Cyclin-dependent Kinase Substrate Research Articles

Differentially Expressed Genes of Human Microvascular Endothelial Cells in Response to Anti-Dengue Virus NS1 Antibodies by Suppression Subtractive Hybridization

It has been previously shown that anti-dengue virus (DENV) nonstructural protein NS1 antibodies could act as autoantibodies that direct against one or more of the host's own proteins, which has potential implications for dengue hemorrhagic fever pathogenesis. In the present study, we have employed suppression subtractive hybridization (SSH) to identify the differentially expressed genes from human microvascular endothelial cells (HMEC-1) in response to anti-dengue virus type 2 NS1 antibodies (anti-DENV2 NS1 Abs). A total of 35 clones from the SSH cDNA library were randomly selected for further analysis using bioinformatics tools after vector screening. After searching for sequence homology in NCBI GenBank database with BLASTN and BLASTX programs, 23 obtained sequences with significant matches (E-values <1×10(-4)) in the SSH library. The predicted genes in the subtracted library include immune response molecules (CD59 antigen preproprotein preproprotein, MURR1), signal transduction molecules (Nuclear casein kinase and cyclin-dependent kinase substrate 1), calcium-binding proteins (S100A6, Annexin A2 isoform 1/2), and cell-membrane component (Yip1 domain family). From these clones, 5 upregulated genes were selected for differential expression profiling by real-time RT-PCR to confirm their upregulated status. The results confirmed their differential upregulation, and thus verified the success of SSHs and the likely involvement of these genes in dengue pathogenesis.

Comprehensive Proteomics Analysis Reveals New Substrates and Regulators of the Fission Yeast Clp1/Cdc14 Phosphatase

The conserved family of Cdc14 phosphatases targets cyclin-dependent kinase substrates in yeast, mediating late mitotic signaling events. To discover substrates and regulators of the Schizosaccharomyces pombe Cdc14 phosphatase Clp1, TAP-tagged Clp1, and a substrate trapping mutant (Clp1-C286S) were purified from asynchronous and mitotic (prometaphase and anaphase) cells and binding partners were identified by 2D-LC-MS/MS. Over 100 Clp1-interacting proteins were consistently identified, over 70 of these were enriched in Clp1-C286S-TAP (potential substrates) and we and others detected Cdk1 phosphorylation sites in over half (44/73) of these potential substrates. According to GO annotations, Clp1-interacting proteins are involved in many essential cellular processes including mitosis, cytokinesis, ribosome biogenesis, transcription, and trafficking among others. We confirmed association and dephosphorylation of multiple candidate substrates, including a key scaffolding component of the septation initiation network called Cdc11, an essential kinase of the conserved morphogenesis-related NDR kinase network named Shk1, and multiple Mlu1-binding factor transcriptional regulators. In addition, we identified Sal3, a nuclear β-importin, as the sole karyopherin required for Clp1 nucleoplasmic shuttling, a key mode of Cdc14 phosphatase regulation. Finally, a handful of proteins were more abundant in wild type Clp1-TAP versus Clp1-C286S-TAP, suggesting that they may directly regulate Clp1 signaling or serve as scaffolding platforms to localize Clp1 activity.

Immunocytochemical studies on the nuclear ubiquitous casein and cyclin-dependent kinases substrate following 5-aminolevulinicacid-mediated photodynamic therapy on MCF-7 cells

Recent data indicates that nuclear ubiquitous casein and cyclin-dependent kinases substrate (NUCKS) may play role in tumor growth. In present study authors examined whether photodynamic therapy with 5-aminolevulinic acid (5-ALA) induces NUCKS expression in breast cancer cell line, MCF-7. In the experiment concentration of 5-ALA was 6.5mM. Excitation wavelength was 630 ± 20 nm, total light dose of light 5 or 10 J/cm(2) and irradiance 60 mW/cm(2) was used. Cells were collected at established time points and Western blot and immunocytochemical studies were performed using antibody against NUCKS. Studies proved strong cytotoxic effects in cells following PDT with 6.5mM of precursor and 10 J/cm(2). Western blot analysis revealed the strongest expression of NUCKS at 7h after PDT. At next time points, 18 and 24h, expression of NUCKS decreased and became similar to that of control group. Further immunocytochemical studies showed very strong expression of NUCKS following PDT with 5-ALA and light irradiation of 5 J/cm(2). Early, at 0 h, that expression was predominantly seen in nuclei, while at 7h expression of NUCKS was observed in disseminated manner within entire cells in both nuclei and cytoplasm, with prevalence of cytoplasmic staining. Authors suggest that NUCKS is involved in cellular responses following PDT, and since parallel induction of NUCKS and proapoptotic marker Bax and inhibition of anti-apoptotic Bcl-2 was observed, this protein might also be involved in induction of apoptosis following PDT.

Abstract 700: Gene expression profiling of cyclin-dependent kinase (CDK) inhibition in cancer cells.

Abstract Cyclin-dependent kinases (CDKs) form complexes with partner cyclins to regulate cell cycle progression and transcription. CDK1, CDK2, CDK4 and CDK6 all regulate cell cycle progression and CDK8 and CDK9 are regulators of transcription. CDK7 is a unique member of this family because it can regulate the cell cycle CDKs as part of the CDK-activating kinase (CAK) and also transcription in conjunction with the TFIIH transcription factor by phosphorylating the COOH-terminal domain of RNA polymerase II (Pol II CTD). A hallmark of cancer is deregulated cell cycle progression and many cancers have abnormal CDK activity which makes CDKs a good target for cancer therapy. Here we show BS-194, a selective and potent CDK inhibitor, which inhibits CDK2, CDK1, CDK5, CDK7 and CDK9 (IC50 = 3, 30, 30, 250 and 90nmol/L, respectively). In vitro cell based assays have shown that BS-194 inhibits the phosphorylation of CDK substrates, Rb and RNA Poll II, down regulation of cyclins A, E and D1 and cell cycle arrest in the S and G2/M phases. BS-194 also has potent anti-proliferative activity in 60 cancer cell lines tested (mean GI50 = 28nmol/L). BS-194 is orally bioavailable and shows potent in vivo tumour growth inhibition of xenograft models of MCF7 and HCT116 cells. We have used BS-194 as a potent inhibitor of CDK activity in HCT116 cells and performed gene microarray analysis to determine novel pathways and identify novel biomarkers associated with CDK inhibition. In summary, the gene microarray has identified genes differentially expressed in response to BS-194 treatment that are primarily involved in cell cycle, apoptosis and transcription pathways. Citation Format: Silvia Ottaviani, Sean Delaney, Hetal Patel, Manikandan Periyasamy, Alexander Bondke, Brian Slafer, Richard Starkey, Sebastian H.B. Kroll, Matthew J. Fuchter, Anthony G.M. Barrett, R. Charles Coombes, Simak Ali. Gene expression profiling of cyclin-dependent kinase (CDK) inhibition in cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 700. doi:10.1158/1538-7445.AM2013-700

Tubulin Polymerization Promoting Protein 1 (Tppp1) Phosphorylation by Rho-associated Coiled-coil Kinase (Rock) and Cyclin-dependent Kinase 1 (Cdk1) Inhibits Microtubule Dynamics to Increase Cell Proliferation

Tubulin polymerization promoting protein 1 (Tppp1) regulates microtubule (MT) dynamics via promoting MT polymerization and inhibiting histone deacetylase 6 (Hdac6) activity to increase MT acetylation. Our results reveal that as a consequence, Tppp1 inhibits cell proliferation by delaying the G1/S-phase and the mitosis to G1-phase transitions. We show that phosphorylation of Tppp1 by Rho-associated coiled-coil kinase (Rock) prevents its Hdac6 inhibitory activity to enable cells to enter S-phase. Whereas, our analysis of the role of Tppp1 during mitosis revealed that inhibition of its MT polymerizing and Hdac6 regulatory activities were necessary for cells to re-enter the G1-phase. During this investigation, we also discovered that Tppp1 is a novel Cyclin B/Cdk1 (cyclin-dependent kinase) substrate and that Cdk phosphorylation of Tppp1 inhibits its MT polymerizing activity. Overall, our results show that dual Rock and Cdk phosphorylation of Tppp1 inhibits its regulation of the cell cycle to increase cell proliferation.

Bioinformatic survey for new physiological substrates of Cyclin-dependent kinase 5

Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase predominantly active in the nervous system where it regulates several processes such as neuronal migration, cytoskeletal dynamics, axonal guidance, and neurotransmission.We constructed a position specific scoring matrix (PSSM) based on a dataset of sites shown to be phosphorylated both in vivo and in vitro by Cdk5. This dataset was curated manually through an exhaustive search of published experimental data. We then used this PSSM to perform a search in the mouse proteome through Scansite, a web-based tool for matching sequence patterns in large databases. Considering a stringent cut-off score of 0.5, we identified 354 new putative sites present in 291 proteins. In order to assess the robustness of our results, ten random subsets (of 80 sites each) of the original dataset were used to construct new PSSMs, which were then used as input for a new Scansite search, leading to the recovery of 81% of the 354 sites by at least 5 PSSMs.In order to reduce the number of false positives in our sequence-based approach, we evaluated which of these predicted sites were phosphorylated in vivo as determined by multiple phosphoproteomics studies carried out through mass spectrometry and available in the PhosphoSitePlus database. This step resulted in a very promising list of 132 putative phosphorylation sites for Cdk5, of which, 51 are specifically phosphorylated in brain tissue, and some are involved in functions regulated by Cdk5 such as axonal growth, synaptic plasticity and neurotransmission. Other phosphorylation sites in our list suggest that Cdk5 might regulate processes through mechanisms not previously recognized such as the control of mRNA splicing.

5′-OH-5-nitro-Indirubin oxime (AGM130), an Indirubin derivative, induces apoptosis of Imatinib-resistant chronic myeloid leukemia cells

Imatinib is a highly effective drug for the treatment of chronic myeloid leukemia (CML) that targets the BCR–ABL kinase. However, a number of patients have CML that is resistant to Imatinib treatment. In this report, we developed AGM130 as a potential therapeutic drug for Imatinib-resistant CML treatment. The AGM130 compound is derived from Indirubin, which is an ingredient of Danggui Longhui Wan and known as a cyclin-dependent kinase (CDK) inhibitor. The water solubility of AGM130 is more enhanced than that of the original form of Indirubin, which has very poor water solubility. Our data showed that the AGM130 compound efficiently decreased the viability of CML-derived K562 cells. Moreover, this compound also efficiently decreased the viability of Imatinib-resistant K562 cells in in vitro and in vivo systems. In addition, like Indirubin, AGM130 also inhibited phosphorylation of retinoblastoma protein (Rb), which is a major substrate of CDK. Conclusively, our data suggest that AGM130 is a strong candidate for treating Imatinib-resistant CML.

Controlling DNA-end resection: a new task for CDKs

DNA double-strand breaks (DSBs) are repaired by two major pathways: homologous recombination (HR) and non-homologous end-joining (NHEJ). The choice between HR and NHEJ is highly regulated during the cell cycle. DNA-end resection, an evolutionarily conserved process that generates long stretches of single-stranded DNA, plays a critical role in pathway choice, as it commits cells to HR, while, at the same time, suppressing NHEJ. As erroneous DSB repair is a major source of genomic instability-driven tumorigenesis, DNA-end resection factors, and in particular their regulation by post-translational modifications, have become the subject of extensive research over the past few years. Recent work has implicated phosphorylation at S/T-P motifs by cyclin-dependent kinases (CDKs) as a major regulatory mechanism of DSB repair. Intriguingly, CDK activity was found to be critically important for the coordinated and timely execution of DNA-end resection, and key players in this process were subsequently identified as CDK substrates. In this mini review, we provide an overview of the current understanding of how the DNA-end resection machinery in yeast and human cells is controlled by CDK-mediated phosphorylation.

Introduction: Current Themes on Cell Cycle and Cancer

Introduction: Current Themes on Cell Cycle and Cancer

BAY 1000394, a Novel Cyclin-Dependent Kinase Inhibitor, with Potent Antitumor Activity in Mono- and in Combination Treatment upon Oral Application

Deregulated activity of cyclin-dependent kinases (CDK) results in loss of cell-cycle checkpoint function and increased expression of antiapoptotic proteins, which has been directly linked to the molecular pathology of cancer. BAY 1000394 inhibits the activity of cell-cycle CDKs CDK1, CDK2, CDK3, CDK4, and of transcriptional CDKs CDK7 and CDK9 with IC(50) values in the range between 5 and 25 nmol/L. Cell proliferation was inhibited at low nanomolar concentration in a broad spectrum of human cancer cell lines. In cell-based assays, the inhibition of phosphorylation of the CDK substrates retinoblastoma protein, nucleophosmin, and RNA polymerase II was shown. Cell-cycle profiles were consistent with inhibition of CDK 1, 2, and 4 as shown in cell-cycle block and release experiments. The physicochemical and pharmacokinetic properties of BAY 1000394 facilitate rapid absorption and moderate oral bioavailability. The compound potently inhibits growth of various human tumor xenografts on athymic mice including models of chemotherapy resistance upon oral dosing. Furthermore, BAY 1000394 shows more than additive efficacy when combined with cisplatin and etoposide. These results suggest that BAY 1000394 is a potent pan-CDK inhibitor and a novel oral cytotoxic agent currently in phase I clinical trials.

Nestin protects mouse podocytes against high glucose‐induced apoptosis by a Cdk5‐dependent mechanism

Podocyte apoptosis contributes to the pathogenesis of diabetic nephropathy (DN). However, the mechanisms that mediate hyperglycemia-induced podocyte apoptosis remain poorly understood. Recent findings indicate that the disruption of the cytoskeleton is related to the podocyte apoptosis. In the present study, we investigated the involvement of nestin, an important cytoskeleton-associated class VI intermediate filament (IF) protein, in the high glucose (HG)-induced podocyte apoptosis. Our data showed that HG decreased the expression level of nestin, either mRNA or protein, in a time-dependent manner in cultured podocytes. Also, through knockdown of nestin expression by miRNA interference, the HG-induced podocyte apoptotic rate was significantly increased. The expression of cleaved caspase-3 was also markedly elevated. Considering that nestin is a substrate of cyclin-dependent kinase 5 (Cdk5), we further assessed the expression of Cdk5 in HG-treated podocytes. The results showed that HG stimulation increased the protein and mRNA expression of Cdk5 in a time-dependent manner in cultured mouse podocytes. The protein activator of Cdk5, p35, was also increased in a time-dependent manner by HG stimulation, and downregulation of Cdk5 by miRNA interference attenuated the nestin reduction in HG-treated podocytes; the HG-induced podocyte apoptosis, the increased cleaved caspase-3 expression and the Bax/Bcl-2 ratio were all effectively attenuated. These data suggested that nestin, which is dependent on Cdk5 regulation, plays a cytoprotective role in HG-induced podocyte apoptosis.

Regulation of N-type Voltage-Gated Calcium Channels and Presynaptic Function by Cyclin-Dependent Kinase 5

N-type voltage-gated calcium channels localize topresynaptic nerve terminals and mediate key eventsincluding synaptogenesis and neurotransmission.While several kinases have been implicated in the modulation of calcium channels, their impact on presynaptic functions remains unclear. Here we report that the N-type calcium channel is a substrate for cyclin-dependent kinase 5 (Cdk5). The pore-forming α(1) subunit of the N-type calcium channel is phosphorylated in the C-terminal domain, and phosphorylation results in enhanced calcium influx due to increased channel open probability. Phosphorylation of the N-type calcium channel by Cdk5 facilitates neurotransmitter release and alters presynaptic plasticity by increasing the number of docked vesicles at the synaptic cleft. These effects are mediated by an altered interaction between N-type calcium channels and RIM1, which tethers presynaptic calcium channels to the active zone. Collectively, our results highlight a molecular mechanism by which N-type calcium channels are regulated by Cdk5 to affect presynaptic function.

CDK2 regulates Foxp3 activity through protein destabilization (123.7)

Abstract Foxp3 is a transcription factor that directs development of the regulatory T cell (Treg) lineage. While the signals that regulate expression of the foxp3 gene are established, it remains unclear how the activity of the Foxp3 protein is controlled. Examination of the primary structure of Foxp3 revealed four putative cyclin-dependent kinase (CDK) substrate motifs: S/T-P. In vitro kinase and mass spectrometry analyses showed that Foxp3 can be phosphorylated on at least three of these motifs by the E-type cyclin-dependent kinase, CDK2. Ser/Ala and Thr/Ala mutations within these motifs (S/T&amp;gt;A, or STAble) resulted in an increase in the stability, measured through a CHX assay, and steady-state level of Foxp3 protein within the cell. Conventional CD4 cells transduced with the STAble mutant of Foxp3 exhibited increased CD25 expression, repression of IL-2, and suppressive function compared to CD4 cells transduced with wild type Foxp3, suggesting that phosphorylation of Foxp3 by CDK2 may negatively regulate its function. Consistent with this, natural Foxp3+ Tregs from mice genetically deficient for CDK2 likewise exhibited a gain of suppressive function compared to wild type Tregs. Based on these data, we hypothesize that mitogenic signaling through CDK2 negatively regulates Foxp3 activity and Treg function through phosphorylation-dependent protein destabilization.

Abstract 3050: Inducing apoptosis in mantle cell lymphoma using inhibitors of cyclin-dependent kinases and the Bcl-2 inhibitor ABT-737

Abstract Mantle cell lymphoma (MCL) is a cyclin D1 over-expressing B cell lymphoma which displays unregulated cell cycle progression driven by increased cyclin-dependent kinase (CDK) activity. We are investigating selective small molecule CDK inhibitors as potential therapeutics in MCL. AZD5438, flavopiridol, PD-0332991 and SNS-032 have distinct efficacies against different groups of CDKs. We hypothesize that inhibiting CDK-7 and -9 will be more effective in causing cell death in MCL than inhibiting CDK-1,-2,-4 and- 6. In Jeko-1 cells, AZD5438 and flavopiridol displayed time- and dose-dependent inhibition of cell proliferation, inhibition of the phosphorylation of CDK substrates, and G1 cell cycle arrest; while PD-0332991 showed a strong cytostatic effect by inhibiting cell proliferation and arresting cells at the G1 phase, but not inducing apoptosis to the same extent as flavopiridol and AZD5438. In addition, AZD5438, flavopiridol and SNS-032 induced caspase-3 activation and down regulation of Mcl-1, but no apoptotic effect was shown in PD-0332991 treated cells. These differential effects may be associated with essential survival functions conferred by genes regulated by CDK7/9 including the pro-survival protein Mcl-1. However, there were no apoptotic effects observed with any of these CDK inhibitors in Granta-519 cells, which may due to high Bcl-2 levels. We are now exploring combinations of CDK7/9 inhibitors with a small molecule inhibitor of Bcl-2 function. We expect CDK7/9 inhibition will reduce Mcl-1 expression at the transcriptional level and thereby sensitize both Jeko-1 and Granta-519 cells to Bcl-2 inhibition. We will also investigate Mcl-1 and Bcl-2 levels in clinical samples to see if there is a correlation with outcomes. Our expectation is that Mcl-1/Bcl-2 levels may ultimately become a useful prognostic and predictive biomarker in MCL. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3050. doi:1538-7445.AM2012-3050

Protein phosphatases and their regulation in the control of mitosis

Cell cycle transitions depend on protein phosphorylation and dephosphorylation. The discovery of cyclin-dependent kinases (CDKs) and their mode of activation by their cyclin partners explained many important aspects of cell cycle control. As the cell cycle is basically a series of recurrences of a defined set of events, protein phosphatases must obviously be as important as kinases. However, our knowledge about phosphatases lags well behind that of kinases. We still do not know which phosphatase(s) is/are truly responsible for dephosphorylating CDK substrates, and we know very little about whether and how protein phosphatases are regulated. Here, we summarize our present understanding of the phosphatases that are important in the control of the cell cycle and pose the questions that need to be answered as regards the regulation of protein phosphatases.

Cdc14-dependent dephosphorylation of Inn1 contributes to Inn1-Cyk3 complex formation

In Saccharomyces cerevisiae the Cdc14 phosphatase plays a well-established role in reverting phosphorylation events on substrates of the mitotic cyclin-dependent kinase (M-Cdk1), thereby promoting mitotic exit and downregulation of M-Cdk1 activity. Cdc14 localizes at the site of cell cleavage after M-Cdk1 inactivation, suggesting that Cdc14 may perform a crucial, yet ill-defined, role during cytokinesis. Here, we identified Inn1, as a novel direct substrate of both M-Cdk1 and Cdc14. Cdc14 colocalizes with Inn1 at the cell division site and interacts with the C-terminal proline-rich domain of Inn1 that mediates its binding to the SH3-domain-containing proteins Hof1 and Cyk3. We show that phosphorylation of Inn1 by Cdk1 partially perturbs the interaction of Inn1 with Cyk3 thereby reducing the levels of Cyk3 at the cell division site. We propose that Cdc14 counteracts Cdk1 phosphorylation of Inn1 to facilitate Inn1-Cyk3 complex formation and so promote cytokinesis.

CR8, a selective and potent CDK inhibitor, provides neuroprotection in experimental traumatic brain injury.

Traumatic brain injury (TBI) induces secondary injury mechanisms, including cell cycle activation (CCA), that leads to neuronal death and neurological dysfunction. We recently reported that delayed administration of roscovitine, a relatively selective cyclin-dependent kinase (CDK) inhibitor, inhibits CCA and attenuates neurodegeneration and functional deficits following controlled cortical impact (CCI) injury in mice. Here we evaluated the neuroprotective potential of CR8, a more potent second-generation roscovitine analog, using the mouse CCI model. Key CCA markers (cyclin A and B1) were significantly up-regulated in the injured cortex following TBI, and phosphorylation of CDK substrates was increased. Central administration of CR8 after TBI, at a dose 20 times less than previously required for roscovitine, attenuated CCA pathways and reduced post-traumatic apoptotic cell death at 24h post-TBI. Central administration of CR8, at 3h after TBI, significantly attenuated sensorimotor and cognitive deficits, decreased lesion volume, and improved neuronal survival in the cortex and dentate gyrus. Moreover, unlike roscovitine treatment in the same model, CR8 also attenuated post-traumatic neurodegeneration in the CA3 region of the hippocampus and thalamus at 21days. Furthermore, delayed systemic administration of CR8, at a dose 10 times less than previously required for roscovitine, significantly improved cognitive performance after CCI. These findings further demonstrate the neuroprotective potential of cell cycle inhibitors following experimental TBI. Given the increased potency and efficacy of CR8 as compared to earlier purine analog types of CDK inhibitors, this drug should be considered as a candidate for future clinical trials of TBI.

Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast.

Eukaryotic chromosomes are replicated from multiple origins that initiate throughout the S-phase of the cell cycle. Why all origins do not fire simultaneously at the beginning of S-phase is not known, but two kinase activities, cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), are continually required throughout the S-phase for all replication initiation events. Here, we show that the two CDK substrates Sld3 and Sld2 and their binding partner Dpb11, together with the DDK subunit Dbf4 are in low abundance in the budding yeast, Saccharomyces cerevisiae. Over-expression of these factors is sufficient to allow late firing origins of replication to initiate early and together with deletion of the histone deacetylase RPD3, promotes the firing of heterochromatic, dormant origins. We demonstrate that the normal programme of origin firing prevents inappropriate checkpoint activation and controls S-phase length in budding yeast. These results explain how the competition for limiting DDK kinase and CDK targets at origins regulates replication initiation kinetics during S-phase and establishes a unique system with which to investigate the biological roles of the temporal programme of origin firing.

Mitotic Exit Control: A Space and Time Odyssey

The mitotic exit network (MEN), a protein kinase cascade under the switch-like control of the small GTPase Tem1, triggers exit from mitosis in budding yeast. Now it emerges that signals from both Tem1 and the yeast Polo kinase Cdc5 converge onto the MEN kinase Cdc15 to accurately restrict MEN activation to late mitosis.

Quantitative phosphoproteomics of transforming growth factor‐β signaling in colon cancer cells

The transforming growth factor-β (TGF-β) signaling pathway progresses through a series of protein phosphorylation regulated steps. Smad4 is a key mediator of the classical TGF-β signaling pathway; however, reports suggest that TGF-β can activate other cellular pathways independent of Smad4. By investigating the TGF-β-regulated phosphoproteome, we aimed to uncover new functions controlled by TGF-β. We applied titanium dioxide to enrich phosphopeptides from stable isotope labeling with amino acids in cell culture (SILAC)-labeled SW480 cells stably expressing Smad4 and profiled them by mass spectrometry. TGF-β stimulation for 30 min resulted in the induction of 17 phosphopeptides and the repression of 8 from a total of 149 unique phosphopeptides. Proteins previously not known to be phosphorylated by TGF-β including programmed cell death protein 4, nuclear ubiquitous casein and cyclin-dependent kinases substrate, hepatoma-derived growth factor and cell division kinases amongst others were induced following TGF-β stimulation, while the phosphorylation of TRAF2 and NCK-interacting protein kinase are examples of proteins whose phosphorylation status was repressed. This phosphoproteomic screen has identified new TGF-β-modulated phosphorylation responses in colon carcinoma cells.