1
|
Henderson JM, Ljubojevic N, Belian S, Chaze T, Castaneda D, Battistella A, Giai Gianetto Q, Matondo M, Descroix S, Bassereau P, Zurzolo C. Tunnelling nanotube formation is driven by Eps8/IRSp53-dependent linear actin polymerization. EMBO J 2023; 42:e113761. [PMID: 38009333 PMCID: PMC10711657 DOI: 10.15252/embj.2023113761] [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: 02/13/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/28/2023] Open
Abstract
Tunnelling nanotubes (TNTs) connect distant cells and mediate cargo transfer for intercellular communication in physiological and pathological contexts. How cells generate these actin-mediated protrusions to span lengths beyond those attainable by canonical filopodia remains unknown. Through a combination of micropatterning, microscopy, and optical tweezer-based approaches, we demonstrate that TNTs formed through the outward extension of actin achieve distances greater than the mean length of filopodia and that branched Arp2/3-dependent pathways attenuate the extent to which actin polymerizes in nanotubes, thus limiting their occurrence. Proteomic analysis using epidermal growth factor receptor kinase substrate 8 (Eps8) as a positive effector of TNTs showed that, upon Arp2/3 inhibition, proteins enhancing filament turnover and depolymerization were reduced and Eps8 instead exhibited heightened interactions with the inverted Bin/Amphiphysin/Rvs (I-BAR) domain protein IRSp53 that provides a direct connection with linear actin polymerases. Our data reveals how common protrusion players (Eps8 and IRSp53) form tunnelling nanotubes, and that when competing pathways overutilizing such proteins and monomeric actin in Arp2/3 networks are inhibited, processes promoting linear actin growth dominate to favour tunnelling nanotube formation.
Collapse
Affiliation(s)
- J Michael Henderson
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and InfectionCNRS UMR 3691, Université de Paris, Institut PasteurParisFrance
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico‐Chimie CurieParisFrance
- Present address:
Department of ChemistryBowdoin CollegeBrunswickMEUSA
| | - Nina Ljubojevic
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and InfectionCNRS UMR 3691, Université de Paris, Institut PasteurParisFrance
- Sorbonne UniversitéParisFrance
| | - Sevan Belian
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and InfectionCNRS UMR 3691, Université de Paris, Institut PasteurParisFrance
- Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Thibault Chaze
- Proteomics Platform, Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut PasteurParisFrance
| | - Daryl Castaneda
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and InfectionCNRS UMR 3691, Université de Paris, Institut PasteurParisFrance
- Keele UniversityKeeleUK
| | - Aude Battistella
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico‐Chimie CurieParisFrance
| | - Quentin Giai Gianetto
- Proteomics Platform, Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut PasteurParisFrance
- Bioinformatics and Biostatistics Hub, Computational Biology DepartmentCNRS USR 3756, Institut PasteurParisFrance
| | - Mariette Matondo
- Proteomics Platform, Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut PasteurParisFrance
| | - Stéphanie Descroix
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico‐Chimie CurieParisFrance
- Institut Pierre‐Gilles de GennesParisFrance
| | - Patricia Bassereau
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico‐Chimie CurieParisFrance
| | - Chiara Zurzolo
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and InfectionCNRS UMR 3691, Université de Paris, Institut PasteurParisFrance
- Department of Molecular Medicine and Medical BiotechnologyUniversity of Naples Federico IINaplesItaly
| |
Collapse
|
2
|
Junk P, Kiel C. Structure-based prediction of Ras-effector binding affinities and design of "branchegetic" interface mutations. Structure 2023; 31:870-883.e5. [PMID: 37167973 DOI: 10.1016/j.str.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
Ras is a central cellular hub protein controlling multiple cell fates. How Ras interacts with a variety of potential effector proteins is relatively unexplored, with only some key effectors characterized in great detail. Here, we have used homology modeling based on X-ray and AlphaFold2 templates to build structural models for 54 Ras-effector complexes. These models were used to estimate binding affinities using a supervised learning regressor. Furthermore, we systematically introduced Ras "branch-pruning" (or branchegetic) mutations to identify 200 interface mutations that affect the binding energy with at least one of the model structures. The impacts of these branchegetic mutants were integrated into a mathematical model to assess the potential for rewiring interactions at the Ras hub on a systems level. These findings have provided a quantitative understanding of Ras-effector interfaces and their impact on systems properties of a key cellular hub.
Collapse
Affiliation(s)
- Philipp Junk
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland.
| | - Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland; Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| |
Collapse
|
3
|
Ternet C, Junk P, Sevrin T, Catozzi S, Wåhlén E, Heldin J, Oliviero G, Wynne K, Kiel C. Analysis of context-specific KRAS-effector (sub)complexes in Caco-2 cells. Life Sci Alliance 2023; 6:e202201670. [PMID: 36894174 PMCID: PMC9998658 DOI: 10.26508/lsa.202201670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Ras is a key switch controlling cell behavior. In the GTP-bound form, Ras interacts with numerous effectors in a mutually exclusive manner, where individual Ras-effectors are likely part of larger cellular (sub)complexes. The molecular details of these (sub)complexes and their alteration in specific contexts are not understood. Focusing on KRAS, we performed affinity purification (AP)-mass spectrometry (MS) experiments of exogenously expressed FLAG-KRAS WT and three oncogenic mutants ("genetic contexts") in the human Caco-2 cell line, each exposed to 11 different culture media ("culture contexts") that mimic conditions relevant in the colon and colorectal cancer. We identified four effectors present in complex with KRAS in all genetic and growth contexts ("context-general effectors"). Seven effectors are found in KRAS complexes in only some contexts ("context-specific effectors"). Analyzing all interactors in complex with KRAS per condition, we find that the culture contexts had a larger impact on interaction rewiring than genetic contexts. We investigated how changes in the interactome impact functional outcomes and created a Shiny app for interactive visualization. We validated some of the functional differences in metabolism and proliferation. Finally, we used networks to evaluate how KRAS-effectors are involved in the modulation of functions by random walk analyses of effector-mediated (sub)complexes. Altogether, our work shows the impact of environmental contexts on network rewiring, which provides insights into tissue-specific signaling mechanisms. This may also explain why KRAS oncogenic mutants may be causing cancer only in specific tissues despite KRAS being expressed in most cells and tissues.
Collapse
Affiliation(s)
- Camille Ternet
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Philipp Junk
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Thomas Sevrin
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Simona Catozzi
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Erik Wåhlén
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Johan Heldin
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Christina Kiel
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
4
|
Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
Collapse
|
5
|
Gan W, Wang C, Pan Q, Li Y, Guo Y, Fan D, Peng Y, Rao Z, Xu S, Zheng P, Zhu W. Discovery of novel 4-arylamino-quinazoline derivatives as EGFRL858R/T790M inhibitors with the potential to inhibit the non-small cell lung cancers. Bioorg Chem 2022; 127:105994. [DOI: 10.1016/j.bioorg.2022.105994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 12/20/2022]
|
6
|
Kemmer S, Berdiel-Acer M, Reinz E, Sonntag J, Tarade N, Bernhardt S, Fehling-Kaschek M, Hasmann M, Korf U, Wiemann S, Timmer J. Disentangling ERBB Signaling in Breast Cancer Subtypes-A Model-Based Analysis. Cancers (Basel) 2022; 14:2379. [PMID: 35625984 PMCID: PMC9139462 DOI: 10.3390/cancers14102379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Targeted therapies have shown striking success in the treatment of cancer over the last years. However, their specific effects on an individual tumor appear to be varying and difficult to predict. Using an integrative modeling approach that combines mechanistic and regression modeling, we gained insights into the response mechanisms of breast cancer cells due to different ligand-drug combinations. The multi-pathway model, capturing ERBB receptor signaling as well as downstream MAPK and PI3K pathways was calibrated on time-resolved data of the luminal breast cancer cell lines MCF7 and T47D across an array of four ligands and five drugs. The same model was then successfully applied to triple negative and HER2-positive breast cancer cell lines, requiring adjustments mostly for the respective receptor compositions within these cell lines. The additional relevance of cell-line-specific mutations in the MAPK and PI3K pathway components was identified via L1 regularization, where the impact of these mutations on pathway activation was uncovered. Finally, we predicted and experimentally validated the proliferation response of cells to drug co-treatments. We developed a unified mathematical model that can describe the ERBB receptor and downstream signaling in response to therapeutic drugs targeting this clinically relevant signaling network in cell line that represent three major subtypes of breast cancer. Our data and model suggest that alterations in this network could render anti-HER therapies relevant beyond the HER2-positive subtype.
Collapse
Affiliation(s)
- Svenja Kemmer
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany; (S.K.); (M.F.-K.)
- FDM—Freiburg Center for Data Analysis and Modeling, University of Freiburg, 79104 Freiburg, Germany
| | - Mireia Berdiel-Acer
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany; (M.B.-A.); (E.R.); (J.S.); (N.T.); (S.B.); (U.K.)
| | - Eileen Reinz
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany; (M.B.-A.); (E.R.); (J.S.); (N.T.); (S.B.); (U.K.)
| | - Johanna Sonntag
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany; (M.B.-A.); (E.R.); (J.S.); (N.T.); (S.B.); (U.K.)
| | - Nooraldeen Tarade
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany; (M.B.-A.); (E.R.); (J.S.); (N.T.); (S.B.); (U.K.)
- Faculty of Biosciences, University of Heidelberg, 69117 Heidelberg, Germany
| | - Stephan Bernhardt
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany; (M.B.-A.); (E.R.); (J.S.); (N.T.); (S.B.); (U.K.)
| | - Mirjam Fehling-Kaschek
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany; (S.K.); (M.F.-K.)
- FDM—Freiburg Center for Data Analysis and Modeling, University of Freiburg, 79104 Freiburg, Germany
| | | | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany; (M.B.-A.); (E.R.); (J.S.); (N.T.); (S.B.); (U.K.)
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany; (M.B.-A.); (E.R.); (J.S.); (N.T.); (S.B.); (U.K.)
| | - Jens Timmer
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany; (S.K.); (M.F.-K.)
- FDM—Freiburg Center for Data Analysis and Modeling, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
7
|
Duan D, Hanson M, Holland DO, Johnson ME. Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis. Sci Rep 2022; 12:5413. [PMID: 35354856 PMCID: PMC8967901 DOI: 10.1038/s41598-022-09259-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/21/2022] [Indexed: 11/25/2022] Open
Abstract
Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at copy numbers within a cell and across cell types varying from hundreds (e.g. auxilin) to millions (e.g. clathrin). These variations contain important information about function, but without integration with the interaction network, they cannot capture how supply and demand for each protein depends on binding to shared and distinct partners. Here we construct the interface-resolved network of 82 proteins involved in CME and establish a metric, a stoichiometric balance ratio (SBR), that quantifies whether each protein in the network has an abundance that is sub- or super-stoichiometric dependent on the global competition for binding. We find that highly abundant proteins (like clathrin) are super-stoichiometric, but that not all super-stoichiometric proteins are highly abundant, across three cell populations (HeLa, fibroblast, and neuronal synaptosomes). Most strikingly, within all cells there is significant competition to bind shared sites on clathrin and the central AP-2 adaptor by other adaptor proteins, resulting in most being in excess supply. Our network and systematic analysis, including response to perturbations of network components, show how competition for shared binding sites results in functionally similar proteins having widely varying stoichiometries, due to variations in both abundance and their unique network of binding partners.
Collapse
Affiliation(s)
- Daisy Duan
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Meretta Hanson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | | | - Margaret E Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA.
| |
Collapse
|
8
|
Catozzi S, Ternet C, Gourrege A, Wynne K, Oliviero G, Kiel C. Reconstruction and analysis of a large-scale binary Ras-effector signaling network. Cell Commun Signal 2022; 20:24. [PMID: 35246154 PMCID: PMC8896392 DOI: 10.1186/s12964-022-00823-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/18/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Ras is a key cellular signaling hub that controls numerous cell fates via multiple downstream effector pathways. While pathways downstream of effectors such as Raf, PI3K and RalGDS are extensively described in the literature, how other effectors signal downstream of Ras is often still enigmatic. METHODS A comprehensive and unbiased Ras-effector network was reconstructed downstream of 43 effector proteins (converging onto 12 effector classes) using public pathway and protein-protein interaction (PPI) databases. The output is an oriented graph of pairwise interactions defining a 3-layer signaling network downstream of Ras. The 2290 proteins comprising the network were studied for their implication in signaling crosstalk and feedbacks, their subcellular localizations, and their cellular functions. RESULTS The final Ras-effector network consists of 2290 proteins that are connected via 19,080 binary PPIs, increasingly distributed across the downstream layers, with 441 PPIs in layer 1, 1660 in layer 2, and 16,979 in layer 3. We identified a high level of crosstalk among proteins of the 12 effector classes. A class-specific Ras sub-network was generated in CellDesigner (.xml file) and a functional enrichment analysis thereof shows that 58% of the processes have previously been associated to a respective effector pathway, with the remaining providing insights into novel and unexplored functions of specific effector pathways. CONCLUSIONS Our large-scale and cell general Ras-effector network is a crucial steppingstone towards defining the network boundaries. It constitutes a 'reference interactome' and can be contextualized for specific conditions, e.g. different cell types or biopsy material obtained from cancer patients. Further, it can serve as a basis for elucidating systems properties, such as input-output relationships, crosstalk, and pathway redundancy. Video Abstract.
Collapse
Affiliation(s)
- Simona Catozzi
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Camille Ternet
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Alize Gourrege
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland. .,Department of Molecular Medicine, University of Pavia, 27100, Pavia, Italy.
| |
Collapse
|
9
|
Burge RA, Hobbs GA. Not all RAS mutations are equal: A detailed review of the functional diversity of RAS hot spot mutations. Adv Cancer Res 2022; 153:29-61. [PMID: 35101234 DOI: 10.1016/bs.acr.2021.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The RAS family of small GTPases are among the most frequently mutated oncogenes in human cancer. Approximately 20% of cancers harbor a RAS mutation, and >150 different missense mutations have been detected. Many of these mutations have mutant-specific biochemical defects that alter nucleotide binding and hydrolysis, effector interactions and cell signaling, prompting renewed efforts in the development of anti-RAS therapies, including the mutation-specific strategies. Previously viewed as undruggable, the recent FDA approval of a KRASG12C-selective inhibitor has offered real promise to the development of allele-specific RAS therapies. A broader understanding of the mutational consequences on RAS function must be developed to exploit additional allele-specific vulnerabilities. Approximately 94% of RAS mutations occur at one of three mutational "hot spots" at Gly12, Gly13 and Gln61. Further, the single-nucleotide substitutions represent >99% of these mutations. Within this scope, we discuss the mutational frequencies of RAS isoforms in cancer, mutant-specific effector interactions and biochemical properties. By limiting our analysis to this mutational subset, we simplify the analysis while only excluding a small percentage of total mutations. Combined, these data suggest that the presence or absence of select RAS mutations in human cancers can be linked to their biochemical properties. Continuing to examine the biochemical differences in each RAS-mutant protein will continue to provide additional breakthroughs in allele-specific therapeutic strategies.
Collapse
Affiliation(s)
- Rachel A Burge
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - G Aaron Hobbs
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
| |
Collapse
|
10
|
Catozzi S, Halasz M, Kiel C. Predicted 'wiring landscape' of Ras-effector interactions in 29 human tissues. NPJ Syst Biol Appl 2021; 7:10. [PMID: 33580066 PMCID: PMC7881153 DOI: 10.1038/s41540-021-00170-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023] Open
Abstract
Ras is a plasma membrane (PM)-associated signaling hub protein that interacts with its partners (effectors) in a mutually exclusive fashion. We have shown earlier that competition for binding and hence the occurrence of specific binding events at a hub protein can modulate the activation of downstream pathways. Here, using a mechanistic modeling approach that incorporates high-quality proteomic data of Ras and 56 effectors in 29 (healthy) human tissues, we quantified the amount of individual Ras-effector complexes, and characterized the (stationary) Ras "wiring landscape" specific to each tissue. We identified nine effectors that are in significant amount in complex with Ras in at least one of the 29 tissues. We simulated both mutant- and stimulus-induced network re-configurations, and assessed their divergence from the reference scenario, specifically discussing a case study for two stimuli in three epithelial tissues. These analyses pointed to 32 effectors that are in significant amount in complex with Ras only if they are additionally recruited to the PM, e.g. via membrane-binding domains or domains binding to activated receptors at the PM. Altogether, our data emphasize the importance of tissue context for binding events at the Ras signaling hub.
Collapse
Affiliation(s)
- Simona Catozzi
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Christina Kiel
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland.
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland.
| |
Collapse
|
11
|
Kiel C, Matallanas D, Kolch W. The Ins and Outs of RAS Effector Complexes. Biomolecules 2021; 11:236. [PMID: 33562401 PMCID: PMC7915224 DOI: 10.3390/biom11020236] [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: 01/10/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
RAS oncogenes are among the most commonly mutated proteins in human cancers. They regulate a wide range of effector pathways that control cell proliferation, survival, differentiation, migration and metabolic status. Including aberrations in these pathways, RAS-dependent signaling is altered in more than half of human cancers. Targeting mutant RAS proteins and their downstream oncogenic signaling pathways has been elusive. However, recent results comprising detailed molecular studies, large scale omics studies and computational modeling have painted a new and more comprehensive portrait of RAS signaling that helps us to understand the intricacies of RAS, how its physiological and pathophysiological functions are regulated, and how we can target them. Here, we review these efforts particularly trying to relate the detailed mechanistic studies with global functional studies. We highlight the importance of computational modeling and data integration to derive an actionable understanding of RAS signaling that will allow us to design new mechanism-based therapies for RAS mutated cancers.
Collapse
Affiliation(s)
- Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - David Matallanas
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
12
|
Rukhlenko O, Kholodenko BN, Kolch W. Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing. Curr Opin Struct Biol 2020; 67:61-68. [PMID: 33126139 DOI: 10.1016/j.sbi.2020.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 11/17/2022]
Abstract
Macromolecular protein assemblies govern many cellular processes and are disturbed in many diseases including cancer. Often seen as static molecular machines, protein complexes involved in signal transduction networks exhibit intricate dynamics that are critical for their function. Using the RAS-RAF-MEK-ERK pathway as example we discuss recent progress in our understanding of protein complex dynamics achieved through mathematical modelling, computational simulations and structural studies. The emerging picture highlights that both spatial and temporal dynamics cooperate to enable correct signal processing and the fine tuning of timing, duration and strengths of signalling. These dynamic processes are subverted by oncogenic mutations and contribute to tumorigenesis and drug resistance.
Collapse
Affiliation(s)
- Oleksii Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris N Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
| |
Collapse
|
13
|
Ibáňez Gaspar V, Catozzi S, Ternet C, Luthert PJ, Kiel C. Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context. Small GTPases 2020; 12:209-225. [PMID: 32057289 PMCID: PMC7939564 DOI: 10.1080/21541248.2020.1724596] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer is the second leading cause of death globally, and colorectal cancer (CRC) is among the five most common cancers. The small GTPase KRAS is an oncogene that is mutated in ~30% of all CRCs. Pharmacological treatments of CRC are currently unsatisfactory, but much hope rests on network-centric approaches to drug development and cancer treatment. These approaches, however, require a better understanding of how networks downstream of Ras oncoproteins are connected in a particular tissue context – here colon and CRC. Previously we have shown that competition for binding to a ‘hub’ protein, such as Ras, can induce a rewiring of signal transduction networks. In this study, we analysed 56 established and predicted effectors that contain a structural domain with the potential ability to bind to Ras oncoproteins and their link to pathways coordinating intestinal homoeostasis and barrier function. Using protein concentrations in colon tissue and Ras-effector binding affinities, a computational network model was generated that predicted how effectors differentially and competitively bind to Ras in colon context. The model also predicted both qualitative and quantitative changes in Ras-effector complex formations with increased levels of active Ras – to simulate its upregulation in cancer – simply as an emergent property of competition for the same binding interface on the surface of Ras. We also considered how the number of Ras-effector complexes at the membrane can be increased by additional domains present in some effectors that are recruited to the membrane in response to specific conditions (inputs/stimuli/growth factors) in colon context and CRC.
Collapse
Affiliation(s)
- Verónica Ibáňez Gaspar
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
| | - Simona Catozzi
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
| | - Camille Ternet
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
| | - Philip J Luthert
- UCL Institute of Ophthalmology, and NIHR Moorfields Biomedical Research Centre, University College London, London, UK
| | - Christina Kiel
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
| |
Collapse
|
14
|
Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan CJ, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ, Kolch W. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS G13D. Nat Commun 2020; 11:499. [PMID: 31980649 PMCID: PMC6981206 DOI: 10.1038/s41467-019-14224-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.
Collapse
Affiliation(s)
- Susan A Kennedy
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Mohamed-Ali Jarboui
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Werner Siemens Imaging Center, University of Tübingen, Tübingen, Germany
| | - Sriganesh Srihari
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
- QIMR-Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Cinzia Raso
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Kenneth Bryan
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Layal Dernayka
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Theodosia Charitou
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Manuel Bernal-Llinares
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | | | | | - David Matallanas
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Jasna Curak
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Thierry LeBihan
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Lisa Imrie
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Priyanka Pillai
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Miriam A Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Erik Fasterius
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cristina Al-Khalili Szigyarto
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - James Breen
- School of Biological Sciences, University of Adelaide Bioinformatics Hub, Adelaide, SA, Australia
- Computational & Systems Biology Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Christina Kiel
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Luis Serrano
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Computer Science, University College Dublin, Dublin, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Owen Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Studies, Glasgow University, Glasgow, UK
| | - Steven Shave
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Manfred Auer
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Horn
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Franziska Klose
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
| | - David J Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland.
- Conway Institute, University College Dublin, Dublin, Ireland.
- School of Medicine, University College Dublin, Dublin, Ireland.
| |
Collapse
|
15
|
Domingo J, Baeza-Centurion P, Lehner B. The Causes and Consequences of Genetic Interactions (Epistasis). Annu Rev Genomics Hum Genet 2019; 20:433-460. [PMID: 31082279 DOI: 10.1146/annurev-genom-083118-014857] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The same mutation can have different effects in different individuals. One important reason for this is that the outcome of a mutation can depend on the genetic context in which it occurs. This dependency is known as epistasis. In recent years, there has been a concerted effort to quantify the extent of pairwise and higher-order genetic interactions between mutations through deep mutagenesis of proteins and RNAs. This research has revealed two major components of epistasis: nonspecific genetic interactions caused by nonlinearities in genotype-to-phenotype maps, and specific interactions between particular mutations. Here, we provide an overview of our current understanding of the mechanisms causing epistasis at the molecular level, the consequences of genetic interactions for evolution and genetic prediction, and the applications of epistasis for understanding biology and determining macromolecular structures.
Collapse
Affiliation(s)
- Júlia Domingo
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , , .,Universitat Pompeu Fabra, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
16
|
Baeza-Centurion P, Miñana B, Schmiedel JM, Valcárcel J, Lehner B. Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing. Cell 2019; 176:549-563.e23. [PMID: 30661752 DOI: 10.1016/j.cell.2018.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/29/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023]
Abstract
Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modeling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighboring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.
Collapse
Affiliation(s)
- Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Belén Miñana
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Jörn M Schmiedel
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| |
Collapse
|
17
|
Stöcker BK, Köster J, Zamir E, Rahmann S. Modeling and simulating networks of interdependent protein interactions. Integr Biol (Camb) 2018; 10:290-305. [PMID: 29676773 DOI: 10.1039/c8ib00012c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of these systems emerge not only from the protein interactions themselves but also from the dependencies between these interactions, as generated by allosteric effects or mutual exclusion due to steric hindrance. Therefore, formal models for integrating and utilizing information about interaction dependencies are of high interest. Here, we describe an approach for endowing protein networks with interaction dependencies using propositional logic, thereby obtaining constrained protein interaction networks ("constrained networks"). The construction of these networks is based on public interaction databases as well as text-mined information about interaction dependencies. We present an efficient data structure and algorithm to simulate protein complex formation in constrained networks. The efficiency of the model allows fast simulation and facilitates the analysis of many proteins in large networks. In addition, this approach enables the simulation of perturbation effects, such as knockout of single or multiple proteins and changes of protein concentrations. We illustrate how our model can be used to analyze a constrained human adhesome protein network, which is responsible for the formation of diverse and dynamic cell-matrix adhesion sites. By comparing protein complex formation under known interaction dependencies versus without dependencies, we investigate how these dependencies shape the resulting repertoire of protein complexes. Furthermore, our model enables investigating how the interplay of network topology with interaction dependencies influences the propagation of perturbation effects across a large biochemical system. Our simulation software CPINSim (for Constrained Protein Interaction Network Simulator) is available under the MIT license at http://github.com/BiancaStoecker/cpinsim and as a Bioconda package (https://bioconda.github.io).
Collapse
Affiliation(s)
- Bianca K Stöcker
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
| | | | | | | |
Collapse
|
18
|
Holland DO, Johnson ME. Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis. PLoS Comput Biol 2018. [PMID: 29518071 PMCID: PMC5860782 DOI: 10.1371/journal.pcbi.1006022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that ‘leftover’ proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles. Protein copy numbers are often found to be stoichiometrically balanced for subunits of multi-protein complexes. Imbalance is believed to be deleterious because it lowers complex yield (the dosage balance hypothesis) and increases the risk of misinteractions, but imbalance may also provide unexplored functional benefits. We show here that the benefits of stoichiometric balance can extend to larger networks of interacting proteins. We develop a method to quantify to what degree protein networks are balanced, and apply it to two networks. We find that the clathrin-mediated endocytosis system in yeast is statistically balanced, but not perfectly so, and explore the consequences of imbalance in the form of misinteractions and endocytic function. We also show that biological networks are more robust to misinteractions than random networks when balanced, but are more sensitive to misinteractions under imbalance. This suggests evolutionary pressure for proteins to be balanced and that any conserved imbalance should occur for functional reasons. We explore one such reason in the form of bottlenecking the endocytosis process. Our method can be generalized to other networks and used to identify out-of-balance proteins. Our results provide insight into how network design, expression level regulation, and cell fitness are intertwined.
Collapse
Affiliation(s)
- David O. Holland
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Margaret E. Johnson
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
19
|
Stojanovski K, Ferrar T, Benisty H, Uschner F, Delgado J, Jimenez J, Solé C, de Nadal E, Klipp E, Posas F, Serrano L, Kiel C. Interaction Dynamics Determine Signaling and Output Pathway Responses. Cell Rep 2017; 19:136-149. [PMID: 28380353 DOI: 10.1016/j.celrep.2017.03.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 12/27/2016] [Accepted: 03/08/2017] [Indexed: 12/28/2022] Open
Abstract
The understanding of interaction dynamics in signaling pathways can shed light on pathway architecture and provide insights into targets for intervention. Here, we explored the relevance of kinetic rate constants of a key upstream osmosensor in the yeast high-osmolarity glycerol-mitogen-activated protein kinase (HOG-MAPK) pathway to signaling output responses. We created mutant pairs of the Sln1-Ypd1 complex interface that caused major compensating changes in the association (kon) and dissociation (koff) rate constants (kinetic perturbations) but only moderate changes in the overall complex affinity (Kd). Yeast cells carrying a Sln1-Ypd1 mutant pair with moderate increases in kon and koff displayed a lower threshold of HOG pathway activation than wild-type cells. Mutants with higher kon and koff rates gave rise to higher basal signaling and gene expression but impaired osmoadaptation. Thus, the kon and koff rates of the components in the Sln1 osmosensor determine proper signaling dynamics and osmoadaptation.
Collapse
Affiliation(s)
- Klement Stojanovski
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Tony Ferrar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Hannah Benisty
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Friedemann Uschner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Javier Delgado
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Javier Jimenez
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Carme Solé
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Eulalia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain.
| |
Collapse
|
20
|
Zhu Z, Teng Z, van Duijnhoven FJB, Dong M, Qian Y, Yu H, Yang J, Han R, Su J, Du W, Huang X, Zhou J, Yu X, Kampman E, Wu M. Interactions between RASA2, CADM1, HIF1AN gene polymorphisms and body fatness with breast cancer: a population-based case-control study in China. Oncotarget 2017; 8:98258-98269. [PMID: 29228687 PMCID: PMC5716727 DOI: 10.18632/oncotarget.21530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/03/2017] [Indexed: 01/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have indicated that gene polymorphisms in alleles of RAS p21 protein activator 2 (RASA2), cell adhesion molecule 1 (CADM1) and hypoxia inducible factor 1 alpha subunit inhibitor (HIF1AN) are associated with the risk of obesity. In this study, we explored the interactions between candidate SNPs of RASA2 (rs16851483), CADM1 (rs12286929) and HIF1AN (rs17094222) and body fatness for breast cancer risk. Unconditional logistic regression models were applied to measure the associations of related factors with breast cancer by odds ratios (ORs) and 95% confidence intervals (CIs). It was observed that cases had a statistically higher body mass index (BMI ≥ 28 kg/m2, OR = 1.77), waist circumference (WC ≥ 90cm, OR = 2.89) and waist-to-hip ratio (WHR ≥ 0.9, OR = 3.41) as compared to controls. Significant differences were also found in the genotype distributions of RASA2 rs16851483 T/T homozygote and CADM1 rs12286929 G/A heterozygote between cases and controls, with an OR of 1.68 (95% CI: 1.10-2.56) and 0.80 (95% CI: 0.64-0.99), respectively. Furthermore, significant interactions were observed between polymorphisms of three genes and body fatness for the risk of breast cancer based on both additive and multiplicative scales. These results of our study suggest that body fatness possibly plays an important role in the development of breast cancer and this risk might be modified by specific genotypes of some potential genes, especially for obese women in China.
Collapse
Affiliation(s)
- Zheng Zhu
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Zhimei Teng
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | | | - Meihua Dong
- Department of Chronic Disease Control, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Yun Qian
- Department of Chronic Disease Control, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Hao Yu
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Jie Yang
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Renqiang Han
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Jian Su
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Wencong Du
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Xingyu Huang
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Jinyi Zhou
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Xiaojin Yu
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Ellen Kampman
- Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Ming Wu
- Department of Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| |
Collapse
|
21
|
Holland DO, Shapiro BH, Xue P, Johnson ME. Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks. Sci Rep 2017; 7:5631. [PMID: 28717235 PMCID: PMC5514078 DOI: 10.1038/s41598-017-05686-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/01/2017] [Indexed: 01/30/2023] Open
Abstract
Protein-protein interactions networks (PPINs) are known to share a highly conserved structure across all organisms. What is poorly understood, however, is the structure of the child interface interaction networks (IINs), which map the binding sites proteins use for each interaction. In this study we analyze four independently constructed IINs from yeast and humans and find a conserved structure of these networks with a unique topology distinct from the parent PPIN. Using an IIN sampling algorithm and a fitness function trained on the manually curated PPINs, we show that IIN topology can be mostly explained as a balance between limits on interface diversity and a need for physico-chemical binding complementarity. This complementarity must be optimized both for functional interactions and against mis-interactions, and this selectivity is encoded in the IIN motifs. To test whether the parent PPIN shapes IINs, we compared optimal IINs in biological PPINs versus random PPINs. We found that the hubs in biological networks allow for selective binding with minimal interfaces, suggesting that binding specificity is an additional pressure for a scale-free-like PPIN. We confirm through phylogenetic analysis that hub interfaces are strongly conserved and rewiring of interactions between proteins involved in endocytosis preserves interface binding selectivity.
Collapse
Affiliation(s)
- David O Holland
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Benjamin H Shapiro
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pei Xue
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
| |
Collapse
|
22
|
Koseska A, Bastiaens PI. Cell signaling as a cognitive process. EMBO J 2017; 36:568-582. [PMID: 28137748 PMCID: PMC5331751 DOI: 10.15252/embj.201695383] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/13/2016] [Accepted: 12/20/2016] [Indexed: 12/17/2022] Open
Abstract
Cellular identity as defined through morphology and function emerges from intracellular signaling networks that communicate between cells. Based on recursive interactions within and among these intracellular networks, dynamical solutions in terms of biochemical behavior are generated that can differ from those in isolated cells. In this way, cellular heterogeneity in tissues can be established, implying that cell identity is not intrinsically predetermined by the genetic code but is rather dynamically maintained in a cognitive manner. We address how to experimentally measure the flow of information in intracellular biochemical networks and demonstrate that even simple causality motifs can give rise to rich, context-dependent dynamic behavior. The concept how intercellular communication can result in novel dynamical solutions is applied to provide a contextual perspective on cell differentiation and tumorigenesis.
Collapse
Affiliation(s)
- Aneta Koseska
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Philippe Ih Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund, Dortmund, Germany
| |
Collapse
|
23
|
Kirk IK, Weinhold N, Belling K, Skakkebæk NE, Jensen TS, Leffers H, Juul A, Brunak S. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations. Cell Syst 2017; 4:357-364.e3. [PMID: 28215527 DOI: 10.1016/j.cels.2017.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 10/23/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
Abstract
Gene copy-number changes influence phenotypes through gene-dosage alteration and subsequent changes of protein complex stoichiometry. Human trisomies where gene copy numbers are increased uniformly over entire chromosomes provide generic cases for studying these relationships. In most trisomies, gene and protein level alterations have fatal consequences. We used genome-wide protein-protein interaction data to identify chromosome-specific patterns of protein interactions. We found that some chromosomes encode proteins that interact infrequently with each other, chromosome 21 in particular. We combined the protein interaction data with transcriptome data from human brain tissue to investigate how this pattern of global interactions may affect cellular function. We identified highly connected proteins that also had coordinated gene expression. These proteins were associated with important neurological functions affecting the characteristic phenotypes for Down syndrome and have previously been validated in mouse knockout experiments. Our approach is general and applicable to other gene-dosage changes, such as arm-level amplifications in cancer.
Collapse
Affiliation(s)
- Isa Kristina Kirk
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nils Weinhold
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kirstine Belling
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Erik Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas Skøt Jensen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Henrik Leffers
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| |
Collapse
|
24
|
Adlung L, Kar S, Wagner MC, She B, Chakraborty S, Bao J, Lattermann S, Boerries M, Busch H, Wuchter P, Ho AD, Timmer J, Schilling M, Höfer T, Klingmüller U. Protein abundance of AKT and ERK pathway components governs cell type-specific regulation of proliferation. Mol Syst Biol 2017; 13:904. [PMID: 28123004 PMCID: PMC5293153 DOI: 10.15252/msb.20167258] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Signaling through the AKT and ERK pathways controls cell proliferation. However, the integrated regulation of this multistep process, involving signal processing, cell growth and cell cycle progression, is poorly understood. Here, we study different hematopoietic cell types, in which AKT and ERK signaling is triggered by erythropoietin (Epo). Although these cell types share the molecular network topology for pro‐proliferative Epo signaling, they exhibit distinct proliferative responses. Iterating quantitative experiments and mathematical modeling, we identify two molecular sources for cell type‐specific proliferation. First, cell type‐specific protein abundance patterns cause differential signal flow along the AKT and ERK pathways. Second, downstream regulators of both pathways have differential effects on proliferation, suggesting that protein synthesis is rate‐limiting for faster cycling cells while slower cell cycles are controlled at the G1‐S progression. The integrated mathematical model of Epo‐driven proliferation explains cell type‐specific effects of targeted AKT and ERK inhibitors and faithfully predicts, based on the protein abundance, anti‐proliferative effects of inhibitors in primary human erythroid progenitor cells. Our findings suggest that the effectiveness of targeted cancer therapy might become predictable from protein abundance.
Collapse
Affiliation(s)
- Lorenz Adlung
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandip Kar
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany.,Department of Chemistry, Indian Institute of Technology, Mumbai, India
| | - Marie-Christine Wagner
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bin She
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sajib Chakraborty
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Bao
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany
| | - Susen Lattermann
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Wuchter
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany.,Institute for Transfusion Medicine and Immunology, University of Heidelberg, Mannheim, Germany
| | - Anthony D Ho
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Jens Timmer
- Center for Biological Signaling Studies (BIOSS), Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Marcel Schilling
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany .,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Ursula Klingmüller
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany .,Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| |
Collapse
|
25
|
Crépieux P, Poupon A, Langonné-Gallay N, Reiter E, Delgado J, Schaefer MH, Bourquard T, Serrano L, Kiel C. A Comprehensive View of the β-Arrestinome. Front Endocrinol (Lausanne) 2017; 8:32. [PMID: 28321204 PMCID: PMC5337525 DOI: 10.3389/fendo.2017.00032] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/07/2017] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are membrane receptors critically involved in sensing the environment and orchestrating physiological processes. As such, they transduce extracellular signals such as hormone, neurotransmitters, ions, and light into an integrated cell response. The intracellular trafficking, internalization, and signaling ability of ligand-activated GPCRs are controlled by arrestins, adaptor proteins that they interact with upon ligand binding. β-arrestins 1 and 2 in particular are now considered as hub proteins assembling multiprotein complexes to regulate receptor fate and transduce diversified cell responses. While more than 400 β-arrestin interaction partners have been identified so far, much remains to be learnt on how discrimination between so many binding partners is accomplished. Here, we gathered the interacting partners of β-arrestins through database mining and manual curation of the literature to map the β-arrestin interactome (β-arrestinome). We discussed several parameters that determine compatible (AND) or mutually exclusive (XOR) binding of β-arrestin interactors, such as structural constraints, intracellular abundance, or binding affinity.
Collapse
Affiliation(s)
- Pascale Crépieux
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France
- «Biology and Bioinformatics of Signaling Systems (BIOS)» Group, CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
- *Correspondence: Pascale Crépieux,
| | - Anne Poupon
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France
- «Biology and Bioinformatics of Signaling Systems (BIOS)» Group, CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Nathalie Langonné-Gallay
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France
- «Biology and Bioinformatics of Signaling Systems (BIOS)» Group, CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Eric Reiter
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France
- «Biology and Bioinformatics of Signaling Systems (BIOS)» Group, CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Javier Delgado
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Martin H. Schaefer
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Thomas Bourquard
- INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, Nouzilly, France
- «Biology and Bioinformatics of Signaling Systems (BIOS)» Group, CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
26
|
Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH. HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Res 2016; 45:D408-D414. [PMID: 27794551 PMCID: PMC5210659 DOI: 10.1093/nar/gkw985] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/28/2016] [Accepted: 10/14/2016] [Indexed: 01/01/2023] Open
Abstract
The increasing number of experimentally detected interactions between proteins makes it difficult for researchers to extract the interactions relevant for specific biological processes or diseases. This makes it necessary to accompany the large-scale detection of protein–protein interactions (PPIs) with strategies and tools to generate meaningful PPI subnetworks. To this end, we generated the Human Integrated Protein–Protein Interaction rEference or HIPPIE (http://cbdm.uni-mainz.de/hippie/). HIPPIE is a one-stop resource for the generation and interpretation of PPI networks relevant to a specific research question. We provide means to generate highly reliable, context-specific PPI networks and to make sense out of them. We just released the second major update of HIPPIE, implementing various new features. HIPPIE grew substantially over the last years and now contains more than 270 000 confidence scored and annotated PPIs. We integrated different types of experimental information for the confidence scoring and the construction of context-specific networks. We implemented basic graph algorithms that highlight important proteins and interactions. HIPPIE's graphical interface implements several ways for wet lab and computational scientists alike to access the PPI data.
Collapse
Affiliation(s)
- Gregorio Alanis-Lobato
- Faculty of Biology, Johannes Gutenberg Universität, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg Universität, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Martin H Schaefer
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
27
|
Hu JX, Thomas CE, Brunak S. Network biology concepts in complex disease comorbidities. Nat Rev Genet 2016; 17:615-29. [PMID: 27498692 DOI: 10.1038/nrg.2016.87] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The co-occurrence of diseases can inform the underlying network biology of shared and multifunctional genes and pathways. In addition, comorbidities help to elucidate the effects of external exposures, such as diet, lifestyle and patient care. With worldwide health transaction data now often being collected electronically, disease co-occurrences are starting to be quantitatively characterized. Linking network dynamics to the real-life, non-ideal patient in whom diseases co-occur and interact provides a valuable basis for generating hypotheses on molecular disease mechanisms, and provides knowledge that can facilitate drug repurposing and the development of targeted therapeutic strategies.
Collapse
Affiliation(s)
- Jessica Xin Hu
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Cecilia Engel Thomas
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark.,Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| |
Collapse
|
28
|
Varusai TM, Kolch W, Kholodenko BN, Nguyen LK. Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses. MOLECULAR BIOSYSTEMS 2016; 11:2750-62. [PMID: 26266875 DOI: 10.1039/c5mb00385g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-protein interactions (PPIs) defined as reversible association of two proteins to form a complex, are undoubtedly among the most common interaction motifs featured in cells. Recent large-scale proteomic studies have revealed an enormously complex interactome of the cell, consisting of tens of thousands of PPIs with numerous signalling hubs. PPIs have functional roles in regulating a wide range of cellular processes including signal transduction and post-translational modifications, and de-regulation of PPIs is implicated in many diseases including cancers and neuro-degenerative disorders. Despite the ubiquitous appearance and physiological significance of PPIs, our understanding of the dynamic and functional consequences of these simple motifs remains incomplete, particularly when PPIs occur within large biochemical networks. We employ quantitative, dynamic modelling to computationally analyse salient dynamic features of the PPI motifs and PPI-containing signalling networks varying in topological architecture. Our analyses surprisingly reveal that simple reversible PPI motifs, when being embedded into signalling cascades, could give rise to extremely rich and complex regulatory dynamics in the absence of explicit positive and negative feedback loops. Our work represents a systematic investigation of the dynamic properties of PPIs in signalling networks, and the results shed light on how this simple event may potentiate diverse and intricate behaviours in vivo.
Collapse
Affiliation(s)
- Thawfeek M Varusai
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | | | | |
Collapse
|
29
|
Beltran-Sastre V, Benisty H, Burnier J, Berger I, Serrano L, Kiel C. Tuneable endogenous mammalian target complementation via multiplexed plasmid-based recombineering. Sci Rep 2015; 5:17432. [PMID: 26612112 PMCID: PMC4661934 DOI: 10.1038/srep17432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/29/2015] [Indexed: 12/26/2022] Open
Abstract
Understanding the quantitative functional consequences of human disease mutations requires silencing of endogenous genes and expression of mutants at close to physiological levels. Changing protein levels above or below these levels is also important for system perturbation and modelling. Fast design optimization demands flexible interchangeable cassettes for endogenous gene silencing and tuneable expression. Here, we introduce ‘TEMTAC’, a multigene recombineering and delivery system for simultaneous siRNA-based knockdown and regulated mutant (or other variant) expression with different dynamic ranges. We show its applicability by confirming known phenotypic effects for selected mutations for BRAF, HRAS, and SHP2.
Collapse
Affiliation(s)
- Violeta Beltran-Sastre
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Hannah Benisty
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Julia Burnier
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Imre Berger
- European Molecular Biology Laboratory, Grenoble Outstation, B.P. 181, Grenoble, France.,The School of Biochemistry, University of Bristol, Clifton BS8 1TD, United Kingdom
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| |
Collapse
|
30
|
Muratcioglu S, Guven-Maiorov E, Keskin Ö, Gursoy A. Advances in template-based protein docking by utilizing interfaces towards completing structural interactome. Curr Opin Struct Biol 2015; 35:87-92. [PMID: 26539658 DOI: 10.1016/j.sbi.2015.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 11/27/2022]
Abstract
The increase in the number of structurally determined protein complexes strengthens template-based docking (TBD) methods for modelling protein-protein interactions (PPIs). These methods utilize the known structures of protein complexes as templates to predict the quaternary structure of the target proteins. The templates may be partial or complete structures. Interface based (partial) methods have recently gained interest due in part to the observation that the interface regions are reusable. We describe how available template interfaces can be used to obtain the structural models of protein interactions. Despite the agreement that a majority of the protein complexes can be modelled using the available Protein Data Bank (PDB) structures, a handful of studies argue that we need more template proteins to increase the structural coverage of PPIs. We also discuss the performance of the interface TBD methods at large scale, and the significance of capturing multiple conformations for improving accuracy.
Collapse
Affiliation(s)
- Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, 34450 Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, 34450 Istanbul, Turkey
| | - Emine Guven-Maiorov
- Department of Chemical and Biological Engineering, Koc University, 34450 Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, 34450 Istanbul, Turkey
| | - Özlem Keskin
- Department of Chemical and Biological Engineering, Koc University, 34450 Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, 34450 Istanbul, Turkey
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, 34450 Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, 34450 Istanbul, Turkey.
| |
Collapse
|
31
|
Arafeh R, Qutob N, Emmanuel R, Keren-Paz A, Madore J, Elkahloun A, Wilmott JS, Gartner JJ, Di Pizio A, Winograd-Katz S, Sindiri S, Rotkopf R, Dutton-Regester K, Johansson P, Pritchard AL, Waddell N, Hill VK, Lin JC, Hevroni Y, Rosenberg SA, Khan J, Ben-Dor S, Niv MY, Ulitsky I, Mann GJ, Scolyer RA, Hayward NK, Samuels Y. Recurrent inactivating RASA2 mutations in melanoma. Nat Genet 2015; 47:1408-10. [PMID: 26502337 PMCID: PMC4954601 DOI: 10.1038/ng.3427] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/29/2015] [Indexed: 02/07/2023]
Abstract
Analysis of 501 melanoma exomes identified RASA2, encoding a RasGAP, as a tumor-suppressor gene mutated in 5% of melanomas. Recurrent loss-of-function mutations in RASA2 were found to increase RAS activation, melanoma cell growth and migration. RASA2 expression was lost in ≥30% of human melanomas and was associated with reduced patient survival. These findings identify RASA2 inactivation as a melanoma driver and highlight the importance of RasGAPs in cancer.
Collapse
Affiliation(s)
- Rand Arafeh
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Nouar Qutob
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Rafi Emmanuel
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jason Madore
- Melanoma Institute Australia, Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Abdel Elkahloun
- National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - James S Wilmott
- Melanoma Institute Australia, Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jared J Gartner
- National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Antonella Di Pizio
- Institute of Biochemistry, Food Science and Nutrition, Hebrew University, Rehovot, Israel
| | - Sabina Winograd-Katz
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sivasish Sindiri
- National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Ron Rotkopf
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | | | - Peter Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Victoria K Hill
- National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Jimmy C Lin
- National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Yael Hevroni
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Steven A Rosenberg
- National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Javed Khan
- National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Shifra Ben-Dor
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, Hebrew University, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Graham J Mann
- Melanoma Institute Australia, Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Centre for Cancer Research, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Yardena Samuels
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
32
|
Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R. The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway. Sci Rep 2015; 5:13128. [PMID: 26293885 PMCID: PMC4544004 DOI: 10.1038/srep13128] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/17/2015] [Indexed: 12/22/2022] Open
Abstract
Activated Toll-like receptors (TLRs) cluster in lipid rafts and induce pro- and anti-tumor responses. The organization of the assembly is critical to the understanding of how these key receptors control major signaling pathways in the cell. Although several models for individual interactions were proposed, the entire TIR-domain signalosome architecture has not been worked out, possibly due to its complexity. We employ a powerful algorithm, crystal structures and experimental data to model the TLR4 and its cluster. The architecture that we obtain with 8 MyD88 molecules provides the structural basis for the MyD88-templated myddosome helical assembly and receptor clustering; it also provides clues to pro- and anti-inflammatory signaling pathways branching at the signalosome level to Mal/MyD88 and TRAM/TRIF pro- and anti-inflammatory pathways. The assembly of MyD88 death domain (DD) with TRAF3 (anti-viral/anti-inflammatory) and TRAF6 (pro-inflammatory) suggest that TRAF3/TRAF6 binding sites on MyD88 DD partially overlap, as do IRAK4 and FADD. Significantly, the organization illuminates mechanisms of oncogenic mutations, demonstrates that almost all TLR4 parallel pathways are competitive and clarifies decisions at pathway branching points. The architectures are compatible with the currently-available experimental data and provide compelling insights into signaling in cancer and inflammation pathways.
Collapse
Affiliation(s)
- Emine Guven-Maiorov
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
- Department of Computer Engineering, Koc University, Istanbul, Turkey
| | - Carter VanWaes
- Clinical Genomic Unit, Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Zhong Chen
- Clinical Genomic Unit, Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
33
|
Bourquard T, Landomiel F, Reiter E, Crépieux P, Ritchie DW, Azé J, Poupon A. Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex. Sci Rep 2015; 5:10760. [PMID: 26030356 PMCID: PMC4649906 DOI: 10.1038/srep10760] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/26/2015] [Indexed: 12/22/2022] Open
Abstract
β-arrestins serve as signaling scaffolds downstream of G protein-coupled receptors, and thus play a crucial role in a plethora of cellular processes. Although it is largely accepted that the ability of β-arrestins to interact simultaneously with many protein partners is key in G protein-independent signaling of GPCRs, only the precise knowledge of these multimeric arrangements will allow a full understanding of the dynamics of these interactions and their functional consequences. However, current experimental procedures for the determination of the three-dimensional structures of protein-protein complexes are not well adapted to analyze these short-lived, multi-component assemblies. We propose a model of the receptor/β-arrestin/Erk1 signaling module, which is consistent with most of the available experimental data. Moreover, for the β-arrestin/Raf1 and the β-arrestin/ERK interactions, we have used the model to design interfering peptides and shown that they compete with both partners, hereby demonstrating the validity of the predicted interaction regions.
Collapse
Affiliation(s)
- Thomas Bourquard
- 1] BIOS group, INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais, 37041 Tours, France; IFCE, Nouzilly, F-37380 France [2] INRIA Nancy, 615 Rue du Jardin Botanique, Villers-lès-Nancy, 54600 France
| | - Flavie Landomiel
- BIOS group, INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais, 37041 Tours, France; IFCE, Nouzilly, F-37380 France
| | - Eric Reiter
- BIOS group, INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais, 37041 Tours, France; IFCE, Nouzilly, F-37380 France
| | - Pascale Crépieux
- BIOS group, INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais, 37041 Tours, France; IFCE, Nouzilly, F-37380 France
| | - David W Ritchie
- INRIA Nancy, 615 Rue du Jardin Botanique, Villers-lès-Nancy, 54600 France
| | - Jérôme Azé
- Bioinformatics group - AMIB INRIA - Laboratoire de Recherche en Informatique, Université Paris-Sud, Orsay, 91405 France
| | - Anne Poupon
- BIOS group, INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; CNRS, UMR7247, F-37380 Nouzilly, France; Université François Rabelais, 37041 Tours, France; IFCE, Nouzilly, F-37380 France
| |
Collapse
|
34
|
Toufighi K, Yang JS, Luis NM, Aznar Benitah S, Lehner B, Serrano L, Kiel C. Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PLoS Comput Biol 2015; 11:e1004256. [PMID: 25946651 PMCID: PMC4422705 DOI: 10.1371/journal.pcbi.1004256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/25/2015] [Indexed: 12/19/2022] Open
Abstract
The molecular details underlying the time-dependent assembly of protein complexes in cellular networks, such as those that occur during differentiation, are largely unexplored. Focusing on the calcium-induced differentiation of primary human keratinocytes as a model system for a major cellular reorganization process, we look at the expression of genes whose products are involved in manually-annotated protein complexes. Clustering analyses revealed only moderate co-expression of functionally related proteins during differentiation. However, when we looked at protein complexes, we found that the majority (55%) are composed of non-dynamic and dynamic gene products ('di-chromatic'), 19% are non-dynamic, and 26% only dynamic. Considering three-dimensional protein structures to predict steric interactions, we found that proteins encoded by dynamic genes frequently interact with a common non-dynamic protein in a mutually exclusive fashion. This suggests that during differentiation, complex assemblies may also change through variation in the abundance of proteins that compete for binding to common proteins as found in some cases for paralogous proteins. Considering the example of the TNF-α/NFκB signaling complex, we suggest that the same core complex can guide signals into diverse context-specific outputs by addition of time specific expressed subunits, while keeping other cellular functions constant. Thus, our analysis provides evidence that complex assembly with stable core components and competition could contribute to cell differentiation.
Collapse
Affiliation(s)
- Kiana Toufighi
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jae-Seong Yang
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuno Miguel Luis
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Salvador Aznar Benitah
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
| | - Ben Lehner
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
| |
Collapse
|
35
|
Abstract
Immunoblotting (also known as Western blotting) combined with digital image analysis can be a reliable method for analyzing the abundance of proteins and protein modifications, but not every immunoblot-analysis combination produces an accurate result. I illustrate how sample preparation, protocol implementation, detection scheme, and normalization approach profoundly affect the quantitative performance of immunoblotting. This study implemented diagnostic experiments that assess an immunoblot-analysis workflow for accuracy and precision. The results showed that ignoring such diagnostics can lead to pseudoquantitative immunoblot data that markedly overestimate or underestimate true differences in protein abundance.
Collapse
Affiliation(s)
- Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA. E-mail:
| |
Collapse
|
36
|
Dodson EJ, Fishbain-Yoskovitz V, Rotem-Bamberger S, Schueler-Furman O. Versatile communication strategies among tandem WW domain repeats. Exp Biol Med (Maywood) 2015; 240:351-60. [PMID: 25710931 PMCID: PMC4436281 DOI: 10.1177/1535370214566558] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands.
Collapse
Affiliation(s)
- Emma Joy Dodson
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Vered Fishbain-Yoskovitz
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| |
Collapse
|
37
|
Majerciak V, Lu M, Li X, Zheng ZM. Attenuation of the suppressive activity of cellular splicing factor SRSF3 by Kaposi sarcoma-associated herpesvirus ORF57 protein is required for RNA splicing. RNA (NEW YORK, N.Y.) 2014; 20:1747-1758. [PMID: 25234929 PMCID: PMC4201827 DOI: 10.1261/rna.045500.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/04/2014] [Indexed: 05/29/2023]
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) ORF57 is a multifunctional post-transcriptional regulator essential for viral gene expression during KSHV lytic infection. ORF57 requires interactions with various cellular proteins for its function. Here, we identified serine/arginine-rich splicing factor 3 (SRSF3, formerly known as SRp20) as a cellular cofactor involved in ORF57-mediated splicing of KSHV K8β RNA. In the absence of ORF57, SRSF3 binds to a suboptimal K8β intron and inhibits K8β splicing. Knockdown of SRSF3 promotes K8β splicing, mimicking the effect of ORF57. The N-terminal half of ORF57 binds to the RNA recognition motif of SRSF3, which prevents SRSF3 from associating with the K8β intron RNA and therefore attenuates the suppressive effect of SRSF3 on K8β splicing. ORF57 also promotes splicing of heterologous non-KSHV transcripts that are negatively regulated by SRSF3, indicating that the effect of ORF57 on SRSF3 activity is independent of RNA target. SPEN proteins, previously identified as ORF57-interacting partners, suppress ORF57 splicing activity by displacing ORF57 from SRSF3-RNA complexes. In summary, we have identified modulation of SRSF3 activity as the molecular mechanism by which ORF57 promotes RNA splicing.
Collapse
Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Mathew Lu
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Xiaofan Li
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| |
Collapse
|
38
|
Doupé DP, Perrimon N. Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools. Sci Signal 2014; 7:re1. [PMID: 24692594 PMCID: PMC4319366 DOI: 10.1126/scisignal.2005077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The use of genome-wide proteomic and RNA interference approaches has moved our understanding of signal transduction from linear pathways to highly integrated networks centered on core nodes. However, probing the dynamics of flow of information through such networks remains technically challenging. In particular, how the temporal dynamics of an individual pathway can elicit distinct outcomes in a single cell type and how multiple pathways may interact sequentially or synchronously to influence cell fate remain open questions in many contexts. The development of fluorescence-based reporters and optogenetic regulators of pathway activity enables the analysis of signaling in living cells and organisms with unprecedented spatiotemporal resolution and holds the promise of addressing these key questions. We present a brief overview of the evidence for the importance of temporal dynamics in cellular regulation, introduce these fluorescence-based tools, and highlight specific studies that leveraged these tools to probe the dynamics of information flow through signaling networks. In particular, we highlight two studies in Caenorhabditis elegans sensory neurons and cultured mammalian cells that demonstrate the importance of signal dynamics in determining cellular responses.
Collapse
Affiliation(s)
- David P Doupé
- 1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | |
Collapse
|
39
|
Johnsson N. Analyzing protein-protein interactions in the post-interactomic era. Are we ready for the endgame? Biochem Biophys Res Commun 2014; 445:739-45. [PMID: 24548408 DOI: 10.1016/j.bbrc.2014.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/05/2014] [Indexed: 11/16/2022]
Abstract
Mapping protein-protein interactions in genome-wide scales revealed thousands of novel binding partners in each of the explored model organisms. Organizing these hits in comprehensive ways is becoming increasingly important for systems biology approaches to understand complex cellular processes and diseases. However, proteome wide interaction techniques and their resulting global networks are not revealing the topologies of networks that are truly operating in the cell. In this short review I will discuss which prerequisites have to be fulfilled and which experimental methods might be practicable to translate primary protein interaction data into network presentations that help in understanding cellular processes.
Collapse
Affiliation(s)
- Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, James-Franck-Ring N27, D-89081 Ulm, Germany.
| |
Collapse
|
40
|
Abstract
The editorial staff and distinguished scientists in the field of cell signaling nominated diverse research as advances for 2013. Breakthroughs in understanding how spatial and temporal signals control cellular behavior ranged from filtering high-frequency stimuli to interpreting circadian inputs. This year's nominations also highlight the importance of understanding cell signaling in the context of physiology and disease, such as links between the nervous system and cancer. Furthermore, the application of new techniques to study cell signaling--such as optogenetics, DNA editing with CRISPR-Cas9, and sequencing untranslated regions of transcripts--continues to expand the realm and impact of signaling research.
Collapse
Affiliation(s)
- Jason D Berndt
- 1Associate Editor of Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, N.W., Washington, DC 20005, USA
| | | |
Collapse
|