as key modulators of complex pattern formation and tissue regeneration. We also discuss opportunities for the development of new therapeutic approaches in regenerative medicine applications by exploiting this fundamental biological phenomenon.
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44
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Vieira WA, McCusker CD. Hierarchical pattern formation during amphibian limb regeneration. Biosystems 2019; 183:103989. [PMID: 31295535 DOI: 10.1016/j.biosystems.2019.103989] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/03/2019] [Accepted: 07/06/2019] [Indexed: 12/28/2022]
Abstract
In 1901 T.H. Morgan proposed in "Regeneration" that pattern formation in amphibian limb regeneration is a stepwise process. Since, biologist have continued to piece together the molecular components of this process to better understand the "patterning code" responsible for regenerate formation. Within this context, several different models have been proposed; however, all are based on one of two underlying hypotheses. The first is the "morphogen hypothesis" that dictates that pattern emerges from localized expression of signaling molecules, which produce differing position-specific cellular responses in receptive cells depending on the intensity of the signal. The second hypothesis is that cells in the remaining tissues retain memory of their patterning information, and use this information to generate new cells with the missing positional identities. A growing body of evidence supports the possibility that these two mechanisms are not mutually exclusive. Here, we propose our theory of hierarchical pattern formation, which consists of 4 basic steps. The first is the existence of cells with positional memory. The second is the communication of positional information through cell-cell interactions in a regeneration-permissive environment. The third step is the induction of molecular signaling centers. And the last step is the interpretation of these signals by specialized cell types to ultimately restore the limb in its entirety. Biological codes are intertwined throughout this model, and we will discuss their multiple roles and mechanisms.
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Affiliation(s)
- Warren A Vieira
- Department of Biology, University of Massachusetts, Boston, MA, USA
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45
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Paredes LC, Olsen Saraiva Camara N, Braga TT. Understanding the Metabolic Profile of Macrophages During the Regenerative Process in Zebrafish. Front Physiol 2019; 10:617. [PMID: 31178754 PMCID: PMC6543010 DOI: 10.3389/fphys.2019.00617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/01/2019] [Indexed: 12/14/2022] Open
Abstract
In contrast to mammals, lower vertebrates, including zebrafish (Danio rerio), have the ability to regenerate damaged or lost tissues, such as the caudal fin, which makes them an ideal model for tissue and organ regeneration studies. Since several diseases involve the process of transition between fibrosis and tissue regeneration, it is necessary to attain a better understanding of these processes. It is known that the cells of the immune system, especially macrophages, play essential roles in regeneration by participating in the removal of cellular debris, release of pro- and anti-inflammatory factors, remodeling of components of the extracellular matrix and alteration of oxidative patterns during proliferation and angiogenesis. Immune cells undergo phenotypical and functional alterations throughout the healing process due to growth factors and cytokines that are produced in the tissue microenvironment. However, some aspects of the molecular mechanisms through which macrophages orchestrate the formation and regeneration of the blastema remain unclear. In the present review, we outline how macrophages orchestrate the regenerative process in zebrafish and give special attention to the redox balance in the context of tail regeneration.
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Affiliation(s)
| | - Niels Olsen Saraiva Camara
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, Brazil.,Nephrology Division, Federal University of São Paulo, São Paulo, Brazil.,Renal Pathophysiology Laboratory, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
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46
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Hosseini S, Ha NT, Simianer H, Falker-Gieske C, Brenig B, Franke A, Hörstgen-Schwark G, Tetens J, Herzog S, Sharifi AR. Genetic mechanism underlying sexual plasticity and its association with colour patterning in zebrafish (Danio rerio). BMC Genomics 2019; 20:341. [PMID: 31060508 PMCID: PMC6503382 DOI: 10.1186/s12864-019-5722-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 04/22/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Elevated water temperature, as is expected through climate change, leads to masculinization in fish species with sexual plasticity, resulting in changes in population dynamics. These changes are one important ecological consequence, contributing to the risk of extinction in small and inbred fish populations under natural conditions, due to male-biased sex ratio. Here we investigated the effect of elevated water temperature during embryogenesis on sex ratio and sex-biased gene expression profiles between two different tissues, namely gonad and caudal fin of adult zebrafish males and females, to gain new insights into the molecular mechanisms underlying sex determination (SD) and colour patterning related to sexual attractiveness. RESULTS Our study demonstrated sex ratio imbalances with 25.5% more males under high-temperature condition, resulting from gonadal masculinization. The result of transcriptome analysis showed a significantly upregulated expression of male SD genes (e.g. dmrt1, amh, cyp11c1 and sept8b) and downregulation of female SD genes (e.g. zp2.1, vtg1, cyp19a1a and bmp15) in male gonads compared to female gonads. Contrary to expectations, we found highly differential expression of colour pattern (CP) genes in the gonads, suggesting the 'neofunctionalisation' of those genes in the zebrafish reproduction system. However, in the caudal fin, no differential expression of CP genes was identified, suggesting the observed differences in colouration between males and females in adult fish may be due to post-transcriptional regulation of key enzymes involved in pigment synthesis and distribution. CONCLUSIONS Our study demonstrates male-biased sex ratio under high temperature condition and support a polygenic SD (PSD) system in laboratory zebrafish. We identify a subset of pathways (tight junction, gap junction and apoptosis), enriched for SD and CP genes, which appear to be co-regulated in the same pathway, providing evidence for involvement of those genes in the regulation of phenotypic sexual dimorphism in zebrafish.
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Affiliation(s)
- Shahrbanou Hosseini
- Department of Animal Sciences, University of Goettingen, Goettingen, Germany. .,Center for Integrated Breeding Research, University of Goettingen, Goettingen, Germany.
| | - Ngoc-Thuy Ha
- Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Goettingen, Germany
| | - Henner Simianer
- Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Goettingen, Germany
| | - Clemens Falker-Gieske
- Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Goettingen, Germany
| | - Bertram Brenig
- Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Goettingen, Germany.,Institute of Veterinary Medicine, University of Goettingen, Goettingen, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | | | - Jens Tetens
- Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Goettingen, Germany
| | - Sebastian Herzog
- Max Planck Institute for Dynamics and Self-Organization, Goettingen, Germany.,Department for Computational Neuroscience, 3rd Physics Institute-Biophysics, University of Goettingen, Goettingen, Germany
| | - Ahmad Reza Sharifi
- Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Goettingen, Germany
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Mitra S, Sharma P, Kaur S, Khursheed MA, Gupta S, Chaudhary M, Kurup AJ, Ramachandran R. Dual regulation of lin28a by Myc is necessary during zebrafish retina regeneration. J Cell Biol 2019; 218:489-507. [PMID: 30606747 PMCID: PMC6363449 DOI: 10.1083/jcb.201802113] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/31/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
Cellular reprogramming leading to induction of Muller glia-derived progenitor cells (MGPCs) with stem cell characteristics is essential for zebrafish retina regeneration. Although several regeneration-specific genes are characterized, the significance of MGPC-associated Mycb induction remains unknown. Here, we show that early expression of Mycb induces expression of genes like ascl1a, a known activator of lin28a in MGPCs. Notably, mycb is simultaneously activated by Ascl1a and repressed by Insm1a in regenerating retina. Here, we unravel a dual role of Mycb in lin28a expression, both as an activator through Ascl1a in MGPCs and a repressor in combination with Hdac1 in neighboring cells. Myc inhibition reduces the number of MGPCs and abolishes normal regeneration. Myc in collaboration with Hdac1 inhibits her4.1, an effector of Delta-Notch signaling. Further, we also show the repressive role of Delta-Notch signaling on lin28a expression in post-injured retina. Our studies reveal mechanistic understanding of Myc pathway during zebrafish retina regeneration, which could pave way for therapeutic intervention during mammalian retina regeneration.
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Affiliation(s)
- Soumitra Mitra
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Poonam Sharma
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Simran Kaur
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Mohammad Anwar Khursheed
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Shivangi Gupta
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Mansi Chaudhary
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Akshai J Kurup
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Rajesh Ramachandran
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
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Schmidt JR, Geurtzen K, von Bergen M, Schubert K, Knopf F. Glucocorticoid Treatment Leads to Aberrant Ion and Macromolecular Transport in Regenerating Zebrafish Fins. Front Endocrinol (Lausanne) 2019; 10:674. [PMID: 31636606 PMCID: PMC6787175 DOI: 10.3389/fendo.2019.00674] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
Abstract
Long-term glucocorticoid administration in patients undergoing immunosuppressive and anti-inflammatory treatment is accompanied by impaired bone formation and increased fracture risk. Furthermore, glucocorticoid treatment can lead to impaired wound healing and altered cell metabolism. Recently, we showed that exposure of zebrafish to the glucocorticoid prednisolone during fin regeneration impacts negatively on the length, bone formation, and osteoblast function of the regenerate. The underlying cellular and molecular mechanisms of impairment, however, remain incompletely understood. In order to further elucidate the anti-regenerative effects of continued glucocorticoid exposure on fin tissues, we performed proteome profiling of fin regenerates undergoing prednisolone treatment, in addition to profiling of homeostatic fin tissue and fins undergoing undisturbed regeneration. By using LC-MS (liquid chromatography-mass spectrometry) we identified more than 6,000 proteins across all tissue samples. In agreement with previous reports, fin amputation induces changes in chromatin structure and extracellular matrix (ECM) composition within the tissue. Notably, prednisolone treatment leads to impaired expression of selected ECM components in the fin regenerate. Moreover, the function of ion transporting ATPases and other proteins involved in macromolecule and vesicular transport mechanisms of the cell appears to be altered by prednisolone treatment. In particular, acidification of membrane-enclosed organelles such as lysosomes is inhibited. Taken together, our data indicate that continued synthetic glucocorticoid exposure in zebrafish deteriorates cellular trafficking processes in the regenerating fin, which interferes with appropriate tissue restoration upon injury.
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Affiliation(s)
- Johannes R. Schmidt
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Karina Geurtzen
- CRTD—Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- *Correspondence: Kristin Schubert
| | - Franziska Knopf
- CRTD—Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Healthy Aging, Technische Universität (TU) Dresden, Dresden, Germany
- Franziska Knopf
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Vieira WA, McCusker CD. Regenerative Models for the Integration and Regeneration of Head Skeletal Tissues. Int J Mol Sci 2018; 19:E3752. [PMID: 30486286 PMCID: PMC6321600 DOI: 10.3390/ijms19123752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 12/19/2022] Open
Abstract
Disease of, or trauma to, the human jaw account for thousands of reconstructive surgeries performed every year. One of the most popular and successful treatment options in this context involves the transplantation of bone tissue from a different anatomical region into the affected jaw. Although, this method has been largely successful, the integration of the new bone into the existing bone is often imperfect, and the integration of the host soft tissues with the transplanted bone can be inconsistent, resulting in impaired function. Unlike humans, several vertebrate species, including fish and amphibians, demonstrate remarkable regenerative capabilities in response to jaw injury. Therefore, with the objective of identifying biological targets to promote and engineer improved outcomes in the context of jaw reconstructive surgery, we explore, compare and contrast the natural mechanisms of endogenous jaw and limb repair and regeneration in regenerative model organisms. We focus on the role of different cell types as they contribute to the regenerating structure; how mature cells acquire plasticity in vivo; the role of positional information in pattern formation and tissue integration, and limitations to endogenous regenerative and repair mechanisms.
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Affiliation(s)
- Warren A Vieira
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
| | - Catherine D McCusker
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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50
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de Pater E, Trompouki E. Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis. Front Cell Dev Biol 2018; 6:124. [PMID: 30374440 PMCID: PMC6196227 DOI: 10.3389/fcell.2018.00124] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is an optimal system for studying stem cell maintenance and lineage differentiation under physiological and pathological conditions. In vertebrate organisms, billions of differentiated hematopoietic cells need to be continuously produced to replenish the blood cell pool. Disruptions in this process have immediate consequences for oxygen transport, responses against pathogens, maintenance of hemostasis and vascular integrity. Zebrafish is a widely used and well-established model for studying the hematopoietic system. Several new hematopoietic regulators were identified in genetic and chemical screens using the zebrafish model. Moreover, zebrafish enables in vivo imaging of hematopoietic stem cell generation and differentiation during embryogenesis, and adulthood. Finally, zebrafish has been used to model hematopoietic diseases. Recent technological advances in single-cell transcriptome analysis, epigenetic regulation, proteomics, metabolomics, and processing of large data sets promise to transform the current understanding of normal, abnormal, and malignant hematopoiesis. In this perspective, we discuss how the zebrafish model has proven beneficial for studying physiological and pathological hematopoiesis and how these novel technologies are transforming the field.
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Affiliation(s)
- Emma de Pater
- Department of Hematology, Erasmus MC, Rotterdam, Netherlands
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
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