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Armingol E, Baghdassarian HM, Lewis NE. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet 2024; 25:381-400. [PMID: 38238518 PMCID: PMC11139546 DOI: 10.1038/s41576-023-00685-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
Abstract
No cell lives in a vacuum, and the molecular interactions between cells define most phenotypes. Transcriptomics provides rich information to infer cell-cell interactions and communication, thus accelerating the discovery of the roles of cells within their communities. Such research relies heavily on algorithms that infer which cells are interacting and the ligands and receptors involved. Specific pressures on different research niches are driving the evolution of next-generation computational tools, enabling new conceptual opportunities and technological advances. More sophisticated algorithms now account for the heterogeneity and spatial organization of cells, multiple ligand types and intracellular signalling events, and enable the use of larger and more complex datasets, including single-cell and spatial transcriptomics. Similarly, new high-throughput experimental methods are increasing the number and resolution of interactions that can be analysed simultaneously. Here, we explore recent progress in cell-cell interaction research and highlight the diversification of the next generation of tools, which have yielded a rich ecosystem of tools for different applications and are enabling invaluable discoveries.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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2
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Ghomlaghi M, Theocharous M, Hoang N, Shin SY, von Kriegsheim A, O’ Neill E, Zhang T, Nguyen LK. Integrative modeling and analysis of signaling crosstalk reveal molecular switches coordinating Yes-associated protein transcriptional activities. iScience 2024; 27:109031. [PMID: 38380257 PMCID: PMC10877689 DOI: 10.1016/j.isci.2024.109031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 12/07/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
The transcriptional co-activator YAP forms complexes with distinct transcription factors, controlling cell fate decisions, such as proliferation and apoptosis. However, the mechanisms underlying its context-dependent function are poorly defined. This study explores the interplay between the TGF-β and Hippo pathways and their influence on YAP's association with specific transcription factors. By integrating iterative mathematical modeling with experimental validation, we uncover molecular switches, predominantly controlled by RASSF1A and ITCH, which dictate the formation of YAP-SMAD (proliferative) and YAP-p73 (apoptotic) complexes. Our results show that RASSF1A enhances the formation of apoptotic complexes, whereas ITCH promotes the formation of proliferative complexes. Notably, higher levels of ITCH transform YAP-SMAD activity from a transient to a sustained state, impacting cellular behaviors. Extending these findings to various breast cancer cell lines highlights the role of cellular context in YAP regulation. Our study provides new insights into the mechanisms of YAP transcriptional activities and their therapeutic implications.
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Affiliation(s)
- Milad Ghomlaghi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mandy Theocharous
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Nhan Hoang
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sung-Young Shin
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Alex von Kriegsheim
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Eric O’ Neill
- CRUK/MRC Institute for Radiation Oncology and Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Tao Zhang
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Lan K. Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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3
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Goetz A, Akl H, Dixit P. The ability to sense the environment is heterogeneously distributed in cell populations. eLife 2024; 12:RP87747. [PMID: 38293960 PMCID: PMC10942581 DOI: 10.7554/elife.87747] [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] [Indexed: 02/01/2024] Open
Abstract
Channel capacity of signaling networks quantifies their fidelity in sensing extracellular inputs. Low estimates of channel capacities for several mammalian signaling networks suggest that cells can barely detect the presence/absence of environmental signals. However, given the extensive heterogeneity and temporal stability of cell state variables, we hypothesize that the sensing ability itself may depend on the state of the cells. In this work, we present an information-theoretic framework to quantify the distribution of sensing abilities from single-cell data. Using data on two mammalian pathways, we show that sensing abilities are widely distributed in the population and most cells achieve better resolution of inputs compared to an 'average cell'. We verify these predictions using live-cell imaging data on the IGFR/FoxO pathway. Importantly, we identify cell state variables that correlate with cells' sensing abilities. This information-theoretic framework will significantly improve our understanding of how cells sense in their environment.
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Affiliation(s)
- Andrew Goetz
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
| | - Hoda Akl
- Department of Physics, University of FloridaGainesvilleUnited States
| | - Purushottam Dixit
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Systems Biology Institute, Yale UniversityWest HavenUnited States
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4
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Goetz A, Akl H, Dixit P. The ability to sense the environment is heterogeneously distributed in cell populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531554. [PMID: 36945613 PMCID: PMC10028875 DOI: 10.1101/2023.03.07.531554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Channel capacity of signaling networks quantifies their fidelity in sensing extracellular inputs. Low estimates of channel capacities for several mammalian signaling networks suggest that cells can barely detect the presence/absence of environmental signals. However, given the extensive heterogeneity and temporal stability of cell state variables, we hypothesize that the sensing ability itself may depend on the state of the cells. In this work, we present an information theoretic framework to quantify the distribution of sensing abilities from single cell data. Using data on two mammalian pathways, we show that sensing abilities are widely distributed in the population and most cells achieve better resolution of inputs compared to an " average cell ". We verify these predictions using live cell imaging data on the IGFR/FoxO pathway. Importantly, we identify cell state variables that correlate with cells' sensing abilities. This information theoretic framework will significantly improve our understanding of how cells sense in their environment.
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5
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Madsen RR, Toker A. PI3K signaling through a biochemical systems lens. J Biol Chem 2023; 299:105224. [PMID: 37673340 PMCID: PMC10570132 DOI: 10.1016/j.jbc.2023.105224] [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: 05/08/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Following 3 decades of extensive research into PI3K signaling, it is now evidently clear that the underlying network does not equate to a simple ON/OFF switch. This is best illustrated by the multifaceted nature of the many diseases associated with aberrant PI3K signaling, including common cancers, metabolic disease, and rare developmental disorders. However, we are still far from a complete understanding of the fundamental control principles that govern the numerous phenotypic outputs that are elicited by activation of this well-characterized biochemical signaling network, downstream of an equally diverse set of extrinsic inputs. At its core, this is a question on the role of PI3K signaling in cellular information processing and decision making. Here, we review the determinants of accurate encoding and decoding of growth factor signals and discuss outstanding questions in the PI3K signal relay network. We emphasize the importance of quantitative biochemistry, in close integration with advances in single-cell time-resolved signaling measurements and mathematical modeling.
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Affiliation(s)
- Ralitsa R Madsen
- MRC-Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.
| | - Alex Toker
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
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6
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Ho KKY, Srivastava S, Kinnunen PC, Garikipati K, Luker GD, Luker KE. Oscillatory ERK Signaling and Morphology Determine Heterogeneity of Breast Cancer Cell Chemotaxis via MEK-ERK and p38-MAPK Signaling Pathways. Bioengineering (Basel) 2023; 10:bioengineering10020269. [PMID: 36829763 PMCID: PMC9952091 DOI: 10.3390/bioengineering10020269] [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: 12/26/2022] [Revised: 01/24/2023] [Accepted: 02/12/2023] [Indexed: 02/22/2023] Open
Abstract
Chemotaxis, regulated by oscillatory signals, drives critical processes in cancer metastasis. Crucial chemoattractant molecules in breast cancer, CXCL12 and EGF, drive the activation of ERK and Akt. Regulated by feedback and crosstalk mechanisms, oscillatory signals in ERK and Akt control resultant changes in cell morphology and chemotaxis. While commonly studied at the population scale, metastasis arises from small numbers of cells that successfully disseminate, underscoring the need to analyze processes that cancer cells use to connect oscillatory signaling to chemotaxis at single-cell resolution. Furthermore, little is known about how to successfully target fast-migrating cells to block metastasis. We investigated to what extent oscillatory networks in single cells associate with heterogeneous chemotactic responses and how targeted inhibitors block signaling processes in chemotaxis. We integrated live, single-cell imaging with time-dependent data processing to discover oscillatory signal processes defining heterogeneous chemotactic responses. We identified that short ERK and Akt waves, regulated by MEK-ERK and p38-MAPK signaling pathways, determine the heterogeneous random migration of cancer cells. By comparison, long ERK waves and the morphological changes regulated by MEK-ERK signaling, determine heterogeneous directed motion. This study indicates that treatments against chemotaxis in consider must interrupt oscillatory signaling.
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Affiliation(s)
- Kenneth K. Y. Ho
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siddhartha Srivastava
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Patrick C. Kinnunen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Krishna Garikipati
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Institute for Computational Discovery & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gary D. Luker
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence: (G.D.L.); (K.E.L.)
| | - Kathryn E. Luker
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence: (G.D.L.); (K.E.L.)
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7
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Diaz-Vegas A, Norris DM, Jall-Rogg S, Cooke KC, Conway OJ, Shun-Shion AS, Duan X, Potter M, van Gerwen J, Baird HJ, Humphrey SJ, James DE, Fazakerley DJ, Burchfield JG. A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology. Life Sci Alliance 2023; 6:e202201585. [PMID: 36283703 PMCID: PMC9595207 DOI: 10.26508/lsa.202201585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Insulin-induced GLUT4 translocation to the plasma membrane in muscle and adipocytes is crucial for whole-body glucose homeostasis. Currently, GLUT4 trafficking assays rely on overexpression of tagged GLUT4. Here we describe a high-content imaging platform for studying endogenous GLUT4 translocation in intact adipocytes. This method enables high fidelity analysis of GLUT4 responses to specific perturbations, multiplexing of other trafficking proteins and other features including lipid droplet morphology. Using this multiplexed approach we showed that Vps45 and Rab14 are selective regulators of GLUT4, but Trarg1, Stx6, Stx16, Tbc1d4 and Rab10 knockdown affected both GLUT4 and TfR translocation. Thus, GLUT4 and TfR translocation machinery likely have some overlap upon insulin-stimulation. In addition, we identified Kif13A, a Rab10 binding molecular motor, as a novel regulator of GLUT4 traffic. Finally, comparison of endogenous to overexpressed GLUT4 highlights that the endogenous GLUT4 methodology has an enhanced sensitivity to genetic perturbations and emphasises the advantage of studying endogenous protein trafficking for drug discovery and genetic analysis of insulin action in relevant cell types.
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Affiliation(s)
- Alexis Diaz-Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sigrid Jall-Rogg
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Olivia J Conway
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Xiaowen Duan
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Meg Potter
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Julian van Gerwen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Harry Jm Baird
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
- School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - James G Burchfield
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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8
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Hart A, Nguyen LK. Meta-Dynamic Network Modelling for Biochemical Networks. Methods Mol Biol 2023; 2634:167-189. [PMID: 37074579 DOI: 10.1007/978-1-0716-3008-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
ODE modelling requires accurate knowledge of parameter and state variable values to deliver accurate and robust predictions. Parameters and state variables, however, are rarely static and immutable entities, especially in a biological context. This observation undermines the predictions made by ODE models that rely on specific parameter and state variable values and limits the contexts in which their predictions remain accurate and useful. Meta-dynamic network (MDN) modelling is a technique that can be synergistically integrated into an ODE modelling pipeline to assist in overcoming these limitations. The core mechanic of MDN modelling is the generation of a large number of model instances, each with a unique set of parameters and/or state variable values, followed by the simulation of each to determine how parameter and state variable variation affects protein dynamics. This process reveals the range of possible protein dynamics for a given network topology. Since MDN modelling is integrated with traditional ODE modelling, it can also be used to investigate the underlying causal mechanics. This technique is particularly suited to the investigation of network behaviors in systems that are highly heterogenous or systems wherein the network properties can change over time. MDN is a collection of principles rather than a strict protocol, so in this chapter, we have introduced the core principles using an example, the Hippo-ERK crosstalk signalling network.
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Affiliation(s)
- Anthony Hart
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia.
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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9
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Su M, Zhang X, Yuan J, Zhang X, Li F. The Role of Insulin-like Peptide in Maintaining Hemolymph Glucose Homeostasis in the Pacific White Shrimp Litopenaeus vannamei. Int J Mol Sci 2022; 23:ijms23063268. [PMID: 35328689 PMCID: PMC8948857 DOI: 10.3390/ijms23063268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023] Open
Abstract
Insulin-like peptide (ILP) has been identified in various crustaceans, but whether it has a similar function in regulating hemolymph glucose as vertebrate insulin is unclear. We analyzed the components of hemolymph sugar in the Pacific white shrimp, Litopenaeus vannamei, and investigated the changes of hemolymph glucose concentration and the expressions of ILP and glucose metabolism genes under different treatments. We found glucose was a major component of hemolymph sugar in shrimp. Starvation caused hemolymph glucose to rise first and then decline, and the raised hemolymph glucose after exogenous glucose injection returned to basal levels within a short time, indicating that shrimp have a regulatory mechanism to maintain hemolymph glucose homeostasis. In addition, injections of bovine insulin and recombinant LvILP protein both resulted in a fast decline in hemolymph glucose. Notably, RNA interference of LvILP did not significantly affect hemolymph glucose levels, but it inhibited exogenous glucose clearance. Based on the detection of glucose metabolism genes, we found LvILP might maintain hemolymph glucose stability by regulating the expression of these genes. These results suggest that ILP has a conserved function in shrimp similar to insulin in vertebrates and plays an important role in maintaining hemolymph glucose homeostasis.
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Affiliation(s)
- Manwen Su
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.S.); (J.Y.); (X.Z.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.S.); (J.Y.); (X.Z.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.S.); (J.Y.); (X.Z.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.S.); (J.Y.); (X.Z.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.S.); (J.Y.); (X.Z.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Roy A, Han VZ, Bard AM, Wehle DT, Smith SEP, Ramirez JM, Kalume F, Millen KJ. Non-synaptic Cell-Autonomous Mechanisms Underlie Neuronal Hyperactivity in a Genetic Model of PIK3CA-Driven Intractable Epilepsy. Front Mol Neurosci 2021; 14:772847. [PMID: 34899181 PMCID: PMC8662737 DOI: 10.3389/fnmol.2021.772847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022] Open
Abstract
Patients harboring mutations in the PI3K-AKT-MTOR pathway-encoding genes often develop a spectrum of neurodevelopmental disorders including epilepsy. A significant proportion remains unresponsive to conventional anti-seizure medications. Understanding mutation-specific pathophysiology is thus critical for molecularly targeted therapies. We previously determined that mouse models expressing a patient-related activating mutation in PIK3CA, encoding the p110α catalytic subunit of phosphoinositide-3-kinase (PI3K), are epileptic and acutely treatable by PI3K inhibition, irrespective of dysmorphology. Here we report the physiological mechanisms underlying this dysregulated neuronal excitability. In vivo, we demonstrate epileptiform events in the Pik3ca mutant hippocampus. By ex vivo analyses, we show that Pik3ca-driven hyperactivation of hippocampal pyramidal neurons is mediated by changes in multiple non-synaptic, cell-intrinsic properties. Finally, we report that acute inhibition of PI3K or AKT, but not MTOR activity, suppresses the intrinsic hyperactivity of the mutant neurons. These acute mechanisms are distinct from those causing neuronal hyperactivity in other AKT-MTOR epileptic models and define parameters to facilitate the development of new molecularly rational therapeutic interventions for intractable epilepsy.
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Affiliation(s)
- Achira Roy
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Victor Z Han
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Biology, University of Washington, Seattle, WA, United States
| | - Angela M Bard
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Devin T Wehle
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States.,Graduate Program in Neuroscience, University of Washington, Seattle, WA, United States
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States.,Department of Neurological Surgery, University of Washington, Seattle, WA, United States.,Department of Physiology and Biophysics, University of Washington, Seattle, WA, United States
| | - Franck Kalume
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Neurological Surgery, University of Washington, Seattle, WA, United States.,Department of Pharmacology, University of Washington, Seattle, WA, United States
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
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11
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Yang P, Huang H, Liu C. Feature selection revisited in the single-cell era. Genome Biol 2021; 22:321. [PMID: 34847932 PMCID: PMC8638336 DOI: 10.1186/s13059-021-02544-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
Recent advances in single-cell biotechnologies have resulted in high-dimensional datasets with increased complexity, making feature selection an essential technique for single-cell data analysis. Here, we revisit feature selection techniques and summarise recent developments. We review their application to a range of single-cell data types generated from traditional cytometry and imaging technologies and the latest array of single-cell omics technologies. We highlight some of the challenges and future directions and finally consider their scalability and make general recommendations on each type of feature selection method. We hope this review stimulates future research and application of feature selection in the single-cell era.
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Affiliation(s)
- Pengyi Yang
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, 2006, Australia.
- Computational Systems Biology Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia.
- Charles Perkins Centre, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Hao Huang
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, 2006, Australia
- Computational Systems Biology Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Chunlei Liu
- Computational Systems Biology Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
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12
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Ghomlaghi M, Yang G, Shin SY, James DE, Nguyen LK. Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1. PLoS Comput Biol 2021; 17:e1008513. [PMID: 34529665 PMCID: PMC8478217 DOI: 10.1371/journal.pcbi.1008513] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 09/28/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022] Open
Abstract
The PI3K/MTOR signalling network regulates a broad array of critical cellular processes, including cell growth, metabolism and autophagy. The mechanistic target of rapamycin (MTOR) kinase functions as a core catalytic subunit in two physically and functionally distinct complexes mTORC1 and mTORC2, which also share other common components including MLST8 (also known as GβL) and DEPTOR. Despite intensive research, how mTORC1 and 2 assembly and activity are coordinated, and how they are functionally linked remain to be fully characterized. This is due in part to the complex network wiring, featuring multiple feedback loops and intricate post-translational modifications. Here, we integrate predictive network modelling, in vitro experiments and -omics data analysis to elucidate the emergent dynamic behaviour of the PI3K/MTOR network. We construct new mechanistic models that encapsulate critical mechanistic details, including mTORC1/2 coordination by MLST8 (de)ubiquitination and the Akt-to-mTORC2 positive feedback loop. Model simulations validated by experimental studies revealed a previously unknown biphasic, threshold-gated dependence of mTORC1 activity on the key mTORC2 subunit SIN1, which is robust against cell-to-cell variation in protein expression. In addition, our integrative analysis demonstrates that ubiquitination of MLST8, which is reversed by OTUD7B, is regulated by IRS1/2. Our results further support the essential role of MLST8 in enabling both mTORC1 and 2’s activity and suggest MLST8 as a viable therapeutic target in breast cancer. Overall, our study reports a new mechanistic model of PI3K/MTOR signalling incorporating MLST8-mediated mTORC1/2 formation and unveils a novel regulatory linkage between mTORC1 and mTORC2. Signalling networks are the key information-processing machineries that underpin the ability of living cells to respond proportionately to extra- (and intra-) cellular cues. The PI3K/MTOR signalling network is one of the most important signalling networks in human cells that regulates cellular response to critical hormones such as insulin; yet our understanding of the network behaviour remains far from complete. Here, we employed a highly integrative approach that combines predictive mathematical modelling, biological experimentation, and data analysis to gain novel systems-level insights into PI3K/MTOR signalling. We constructed new mathematical models of this complex network incorporating important regulatory mechanisms. In contrary to commonly-held views that mTORC2 lies upstream and is a positive regulator of mTORC1, we found that their relationship is highly non-linear and dose dependent. This finding has major implications for anti-mTORC2 therapy as depending on the cellular contexts, inhibiting mTORC2 may either reduce or enhance mTORC1 activation, the latter could inadvertently dampen the effect of mTORC2 blockade. Furthermore, our results demonstrate that MLST8 is required for the assembly and activity of both MTOR complexes and suggest MLST8 is a viable therapeutic target in breast cancer.
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Affiliation(s)
- Milad Ghomlaghi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Guang Yang
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Sung-Young Shin
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Monash University, Melbourne, Australia
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13
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Kearney AL, Norris DM, Ghomlaghi M, Kin Lok Wong M, Humphrey SJ, Carroll L, Yang G, Cooke KC, Yang P, Geddes TA, Shin S, Fazakerley DJ, Nguyen LK, James DE, Burchfield JG. Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis. eLife 2021; 10:e66942. [PMID: 34253290 PMCID: PMC8277355 DOI: 10.7554/elife.66942] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/30/2021] [Indexed: 01/16/2023] Open
Abstract
The phosphoinositide 3-kinase (PI3K)-Akt network is tightly controlled by feedback mechanisms that regulate signal flow and ensure signal fidelity. A rapid overshoot in insulin-stimulated recruitment of Akt to the plasma membrane has previously been reported, which is indicative of negative feedback operating on acute timescales. Here, we show that Akt itself engages this negative feedback by phosphorylating insulin receptor substrate (IRS) 1 and 2 on a number of residues. Phosphorylation results in the depletion of plasma membrane-localised IRS1/2, reducing the pool available for interaction with the insulin receptor. Together these events limit plasma membrane-associated PI3K and phosphatidylinositol (3,4,5)-trisphosphate (PIP3) synthesis. We identified two Akt-dependent phosphorylation sites in IRS2 at S306 (S303 in mouse) and S577 (S573 in mouse) that are key drivers of this negative feedback. These findings establish a novel mechanism by which the kinase Akt acutely controls PIP3 abundance, through post-translational modification of the IRS scaffold.
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Affiliation(s)
- Alison L Kearney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Dougall M Norris
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of CambridgeCambridgeUnited Kingdom
| | - Milad Ghomlaghi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash UniversityClaytonAustralia
- Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Martin Kin Lok Wong
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Luke Carroll
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Guang Yang
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Pengyi Yang
- Charles Perkins Centre, School of Mathematics and Statistics, University of SydneySydneyAustralia
- Computational Systems Biology Group, Children's Medical Research Institute, University of SydneyWestmeadAustralia
| | - Thomas A Geddes
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
- Computational Systems Biology Group, Children's Medical Research Institute, University of SydneyWestmeadAustralia
| | - Sungyoung Shin
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash UniversityClaytonAustralia
- Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of CambridgeCambridgeUnited Kingdom
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash UniversityClaytonAustralia
- Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
- School of Medical Sciences, University of SydneySydneyAustralia
| | - James G Burchfield
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
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