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Thibault S, Wong AL, Buxbaum LJ. Cognitive neuropsychological and neuroanatomic predictors of naturalistic action performance in left hemisphere stroke: a retrospective analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601398. [PMID: 39005391 PMCID: PMC11244907 DOI: 10.1101/2024.07.01.601398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Individuals who have experienced a left hemisphere cerebrovascular accident (LCVA) have been shown to make errors in naturalistic action tasks designed to assess the ability to perform everyday activities such as preparing a cup of coffee. Naturalistic action errors in this population are often attributed to limb apraxia, a common deficit in the representation and performance of object-related actions. However, naturalistic action impairments are also observed in right hemisphere stroke and traumatic brain injury, populations infrequently associated with apraxia, and errors across all these populations are influenced by overall severity. Based on these and other data, an alternative (though not mutually exclusive) account is that naturalistic action errors in LCVA are also a consequence of deficits in general attentional resource availability or allocation. In this study, we conducted a retrospective analysis of data from a large group of 51 individuals with LCVA who had completed a test of naturalistic action, along with a battery of tests assessing praxis, attention allocation and control, reasoning, and language abilities to determine which of these capacities contribute uniquely to naturalistic action impairments. Using a regularized regression method, we found that naturalistic action impairments are predicted by both praxis deficits (hand posture sequencing and gesture recognition), as well as attention allocation and control deficits (orienting and dividing attention), along with language comprehension ability and age. Using support vector regression-lesion symptom mapping (SVR-LSM), we also demonstrated that naturalistic action impairments are associated with lesions to posterior middle temporal gyrus and anterior inferior parietal lobule - regions known to be implicated in praxis; as well the middle frontal gyrus that has been implicated in both praxis and attention allocation and control. Taken together, these findings support the hypothesis that naturalistic action impairments in LCVA are a consequence of apraxia as well as deficits in attention allocation and control.
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Affiliation(s)
- Simon Thibault
- Moss Rehabilitation Research Institute, Thomas Jefferson University, Elkins Park, PA
| | - Aaron L. Wong
- Moss Rehabilitation Research Institute, Thomas Jefferson University, Elkins Park, PA
- Department of Rehabilitation Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Laurel J. Buxbaum
- Moss Rehabilitation Research Institute, Thomas Jefferson University, Elkins Park, PA
- Department of Rehabilitation Medicine, Thomas Jefferson University, Philadelphia, PA
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2
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Dintzner E, Bandekar SJ, Leon K, Cechova K, Vafabakhsh R, Araç D. The far extracellular CUB domain of the adhesion GPCR ADGRG6/GPR126 is a key regulator of receptor signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580607. [PMID: 38766069 PMCID: PMC11100614 DOI: 10.1101/2024.02.16.580607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Adhesion G Protein-coupled receptors (aGPCRs) transduce extracellular adhesion signals into cytoplasmic signaling pathways. ADGRG6/GPR126 is an aGPCR critical for axon myelination, heart development and ear development; and is associated with developmental diseases and cancers. ADGRG6 has a large, alternatively-spliced, five-domain extracellular region (ECR) that samples different conformations and regulates receptor signaling. However, the molecular details of how the ECR regulates signaling are unclear. Herein, we studied the conformational dynamics of the conserved CUB domain which is located at the distal N-terminus of the ECR and is deleted in an alternatively-spliced isoform ( Δ CUB). We showed that the Δ CUB isoform has decreased signaling. Molecular dynamics simulations suggest that the CUB domain is involved in interdomain contacts to maintain a compact ECR conformation. A cancer-associated CUB domain mutant, C94Y, drastically perturbs the ECR conformation and results in elevated signaling, whereas another CUB mutant, Y96A, located near a conserved Ca 2+ -binding site, decreases signaling. Our results suggest an ECR-mediated mechanism for ADGRG6 regulation in which the CUB domain instructs conformational changes within the ECR to regulate receptor signaling.
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3
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Jeong R, Bulyk ML. Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589213. [PMID: 38659802 PMCID: PMC11042205 DOI: 10.1101/2024.04.12.589213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Most genetic loci associated with complex traits and diseases through genome-wide association studies (GWAS) are noncoding, suggesting that the causal variants likely have gene regulatory effects. However, only a small number of loci have been linked to expression quantitative trait loci (eQTLs) detected currently. To better understand the potential reasons for many trait-associated loci lacking eQTL colocalization, we investigated whether chromatin accessibility QTLs (caQTLs) in lymphoblastoid cell lines (LCLs) explain immune-mediated disease associations that eQTLs in LCLs did not. The power to detect caQTLs was greater than that of eQTLs and was less affected by the distance from the transcription start site of the associated gene. Meta-analyzing LCL eQTL data to increase the sample size to over a thousand led to additional loci with eQTL colocalization, demonstrating that insufficient statistical power is still likely to be a factor. Moreover, further eQTL colocalization loci were uncovered by surveying eQTLs of other immune cell types. Altogether, insufficient power and context-specificity of eQTLs both contribute to the 'missing regulation.'
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Affiliation(s)
- Raehoon Jeong
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA 02138, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA 02138, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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4
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Avalos PN, Wong LL, Forsthoefel DJ. Extracellular vesicles promote proliferation in an animal model of regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586206. [PMID: 38712279 PMCID: PMC11071309 DOI: 10.1101/2024.03.22.586206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Extracellular vesicles (EVs) are secreted nanoparticles composed of a lipid bilayer that carry lipid, protein, and nucleic acid cargo between cells as a mode of intercellular communication. Although EVs can promote tissue repair in mammals, their roles in animals with greater regenerative capacity are not well understood. Planarian flatworms are capable of whole body regeneration due to pluripotent somatic stem cells called neoblasts that proliferate in response to injury. Here, using transmission electron microscopy, nanoparticle tracking analysis, and protein content examination, we showed that EVs enriched from the tissues of the planarian Schmidtea mediterranea had similar morphology and size as other eukaryotic EVs, and that these EVs carried orthologs of the conserved EV biogenesis regulators ALIX and TSG101. PKH67-labeled EVs were taken up more quickly by S/G2 neoblasts than G1 neoblasts/early progeny and differentiated cells. When injected into living planarians, EVs from regenerating tissue fragments enhanced upregulation of neoblast-associated transcripts. In addition, EV injection increased the number of F-ara-EdU-labelled cells by 49% as compared to buffer injection only. Our findings demonstrate that regenerating planarians produce EVs that promote stem cell proliferation, and suggest the planarian as an amenable in vivo model for the study of EV function during regeneration.
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Affiliation(s)
- Priscilla N. Avalos
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Lily L. Wong
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - David J. Forsthoefel
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
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5
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Tang VT, Xiang J, Chen Z, McCormick J, Abbineni PS, Chen XW, Hoenerhoff M, Emmer BT, Khoriaty R, Lin JD, Ginsburg D. Functional overlap between the mammalian Sar1a and Sar1b paralogs in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582310. [PMID: 38463989 PMCID: PMC10925261 DOI: 10.1101/2024.02.27.582310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Proteins carrying a signal peptide and/or a transmembrane domain enter the intracellular secretory pathway at the endoplasmic reticulum (ER) and are transported to the Golgi apparatus via COPII vesicles or tubules. SAR1 initiates COPII coat assembly by recruiting other coat proteins to the ER membrane. Mammalian genomes encode two SAR1 paralogs, SAR1A and SAR1B. While these paralogs exhibit ~90% amino acid sequence identity, it is unknown whether they perform distinct or overlapping functions in vivo. We now report that genetic inactivation of Sar1a in mice results in lethality during mid-embryogenesis. We also confirm previous reports that complete deficiency of murine Sar1b results in perinatal lethality. In contrast, we demonstrate that deletion of Sar1b restricted to hepatocytes is compatible with survival, though resulting in hypocholesterolemia that can be rescued by adenovirus-mediated overexpression of either SAR1A or SAR1B. To further examine the in vivo function of these 2 paralogs, we genetically engineered mice with the Sar1a coding sequence replacing that of Sar1b at the endogenous Sar1b locus. Mice homozygous for this allele survive to adulthood and are phenotypically normal, demonstrating complete or near-complete overlap in function between the two SAR1 protein paralogs in mice. These data also suggest upregulation of SAR1A gene expression as a potential approach for the treatment of SAR1B deficiency (chylomicron retention disease) in humans.
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Affiliation(s)
- Vi T. Tang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Jie Xiang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Zhimin Chen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Joseph McCormick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Prabhodh S. Abbineni
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Mark Hoenerhoff
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Rami Khoriaty
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Jiandie D. Lin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - David Ginsburg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109
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6
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Sosa J, Oyelakin A, Sinha S. The Reign of Follistatin in Tumors and Their Microenvironment: Implications for Drug Resistance. BIOLOGY 2024; 13:130. [PMID: 38392348 PMCID: PMC10887188 DOI: 10.3390/biology13020130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/10/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Follistatin (FST) is a potent neutralizer of the transforming growth factor-β superfamily and is associated with normal cellular programs and various hallmarks of cancer, such as proliferation, migration, angiogenesis, and immune evasion. The aberrant expression of FST by solid tumors is a well-documented observation, yet how FST influences tumor progression and therapy response remains unclear. The recent surge in omics data has revealed new insights into the molecular foundation underpinning tumor heterogeneity and its microenvironment, offering novel precision medicine-based opportunities to combat cancer. In this review, we discuss these recent FST-centric studies, thereby offering an updated perspective on the protean role of FST isoforms in shaping the complex cellular ecosystem of tumors and in mediating drug resistance.
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Affiliation(s)
- Jennifer Sosa
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Akinsola Oyelakin
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA 98101, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA 98101, USA
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
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7
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Chamness LM, Kuntz CP, McKee AG, Penn WD, Hemmerich CM, Rusch DB, Woods H, Dyotima, Meiler J, Schlebach JP. Divergent Folding-Mediated Epistasis Among Unstable Membrane Protein Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.25.554866. [PMID: 37662415 PMCID: PMC10473758 DOI: 10.1101/2023.08.25.554866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency. Though protein stability is known to shape evolution, it is unclear how cotranslational folding constraints modulate the synergistic, epistatic interactions between mutations. We therefore compared the pairwise interactions formed by mutations that disrupt the membrane topology (V276T) or tertiary structure (W107A) of GnRHR. Using deep mutational scanning, we evaluated how the plasma membrane expression of these variants is modified by hundreds of secondary mutations. An analysis of 251 mutants in three genetic backgrounds reveals that V276T and W107A form distinct epistatic interactions that depend on both the severity and the mechanism of destabilization. V276T forms predominantly negative epistatic interactions with destabilizing mutations in soluble loops. In contrast, W107A forms positive interactions with mutations in both loops and transmembrane domains that reflect the diminishing impacts of the destabilizing mutations in variants that are already unstable. These findings reveal how epistasis is remodeled by conformational defects in membrane proteins and in unstable proteins more generally.
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Affiliation(s)
- Laura M. Chamness
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Charles P. Kuntz
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Andrew G. McKee
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Wesley D. Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | | | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | - Hope Woods
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Dyotima
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC, Germany
| | - Jonathan P. Schlebach
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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8
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Bandekar SJ, Garbett K, Kordon SP, Dintzner E, Shearer T, Sando RC, Araç D. Structure of the extracellular region of the adhesion GPCR CELSR1 reveals a compact module which regulates G protein-coupling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577439. [PMID: 38328199 PMCID: PMC10849658 DOI: 10.1101/2024.01.26.577439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cadherin EGF Laminin G seven-pass G-type receptors (CELSRs or ADGRCs) are conserved adhesion G protein-coupled receptors which are essential for animal development. CELSRs have extracellular regions (ECRs) containing 23 adhesion domains which couple adhesion to intracellular signaling. However, molecular-level insight into CELSR function is sparsely available. We report the 4.3 Å cryo-EM reconstruction of the mCELSR1 ECR with 13 domains resolved in the structure. These domains form a compact module mediated by interdomain interactions with contact between the N- and C-terminal domains. We show the mCELSR1 ECR forms an extended species in the presence of Ca 2+ , which we propose represents the antiparallel cadherin repeat dimer. Using assays for adhesion and G protein-coupling, we assign the N-terminal CADH1-8 module as necessary for cell adhesion and we show the C-terminal CAHD9-GAIN module regulates signaling. Our work provides important molecular context to the literature on CELSR function and opens the door towards further mechanistic studies.
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9
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Vila-Farré M, Rozanski A, Ivanković M, Cleland J, Brand JN, Thalen F, Grohme MA, von Kannen S, Grosbusch AL, Vu HTK, Prieto CE, Carbayo F, Egger B, Bleidorn C, Rasko JEJ, Rink JC. Evolutionary dynamics of whole-body regeneration across planarian flatworms. Nat Ecol Evol 2023; 7:2108-2124. [PMID: 37857891 PMCID: PMC10697840 DOI: 10.1038/s41559-023-02221-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 09/14/2023] [Indexed: 10/21/2023]
Abstract
Regenerative abilities vary dramatically across animals. Even amongst planarian flatworms, well-known for complete regeneration from tiny body fragments, some species have restricted regeneration abilities while others are almost entirely regeneration incompetent. Here, we assemble a diverse live collection of 40 planarian species to probe the evolution of head regeneration in the group. Combining quantification of species-specific head-regeneration abilities with a comprehensive transcriptome-based phylogeny reconstruction, we show multiple independent transitions between robust whole-body regeneration and restricted regeneration in freshwater species. RNA-mediated genetic interference inhibition of canonical Wnt signalling in RNA-mediated genetic interference-sensitive species bypassed all head-regeneration defects, suggesting that the Wnt pathway is linked to the emergence of planarian regeneration defects. Our finding that Wnt signalling has multiple roles in the reproductive system of the model species Schmidtea mediterranea raises the possibility that a trade-off between egg-laying, asexual reproduction by fission/regeneration and Wnt signalling drives regenerative trait evolution. Although quantitative comparisons of Wnt signalling levels, yolk content and reproductive strategy across our species collection remained inconclusive, they revealed divergent Wnt signalling roles in the reproductive system of planarians. Altogether, our study establishes planarians as a model taxon for comparative regeneration research and presents a framework for the mechanistic evolution of regenerative abilities.
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Affiliation(s)
- Miquel Vila-Farré
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Andrei Rozanski
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mario Ivanković
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - James Cleland
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jeremias N Brand
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Felix Thalen
- Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen, Germany
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
| | - Markus A Grohme
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Hanh T-K Vu
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carlos E Prieto
- Department of Zoology & Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Fernando Carbayo
- Laboratório de Ecologia e Evolução. Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil
| | - Bernhard Egger
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Christoph Bleidorn
- Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen, Germany
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Jochen C Rink
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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Molina MD, Abduljabbar D, Guixeras A, Fraguas S, Cebrià F. LIM-HD transcription factors control axial patterning and specify distinct neuronal and intestinal cell identities in planarians. Open Biol 2023; 13:230327. [PMID: 38086422 PMCID: PMC10715919 DOI: 10.1098/rsob.230327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
Adult planarians can regenerate the gut, eyes and even a functional brain. Proper identity and patterning of the newly formed structures require signals that guide and commit their adult stem cells. During embryogenesis, LIM-homeodomain (LIM-HD) transcription factors act in a combinatorial 'LIM code' to control cell fate determination and differentiation. However, our understanding about the role these genes play during regeneration and homeostasis is limited. Here, we report the full repertoire of LIM-HD genes in Schmidtea mediterranea. We found that lim homeobox (lhx) genes appear expressed in complementary patterns along the cephalic ganglia and digestive system of the planarian, with some of them being co-expressed in the same cell types. We have identified that Smed-islet1, -lhx1/5-1, -lhx2/9-3, -lhx6/8, -lmx1a/b-2 and -lmx1a/b-3 are essential to pattern and size the planarian brain as well as for correct regeneration of specific subpopulations of dopaminergic, serotonergic, GABAergic and cholinergic neurons, while Smed-lhx1/5.2 and -lhx2/9.2 are required for the proper expression of intestinal cell type markers, specifically the goblet subtype. LIM-HD are also involved in controlling axonal pathfinding (lhx6/8), axial patterning (islet1, lhx1/5-1, lmx1a/b-3), head/body proportions (islet2) and stem cell proliferation (lhx3/4, lhx2/9-3, lmx1a/b-2, lmx1a/b-3). Altogether, our results suggest that planarians might present a combinatorial LIM code that controls axial patterning and axonal growing and specifies distinct neuronal and intestinal cell identities.
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Affiliation(s)
- M. Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Dema Abduljabbar
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Anna Guixeras
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Susanna Fraguas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Francesc Cebrià
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
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11
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Tsukahara T, Kethireddy S, Bonefas K, Chen A, Sutton BLM, Dou Y, Iwase S, Sutton MA. Division of labor among H3K4 Methyltransferases Defines Distinct Facets of Homeostatic Plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558734. [PMID: 37790395 PMCID: PMC10542164 DOI: 10.1101/2023.09.20.558734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Heterozygous mutations in any of the six H3K4 methyltransferases (KMT2s) result in monogenic neurodevelopmental disorders, indicating nonredundant yet poorly understood roles of this enzyme family in neurodevelopment. Recent evidence suggests that histone methyltransferase activity may not be central to KMT2 functions; however, the enzymatic activity is evolutionarily conserved, implicating the presence of selective pressure to maintain the catalytic activity. Here, we show that H3K4 methylation is dynamically regulated during prolonged alteration of neuronal activity. The perturbation of H3K4me by the H3.3K4M mutant blocks synaptic scaling, a form of homeostatic plasticity that buffers the impact of prolonged reductions or increases in network activity. Unexpectedly, we found that the six individual enzymes are all necessary for synaptic scaling and that the roles of KMT2 enzymes segregate into evolutionary-defined subfamilies: KMT2A and KMT2B (fly-Trx homologs) for synaptic downscaling, KMT2C and KMT2D (Trr homologs) for upscaling, and KMT2F and KMT2G (dSet homologs) for both directions. Selective blocking of KMT2A enzymatic activity by a small molecule and targeted disruption of the enzymatic domain both blocked the synaptic downscaling and interfered with the activity-dependent transcriptional program. Furthermore, our study revealed specific phases of synaptic downscaling, i.e., induction and maintenance, in which KMT2A and KMT2B play distinct roles. These results suggest that mammalian brains have co-opted intricate H3K4me installation to achieve stability of the expanding neuronal circuits.
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Affiliation(s)
- Takao Tsukahara
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Saini Kethireddy
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan
| | - Katherine Bonefas
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Alex Chen
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Brendan LM Sutton
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Yali Dou
- Department of Medicine and Department of Biochemistry and Molecular Medicine, Keck School of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Shigeki Iwase
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Michael A. Sutton
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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12
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Chen JJ, Lei K. The known, unknown, and unknown unknowns of cell-cell communication in planarian regeneration. Zool Res 2023; 44:981-992. [PMID: 37721107 PMCID: PMC10559094 DOI: 10.24272/j.issn.2095-8137.2023.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023] Open
Abstract
Planarians represent the most primitive bilateral triploblastic animals. Most planarian species exhibit mechanisms for whole-body regeneration, exemplified by the regeneration of their cephalic ganglion after complete excision. Given their robust whole-body regeneration capacity, planarians have been model organisms in regenerative research for more than 240 years. Advancements in research tools and techniques have progressively elucidated the mechanisms underlying planarian regeneration. Accurate cell-cell communication is recognized as a fundamental requirement for regeneration. In recent decades, mechanisms associated with such communication have been revealed at the cellular level. Notably, stem cells (neoblasts) have been identified as the source of all new cells during planarian homeostasis and regeneration. The interplay between neoblasts and somatic cells affects the identities and proportions of various tissues during homeostasis and regeneration. Here, this review outlines key discoveries regarding communication between stem cell compartments and other cell types in planarians, as well as the impact of communication on planarian regeneration. Additionally, this review discusses the challenges and potential directions of future planarian research, emphasizing the sustained impact of this field on our understanding of animal regeneration.
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Affiliation(s)
- Jia-Jia Chen
- School of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Kai Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China. E-mail:
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13
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Su-Tobon Q, Fan J, Feeney K, Ren H, Autissier P, Wang P, Huang Y, Niu J. CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555185. [PMID: 37693461 PMCID: PMC10491168 DOI: 10.1101/2023.08.29.555185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Recent advances in gene editing and precise regulation of gene expression based on CRISPR technologies have provided powerful tools for the understanding and manipulation of gene functions. Fusing RNA aptamers to the sgRNA of CRISPR can recruit cognate RNA-binding protein (RBP) effectors to target genomic sites, and the expression of sgRNA containing different RNA aptamers permit simultaneous multiplexed and multifunctional gene regulations. Here, we report an intracellular directed evolution platform for RNA aptamers against intracellularly expressed RBPs. We optimized a bacterial CRISPR-hybrid system coupled with FACS, and identified novel high affinity RNA aptamers orthogonal to existing aptamer-RBP pairs. Application of orthogonal aptamer-RBP pairs in multiplexed CRISPR allowed effective simultaneous transcriptional activation and repression of endogenous genes in mammalian cells.
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14
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Fan Y, Chai C, Li P, Zou X, Ferrell JE, Wang B. Ultrafast distant wound response is essential for whole-body regeneration. Cell 2023; 186:3606-3618.e16. [PMID: 37480850 PMCID: PMC10957142 DOI: 10.1016/j.cell.2023.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/11/2023] [Accepted: 06/23/2023] [Indexed: 07/24/2023]
Abstract
Injury induces systemic responses, but their functions remain elusive. Mechanisms that can rapidly synchronize wound responses through long distances are also mostly unknown. Using planarian flatworms capable of whole-body regeneration, we report that injury induces extracellular signal-regulated kinase (Erk) activity waves to travel at a speed 10-100 times faster than those in other multicellular tissues. This ultrafast propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. The morphological properties of muscles allow them to act as superhighways for propagating and disseminating wound signals. Inhibiting Erk propagation prevents tissues distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues shortly after the first injury. Our findings provide a mechanism for long-range signal propagation in large, complex tissues to coordinate responses across cell types and highlight the function of feedback between spatially separated tissues during whole-body regeneration.
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Affiliation(s)
- Yuhang Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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15
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Pio-Lopez L, Bischof J, LaPalme JV, Levin M. The scaling of goals from cellular to anatomical homeostasis: an evolutionary simulation, experiment and analysis. Interface Focus 2023; 13:20220072. [PMID: 37065270 PMCID: PMC10102734 DOI: 10.1098/rsfs.2022.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/02/2023] [Indexed: 04/18/2023] Open
Abstract
Complex living agents consist of cells, which are themselves competent sub-agents navigating physiological and metabolic spaces. Behaviour science, evolutionary developmental biology and the field of machine intelligence all seek to understand the scaling of biological cognition: what enables individual cells to integrate their activities to result in the emergence of a novel, higher-level intelligence with large-scale goals and competencies that belong to it and not to its parts? Here, we report the results of simulations based on the TAME framework, which proposes that evolution pivoted the collective intelligence of cells during morphogenesis of the body into traditional behavioural intelligence by scaling up homeostatic competencies of cells in metabolic space. In this article, we created a minimal in silico system (two-dimensional neural cellular automata) and tested the hypothesis that evolutionary dynamics are sufficient for low-level setpoints of metabolic homeostasis in individual cells to scale up to tissue-level emergent behaviour. Our system showed the evolution of the much more complex setpoints of cell collectives (tissues) that solve a problem in morphospace: the organization of a body-wide positional information axis (the classic French flag problem in developmental biology). We found that these emergent morphogenetic agents exhibit a number of predicted features, including the use of stress propagation dynamics to achieve the target morphology as well as the ability to recover from perturbation (robustness) and long-term stability (even though neither of these was directly selected for). Moreover, we observed an unexpected behaviour of sudden remodelling long after the system stabilizes. We tested this prediction in a biological system-regenerating planaria-and observed a very similar phenomenon. We propose that this system is a first step towards a quantitative understanding of how evolution scales minimal goal-directed behaviour (homeostatic loops) into higher-level problem-solving agents in morphogenetic and other spaces.
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Affiliation(s)
- Léo Pio-Lopez
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | | | | | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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16
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Kaethner M, Epping K, Bernthaler P, Rudolf K, Thomann I, Leitschuh N, Bergmann M, Spiliotis M, Koziol U, Brehm K. Transforming growth factor-β signalling regulates protoscolex formation in the Echinococcus multilocularis metacestode. Front Cell Infect Microbiol 2023; 13:1153117. [PMID: 37033489 PMCID: PMC10073696 DOI: 10.3389/fcimb.2023.1153117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/23/2023] [Indexed: 04/11/2023] Open
Abstract
The lethal zoonosis alveolar echinococcosis (AE) is caused by tumor-like, infiltrative growth of the metacestode larval stage of the tapeworm Echinococcus multilocularis. We previously showed that the metacestode is composed of posteriorized tissue and that the production of the subsequent larval stage, the protoscolex, depends on re-establishment of anterior identities within the metacestode germinative layer. It is, however, unclear so far how protoscolex differentiation in Echinococcus is regulated. We herein characterized the full complement of E. multilocularis TGFβ/BMP receptors, which is composed of one type II and three type I receptor serine/threonine kinases. Functional analyzes showed that all Echinococcus TGFβ/BMP receptors are enzymatically active and respond to host derived TGFβ/BMP ligands for activating downstream Smad transcription factors. In situ hybridization experiments demonstrated that the Echinococcus TGFβ/BMP receptors are mainly expressed by nerve and muscle cells within the germinative layer and in developing brood capsules. Interestingly, the production of brood capsules, which later give rise to protoscoleces, was strongly suppressed in the presence of inhibitors directed against TGFβ/BMP receptors, whereas protoscolex differentiation was accelerated in response to host BMP2 and TGFβ. Apart from being responsive to host TGFβ/BMP ligands, protoscolex production also correlated with the expression of a parasite-derived TGFβ-like ligand, EmACT, which is expressed in early brood capsules and which is strongly expressed in anterior domains during protoscolex development. Taken together, these data indicate an important role of TGFβ/BMP signalling in Echinococcus anterior pole formation and protoscolex development. Since TGFβ is accumulating around metacestode lesions at later stages of the infection, the host immune response could thus serve as a signal by which the parasite senses the time point at which protoscoleces must be produced. Overall, our data shed new light on molecular mechanisms of host-parasite interaction during AE and are relevant for the development of novel treatment strategies.
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Affiliation(s)
- Marc Kaethner
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Kerstin Epping
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Peter Bernthaler
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Kilian Rudolf
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Irena Thomann
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Nadine Leitschuh
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Laboratory of Microbiology and Biotechnology, Department of Food Technology, Fulda University of Applied Sciences, Fulda, Germany
| | - Monika Bergmann
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Markus Spiliotis
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Uriel Koziol
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Klaus Brehm
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
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17
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Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers B, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Multiscale integration of human and single-cell variations reveals unadjuvanted vaccine high responders are naturally adjuvanted. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.20.23287474. [PMID: 37090674 PMCID: PMC10120791 DOI: 10.1101/2023.03.20.23287474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Advances in multimodal single cell analysis can empower high-resolution dissection of human vaccination responses. The resulting data capture multiple layers of biological variations, including molecular and cellular states, vaccine formulations, inter- and intra-subject differences, and responses unfolding over time. Transforming such data into biological insight remains a major challenge. Here we present a systematic framework applied to multimodal single cell data obtained before and after influenza vaccination without adjuvants or pandemic H5N1 vaccination with the AS03 adjuvant. Our approach pinpoints responses shared across or unique to specific cell types and identifies adjuvant specific signatures, including pro-survival transcriptional states in B lymphocytes that emerged one day after vaccination. We also reveal that high antibody responders to the unadjuvanted vaccine have a distinct baseline involving a rewired network of cell type specific transcriptional states. Remarkably, the status of certain innate immune cells in this network in high responders of the unadjuvanted vaccine appear "naturally adjuvanted": they resemble phenotypes induced early in the same cells only by vaccination with AS03. Furthermore, these cell subsets have elevated frequency in the blood at baseline and increased cell-intrinsic phospho-signaling responses after LPS stimulation ex vivo in high compared to low responders. Our findings identify how variation in the status of multiple immune cell types at baseline may drive robust differences in innate and adaptive responses to vaccination and thus open new avenues for vaccine development and immune response engineering in humans.
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Affiliation(s)
- Matthew P. Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Brian Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juan A. Quiel
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Arjun Jain
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Pamela L. Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cell Signaling and Immunity Section, NIAID, NIH, Bethesda, MD, USA
| | - John S. Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
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18
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Fan Y, Chai C, Li P, Zou X, Ferrell JE, Wang B. Ultrafast and long-range coordination of wound responses is essential for whole-body regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532844. [PMID: 36993633 PMCID: PMC10055111 DOI: 10.1101/2023.03.15.532844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Injury induces systemic, global responses whose functions remain elusive. In addition, mechanisms that rapidly synchronize wound responses through long distances across the organismal scale are mostly unknown. Using planarians, which have extreme regenerative ability, we report that injury induces Erk activity to travel in a wave-like manner at an unexpected speed (∼1 mm/h), 10-100 times faster than those measured in other multicellular tissues. This ultrafast signal propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. Combining experiments and computational models, we show that the morphological properties of muscles allow them to minimize the number of slow intercellular signaling steps and act as bidirectional superhighways for propagating wound signals and instructing responses in other cell types. Inhibiting Erk propagation prevents cells distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues within a narrow time window after the first injury. These results suggest that rapid responses in uninjured tissues far from wounds are essential for regeneration. Our findings provide a mechanism for long-range signal propagation in large and complex tissues to coordinate cellular responses across diverse cell types, and highlights the function of feedback between spatially separated tissues during whole-body regeneration.
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Affiliation(s)
- Yuhang Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - James E. Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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19
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Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration. Nat Commun 2023; 14:298. [PMID: 36653403 PMCID: PMC9849279 DOI: 10.1038/s41467-023-35937-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process; the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the Wnt/β-catenin signal specifies anterior versus posterior identity. Initially, both wnt1 and notum (Wnt inhibitor) are expressed in all wounds, but 48 hours later they are restricted to posterior or anterior facing wounds, respectively, by an unknown mechanism. Here we show that 12 hours after amputation, the chromatin accessibility of cells in the wound region changes according to the polarity of the pre-existing tissue in a Wnt/β-catenin-dependent manner. Genomic analyses suggest that homeobox transcription factors and chromatin-remodeling proteins are direct Wnt/β-catenin targets, which trigger the expression of posterior effectors. Finally, we identify FoxG as a wnt1 up-stream regulator, probably via binding to its first intron enhancer region.
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20
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Petersen CP. Wnt signaling in whole-body regeneration. Curr Top Dev Biol 2023; 153:347-380. [PMID: 36967200 DOI: 10.1016/bs.ctdb.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Regeneration abilities are widespread among animals and select species can restore any body parts removed by wounds that sever the major body axes. This capability of whole-body regeneration as exemplified in flatworm planarians, Acoels, and Cnidarians involves initial responses to injury, the assessment of wound site polarization, determination of missing tissue and programming of blastema fate, and patterned outgrowth to restore axis content and proportionality. Wnt signaling drives many shared and conserved aspects of the biology of whole-body regeneration in the planarian species Schmidtea mediterranea and Dugesia japonica, in the Acoel Hofstenia miamia, and in Cnidarians Hydra and Nematostella. These overlapping mechanisms suggest whole-body regeneration might be an ancestral property across diverse animal taxa.
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Affiliation(s)
- Christian P Petersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States; Robert Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, United States.
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21
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Ge XY, Han X, Zhao YL, Cui GS, Yang YG. An insight into planarian regeneration. Cell Prolif 2022; 55:e13276. [PMID: 35811385 PMCID: PMC9436907 DOI: 10.1111/cpr.13276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/22/2022] [Accepted: 05/17/2022] [Indexed: 11/29/2022] Open
Abstract
Background Planarian has attracted increasing attentions in the regeneration field for its usefulness as an important biological model organism attributing to its strong regeneration ability. Both the complexity of multiple regulatory networks and their coordinate functions contribute to the maintenance of normal cellular homeostasis and the process of regeneration in planarian. The polarity, size, location and number of regeneration tissues are regulated by diverse mechanisms. In this review we summarize the recent advances about the importance genetic and molecular mechanisms for regeneration control on various tissues in planarian. Methods A comprehensive literature search of original articles published in recent years was performed in regards to the molecular mechanism of each cell types during the planarian regeneration, including neoblast, nerve system, eye spot, excretory system and epidermal. Results Available molecular mechanisms gave us an overview of regeneration process in every tissue. The sense of injuries and initiation of regeneration is regulated by diverse genes like follistatin and ERK signaling. The Neoblasts differentiate into tissue progenitors under the regulation of genes such as egfr‐3. The regeneration polarity is controlled by Wnt pathway, BMP pathway and bioelectric signals. The neoblast within the blastema differentiate into desired cell types and regenerate the missing tissues. Those tissue specific genes regulate the tissue progenitor cells to differentiate into desired cell types to complete the regeneration process. Conclusion All tissue types in planarian participate in the regeneration process regulated by distinct molecular factors and cellular signaling pathways. The neoblasts play vital roles in tissue regeneration and morphology maintenance. These studies provide new insights into the molecular mechanisms for regulating planarian regeneration.
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Affiliation(s)
- Xin-Yang Ge
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Xiao Han
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Guan-Shen Cui
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
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22
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Scimone ML, Cloutier JK, Maybrun CL, Reddien PW. The planarian wound epidermis gene equinox is required for blastema formation in regeneration. Nat Commun 2022; 13:2726. [PMID: 35585061 PMCID: PMC9117669 DOI: 10.1038/s41467-022-30412-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/09/2022] [Indexed: 11/25/2022] Open
Abstract
Regeneration often involves the formation of a blastema, an outgrowth or regenerative bud formed at the plane of injury where missing tissues are produced. The mechanisms that trigger blastema formation are therefore fundamental for regeneration. Here, we identify a gene, which we named equinox, that is expressed within hours of injury in the planarian wound epidermis. equinox encodes a predicted secreted protein that is conserved in many animal phyla. Following equinox inhibition, amputated planarians fail to maintain wound-induced gene expression and to subsequently undergo blastema outgrowth. Associated with these defects is an inability to reestablish lost positional information needed for missing tissue specification. Our findings link the planarian wound epidermis, through equinox, to regeneration of positional information and blastema formation, indicating a broad regulatory role of the wound epidermis in diverse regenerative contexts.
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Affiliation(s)
- M Lucila Scimone
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Jennifer K Cloutier
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Harvard/MIT MD-PhD, Harvard Medical School, Boston, MA, 02115, USA
| | - Chloe L Maybrun
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Peter W Reddien
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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23
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Reddien PW. Positional Information and Stem Cells Combine to Result in Planarian Regeneration. Cold Spring Harb Perspect Biol 2022; 14:a040717. [PMID: 34518341 PMCID: PMC9121904 DOI: 10.1101/cshperspect.a040717] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The capacity for regeneration is broad in the animal kingdom. Planarians are flatworms that can regenerate any missing body part and their regenerative powers have combined with ease of experimentation to make them a classic regeneration model for more than a century. Pluripotent stem cells called neoblasts generate missing planarian tissues. Fate specification happens in the neoblasts, and this can occur in response to regeneration instructions in the form of positional information. Fate specification can lead to differentiating cells in single steps rather than requiring a long lineage hierarchy. Planarians display constitutive expression of positional information from muscle cells, which is required for patterned maintenance of tissues in tissue turnover. Amputation leads to the rapid resetting of positional information in a process triggered by wound signaling and the resetting of positional information is required for regeneration. These findings suggest a model for planarian regeneration in which adult positional information resets after injury to regulate stem cells to bring about the replacement of missing parts.
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Affiliation(s)
- Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
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24
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Sarkar SR, Dubey VK, Jahagirdar A, Lakshmanan V, Haroon MM, Sowndarya S, Sowdhamini R, Palakodeti D. DDX24 is required for muscle fiber organization and the suppression of wound-induced Wnt activity necessary for pole re-establishment during planarian regeneration. Dev Biol 2022; 488:11-29. [PMID: 35523320 DOI: 10.1016/j.ydbio.2022.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/06/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
Abstract
Planarians have a remarkable ability to undergo whole-body regeneration. Successful regeneration outcome is determined by processes like polarity establishment at the wound site, which is followed by pole (organizer) specification. Interestingly, these determinants are almost exclusively expressed by muscles in these animals. However, the molecular toolkit that enables the functional versatility of planarian muscles remains poorly understood. Here we report that SMED_DDX24, a D-E-A-D Box RNA helicase, is necessary for planarian survival and regeneration. We found that DDX24 is enriched in muscles and its knockdown disrupts muscle fiber organization. This leads to defective pole specification, which in turn results in misregulation of many positional control genes specifically during regeneration. ddx24 RNAi also upregulates wound-induced Wnt signalling. Suppressing this ectopic Wnt activity rescues the knockdown phenotype by enabling better anterior pole regeneration. To summarize, our work highlights the role of an RNA helicase in muscle fiber organization, and modulating amputation-induced wnt levels, both of which seem critical for pole re-organization, thereby regulating whole-body regeneration.
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Affiliation(s)
- Souradeep R Sarkar
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bengaluru, 560065, India; Integrative Chemical Biology (ICB), Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, 560065, India
| | - Vinay Kumar Dubey
- Integrative Chemical Biology (ICB), Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, 560065, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anusha Jahagirdar
- Integrative Chemical Biology (ICB), Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, 560065, India
| | - Vairavan Lakshmanan
- Integrative Chemical Biology (ICB), Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, 560065, India
| | - Mohamed Mohamed Haroon
- Integrative Chemical Biology (ICB), Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, 560065, India; SASTRA University, Thanjavur, 613401, India
| | - Sai Sowndarya
- Integrative Chemical Biology (ICB), Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bengaluru, 560065, India
| | - Dasaradhi Palakodeti
- Integrative Chemical Biology (ICB), Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, 560065, India.
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25
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Luo L, Santos A, Konganti K, Hillhouse A, Lambertz IU, Zheng Y, Gunaratna RT, Threadgill DW, Fuchs-Young RS. Overexpression of IGF-1 During Early Development Expands the Number of Mammary Stem Cells and Primes them for Transformation. Stem Cells 2022; 40:273-289. [DOI: 10.1093/stmcls/sxab018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Insulin-like growth factor I (IGF-1) has been implicated in breast cancer due to its mitogenic and anti-apoptotic effects. Despite substantial research on the role of IGF-1 in tumor progression, the relationship of IGF-1 to tissue stem cells, particularly in mammary tissue, and the resulting tumor susceptibility has not been elucidated. Previous studies with the BK5.IGF-1 transgenic (Tg) mouse model reveals that IGF-1 does not act as a classical, post-carcinogen tumor promoter in the mammary gland. Pre-pubertal Tg mammary glands display increased numbers and enlarged sizes of terminal end buds, a niche for mammary stem cells (MaSCs). Here we show that MaSCs from both wild type (WT) and Tg mice expressed IGF-1R and that overexpression of Tg IGF-1 increased numbers of MaSCs by undergoing symmetric division, resulting in an expansion of the MaSC and luminal progenitor (LP) compartments in pre-pubertal female mice. This expansion was maintained post-pubertally and validated by mammosphere assays in vitro and transplantation assays in vivo. The addition of recombinant IGF-1 promoted, and IGF-1R downstream inhibitors decreased mammosphere formation. Single-cell transcriptomic profiles generated from two related platforms reveal that IGF-1 stimulated quiescent MaSCs to enter the cell cycle and increased their expression of genes involved in proliferation, plasticity, tumorigenesis, invasion, and metastasis. This study identifies a novel, pro-tumorigenic mechanism, where IGF-1 increases the number of transformation-susceptible carcinogen targets during the early stages of mammary tissue development, and “primes” their gene expression profiles for transformation.
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Affiliation(s)
- Linjie Luo
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andres Santos
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Department of Anatomic Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences & Society, Texas A&M University, College Station, TX, USA
| | - Andrew Hillhouse
- Texas A&M Institute for Genome Sciences & Society, Texas A&M University, College Station, TX, USA
| | - Isabel U Lambertz
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Yuanning Zheng
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Ramesh T Gunaratna
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Texas A&M Institute for Genome Sciences & Society, Texas A&M University, College Station, TX, USA
| | - Robin S Fuchs-Young
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
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26
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Benham-Pyle BW, Brewster CE, Kent AM, Mann FG, Chen S, Scott AR, Box AC, Sánchez Alvarado A. Identification of rare, transient post-mitotic cell states that are induced by injury and required for whole-body regeneration in Schmidtea mediterranea. Nat Cell Biol 2021; 23:939-952. [PMID: 34475533 PMCID: PMC8855990 DOI: 10.1038/s41556-021-00734-6] [Citation(s) in RCA: 15] [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: 05/17/2020] [Accepted: 07/14/2021] [Indexed: 01/02/2023]
Abstract
Regeneration requires the coordination of stem cells, their progeny and distant differentiated tissues. Here, we present a comprehensive atlas of whole-body regeneration in Schmidtea mediterranea and identify wound-induced cell states. An analysis of 299,998 single-cell transcriptomes captured from regeneration-competent and regeneration-incompetent fragments identified transient regeneration-activated cell states (TRACS) in the muscle, epidermis and intestine. TRACS were independent of stem cell division with distinct spatiotemporal distributions, and RNAi depletion of TRACS-enriched genes produced regeneration defects. Muscle expression of notum, follistatin, evi/wls, glypican-1 and junctophilin-1 was required for tissue polarity. Epidermal expression of agat-1/2/3, cyp3142a1, zfhx3 and atp1a1 was important for stem cell proliferation. Finally, expression of spectrinβ and atp12a in intestinal basal cells, and lrrk2, cathepsinB, myosin1e, polybromo-1 and talin-1 in intestinal enterocytes regulated stem cell proliferation and tissue remodelling, respectively. Our results identify cell types and molecules that are important for regeneration, indicating that regenerative ability can emerge from coordinated transcriptional plasticity across all three germ layers.
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Affiliation(s)
- Blair W Benham-Pyle
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Howard Hughes Institute for Medical Research, Kansas City, MO, USA.
| | | | - Aubrey M Kent
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Frederick G Mann
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Howard Hughes Institute for Medical Research, Kansas City, MO, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Andrew C Box
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Howard Hughes Institute for Medical Research, Kansas City, MO, USA.
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27
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Srivastava M. Beyond Casual Resemblances: Rigorous Frameworks for Comparing Regeneration Across Species. Annu Rev Cell Dev Biol 2021; 37:415-440. [PMID: 34288710 DOI: 10.1146/annurev-cellbio-120319-114716] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells are discussed as examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mansi Srivastava
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;
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28
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Bohr TE, Shiroor DA, Adler CE. Planarian stem cells sense the identity of the missing pharynx to launch its targeted regeneration. eLife 2021; 10:e68830. [PMID: 34156924 PMCID: PMC8219383 DOI: 10.7554/elife.68830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
In order to regenerate tissues successfully, stem cells must detect injuries and restore missing cell types through largely unknown mechanisms. Planarian flatworms have an extensive stem cell population responsible for regenerating any organ after amputation. Here, we compare planarian stem cell responses to different injuries by either amputation of a single organ, the pharynx, or removal of tissues from other organs by decapitation. We find that planarian stem cells adopt distinct behaviors depending on what tissue is missing to target progenitor and tissue production towards missing tissues. Loss of non-pharyngeal tissues only increases non-pharyngeal progenitors, while pharynx removal selectively triggers division and expansion of pharynx progenitors. By pharmacologically inhibiting either mitosis or activation of the MAP kinase ERK, we identify a narrow window of time during which stem cell division and ERK signaling produces pharynx progenitors necessary for regeneration. These results indicate that planarian stem cells can tailor their output to match the regenerative needs of the animal.
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Affiliation(s)
- Tisha E Bohr
- Department of Molecular Medicine, Cornell University College of Veterinary MedicineIthacaUnited States
| | - Divya A Shiroor
- Department of Molecular Medicine, Cornell University College of Veterinary MedicineIthacaUnited States
| | - Carolyn E Adler
- Department of Molecular Medicine, Cornell University College of Veterinary MedicineIthacaUnited States
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29
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Ramirez AN, Loubet-Senear K, Srivastava M. A Regulatory Program for Initiation of Wnt Signaling during Posterior Regeneration. Cell Rep 2021; 32:108098. [PMID: 32877680 DOI: 10.1016/j.celrep.2020.108098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/03/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Whole-body regeneration relies on the re-establishment of body axes for patterning of new tissue. Wnt signaling is required to correctly regenerate tissues along the primary axis in many animals. However, the causal mechanisms that first launch Wnt signaling during regeneration are poorly characterized. We use the acoel worm Hofstenia miamia to identify processes that initiate Wnt signaling during posterior regeneration and find that the ligand wnt-3 is upregulated early in posterior-facing wounds. Functional studies reveal that wnt-3 is required to regenerate posterior tissues. wnt-3 is expressed in stem cells, it is needed for their proliferation, and its function is stem cell dependent. Chromatin accessibility data reveal that wnt-3 activation requires input from the general wound response. In addition, the expression of a different Wnt ligand, wnt-1, before amputation is required for wound-induced activation of wnt-3. Our study establishes a gene regulatory network for initiating Wnt signaling in posterior tissues in a bilaterian.
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Affiliation(s)
- Alyson N Ramirez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kaitlyn Loubet-Senear
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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30
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Cloutier JK, McMann CL, Oderberg IM, Reddien PW. activin-2 is required for regeneration of polarity on the planarian anterior-posterior axis. PLoS Genet 2021; 17:e1009466. [PMID: 33780442 PMCID: PMC8057570 DOI: 10.1371/journal.pgen.1009466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/20/2021] [Accepted: 03/03/2021] [Indexed: 01/16/2023] Open
Abstract
Planarians are flatworms and can perform whole-body regeneration. This ability involves a mechanism to distinguish between anterior-facing wounds that require head regeneration and posterior-facing wounds that require tail regeneration. How this head-tail regeneration polarity decision is made is studied to identify principles underlying tissue-identity specification in regeneration. We report that inhibition of activin-2, which encodes an Activin-like signaling ligand, resulted in the regeneration of ectopic posterior-facing heads following amputation. During tissue turnover in uninjured planarians, positional information is constitutively expressed in muscle to maintain proper patterning. Positional information includes Wnts expressed in the posterior and Wnt antagonists expressed in the anterior. Upon amputation, several wound-induced genes promote re-establishment of positional information. The head-versus-tail regeneration decision involves preferential wound induction of the Wnt antagonist notum at anterior-facing over posterior-facing wounds. Asymmetric activation of notum represents the earliest known molecular distinction between head and tail regeneration, yet how it occurs is unknown. activin-2 RNAi animals displayed symmetric wound-induced activation of notum at anterior- and posterior-facing wounds, providing a molecular explanation for their ectopic posterior-head phenotype. activin-2 RNAi animals also displayed anterior-posterior (AP) axis splitting, with two heads appearing in anterior blastemas, and various combinations of heads and tails appearing in posterior blastemas. This was associated with ectopic nucleation of anterior poles, which are head-tip muscle cells that facilitate AP and medial-lateral (ML) pattern at posterior-facing wounds. These findings reveal a role for Activin signaling in determining the outcome of AP-axis-patterning events that are specific to regeneration. A central problem in animal regeneration is how animals determine what body part to regenerate. Planarians are flatworms that can regenerate any missing body region, and are studied to identify mechanisms underlying regeneration. At transverse amputation planes, a poorly understood mechanism specifies regeneration of either a head or a tail. This head-versus-tail regeneration decision-making process is referred to as regeneration polarity and has been studied for over a century to identify mechanisms that specify what to regenerate. The gene notum, which encodes a Wnt antagonist, is induced within hours after injury preferentially at anterior-facing wounds, where it specifies head regeneration. We report that Activin signaling is required for regeneration polarity, and the underlying asymmetric activation of notum at anterior- over posterior-facing wounds. We propose that Activin signaling is involved in regeneration-specific responses broadly in the animal kingdom.
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Affiliation(s)
- Jennifer K. Cloutier
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD, United States of America
- Harvard/MIT MD-PhD, Harvard Medical School, Boston, MA, United States of America
| | - Conor L. McMann
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD, United States of America
| | - Isaac M. Oderberg
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD, United States of America
| | - Peter W. Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD, United States of America
- * E-mail:
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31
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Stelman CR, Smith BM, Chandra B, Roberts-Galbraith RH. CBP/p300 homologs CBP2 and CBP3 play distinct roles in planarian stem cell function. Dev Biol 2021; 473:130-143. [PMID: 33607113 DOI: 10.1016/j.ydbio.2021.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/19/2022]
Abstract
Chromatin modifications function as critical regulators of gene expression and cellular identity, especially in the regulation and maintenance of the pluripotent state. However, many studies of chromatin modification in stem cells-and pluripotent stem cells in particular-are performed in mammalian stem cell culture, an in vitro condition mimicking a very transient state during mammalian development. Thus, new models for studying pluripotent stem cells in vivo could be helpful for understanding the roles of chromatin modification, for confirming prior in vitro studies, and for exploring evolution of the pluripotent state. The freshwater flatworm, Schmidtea mediterranea, is an excellent model for studying adult pluripotent stem cells, particularly in the context of robust, whole-body regeneration. To identify chromatin modifying and remodeling enzymes critical for planarian regeneration and stem cell maintenance, we took a candidate approach and screened planarian homologs of 25 genes known to regulate chromatin biology in other organisms. Through our study, we identified six genes with novel functions in planarian homeostasis, regeneration, and behavior. Of the list of genes characterized, we identified five planarian homologs of the mammalian CREB-Binding Protein (CBP) and p300 family of histone acetyltransferases, representing an expansion of this family in planarians. We find that two planarian CBP family members are required for planarian survival, with knockdown of Smed-CBP2 and Smed-CBP3 causing distinct defects in stem cell maintenance or function. Loss of CBP2 causes a quick, dramatic loss of stem cells, while knockdown of CBP3 affects stem cells more narrowly, influencing differentiation of several cell types that include neuronal subtypes and cells of the eye. Further, we find that Smed-CBP1 is required for planarian fissioning behavior. We propose that the division of labor among a diversified CBP family in planarians presents an opportunity to dissect specific functions of a broadly important histone acetyltransferase family.
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Affiliation(s)
- Clara R Stelman
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Britessia M Smith
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Bidushi Chandra
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Rachel H Roberts-Galbraith
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Cellular Biology, University of Georgia, Athens, GA, USA.
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32
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Abarca-Buis RF, Mandujano-Tinoco EA, Cabrera-Wrooman A, Krötzsch E. The complexity of TGFβ/activin signaling in regeneration. J Cell Commun Signal 2021; 15:7-23. [PMID: 33481173 DOI: 10.1007/s12079-021-00605-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
The role of transforming growth factor β TGFβ/activin signaling in wound repair and regeneration is highly conserved in the animal kingdom. Various studies have shown that TGF-β/activin signaling can either promote or inhibit different aspects of the regeneration process (i.e., proliferation, differentiation, and re-epithelialization). It has been demonstrated in several biological systems that some of the different cellular responses promoted by TGFβ/activin signaling depend on the activation of Smad-dependent or Smad-independent signal transduction pathways. In the context of regeneration and wound healing, it has been shown that the type of R-Smad stimulated determines the different effects that can be obtained. However, neither the possible roles of Smad-independent pathways nor the interaction of the TGFβ/activin pathway with other complex signaling networks involved in the regenerative process has been studied extensively. Here, we review the important aspects concerning the TGFβ/activin signaling pathway in the regeneration process. We discuss data regarding the role of TGF-β/activin in the most common animal regenerative models to demonstrate how this signaling promotes or inhibits regeneration, depending on the cellular context.
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Affiliation(s)
- René Fernando Abarca-Buis
- Laboratory of Connective Tissue, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación "Luís Guillermo Ibarra Ibarra", Calzada México-Xochimilco No. 289, Col. Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico.
| | - Edna Ayerim Mandujano-Tinoco
- Laboratory of Connective Tissue, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación "Luís Guillermo Ibarra Ibarra", Calzada México-Xochimilco No. 289, Col. Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico
| | - Alejandro Cabrera-Wrooman
- Laboratory of Connective Tissue, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación "Luís Guillermo Ibarra Ibarra", Calzada México-Xochimilco No. 289, Col. Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico
| | - Edgar Krötzsch
- Laboratory of Connective Tissue, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación "Luís Guillermo Ibarra Ibarra", Calzada México-Xochimilco No. 289, Col. Arenal de Guadalupe, Tlalpan, 14389, Mexico City, Mexico
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33
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Winkler J, De Meyer A, Mylle E, Storme V, Grones P, Van Damme D. Nanobody-Dependent Delocalization of Endocytic Machinery in Arabidopsis Root Cells Dampens Their Internalization Capacity. FRONTIERS IN PLANT SCIENCE 2021. [PMID: 33815429 DOI: 10.1101/2020.02.27.968446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant cells perceive and adapt to an ever-changing environment by modifying their plasma membrane (PM) proteome. Whereas secretion deposits new integral membrane proteins, internalization by endocytosis removes membrane proteins and associated ligands, largely with the aid of adaptor protein (AP) complexes and the scaffolding molecule clathrin. Two AP complexes function in clathrin-mediated endocytosis at the PM in plant cells, the heterotetrameric AP-2 complex and the hetero-octameric TPLATE complex (TPC). Whereas single subunit mutants in AP-2 develop into viable plants, genetic mutation of a single TPC subunit causes fully penetrant male sterility and silencing single subunits leads to seedling lethality. To address TPC function in somatic root cells, while minimizing indirect effects on plant growth, we employed nanobody-dependent delocalization of a functional, GFP-tagged TPC subunit, TML, in its respective homozygous genetic mutant background. In order to decrease the amount of functional TPC at the PM, we targeted our nanobody construct to the mitochondria and fused it to TagBFP2 to visualize it independently of its bait. We furthermore limited the effect of our delocalization to those tissues that are easily accessible for live-cell imaging by expressing it from the PIN2 promoter, which is active in root epidermal and cortex cells. With this approach, we successfully delocalized TML from the PM. Moreover, we also show co-recruitment of TML-GFP and AP2A1-TagRFP to the mitochondria, suggesting that our approach delocalized complexes, rather than individual adaptor complex subunits. In line with the specific expression domain, we only observed minor effects on root growth, yet realized a clear reduction of endocytic flux in epidermal root cells. Nanobody-dependent delocalization in plants, here exemplified using a TPC subunit, has the potential to be widely applicable to achieve specific loss-of-function analysis of otherwise lethal mutants.
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Affiliation(s)
- Joanna Winkler
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Andreas De Meyer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Peter Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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34
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Forsthoefel DJ, Cejda NI, Khan UW, Newmark PA. Cell-type diversity and regionalized gene expression in the planarian intestine. eLife 2020; 9:e52613. [PMID: 32240093 PMCID: PMC7117911 DOI: 10.7554/elife.52613] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.
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Affiliation(s)
- David J Forsthoefel
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Nicholas I Cejda
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
| | - Umair W Khan
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Phillip A Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
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35
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Tewari AG, Stern SR, Oderberg IM, Reddien PW. Cellular and Molecular Responses Unique to Major Injury Are Dispensable for Planarian Regeneration. Cell Rep 2019; 25:2577-2590.e3. [PMID: 30485821 PMCID: PMC6475882 DOI: 10.1016/j.celrep.2018.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/11/2018] [Accepted: 10/31/2018] [Indexed: 11/18/2022] Open
Abstract
The fundamental requirements for regeneration are poorly understood. Planarians can robustly regenerate all tissues after injury, involving stem cells, positional information, and a set of cellular and molecular responses collectively called the "missing tissue" or "regenerative" response. follistatin, which encodes an extracellular Activin inhibitor, is required for the missing tissue response after head amputation and for subsequent regeneration. We found that follistatin is required for the missing tissue response regardless of the wound context, but causes regeneration failure only after head amputation. This head regeneration failure involves follistatin-mediated regulation of Wnt signaling at wounds and is not a consequence of a diminished missing tissue response. All tested contexts of regeneration, including head regeneration, could occur with a defective missing tissue response, but at a slower pace. Our findings suggest that major cellular and molecular programs induced specifically by large injuries function to accelerate regeneration but are dispensable for regeneration itself.
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Affiliation(s)
- Aneesha G Tewari
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah R Stern
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isaac M Oderberg
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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36
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Gehrke AR, Neverett E, Luo YJ, Brandt A, Ricci L, Hulett RE, Gompers A, Ruby JG, Rokhsar DS, Reddien PW, Srivastava M. Acoel genome reveals the regulatory landscape of whole-body regeneration. Science 2019; 363:363/6432/eaau6173. [PMID: 30872491 DOI: 10.1126/science.aau6173] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
Whole-body regeneration is accompanied by complex transcriptomic changes, yet the chromatin regulatory landscapes that mediate this dynamic response remain unexplored. To decipher the regulatory logic that orchestrates regeneration, we sequenced the genome of the acoel worm Hofstenia miamia, a highly regenerative member of the sister lineage of other bilaterians. Epigenomic profiling revealed thousands of regeneration-responsive chromatin regions and identified dynamically bound transcription factor motifs, with the early growth response (EGR) binding site as the most variably accessible during Hofstenia regeneration. Combining egr inhibition with chromatin profiling suggests that Egr functions as a pioneer factor to directly regulate early wound-induced genes. The genetic connections inferred by this approach allowed the construction of a gene regulatory network for whole-body regeneration, enabling genomics-based comparisons of regeneration across species.
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Affiliation(s)
- Andrew R Gehrke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Emily Neverett
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Brandt
- Department of Chemistry, University of California, Berkeley, CA 94703, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Annika Gompers
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - J Graham Ruby
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94703, USA
| | - Peter W Reddien
- Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. .,Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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37
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Zhao XS, Huang XJ. Seeking biomarkers for acute graft-versus-host disease: where we are and where we are heading? Biomark Res 2019; 7:17. [PMID: 31406575 PMCID: PMC6685226 DOI: 10.1186/s40364-019-0167-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/10/2019] [Indexed: 12/16/2022] Open
Abstract
Acute graft-versus-host disease (aGVHD) is one of the most important complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT), which would seriously affect the clinical outcomes of patients. Early diagnosis and early intervention are keys for improving its curative efficacy. Thus, seeking the biomarkers of aGVHD that can accurately identify and diagnose aGVHD is very important to guiding the intervention and treatment of aGVHD. For the past decades, many studies have focused on searching for aGVHD-related biological markers to assist in diagnosis, early warning, and risk stratification. Unfortunately, until now, no reliable aGVHD biomarker is available that is recognized and widely used in clinical practice. With the continuous development of biological technology, as well as our in-depth understanding of the pathophysiologic mechanism of aGVHD, the selection, examination and application of biological markers have changed much. In this review, we summarized the progress of aGVHD biological marker screening, identification, preliminary clinical application, and look forward to a promising development direction in the future.
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Affiliation(s)
- Xiao-Su Zhao
- 1Peking University Peopl's Hospital, Peking University Institute of Hematology, No.11 Xizhimen South Street, Beijing, 100044 China.,National Clinical Research Center for Hematologic Disease, Beijing, China.,3Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xiao-Jun Huang
- 1Peking University Peopl's Hospital, Peking University Institute of Hematology, No.11 Xizhimen South Street, Beijing, 100044 China.,National Clinical Research Center for Hematologic Disease, Beijing, China.,3Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China.,4Peking-Tsinghua Center for Life Sciences, Beijing, China
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38
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The Cellular and Molecular Basis for Planarian Regeneration. Cell 2019; 175:327-345. [PMID: 30290140 DOI: 10.1016/j.cell.2018.09.021] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 01/03/2023]
Abstract
Regeneration is one of the great mysteries of biology. Planarians are flatworms capable of dramatic feats of regeneration, which have been studied for over 2 centuries. Recent findings identify key cellular and molecular principles underlying these feats. A stem cell population (neoblasts) generates new cells and is comprised of pluripotent stem cells (cNeoblasts) and fate-specified cells (specialized neoblasts). Positional information is constitutively active and harbored primarily in muscle, where it acts to guide stem cell-mediated tissue turnover and regeneration. I describe here a model in which positional information and stem cells combine to enable regeneration.
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39
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Kim MM, Schlussel L, Zhao L, Himburg HA. Dickkopf-1 Treatment Stimulates Hematopoietic Regenerative Function in Infused Endothelial Progenitor Cells. Radiat Res 2019; 192:53-62. [PMID: 31081743 DOI: 10.1667/rr15361.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Acute high-dose radiation injury damages the bone marrow hematopoietic stem and progenitor cell compartment. This damage compromises the functional ability of the bone marrow to produce mature blood cells and results in an increased risk of death due to hematopoietic complications. Past work has shown that the bone marrow endothelium provides critical cues, which promote hematopoietic stem cell regeneration after injury. Additionally, transfusion of endothelial cells after radiation injury has been shown to promote recovery of both the bone marrow vasculature and hematopoietic systems. In this work, we examined the regenerative capacity of intravenous infusion of umbilical cord-blood derived endothelial progenitor cells (EPCs) since this is a cell source which is easy to obtain, expand and cryopreserve. We show that pre-treatment with the Wnt-antagonist Dickkopf1 (Dkk1) augments EPC regenerative function in an allogeneic mouse transplant model. Here, hematopoietic recovery was assessed in Balb/c mice after 5 Gy total-body irradiation and transplantation with C57/BL6-derived EPCs either with or without Dkk1 pre-treatment. The Dkk1-treated EPC group had significantly faster recovery of peripheral white blood cells, total bone marrow cellularity, bone marrow progenitors and BM endothelial cells compared to EPC treatment alone or saline controls. Importantly, after an LD50/30 dose of 8 Gy in the Balb/c mouse, Dkk1-treated EPCs were able to rescue 100% of irradiated mice versus 80% in the EPC control group and only 33% in the saline-treated group. To understand how Dkk1 induces regenerative function in the EPCs, we screened for pro-regenerative factors secreted by the EPC in response to Dkk1. Dkk1-treated EPCs were observed to secrete high levels of the anti-fibrotic protein follistatin as well as several proteins known to promote regeneration including EGF, VEGF and G-CSF. This work demonstrates the potential for Dkk1-treated EPCs as a rescue therapeutic for victims of acute radiation injury.
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Affiliation(s)
- Mindy M Kim
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, California
| | - Lauren Schlussel
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, California
| | - Liman Zhao
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, California
| | - Heather A Himburg
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, California
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40
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Li DJ, McMann CL, Reddien PW. Nuclear receptor NR4A is required for patterning at the ends of the planarian anterior-posterior axis. eLife 2019; 8:42015. [PMID: 31025936 PMCID: PMC6534381 DOI: 10.7554/elife.42015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/25/2019] [Indexed: 02/07/2023] Open
Abstract
Positional information is fundamental to animal regeneration and tissue turnover. In planarians, muscle cells express signaling molecules to promote positional identity. At the ends of the anterior-posterior (AP) axis, positional identity is determined by anterior and posterior poles, which are putative organizers. We identified a gene, nr4A, that is required for anterior- and posterior-pole localization to axis extremes. nr4A encodes a nuclear receptor expressed predominantly in planarian muscle, including strongly at AP-axis ends and the poles. nr4A RNAi causes patterning gene expression domains to retract from head and tail tips, and ectopic anterior and posterior anatomy (e.g., eyes) to iteratively appear more internally. Our study reveals a novel patterning phenotype, in which pattern-organizing cells (poles) shift from their normal locations (axis extremes), triggering abnormal tissue pattern that fails to reach equilibrium. We propose that nr4A promotes pattern at planarian AP axis ends through restriction of patterning gene expression domains. Many animals are able to regenerate tissue that has been lost through illness or injury. Flatworms called planarians have long been used to study tissue regeneration because of their remarkable ability to completely regenerate their whole body from small pieces of tissue. Furthermore, the stem cells of adult planarians continually produce new cells to replace dying cells in a process called tissue turnover. For regeneration and tissue turnover to be successful, it is important for the new cells to form in the right location in the body; for example, new eye cells need to form in the head. Genes known as position control genes are active in muscle at specific locations along the body of a flatworm to regulate both regeneration and tissue turnover. However, it was not clear how these genes coordinate with stem cells to produce new cells in the correct positions in the body. Li et al. examined the effects of a gene known as nr4A that is particularly active in muscle at the head and tail ends of planarians. Using a technique called RNA interference to decrease the activity of nr4A in planarians disrupted the patterns of tissues at each end of the flatworms. Over time, the activity of the position control genes also became restricted to locations progressively farther away from the head and tail. As a result, cells that were intended to replace tissues in the head or tail were deposited increasingly far away from these locations. For example, new eyes formed repeatedly in the planarians, with each set farther away from the head tip than the last. Li et al. propose that these disruptions of normal tissue patterning ensue because the cells that organize such patterns at the ends of the planarian (the poles) are themselves misplaced within the existing body pattern. The nr4A gene can be found in a wide range of animal species. Understanding how this gene affects tissue patterns in planarians could therefore also help researchers to discover how adult tissue patterns form and are maintained in animals more generally.
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Affiliation(s)
- Dayan J Li
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, United States
| | - Conor L McMann
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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41
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Cote LE, Simental E, Reddien PW. Muscle functions as a connective tissue and source of extracellular matrix in planarians. Nat Commun 2019; 10:1592. [PMID: 30962434 PMCID: PMC6453901 DOI: 10.1038/s41467-019-09539-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/15/2019] [Indexed: 12/24/2022] Open
Abstract
Regeneration and tissue turnover require new cell production and positional information. Planarians are flatworms capable of regenerating all body parts using a population of stem cells called neoblasts. The positional information required for tissue patterning is primarily harbored by muscle cells, which also control body contraction. Here we produce an in silico planarian matrisome and use recent whole-animal single-cell-transcriptome data to determine that muscle is a major source of extracellular matrix (ECM). No other ECM-secreting, fibroblast-like cell type was detected. Instead, muscle cells express core ECM components, including all 19 collagen-encoding genes. Inhibition of muscle-expressed hemicentin-1 (hmcn-1), which encodes a highly conserved ECM glycoprotein, results in ectopic peripheral localization of cells, including neoblasts, outside of the muscle layer. ECM secretion and hmcn-1-dependent maintenance of tissue separation indicate that muscle functions as a planarian connective tissue, raising the possibility of broad roles for connective tissue in adult positional information. How the cellular source of positional information compares across regenerative animals is unclear. Here, the authors find that planarian muscle, which harbours positional information, acts as a connective tissue by being a major site of matrisome gene expression and by maintaining tissue architecture.
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Affiliation(s)
- Lauren E Cote
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main St, Cambridge, MA, 02142, USA
| | - Eric Simental
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main St, Cambridge, MA, 02142, USA.,University of California San Francisco, 600 16th Street, San Francisco, CA, 94143, USA
| | - Peter W Reddien
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main St, Cambridge, MA, 02142, USA.
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42
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Unveiling Mesenchymal Stromal Cells' Organizing Function in Regeneration. Int J Mol Sci 2019; 20:ijms20040823. [PMID: 30769851 PMCID: PMC6413004 DOI: 10.3390/ijms20040823] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/03/2019] [Accepted: 02/11/2019] [Indexed: 12/16/2022] Open
Abstract
Regeneration is a fundamental process attributed to the functions of adult stem cells. In the last decades, delivery of suspended adult stem cells is widely adopted in regenerative medicine as a leading means of cell therapy. However, adult stem cells cannot complete the task of human body regeneration effectively by themselves as far as they need a receptive microenvironment (the niche) to engraft and perform properly. Understanding the mechanisms underlying mammalian regeneration leads us to an assumption that improved outcomes of cell therapy require a specific microenvironment that is generated in damaged areas prior to stem cell delivery. To a certain extent, it may be achieved by the delivery of mesenchymal stromal cells (MSCs), not in dispersed form, but rather in self-organized cell sheets (CS) ⁻ tissue-like structures comprised of viable cells and microenvironment components: extracellular matrix and soluble factors deposited in the matrix. In this review, we highlight the potential role of MSCs as regeneration organizers and speculate that this function emerges in CS. This concept shifts our understanding of the therapeutic mechanism underlying a widely known CS-based delivery method for regenerative medicine.
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43
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Shinji J, Gotoh H, Miyanishi H, Lavine MD, Lavine LC. The activin signaling transcription factor Smox is an essential regulator of appendage size during regeneration after autotomy in the crayfish. Evol Dev 2018; 21:44-55. [DOI: 10.1111/ede.12277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junpei Shinji
- Department of Entomology; Washington State University; Pullman Washington
| | - Hiroki Gotoh
- Graduate School of Bioagricultural Sciences; Nagoya University, Furo-cho, Chikusa-ku; Nagoya Japan
| | - Hiroshi Miyanishi
- Faculty of Agriculture; University of Miyazaki, Gakuen-kibanadai-nishi; Miyazaki Japan
| | - Mark D. Lavine
- Department of Entomology; Washington State University; Pullman Washington
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44
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Rojo-Laguna JI, Garcia-Cabot S, Saló E. Tissue transplantation in planarians: A useful tool for molecular analysis of pattern formation. Semin Cell Dev Biol 2018; 87:116-124. [PMID: 29787860 DOI: 10.1016/j.semcdb.2018.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 01/03/2023]
Abstract
Freshwater planarians are well known for their remarkable plasticity and regenerative capabilities. Most studies of planarian regeneration have specifically examined regeneration after transverse or longitudinal sectioning or during homeostasis in intact adults. However, tissue transplantation, first performed over a century ago, constitutes another important tool in the study of regeneration in planarians, and can be easily performed given this species' extraordinary healing capacity and its lack of a circulatory system. Studies conducted to date have demonstrated the viability of transplantations involving a variety of tissue types of different positional identities, affecting any of the 3 main body axes. Moreover, these grafting experiments have shown that tissues possess axial positional identities, which are retained following transplantation. The confrontation between different positional identities that occurs after any type of tissue transplantation is resolved by the formation of a blastema, consisting of undifferentiated tissue produced by adult pluripotent stem cells (neoblasts). This blastema intercalates the positional identities of the graft and host tissues. The recent discovery of pathways involved in planarian growth, patterning, and organogenesis, as well as corresponding molecular markers, makes tissue transplantation a vital new tool with which to explore pattern formation. Here, we discuss the different grafting approaches used in planarians, and the corresponding intercalary regenerative response, placing particular emphasis on the respective contributions of donor and host tissue. Moreover, we discuss the temporal induction of blastema formation, and present new molecular data on the generation of an ectopic anterior/posterior axis in response to dorsal/ventral confrontations between host and donor tissue.
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Affiliation(s)
- Jose Ignacio Rojo-Laguna
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Catalunya, Spain
| | - Sergi Garcia-Cabot
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Catalunya, Spain
| | - Emili Saló
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Catalunya, Spain.
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45
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Neoblast-enriched zinc finger protein FIR1 triggers local proliferation during planarian regeneration. Protein Cell 2018; 10:43-59. [PMID: 29557542 PMCID: PMC6321819 DOI: 10.1007/s13238-018-0512-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/09/2018] [Indexed: 11/30/2022] Open
Abstract
Regeneration, relying mainly on resident adult stem cells, is widespread. However, the mechanism by which stem cells initiate proliferation during this process in vivo is unclear. Using planarian as a model, we screened 46 transcripts showing potential function in the regulation of local stem cell proliferation following 48 h regeneration. By analyzing the regeneration defects and the mitotic activity of animals under administration of RNA interference (RNAi), we identified factor for initiating regeneration 1 (Fir1) required for local proliferation. Our findings reveal that Fir1, enriched in neoblasts, promotes planarian regeneration in any tissue-missing context. Further, we demonstrate that DIS3 like 3′-5′ exoribonuclease 2 (Dis3l2) is required for Fir1 phenotype. Besides, RNAi knockdown of Fir1 causes a decrease of neoblast wound response genes following amputation. These findings suggest that Fir1 recognizes regenerative signals and promotes DIS3L2 proteins to trigger neoblast proliferation following amputation and provide a mechanism critical for stem cell response to injury.
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46
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Rossi L, Salvetti A. Planarian stem cell niche, the challenge for understanding tissue regeneration. Semin Cell Dev Biol 2018. [PMID: 29534938 DOI: 10.1016/j.semcdb.2018.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Stem cell fate depends on surrounding microenvironment, the so called niche. For this reason, understanding stem cell niche is one of the most challenging target in cell biology field and need to be unraveled with in vivo studies. Planarians offer this unique opportunity, as their stem cells, the neoblasts, are abundant, highly characterized and genetically modifiable by RNA interference in alive animals. However, despite impressive advances have been done in the understanding planarian stem cells and regeneration, only a few information is available in defining signals from differentiated tissues, which affect neoblast stemness and fate. Here, we review on molecular factors that have been found activated in differentiated tissues and directly or indirectly affect neoblast behavior, and we suggest future directions for unravelling this challenge in understanding planarian stem cells.
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Affiliation(s)
- Leonardo Rossi
- Departement of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Via Volta 4 Pisa, Italy
| | - Alessandra Salvetti
- Departement of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Via Volta 4 Pisa, Italy.
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47
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Rink JC. Stem Cells, Patterning and Regeneration in Planarians: Self-Organization at the Organismal Scale. Methods Mol Biol 2018; 1774:57-172. [PMID: 29916155 DOI: 10.1007/978-1-4939-7802-1_2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The establishment of size and shape remains a fundamental challenge in biological research that planarian flatworms uniquely epitomize. Planarians can regenerate complete and perfectly proportioned animals from tiny and arbitrarily shaped tissue pieces; they continuously renew all organismal cell types from abundant pluripotent stem cells, yet maintain shape and anatomy in the face of constant turnover; they grow when feeding and literally degrow when starving, while scaling form and function over as much as a 40-fold range in body length or an 800-fold change in total cell numbers. This review provides a broad overview of the current understanding of the planarian stem cell system, the mechanisms that pattern the planarian body plan and how the interplay between patterning signals and cell fate choices orchestrates regeneration. What emerges is a conceptual framework for the maintenance and regeneration of the planarian body plan on basis of the interplay between pluripotent stem cells and self-organizing patterns and further, the general utility of planarians as model system for the mechanistic basis of size and shape.
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Affiliation(s)
- Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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48
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Abstract
Planarians have gained a well-deserved reputation as an excellent model organism for research on the biology of adult stem cells and their role in regeneration. Though less widely recognized, these animals also offer many advantages for investigating mechanisms and functions of programmed cell death in self-renewing tissues. Apoptosis complements stem cell division during physiological cell turnover and constitutes a prominent feature of the tissue remodeling process that restores anatomical scale and proportion during regeneration. One technical advantage to studying apoptosis in planarians is the availability of a whole-mount TUNEL assay for visualizing dying cells throughout the animal. Here, we provide a detailed protocol for this assay that is likely to benefit researchers investigating planarian cell death in either physiological or pathological contexts.
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49
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Generic wound signals initiate regeneration in missing-tissue contexts. Nat Commun 2017; 8:2282. [PMID: 29273738 PMCID: PMC5741630 DOI: 10.1038/s41467-017-02338-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/22/2017] [Indexed: 11/08/2022] Open
Abstract
Despite the identification of numerous regulators of regeneration in different animal models, a fundamental question remains: why do some wounds trigger the full regeneration of lost body parts, whereas others resolve by mere healing? By selectively inhibiting regeneration initiation, but not the formation of a wound epidermis, here we create headless planarians and finless zebrafish. Strikingly, in both missing-tissue contexts, injuries that normally do not trigger regeneration activate complete restoration of heads and fin rays. Our results demonstrate that generic wound signals have regeneration-inducing power. However, they are interpreted as regeneration triggers only in a permissive tissue context: when body parts are missing, or when tissue-resident polarity signals, such as Wnt activity in planarians, are modified. Hence, the ability to decode generic wound-induced signals as regeneration-initiating cues may be the crucial difference that distinguishes animals that regenerate from those that cannot. Some wounds trigger regeneration, while others simply heal but how this is regulated is unclear. Here, by manipulating ERK and Wnt signalling pathways, the authors create headless planarians and finless zebrafish and show that wounds that normally only trigger wound healing can activate regeneration of heads and bones.
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50
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Abstract
Muscles are traditionally considered in the context of force generation. Scimone et al. (2017), reporting in Nature, now examine muscles in a developmental setting and find unexpected roles for distinct planarian muscle fibers. The authors show that muscles provide patterning signals to promote regeneration and guide tissue growth after injury.
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