1
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Pilo CA, Baffi TR, Kornev AP, Kunkel MT, Malfavon M, Chen DH, Rossitto LA, Chen DX, Huang LC, Longman C, Kannan N, Raskind WH, Gonzalez DJ, Taylor SS, Gorrie G, Newton AC. Mutations in protein kinase Cγ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition. Sci Signal 2022; 15:eabk1147. [PMID: 36166510 PMCID: PMC9810342 DOI: 10.1126/scisignal.abk1147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca2+-regulated protein kinase Cγ (PKCγ), leading to Purkinje cell degeneration and progressive cerebellar dysfunction. Most of the identified mutations cluster in the DAG-sensing C1 domains. Here, we found with a FRET-based activity reporter that SCA14-associated PKCγ mutations, including a previously undescribed variant, D115Y, enhanced the basal activity of the kinase by compromising its autoinhibition. Unlike other mutations in PKC that impair its autoinhibition but lead to its degradation, the C1 domain mutations protected PKCγ from such down-regulation. This enhanced basal signaling rewired the brain phosphoproteome, as revealed by phosphoproteomic analysis of cerebella from mice expressing a human SCA14-associated H101Y mutant PKCγ transgene. Mutations that induced a high basal activity in vitro were associated with earlier average age of onset in patients. Furthermore, the extent of disrupted autoinhibition, but not agonist-stimulated activity, correlated with disease severity. Molecular modeling indicated that almost all SCA14 variants not within the C1 domain were located at interfaces with the C1B domain, suggesting that mutations in and proximal to the C1B domain are a susceptibility for SCA14 because they uniquely enhance PKCγ basal activity while protecting the enzyme from down-regulation. These results provide insight into how PKCγ activation is modulated and how deregulation of the cerebellar phosphoproteome by SCA14-associated mutations affects disease progression.
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Affiliation(s)
- Caila A. Pilo
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA 92037, USA
| | - Timothy R. Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Maya T. Kunkel
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mario Malfavon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Dong-Hui Chen
- Department of Neurology, University of Washington Seattle, WA 98195, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA 92037, USA
| | - Daniel X. Chen
- Department of Neurology, University of Washington Seattle, WA 98195, USA
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Cheryl Longman
- Queen Elizabeth University Hospital, Glasgow, Scotland G51 4TF, United Kingdom
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wendy H. Raskind
- Department of Medicine/Medical Genetics, University of Washington Seattle, WA 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington Seattle, WA 98195, USA
- Mental Illness Research, Education and Clinical Center, Department of Veterans Affairs, Seattle, WA 98108, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - George Gorrie
- Queen Elizabeth University Hospital, Glasgow, Scotland G51 4TF, United Kingdom
| | - Alexandra C. Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
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2
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Baffi TR, Newton AC. Protein kinase C: release from quarantine by mTORC2. Trends Biochem Sci 2022; 47:518-530. [DOI: 10.1016/j.tibs.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 01/31/2023]
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3
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Abstract
The family of AGC kinases not only regulate cellular biology by phosphorylating substrates, but are themselves controlled by phosphorylation. Phosphorylation generally occurs at two conserved regions in these kinases: a loop near the entrance to the active site, termed the activation loop, that correctly aligns residues for catalysis, and a C-terminal tail whose phosphorylation at a site termed the hydrophobic motif stabilizes the active conformation. Whereas phosphorylation of the activation loop is well established to be catalyzed by the phosphoinositide-dependent kinase 1 (PDK1), the mechanism of phosphorylation of the C-tail hydrophobic motif has been controversial. For a subset of AGC kinases, which includes most protein kinase C (PKC) isozymes and Akt, phosphorylation of the hydrophobic motif in cells was shown to depend on mTORC2 over 15 years ago, yet whether by direct phosphorylation or by another mechanism has remained elusive. The recent identification of a novel and evolutionarily conserved phosphorylation site on the C-tail termed the TOR-Interaction Motif (TIM) has finally unraveled the mystery of how mTORC2 regulates its client kinases. mTORC2 does not directly phosphorylate the hydrophobic motif, rather it converts kinases such as PKC and Akt into a conformation that can ultimately autophosphorylate at the hydrophobic motif. Identification of the direct mTOR phosphorylation that facilitates auto-regulation of the C-tail hydrophobic motif revises the activation mechanisms of mTOR-regulated AGC kinases. This new twist to an old tail opens avenues for therapeutic intervention. Significance Statement The enzyme mTORC2 has been an enigmatic regulator of AGC kinases such as protein kinase C (PKC) and Akt. The recent discovery of a motif named the TOR Interaction Motif in the C-tail of these kinases solves the mystery: mTORC2 marks these kinases for maturity by, ultimately, facilitating autophosphorylation another C-tail site, the hydrophobic motif.
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4
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Baffi TR, Lordén G, Wozniak JM, Feichtner A, Yeung W, Kornev AP, King CC, Del Rio JC, Limaye AJ, Bogomolovas J, Gould CM, Chen J, Kennedy EJ, Kannan N, Gonzalez DJ, Stefan E, Taylor SS, Newton AC. mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. Sci Signal 2021; 14:eabe4509. [PMID: 33850054 PMCID: PMC8208635 DOI: 10.1126/scisignal.abe4509] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complex mTORC2 is accepted to be the kinase that controls the phosphorylation of the hydrophobic motif, a key regulatory switch for AGC kinases, although whether mTOR directly phosphorylates this motif remains controversial. Here, we identified an mTOR-mediated phosphorylation site that we termed the TOR interaction motif (TIM; F-x3-F-pT), which controls the phosphorylation of the hydrophobic motif of PKC and Akt and the activity of these kinases. The TIM is invariant in mTORC2-dependent AGC kinases, is evolutionarily conserved, and coevolved with mTORC2 components. Mutation of this motif in Akt1 and PKCβII abolished cellular kinase activity by impairing activation loop and hydrophobic motif phosphorylation. mTORC2 directly phosphorylated the PKC TIM in vitro, and this phosphorylation event was detected in mouse brain. Overexpression of PDK1 in mTORC2-deficient cells rescued hydrophobic motif phosphorylation of PKC and Akt by a mechanism dependent on their intrinsic catalytic activity, revealing that mTORC2 facilitates the PDK1 phosphorylation step, which, in turn, enables autophosphorylation. Structural analysis revealed that PKC homodimerization is driven by a TIM-containing helix, and biophysical proximity assays showed that newly synthesized, unphosphorylated PKC dimerizes in cells. Furthermore, disruption of the dimer interface by stapled peptides promoted hydrophobic motif phosphorylation. Our data support a model in which mTORC2 relieves nascent PKC dimerization through TIM phosphorylation, recruiting PDK1 to phosphorylate the activation loop and triggering intramolecular hydrophobic motif autophosphorylation. Identification of TIM phosphorylation and its role in the regulation of PKC provides the basis for AGC kinase regulation by mTORC2.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Charles C King
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jason C Del Rio
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ameya J Limaye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Julius Bogomolovas
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Christine M Gould
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ju Chen
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
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Abstract
Whereas protein kinases have been successfully targeted for a variety of diseases, protein phosphatases remain an underutilized therapeutic target, in part because of incomplete characterization of their effects on signaling networks. The pleckstrin homology domain leucine-rich repeat protein phosphatase (PHLPP) is a relatively new player in the cell signaling field, and new roles in controlling the balance among cell survival, proliferation, and apoptosis are being increasingly identified. Originally characterized for its tumor-suppressive function in deactivating the prosurvival kinase Akt, PHLPP may have an opposing role in promoting survival, as recent evidence suggests. Additionally, identification of the transcription factor STAT1 as a substrate unveils a role for PHLPP as a critical mediator of transcriptional programs in cancer and the inflammatory response. This review summarizes the current knowledge of PHLPP as both a tumor suppressor and an oncogene and highlights emerging functions in regulating gene expression and the immune system. Understanding the context-dependent functions of PHLPP is essential for appropriate therapeutic intervention.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
| | - Ksenya Cohen-Katsenelson
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
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6
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Van AAN, Kunkel MT, Baffi TR, Lordén G, Antal CE, Banerjee S, Newton AC. Protein kinase C fusion proteins are paradoxically loss of function in cancer. J Biol Chem 2021; 296:100445. [PMID: 33617877 PMCID: PMC8008189 DOI: 10.1016/j.jbc.2021.100445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/02/2022] Open
Abstract
Within the AGC kinase superfamily, gene fusions resulting from chromosomal rearrangements have been most frequently described for protein kinase C (PKC), with gene fragments encoding either the C-terminal catalytic domain or the N-terminal regulatory moiety fused to other genes. Kinase fusions that eliminate regulatory domains are typically gain of function and often oncogenic. However, several quality control pathways prevent accumulation of aberrant PKC, suggesting that PKC fusions may paradoxically be loss of function. To explore this topic, we used biochemical, cellular, and genome editing approaches to investigate the function of fusions that retain the portion of the gene encoding either the catalytic domain or regulatory domain of PKC. Overexpression studies revealed that PKC catalytic domain fusions were constitutively active but vulnerable to degradation. Genome editing of endogenous genes to generate a cancer-associated PKC fusion resulted in cells with detectable levels of fusion transcript but no detectable protein. Hence, PKC catalytic domain fusions are paradoxically loss of function as a result of their instability, preventing appreciable accumulation of protein in cells. Overexpression of a PKC regulatory domain fusion suppressed both basal and agonist-induced endogenous PKC activity, acting in a dominant-negative manner by competing for diacylglycerol. For both catalytic and regulatory domain fusions, the PKC component of the fusion proteins mediated the effects of the full-length fusions on the parameters examined, suggesting that the partner protein is dispensable in these contexts. Taken together, our findings reveal that PKC gene fusions are distinct from oncogenic fusions and present a mechanism by which loss of PKC function occurs in cancer.
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Affiliation(s)
- An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Maya T Kunkel
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Corina E Antal
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Sourav Banerjee
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA.
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7
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Van AAN, Kunkel MT, Baffi TR, Antal CE, Newton AC. Protein Kinase C Fusions Reveal Another Mechanism for Loss of Protein Kinase C Function in Cancer. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Van AN, Baffi TR, Kunkel MT, Antal CE, Newton AC. Fusion Gene
TANC2‐PRKCA
Reveals Another Mechanism for Loss of Protein Kinase C Function in Cancer. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.815.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- An‐Angela N. Van
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaCA
| | - Timothy R. Baffi
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaCA
| | - Maya T. Kunkel
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
| | - Corina E. Antal
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaCA
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9
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Baffi TR, Van AAN, Zhao W, Mills GB, Newton AC. Protein Kinase C Quality Control by Phosphatase PHLPP1 Unveils Loss-of-Function Mechanism in Cancer. Mol Cell 2019; 74:378-392.e5. [PMID: 30904392 DOI: 10.1016/j.molcel.2019.02.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/26/2018] [Accepted: 02/12/2019] [Indexed: 02/02/2023]
Abstract
Protein kinase C (PKC) isozymes function as tumor suppressors in increasing contexts. In contrast to oncogenic kinases, whose function is acutely regulated by transient phosphorylation, PKC is constitutively phosphorylated following biosynthesis to yield a stable, autoinhibited enzyme that is reversibly activated by second messengers. Here, we report that the phosphatase PHLPP1 opposes PKC phosphorylation during maturation, leading to the degradation of aberrantly active species that do not become autoinhibited. Cancer-associated hotspot mutations in the pseudosubstrate of PKCβ that impair autoinhibition result in dephosphorylated and unstable enzymes. Protein-level analysis reveals that PKCα is fully phosphorylated at the PHLPP site in over 5,000 patient tumors, with higher PKC levels correlating (1) inversely with PHLPP1 levels and (2) positively with improved survival in pancreatic adenocarcinoma. Thus, PHLPP1 provides a proofreading step that maintains the fidelity of PKC autoinhibition and reveals a prominent loss-of-function mechanism in cancer by suppressing the steady-state levels of PKC.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Wei Zhao
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
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10
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Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. Sci Rep 2018; 8:6518. [PMID: 29695735 PMCID: PMC5916945 DOI: 10.1038/s41598-018-24457-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/23/2018] [Indexed: 11/09/2022] Open
Abstract
Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies. We identify 32 functional domains enriched in cancer variants and PTMs and generate mechanistic hypotheses on overlapping variant and PTM sites by aggregating information at the residue, protein, pathway and species level from these resources. We experimentally test the hypothesis that S768 phosphorylation in the C-helix of EGFR is inhibitory by showing that oncogenic variants altering S768 phosphorylation increase basal EGFR activity. In contrast, oncogenic variants altering conserved phosphorylation sites in the ‘hydrophobic motif’ of PKCβII (S660F and S660C) are loss-of-function in that they reduce kinase activity and enhance membrane translocation. Our studies provide a framework for integrative, consistent, and reproducible annotation of the cancer kinomes.
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Affiliation(s)
- Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Karen E Ross
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Krzysztof J Kochut
- Department of Computer Science, University of Georgia, Athens, GA, 30602, USA
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Peter D'Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY, 10016, USA
| | - Daniel McSkimming
- Genome, Environment, and Microbiome (GEM) Center of Excellence, University at Buffalo, Buffalo, NY, 14203, USA
| | - Cecilia Arighi
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Darren A Natale
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | | | - Pascale Gaudet
- SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Cathy Wu
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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11
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Van AN, Baffi TR, Kunkel MT, Antal CE, Newton AC. Cancer‐Associated Fusions of the Protein Kinase C Kinase Domain are Loss‐of‐Function. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.687.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- An‐Angela N. Van
- PharmacologyU.C. San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramU.C. San DiegoLa JollaCA
| | - Timothy R. Baffi
- PharmacologyU.C. San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramU.C. San DiegoLa JollaCA
| | | | - Corina E. Antal
- PharmacologyU.C. San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramU.C. San DiegoLa JollaCA
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12
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Baffi TR, Gould CM, Wang Z, Gutkind S, Newton AC. mTORC2 Regulates the Maturation of Protein Kinase C by Folding and Phosphorylation. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.687.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Timothy R. Baffi
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramLa JollaCA
| | - Christine M. Gould
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramLa JollaCA
| | - Zhiyong Wang
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Basic ScienceMoores Cancer CenterLa JollaCA
| | - Silvio Gutkind
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Basic ScienceMoores Cancer CenterLa JollaCA
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13
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McSkimming DI, Dastgheib S, Baffi TR, Byrne DP, Ferries S, Scott ST, Newton AC, Eyers CE, Kochut KJ, Eyers PA, Kannan N. KinView: a visual comparative sequence analysis tool for integrated kinome research. Mol Biosyst 2016; 12:3651-3665. [PMID: 27731453 PMCID: PMC5508867 DOI: 10.1039/c6mb00466k] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats.
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Affiliation(s)
| | - Shima Dastgheib
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Steven Thomas Scott
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Krzysztof J Kochut
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. and Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
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