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Ness N, Brancaccio M. Network-level time computations in the suprachiasmatic nucleus. Cell Res 2024; 34:471-472. [PMID: 38720097 PMCID: PMC11217402 DOI: 10.1038/s41422-024-00969-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024] Open
Affiliation(s)
- Natalie Ness
- Department of Brain Science, Imperial College London, London, UK
- UK Dementia Research Institute at Imperial College London, London, UK
| | - Marco Brancaccio
- Department of Brain Science, Imperial College London, London, UK.
- UK Dementia Research Institute at Imperial College London, London, UK.
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2
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Mim MS, Kumar N, Levis M, Unger MF, Miranda G, Gazzo D, Robinett T, Zartman JJ. Piezo regulates epithelial topology and promotes precision in organ size control. Cell Rep 2024; 43:114398. [PMID: 38935502 DOI: 10.1016/j.celrep.2024.114398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Mechanosensitive Piezo channels regulate cell division, cell extrusion, and cell death. However, systems-level functions of Piezo in regulating organogenesis remain poorly understood. Here, we demonstrate that Piezo controls epithelial cell topology to ensure precise organ growth by integrating live-imaging experiments with pharmacological and genetic perturbations and computational modeling. Notably, the knockout or knockdown of Piezo increases bilateral asymmetry in wing size. Piezo's multifaceted functions can be deconstructed as either autonomous or non-autonomous based on a comparison between tissue-compartment-level perturbations or between genetic perturbation populations at the whole-tissue level. A computational model that posits cell proliferation and apoptosis regulation through modulation of the cutoff tension required for Piezo channel activation explains key cell and tissue phenotypes arising from perturbations of Piezo expression levels. Our findings demonstrate that Piezo promotes robustness in regulating epithelial topology and is necessary for precise organ size control.
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Affiliation(s)
- Mayesha Sahir Mim
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA; Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Nilay Kumar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Megan Levis
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA; Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Maria F Unger
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gabriel Miranda
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - David Gazzo
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA; Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trent Robinett
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jeremiah J Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA; Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
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3
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Ho KYL, An K, Carr RL, Dvoskin AD, Ou AYJ, Vogl W, Tanentzapf G. Maintenance of hematopoietic stem cell niche homeostasis requires gap junction-mediated calcium signaling. Proc Natl Acad Sci U S A 2023; 120:e2303018120. [PMID: 37903259 PMCID: PMC10636368 DOI: 10.1073/pnas.2303018120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023] Open
Abstract
Regulation of stem cells requires coordination of the cells that make up the stem cell niche. Here, we describe a mechanism that allows communication between niche cells to coordinate their activity and shape the signaling environment surrounding resident stem cells. Using the Drosophila hematopoietic organ, the lymph gland, we show that cells of the hematopoietic niche, the posterior signaling center (PSC), communicate using gap junctions (GJs) and form a signaling network. This network allows PSC cells to exchange Ca2+ signals repetitively which regulate the hematopoietic niche. Disruption of Ca2+ signaling in the PSC or the GJ-mediated network connecting niche cells causes dysregulation of the PSC and blood progenitor differentiation. Analysis of PSC-derived cell signaling shows that the Hedgehog pathway acts downstream of GJ-mediated Ca2+ signaling to modulate the niche microenvironment. These data show that GJ-mediated communication between hematopoietic niche cells maintains their homeostasis and consequently controls blood progenitor behavior.
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Affiliation(s)
- Kevin Y. L. Ho
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Kevin An
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Rosalyn L. Carr
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
- British Columbia Children’s Hospital Research Institute, British Columbia Children’s Hospital, Vancouver, BCV5Z 4H4, Canada
| | - Alexandra D. Dvoskin
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Annie Y. J. Ou
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
- School of Kinesiology, University of British Columbia, Vancouver, BCV6T 1Z1, Canada
| | - Wayne Vogl
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Guy Tanentzapf
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
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4
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Chang M, Montagne K, Furukawa KS, Ushida T. Intracellular calcium ion transients evoked by cell poking independently of released autocrine ATP in Madin-Darby canine kidney cells. Cell Biochem Funct 2023; 41:845-856. [PMID: 37515551 DOI: 10.1002/cbf.3834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/31/2023]
Abstract
The mechanical stimulation induced by poking cells with a glass needle activates Piezo1 receptors and the adenosine triphosphate (ATP) autocrine pathway, thus increasing intracellular Ca2+ concentration. The differences between the increase in intracellular Ca2+ concentration induced by cell poking and by ATP-only stimulation have not been investigated. In this study, we investigated the Ca2+ signaling mechanism induced by autocrine ATP release during Madin-Darby Canine Kidney cell membrane deformation by cell poking. The results suggest that the pathways for supplying Ca2+ into the cytoplasm were not identical between cell poking and conventional ATP stimulation. The functions of the G protein-coupled receptor (GPCR) subunits (Gα $\alpha $ q, Gβ γ $\beta \gamma $ ), ATP-activated receptor and the upstream Ca2+ release signal from the intracellular endoplasmic reticulum Ca2+ store, were investigated. The results show that Gα $\alpha $ q plays a major role in the Ca2+ response evoked by ATP-only stimulation, while cell poking induces a Ca2+ response requiring the involvement of both Gα $\alpha $ q and Gβ γ $\beta \gamma $ units simultaneously. These results suggest that GPCR are not only activated by ATP-only stimulation or autocrine ATP release during Ca2+ signaling, but also activated by the mechanical effects of cell poking.
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Affiliation(s)
- Minki Chang
- Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kevin Montagne
- Department of Mechanical Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Katsuko S Furukawa
- Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Department of Mechanical Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Takashi Ushida
- Department of Mechanical Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
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5
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Carrisoza-Gaytan R, Kroll KT, Hiratsuka K, Gupta NR, Morizane R, Lewis JA, Satlin LM. Functional maturation of kidney organoid tubules: PIEZO1-mediated Ca 2+ signaling. Am J Physiol Cell Physiol 2023; 324:C757-C768. [PMID: 36745528 PMCID: PMC10027089 DOI: 10.1152/ajpcell.00288.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/07/2023]
Abstract
Kidney organoids cultured on adherent matrices in the presence of superfusate flow generate vascular networks and exhibit more mature podocyte and tubular compartments compared with static controls (Homan KA, Gupta N, Kroll KT, Kolesky DB, Skylar-Scott M, Miyoshi T, Mau D, Valerius MT, Ferrante T, Bonventre JV, Lewis JA, Morizane R. Nat Methods 16: 255-262, 2019; Takasato M, Er PX, Chiu HS, Maier B, Baillie GJ, Ferguson C, Parton RG, Wolvetang EJ, Roost MS, Chuva de Sousa Lopes SM, Little MH. Nature 526: 564-568, 2015.). However, their physiological function has yet to be systematically investigated. Here, we measured mechano-induced changes in intracellular Ca2+ concentration ([Ca2+]i) in tubules isolated from organoids cultured for 21-64 days, microperfused in vitro or affixed to the base of a specimen chamber, and loaded with fura-2 to measure [Ca2+]i. A rapid >2.5-fold increase in [Ca2+]i from a baseline of 195.0 ± 22.1 nM (n = 9; P ≤ 0.001) was observed when microperfused tubules from organoids >40 days in culture were subjected to luminal flow. In contrast, no response was detected in tubules isolated from organoids <30 days in culture. Nonperfused tubules (41 days) subjected to a 10-fold increase in bath flow rate also exhibited a threefold increase in [Ca2+]i from baseline (P < 0.001). Mechanosensitive PIEZO1 channels contribute to the flow-induced [Ca2+]i response in mouse distal tubule (Carrisoza-Gaytan R, Dalghi MG, Apodaca GL, Kleyman TR, Satlin LM. The FASEB J 33: 824.25, 2019.). Immunodetectable apical and basolateral PIEZO1 was identified in tubular structures by 21 days in culture. Basolateral PIEZO1 appeared to be functional as basolateral exposure of nonperfused tubules to the PIEZO1 activator Yoda 1 increased [Ca2+]i (P ≤ 0.001) in segments from organoids cultured for >30 days, with peak [Ca2+]i increasing with advancing days in culture. These results are consistent with a maturational increase in number and/or activity of flow/stretch-sensitive Ca2+ channels, including PIEZO1, in tubules of static organoids in culture.
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Affiliation(s)
- Rolando Carrisoza-Gaytan
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Katharina T Kroll
- Paulson School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States
| | - Ken Hiratsuka
- Paulson School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
| | - Navin R Gupta
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
| | - Ryuji Morizane
- Paulson School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
| | - Jennifer A Lewis
- Paulson School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
| | - Lisa M Satlin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, United States
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Velagala V, Soundarrajan DK, Unger MF, Gazzo D, Kumar N, Li J, Zartman J. The multimodal action of G alpha q in coordinating growth and homeostasis in the Drosophila wing imaginal disc. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.08.523049. [PMID: 36711848 PMCID: PMC9881979 DOI: 10.1101/2023.01.08.523049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background G proteins mediate cell responses to various ligands and play key roles in organ development. Dysregulation of G-proteins or Ca 2+ signaling impacts many human diseases and results in birth defects. However, the downstream effectors of specific G proteins in developmental regulatory networks are still poorly understood. Methods We employed the Gal4/UAS binary system to inhibit or overexpress Gαq in the wing disc, followed by phenotypic analysis. Immunohistochemistry and next-gen RNA sequencing identified the downstream effectors and the signaling cascades affected by the disruption of Gαq homeostasis. Results Here, we characterized how the G protein subunit Gαq tunes the size and shape of the wing in the larval and adult stages of development. Downregulation of Gαq in the wing disc reduced wing growth and delayed larval development. Gαq overexpression is sufficient to promote global Ca 2+ waves in the wing disc with a concomitant reduction in the Drosophila final wing size and a delay in pupariation. The reduced wing size phenotype is further enhanced when downregulating downstream components of the core Ca 2+ signaling toolkit, suggesting that downstream Ca 2+ signaling partially ameliorates the reduction in wing size. In contrast, Gαq -mediated pupariation delay is rescued by inhibition of IP 3 R, a key regulator of Ca 2+ signaling. This suggests that Gαq regulates developmental phenotypes through both Ca 2+ -dependent and Ca 2+ -independent mechanisms. RNA seq analysis shows that disruption of Gαq homeostasis affects nuclear hormone receptors, JAK/STAT pathway, and immune response genes. Notably, disruption of Gαq homeostasis increases expression levels of Dilp8, a key regulator of growth and pupariation timing. Conclusion Gαq activity contributes to cell size regulation and wing metamorphosis. Disruption to Gαq homeostasis in the peripheral wing disc organ delays larval development through ecdysone signaling inhibition. Overall, Gαq signaling mediates key modules of organ size regulation and epithelial homeostasis through the dual action of Ca 2+ -dependent and independent mechanisms.
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7
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McMillen P, Walker SI, Levin M. Information Theory as an Experimental Tool for Integrating Disparate Biophysical Signaling Modules. Int J Mol Sci 2022; 23:ijms23179580. [PMID: 36076979 PMCID: PMC9455895 DOI: 10.3390/ijms23179580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/13/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022] Open
Abstract
There is a growing appreciation in the fields of cell biology and developmental biology that cells collectively process information in time and space. While many powerful molecular tools exist to observe biophysical dynamics, biologists must find ways to quantitatively understand these phenomena at the systems level. Here, we present a guide for the application of well-established information theory metrics to biological datasets and explain these metrics using examples from cell, developmental and regenerative biology. We introduce a novel computational tool named after its intended purpose, calcium imaging, (CAIM) for simple, rigorous application of these metrics to time series datasets. Finally, we use CAIM to study calcium and cytoskeletal actin information flow patterns between Xenopus laevis embryonic animal cap stem cells. The tools that we present here should enable biologists to apply information theory to develop a systems-level understanding of information processing across a diverse array of experimental systems.
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Affiliation(s)
- Patrick McMillen
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Sara I. Walker
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85281, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
- Correspondence:
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8
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Pai VP, Cooper BG, Levin M. Screening Biophysical Sensors and Neurite Outgrowth Actuators in Human Induced-Pluripotent-Stem-Cell-Derived Neurons. Cells 2022; 11:cells11162470. [PMID: 36010547 PMCID: PMC9406775 DOI: 10.3390/cells11162470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
All living cells maintain a charge distribution across their cell membrane (membrane potential) by carefully controlled ion fluxes. These bioelectric signals regulate cell behavior (such as migration, proliferation, differentiation) as well as higher-level tissue and organ patterning. Thus, voltage gradients represent an important parameter for diagnostics as well as a promising target for therapeutic interventions in birth defects, injury, and cancer. However, despite much progress in cell and molecular biology, little is known about bioelectric states in human stem cells. Here, we present simple methods to simultaneously track ion dynamics, membrane voltage, cell morphology, and cell activity (pH and ROS), using fluorescent reporter dyes in living human neurons derived from induced neural stem cells (hiNSC). We developed and tested functional protocols for manipulating ion fluxes, membrane potential, and cell activity, and tracking neural responses to injury and reinnervation in vitro. Finally, using morphology sensor, we tested and quantified the ability of physiological actuators (neurotransmitters and pH) to manipulate nerve repair and reinnervation. These methods are not specific to a particular cell type and should be broadly applicable to the study of bioelectrical controls across a wide range of combinations of models and endpoints.
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Affiliation(s)
- Vaibhav P. Pai
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Ben G. Cooper
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
- Correspondence:
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9
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Varadarajan S, Chumki SA, Stephenson RE, Misterovich ER, Wu JL, Dudley CE, Erofeev IS, Goryachev AB, Miller AL. Mechanosensitive calcium flashes promote sustained RhoA activation during tight junction remodeling. J Cell Biol 2022; 221:213049. [PMID: 35254388 PMCID: PMC8906493 DOI: 10.1083/jcb.202105107] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/03/2021] [Accepted: 02/02/2022] [Indexed: 11/22/2022] Open
Abstract
Epithelial cell–cell junctions remodel in response to mechanical stimuli to maintain barrier function. Previously, we found that local leaks in tight junctions (TJs) are rapidly repaired by local, transient RhoA activation, termed “Rho flares,” but how Rho flares are regulated is unknown. Here, we discovered that intracellular calcium flashes and junction elongation are early events in the Rho flare pathway. Both laser-induced and naturally occurring TJ breaks lead to local calcium flashes at the site of leaks. Additionally, junction elongation induced by optogenetics increases Rho flare frequency, suggesting that Rho flares are mechanically triggered. Depletion of intracellular calcium or inhibition of mechanosensitive calcium channels (MSCs) reduces the amplitude of calcium flashes and diminishes the sustained activation of Rho flares. MSC-dependent calcium influx is necessary to maintain global barrier function by regulating reinforcement of local TJ proteins via junction contraction. In all, we uncovered a novel role for MSC-dependent calcium flashes in TJ remodeling, allowing epithelial cells to repair local leaks induced by mechanical stimuli.
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Affiliation(s)
| | - Shahana A Chumki
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI
| | - Rachel E Stephenson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Eileen R Misterovich
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Jessica L Wu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Claire E Dudley
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Ivan S Erofeev
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, Scotland
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, Scotland
| | - Ann L Miller
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI
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10
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Inference of trajectory presence by tree dimension and subset specificity by subtree cover. PLoS Comput Biol 2022; 18:e1009829. [PMID: 35134060 PMCID: PMC8884548 DOI: 10.1371/journal.pcbi.1009829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/28/2022] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
The complexity of biological processes such as cell differentiation is reflected in dynamic transitions between cellular states. Trajectory inference arranges the states into a progression using methodologies propelled by single-cell biology. However, current methods, all returning a best trajectory, do not adequately assess statistical significance of noisy patterns, leading to uncertainty in inferred trajectories. We introduce a tree dimension test for trajectory presence in multivariate data by a dimension measure of Euclidean minimum spanning tree, a test statistic, and a null distribution. Computable in linear time to tree size, the tree dimension measure summarizes the extent of branching more effectively than globally insensitive number of leaves or tree diameter indifferent to secondary branches. The test statistic quantifies trajectory presence and its null distribution is estimated under the null hypothesis of no trajectory in data. On simulated and real single-cell datasets, the test outperformed the intuitive number of leaves and tree diameter statistics. Next, we developed a measure for the tissue specificity of the dynamics of a subset, based on the minimum subtree cover of the subset in a minimum spanning tree. We found that tissue specificity of pathway gene expression dynamics is conserved in human and mouse development: several signal transduction pathways including calcium and Wnt signaling are most tissue specific, while genetic information processing pathways such as ribosome and mismatch repair are least so. Neither the tree dimension test nor the subset specificity measure has any user parameter to tune. Our work opens a window to prioritize cellular dynamics and pathways in development and other multivariate dynamical systems. Modern biology now routinely studies transcriptome profiles during development. This practice demands computational methods to quantify dynamical changes in cellular states and their heterogeneity. Many methods process single-cell transcriptome data to reconstruct cellular trajectories, which are orderings of cells as they progress from an early to a late developmental stage. Due to noise in transcriptome data, there is a great need to quantify how likely observed data present a trajectory-like pattern due to chance. To address this need, we developed a tree dimension test to quantify evidence for trajectory presence in multivariate data based on graph-theoretical concepts. By this test, one may reject trajectory presence due to low data quality, or accept a trajectory with high statistical significance. Now one can rank biological pathways by their trajectory quality. We also introduce a subset specificity measure to quantify how cellular or pathway dynamics are tissue specific. We found that pathway tissue specificity is highly conserved between human and mouse. Trajectory presence testing and subset specificity offer a unique informatics tool set to study developmental biology.
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11
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Ho KYL, Khadilkar RJ, Carr RL, Tanentzapf G. A gap-junction-mediated, calcium-signaling network controls blood progenitor fate decisions in hematopoiesis. Curr Biol 2021; 31:4697-4712.e6. [PMID: 34480855 DOI: 10.1016/j.cub.2021.08.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/28/2021] [Accepted: 08/06/2021] [Indexed: 11/24/2022]
Abstract
Stem cell homeostasis requires coordinated fate decisions among stem cells that are often widely distributed within a tissue at varying distances from their stem cell niche. This requires a mechanism to ensure robust fate decisions within a population of stem cells. Here, we show that, in the Drosophila hematopoietic organ, the lymph gland (LG), gap junctions form a network that coordinates fate decisions between blood progenitors. Using live imaging of calcium signaling in intact LGs, we find that blood progenitors are connected through a signaling network. Blocking gap junction function disrupts this network, alters the pattern of encoded calcium signals, and leads to loss of progenitors and precocious blood cell differentiation. Ectopic and uniform activation of the calcium-signaling mediator CaMKII restores progenitor homeostasis when gap junctions are disrupted. Overall, these data show that gap junctions equilibrate cell signals between blood progenitors to coordinate fate decisions and maintain hematopoietic homeostasis.
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Affiliation(s)
- Kevin Y L Ho
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rohan J Khadilkar
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Advanced Centre for Treatment, Research and Education in Cancer-Tata Memorial Centre (ACTREC-TMC), Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - Rosalyn L Carr
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Guy Tanentzapf
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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12
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Minh-Thai TN, Samarasinghe S, Levin M. A Comprehensive Conceptual and Computational Dynamics Framework for Autonomous Regeneration Systems. ARTIFICIAL LIFE 2021; 27:80-104. [PMID: 34473826 DOI: 10.1162/artl_a_00343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological organisms regenerate structure and function after damage. Despite the long history of research on molecular mechanisms, many questions remain about algorithms by which cells can cooperate towards the same invariant morphogenetic outcomes. Therefore, conceptual frameworks are needed not only for motivating hypotheses for advancing the understanding of regeneration processes in living organisms, but also for regenerative medicine and synthetic biology. Inspired by planarian regeneration, this study offers a novel generic conceptual framework that hypothesizes mechanisms and algorithms by which cell collectives may internally represent an anatomical target morphology towards which they build after damage. Further, the framework contributes a novel nature-inspired computing method for self-repair in engineering and robotics. Our framework, based on past in vivo and in silico studies on planaria, hypothesizes efficient novel mechanisms and algorithms to achieve complete and accurate regeneration of a simple in silico flatwormlike organism from any damage, much like the body-wide immortality of planaria, with minimal information and algorithmic complexity. This framework that extends our previous circular tissue repair model integrates two levels of organization: tissue and organism. In Level 1, three individual in silico tissues (head, body, and tail-each with a large number of tissue cells and a single stem cell at the centre) repair themselves through efficient local communications. Here, the contribution extends our circular tissue model to other shapes and invests them with tissue-wide immortality through an information field holding the minimum body plan. In Level 2, individual tissues combine to form a simple organism. Specifically, the three stem cells form a network that coordinates organism-wide regeneration with the help of Level 1. Here we contribute novel concepts for collective decision-making by stem cells for stem cell regeneration and large-scale recovery. Both levels (tissue cells and stem cells) represent networks that perform simple neural computations and form a feedback control system. With simple and limited cellular computations, our framework minimises computation and algorithmic complexity to achieve complete recovery. We report results from computer simulations of the framework to demonstrate its robustness in recovering the organism after any injury. This comprehensive hypothetical framework that significantly extends the existing biological regeneration models offers a new way to conceptualise the information-processing aspects of regeneration, which may also help design living and non-living self-repairing agents.
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Affiliation(s)
- Tran Nguyen Minh-Thai
- Lincoln University, Complex Systems, Big Data and Informatics Initiative (CSBII)
- Can Tho University, College of Information and Communication Technology
| | - Sandhya Samarasinghe
- Lincoln University, Complex Systems, Big Data and Informatics Initiative (CSBII).
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13
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Mestril S, Kim R, Hinman SS, Gomez SM, Allbritton NL. Stem/Proliferative and Differentiated Cells within Primary Murine Colonic Epithelium Display Distinct Intracellular Free Ca 2+ Signal Codes. Adv Healthc Mater 2021; 10:e2101318. [PMID: 34510822 DOI: 10.1002/adhm.202101318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/24/2021] [Indexed: 11/11/2022]
Abstract
The second messenger, intracellular free calcium (Ca2+ ), acts to transduce mitogenic and differentiation signals incoming to the colonic epithelium. A self-renewing monolayer of primary murine colonic epithelial cells is formed over a soft, transparent hydrogel matrix for the scalable analysis of intracellular Ca2+ transients. Cultures that are enriched for stem/proliferative cells exhibit repetitive, high frequency (≈25 peaks h-1 ), and short pulse width (≈25 s) Ca2+ transients. Upon cell differentiation the transient frequency declines by 50% and pulse width widens by 200%. Metabolites and growth factors that are known to modulate stem cell proliferation and differentiation through Wnt and Notch signaling pathways, including CHIR-99021, N-[(3,5-Difluorophenyl)acetyl]-L-alanyl-2-phenylglycine-1,1-dimethylethyl ester (DAPT), bone morphogenetic proteins (BMPs), and butyrate, also modulate Ca2+ oscillation patterns in a consistent manner. Increasing the stiffness of the supportive matrix from 200 Pa to 3 GPa shifts Ca2+ transient patterns toward those resembling differentiated cells. The ability to monitor Ca2+ oscillations with the spatial and temporal resolution offered by this platform, combined with its amenability to high-content screens, provides a powerful tool for investigating real-time communication within a wide range of primary tissues in addition to the colonic epithelium.
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Affiliation(s)
- Sebastian Mestril
- Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill and North Carolina State University Chapel Hill NC 27599 USA
| | - Raehyun Kim
- Department of Bioengineering University of Washington Seattle WA 98195 USA
| | - Samuel S. Hinman
- Department of Bioengineering University of Washington Seattle WA 98195 USA
| | - Shawn M. Gomez
- Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill and North Carolina State University Chapel Hill NC 27599 USA
- Department of Pharmacology University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
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Vernale A, Prünster MM, Marchianò F, Debost H, Brouilly N, Rocher C, Massey-Harroche D, Renard E, Le Bivic A, Habermann BH, Borchiellini C. Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis. BMC Ecol Evol 2021; 21:160. [PMID: 34418961 PMCID: PMC8380372 DOI: 10.1186/s12862-021-01866-x] [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: 03/16/2021] [Accepted: 06/18/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The ancestral presence of epithelia in Metazoa is no longer debated. Porifera seem to be one of the best candidates to be the sister group to all other Metazoa. This makes them a key taxon to explore cell-adhesion evolution on animals. For this reason, several transcriptomic, genomic, histological, physiological and biochemical studies focused on sponge epithelia. Nevertheless, the complete and precise protein composition of cell-cell junctions and mechanisms that regulate epithelial morphogenetic processes still remain at the center of attention. RESULTS To get insights into the early evolution of epithelial morphogenesis, we focused on morphogenic characteristics of the homoscleromorph sponge Oscarella lobularis. Homoscleromorpha are a sponge class with a typical basement membrane and adhaerens-like junctions unknown in other sponge classes. We took advantage of the dynamic context provided by cell dissociation-reaggregation experiments to explore morphogenetic processes in epithelial cells in a non-bilaterian lineage by combining fluorescent and electron microscopy observations and RNA sequencing approaches at key time-points of the dissociation and reaggregation processes. CONCLUSIONS Our results show that part of the molecular toolkit involved in the loss and restoration of epithelial features such as cell-cell and cell-matrix adhesion is conserved between Homoscleromorpha and Bilateria, suggesting their common role in the last common ancestor of animals. In addition, sponge-specific genes are differently expressed during the dissociation and reaggregation processes, calling for future functional characterization of these genes.
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Affiliation(s)
- Amélie Vernale
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Maria Mandela Prünster
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Turing Center for Living Systems (CENTURI), Marseille, France
| | - Fabio Marchianò
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Turing Center for Living Systems (CENTURI), Marseille, France
| | - Henry Debost
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Nicolas Brouilly
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Caroline Rocher
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
| | - Dominique Massey-Harroche
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Emmanuelle Renard
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - André Le Bivic
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France
| | - Bianca H Habermann
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France.
- Aix Marseille Univ, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Turing Center for Living Systems (CENTURI), Marseille, France.
| | - Carole Borchiellini
- Aix Marseille Univ, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France.
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15
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Sun C, Jin K, Zuo Q, Sun H, Song J, Zhang Y, Chen G, Li B. Characterization of Alternative Splicing (AS) Events during Chicken ( Gallus gallus) Male Germ-Line Stem Cell Differentiation with Single-Cell RNA-seq. Animals (Basel) 2021; 11:ani11051469. [PMID: 34065391 PMCID: PMC8160964 DOI: 10.3390/ani11051469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Studies have shown that alternative splicing (AS) has been utilized in a wide variety of life processes. However, there are very few studies on AS during germ cell development. In this study, we preliminarily investigated the variation of variable shear events during the formation of chicken germ cells through the RNA-seq data analysis of embryonic stem cells (ESCs), gonad PGCs (gPGCs), and spermatogonia stem cells (SSCs), and the critical AS mode for several crucial stage-specific genes, which were identified during germ cell development. The results of this study lay a theoretical foundation for further analysis of the regulation mechanism of key genes involved in germ cell formation. Abstract Alternative splicing (AS) is a ubiquitous, co-transcriptional, and post-transcriptional regulation mechanism during certain developmental processes, such as germ cell differentiation. A thorough understanding of germ cell differentiation will help us to open new avenues for avian reproduction, stem cell biology, and advances in medicines for human consumption. Here, based on single-cell RNA-seq, we characterized genome-wide AS events in manifold chicken male germ cells: embryonic stem cells (ESCs), gonad primordial germ cells (gPGCs), and spermatogonia stem cells (SSCs). A total of 38,494 AS events from 15,338 genes were detected in ESCs, with a total of 48,955 events from 14,783 genes and 49,900 events from 15,089 genes observed in gPGCs and SSCs, respectively. Moreover, this distribution of AS events suggests the diverse splicing feature of ESCs, gPGCs, and SSCs. Finally, several crucial stage-specific genes, such as NANOG, POU5F3, LIN28B, BMP4, STRA8, and LHX9, were identified in AS events that were transmitted in ESCs, gPGCs, and SSCs. The gene expression results of the RNA-seq data were validated by qRT-PCR. In summary, we provided a comprehensive atlas of the genome-wide scale of the AS event landscape in male chicken germ-line cells and presented its distribution for the first time. This research may someday improve treatment options for men suffering from male infertility.
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Affiliation(s)
- Changhua Sun
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Department of Food Technology, College of Biochemical Engineering, Yangzhou Polytechnic College, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Kai Jin
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Qisheng Zuo
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Sun
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Jiuzhou Song
- Animal & Avian Sciences, University of Maryland, College Park, MD 20741, USA;
| | - Yani Zhang
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Bichun Li
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Abstract
Meaning has traditionally been regarded as a problem for philosophers and psychologists. Advances in cognitive science since the early 1960s, however, broadened discussions of meaning, or more technically, the semantics of perceptions, representations, and/or actions, into biology and computer science. Here, we review the notion of “meaning” as it applies to living systems, and argue that the question of how living systems create meaning unifies the biological and cognitive sciences across both organizational and temporal scales.
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17
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Multiscale imaging of basal cell dynamics in the functionally mature mammary gland. Proc Natl Acad Sci U S A 2020; 117:26822-26832. [PMID: 33033227 DOI: 10.1073/pnas.2016905117] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The mammary epithelium is indispensable for the continued survival of more than 5,000 mammalian species. For some, the volume of milk ejected in a single day exceeds their entire blood volume. Here, we unveil the spatiotemporal properties of physiological signals that orchestrate the ejection of milk from alveolar units and its passage along the mammary ductal network. Using quantitative, multidimensional imaging of mammary cell ensembles from GCaMP6 transgenic mice, we reveal how stimulus evoked Ca2+ oscillations couple to contractions in basal epithelial cells. Moreover, we show that Ca2+-dependent contractions generate the requisite force to physically deform the innermost layer of luminal cells, compelling them to discharge the fluid that they produced and housed. Through the collective action of thousands of these biological positive-displacement pumps, each linked to a contractile ductal network, milk begins its passage toward the dependent neonate, seconds after the command.
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18
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Schade-Mann T, Münkner S, Eckrich T, Engel J. Calcium signaling in interdental cells during the critical developmental period of the mouse cochlea. Hear Res 2020; 389:107913. [PMID: 32120242 DOI: 10.1016/j.heares.2020.107913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 11/18/2022]
Abstract
The tectorial membrane (TM), a complex acellular structure that covers part of the organ of Corti and excites outer hair cells, is required for normal hearing. It consists of collagen fibrils and various glycoproteins, which are synthesized in embryonic and postnatal development by different cochlear cell types including the interdental cells (IDCs). At its modiolar side, the TM is fixed to the apical surfaces of IDCs, which form the covering epithelium of the spiral limbus. We performed confocal membrane imaging and Ca2+ imaging in IDCs of the developing mouse cochlea from birth to postnatal day 18 (P18). Using the fluorescent membrane markers FM 4-64 and CellMask™ Deep Red on explanted whole-mount cochlear epithelium, we identified the morphology of IDCs at different z-levels of the spiral limbus. Ca2+ imaging of Fluo-8 AM-loaded cochlear epithelia revealed spontaneous intracellular Ca2+ transients in IDCs at P0/1, P4/5, and P18. Their relative frequency was lowest on P0/1, increased by a factor of 12.5 on P4/5 and decreased to twice the initial value on P18. At all three ages, stimulation of IDCs with the trinucleotides ATP and UTP at 1 and 10 μM elicited Ca2+ transients of varying amplitude and shape. Before the onset of hearing, IDCs responded with robust Ca2+ oscillations. At P18, after the onset of hearing, ATP stimulation either caused Ca2+ oscillations or an initial Ca2+ peak followed by a plateau while the UTP response was unchanged from that at pre-hearing stage. Parameters of spontaneous and nucleotide-evoked Ca2+ transients such as amplitude, decay time and duration were markedly reduced during cochlear development, whereas the kinetics of the Ca2+ rise did not show relevant changes. Whether low-frequency spontaneous Ca2+ transients are necessary for the formation and maintenance of the tectorial membrane e.g. by regulating gene transcription needs to be elucidated in further studies.
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Affiliation(s)
- Thore Schade-Mann
- Dept. of Biophysics & CIPMM, Hearing Research, Saarland University, Homburg, Germany; Department of Otolaryngology, Head and Neck Surgery, Tübingen University Medical Centre, Germany
| | - Stefan Münkner
- Dept. of Biophysics & CIPMM, Hearing Research, Saarland University, Homburg, Germany
| | - Tobias Eckrich
- Dept. of Biophysics & CIPMM, Hearing Research, Saarland University, Homburg, Germany
| | - Jutta Engel
- Dept. of Biophysics & CIPMM, Hearing Research, Saarland University, Homburg, Germany.
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19
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Huizar F, Soundarrajan D, Paravitorghabeh R, Zartman J. Interplay between morphogen-directed positional information systems and physiological signaling. Dev Dyn 2020; 249:328-341. [PMID: 31794137 PMCID: PMC7328709 DOI: 10.1002/dvdy.140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
The development of an organism from an undifferentiated single cell into a spatially complex structure requires spatial patterning of cell fates across tissues. Positional information, proposed by Lewis Wolpert in 1969, has led to the characterization of many components involved in regulating morphogen signaling activity. However, how morphogen gradients are established, maintained, and interpreted by cells still is not fully understood. Quantitative and systems-based approaches are increasingly needed to define general biological design rules that govern positional information systems in developing organisms. This short review highlights a selective set of studies that have investigated the roles of physiological signaling in modulating and mediating morphogen-based pattern formation. Similarities between neural transmission and morphogen-based pattern formation mechanisms suggest underlying shared principles of active cell-based communication. Within larger tissues, neural networks provide directed information, via physiological signaling, that supplements positional information through diffusion. Further, mounting evidence demonstrates that physiological signaling plays a role in ensuring robustness of morphogen-based signaling. We conclude by highlighting several outstanding questions regarding the role of physiological signaling in morphogen-based pattern formation. Elucidating how physiological signaling impacts positional information is critical for understanding the close coupling of developmental and cellular processes in the context of development, disease, and regeneration.
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Affiliation(s)
- Francisco Huizar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
- Bioengineering Graduate Program, University of Notre Dame, South Bend, Indiana
| | - Dharsan Soundarrajan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
| | - Ramezan Paravitorghabeh
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
| | - Jeremiah Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
- Bioengineering Graduate Program, University of Notre Dame, South Bend, Indiana
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20
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Gou J, Stotsky JA, Othmer HG. Growth control in the Drosophila wing disk. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1478. [PMID: 31917525 DOI: 10.1002/wsbm.1478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/02/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022]
Abstract
The regulation of size and shape is a fundamental requirement of biological development and has been a subject of scientific study for centuries, but we still lack an understanding of how organisms know when to stop growing. Imaginal wing disks of the fruit fly Drosophila melanogaster, which are precursors of the adult wings, are an archetypal tissue for studying growth control. The growth of the disks is dependent on many inter- and intra-organ factors such as morphogens, mechanical forces, nutrient levels, and hormones that influence gene expression and cell growth. Extracellular signals are transduced into gene-control signals via complex signal transduction networks, and since cells typically receive many different signals, a mechanism for integrating the signals is needed. Our understanding of the effect of morphogens on tissue-level growth regulation via individual pathways has increased significantly in the last half century, but our understanding of how multiple biochemical and mechanical signals are integrated to determine whether or not a cell decides to divide is still rudimentary. Numerous fundamental questions are involved in understanding the decision-making process, and here we review the major biochemical and mechanical pathways involved in disk development with a view toward providing a basis for beginning to understand how multiple signals can be integrated at the cell level, and how this translates into growth control at the level of the imaginal disk. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Cellular Models.
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Affiliation(s)
- Jia Gou
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota
| | - Jay A Stotsky
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota
| | - Hans G Othmer
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota
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21
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Manicka S, Levin M. Modeling somatic computation with non-neural bioelectric networks. Sci Rep 2019; 9:18612. [PMID: 31819119 PMCID: PMC6901451 DOI: 10.1038/s41598-019-54859-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/13/2019] [Indexed: 02/08/2023] Open
Abstract
The field of basal cognition seeks to understand how adaptive, context-specific behavior occurs in non-neural biological systems. Embryogenesis and regeneration require plasticity in many tissue types to achieve structural and functional goals in diverse circumstances. Thus, advances in both evolutionary cell biology and regenerative medicine require an understanding of how non-neural tissues could process information. Neurons evolved from ancient cell types that used bioelectric signaling to perform computation. However, it has not been shown whether or how non-neural bioelectric cell networks can support computation. We generalize connectionist methods to non-neural tissue architectures, showing that a minimal non-neural Bio-Electric Network (BEN) model that utilizes the general principles of bioelectricity (electrodiffusion and gating) can compute. We characterize BEN behaviors ranging from elementary logic gates to pattern detectors, using both fixed and transient inputs to recapitulate various biological scenarios. We characterize the mechanisms of such networks using dynamical-systems and information-theory tools, demonstrating that logic can manifest in bidirectional, continuous, and relatively slow bioelectrical systems, complementing conventional neural-centric architectures. Our results reveal a variety of non-neural decision-making processes as manifestations of general cellular biophysical mechanisms and suggest novel bioengineering approaches to construct functional tissues for regenerative medicine and synthetic biology as well as new machine learning architectures.
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Affiliation(s)
- Santosh Manicka
- Allen Discovery Center, 200 College Ave., Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Allen Discovery Center, 200 College Ave., Tufts University, Medford, MA, 02155, USA.
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22
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Toward Decoding Bioelectric Events in Xenopus Embryogenesis: New Methodology for Tracking Interplay Between Calcium and Resting Potentials In Vivo. J Mol Biol 2019; 432:605-620. [PMID: 31711960 DOI: 10.1016/j.jmb.2019.10.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022]
Abstract
Although chemical signaling during embryogenesis is readily addressed by a plethora of available techniques, the developmental functions of ionic signaling are still poorly understood. It is increasingly realized that bioelectric events in nonneural cells are critical for pattern regulation, but their study has been hampered by difficulties in monitoring and manipulating them in vivo. Recent developments in visualizing electrical signaling dynamics in the field of neuroscience have facilitated functional experiments that reveal instructive developmental bioelectric signals. However, there is a pressing need for additional tools to explore time-dependent ionic signaling to understand complex endogenous dynamics. Here, we present methodological advances, including 4D imaging and data analysis, for improved tracking of calcium flux in the Xenopus laevis embryo, lowering the barrier for in vivo physiology work in this important model system. Using these techniques, we investigated the relationship between bioelectric ion channel activity and calcium, finding that cell hyperpolarization and depolarization both induce persistent static elevation of cytoplasmic calcium levels that fade over developmental time. These calcium changes correlate with increased cell mobility in early embryos and abnormal craniofacial morphology in later embryos. We thus highlight membrane potential modulation as a tractable tool for modulation of signaling cascades that rely on calcium as a transduction mechanism. The methods we describe facilitate the study of important novel aspects of developmental physiology, are extendable to numerous classes of existing and forthcoming fluorescent physiological reporters, and establish highly accessible, inexpensive protocols for their investigation.
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Zhao D, Han X, Huang L, Wang J, Zhang X, Jeon JH, Zhao Q, Dong JT. Transcription factor ZFHX3 regulates calcium influx in mammary epithelial cells in part via the TRPV6 calcium channel. Biochem Biophys Res Commun 2019; 519:366-371. [PMID: 31519324 DOI: 10.1016/j.bbrc.2019.08.148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 12/19/2022]
Abstract
Zinc finger homeobox 3 (ZFHX3) is a transcription factor that regulates multiple cellular processes including cell proliferation, differentiation and neoplastic development. It is also involved in the function of steroid hormones estrogen and progesterone and the peptide hormone prolactin in mammary epithelial cells. In this study, we investigated whether and how ZFHX3 regulates intracellular calcium homeostasis in mammary epithelial cells. We found that ZFHX3 affected both store operated calcium entry and store independent calcium entry (SOCE and SICE). Simultaneously, the expression of the calcium channel TRPV6 was regulated by ZFHX3, as demonstrated by expression analysis and luciferase reporter assay. In cells with knockdown of ZFHX3, calcium entry was partially rescued by the overexpression of wild type but not the pore mutants of TRPV6. In addition, overexpression of TRPV6 promoted differentiation of the MCF10A mammary epithelial cells in three-dimensional culture, which is consistent with our previous findings that ZFHX3 is essential for mammary gland differentiation. These findings suggest that ZFHX3 plays an important role in intracellular calcium homeostasis in mammary epithelial cells, at least in part, by regulating TRPV6.
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Affiliation(s)
- Dan Zhao
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xueying Han
- Department of Zoology and Developmental Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Lili Huang
- Department of Zoology and Developmental Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jianpeng Wang
- Department of Zoology and Developmental Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xi Zhang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ju-Hong Jeon
- Department of Physiology, Seoul National University College of Medicine, Seoul, 110-799, South Korea
| | - Qiang Zhao
- Department of Zoology and Developmental Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Jin-Tang Dong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China; Department of Hematology and Medical Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, GA, USA.
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24
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Miller WB, Torday JS, Baluška F. The N-space Episenome unifies cellular information space-time within cognition-based evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:112-139. [PMID: 31415772 DOI: 10.1016/j.pbiomolbio.2019.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
Self-referential cellular homeostasis is maintained by the measured assessment of both internal status and external conditions based within an integrated cellular information field. This cellular field attachment to biologic information space-time coordinates environmental inputs by connecting the cellular senome, as the sum of the sensory experiences of the cell, with its genome and epigenome. In multicellular organisms, individual cellular information fields aggregate into a collective information architectural matrix, termed a N-space Episenome, that enables mutualized organism-wide information management. It is hypothesized that biological organization represents a dual heritable system constituted by both its biological materiality and a conjoining N-space Episenome. It is further proposed that morphogenesis derives from reciprocations between these inter-related facets to yield coordinated multicellular growth and development. The N-space Episenome is conceived as a whole cell informational projection that is heritable, transferable via cell division and essential for the synchronous integration of the diverse self-referential cells that constitute holobionts.
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Affiliation(s)
| | - John S Torday
- Department of Pediatrics, Harbor-UCLA Medical Center, USA.
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25
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Brodskiy PA, Wu Q, Soundarrajan DK, Huizar FJ, Chen J, Liang P, Narciso C, Levis MK, Arredondo-Walsh N, Chen DZ, Zartman JJ. Decoding Calcium Signaling Dynamics during Drosophila Wing Disc Development. Biophys J 2019; 116:725-740. [PMID: 30704858 PMCID: PMC6382932 DOI: 10.1016/j.bpj.2019.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/04/2018] [Accepted: 01/04/2019] [Indexed: 01/07/2023] Open
Abstract
The robust specification of organ development depends on coordinated cell-cell communication. This process requires signal integration among multiple pathways, relying on second messengers such as calcium ions. Calcium signaling encodes a significant portion of the cellular state by regulating transcription factors, enzymes, and cytoskeletal proteins. However, the relationships between the inputs specifying cell and organ development, calcium signaling dynamics, and final organ morphology are poorly understood. Here, we have designed a quantitative image-analysis pipeline for decoding organ-level calcium signaling. With this pipeline, we extracted spatiotemporal features of calcium signaling dynamics during the development of the Drosophila larval wing disc, a genetic model for organogenesis. We identified specific classes of wing phenotypes that resulted from calcium signaling pathway perturbations, including defects in gross morphology, vein differentiation, and overall size. We found four qualitative classes of calcium signaling activity. These classes can be ordered based on agonist stimulation strength Gαq-mediated signaling. In vivo calcium signaling dynamics depend on both receptor tyrosine kinase/phospholipase C γ and G protein-coupled receptor/phospholipase C β activities. We found that spatially patterned calcium dynamics correlate with known differential growth rates between anterior and posterior compartments. Integrated calcium signaling activity decreases with increasing tissue size, and it responds to morphogenetic perturbations that impact organ growth. Together, these findings define how calcium signaling dynamics integrate upstream inputs to mediate multiple response outputs in developing epithelial organs.
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Affiliation(s)
- Pavel A Brodskiy
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Qinfeng Wu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Dharsan K Soundarrajan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Francisco J Huizar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Jianxu Chen
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Peixian Liang
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Cody Narciso
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Megan K Levis
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana
| | | | - Danny Z Chen
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana
| | - Jeremiah J Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana.
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