FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer

Abstract

The transcription factor FOXM1 contributes to cell cycle progression and is significantly upregulated in basal-like breast cancer (BLBC). Despite its importance in normal and cancer cell cycles, we lack a complete understanding of mechanisms that regulate FOXM1. We identified USP21 in an RNAi-based screen for deubiquitinases that control FOXM1 abundance. USP21 increases the stability of FOXM1, and USP21 binds and deubiquitinates FOXM1 in vivo and in vitro, indicating a direct enzyme-substrate relationship. Depleting USP21 downregulates the FOXM1 transcriptional network and causes a significant delay in cell cycle progression. Significantly, USP21 depletion sensitized BLBC cell lines and mouse xenograft tumors to paclitaxel, an anti-mitotic, frontline therapy in BLBC treatment. USP21 is the most frequently amplified deubiquitinase in BLBC patient tumors, and its amplification co-occurs with the upregulation of FOXM1 protein. Altogether, these data suggest a role for USP21 in the proliferation and potentially treatment of FOXM1-high, USP21-high BLBC.

Keywords: breast cancer; cell cycle; chemotherapy; deubiquitinase; deubiquitination; gene regulation; transcription; ubiquitination.

Figure 1.. USP21 Binds and Regulates FOXM1 Abundance

(A) HeLa cells treated with vehicle or 2.5, 5, or 10 mM PR-619 for 8 h were analyzed by immunoblot (IB). (B) HeLa cells were transfected with a pool of four siRNAs targeting respective DUBs. FOXM1 stability was assessed by IB 72 h after transfection. (C) FOXM1 levels were assessed by IB following transfection of Myc-FOXM1b and FLAG-HA-USP21 in 293T cells 48 h after transfection. (D) FLAG-FOXM1b and Myc-USP21 were co-expressed in 293T cells. Protein complexes were immunopurified with anti-Myc and analyzed by IB. (E) HA-FOXM1b and Myc-USP21 were co-expressed in 293T cells. Lysates were immunopurified with anti-mouse immunoglobulin G (IgG) or anti-HA and analyzed by IB. (F) Endogenous USP21 was immunopurified from HeLa whole-cell lysates and analyzed by IB. (G) Recombinant 6xHIS-FOXM1b was incubated with recombinant GST-USP21. Complexes were captured on glutathione (GSH) agarose beads and analyzed by IB.

Figure 2.. USP21 Protects FOXM1 from Proteasomal Degradation

(A) HeLa cells were transfected with the indicated siRNAs. After 48 h, HeLa cells were treated with 10 μM MG132 or vehicle for 6 h. (B) 293T cells transfected with the indicated plasmids were lysed under denaturing conditions and subjected to Ni-NTA pull-down. The ubiquitination status of FOXM1 in each condition was assessed by IB. (C) Top: 293T cells were transfected with the indicated plasmids. After 48 h, 100 ng/mL of cycloheximide was added to the cells and samples were taken every 4 h for 16 h. Bottom: densitometry analysis performed on corresponding IBs to assess FOXM1 half-life in the indicated conditions.

Figure 3.. USP21 Affects Growth through Modulation of the FOXM1 Transcriptional Network

(A) FOXM1 transcriptional activity was measured by quantifying luciferase activity in 293T cells expressing the 6x-DBE FOXM1 luciferase reporter with and without USP21 overexpression. Error bars represent SEM. (B) Relative abundance of FOXM1 target transcripts was assessed by RT-qPCR following RNA extraction from MDA-MB-231 cells transfected with the indicated siRNA for 72 h. Each condition represents means of triplicates. Error bars represent min-max. *p ≤ 0.05 based on Student’s t test performed on ΔCt values. (C) IB of cells used in (B) showing protein levels of various FOXM1 targets. (D) Mitosis was scored by measuring P-H3-positive cells by flow cytometry in MDA-MB-231 cells transfected with the indicated siRNA or plasmids following release from aphidicolin synchronization at the indicated times. (E) Growth was measured as the percentage of confluence in the dish every 6 h over 120 h in MDA-MB-468 (left) and MDA-MB-231 pINDUCER20 FOXM1b cells (right) treated with the indicated siRNAs (or 10 ng/mL of doxycycline) using the IncuCyte live-cell imaging system. Each point represents mean of triplicates. Error bars represent SEM. **p ≤ 0.01 based on linear regression analysis.

Figure 4.. Amplification of FOXM1 and USP21 Is Linked to Proliferation in BLBC

(A) Top: log2 median FOXM1 expression in TCGA breast cancers compared with proliferation score and subtype. Bottom: log2 median FOXM1 expression and 7 FOXM1 target genes ordered by FOXM1 expression. PAM50 breast cancer subtypes: basal like, red; HER2 enriched, hot pink; luminal A, dark blue; luminal B, light blue; normal like, green. (B) Analysis comparing mRNA overexpression (Z score threshold ± 2) and CNA amplification of 92 DUBs in 482 tumor samples from the TCGA breast invasive carcinoma dataset. (C) FOXM1 and USP21 abundance assessed by IB in a panel of breast cancer cell lines. Breast cancer subtype denoted by color (normal, green; luminal, blue; HER2, pink; BLBC, red). (D) Volcano plot showing protein expression levels in USP21-amplified patient tumors based on RPPA data from the TCGA breast cancer dataset.

Figure 5.. USP21 Knockdown Sensitizes BLBC Cells to Paclitaxel

(A) Relative viability of MDA-MB-231 cells (pINDUCER20 FOXM1b transduced) (top), MDA-MB-468 cells (middle), and SUM149 cells (bottom) treated with the indicated siRNA and exposed to the indicated concentration of paclitaxel (and 10 ng/mL of doxycycline [Dox] in siUSP21 + Dox) for 72 h. Each condition represents mean of triplicates. Error bars represent SEM. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, and ****p ≤ 0.0001 based on two-way ANOVA with post hoc pairwise analysis. IB confirming expression of FOXM1 and USP21 is shown to the right for each corresponding experiment. (B) Quantification of mean tumor volume of SUM149 mouse xenograft for the indicated conditions. For each condition, n = 3. Error bars represent SEM. **p ≤ 0.01 and ***p ≤ 0.001 based on paired t test of respective measurements.