A kinetic model for RNA-interference of focal adhesions

BMC Systems Biology

Ulrich S Schwarz¹  Max Hoffmann¹ 

[1] Institute for Theoretical Physics, , Philosophenweg 19, 69120 Heidelberg, Germany

关键词: Sensitivity analysis;    Bifurcation analysis;    Timescales;    Parameter estimation;    Dynamic model;    Rac/Rho signaling pathways;    RNA interference;    Focal adhesions;    Cell-matrix adhesion;   

Others  :  1143330
DOI  :  10.1186/1752-0509-7-2

 received in 2012-07-21, accepted in 2012-12-21,  发布年份 2013

【 摘 要 】

Background

Focal adhesions are integrin-based cell-matrix contacts that transduce and integrate mechanical and biochemical cues from the environment. They develop from smaller and more numerous focal complexes under the influence of mechanical force and are key elements for many physiological and disease-related processes, including wound healing and metastasis. More than 150 different proteins localize to focal adhesions and have been systematically classified in the adhesome project (http://www.adhesome.org webcite). First RNAi-screens have been performed for focal adhesions and the effect of knockdown of many of these components on the number, size, shape and location of focal adhesions has been reported.

Results

We have developed a kinetic model for RNA interference of focal adhesions which represents some of its main elements: a spatially layered structure, signaling through the small GTPases Rac and Rho, and maturation from focal complexes to focal adhesions under force. The response to force is described by two complementary scenarios corresponding to slip and catch bond behavior, respectively. Using estimated and literature values for the model parameters, three time scales of the dynamics of RNAi-influenced focal adhesions are identified: a sub-minute time scale for the assembly of focal complexes, a sub-hour time scale for the maturation to focal adhesions, and a time scale of days that controls the siRNA-mediated knockdown. Our model shows bistability between states dominated by focal complexes and focal adhesions, respectively. Catch bonding strongly extends the range of stability of the state dominated by focal adhesions. A sensitivity analysis predicts that knockdown of focal adhesion components is more efficient for focal adhesions with slip bonds or if the system is in a state dominated by focal complexes. Knockdown of Rho leads to an increase of focal complexes.

Conclusions

The suggested model provides a kinetic description of the effect of RNA-interference of focal adhesions. Its predictions are in good agreement with known experimental results and can now guide the design of RNAi-experiments. In the future, it can be extended to include more components of the adhesome. It also could be extended by spatial aspects, for example by the differential activation of the Rac- and Rho-pathways in different parts of the cell.

【 授权许可】

   
2013 Hoffmann and Schwarz; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

Figure 8.

Figure 9.

Figure 10.

【 参考文献 】

• [1]Geiger B, Spatz JP, Bershadsky AD: Environmental sensing through focal adhesions. Nat Rev Mol Cell Biol 2009, 10:21-33.
• [2]Parsons JT, Horwitz AR, Schwartz MA: Cell adhesion: integrating cytoskeletal dynamics and cellular tension. Nat Rev Mol Cell Biol 2010, 11(9):633-643.
• [3]Geiger B, Yamada KM: Molecular architecture and function of matrix adhesions. Cold Spring Harbor Perspect Biol 2011, 3(5):1-21.
• [4]Zaidel-Bar R, Itzkovitz S, Ma’ayan A, Iyengar R, Geiger B: Functional atlas of the integrin adhesome. Nat Cell Biol 2007, 9(8):858-867.
• [5]Zaidel-Bar R, Geiger B: The switchable integrin adhesome. J Cell Sci 2010, 123:1385-1388.
• [6]Whittaker CA, Bergeron KF, Whittle J, Brandhorst BP, Burke RD, Hynes RO: The echinoderm adhesome. Dev Biol 2006, 300:252-266.
• [7]Byron A, Morgan MR, Humphries MJ: Adhesion signalling complexes. Cur Biol 2010, 20(24):R1063—R1067.
• [8]Ridley AJ, Hall A: The small GTP-binding protein rho regulates the assembly of focal adhesions and actin stress fibers in response to growth factors. Cell 1992, 70(3):389-399.
• [9]Ridley AJ, Paterson HF, Johnston CL, Diekmann D, Hall A: The small GTP-binding protein rac regulates growth factor-induced membrane ruffling. Cell 1992, 70(3):401-410.
• [10]Etienne-Manneville S, Hall A: Rho GTPases in cell biology. Nature 2002, 420(6916):629-635.
• [11]Zeng Y, Lai T, Koh CG, LeDuc PR, Chiam KH: Investigating circular dorsal ruffles through varying substrate stiffness and mathematical modeling. Biophys J 2011, 101(9):2122-2130.
• [12]Besser A, Schwarz US: Coupling biochemistry and mechanics in cell adhesion: a model for inhomogeneous stress fiber contraction. New J Phys 2007, 9(11):425.
• [13]Welf ES, Haugh JM: Stochastic Dynamics of Membrane Protrusion Mediated by the DOCK180/Rac Pathway in Migrating Cells. Cell Mol Bioeng 2010, 3:30-39.
• [14]Civelekoglu-Scholey G, Orr AW, Novak I, Meister JJ, Schwartz MA, Mogilner A: Model of coupled transient changes of Rac, Rho, adhesions and stress fibers alignment in endothelial cells responding to shear stress. J Theor Biol 2005, 232(4):569-585.
• [15]Takai Y, Sasaki T, Matozaki T: Small GTP-binding proteins. Phys rev 2001, 81:153-208.
• [16]Rottner K, Hall A, Small JV: Interplay between Rac and Rho in the control of substrate contact dynamics. Curr Biol 1999, 9(12):640-648.
• [17]Sander EE, ten Klooster JP, van Delft S, van der Kammen RA, Collard JG: Rac downregulates Rho activity: reciprocal balance between both GTPases determines cellular morphology and migratory behavior. J Cell Biol 1999, 147(5):1009-1022.
• [18]Burridge K, Wennerberg K: Rho and Rac take center stage. Cell 2004, 116:167-179.
• [19]Machacek M, Hodgson L, Welch C, Elliott H, Pertz O, Nalbant P, Abell A, Johnson GL, Hahn KM, Danuser G: Coordination of Rho GTPase activities during cell protrusion. Nature 2009, 461(7260):99-103.
• [20]Brown CM, Hebert B, Kolin DL, Zareno J, Whitmore L, Horwitz AR, Wiseman PW: Probing the integrin-actin linkage using high-resolution protein velocity mapping. J Cell Sci 2006, 119:5204-5214.
• [21]Hu K, Ji L, Applegate KT, Danuser G, Waterman-Storer CM: Differential transmission of actin motion within focal adhesions. Science 2007, 315(5808):111-115.
• [22]Patla I, Volberg T, Elad N, Hirschfeld-Warneken V, Grashoff C, Fässler R, Spatz JP, Geiger B, Medalia O: Dissecting the molecular architecture of integrin adhesion sites by cryo-electron tomography. Nat Cell Biol 2010, 12(9):909-915.
• [23]Shtengel G, Galbraith JA, Galbraith CG, Lippincott-Schwartz J, Gillette JM, Manley S, Sougrat R, Waterman CM, Kanchanawong P, Davidson MW, Fetter RD, Hess HF: Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. PNAS 2009, 106(9):3125-3130.
• [24]Kanchanawong P, Shtengel G, Pasapera AM, Ramko EB, Davidson MW, Hess HF, Waterman CM: Nanoscale architecture of integrin-based cell adhesions. Nature 2010, 468(7323):580-584.
• [25]Xu K, Babcock HP, Zhuang X: Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods 2012, 9(2):185-188.
• [26]Schwarz US, Gardel ML: United we stand - integrating the actin cytoskeleton and cell-matrix adhesions in cellular mechanotransduction. J Cell Sci 2012, 125:1-10.
• [27]Ponti A, Machacek M, Gupton SL, Waterman-Storer CM, Danuser G: Two distinct actin networks drive the protrusion of migrating cells. Science 2004, 305(5691):1782-1786.
• [28]Gardel ML, Sabass B, Ji L, Danuser G, Schwarz US, Waterman CM: Traction stress in focal adhesions correlates biphasically with actin retrograde flow speed. J Cell Biol 2008, 183(6):999-1005.
• [29]Gardel ML, Schneider IC, Aratyn-Schaus Y, Waterman CM: Mechanical Integration of Actin and Adhesion Dynamics in Cell Migration. Ann Rev Cell and Dev Biol 2010, 26:315-333.
• [30]Abercrombie M, Heaysman J, Pegrum S: The locomotion of fibroblasts in culture. IV. Electron microscopy of the leading lamella. Exp Cell Res 1971, 67:359-367.
• [31]Choi CK, Vicente-Manzanares M, Zareno J, Whitmore LA, Mogilner A, Horwitz AR: Actin and alpha-actinin orchestrate the assembly and maturation of nascent adhesions in a myosin II motor-independent manner. Nat Cell Biol 2008, 10(9):1039-1050.
• [32]Walcott S, Kim DH, Wirtz D, Sun SX: Nucleation and decay initiation are the stiffness-sensitive phases of focal adhesion maturation. Biophys J 2011, 101(12):2919-2928.
• [33]Choquet D, Felsenfeld DP, Sheetz MP: Extracellular matrix rigidity causes strengthening of integrin-cytoskeleton linkages. Cell 1997, 88:39-48.
• [34]Balaban NQ, Schwarz US, Riveline D, Goichberg P, Tzur G, Sabanay I, Mahalu D, Safran S, Bershadsky A, Addadi L, Geiger B: Force and focal adhesion assembly: a close relationship studied using elastic micropatterned substrates. Nat Cell Biol 2001, 3(5):466-472.
• [35]Riveline D, Zamir E, Balaban NQ, Schwarz US, Ishizaki T, Narumiya S, Kam Z, Geiger B, Bershadsky AD: Focal contacts as mechanosensors: externally applied local mechanical force induces growth of focal contacts by an mDia1-dependent and ROCK-independent mechanism. J Cell Biol 2001, 153(6):1175-1186.
• [36]Galbraith CG, Yamada KM, Sheetz MP: The relationship between force and focal complex development. J Cell Biol 2002, 159(4):695-705.
• [37]Geiger B, Bershadsky A: Exploring the neighborhood: adhesion-coupled cell mechanosensors. Cell 2002, 110(2):139-142.
• [38]Zamir E, Katz M, Posen Y, Erez N, Yamada KM, Katz BZ, Lin S, Lin DC, Bershadsky A, Kam Z, Geiger B: Dynamics and segregation of cell-matrix adhesions in cultured fibroblasts. Nat Cell Biol 2000, 2(4):191-196.
• [39]Dembo M, Wang YL: Stresses at the cell-to-substrate interface during locomotion of fibroblasts. Biophys J 1999, 76(4):2307-2316.
• [40]Butler JP, Tolić-Nørrelykke IM, Fabry B, Fredberg JJ: Traction fields, moments, and strain energy that cells exert on their surroundings. Am J Phys Cell phys 2002, 282(3):C595—C605.
• [41]Sabass B, Gardel ML, Waterman CM, Schwarz US: High resolution traction force microscopy based on experimental and computational advances. Biophys J 2008, 94:207-220.
• [42]Bell GI: Models for the specific adhesion of cells to cells. Science 1978, 200(4342):618-627.
• [43]Dembo M, Torney DC, Saxman K, Hammer D: The Reaction-Limited Kinetics of Membrane-to-Surface Adhesion and Detachment. PNAS 1988, 234(1274):55-83.
• [44]Zhu C, Lou J, McEver RP: Catch bonds: physical models, structural bases, biological function and rheological relevance. Biorheology 2005, 42(6):443-462.
• [45]Thomas WE, Vogel V, Sokurenko E: Biophysics of catch bonds. Ann Rev Biophyscs 2008, 37:399-416.
• [46]Thomas W: Catch bonds in adhesion. Ann Rev Biomed Eng 2008, 10:39-57.
• [47]Kong F, García AJ, Mould AP, Humphries MJ, Zhu C: Demonstration of catch bonds between an integrin and its ligand. J Cell Biol 2009, 185(7):1275-1284.
• [48]Albuquerque MLC, Flozak AS: Lamellipodial motility in wounded endothelial cells exposed to physiologic flow is associated with different patterns of beta1-integrin and vinculin localization. J Cel Phys 2003, 195:50-60.
• [49]Xu Y, Benlimame N, Su J, He Q, Alaoui-Jamali MA: Regulation of focal adhesion turnover by ErbB signalling in invasive breast cancer cells. British J Cancer 2009, 100(4):633-643.
• [50]Lecuit T, Lenne PF: Cell surface mechanics and the control of cell shape, tissue patterns and morphogenesis. Nat Rev Mol Cell Biol 2007, 8(8):633-644.
• [51]Guilak F, Cohen DM, Estes BT, Gimble JM, Liedtke W, Chen CS: Control of stem cell fate by physical interactions with the extracellular matrix. Cell Stem Cell 2009, 5:17-26.
• [52]Echeverri CJ, Perrimon N: High-throughput RNAi screening in cultured cells: a user’s guide. Nat Rev Genet 2006, 7(5):373-384.
• [53]Rana TM: Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 2007, 8:23-36.
• [54]Johnson PH(Ed): RNA interference: application to drug discovery and challenges to pharmaceutical development. Hoboken, NJ, USA: Wiley; 2011.
• [55]Simpson KJ, Selfors LM, Bui J, Reynolds A, Leake D, Khvorova A, Brugge JS: Identification of genes that regulate epithelial cell migration using an siRNA screening approach. Nat Cell Biol 2008, 10(9):1027-1038.
• [56]Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wünsche A, Satagopam V, Schmitz MHA, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters JM, Hyman AA, Durbin R, Pepperkok R, Ellenberg J: Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 2010, 464(7289):721-727.
• [57]Hutchins JRA, Toyoda Y, Hegemann B, Poser I, Hériché JK, Sykora MM, Augsburg M, Hudecz O, Buschhorn BA, Bulkescher J, Conrad C, Comartin D, Schleiffer A, Sarov M, Pozniakovsky A, Slabicki MM, Schloissnig S, Steinmacher I, Leuschner M, Ssykor A, Lawo S, Pelletier L, Stark H, Nasmyth K, Ellenberg J, Durbin R, Buchholz F, Mechtler K, Hyman AA, Peters JM: Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 2010, 328(5978):593-599.
• [58]Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ: Identification of host proteins required for HIV infection through a functional genomic screen. Science 2008, 319(5865):921-926.
• [59]Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, Sultana H, Brass AL, Adametz R, Tsui M, Qian F, Montgomery RR, Lev S, Mason PW, Koski RA, Elledge SJ, Xavier RJ, Agaisse H, Fikrig E: RNA interference screen for human genes associated with West Nile virus infection. Nature 2008, 455(7210):242-245.
• [60]Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, Xavier RJ, Chung RT: A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host & Microbe 2009, 5(3):298-307.
• [61]Krueger U, Bergauer T, Kaufmann B, Wolter I, Pilk S, Heider-Fabian M, Kirch S, Artz-Oppitz C, Isselhorst M, Konrad J: Insights into effective RNAi gained from large-scale siRNA validation screening. Oligonucleotides 2007, 17(2):237-250.
• [62]Winograd-Katz SE, Itzkovitz S, Kam Z, Geiger B: Multiparametric analysis of focal adhesion formation by RNAi-mediated gene knockdown. J Cell Biol 2009, 186(3):423-436.
• [63]Prager-Khoutorsky M, Lichtenstein A, Krishnan R, Rajendran K, Mayo A, Kam Z, Geiger B, Bershadsky AD: Fibroblast polarization is a matrix-rigidity-dependent process controlled by focal adhesion mechanosensing. Nat Cell Biol 2011, 13(12):1457-1465.
• [64]Nicolas A, Geiger B, Safran SA: Cell mechanosensitivity controls the anisotropy of focal adhesions. PNAS 2004, 101(34):12520-12525.
• [65]Nicolas A, Safran SA: Limitation of cell adhesion by the elasticity of the extracellular matrix. Biophys J 2006, 91:61-73.
• [66]Shemesh T, Geiger B, Bershadsky AD, Kozlov MM: Focal adhesions as mechanosensors: a physical mechanism. PNAS 2005, 102(35):12383-12388.
• [67]Walcott S, Sun SX: A mechanical model of actin stress fiber formation and substrate elasticity sensing in adherent cells. PNAS 2010, 107(17):7757-62.
• [68]Olberding JE, Thouless MD, Arruda EM, Garikipati K: The non-equilibrium thermodynamics and kinetics of focal adhesion dynamics. PLoS ONE 2010, 5(8):e12043.
• [69]Gao H, Qian J, Chen B: Probing mechanical principles of focal contacts in cell-matrix adhesion with a coupled stochastic-elastic modelling framework. J R Soc, Interface 2011, 8(62):1217-1232.
• [70]Macdonald A, Horwitz AR, Lauffenburger DA: Kinetic model for lamellipodal actin-integrin ’clutch’ dynamics. Cell Adhesion & Migration 2008, 2(2):95-105.
• [71]Bartlett DW, Davis ME: Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging. Nucleic Acids Res 2006, 34:322-333.
• [72]Cuccato G, Polynikis A, Siciliano V, Graziano M, di Bernardo M, di Bernardo D: Modeling RNA interference in mammalian cells. BMC Syst Biol 2011, 5:19. BioMed Central Full Text
• [73]Levine E, Zhang Z, Kuhlman T, Hwa T: Quantitative characteristics of gene regulation by small RNA. PLoS Biol 2007, 5(9):e229.
• [74]Khanin R, Vinciotti V: Computational modeling of post-transcriptional gene regulation by microRNAs. J Comput Biol 2008, 15(3):305-316.
• [75]Malphettes L, Fussenegger M: Impact of RNA interference on gene networks. Metabo eng 2006, 8(6):672-683.
• [76]Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS: Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 2009, 27(6):549-555.
• [77]Lämmermann T, Bader BL, Monkley SJ, Worbs T, Wedlich-Söldner R, Hirsch K, Keller M, Förster R, Critchley DR, Fässler R, Sixt M: Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature 2008, 453(7191):51-55.
• [78]Shawlot W, Deng JM, Fohn LE, Behringer RR: Restricted beta-galactosidase expression of a hygromycin-lacZ gene targeted to the beta-actin locus and embryonic lethality of beta-actin mutant mice. Transgenic Res 1998, 7(2):95-103.
• [79]Perrin BJ, Ervasti JM: The actin gene family: function follows isoform. Cytoskeleton 2010, 67(10):630-634.
• [80]Pertz O: Spatio-temporal Rho GTPase signaling - where are we now? J Cell Sci 2010, 123:1841-1850.
• [81]Hotchin NA, Kidd AG, Altroff H, Mardon HJ: Differential activation of focal adhesion kinase, Rho and Rac by the ninth and tenth FIII domains of fibronectin. J Cell Sci 1999, 112:2937-2946.
• [82]Ren XD, Kiosses WB, Sieg DJ, Otey CA, Schlaepfer DD, Schwartz MA: Focal adhesion kinase suppresses Rho activity to promote focal adhesion turnover. J Cell Sci 2000, 113:3673-3678.
• [83]Evans E, Ritchie K: Dynamic strength of molecular adhesion bonds. Biophys J 1997, 72(4):1541-1555.
• [84]Evans EA, Calderwood DA: Forces and bond dynamics in cell adhesion. Science 2007, 316(5828):1148-1153.
• [85]Zimerman B, Volberg T, Geiger B: Early molecular events in the assembly of the focal adhesion-stress fiber complex during fibroblast spreading. Cell Motility and the Cytoskeleton 2004, 58(3):143-159.
• [86]Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P: Molecular Biology of the Cell. New York, NY, United States of America: Garland Science; 2007.
• [87]Mori Y, Jilkine A, Edelstein-Keshet L: Wave-pinning and cell polarity from a bistable reaction-diffusion system. Biophys J 2008, 94(9):3684-3697.
• [88]Wolgemuth CW, Stajic J, Mogilner A: Redundant Mechanisms for Stable Cell Locomotion Revealed by Minimal Models. Biophys J 2011, 101(3):545-553.
• [89]Izzard CS: A precursor of the focal contact in cultured fibroblasts. Cell Motility and the Cytoskeleton 1988, 10(1-2):137-142.
• [90]Zaidel-Bar R, Ballestrem C, Kam Z, Geiger B: Early molecular events in the assembly of matrix adhesions at the leading edge of migrating cells. J Cell Sci 2003, 116:4605-4613.
• [91]Cohen M, Joester D, Geiger B, Addadi L: Spatial and temporal sequence of events in cell adhesion: from molecular recognition to focal adhesion assembly. ChemBioChem 2004, 5(10):1393-1399.
• [92]Dourdin N, Bhatt AK, Dutt P, Greer PA, Arthur JS, Elce JS, Huttenlocher A: Reduced cell migration and disruption of the actin cytoskeleton in calpain-deficient embryonic fibroblasts. J Biol Chem 2001, 276(51):48382-48388.
• [93]Bate N, Gingras AR, Bachir A, Horwitz R, Ye F, Patel B, Goult BT, Critchley DR: Talin contains a C-terminal calpain2 cleavage site important in focal adhesion dynamics. PLoS ONE 2012, 7(4):e34461.
• [94]Meves A, Stremmel C, Gottschalk K, Fässler R: The Kindlin protein family: new members to the club of focal adhesion proteins. Trends in Cell Biol 2009, 19(10):504-513.
• [95]Kahner BN, Kato H, Banno A, Ginsberg MH, Shattil SJ, Ye F: Kindlins, integrin activation and the regulation of talin recruitment to αIIbβ3. PLoS ONE 2012, 7(3):e34056.
• [96]Margadant C, Kreft M, de Groot D J, Norman JC, Sonnenberg A: Distinct Roles of Talin and Kindlin in Regulating Integrin α5β1 Function and Trafficking. Curr Biol 2012, 22(17):1554-1563.
• [97]Zhao Y, Malinin NL, Meller J, Ma Y, West XZ, Qin J, Podrez EA, Byzova TV: Regulation of cell adhesion and migration by Kindlin-3 cleavage by calpain. J Biol Chem 2012, 287(47):40012-40020.
• [98]Heinrich R, Rapoport TA: A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector. Eur J Biochem / FEBS 1974, 42:97-105.
• [99]Kacser H, Burns JA: The control of flux. Symp Soc Exp Biol 1973, 27:65-104.
• [100]Klipp E, Liebermeister W, Wierling C, Kowald A, Lehrach H, Herwig R: Systems Biology. Weinheim, Germany: Wiley-VCH; 2009.
• [101]Shemesh T, Verkhovsky AB, Svitkina TM, Bershadsky AD, Kozlov MM: Role of focal adhesions and mechanical stresses in the formation and progression of the lamellipodium-lamellum interface [corrected]. Biophys J 2009, 97(5):1254-1264.
• [102]Shemesh T, Bershadsky AD, Kozlov MM: Physical model for self-organization of actin cytoskeleton and adhesion complexes at the cell front. Biophys J 2012, 102(8):1746-1756.