DBC1 Regulates p53 Stability via Inhibition of CBP-Dependent p53 Polyubiquitination

Abstract

The control of p53 protein stability is critical to its tumor suppressor functions. The CREB binding protein (CBP) transcriptional co-activator co-operates with MDM2 to maintain normally low physiological p53 levels in cells via exclusively cytoplasmic E4 polyubiquitination activity. Using mass spectrometry to identify nuclear and cytoplasmic CBP-interacting proteins that regulate compartmentalized CBP E4 activity, we identified deleted in breast cancer 1 (DBC1) as a stoichiometric CBP-interacting protein that negatively regulates CBP-dependent p53 polyubiquitination, stabilizes p53, and augments p53-dependent apoptosis. TCGA analysis demonstrated that solid tumors often retain wild-type p53 alleles in conjunction with DBC1 loss, supporting the hypothesis that DBC1 is selected for disruption during carcinogenesis as a surrogate for p53 functional loss. Because DBC1 maintains p53 stability in the nucleus, where p53 exerts its tumor-suppressive transcriptional function, replacement of DBC1 functionality in DBC1-deleted tumors might enhance p53 function and chemosensitivity for therapeutic benefit.

Keywords: CBP; DBC1; apoptosis; p53; ubiquitin.

Figure 1.. Identification of CBP-Interacting Proteins in U2OS Cells

(A) Identification of activators and/or inhibitors of CBP E3 activity. (Left) CBP IP from nuclear fractions (lane 1) or cytoplasmic fractions (lanes 2–9), followed by incubation of cytoplasmic CBP IPs with either nuclear lysate (lanes 3–5) or nuclear lysate after CBP immunodepletion (lanes 7–9), followed by in vitro CBP E3 autoubiquitination assay (addition of ubiquitin reaction components ATP, ubiquitin (Ub), E1, and E2 to the washed IP; lanes 1–5 and 7–9) or mock assay (no reaction components, buffer only; lane 6) and immunoblotting of the reaction products with the indicated antibodies. (Right) CBP IP from cytoplasmic fractions (lane 1) or nuclear fractions (lanes 2–9), followed by incubation of nuclear CBP IPs with either cytoplasmic lysate (lanes 3–5) or cytoplasmic lysate after CBP immunodepletion (lanes 7–9), followed by in vitro CBP E3 autoubiquitination assay and immunoblotting of the reaction products with the indicated antibodies. See also Figure S1. (B) CBP IP from cytoplasmic and nuclear fractions of U2OS cells, followed by silver staining (top) or CBP immunoblotting (middle). (Bottom) Immunoblot of cytoplasmic and nuclear fractions for CBP and nuclear (Rb) and cytoplasmic (tubulin) specific markers. (C) Graphical representation of the average total spectra of CBP identified by MudPIT analyses from cytoplasmic and nuclear CBP immunoprecipitations from two separate experiments. (D) Venn diagrams of the number of overlapping and non-overlapping CBP-interacting proteins from cytoplasmic and nuclear CBP IPs identified by MudPIT from two separate experiments (upper) and common to both experiments (lower).

Figure 2.. DBC1 Is a CBP-Interacting Protein

(A) Graphical representation of total spectra of DBC1 identified by MudPIT analysis from cytoplasmic and nuclear CBP IPs from two separate experiments. (B) U2OS cells were transfected with FLAG-tagged CBP and myc-tagged DBC1 for 48 h, followed by FLAG IP (top) of nuclear and cytoplasmic lysates and immunoblotting of IPs using anti-FLAG and anti-myc antibodies. (Bottom) Immunoblotting of nuclear and cytoplasmic lysates used in each IP with indicated antibodies. (C) CBP or DBC1 IPs (top) from cytoplasmic and nuclear fractions of U2OS cells (left) and H1299 cells (right), followed by immunoblotting. (Bottom) Immunoblots of nuclear and cytoplasmic lysates used in each IP. (D) Immunofluorescent staining of U2OS cells using anti-CBP and anti-DBC1 antibodies. Images are representative of three independent experiments. See also Figure S2. (E) Graphical representation of TCGA data showing the percentage of tumors with DBC1 alterations retaining wild-type p53. (F) Graphical representation of TCGA data showing the percentage of human breast, lung, or prostate cancers with DBC1 loss retaining not only wild-type CBP and p53 but also wild-type status of the key p53 regulators MDM2 (non-amplified) and CDKN2A (not deleted).

Figure 3.. DBC1 Interacts with N- and C-Terminal Regions of CBP and Regulates Nuclear CBP E3 Ubiquitin Ligase Activity

(A) Schematic diagram of full-length DBC1, full-length CBP, and deletion mutants of DBC1 and CBP. NLS, nuclear localization signal; NES, nuclear export sequence; CH1, CH2, and CH3, cysteine-histidine regions. (B and C) Plasmids encoding FLAG-tagged full-length CBP, along with myc-tagged full-length DBC1, DBC1 deletion constructs, or vector (B), or myc-tagged full-length DBC1, along with FLAG-tagged full-length CBP, CBP deletion constructs, or vector (C), were transfected into U2OS cells, followed by IPs with anti-FLAG antibody and immunoblotting with anti-FLAG and anti-myc antibodies. Right panels show immunoblotting of lysates. (D) CBP IP from cytoplasmic and nuclear fractions of U2OS cells transfected with control or DBC1 siRNA, followed by in vitro CBP E3 autoubiquitination assay and immunoblotting of ubiquitination reactions. (E) Quantification of CBP autoubiquitination in (D) by densitometry. Error bars represents mean ± SEM from three independent experiments. Right panel shows immunoblotting of lysates used for IPs in (D) with the indicated antibodies.

Figure 4.. DBC1 Depletion Decreases p53 Half-Life in U2OS Cells

(A) U2OS cells treated with 100 μM cycloheximide (Sigma) for up to 90 min were harvested for immunoblotting using anti-p53 antibody. See also Figure S3. (B) Quantification of relative p53 protein level post-cycloheximide treatment. (Left) Error bars represent mean ± SD from three independent experiments. (Right) Derived p53 half-life is displayed in the table. (C) Immunoblotting of lysates from (A). (D) p53 IPs from cytoplasmic and nuclear fractions of U2OS cells treated with control, CBP, DBC1, or CBP-DBC1 siRNA, followed by immunoblotting with anti-p53 and ubiquitin antibodies. (E) Immunoblotting of cytoplasmic and nuclear lysates from (D).

Figure 5.. Re-expression of DBC1 Reduces p53 Polyubiquitination and Stabilizes p53 in DBC1-Depleted Cells

(A and B) p53 IPs from cytoplasmic and nuclear fractions of U2OS cells (A) stably expressing DBC1 shRNA transfected with either empty vector or DBC1(1–470)* or (B) transfected with constructs in (A) and DBC1(698–923), followed by immunoblotting. Cells expressing control shRNA were included in this experiment. (C and D) Immunoblots of U2OS nuclear and cytoplasmic fractions used in (A) and (B), showing (C) DBC1 knockdown, (D) overexpression of DBC1(1–470)*, and overexpression of DBC1(698–923) in DBC1 shRNA-expressing cells. (E and F) U2OS cells stably expressing DBC1 shRNA, transfected with either empty vector or DBC1(1–470)*, were treated with 100 μM cycloheximide for up to 90 min and harvested for subcellular fractionation, followed by immunoblotting of (E) cytoplasm and (F) nuclear fractions with p53, tubulin, and lamin a/c antibodies. (G and H) Quantification of p53 half-life in the cytoplasmic (G) and nuclear (H) fractions from (E) and (F). Error bars represent mean ± SD from three independent experiments. (I and J) Immunoblots of cytoplasmic (I) and nuclear (J) lysates from (E) and (F), showing overexpression of DBC1(1–470)*, in U2OS cells stably expressing DBC1 shRNA.

Figure 6.. Opposing Roles of CBP and DBC1 in Apoptosis

(A) U2OS cells were untreated or treated with 2 μM doxorubicin, followed by p53 IP (left) from cytoplasmic and nuclear lysates, respectively, followed by immunoblotting. Lysates were calibrated for p53 levels by immunoblotting (right) to allow equal levels of p53 in each IP. See also Figures S4A, S4B, and S5. (B) U2OS cells were untreated or treated with 2 μM doxorubicin, 25 μM cisplatin, or 1 μM staurosporine for 6 h, followed by immunoblotting of cytoplasmic and nuclear lysates. See also Figure S4C. (C) CBP IPs from cytoplasmic and nuclear fractions in (B), followed by immunoblotting with CBP and DBC1 antibodies. (D) U2OS cells were untreated or treated with 2 μM doxorubicin or 1 μM staurosporine for 1 and 6 h, followed by qRT-PCR to determine DBC1 mRNA levels. Graph shows DBC1 mRNA levels relative to no treatment control. Error bars represent mean ± SEM from three independent experiments. RNA level was normalized to GAPDH. (E) Immunofluorescence of U2OS cells untreated or treated with 25 μM cisplatin, 2 μM doxorubicin, or 1 μM staurosporine for 6 h and stained with DBC1 antibody. (F) U2OS cells stably expressing control shRNA, CBP shRNA, DBC1 shRNA, or CBP-DBC1 shRNAs were treated with 25 μM cisplatin for 24 h, followed by cell permeabilization, staining with anti-cleaved caspase-3 antibody, and analysis by flow cytometry. Graph shows the percentage of cells with cleaved caspase-3. Error bars represent mean ± SEM from three independent experiments. (G) U2OS cells stably expressing control, CBP, DBC1, or CBP-DBC1 shRNAs were treated with 25 μM cisplatin for 24 h, followed by cell lysis and immunoblotting with the indicated antibodies. See also Figure S6A.

Figure 7.. DBC1 Overexpression Promotes p53-Dependent Apoptosis

(A–C) Representative flow cytometry histograms for apoptosis using U2OS cells (A), MCF-7 cells (B), and MCF-10A cells (C). Analysis of apoptosis by flow cytometry of annexin-PI-stained U2OS, MCF-7, and MCF-10A cells transfected with either empty vector or myc-DBC1 and treated with 25 μM cisplatin. Percentages in the Q2 and Q4 quadrants represent the early and late apoptotic populations, resepctively. See also Figure S6B. (D–F) Quantification of apoptosis measured by flow cytometry from three independent experiments for U2OS cells (D), MCF-7 cells (E), and MCF-10A cells (F) treated as in (A)–(C). Error bars represent mean ± SEM from three independent experiments. (G–H) U2OS cells (G), MCF-7 cells (H), and MCF-10A cells (H) transfected with either empty vector or myc-DBC1 were treated with 25 μM cisplatin, followed by cell lysis and immunoblotting using the indicated antibodies. (I) U2OS cells were treated with either control siRNA or p53 siRNA, followed by transfection with empty vector or full-length myc-DBC1 plasmids. 24 h before lysis, cells were exposed to 25 μM cisplatin. Lysed cells were subjected to immunoblotting using the indicated antibodies.