Stabilization of GTSE1 by cyclin D1-CDK4/6-mediated phosphorylation promotes cell proliferation with implications for cancer prognosis

Abstract

In healthy cells, cyclin D1 is expressed during the G1 phase of the cell cycle, where it activates CDK4 and CDK6. Its dysregulation is a well-established oncogenic driver in numerous human cancers. The cancer-related function of cyclin D1 has been primarily studied by focusing on the phosphorylation of the retinoblastoma (RB) gene product. Here, using an integrative approach combining bioinformatic analyses and biochemical experiments, we show that GTSE1 (G-Two and S phases expressed protein 1), a protein positively regulating cell cycle progression, is a previously unrecognized substrate of cyclin D1-CDK4/6 in tumor cells overexpressing cyclin D1 during G1 and subsequent phases. The phosphorylation of GTSE1 mediated by cyclin D1-CDK4/6 inhibits GTSE1 degradation, leading to high levels of GTSE1 across all cell cycle phases. Functionally, the phosphorylation of GTSE1 promotes cellular proliferation and is associated with poor prognosis within a pan-cancer cohort. Our findings provide insights into cyclin D1's role in cell cycle control and oncogenesis beyond RB phosphorylation.

Keywords: CDK4; CDK6; biochemistry; cell proliferation; chemical biology; cullin-RING ligases; cyclin D1; human.

Figure 1.. Identification of GTSE1 as a cyclin D1–CDK4 substrate with prognostic significance in cancer.

(A) Differential proteomic profiling of AMBRA1 knockout (KO) U2OS cells compared to parental U2OS cells (Chaikovsky et al., 2021). Proteins with adjusted p-value <0.05 were ranked by the log2 fold change (Log2FC) to quantify expression changes between AMBRA1 KO and parental cells. The top 30 upregulated proteins in this analysis are presented. Statistical significance was assessed by false discovery rate (FDR). (B) Subset of proteins from (A) containing a canonical CDK phosphorylation consensus motif [S/T*]PX[K/R]. Annotated list of phosphorylated proteins was generated using PhosphoSitePlus database (Hornbeck et al., 2015). (C) Subset of proteins from (B) whose abundance was reverted to basal levels following treatment of AMBRA1 KO U2OS cells with Palbociclib (Chaikovsky et al., 2021) (Log2FC_ambra) with adjusted p-values (adjp_ambra) <0.001 were ranked by log2 fold change (Log2FC) from the original shotgun proteomic analysis (A) to integrate expression changes between AMBRA1 KO and parental cells under Palbociclib-treated versus untreated condition. (D) Kaplan–Meier curves representing the overall survival analysis based on the 50% upper versus lower expression levels of GTSE1. Survival analysis was conducted across various cancer cohorts, including ACC, KIRP, KIRC, LGG, LUAD, MESO, PAAD, and SKCM (see also Figure 1—figure supplement 1). The hazard ratio (HR) was calculated to estimate the relative risk, and significance was assessed using the log-rank test with a threshold of p < 0.05. Curves were generated using the GEPIA2 platform (Tang et al., 2019). (E) Transcriptomic analysis of GTSE1 in various cancer types, contrasting tumor (red) and normal tissue (blue) expression levels, using data derived from The Cancer Genome Atlas (TCGA) (The Cancer Genome Atlas Research Network et al., 2013). Statistical significance assessed by FDR, p < 0.05. (F) Survival map of various cancer types according to the indicated gene expression levels (50% upper and lower expression). Color intensity indicates the log of the HR, with red and blue representing poorer and better survival, respectively. Statistically significant differences in survival are denoted by highlighted contour squares, based on the log-rank test. Generated with GEPIA2 platform (Tang et al., 2019), using TCGA data.

Figure 1—figure supplement 1.. Identification of GTSE1 as a D-type cyclin substrate and Its prognostic significance in cancer.

(A) Schematic of the bioinformatics workflow implemented to identify potential substrates of the D-type cyclins.The process integrates proteomic data from AMBRA1 knockout (KO) U2OS cells versus parental cells (Chaikovsky et al., 2021), protein annotations of the CDK phosphorylation consensus site [S/T*]PX[K/R] from PhosphoSitePlus (Hornbeck et al., 2015), and cancer-related databases. (B) Kaplan–Meier curves representing the overall survival analysis based on the 50% upper versus lower expression levels of GTSE1. Survival analysis was conducted across the indicated cancer cohorts. The hazard ratio (HR) was calculated to estimate the relative risk, and significance was assessed using the log-rank test with a threshold of p < 0.05. Curves were generated using the GEPIA2 platform (Tang et al., 2019).

Figure 2.. Cyclin D1–CDK4 promotes GTSE1 phosphorylation on four serine residues.

(A) Immunoblot analysis following transient transfection of the indicated proteins in HEK293T cells detailing their phosphorylation status via differential mobility in phos-tag gels in the presence or absence of cyclin D1–CDK4 co-expression. (B, C) The indicated purified, recombinant proteins were incubated in the presence or absence of recombinant cyclin D1–CDK4 complex. ERK2 was used as a negative control. Post-incubation, differential phosphorylation was analyzed using phos-tag gels to detect mobility shifts. Immunoblot analysis was conducted to verify the presence of the recombinant proteins as indicated. (D) HEK293T cells transfected with either the indicated Flag-tagged proteins or an empty vector (EV). Cell lysates were subjected to immunoprecipitation followed by immunoblot analysis. Inputs (5%) represent whole-cell extracts before pull down. (E) Schematic representation of candidate CDK phosphorylation sites in GTSE1, as indicated by the PhosphoSitePlus database (Hornbeck et al., 2015). (F) HEK293T cells were transiently transfected with the indicated HA-GTSE1 mutants, in the presence or absence of cyclin D1–CDK4 co-expression. Changes in protein migration were analyzed by phos-tag gels. (G) Immunoblot and phos-tag gel analysis displaying cell cycle synchronization effects following 72 hr of serum starvation in parental T98G cells and AMBRA1 KO T98G cells. Cells were collected at various time points post-serum re-supplementation as indicated, followed by immunoblotting with the indicated antibodies. (H) HA-tagged wild-type GTSE1 (left) or GTSE1 mutated at positions 91, 261, 454, and 724 (Tetra SA) (right) was subjected to co-expression with various cyclins and CDKs, in the presence or absence of the indicated kinase inhibitors to observe the impact on phosphorylation. (I) Box plot showing GTSE1 phosphorylation levels normalized to total GTSE1 protein abundance across a pan-cancer cohort relative to adjacent normal tissue, utilizing data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) (Varadarajan et al., 2020). Statistical significance was assessed using the Wilcoxon rank-sum test, with a p-value threshold of <0.05. (J) Heatmap illustrating differential abundance in cancer of the three GTSE1 phosphorylation sites found in the current study using CPTAC data (Varadarajan et al., 2020). Color intensity reflects the log2-transformed Z-scores of identified GTSE1 phospho-peptides, indicating relative phosphorylation levels across various tumor cohorts compared to adjacent normal tissues. The complete analysis of all phosphorylation sites can be found in Figure 3—figure supplement 1D.

Figure 2—figure supplement 1.. Evolutionary conservation analysis of GTSE1 phosphorylation sites across species.

(A) Phylogenetic conservation of GTSE1 phosphorylation sites across species. Illustration of the evolutionary conservation of phosphorylation sites within the GTSE1 protein. (B) The sequence alignment highlights identical (red) and similar residues (orange) across a range of species, indicating the conserved nature of these phosphorylation sites in GTSE1 orthologs.

Figure 3.. GTSE1 protein is stabilized upon its phosphorylation by cyclin D1–CDK4.

(A) Immunoblot analysis of whole-cell extracts from parental HCT-116 cells, AMBRA1 knockout (KO) HCT-116 cells, and HCT-116 cells expressing either wild-type cyclin D1 or an AMBRA1-insensitive mutant of cyclin D1 (T286A), in the presence or absence of the CDK4/6 inhibitor Palbociclib. (B) Immunoblot analysis of whole-cell extracts from HCT-116 cells harboring an endogenous mini-AID domain fused to AMBRA1 N-terminus. Cells were subjected to either incubation with auxin and doxycycline to induce AMBRA1 degradation or transfection with cyclin D1(T286A) in the presence or absence of Palbociclib. (C) Cycloheximide (CHX) chase assay in HCT-116 cells with mAID-AMBRA1, treated with or without auxin and doxycycline to induce AMBRA1 degradation. Immunoblot analyses were conducted to assess the stability of GTSE1 and other indicated proteins, with the stable protein SKP1 used as a loading control. (D) Protein stability assessment via CHX chase in U2OS parental cells and AMBRA1 KO clones (C11 and G11). The protein levels of AMBRA1, GTSE1, and cyclin D1 were analyzed by immunoblotting, with tubulin serving as a loading control. (E) U2OS cells stably transduced with retroviruses expressing the indicated GTSE1 constructs were subjected to CHX chase assays. Subsequent immunoblotting was conducted for the indicated proteins, with tubulin utilized as a loading control. (F) Densitometric quantification of GTSE1 band intensity from (E) and two identical experiments normalized using tubulin. Initial band intensity at time 0 is set as the 100% reference point. Error bars represent SEM (n = 3 of biological replicates). (G) Time-lapse microscopy images of U2OS cells stably expressing EGFP-tagged the indicated GTSE1 constructs during a CHX chase. The EGFP signal intensity corresponds to GTSE1 levels, while cells are stained with a far-red cell tracker for cell masking. Scale bars indicate 120 μM. (H) Quantitative analysis of EGFP fluorescence intensity from time-lapse experiment shown in (G) plus two identical experiments. The initial fluorescence intensity was normalized to 100% at time zero. Data represent the mean fluorescence intensity from the three independent measurements, with error bars indicating SEM.(I) U2OS cells were treated with various inhibitors for 3 hr before harvest: the proteasome inhibitor MG132, the CRL inhibitor MLN4924, and the V-ATPase inhibitor Bafilomycin A1. Immunoblot analysis of the indicated proteins was performed, with tubulin as a loading control. p62 and LC3 serve as autophagy inhibition controls, while p27 is used as control for CRL- and ubiquitin–proteasome system (UPS)-dependent degradation.

Figure 3—figure supplement 1.. Functional analysis of GTSE1 phosphorylation by cyclin D1-CDK4.

(A) HEK293T cells transfected with the indicated single Ser-to-Ala mutants of HA-tagged GTSE1, with and without cyclin D1–CDK4 co-expression, followed by analysis of their migration pattern on phos-tag gels. (B) Immunoblot analysis displaying cell cycle synchronization effects following 72 hr of serum starvation in parental T98G cells and AMBRA1 KO T98G cells. Cells were collected at various time points post-serum re-supplementation as indicated, followed by immunoblotting with the indicated antibodies. Cyclin A2 and cyclin B1 serve as S phase and G2-M markers, respectively. pH 3 at Ser10 serves as a mitotic marker. GAPDH serves a loading control. (C) HEK293T cells were subjected to transfection with the indicated variants of HA-tagged GTSE1, with and without FFSS–Cyclin D1–CDK4 co-expression. Where indicated, cells were treated with Palbociclib for 4 hr before harvest. Finally, samples were subjected to western blot analysis with the indicated antibodies. (D) Heatmap illustrating differential abundance of GTSE1 phosphorylation in cancer using Clinical Proteomic Tumor Analysis Consortium (CPTAC) data (Varadarajan et al., 2020). Color intensity reflects the log2-transformed Z-scores of identified GTSE1 phospho-peptides, indicating relative phosphorylation levels across various tumor cohorts compared to adjacent normal tissues. (E) HCT mAID FLAG-AMBRA KI cells underwent pull-down using an anti-FLAG antibody versus an IgG sham pull-down. Where indicated, cells were treated with MLN4924 for 3 hr prior to harvesting. Western blot analysis was performed using the specified antibodies to compare the pull-down fraction with the whole-cell extract (WCE). Vinculin serves as WCE loading control.

Figure 4.. Increased cell proliferation upon cyclin D1–CDK4-mediated phosphorylation and stabilization of GTSE1.

(A) Bubble plot derived from Clinical Proteomic Tumor Analysis Consortium (CPTAC) data analysis showing the correlation between the abundance of the bulk phospho-peptides of GTSE1 and the levels of proteins involved in cell proliferation or cell migration across various cancer types. The color intensity of each bubble represents the Spearman correlation coefficient, while the bubble size indicates the negative log10 transformation of the p-values. Bubbles outlined in black indicate statistically significant correlations with q-value <0.0001, adjusted by Benjamini–Hochberg (BH) method. (B) Growth curve analysis comparing the proliferation of U2OS cells stably expressing GFP-tagged wild-type GTSE1, GTSE1 Tetra SA (phospho-deficient), or GTSE1 Tetra SD (phospho-mimetic). GTSE1 Tetra SD cells proliferated significantly more than cells expressing either wild-type GTSE1 or GTSE1 Tetra SA. Statistical significance was determined using unpaired T-tests with p-values <0.05. Error bars represent the mean ± SEM (n = 3 per condition). (C) Proliferation analysis using CellTrace Far Red dye to assess the division of U2OS cells expressing wild-type GTSE1, Tetra SA, and Tetra SD, alongside a comparison between parental and AMBRA knockout (KO) U2OS cells. Following staining, the dye dilutes progressively with each cell division, allowing for the distinction of successive generations by the relative decrease in fluorescence intensity. Fluorescence-activated cell sorting was employed to accurately measure the dye dilution and thereby quantify the discrete populations representing each generation of the cell line. The gating strategy was implemented to identify live, single cells positive for GFP, as detailed in Figure 4—figure supplement 1C. The percentages of cells in each generation are as follows: Parental (Undivided: 1.9%, Gen 1: 28.6%, Gen 2: 55.0%, Gen 3: 14.3%, Gen 4: 0.46%), AMBRA KO (Undivided: 1.2%, Gen 1: 5.8%, Gen 2: 28.77%, Gen 3: 54.0%, Gen 4: 10.8%), WT GTSE1 (Undivided: 1.2%, Gen 1: 21.7%, Gen 2: 56.36%, Gen 3: 20.7%, Gen 4: 0%), Tetra SA GTSE1 (Undivided: 5.4%, Gen 1: 37.8%, Gen 2: 55.5%, Gen 3: 0%, Gen 4: 1.2%), and Tetra SD GTSE1 (Undivided: 2.52%, Gen 1: 12.3%, Gen 2: 45.9%, Gen 3: 33.52%, Gen 4: 4.96%). See additional biological replicates in Figure 4—figure supplement 1D, E.

Figure 4—figure supplement 1.. GTSE1 phosphorylation status influences cell proliferation and cell cycle progression in cancer.

(A) Bubble plot derived from Clinical Proteomic Tumor Analysis Consortium (CPTAC) data depicting the correlation GTSE1 protein abundance with the levels of proteins involved in cell proliferation or cell migration across various cancer types.Data analysis was performed as detailed in Figure 4A. (B) Growth curves comparing the proliferation of AMBRA1 knockout (KO) clones with that of parental U2OS cells, with graphs displaying mean cell counts at each time point, n = 3 biological replicates per clone. Statistical significance was determined using unpaired T-tests with p-values <0.05. Error bars represent SEM. (C) Gating strategy for FACS analysis shown in Figure 4C. The gating strategy was implemented to identify live, single cells positive for GFP. The fourth panel (proliferation analysis) is the same as the first panel in Figure 4C (GTSE1), which is used here to show the gating strategy. (D, E) Independent biological replicates of cell proliferation analysis using CellTrace as shown in Figure 4C. Generation distribution in D: WT GTSE1 (Undivided: 2.6%, Gen 1: 8.5%, Gen 2: 44.0%, Gen 3: 39.7%, Gen 4: 5.4%), Tetra SA GTSE1 (Undivided: 0.1%, Gen 1: 5.5%, Gen 2: 44.5%, Gen 3: 50.0%, Gen 4: 0%), and Tetra SD GTSE1 (Undivided: 1.0%, Gen 1: 4.5%, Gen 2: 40.0%, Gen 3: 34.4%, Gen 4: 20.0%). Generation distribution in E: WT GTSE1 (Undivided: 16.8%, Gen 1: 52.9%, Gen 2: 27.9%, Gen 3: 2.5%, Gen 4: 0.3%), Tetra SA GTSE1 (Undivided: 22.0%, Gen 1: 49.7%, Gen 2: 24.8%, Gen 3: 3.3%, Gen 4: 0%), and Tetra SD GTSE1 (Undivided: 10.0%, Gen 1: 38.0%, Gen 2: 40.0%, Gen 3: 10.1%, Gen 4: 1.5%). (F) Representative cell cycle analysis of U2OS cells expressing wild-type (WT), Tetra SA, and Tetra SD constructs. Cells were pulsed with EdU and stained with propidium iodide (PI) for DNA content assessment. Cell cycle distribution was quantified by FACS using the gating strategy described in panel C. Graph on the right shows the percentage of cells in each phase of the cell cycle: AMBRA Parental (G1: 42.9%, S: 46.2%, G2/M: 10.8%), AMBRA KO (G1: 35.0%, S: 51.7%, G2/M: 13.0%), WT GTSE1 (G1: 45.0%, S: 43.8%, G2/M: 11.2%), Tetra SA GTSE1 (G1: 45.4%, S: 42.2%, G2/M: 11.8%), and Tetra SD GTSE1 (G1: 38.6%, S: 46.6%, G2/M: 14.0%).