MRP4 regulates various cyclic nucleotide-dependent signaling events including a recently elucidated role in cell migration. We describe a direct, but multifaceted approach to unravel the downstream molecular targets of MRP4 resulting in identification of a unique MRP4 interactome that plays key roles in the fine-tuned regulation of fibroblast migration.
Multidrug resistance protein 4 (MRP4) is a member of the ATP-binding cassette family of membrane transporters and is an endogenous efflux transporter of cyclic nucleotides. By modulating intracellular cyclic nucleotide concentration, MRP4 can regulate multiple cyclic nucleotide-dependent cellular events including cell migration. Previously, we demonstrated that in the absence of MRP4, fibroblast cells contain higher levels of intracellular cyclic nucleotides and can migrate faster. To understand the underlying mechanisms of this finding, we adopted a direct yet multifaceted approach. First, we isolated potential interacting protein complexes of MRP4 from a MRP4 over-expression cell system using immunoprecipitation followed by mass-spectrometry. After identifying unique proteins in the MRP4 interactome, we utilized Ingenuity Pathway Analysis (IPA) to explore the role of these protein-protein interactions in the context of signal transduction. We elucidated the potential role of the MRP4 protein complex in cell migration and identified F-actin as a major mediator of the effect of MRP4 on cell migration. This study also emphasized the role of cAMP and cGMP as key players in the migratory phenomena. Using high-content microscopy, we performed cell-migration assays and observed that the effect of MRP4 on fibroblast migration is completely abolished by disruption of the actin cytoskeleton or inhibition of cAMP-dependent kinase A (PKA). To visualize signaling modulations in a migrating cell in real time, we utilized a FRET-based sensor for measuring PKA activity and found, the presence of more polarized PKA activity near the leading edge of migrating Mrp4-/- fibroblast, compared to Mrp4+/+fibroblasts. This in turn increased cortical actin formation and augmented the process of migration. Our approach enables identification of the proteins acting downstream to MRP4 and provides us with an overview of the mechanism involved in MRP4-dependent regulation of fibroblast migration.
Cell migration is a complicated multi-step process. Studies have shown that during migration cells are polarized into leading and trailing edges. By adhering to the extracellular matrix, the leading edge provides the traction necessary for the cell body to move forward. Finally, the trailing edge releases rear attachments and completes the migration cycle1,2.
Cell polarization for efficient cell migration is regulated by spatial segregation of intracellular signaling. Cellular second messengers, such as cAMP, mediate the compartmentalization of the signaling events required for fine-tuned directional cell migration3,4. Preferential accumulations of cAMP and cAMP-dependent kinase PKA activity at the leading edge play key roles in directional cell migration5,6. By phosphorylating small GTPases such as Ras-related C3 botulinum toxin substrate (Rac) and cell division control protein 42 homolog or Cdc42, PKA activates actin-related protein 2/3 (Arp 2/3) at the leading edge and induces the formation of lamellipodia7-9. PKA also phosphorylates an anti-capping agent, vasodilator stimulated phosphoprotein (VASP), thereby regulates the oscillatory cycles of membrane extension and retraction10,11.
In cells, cAMP levels are regulated by three major processes: i) synthesis by adenylate cyclase, ii) degradation by phosphodiesterases, and iii) transportation by membrane-bound efflux transporters3. Multidrug resistance protein 4 (MRP4), a member of ATP-binding cassette (ABC) family of membrane transporters, functions as an endogenous efflux transporter of cyclic nucleotides. Therefore, MRP4 can regulate intracellular cAMP levels and cAMP-dependent cellular signaling11-13. We have previously shown that in Mrp4-/-, fibroblasts contain relatively higher levels of cyclic nucleotides and migrate faster compared to Mrp4+/+ fibroblasts14. We also reported a biphasic effect of cyclic nucleotides on fibroblast migration. Based on previous studies and our finding that Mrp4-/- fibroblasts contain more polarized cAMP during the course of migration, we hypothesized that this MRP4-mediated regulation of fibroblast migration is cAMP dependent. In order to understand the downstream mechanism, we took a direct yet multifaceted approach.
To identify the proteins associated and in interplay with MRP4, we immunoprecipitated MRP4-containing macromolecular complexes from HEK293 cells that over express MRP4. Using mass-spectrometry, we identified multiple MRP4-interacting proteins and analyzed their interconnectivity using Ingenuity Pathway Analysis (IPA). IPA is a useful tool to analyze protein-protein interactions (both structural and functional) and explore their contributions in particular physiological and pathological events based on the literature and experimental evidences15,16. IPA indicated that F-actin is a major downstream target of MRP4 in the context of cell migration where cAMP and cGMP are the key signaling molecules17. These data were further confirmed by high-content microscopy. High-content microscopy can capture and analyze cell behaviors such as cell migration in a more convenient, accurate and high-throughput manner18. The high-content microscopy data demonstrated that the effect of MRP4 on fibroblast migration is completely abolished upon disruption of the actin cytoskeleton or inhibition of PKA17.
Additionally, we used a Förster resonance energy transfer (FRET)-based PKA sensor to monitor the PKA dynamics in migrating cells in real time. FRET-based kinase sensors usually consist of specific phosphorylation substrate peptides flanked by CFP and YFP fluorophores19-21. pmAKAR3 is an improved and membrane targeted FRET-based PKA sensor that contains forkhead-associated domain 1 (FHA1) and the PKA substrate sequence LRRATLVD5,22. Phosphorylation of pmAKAR3 by the PKA catalytic subunit increases FRET signal between CFP and YFP19. Insertion of a lipid modification domain into the sensor targets it to the plasma membrane for monitoring PKA dynamics, specifically at the membrane compartment23.
Using pmAKAR3, we demonstrated that the leading edge of migrating Mrp4-/- fibroblasts exhibited more polarized PKA activity than Mrp4+/+ fibroblasts, which in turn increased the cortical actin formation at the cell's leading edge17. Together, these events resulted in better cellular polarization and faster directional cell migration in the absence of MRP4. Our specific and direct approach identified key downstream targets for MRP4 and provides an important, but as of yet unexplored mechanism for MRP4-dependent regulation of fibroblast migration.
1. Ingenuity Pathway Analysis
2. High-content Microscopy
3. Förster Resonance Energy Transfer (FRET)
To study the effect of MRP4 on fibroblast migration, we used a wound-healing assay utilizing high-content microscopy14. Precise wounds were made on confluent monolayers of MEFs isolated from either Mrp4-/- or Mrp4+/+ mice, and images were taken at 1 hr intervals for 24 hr. We observed a higher migration rate for Mrp4-/- MEFs compared to Mrp4+/+ MEFs (Figure 2). The wounds were completely healed in less than 15 hr for the Mrp4-/- MEFs, whereas the Mrp4+/+ MEFs required almost 20 hr to cover the wounds.
Polarized accumulation of PKA activity at the leading edge of migrating cells is a key early event for directional migration. PKA activity can be monitored in real time using the pmAKAR3 FRET-based sensor for PKA5,17. To check the specificity of pmAKAR3 for PKA activity, we treated HEK293 cells overexpressing pmAKAR3 or the point mutant pmAKAR3-TA, which contains a threonine-to-alanine mutation at the substrate region for PKA and therefore is irresponsive to PKA phosphorylation with 25 µM forskolin, a cAMP-inducing agent14. We found an increase in FRET signal in cells overexpressing pmAKAR3, but cells overexpressing pmAKAR3-TA remained unchanged (Figure 3). The basal FRET levels were also higher for cells expressing pmAKAR3 compared to the cells expressing pmAKAR3-TA. These data indicated that pmAKAR3 is very specific for PKA activity.
In summary, the methods described in the protocol section are useful tools to study the molecular mechanism associated with a specific cellular event.
Figure 1: Ingenuity Pathway Analysis (IPA) of MRP4 Interactome. Using IPA actin cytoskeleton pathway was identified as one of the major canonical pathways affected by MRP4 interactome. Presented actin signaling network indicates connected proteins (white) and their cross communication with the proteins identified in the MRP4 interactome (pink) inferred from literature and experimental evidences. Please click here to view a larger version of this figure.
Figure 2: Wound-healing Assay using High Content Microscopy. Mrp4+/+and Mrp4-/- mouse embryonic fibroblasts (MEFs) were grown on fibronectin-coated 96-well dishes, and wounds in the monolayers were made precisely using the 96-pin wound-maker. Representative images at different time points are shown with 10X magnification. Please click here to view a larger version of this figure.
Figure 3: Förster Resonance Energy Transfer (FRET)-based Measurement of PKA Activity using pmAKAR3 Sensors. Representative pseudo-color images of N-FRET with 60X magnification for HEK293 cells transfected with pmAKAR3 sensor and pmAKAR3-TA sensor before and after forskolin treatment are shown (top panels). Images in each panel were captured from the same field of view. Color bar indicates the magnitude of the N-FRET. The line graph (bottom panel) represents the change in N-FRET levels after treatment with forskolin. Data represent the average of at least three independent experiments (Mean ± SEM; n = 3). Please click here to view a larger version of this figure.
Cell migration is an intricate process that plays indispensable roles in many important physiological events including wound healing1,2. Aberrant cell migrations may cause catastrophic events, such as tumor metastasis and angiogenesis24,25. Therefore, fine-tuned regulation of cell migration is required to maintain normal body function.
Using high-content microscopy18, we demonstrated that MRP4-deficient MEFs migrate faster compared to wild-type fibroblasts14. In contrast to the conventional scratch wound assay, the microscopy here conducts the wound healing assay in an automated convenient, consistent and high-throughput manner. The software analyzes the cell migration rate based on three separate metrics: i) change in wound width, ii) change in cell confluence within the wound region, and iii) relative wound density (RWD). RWD is a self-normalized metric that measures the spatial cell density inside the wound area relative to the spatial cell density outside of the wound area. Therefore, it is not affected by changes in cell density due to cell proliferation and provides very specific information regarding cell migration which is otherwise difficult to be obtained by the conventional scratch wound assay26. Initially, at the 0 time point, the RWD will be 0% and upon complete wound healing, the RWD will be 100%. All of these metrics are calculated by custom-made software with inbuilt algorithms and the migration information is automatically generated for every time point. The assay is easy to perform but proper washing (70% ethanol) and handling (inside the hood) of the wound-maker is important to prevent contamination. Our data suggested that the RWD kinetics for Mrp4-/- MEFs are significantly higher compared to Mrp4+/+ MEFs.
During migration, cells polarize into leading and trailing edges that ultimately pull the cell body toward the direction of migration1,27. Distinct and segregated signaling events at different regions of a moving cell ensure the polarization process. Polarized accumulation of cAMP and subsequent activation of PKA at the leading edge is a key early step in directional cell migration5. Since MRP4 has very high affinity for cAMP (Km = 45 µM)12, we hypothesize that the effect of MRP4 on cell migration is cAMP-dependent. To identify the proteins acting downstream of MRP4 and simultaneously interacting with MRP4, we characterized MRP4-containing macromolecular complexes by mass-spectrometry. The MRP4 interactome was subjected to multiple analyses including generation of protein networks, path maps, and functional integration to the canonical pathways of the cellular signaling and their respective pictorial representation through the use of IPA. In general, IPA allows scientific users to recognize the molecular and physiological contexts of their genes and proteins of interest. However the analysis is completely based on the literature and experimental evidences. Novel interactions cannot be suggested by IPA. But it can identify which network, the proteins of interest, can potentially form. Additionally users can identify the top diseases and functions that are potentially linked to a particular protein network based on the confidence level (P value). Of interest to our study, the actin cytoskeleton pathway was a major affected pathway with a P value of 6.75 x 10-4. This comprehensive approach also revealed that F-actin is a major protein target for MRP4 and cAMP is the key mediator17. Based on these data, we further studied the underlying molecular mechanisms.
To understand the effect of MRP4 on cAMP dynamics and PKA activity during the course of cell migration, we used FRET-based live-cell imaging techniques. Using FRET-based sensors for cAMP and PKA activity, we confirmed higher cAMP accumulation and higher PKA activity at the leading edge of migrating and polarized fibroblasts22,28. We further demonstrated that in the absence of MRP4, MEFs have more polarized cAMP and PKA activity, which in turn facilitates cortical actin formation and cell migration. The high-content microscopy-based wound-healing assay showed that the effect of MRP4 on cell migration is completely abolished by PKA inhibition or actin disruption, which indicates a direct role of PKA and actin as downstream targets17. Unlike conventional cell population-based assays such as ELISA, use of a FRET-based sensor allows us to identify the downstream effector kinases that regulate various signaling processes and detect the correlation between cyclic nucleotide dynamics and their corresponding kinase activity in real time and space. Additionally it can discriminate intracellular and intercellular heterogeneity during the signaling events. For example it can detect the difference in PKA dynamics in the cells at the wound edge compared to the cells inside the monolayer and away from the wound edge5, whereas ELISA based assays can only detect total intracellular cyclic nucleotide or PKA level in a sample14,17. However the transfection efficacy of particular cell types can be a limiting factor for conducting FRET based assays but the highly efficient transfection reagents can overcome this problem.
Together, our results indicate that in addition to conferring drug resistance, MRP4 also plays important physiological roles by modulating intracellular cAMP dynamics. Using three unique approaches, i) high-content microscopy18, ii) IPA15, and iii) FRET5,28, we have begun to unravel the previously undefined role of MRP4 in cell migration. In general, these useful scientific techniques will allow us to identify new downstream targets of any protein of interest and explore novel molecular mechanisms involved in particular pathological or physiological cell responses. Where IPA provides useful information regarding downstream effectors of the protein of interest and potential regulatory networks; FRET-based live imaging can monitor compartmentalized signaling in real time. High-content microscopy is a convenient high-throughput screening tool to monitor and analyze physiological events, such as cell migration and cell proliferation, over a period of time as a final readout.
The authors have nothing to disclose.
This work was supported by National Institutes of Health grants R01-DK080834 and R01-DK093045. We thank J. Denise Wetzel, CCHMC Medical Writer, for editing of the manuscript.
Lipofectamine 2000 | Invitrogen(Carlsbad, CA) | 11668-027 | |
DMEM | Invitrogen (Carlsbad, CA) | 11965-092 | |
IncuCyte Zoom | Essen BioScience | ||
96-well IncuCyte Image-Lock microplates | Essen BioScience | 4493 | |
Latrunculin B | Sigma-Aldrich (St. Louis, MO). | L5288 | Stock in DMSO |
H-89 | Enzo Life Sciences (Farmingdale, NY) | BML-EI196 | Stock in DMSO |
35-mm glass-bottomed dishes | (MatTek Corporation; Ashland, MA) | P35G-1.5-20-C | |
Fibronectin | Sigma-Aldrich (St. Louis, MO). | F1141 | |
Opti-MEM Reduced Serum Media | Invitrogen (Carlsbad, CA) | 31985-088 | |
FRET microscopy system | Olympus inverted microscope (IX51) | ||
CCD camera | Hamamatsu, Japan | ORCA285 | |
SlideBook software 5.5 | Intelligent Imaging Innovation ( Denver, CO) | ||
Ingenuity Pathway Analysis software | IPA, QIAGEN Redwood City, | ||
Forskolin | Tocris (Ellisville, MO). | 1099 | Stock in100% EtOH |
DMEM F-12 | Invitrogen (Carlsbad, CA) | 11330-057 | |
HBSS | Invitrogen (Carlsbad, CA) | 14025-134 | |
Excel | Microsoft | ||
PBS | Invitrogen(Carlsbad, CA) | 10010-023 | |
Trypsin/EDTA Solution (TE) | Invitrogen(Carlsbad, CA) | R-001-100 | |
Penicillin-Streptomycin | Invitrogen(Carlsbad, CA) | 15140-122 |