Advertisement

Proteomic Analysis of the Human Cyclin-dependent Kinase Family Reveals a Novel CDK5 Complex Involved in Cell Growth and Migration*

  • Shuangbing Xu
    Footnotes
    Affiliations
    From the Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;

    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Xu Li
    Footnotes
    Affiliations
    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Zihua Gong
    Footnotes
    Affiliations
    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Wenqi Wang
    Affiliations
    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Yujing Li
    Affiliations
    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Binoj Chandrasekharan Nair
    Affiliations
    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Hailong Piao
    Affiliations
    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Kunyu Yang
    Affiliations
    From the Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
    Search for articles by this author
  • Gang Wu
    Affiliations
    From the Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
    Search for articles by this author
  • Junjie Chen
    Correspondence
    To whom correspondence should be addressed: Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 66 (Room Y3.6006), Houston, TX 77030. Tel.: 713-792-4863; Fax: 713-745-6141; [email protected]
    Affiliations
    Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
    Search for articles by this author
  • Author Footnotes
    * This work was in part supported by the NIH/NCI Cancer Center Support Grant P30 CA016672. X.L. is a recipient of a Computational Cancer Biology Training Program Fellowship supported by the Cancer Prevention and Research Institute of Texas and a Jeffrey Lee Cousins Fellowship in Lung Cancer Research. This work was supported in part by the Department of Defense (DOD) Era of Hope research scholar award to J.C. (W81XWH-09–1-0409), and by the NSFC to S.X. (81301719). J.C. is also a recipient of an Era of Hope Scholar award from the Department of Defense (W81XWH-05-1-0470).
    This article contains supplemental Figs. S1 to S5 and Tables S1 to S3.
    ¶ These authors contributed equally to this work.
Open AccessPublished:August 05, 2014DOI:https://doi.org/10.1074/mcp.M113.036699
      Cyclin-dependent kinases (CDKs) are the catalytic subunits of a family of mammalian heterodimeric serine/threonine kinases that play critical roles in the control of cell-cycle progression, transcription, and neuronal functions. However, the functions, substrates, and regulation of many CDKs are poorly understood. To systematically investigate these features of CDKs, we conducted a proteomic analysis of the CDK family and identified their associated protein complexes in two different cell lines using a modified SAINT (Significance Analysis of INTeractome) method. The mass spectrometry data were deposited to ProteomeXchange with identifier PXD000593 and DOI 10.6019/PXD000593. We identified 753 high-confidence candidate interaction proteins (HCIPs) in HEK293T cells and 352 HCIPs in MCF10A cells. We subsequently focused on a neuron-specific CDK, CDK5, and uncovered two novel CDK5-binding partners, KIAA0528 and fibroblast growth factor (acidic) intracellular binding protein (FIBP), in non-neuronal cells. We showed that these three proteins form a stable complex, with KIAA0528 and FIBP being required for the assembly and stability of the complex. Furthermore, CDK5-, KIAA0528-, or FIBP-depleted breast cancer cells displayed impaired proliferation and decreased migration, suggesting that this complex is required for cell growth and migration in non-neural cells. Our study uncovers new aspects of CDK functions, which provide direction for further investigation of these critical protein kinases.
      Cell division is a precisely regulated process that is mainly driven by two classes of molecules, cyclin-dependent kinases (CDKs)
      The abbreviations used are:
      CDKs
      Cyclin-dependent kinases
      SAINT
      Significance Analysis of INTeactome
      HCIP
      high-confidence candidate interacting proteins
      PPI
      protein-protein interaction
      shRNA
      short-hairpin RNA
      SFB
      S tag-Flag tag-SBP
      GO
      gene ontology.
      1The abbreviations used are:CDKs
      Cyclin-dependent kinases
      SAINT
      Significance Analysis of INTeactome
      HCIP
      high-confidence candidate interacting proteins
      PPI
      protein-protein interaction
      shRNA
      short-hairpin RNA
      SFB
      S tag-Flag tag-SBP
      GO
      gene ontology.
      and their activating subunits, cyclins (
      • Morgan D.O.
      Cyclin-dependent kinases: engines, clocks, and microprocessors.
      ,
      • Malumbres M.
      • Barbacid M.
      Mammalian cyclin-dependent kinases.
      ,
      • Satyanarayana A.
      • Kaldis P.
      Mammalian cell-cycle regulation: several Cdks, numerous cyclins and diverse compensatory mechanisms.
      ). Cdks are the catalytic subunits of this large family of heterodimeric serine/threonine protein kinases whose best-characterized members are involved in controlling progression throughout the various cell cycle phases (
      • Malumbres M.
      • Barbacid M.
      Mammalian cyclin-dependent kinases.
      ,
      • Malumbres M.
      • Barbacid M.
      Cell cycle, CDKs and cancer: a changing paradigm.
      ,
      • Johnson N.
      • Shapiro G.I.
      Cyclin-dependent kinases (cdks) and the DNA damage response: rationale for cdk inhibitor-chemotherapy combinations as an anticancer strategy for solid tumors.
      ). According to the latest versions of human and mouse genomes, there are 20 genes encoding CDKs and five additional genes encoding a more distant group of proteins named CDK-like (CDKL1-CDKL5) kinases (
      • Malumbres M.
      • Barbacid M.
      Mammalian cyclin-dependent kinases.
      ,
      • Malumbres M.
      • Harlow E.
      • Hunt T.
      • Hunter T.
      • Lahti J.M.
      • Manning G.
      • Morgan D.O.
      • Tsai L.H.
      • Wolgemuth D.J.
      Cyclin-dependent kinases: a family portrait.
      ). The current CDK family consists of 11 classic CDKs (CDK1–11), two newly proposed family members (CDK12 and 13), and additional proteins whose names are based on the presence of a cyclin-binding element (PFTAIRE proteins, including CDK14 and CDK15; PCTAIRE proteins, including CDK16, CDK17, and CDK18) or on a sequence relationship with the original CDKs, such as CDC2-like kinase (CDK19) or cell cycle-related kinase (CDK20).
      The CDK family has been widely studied in the past two decades and implicated in control of cell-cycle progression, gene transcription, and neuronal functions, which are key events required during development, tissue homeostasis, and tumorigenesis (
      • Malumbres M.
      • Barbacid M.
      Cell cycle kinases in cancer.
      ,
      • Malumbres M.
      Physiological relevance of cell cycle kinases.
      ). In addition, because of their catalytic activities, some CDKs are considered druggable targets, and selective inhibitors for these CDKs are being developed for cancer therapy (
      • Johnson N.
      • Shapiro G.I.
      Cyclin-dependent kinases (cdks) and the DNA damage response: rationale for cdk inhibitor-chemotherapy combinations as an anticancer strategy for solid tumors.
      ). Until now, the studies of some CDKs, such as those focused on CDK1, CDK2, CDK4, and CDK6, have been very extensive; however, the physiological roles of other CDKs and their activating partners remain largely unknown. Therefore, we used a modified tandem affinity purification coupled with mass spectrometry analysis (TAP-MS) approach to conduct a proteomic study of the CDK family, with a goal of understanding the regulations and functions of this critical family of protein kinases. An unexpected finding is the identification of a novel CDK5-containing protein complex in non-neuronal cells.
      Despite the recent recognition that many CDKs may have regulatory functions beyond cell cycle control, CDK5 remains the most unusual member of the CDK family (
      • Dhariwala F.A.
      • Rajadhyaksha M.S.
      An unusual member of the Cdk family: Cdk5.
      ). This is because unlike other CDKs, CDK5 is activated by p35 and p39, two proteins that are expressed only in the brain (
      • Tsai L.H.
      • Delalle I.
      • Caviness Jr., V.S.
      • Chae T.
      • Harlow E.
      p35 is a neural-specific regulatory subunit of cyclin-dependent kinase 5.
      ,
      • Lew J.
      • Huang Q.Q.
      • Qi Z.
      • Winkfein R.J.
      • Aebersold R.
      • Hunt T.
      • Wang J.H.
      A brain-specific activator of cyclin-dependent kinase 5.
      ). CDK5 also binds to d-type and E-type cyclins but does not display kinase activity (
      • Contreras-Vallejos E.
      • Utreras E.
      • Gonzalez-Billault C.
      Going out of the brain: non-nervous system physiological and pathological functions of Cdk5.
      ). Therefore, Cdk5 is often regarded as a neuron-specific kinase, which is not involved in cell cycle control, but instead plays an essential role in neuronal development, including neuronal migration, axon guidance, and synaptic plasticity (
      • Lopes J.P.
      • Agostinho P.
      Cdk5: multitasking between physiological and pathological conditions.
      ,
      • Lalioti V.
      • Pulido D.
      • Sandoval I.V.
      Cdk5, the multifunctional surveyor.
      ,
      • Su S.C.
      • Tsai L.H.
      Cyclin-dependent kinases in brain development and disease.
      ,
      • Feldmann G.
      • Mishra A.
      • Hong S.M.
      • Bisht S.
      • Strock C.J.
      • Ball D.W.
      • Goggins M.
      • Maitra A.
      • Nelkin B.D.
      Inhibiting the cyclin-dependent kinase CDK5 blocks pancreatic cancer formation and progression through the suppression of Ras-Ral signaling.
      ).
      However, CDK5 is ubiquitously expressed. Emerging evidence indicates that CDK5 may have extraneuronal functions that comprise transcript-selective translation control, glucose-inducible insulin secretion, vascular angiogenesis, cell adhesion, migration, and wound healing (
      • Contreras-Vallejos E.
      • Utreras E.
      • Gonzalez-Billault C.
      Going out of the brain: non-nervous system physiological and pathological functions of Cdk5.
      ,
      • Rosales J.L.
      • Lee K.Y.
      Extraneuronal roles of cyclin-dependent kinase 5.
      ,
      • Liebl J.
      • Furst R.
      • Vollmar A.M.
      • Zahler S.
      Twice switched at birth: cell cycle-independent roles of the “neuron-specific” cyclin-dependent kinase 5 (Cdk5) in non-neuronal cells.
      ,
      • Arif A.
      Extraneuronal activities and regulatory mechanisms of the atypical cyclin-dependent kinase Cdk5.
      ). Importantly, CDK5 also plays critical roles in the development and progression of many types of human cancers, which include liver cancer (
      • Selvendiran K.
      • Koga H.
      • Ueno T.
      • Yoshida T.
      • Maeyama M.
      • Torimura T.
      • Yano H.
      • Kojiro M.
      • Sata M.
      Luteolin promotes degradation in signal transducer and activator of transcription 3 in human hepatoma cells: an implication for the antitumor potential of flavonoids.
      ), colorectal cancer (
      • Kim E.
      • Chen F.
      • Wang C.C.
      • Harrison L.E.
      CDK5 is a novel regulatory protein in PPARgamma ligand-induced antiproliferation.
      ), pancreatic cancer (
      • Feldmann G.
      • Mishra A.
      • Hong S.M.
      • Bisht S.
      • Strock C.J.
      • Ball D.W.
      • Goggins M.
      • Maitra A.
      • Nelkin B.D.
      Inhibiting the cyclin-dependent kinase CDK5 blocks pancreatic cancer formation and progression through the suppression of Ras-Ral signaling.
      ,
      • Eggers J.P.
      • Grandgenett P.M.
      • Collisson E.C.
      • Lewallen M.E.
      • Tremayne J.
      • Singh P.K.
      • Swanson B.J.
      • Andersen J.M.
      • Caffrey T.C.
      • High R.R.
      • Ouellette M.
      • Hollingsworth M.A.
      Cyclin-dependent kinase 5 is amplified and overexpressed in pancreatic cancer and activated by mutant K-Ras.
      ), prostate cancer (
      • Strock C.J.
      • Park J.I.
      • Nakakura E.K.
      • Bova G.S.
      • Isaacs J.T.
      • Ball D.W.
      • Nelkin B.D.
      Cyclin-dependent kinase 5 activity controls cell motility and metastatic potential of prostate cancer cells.
      ,
      • Hsu F.N.
      • Chen M.C.
      • Chiang M.C.
      • Lin E.
      • Lee Y.T.
      • Huang P.H.
      • Lee G.S.
      • Lin H.
      Regulation of androgen receptor and prostate cancer growth by cyclin-dependent kinase 5.
      ), and lung cancer (
      • Choi H.S.
      • Lee Y.
      • Park K.H.
      • Sung J.S.
      • Lee J.E.
      • Shin E.S.
      • Ryu J.S.
      • Kim Y.H.
      Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population.
      ,
      • Lockwood W.W.
      • Chari R.
      • Coe B.P.
      • Girard L.
      • Macaulay C.
      • Lam S.
      • Gazdar A.F.
      • Minna J.D.
      • Lam W.L.
      DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers.
      ). Unfortunately, precisely how CDK5 functions outside of neuronal tissues and participates in tumorigenesis is largely unknown.
      Our proteomics study of the CDK family led to the discovery of many novel CDK-associated proteins, expanded the roles of CDKs in multiple biological processes, and established comparable interaction networks in two different cell lines. Specifically for CDK5, we uncovered a novel complex that contains CDK5, a previously uncharacterized protein KIAA0528, and fibroblast growth factor (acidic) intracellular binding protein (FIBP). We provide evidence suggesting that this complex is important for regulating cell growth and migration in breast cancer cells and therefore offer a new mechanism of CDK5 function in non-neuronal tissues.

      DISCUSSION

      In this study, we conducted a proteomic analysis and revealed the extensive PPI network of the CDK family. Based on this study, we uncovered a total of 1105 HCIPs, which greatly broadens our current understanding of the functions of the CDK family and provides directions for future investigation. We merged the data obtained from two different cell lines and generated a more complete CDK family interactomes (Fig. 2). We identified several previously unrecognized CDK sub-networks such as CDK11/12/13, CDK10/15/20, and CDK17/18 networks (Fig. 2 and supplemental Figs. S2 and S3). We also compared the differences between the two cell lines (Fig. 3) and found CDKs bind to very different groups of proteins. The difference in HCIPs obtained from these two cell lines could be caused by multiple reasons, including the technical and biological reasons discussed above in the Result section. The biological differences could be more interesting and may prompt further investigation. The endogenous prey protein expression levels can be very different in different tissues or cell lines. Although CABLES1/2 and KIAA0195 are previously reported CDK5-interacting proteins (Fig. 4A), according to protein atlas database, their RNAs and proteins are undetectable in breast tissues, but relatively high in kidney tissues. This might be the reason that we only recovered them in the CDK5 purification in HEK293T cells, an embryonic kidney cell line, but not in MCF10A cells, which are normal breast epithelial cells. Another difference is that MCF10A is a normal breast epithelial cell line, its cell cycle regulation could be different from that of HEK293T cells, which express SV40 T antigen. For example, CDK2 binds to CCNA1/2, CCNH, CCNJ only in HEK293T cells, and CCND1/3 only in MCF10A cells (Fig. 3C). It is possible that this difference could be caused by the inactivation of both p53 and RB pathways by SV40 T antigen in HEK293T cells, while these cell cycle regulatory pathways are intact in MCF10A cells. Future studies will be needed to elucidate the mechanisms underlying the difference of CDK interactomes in these two cell lines.
      More specifically, we identified a novel complex containing CDK5, KIAA0528, and FIBP, and demonstrated that FIBP and KIAA0528 are required for the complex assembly and stability. Importantly, CDK5-, KIAA0528-, or FIBP-depleted breast cancer cells displayed impaired cell growth and decreased cell migration. Given that CDK5 has already been proposed to act in these processes, it is not surprising that KIAA0528 and FIBP are also required for these functions.
      Cyclin-dependent kinase 5 (CDK5) is a unique member of the CDK family (
      • Dhariwala F.A.
      • Rajadhyaksha M.S.
      An unusual member of the Cdk family: Cdk5.
      ). CDK5 is best known as a neuron-specific kinase, which is largely because of the fact that CDK5 activators p35 and p39 are present only in neuronal cells. Of course, CDK5 also can binds to cyclins, such as cyclin D1/D3/E, but binding to these cyclins does not seem to affect its kinase activity (
      • Xiong Y.
      • Zhang H.
      • Beach D.
      D type cyclins associate with multiple protein kinases and the DNA replication and repair factor PCNA.
      ,
      • Miyajima M.
      • Nornes H.O.
      • Neuman T.
      Cyclin E is expressed in neurons and forms complexes with cdk5.
      ). However, cyclin I can bind to and activate Cdk5 (
      • Brinkkoetter P.T.
      • Olivier P.
      • Wu J.S.
      • Henderson S.
      • Krofft R.D.
      • Pippin J.W.
      • Hockenbery D.
      • Roberts J.M.
      • Shankland S.J.
      Cyclin I activates Cdk5 and regulates expression of Bcl-2 and Bcl-XL in postmitotic mouse cells.
      ), which may be involved in antiapoptotic process via the MAPK signaling pathway. Cyclin E has also been shown to form complexes with Cdk5 and controls synapse function by restraining Cdk5 activity in postmitotic neurons (
      • Odajima J.
      • Wills Z.P.
      • Ndassa Y.M.
      • Terunuma M.
      • Kretschmannova K.
      • Deeb T.Z.
      • Geng Y.
      • Gawrzak S.
      • Quadros I.M.
      • Newman J.
      • Das M.
      • Jecrois M.E.
      • Yu Q.
      • Li N.
      • Bienvenu F.
      • Moss S.J.
      • Greenberg M.E.
      • Marto J.A.
      • Sicinski P.
      Cyclin E constrains Cdk5 activity to regulate synaptic plasticity and memory formation.
      ). In agreement with these prior publications, we identified cyclin I and other known CDK5 binding partners, such as CABLES1, CABLES2, and CCND2 as CDK5-interacting proteins (Fig. 4A), which is consistent with findings from previous reports. Importantly, we identified KIAA0528 and FIBP as the major CDK5-associated proteins in three independent cell lines, indicating that these three proteins form a stable complex in non-neuronal cells. Indeed, a recent high-throughput AP-MS study of 32 human kinases including CDK5 also revealed that KIAA0528 and FIBP are CDK5-interacting proteins (
      • Varjosalo M.
      • Sacco R.
      • Stukalov A.
      • van Drogen A.
      • Planyavsky M.
      • Hauri S.
      • Aebersold R.
      • Bennett K.L.
      • Colinge J.
      • Gstaiger M.
      • Superti-Furga G.
      Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS.
      ). Therefore, it is likely that this CDK5/KIAA0528/FIBP complex may play crucial roles in various cellular processes because of its presence in multiple non-neuronal cell lines.
      Although many researchers focus on CDK5 functions in neuronal development, increasing evidence is supporting extra-neuronal roles of CDK5, especially in tumorigenesis (
      • Contreras-Vallejos E.
      • Utreras E.
      • Gonzalez-Billault C.
      Going out of the brain: non-nervous system physiological and pathological functions of Cdk5.
      ,
      • Rosales J.L.
      • Lee K.Y.
      Extraneuronal roles of cyclin-dependent kinase 5.
      ,
      • Liebl J.
      • Furst R.
      • Vollmar A.M.
      • Zahler S.
      Twice switched at birth: cell cycle-independent roles of the “neuron-specific” cyclin-dependent kinase 5 (Cdk5) in non-neuronal cells.
      ,
      • Arif A.
      Extraneuronal activities and regulatory mechanisms of the atypical cyclin-dependent kinase Cdk5.
      ). CDK5 was reported to be active and control cell growth and metastasis in prostate and pancreatic cancers (
      • Feldmann G.
      • Mishra A.
      • Hong S.M.
      • Bisht S.
      • Strock C.J.
      • Ball D.W.
      • Goggins M.
      • Maitra A.
      • Nelkin B.D.
      Inhibiting the cyclin-dependent kinase CDK5 blocks pancreatic cancer formation and progression through the suppression of Ras-Ral signaling.
      ,
      • Strock C.J.
      • Park J.I.
      • Nakakura E.K.
      • Bova G.S.
      • Isaacs J.T.
      • Ball D.W.
      • Nelkin B.D.
      Cyclin-dependent kinase 5 activity controls cell motility and metastatic potential of prostate cancer cells.
      ). CDK5 was also shown to promote prostate cancer cell growth through androgen receptor (
      • Hsu F.N.
      • Chen M.C.
      • Chiang M.C.
      • Lin E.
      • Lee Y.T.
      • Huang P.H.
      • Lee G.S.
      • Lin H.
      Regulation of androgen receptor and prostate cancer growth by cyclin-dependent kinase 5.
      ). Cdk5-mediated phosphorylation of PIKE-A was proposed to induce glioblastoma cell migration and invasion (
      • Liu R.
      • Tian B.
      • Gearing M.
      • Hunter S.
      • Ye K.
      • Mao Z.
      Cdk5-mediated regulation of the PIKE-A-Akt pathway and glioblastoma cell invasion.
      ). Moreover, Cdk5 inhibition led to retarded cell growth in medullary thyroid carcinoma cells, accompanied by reduced phospho-STAT3 (
      • Lin H.
      • Chen M.C.
      • Chiu C.Y.
      • Song Y.M.
      • Lin S.Y.
      Cdk5 regulates STAT3 activation and cell proliferation in medullary thyroid carcinoma cells.
      ). In agreement with these studies, we demonstrated that CDK5 and its two major binding partners, KIAA0528 and FIBP, are required for breast cancer cell growth and migration, highlighting that this major CDK5-containing protein complex is likely responsible for most, if not all, of the CDK5 functions in non-neuronal cells. Our future studies will focus on elucidating the mechanism of this complex and how it may regulate multiple cellular processes and contribute to tumorigenesis by promoting tumor proliferation and migration.
      In conclusion, our proteomic study of the CDK kinase family led us to establish the first CDK interactomes, which will greatly facilitate future studies of this family of kinases, not only in cell cycle regulations, but also in many other cellular processes. More specifically, involvement of the CDK5 complex in the growth and migration of breast cancer cells suggests that CDK5 may be a promising therapeutic target for cancer therapy, especially for those breast cancers with high levels of CDK5, KIAA0528, and/or FIBP expression.

      Acknowledgments

      We thank all the colleagues in Dr. Chen's laboratory for insightful discussion and technical assistance, especially Jingsong Yuan. We thank Drs. Rudy Guerra, Benjamin White (Department of Statistics, Rice University), Susan Tucker, Nianxiang Zhang, and Shelley Herbrich (Department of Bioinformatics & Computer Biology, MD Anderson Cancer Center) for the bioinformatics discussion and assistance. We also want to thank Drs. Steven Gygi and Ross Tomaino (Taplin Mass Spectrometry Facility, Harvard Medical School) for their help with mass spectrometry analysis and providing raw data for the submission.

      REFERENCES

        • Morgan D.O.
        Cyclin-dependent kinases: engines, clocks, and microprocessors.
        Annu. Rev. Cell Dev. Biol. 1997; 13: 261-291
        • Malumbres M.
        • Barbacid M.
        Mammalian cyclin-dependent kinases.
        Trends Biochem. Sci. 2005; 30: 630-641
        • Satyanarayana A.
        • Kaldis P.
        Mammalian cell-cycle regulation: several Cdks, numerous cyclins and diverse compensatory mechanisms.
        Oncogene. 2009; 28: 2925-2939
        • Malumbres M.
        • Barbacid M.
        Cell cycle, CDKs and cancer: a changing paradigm.
        Nat. Rev. Cancer. 2009; 9: 153-166
        • Johnson N.
        • Shapiro G.I.
        Cyclin-dependent kinases (cdks) and the DNA damage response: rationale for cdk inhibitor-chemotherapy combinations as an anticancer strategy for solid tumors.
        Expert Opin. Ther. Targets. 2010; 14: 1199-1212
        • Malumbres M.
        • Harlow E.
        • Hunt T.
        • Hunter T.
        • Lahti J.M.
        • Manning G.
        • Morgan D.O.
        • Tsai L.H.
        • Wolgemuth D.J.
        Cyclin-dependent kinases: a family portrait.
        Nat. Cell Biol. 2009; 11: 1275-1276
        • Malumbres M.
        • Barbacid M.
        Cell cycle kinases in cancer.
        Curr. Opin. Genet. Dev. 2007; 17: 60-65
        • Malumbres M.
        Physiological relevance of cell cycle kinases.
        Physiol. Rev. 2011; 91: 973-1007
        • Dhariwala F.A.
        • Rajadhyaksha M.S.
        An unusual member of the Cdk family: Cdk5.
        Cell. Mol. Neurobiol. 2008; 28: 351-369
        • Tsai L.H.
        • Delalle I.
        • Caviness Jr., V.S.
        • Chae T.
        • Harlow E.
        p35 is a neural-specific regulatory subunit of cyclin-dependent kinase 5.
        Nature. 1994; 371: 419-423
        • Lew J.
        • Huang Q.Q.
        • Qi Z.
        • Winkfein R.J.
        • Aebersold R.
        • Hunt T.
        • Wang J.H.
        A brain-specific activator of cyclin-dependent kinase 5.
        Nature. 1994; 371: 423-426
        • Contreras-Vallejos E.
        • Utreras E.
        • Gonzalez-Billault C.
        Going out of the brain: non-nervous system physiological and pathological functions of Cdk5.
        Cell Signal. 2012; 24: 44-52
        • Lopes J.P.
        • Agostinho P.
        Cdk5: multitasking between physiological and pathological conditions.
        Prog. Neurobiol. 2011; 94: 49-63
        • Lalioti V.
        • Pulido D.
        • Sandoval I.V.
        Cdk5, the multifunctional surveyor.
        Cell Cycle. 2010; 9: 284-311
        • Su S.C.
        • Tsai L.H.
        Cyclin-dependent kinases in brain development and disease.
        Annu. Rev. Cell Dev. Biol. 2011; 27: 465-491
        • Feldmann G.
        • Mishra A.
        • Hong S.M.
        • Bisht S.
        • Strock C.J.
        • Ball D.W.
        • Goggins M.
        • Maitra A.
        • Nelkin B.D.
        Inhibiting the cyclin-dependent kinase CDK5 blocks pancreatic cancer formation and progression through the suppression of Ras-Ral signaling.
        Cancer Res. 2010; 70: 4460-4469
        • Rosales J.L.
        • Lee K.Y.
        Extraneuronal roles of cyclin-dependent kinase 5.
        Bioessays. 2006; 28: 1023-1034
        • Liebl J.
        • Furst R.
        • Vollmar A.M.
        • Zahler S.
        Twice switched at birth: cell cycle-independent roles of the “neuron-specific” cyclin-dependent kinase 5 (Cdk5) in non-neuronal cells.
        Cell Signal. 2011; 23: 1698-1707
        • Arif A.
        Extraneuronal activities and regulatory mechanisms of the atypical cyclin-dependent kinase Cdk5.
        Biochem. Pharmacol. 2012; 84: 985-993
        • Selvendiran K.
        • Koga H.
        • Ueno T.
        • Yoshida T.
        • Maeyama M.
        • Torimura T.
        • Yano H.
        • Kojiro M.
        • Sata M.
        Luteolin promotes degradation in signal transducer and activator of transcription 3 in human hepatoma cells: an implication for the antitumor potential of flavonoids.
        Cancer Res. 2006; 66: 4826-4834
        • Kim E.
        • Chen F.
        • Wang C.C.
        • Harrison L.E.
        CDK5 is a novel regulatory protein in PPARgamma ligand-induced antiproliferation.
        Int. J. Oncol. 2006; 28: 191-194
        • Eggers J.P.
        • Grandgenett P.M.
        • Collisson E.C.
        • Lewallen M.E.
        • Tremayne J.
        • Singh P.K.
        • Swanson B.J.
        • Andersen J.M.
        • Caffrey T.C.
        • High R.R.
        • Ouellette M.
        • Hollingsworth M.A.
        Cyclin-dependent kinase 5 is amplified and overexpressed in pancreatic cancer and activated by mutant K-Ras.
        Clin. Cancer Res. 2011; 17: 6140-6150
        • Strock C.J.
        • Park J.I.
        • Nakakura E.K.
        • Bova G.S.
        • Isaacs J.T.
        • Ball D.W.
        • Nelkin B.D.
        Cyclin-dependent kinase 5 activity controls cell motility and metastatic potential of prostate cancer cells.
        Cancer Res. 2006; 66: 7509-7515
        • Hsu F.N.
        • Chen M.C.
        • Chiang M.C.
        • Lin E.
        • Lee Y.T.
        • Huang P.H.
        • Lee G.S.
        • Lin H.
        Regulation of androgen receptor and prostate cancer growth by cyclin-dependent kinase 5.
        J. Biol. Chem. 2011; 286: 33141-33149
        • Choi H.S.
        • Lee Y.
        • Park K.H.
        • Sung J.S.
        • Lee J.E.
        • Shin E.S.
        • Ryu J.S.
        • Kim Y.H.
        Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population.
        J. Hum. Genet. 2009; 54: 298-303
        • Lockwood W.W.
        • Chari R.
        • Coe B.P.
        • Girard L.
        • Macaulay C.
        • Lam S.
        • Gazdar A.F.
        • Minna J.D.
        • Lam W.L.
        DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers.
        Oncogene. 2008; 27: 4615-4624
        • Shevchenko A.
        • Wilm M.
        • Vorm O.
        • Mann M.
        Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.
        Anal. Chem. 1996; 68: 850-858
        • Elias J.E.
        • Gygi S.P.
        Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.
        Nat. Methods. 2007; 4: 207-214
        • Vizcaino J.A.
        • Cote R.G.
        • Csordas A.
        • Dianes J.A.
        • Fabregat A.
        • Foster J.M.
        • Griss J.
        • Alpi E.
        • Birim M.
        • Contell J.
        • O'Kelly G.
        • Schoenegger A.
        • Ovelleiro D.
        • Perez-Riverol Y.
        • Reisinger F.
        • Rios D.
        • Wang R.
        • Hermjakob H.
        The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
        Nucleic Acids Res. 2013; 41: D1063-D1069
        • Vizcaino J.A.
        • Deutsch E.W.
        • Wang R.
        • Csordas A.
        • Reisinger F.
        • Rios D.
        • Dianes J.A.
        • Sun Z.
        • Farrah T.
        • Bandeira N.
        • Binz P.A.
        • Xenarios I.
        • Eisenacher M.
        • Mayer G.
        • Gatto L.
        • Campos A.
        • Chalkley R.J.
        • Kraus H.J.
        • Albar J.P.
        • Martinez-Bartolome S.
        • Apweiler R.
        • Omenn G.S.
        • Martens L.
        • Jones A.R.
        • Hermjakob H.
        ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
        Nat. Biotechnol. 2014; 32: 223-226
        • Cote R.G.
        • Griss J.
        • Dianes J.A.
        • Wang R.
        • Wright J.C.
        • van den Toorn H.W.
        • van Breukelen B.
        • Heck A.J.
        • Hulstaert N.
        • Martens L.
        • Reisinger F.
        • Csordas A.
        • Ovelleiro D.
        • Perez-Rivevol Y.
        • Barsnes H.
        • Hermjakob H.
        • Vizcaino J.A.
        The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
        Mol. Cell. Proteomics. 2012; 11: 1682-1689
        • Choi H.
        • Larsen B.
        • Lin Z.Y.
        • Breitkreutz A.
        • Mellacheruvu D.
        • Fermin D.
        • Qin Z.S.
        • Tyers M.
        • Gingras A.C.
        • Nesvizhskii A.I.
        SAINT: probabilistic scoring of affinity purification-mass spectrometry data.
        Nat. Methods. 2011; 8: 70-73
        • Saito R.
        • Smoot M.E.
        • Ono K.
        • Ruscheinski J.
        • Wang P.L.
        • Lotia S.
        • Pico A.R.
        • Bader G.D.
        • Ideker T.
        A travel guide to Cytoscape plugins.
        Nat. Methods. 2012; 9: 1069-1076
        • Smoot M.E.
        • Ono K.
        • Ruscheinski J.
        • Wang P.L.
        • Ideker T.
        Cytoscape 2.8: new features for data integration and network visualization.
        Bioinformatics. 2011; 27: 431-432
        • Chatr-Aryamontri A.
        • Breitkreutz B.J.
        • Heinicke S.
        • Boucher L.
        • Winter A.
        • Stark C.
        • Nixon J.
        • Ramage L.
        • Kolas N.
        • O'Donnell L.
        • Reguly T.
        • Breitkreutz A.
        • Sellam A.
        • Chen D.
        • Chang C.
        • Rust J.
        • Livstone M.
        • Oughtred R.
        • Dolinski K.
        • Tyers M.
        The BioGRID interaction database: 2013 update.
        Nucleic Acids Res. 2013; 41: D816-D823
        • Wang J.
        • Leung J.W.
        • Gong Z.
        • Feng L.
        • Shi X.
        • Chen J.
        PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis.
        J. Biol. Chem. 2013; 288: 3174-3183
        • Wang W.
        • Huang J.
        • Wang X.
        • Yuan J.
        • Li X.
        • Feng L.
        • Park J.I.
        • Chen J.
        PTPN14 is required for the density-dependent control of YAP1.
        Genes Dev. 2012; 26: 1959-1971
        • Wang W.
        • Huang J.
        • Chen J.
        Angiomotin-like proteins associate with and negatively regulate YAP1.
        J. Biol. Chem. 2011; 286: 4364-4370
        • Chen D.
        • Sun Y.
        • Wei Y.
        • Zhang P.
        • Rezaeian A.H.
        • Teruya-Feldstein J.
        • Gupta S.
        • Liang H.
        • Lin H.K.
        • Hung M.C.
        • Ma L.
        LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker.
        Nat. Med. 2012; 18: 1511-1517
        • Choi H.
        • Larsen B.
        • Lin Z.Y.
        • Breitkreutz A.
        • Mellacheruvu D.
        • Fermin D.
        • Qin Z.S.
        • Tyers M.
        • Gingras A.C.
        • Nesvizhskii A.I.
        SAINT: probabilistic scoring of affinity purification-mass spectrometry data.
        Nat. Methods. 2011; 8: 70-73
        • Breitkreutz A.
        • Choi H.
        • Sharom J.R.
        • Boucher L.
        • Neduva V.
        • Larsen B.
        • Lin Z.Y.
        • Breitkreutz B.J.
        • Stark C.
        • Liu G.
        • Ahn J.
        • Dewar-Darch D.
        • Reguly T.
        • Tang X.
        • Almeida R.
        • Qin Z.S.
        • Pawson T.
        • Gingras A.C.
        • Nesvizhskii A.I.
        • Tyers M.
        A global protein kinase and phosphatase interaction network in yeast.
        Science. 2010; 328: 1043-1046
        • Wang W.
        • Li X.
        • Huang J.
        • Feng L.
        • Dolinta K.G.
        • Chen J.
        Defining the protein-protein interaction network of the human Hippo pathway.
        Mol. Cell. Proteomics. 2014; 13: 119-131
        • Mellacheruvu D.
        • Wright Z.
        • Couzens A.L.
        • Lambert J.P.
        • St-Denis N.A.
        • Li T.
        • Miteva Y.V.
        • Hauri S.
        • Sardiu M.E.
        • Low T.Y.
        • Halim V.A.
        • Bagshaw R.D.
        • Hubner N.C.
        • Al-Hakim A.
        • Bouchard A.
        • Faubert D.
        • Fermin D.
        • Dunham W.H.
        • Goudreault M.
        • Lin Z.Y.
        • Badillo B.G.
        • Pawson T.
        • Durocher D.
        • Coulombe B.
        • Aebersold R.
        • Superti-Furga G.
        • Colinge J.
        • Heck A.J.
        • Choi H.
        • Gstaiger M.
        • Mohammed S.
        • Cristea I.M.
        • Bennett K.L.
        • Washburn M.P.
        • Raught B.
        • Ewing R.M.
        • Gingras A.C.
        • Nesvizhskii A.I.
        The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.
        Nat. Methods. 2013; 10: 730-736
        • Choi H.
        • Fermin D.
        • Nesvizhskii A.I.
        Significance analysis of spectral count data in label-free shotgun proteomics.
        Mol. Cell. Proteomics. 2008; 7: 2373-2385
        • Sato S.
        • Tomomori-Sato C.
        • Parmely T.J.
        • Florens L.
        • Zybailov B.
        • Swanson S.K.
        • Banks C.A.
        • Jin J.
        • Cai Y.
        • Washburn M.P.
        • Conaway J.W.
        • Conaway R.C.
        A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology.
        Mol. Cell. 2004; 14: 685-691
        • Chen H.H.
        • Wang Y.C.
        • Fann M.J.
        Identification and characterization of the CDK12/cyclin L1 complex involved in alternative splicing regulation.
        Mol. Cell. Biol. 2006; 26: 2736-2745
        • Chen H.H.
        • Wong Y.H.
        • Geneviere A.M.
        • Fann M.J.
        CDK13/CDC2L5 interacts with L-type cyclins and regulates alternative splicing.
        Biochem. Biophys. Res. Commun. 2007; 354: 735-740
        • Zolotukhin A.S.
        • Uranishi H.
        • Lindtner S.
        • Bear J.
        • Pavlakis G.N.
        • Felber B.K.
        Nuclear export factor RBM15 facilitates the access of DBP5 to mRNA.
        Nucleic Acids Res. 2009; 37: 7151-7162
        • Zhou A.
        • Ou A.C.
        • Cho A.
        • Benz Jr., E.J.
        • Huang S.C.
        Novel splicing factor RBM25 modulates Bcl-x pre-mRNA 5′ splice site selection.
        Mol. Cell. Biol. 2008; 28: 5924-5936
        • Zukerberg L.R.
        • Patrick G.N.
        • Nikolic M.
        • Humbert S.
        • Wu C.L.
        • Lanier L.M.
        • Gertler F.B.
        • Vidal M.
        • Van Etten R.A.
        • Tsai L.H.
        Cables links Cdk5 and c-Abl and facilitates Cdk5 tyrosine phosphorylation, kinase upregulation, and neurite outgrowth.
        Neuron. 2000; 26: 633-646
        • Sato H.
        • Nishimoto I.
        • Matsuoka M.
        ik3–2, a relative to ik3–1/cables, is associated with cdk3, cdk5, and c-abl.
        Biochim. Biophys. Acta. 2002; 1574: 157-163
        • Guidato S.
        • McLoughlin D.M.
        • Grierson A.J.
        • Miller C.C.
        Cyclin D2 interacts with cdk-5 and modulates cellular cdk-5/p35 activity.
        J. Neurochem. 1998; 70: 335-340
        • Brinkkoetter P.T.
        • Olivier P.
        • Wu J.S.
        • Henderson S.
        • Krofft R.D.
        • Pippin J.W.
        • Hockenbery D.
        • Roberts J.M.
        • Shankland S.J.
        Cyclin I activates Cdk5 and regulates expression of Bcl-2 and Bcl-XL in postmitotic mouse cells.
        J. Clin. Invest. 2009; 119: 3089-3101
        • Xie X.
        • Gong Z.
        • Mansuy-Aubert V.
        • Zhou Q.L.
        • Tatulian S.A.
        • Sehrt D.
        • Gnad F.
        • Brill L.M.
        • Motamedchaboki K.
        • Chen Y.
        • Czech M.P.
        • Mann M.
        • Kruger M.
        • Jiang Z.Y.
        C2 domain-containing phosphoprotein CDP138 regulates GLUT4 insertion into the plasma membrane.
        Cell Metab. 2011; 14: 378-389
        • Sadacca L.A.
        • Bruno J.
        • Wen J.
        • Xiong W.
        • McGraw T.E.
        Specialized sorting of GLUT4 and its recruitment to the cell surface are independently regulated by distinct Rabs.
        Mol. Biol. Cell. 2013; 24: 2544-2557
        • Kolpakova E.
        • Wiedlocha A.
        • Stenmark H.
        • Klingenberg O.
        • Falnes P.O.
        • Olsnes S.
        Cloning of an intracellular protein that binds selectively to mitogenic acidic fibroblast growth factor.
        Biochem. J. 1998; 336: 213-222
        • Kolpakova E.
        • Frengen E.
        • Stokke T.
        • Olsnes S.
        Organization, chromosomal localization and promoter analysis of the gene encoding human acidic fibroblast growth factor intracellular binding protein.
        Biochem. J. 2000; 352: 629-635
        • Forde N.
        • Mihm M.
        • Canty M.J.
        • Zielak A.E.
        • Baker P.J.
        • Park S.
        • Lonergan P.
        • Smith G.W.
        • Coussens P.M.
        • Ireland J.J.
        • Evans A.C.
        Differential expression of signal transduction factors in ovarian follicle development: a functional role for betaglycan and FIBP in granulosa cells in cattle.
        Physiol. Genomics. 2008; 33: 193-204
        • Yin J.
        • Sobeck A.
        • Xu C.
        • Meetei A.R.
        • Hoatlin M.
        • Li L.
        • Wang W.
        BLAP75, an essential component of Bloom's syndrome protein complexes that maintain genome integrity.
        EMBO J. 2005; 24: 1465-1476
        • Xiong Y.
        • Zhang H.
        • Beach D.
        D type cyclins associate with multiple protein kinases and the DNA replication and repair factor PCNA.
        Cell. 1992; 71: 505-514
        • Miyajima M.
        • Nornes H.O.
        • Neuman T.
        Cyclin E is expressed in neurons and forms complexes with cdk5.
        Neuroreport. 1995; 6: 1130-1132
        • Odajima J.
        • Wills Z.P.
        • Ndassa Y.M.
        • Terunuma M.
        • Kretschmannova K.
        • Deeb T.Z.
        • Geng Y.
        • Gawrzak S.
        • Quadros I.M.
        • Newman J.
        • Das M.
        • Jecrois M.E.
        • Yu Q.
        • Li N.
        • Bienvenu F.
        • Moss S.J.
        • Greenberg M.E.
        • Marto J.A.
        • Sicinski P.
        Cyclin E constrains Cdk5 activity to regulate synaptic plasticity and memory formation.
        Dev. Cell. 2011; 21: 655-668
        • Varjosalo M.
        • Sacco R.
        • Stukalov A.
        • van Drogen A.
        • Planyavsky M.
        • Hauri S.
        • Aebersold R.
        • Bennett K.L.
        • Colinge J.
        • Gstaiger M.
        • Superti-Furga G.
        Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS.
        Nat. Methods. 2013; 10: 307-314
        • Liu R.
        • Tian B.
        • Gearing M.
        • Hunter S.
        • Ye K.
        • Mao Z.
        Cdk5-mediated regulation of the PIKE-A-Akt pathway and glioblastoma cell invasion.
        Proc. Natl. Acad. Sci. U. S. A. 2008; 105: 7570-7575
        • Lin H.
        • Chen M.C.
        • Chiu C.Y.
        • Song Y.M.
        • Lin S.Y.
        Cdk5 regulates STAT3 activation and cell proliferation in medullary thyroid carcinoma cells.
        J. Biol. Chem. 2007; 282: 2776-2784