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Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6

Nature Structural & Molecular Biology volume 22, pages 703–711 (2015)Cite this article

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Abstract

Mig6 is a feedback inhibitor that directly binds, inhibits and drives internalization of ErbB-family receptors. Mig6 selectively targets activated receptors. Here we found that the epidermal growth factor receptor (EGFR) phosphorylates Mig6 on Y394 and that this phosphorylation is primed by prior phosphorylation of an adjacent residue, Y395, by Src. Crystal structures of human EGFR–Mig6 complexes reveal the structural basis for enhanced phosphorylation of primed Mig6 and show how Mig6 rearranges after phosphorylation by EGFR to effectively irreversibly inhibit the same receptor that catalyzed its phosphorylation. This dual phosphorylation site allows Mig6 to inactivate EGFR in a manner that requires activation of the target receptor and that can be modulated by Src. Loss of Mig6 is a driving event in human cancer; analysis of 1,057 gliomas reveals frequent focal deletions of ERRFI1, the gene that encodes Mig6, in EGFR-amplified glioblastomas.

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Figure 1: Identification and validation of EGFR-driven phosphorylation of Mig6 on Y394-Y395.
Figure 2: Characterization of Mig6 Y394-Y395 peptides as substrates for EGFR and Src.
Figure 3: Phosphorylation of Mig6 on Y394-Y395 is essential for binding and inhibition of EGFR and is modulated by Src.
Figure 4: Y394 phosphorylation increases Mig6 potency and is the basis for EGFR inhibition.
Figure 5: Structural snapshots of Mig6 inhibition of EGFR.
Figure 6: Analysis of chromosome 1p copy-number alterations across 1,057 gliomas.
Figure 7: Model for mechanism of feedback inhibition of EGFR by Mig6.

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Acknowledgements

We thank L. Cantley and M. Begley for helpful discussions and sharing unpublished data, and R. McNally for critical reading of the manuscript. We thank P. Cole, D. Leahy and Z. Wang for helpful discussions and for testing the effect of phospho-Mig6 species on the activity of transmembrane EGFR (Supplementary Fig. 4e). We thank P. Janne (Dana-Farber Cancer Institute) for providing cells. We thank beamline personnel at the Northeast Collaborative Access Team at the Advanced Photon Source, Argonne National Laboratory (NE-CAT) for assistance with data collection and processing. NE-CAT is supported by grants from the US National Institutes of Health (NIH). This work was supported in part by NIH grants CA116020 (M.J.E. and M.M.), CA154303 (M.J.E. and M.M.), CA156021 (J.A.M.) and CA178860 (J.A.M.). This work was also supported in part by grants from Samsung Medical Center (J.C.) and the Basic Science Research Program of the National Research Foundation of Korea, Ministry of Science, ICT and Future Planning (grant 2013065771; J.C.).

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  1. Eunyoung Park and Nayoung Kim: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Eunyoung Park, Scott B Ficarro, Yi Zhang, Byung Il Lee, Rameen Beroukhim, Jarrod A Marto & Michael J Eck

  2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA

    Eunyoung Park, Jarrod A Marto & Michael J Eck

  3. Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea

    Nayoung Kim, Ahye Cho, Angela K J Park, Woong-Yang Park & Jeonghee Cho

  4. Samsung Advanced Institute for Health Sciences and Technology, SungKyunKwan University, Seoul, Republic of Korea

    Nayoung Kim, Ahye Cho, Kihong Kim, Angela K J Park, Woong-Yang Park & Jeonghee Cho

  5. Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Scott B Ficarro, Yi Zhang & Jarrod A Marto

  6. Division of Convergence Technology, Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea

    Byung Il Lee

  7. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA

    Bradley Murray, Matthew Meyerson & Rameen Beroukhim

  8. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Matthew Meyerson & Rameen Beroukhim

  9. Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA

    Matthew Meyerson

  10. Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA

    Rameen Beroukhim

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Contributions

E.P. designed and conducted all in vitro biochemical and enzyme kinetic studies and determined all crystal structures. N.K., A.C., K.K., A.K.J.P. and W.-Y.P. designed and carried out cell-based functional studies of Mig6. J.A.M. conceived and supervised proteomics and other mass spectrometry–based experiments. S.B.F. and Y.Z. designed and executed mass spectrometry–based experiments. B.I.L. refined crystal structure 4ZJV. B.M. and R.B. designed and executed genomic analyses of ERRFI1. M.M., J.C. and M.J.E. conceived the study, designed experiments and, together with E.P., S.F., R.B. and J.A.M., wrote and edited the manuscript. All authors commented on the manuscript.

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Correspondence to Jeonghee Cho or Michael J Eck.

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Integrated supplementary information

Supplementary Figure 1 Quantitative phosphoproteomic workflow and identification of EGFR-driven phosphorylation in NIH-3T3 cells.

a, Analytical workflow leading to identification of Mig6 pY394/pY395 site. Tryptic peptides derived from NIH-3T3 cells expressing WT EGFR or various mutant EGFR (Ex20Ins, Ex20Ins/D837A (kinase-dead) or C-terminal deletion mutants) were iTRAQ-labeled (114-WT+EGF, 115-Ex20Ins, 116-Ex20Ins-KD, 117-CT DEL1) and subjected to enrichment and clean-up of phospho-tyrosine-containing peptides using anti-phospho-tyrosine antibodies followed by immobilized metal affinity chromatorgraphy IIMAC). Next, iTRAQ labeled peptides were analyzed by LC-MS/MS, with peptide sequence and phosphorylation site assignments based on the Mascot search algorithm. To complement previous phosphoproteomic studies that focused on the L858R and Ex19Del EGFR mutants, we studied an exon20 insertion mutant (insNPG) and an oncogenic C-terminal deletion mutant (CTDel1), which deletes residues 1010-1152). We included a kinase-dead (D837A) version of the exon20 insertion mutant as a negative control. b, Using this approach we identified a total of 640 phosphopeptides that mapped to 511 unique gene identifiers (≤1% false discovery rate, FDR). The histogram distribution of iTRAQ reporter ion Log-ratios for these 640 phosphopeptides are plotted. Selected phosphorylation sites listed on the right were upregulated at least 8-fold relative to the kinase-dead control in all three experiments (WT+EGF, Ex20Ins, and CTDel). This analysis revealed increased phosphorylation of EGFR itself in addition to adaptor proteins that mediate EGFR and Src signaling (including CrkL, Dok1, Gab3 and Shc1), as well as key downstream signaling proteins including STAT5b and Shp2.

Supplementary Figure 2 Validation and characterization of EGFR-driven phosphorylation of Mig6.

a and b, Characterization of phospho-specific Y394Y395 Mig6 antibody. Expression constructs of WT(a) or L858R or Ex20Ins EGFR mutants (b) were transiently transfected alone or in combination with either WT or Y394F/Y395F Mig6 mutants in HEK-293T cells. The resulting cell lysates were subjected to immunoblotting with an affinity purified rabbit polyclonal antibody raised against a phosphorylated Mig6 peptide (with sequence SSTHpYpYLLPER). The levels of ectopically expressed EGFR and Mig6 proteins were examined by immunoblotting with anti-EGFR or antiflag antibodies. Anti-β-actin was used as a loading control. c and d, EGFR phosphorylates Mig6 segment 1+2 predominately on Y394. Equimolar EGFR and Mig6 (330-399) were mixed under reaction conditions and the fraction of Mig6 in each phosphorylation state (at the Y394/Y395 site) was determined by quantitative mass spectrometry at the indicated time points. Parallel experiments were conducted with L858R mutant EGFR (c) and WT EGFR (d).

Supplementary Figure 3 Phosphorylation of Mig6 on Y394 is essential for binding and inhibition of WT and mutant EGFR.

a, Immunoblotting analysis was performed using cell lysates prepared from the NIH-3T3 cells stably expressing the indicated Mig6 and EGFR variants (corresponding to Fig. 3b in main text) with antibodies against EGFR, p-EGFR (4G10), Mig6 (flag) or p-Mig6. β-actin antibody was used as a loading control. b, Y394F and Y394F/Y395F mutations impair the ability of Mig6 to inhibit constitutive phosphorylation of L858R EGFR. Cell lysates derived from HEK-293T cells transiently cotransfected expression constructs of L858R EGFR with WT or mutant Mig6 as indicated were subjected to immunoblotting with antibodies against EGFR, p-EGFR (4G10), Mig6 (flag), p-Mig6 and β-actin. c, Binding of Mig6 to L858R EGFR is abrogated by erlotinib treatment and by mutation of the Y394/Y395 phosphorylation site. Cell lysates derived from HEK-293T cells transiently transfected with EGFR L858R and Mig6 alone or in combination as indicated were immunoprecipitated with antibodies against EGFR followed by immunoblotting analysis with anti-flag or anti-EGFR antibodies, respectively. Immunoblotting of whole cell lysates as indicated revealed equivalent levels of ectopically expressed EGFR and Mig6. β-actin antibody was used as a loading control.

Supplementary Figure 4 Preparation and characterization of semisynthetic Mig6 phosphoproteins.

a, Scheme for preparation of Mig6 segment 1+2 proteins (residues 330-399) in defined phosphorylation states using intein-mediated expressed protein ligation (EPL). Mig6 residues 330-389 were expressed in the chitin EPL vector pTBX1, modified to encode a glutathione-Stransferase (GST) fusion and a tobacco etch virus (TEV) protease site. Synthetic phosphopeptides corresponding to Mig6 residues 390-399, with Ser 390 replaced by cysteine, were ligated to the Mig6-330-389 fragment following MESNA cleavage (2-mercaptoethanesulfonic acid). Preparation of the doubly-phosphorylated Mig6-pYpY protein is illustrated, analogous procedues were used to prepare the singly-phosphorylated species. Note that this synthetic approach introduces a Ser390Cys substitution. b, Analysis of unphosphorylated Mig6 and semisynthetic Mig6 phosphorylation variants by Coomassie staining and western blotting with phosphospecific antibodies. Parallel SDS-PAGE gels were Coomassie-stained or immunoblotted with anti-phosphotyrosine antibody 4G10, anti-phospho-Mig6, or the anti-phospho-Mig6 further purified by subtractive purification with an immobilized

Mig6 pY394 peptide (anti-phospho-Mig6*). c, Inhibition of EGFR (L858R or wild type) by Mig6 segment 1+2 or semi-synthetic Mig6 segment 1+2 (residues 330-399) in defined phosphorylation states. The kinase was preincubated with increasing concentrations of the indicated Mig6 phosphorylation variant and reaction velocity was measured at steady state (30 minutes after starting the reaction by addition of ATP). Fractional velocities are plotted as a function of Mig6 concentration. Poly[E4Y] was used as a peptide substrate at a concentration of 2.5 mM. d, Inhibition of EGFR L858R by Mig6-YY versus Mig6-pYpY at moderate concentrations (0.16 mM) of peptide substrate poly[E4Y]. Enzyme activity was measured at steady state. Inhibition of L858R EGFR by Mig6-pYpY is well-fit by Morrison’s equation for tightbinding inhibitors (purple curve), but inhibition by the unphosphorylated Mig6-YY protein is not (blue curve). At low concentrations, Mig6-YY exhibits potent inhibition (up to 160 nM Mig6-YY), but inhibition effectively plateaus at higher concentrations. This effect arises from the fact that Mig6-YY is not the actual inhibitory species, and once EGFR is saturated with Mig6-YY (that it

has converted to Mig6-pYY or Mig6-pYpY), little additional phospho-Mig6 is produced. Thus at each point in the titration the reaction contains a mixture of unphosphorylated and phosphorylated Mig6. At low concentrations virtually all of the Mig6 is phosphorylated, while at higher concentrations only a small, nearly fixed amount of inhibitory phospho-Mig6 is present. EGFR L858R was used at a concentration of 100 nM active enzyme. e, Inhibition of EGF-bound, near full-length EGFR by Mig6 segment 1+2 or semi-synthetic Mig6 segment 1+2 (residues 330-399) in defined phosphorylation states. Radiometric kinase assays were performed as previously described by Wang et al. (ref. 33). Briefly, Mig6 was preincubated with 10 nM tEGFR on ice for 10 min before initiating the reaction with 30 μM peptide substrate (Biotin- RAHEEIYHFFFAKKK-COOH). After stopping the reaction, streptavidin Ultralink resin (Pierce) was used to isolate the biotinylated substrate. The resin was washed three times, and incorporated radioactivity was measured by liquid scintillation counting. Turnover was <10%. All reactions were performed in duplicate, which showed values that were generally within 20%.

Supplementary Figure 5 Binding studies of phosphorylated Mig6 (330–399) to EGFR.

a, Kinase-dead EGFR retains the ability to bind phosphorylated Mig6. An excess of semisynthetic Mig6-pYpY was incubated with EGFR D837N and was then analyzed by size-exclusion chromatography and SDS-PAGE. The elution profile (absorbance at 280 nm) is shown in the upper panel, aligned with Coomassie-stained SDS-PAGE of corresponding elution fractions (middle panel) and a western blot with the Mig6-pY394/pY395 specific antisera (lower panel). b, Dissociation of phosphorylated Mig6 (segment 1+2) from EGFR is extremely slow. A two-fold molar excess of EGFR L858R was combined with GST-Mig6 (330-399) and incubated for 20 minutes with or without ATP. The reaction mixture was captured on glutathione agarose beads, which were washed with continuous flow for the indicated time periods before elution with glutathione and analysis by SDS-Page. Note that binding is ATP-dependent, consistent with a requirement for phosphorylation on Y394. Using gel densitometry to measure the ratio of bound EGFR to GST-Mig6, we calculated a t1/2 of ~45 minutes for the complex.

Supplementary Figure 6 Crystal structures of EGFR in complex with Mig6.

a, Electron density map in the region of pY394/pY395 in Mig6-pYpY peptide complex. The 2Fo-Fc map (blue mesh) is contoured at 1.2σ. We also calculated a difference electron density map with coefficients [Fobs(pYpY)-Fobs(YpY)] and phases derived from the apo-EGFR model. The strongest feature in this completely unbiased difference map is a positive peak (> 8σ) in the position of the phosphate group on pTyr394 (green mesh, contoured at 4σ). b, Stereo view of electron density in Mig6 segment 1 + 2 structure. Map is contoured at 1.2σ in region of Mig6 segment 2. Mig6 is shown in yellow, EGFR in blue. Note hydrophobic packing of isoleucines 379 and 382.

Supplementary Figure 7 Enzyme kinetic studies of Mig6 inhibition of WT and mutant EGFR.

a, Mig6 is a peptide-substrate competitive inhibitor with Ki=15.85 nM. Apparent Ki values (Ki app) for Mig6- pYpY (residues 330-399) were determined at a range of poly[E4Y] concentrations; extrapolation to zero substrate concentration by linear least-squares fitting (red line) was used to determine the Ki value. b, EGFR L858R activity was measured at a range of poly[E4Y] concentrations in the presence of increasing concentrations of Mig6-pYpY. Apparent Km values (Kmapp) at each Mig6-pYpY concentration were determined by fitting to the Michaelis-Menten equation using Graphpad PRISM software, and were as follows: no Mig6, Kmapp = 243 μM; 0.04 μM Mig6, Kmapp = 402 μM; 0.16 μM Mig6, Kmapp = 1.29 mM; 0.64 μM Mig6, Kmapp = 2.0 mM, and 2.56 μM Mig6, Kmapp = 1.45 mM. The increase in Kmapp with increasing Mig6-pYpY concentrations indicates a peptide-substrate competitive mechanism of inhibition. c, Comparison of inhibition of WT, L858R (LR), and T790M/V948R (TMVR) EGFR proteins by Mig6-YY. The V948R mutation is on the C-lobe of EGFR in the Mig6 segment 1 binding site. This mutation decreases, but does not abolish inhibition by Mig6. (We expect that the T790M mutation is without effect; the double mutant was used here as we had previously prepared it for an unrelated study).

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Supplementary Data Set 1

Gel and blot original images (PDF 3064 kb)

Supplementary Table 1

Quantitative phosphoproteomic data for WT and mutant EGFR signaling images (XLS 206 kb)

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Park, E., Kim, N., Ficarro, S. et al. Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6. Nat Struct Mol Biol 22, 703–711 (2015). https://doi.org/10.1038/nsmb.3074

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