Sylvia Le Dévédec - Academia.edu (original) (raw)
Papers by Sylvia Le Dévédec
Journal of Clinical Investigation, 2015
PLoS ONE, 2014
In many situations, 3D cell cultures mimic the natural organization of tissues more closely than ... more In many situations, 3D cell cultures mimic the natural organization of tissues more closely than 2D cultures. Conventional methods for phenotyping such 3D cultures use either single or multiple simple parameters based on morphology and fluorescence staining intensity. However, due to their simplicity many details are not taken into account which limits system-level study of phenotype characteristics. Here, we have developed a new image analysis platform to automatically profile 3D cell phenotypes with 598 parameters including morphology, topology, and texture parameters such as wavelet and image moments. As proof of concept, we analyzed mouse breast cancer cells (4T1 cells) in a 384-well plate format following exposure to a diverse set of compounds at different concentrations. The result showed concentration dependent phenotypic trajectories for different biologically active compounds that could be used to classify compounds based on their biological target. To demonstrate the wider applicability of our method, we analyzed the phenotypes of a collection of 44 human breast cancer cell lines cultured in 3D and showed that our method correctly distinguished basal-A, basal-B, luminal and ERBB2+ cell lines in a supervised nearest neighbor classification method. Citation: Di Z, Klop MJD, Rogkoti V-M, Le Dévédec SE, van de Water B, et al. (2014) Ultra High Content Image Analysis and Phenotype Profiling of 3D Cultured Micro-Tissues. PLoS ONE 9(10): e109688.
Cellular and molecular life sciences : CMLS, 2010
Cell migration is essential in a number of processes, including wound healing, angiogenesis and c... more Cell migration is essential in a number of processes, including wound healing, angiogenesis and cancer metastasis. Especially, invasion of cancer cells in the surrounding tissue is a crucial step that requires increased cell motility. Cell migration is a well-orchestrated process that involves the continuous formation and disassembly of matrix adhesions. Those structural anchor points interact with the extra-cellular matrix and also participate in adhesion-dependent signalling. Although these processes are essential for cancer metastasis, little is known about the molecular mechanisms that regulate adhesion dynamics during tumour cell migration. In this review, we provide an overview of recent advanced imaging strategies together with quantitative image analysis that can be implemented to understand the dynamics of matrix adhesions and its molecular components in relation to tumour cell migration. This dynamic cell imaging together with multiparametric image analysis will help in un...
Molecular systems biology, 2014
Over the last decade, the field of cancer metabolism has mainly focused on studying the role of t... more Over the last decade, the field of cancer metabolism has mainly focused on studying the role of tumorigenic metabolic rewiring in supporting cancer proliferation. Here, we perform the first genome‐scale computational study of the metabolic underpinnings of cancer migration. We build genome‐scale metabolic models of the NCI‐60 cell lines that capture the Warburg effect (aerobic glycolysis) typically occurring in cancer cells. The extent of the Warburg effect in each of these cell line models is quantified by the ratio of glycolytic to oxidative ATP flux (AFR), which is found to be highly positively associated with cancer cell migration. We hence predicted that targeting genes that mitigate the Warburg effect by reducing the AFR may specifically inhibit cancer migration. By testing the anti‐migratory effects of silencing such 17 top predicted genes in four breast and lung cancer cell lines, we find that up to 13 of these novel predictions significantly attenuate cell migration either ...
eLife, 2014
Utilizing molecular data to derive functional physiological models tailored for specific cancer c... more Utilizing molecular data to derive functional physiological models tailored for specific cancer cells can facilitate the use of individually tailored therapies. To this end we present an approach termed PRIME for generating cell-specific genome-scale metabolic models (GSMMs) based on molecular and phenotypic data. We build >280 models of normal and cancer cell-lines that successfully predict metabolic phenotypes in an individual manner. We utilize this set of cell-specific models to predict drug targets that selectively inhibit cancerous but not normal cell proliferation. The top predicted target, MLYCD, is experimentally validated and the metabolic effects of MLYCD depletion investigated. Furthermore, we tested cell-specific predicted responses to the inhibition of metabolic enzymes, and successfully inferred the prognosis of cancer patients based on their PRIME-derived individual GSMMs. These results lay a computational basis and a counterpart experimental proof of concept for future personalized metabolic modeling applications, enhancing the search for novel selective anticancer therapies.
Cells are attached to different type of extracellular matrix and move by coupling forces generate... more Cells are attached to different type of extracellular matrix and move by coupling forces generated in the actin cytoskeleton to the extracellular matrix via trans-membrane focal adhesions. Contraction of actin cytoskeleton linked to adhesion induces integrin clustering and focal adhesion maturation. The formation of focal adhesions is controlled by a mechanochemical mechanism in which cytoskeletal tensional forces drive changes in molecular assembly. Since the integrins are mechanotransducers that regulate cell fate, we hypothesized that matrix density and tension-induced maturation of focal adhesions result in changes in protein composition and dynamics that may influence adhesion morphology, strength and signalling. We first aimed to analyse the dynamics of different focal adhesionassociated proteins such as FAK and paxillin in control situation. Here, we describe a method to measure the binding rate and the mobile fraction of individual GFP-tagged focal adhesionassociated proteins by using FLIP (Fluorescence Loss In Photobleaching) -FRAP (Fluorescence Recovery After Photobleaching) technique and combining it with computer modelling [1]. With this method, we found that paxillin and FAK, binding partners share a similar diffusion coefficient (5µm 2 /s) and a similar binding fraction (70%). Surprisingly, both proteins which are well known binding partners, differ in their residence time at focal adhesions by a factor of 10 (10 s for FAK and 100 s for paxillin). Next, we determined the relationship between matrix concentration and protein binding/dissociation at focal adhesions. With the FLIP-FRAP method, we show that decreasing cellular traction forces on focal adhesions by low collagen matrices, increases the turnover of the focal adhesion protein FAK, and paxillin. These findings demonstrate that the molecular binding kinetics of some focal adhesion proteins are sensitive to mechanical environment. 0 50 100 150 200 250 300 0.0 0.2 0.4 0.6 0.8 1.0 Time [s] Re lative fluorescence intensity FLIP 100-150 FLIP 50-100 FLIP 0-50 FRAP 100-150 FRAP 50-100 FRAP 0-50 GFP-paxillin at focal adhesions
Toxicology Letters, 2006
Increasing our knowledge on the molecular and cellular mechanisms of acute renal tubular patholog... more Increasing our knowledge on the molecular and cellular mechanisms of acute renal tubular pathologies will lead to potential novel therapeutic strategies either to prevent the initiation of renal failure or to promote the renal regeneration after injury. Currently many genomic- and proteomic-based techniques are available to identify genes, proteins or protein modifications in relation to renal toxicity. Although we are
Journal of Cell Science, 2012
Focal adhesions (FAs) are specialized membrane associated multi-protein complexes that link the c... more Focal adhesions (FAs) are specialized membrane associated multi-protein complexes that link the cell to the extra-cellular matrix and enable cell proliferation, survival, and motility. Despite the extensive description of the molecular composition of FAs, the complex regulation of FA dynamics is largely unclear. Here, we have applied photobleaching assays on the whole cell to allow the determination of protein dynamics in every single focal adhesion. We identified that the focal adhesion proteins FAK and paxillin exist in two different states: a diffusive cytoplasmic pool and a transiently immobile FA-bound fraction with variable residence times. Interestingly, the average residence time of both proteins increased with focal adhesion size. Moreover, increasing integrin clustering by modulating surface collagen density increased residence time of FAK but not paxillin. Finally, this approach was applied to measure FAK and paxillin dynamics using nocodazole treatment followed by washout. This revealed an opposite residence time of FAK and paxillin in maturing and disassembling FAs, which depends on the ventral and peripheral cellular position of the FAs.
Proceedings of The National Academy of Sciences, 2010
Annexin A1 (AnxA1) is a candidate regulator of the epithelial-to mesenchymal (EMT)-like phenotypi... more Annexin A1 (AnxA1) is a candidate regulator of the epithelial-to mesenchymal (EMT)-like phenotypic switch, a pivotal event in breast cancer progression. We show here that AnxA1 expression is associated with a highly invasive basal-like breast cancer subtype both in a panel of human breast cancer cell lines as in breast cancer patients and that AnxA1 is functionally related to breast cancer progression. AnxA1 knockdown in invasive basal-like breast cancer cells reduced the number of spontaneous lung metastasis, whereas additional expression of AnxA1 enhanced metastatic spread. AnxA1 promotes metastasis formation by enhancing TGFβ/Smad signaling and actin reorganization, which facilitates an EMT-like switch, thereby allowing efficient cell migration and invasion of metastatic breast cancer cells.
Methods in molecular …, 2011
Cell migration, essential in cancer progression, is a complex process comprising a number of spat... more Cell migration, essential in cancer progression, is a complex process comprising a number of spatiotemporally regulated and well-coordinated mechanisms. In order to study (random) cell migration in the context of responses to various external cues (such as ...
Methods in molecular …, 2011
In the last decade, intravital microscopy on breast tumours in mice at single-cell resolution has... more In the last decade, intravital microscopy on breast tumours in mice at single-cell resolution has resulted in important new insight into mechanisms of metastatic behaviour such as migration, invasion, and intravasation of tumour cells; angiogenesis; and the ...
Molecular Imaging and …, 2011
PurposeThe aim of this study is to use multicolor intravital imaging together with an inducible c... more PurposeThe aim of this study is to use multicolor intravital imaging together with an inducible cell model to compare metastatic behavior of control and genetically modified breast cancer cell populations within the intact primary tumor of a mouse.ProcedureGFP-MTLn3-ErbB1 cells were generated with doxycycline-regulated conditional transgene expression using lentiviral TREAutoR3-cyan fluorescent protein (CFP). CFP expression together with tumor cell motility is monitored in vitro and in vivo.ResultsEffective and tight control of doxycycline-induced CFP expression was observed both in vitro and in vivo. Intravital multiphoton microscopy on intact orthotopic tumors allowed a clear discrimination between GFP-only and (GFP + CFP) cell populations, which enables direct comparison of the motility behavior of two different cell populations in the same microenvironment in vivo.ConclusionsThis system is robust and versatile for conditional gene expression and can be used to study the role of individual candidate metastasis genes in vitro and in vivo. This technology will allow investigations of cellular events in cancer metastasis and in particular intravasation within a primary tumor.Electronic supplementary materialThe online version of this article (doi:10.1007/s11307-010-0307-z) contains supplementary material, which is available to authorized users.
Clinical and …, 2009
The occurrence of metastases is a critical determinant of the prognosis for breast cancer patient... more The occurrence of metastases is a critical determinant of the prognosis for breast cancer patients. Effective treatment of breast cancer metastases is ham-pered by a poor understanding of the mechanisms involved in the formation of these secondary tumor deposits. To study ...
The Journal of pharmacology and experimental therapeutics, 2007
Toxicant exposure affects the activity of various protein tyrosine kinases. Using phosphotyrosine... more Toxicant exposure affects the activity of various protein tyrosine kinases. Using phosphotyrosine proteomics, we identified proteins that were differentially phosphorylated before renal cell detachment and apoptosis. Treatment of primary cultured rat proximal tubular epithelial cells with the model nephrotoxicant S-(1,2-dichlorovinyl)-L-cysteine (DCVC) resulted in early reorganization of F-actin stress fibers and formation of lamellipodia, which was followed by cell detachment from the matrix and apoptosis. This was prevented by genistein-mediated inhibition of protein tyrosine kinases and enhanced by inhibition of protein tyrosine phosphatases using vanadate. Phosphotyrosine proteomics revealed that DCVC-induced renal cell apoptosis was preceded by changes in the tyrosine phosphorylation status of a subset of proteins, as identified by matrix-assisted laser desorption ionization/time of flight-mass spectrometry (MS)/MS including actin-related protein 2 (Arp2), cytokeratin 8, t-comp...
Journal of Clinical Investigation, 2015
PLoS ONE, 2014
In many situations, 3D cell cultures mimic the natural organization of tissues more closely than ... more In many situations, 3D cell cultures mimic the natural organization of tissues more closely than 2D cultures. Conventional methods for phenotyping such 3D cultures use either single or multiple simple parameters based on morphology and fluorescence staining intensity. However, due to their simplicity many details are not taken into account which limits system-level study of phenotype characteristics. Here, we have developed a new image analysis platform to automatically profile 3D cell phenotypes with 598 parameters including morphology, topology, and texture parameters such as wavelet and image moments. As proof of concept, we analyzed mouse breast cancer cells (4T1 cells) in a 384-well plate format following exposure to a diverse set of compounds at different concentrations. The result showed concentration dependent phenotypic trajectories for different biologically active compounds that could be used to classify compounds based on their biological target. To demonstrate the wider applicability of our method, we analyzed the phenotypes of a collection of 44 human breast cancer cell lines cultured in 3D and showed that our method correctly distinguished basal-A, basal-B, luminal and ERBB2+ cell lines in a supervised nearest neighbor classification method. Citation: Di Z, Klop MJD, Rogkoti V-M, Le Dévédec SE, van de Water B, et al. (2014) Ultra High Content Image Analysis and Phenotype Profiling of 3D Cultured Micro-Tissues. PLoS ONE 9(10): e109688.
Cellular and molecular life sciences : CMLS, 2010
Cell migration is essential in a number of processes, including wound healing, angiogenesis and c... more Cell migration is essential in a number of processes, including wound healing, angiogenesis and cancer metastasis. Especially, invasion of cancer cells in the surrounding tissue is a crucial step that requires increased cell motility. Cell migration is a well-orchestrated process that involves the continuous formation and disassembly of matrix adhesions. Those structural anchor points interact with the extra-cellular matrix and also participate in adhesion-dependent signalling. Although these processes are essential for cancer metastasis, little is known about the molecular mechanisms that regulate adhesion dynamics during tumour cell migration. In this review, we provide an overview of recent advanced imaging strategies together with quantitative image analysis that can be implemented to understand the dynamics of matrix adhesions and its molecular components in relation to tumour cell migration. This dynamic cell imaging together with multiparametric image analysis will help in un...
Molecular systems biology, 2014
Over the last decade, the field of cancer metabolism has mainly focused on studying the role of t... more Over the last decade, the field of cancer metabolism has mainly focused on studying the role of tumorigenic metabolic rewiring in supporting cancer proliferation. Here, we perform the first genome‐scale computational study of the metabolic underpinnings of cancer migration. We build genome‐scale metabolic models of the NCI‐60 cell lines that capture the Warburg effect (aerobic glycolysis) typically occurring in cancer cells. The extent of the Warburg effect in each of these cell line models is quantified by the ratio of glycolytic to oxidative ATP flux (AFR), which is found to be highly positively associated with cancer cell migration. We hence predicted that targeting genes that mitigate the Warburg effect by reducing the AFR may specifically inhibit cancer migration. By testing the anti‐migratory effects of silencing such 17 top predicted genes in four breast and lung cancer cell lines, we find that up to 13 of these novel predictions significantly attenuate cell migration either ...
eLife, 2014
Utilizing molecular data to derive functional physiological models tailored for specific cancer c... more Utilizing molecular data to derive functional physiological models tailored for specific cancer cells can facilitate the use of individually tailored therapies. To this end we present an approach termed PRIME for generating cell-specific genome-scale metabolic models (GSMMs) based on molecular and phenotypic data. We build >280 models of normal and cancer cell-lines that successfully predict metabolic phenotypes in an individual manner. We utilize this set of cell-specific models to predict drug targets that selectively inhibit cancerous but not normal cell proliferation. The top predicted target, MLYCD, is experimentally validated and the metabolic effects of MLYCD depletion investigated. Furthermore, we tested cell-specific predicted responses to the inhibition of metabolic enzymes, and successfully inferred the prognosis of cancer patients based on their PRIME-derived individual GSMMs. These results lay a computational basis and a counterpart experimental proof of concept for future personalized metabolic modeling applications, enhancing the search for novel selective anticancer therapies.
Cells are attached to different type of extracellular matrix and move by coupling forces generate... more Cells are attached to different type of extracellular matrix and move by coupling forces generated in the actin cytoskeleton to the extracellular matrix via trans-membrane focal adhesions. Contraction of actin cytoskeleton linked to adhesion induces integrin clustering and focal adhesion maturation. The formation of focal adhesions is controlled by a mechanochemical mechanism in which cytoskeletal tensional forces drive changes in molecular assembly. Since the integrins are mechanotransducers that regulate cell fate, we hypothesized that matrix density and tension-induced maturation of focal adhesions result in changes in protein composition and dynamics that may influence adhesion morphology, strength and signalling. We first aimed to analyse the dynamics of different focal adhesionassociated proteins such as FAK and paxillin in control situation. Here, we describe a method to measure the binding rate and the mobile fraction of individual GFP-tagged focal adhesionassociated proteins by using FLIP (Fluorescence Loss In Photobleaching) -FRAP (Fluorescence Recovery After Photobleaching) technique and combining it with computer modelling [1]. With this method, we found that paxillin and FAK, binding partners share a similar diffusion coefficient (5µm 2 /s) and a similar binding fraction (70%). Surprisingly, both proteins which are well known binding partners, differ in their residence time at focal adhesions by a factor of 10 (10 s for FAK and 100 s for paxillin). Next, we determined the relationship between matrix concentration and protein binding/dissociation at focal adhesions. With the FLIP-FRAP method, we show that decreasing cellular traction forces on focal adhesions by low collagen matrices, increases the turnover of the focal adhesion protein FAK, and paxillin. These findings demonstrate that the molecular binding kinetics of some focal adhesion proteins are sensitive to mechanical environment. 0 50 100 150 200 250 300 0.0 0.2 0.4 0.6 0.8 1.0 Time [s] Re lative fluorescence intensity FLIP 100-150 FLIP 50-100 FLIP 0-50 FRAP 100-150 FRAP 50-100 FRAP 0-50 GFP-paxillin at focal adhesions
Toxicology Letters, 2006
Increasing our knowledge on the molecular and cellular mechanisms of acute renal tubular patholog... more Increasing our knowledge on the molecular and cellular mechanisms of acute renal tubular pathologies will lead to potential novel therapeutic strategies either to prevent the initiation of renal failure or to promote the renal regeneration after injury. Currently many genomic- and proteomic-based techniques are available to identify genes, proteins or protein modifications in relation to renal toxicity. Although we are
Journal of Cell Science, 2012
Focal adhesions (FAs) are specialized membrane associated multi-protein complexes that link the c... more Focal adhesions (FAs) are specialized membrane associated multi-protein complexes that link the cell to the extra-cellular matrix and enable cell proliferation, survival, and motility. Despite the extensive description of the molecular composition of FAs, the complex regulation of FA dynamics is largely unclear. Here, we have applied photobleaching assays on the whole cell to allow the determination of protein dynamics in every single focal adhesion. We identified that the focal adhesion proteins FAK and paxillin exist in two different states: a diffusive cytoplasmic pool and a transiently immobile FA-bound fraction with variable residence times. Interestingly, the average residence time of both proteins increased with focal adhesion size. Moreover, increasing integrin clustering by modulating surface collagen density increased residence time of FAK but not paxillin. Finally, this approach was applied to measure FAK and paxillin dynamics using nocodazole treatment followed by washout. This revealed an opposite residence time of FAK and paxillin in maturing and disassembling FAs, which depends on the ventral and peripheral cellular position of the FAs.
Proceedings of The National Academy of Sciences, 2010
Annexin A1 (AnxA1) is a candidate regulator of the epithelial-to mesenchymal (EMT)-like phenotypi... more Annexin A1 (AnxA1) is a candidate regulator of the epithelial-to mesenchymal (EMT)-like phenotypic switch, a pivotal event in breast cancer progression. We show here that AnxA1 expression is associated with a highly invasive basal-like breast cancer subtype both in a panel of human breast cancer cell lines as in breast cancer patients and that AnxA1 is functionally related to breast cancer progression. AnxA1 knockdown in invasive basal-like breast cancer cells reduced the number of spontaneous lung metastasis, whereas additional expression of AnxA1 enhanced metastatic spread. AnxA1 promotes metastasis formation by enhancing TGFβ/Smad signaling and actin reorganization, which facilitates an EMT-like switch, thereby allowing efficient cell migration and invasion of metastatic breast cancer cells.
Methods in molecular …, 2011
Cell migration, essential in cancer progression, is a complex process comprising a number of spat... more Cell migration, essential in cancer progression, is a complex process comprising a number of spatiotemporally regulated and well-coordinated mechanisms. In order to study (random) cell migration in the context of responses to various external cues (such as ...
Methods in molecular …, 2011
In the last decade, intravital microscopy on breast tumours in mice at single-cell resolution has... more In the last decade, intravital microscopy on breast tumours in mice at single-cell resolution has resulted in important new insight into mechanisms of metastatic behaviour such as migration, invasion, and intravasation of tumour cells; angiogenesis; and the ...
Molecular Imaging and …, 2011
PurposeThe aim of this study is to use multicolor intravital imaging together with an inducible c... more PurposeThe aim of this study is to use multicolor intravital imaging together with an inducible cell model to compare metastatic behavior of control and genetically modified breast cancer cell populations within the intact primary tumor of a mouse.ProcedureGFP-MTLn3-ErbB1 cells were generated with doxycycline-regulated conditional transgene expression using lentiviral TREAutoR3-cyan fluorescent protein (CFP). CFP expression together with tumor cell motility is monitored in vitro and in vivo.ResultsEffective and tight control of doxycycline-induced CFP expression was observed both in vitro and in vivo. Intravital multiphoton microscopy on intact orthotopic tumors allowed a clear discrimination between GFP-only and (GFP + CFP) cell populations, which enables direct comparison of the motility behavior of two different cell populations in the same microenvironment in vivo.ConclusionsThis system is robust and versatile for conditional gene expression and can be used to study the role of individual candidate metastasis genes in vitro and in vivo. This technology will allow investigations of cellular events in cancer metastasis and in particular intravasation within a primary tumor.Electronic supplementary materialThe online version of this article (doi:10.1007/s11307-010-0307-z) contains supplementary material, which is available to authorized users.
Clinical and …, 2009
The occurrence of metastases is a critical determinant of the prognosis for breast cancer patient... more The occurrence of metastases is a critical determinant of the prognosis for breast cancer patients. Effective treatment of breast cancer metastases is ham-pered by a poor understanding of the mechanisms involved in the formation of these secondary tumor deposits. To study ...
The Journal of pharmacology and experimental therapeutics, 2007
Toxicant exposure affects the activity of various protein tyrosine kinases. Using phosphotyrosine... more Toxicant exposure affects the activity of various protein tyrosine kinases. Using phosphotyrosine proteomics, we identified proteins that were differentially phosphorylated before renal cell detachment and apoptosis. Treatment of primary cultured rat proximal tubular epithelial cells with the model nephrotoxicant S-(1,2-dichlorovinyl)-L-cysteine (DCVC) resulted in early reorganization of F-actin stress fibers and formation of lamellipodia, which was followed by cell detachment from the matrix and apoptosis. This was prevented by genistein-mediated inhibition of protein tyrosine kinases and enhanced by inhibition of protein tyrosine phosphatases using vanadate. Phosphotyrosine proteomics revealed that DCVC-induced renal cell apoptosis was preceded by changes in the tyrosine phosphorylation status of a subset of proteins, as identified by matrix-assisted laser desorption ionization/time of flight-mass spectrometry (MS)/MS including actin-related protein 2 (Arp2), cytokeratin 8, t-comp...