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Lau TT, Ma HT, Poon RY. Kinesins regulate the heterogeneity in centrosome clustering after whole-genome duplication. Life Sci Alliance 2024; 7:e202402670. [PMID: 39074902 PMCID: PMC11287020 DOI: 10.26508/lsa.202402670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 07/31/2024] Open
Abstract
After whole-genome duplication (WGD), tetraploid cells can undergo multipolar mitosis or pseudo-bipolar mitosis with clustered centrosomes. Kinesins play a crucial role in regulating spindle formation. However, the contribution of kinesin expression levels to the heterogeneity in centrosome clustering observed across different cell lines after WGD remains unclear. We identified two subsets of cell lines: "BP" cells efficiently cluster extra centrosomes for pseudo-bipolar mitosis, and "MP" cells primarily undergo multipolar mitosis after WGD. Diploid MP cells contained higher levels of KIF11 and KIF15 compared with BP cells and showed reduced sensitivity to centrosome clustering induced by KIF11 inhibitors. Moreover, partial inhibition of KIF11 or depletion of KIF15 converted MP cells from multipolar to bipolar mitosis after WGD. Multipolar spindle formation involved microtubules but was independent of kinetochore-microtubule attachment. Silencing KIFC1, but not KIFC3, promoted multipolar mitosis in BP cells, indicating the involvement of specific kinesin-14 family members in counteracting the forces from KIF11/KIF15 after WGD. These findings highlight the collective role of KIF11, KIF15, and KIFC1 in determining the polarity of the mitotic spindle after WGD.
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Affiliation(s)
- Thomas Ty Lau
- https://ror.org/00q4vv597 Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Hoi Tang Ma
- Department of Pathology, The University of Hong Kong, Pok Fu Lam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Randy Yc Poon
- https://ror.org/00q4vv597 Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
- https://ror.org/00q4vv597 State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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2
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Zhao H, Cheng X, Yan L, Mi F, Wang W, Hu Y, Liu X, Fan Y, Min Q, Wang Y, Zhang W, Wu Q, Zhan Q. APC/C-regulated CPT1C promotes tumor progression by upregulating the energy supply and accelerating the G1/S transition. Cell Commun Signal 2024; 22:283. [PMID: 38783346 PMCID: PMC11112774 DOI: 10.1186/s12964-024-01657-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND In addition to functioning as a precise monitoring mechanism in cell cycle, the anaphase-promoting complex/cyclosome (APC/C) is reported to be involved in regulating multiple metabolic processes by facilitating the ubiquitin-mediated degradation of key enzymes. Fatty acid oxidation is a metabolic pathway utilized by tumor cells that is crucial for malignant progression; however, its association with APC/C remains to be explored. METHODS Cell cycle synchronization, immunoblotting, and propidium iodide staining were performed to investigate the carnitine palmitoyltransferase 1 C (CPT1C) expression manner. Proximity ligation assay and co-immunoprecipitation were performed to detect interactions between CPT1C and APC/C. Flow cytometry, 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2 H-tetrazolium, inner salt (MTS) assays, cell-scratch assays, and transwell assays and xenograft transplantation assays were performed to investigate the role of CPT1C in tumor progression in vitro and in vivo. Immunohistochemistry was performed on tumor tissue microarray to evaluate the expression levels of CPT1C and explore its potential clinical value. RESULTS We identified CPT1C as a novel APC/C substrate. CPT1C protein levels exhibited cell cycle-dependent fluctuations, peaking at the G1/S boundary. Elevated CPT1C accelerated the G1/S transition, facilitating tumor cell proliferation in vitro and in vivo. Furthermore, CPT1C enhanced fatty acid utilization, upregulated ATP levels, and decreased reactive oxygen species levels, thereby favoring cell survival in a harsh metabolic environment. Clinically, high CPT1C expression correlated with poor survival in patients with esophageal squamous cell carcinoma. CONCLUSIONS Overall, our results revealed a novel interplay between fatty acid utilization and cell cycle machinery in tumor cells. Additionally, CPT1C promoted tumor cell proliferation and survival by augmenting cellular ATP levels and preserving redox homeostasis, particularly under metabolic stress. Therefore, CPT1C could be an independent prognostic indicator in esophageal squamous cell carcinoma.
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Affiliation(s)
- Huihui Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xinxin Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Liping Yan
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Fang Mi
- State Key Laboratory of Molecular Oncology, National Cancer center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wenqing Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yuying Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xingyang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yuyan Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Qingjie Min
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Qingnan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Peking University International Cancer Institute, Beijing, 100142, China.
- Soochow University Cancer Institute, Suzhou, 215000, China.
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3
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Lin X, He Y, Liu Y, Zhou H, Xu X, Xu J, Zhou K. CDK1 promotes the phosphorylation of KIFC1 to regulate the tumorgenicity of endometrial carcinoma. J Gynecol Oncol 2024; 35:35.e68. [PMID: 38456590 DOI: 10.3802/jgo.2024.35.e68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/25/2023] [Accepted: 02/11/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVE This study aims to clarify the mechanical action of cyclin-dependent protein kinase 1 (CDK1) in the development of endometrial carcinoma (EMCA), which may be associated with the phosphorylation of kinesin family member C1 (KIFC1) and further activate the PI3K/AKT pathway. METHODS The protein and gene expression of CDK1 in EMCA tissues and tumor cell lines were evaluated by western blot, quantitative polymerase chain reaction, and immunohistochemistry staining. Next, Cell Counting Kit-8 and colony formation assay detected cell survival and proliferation. Cell migration and invasion were measured by Transwell assay. Cell apoptosis and cell cycle were tested by flow cytometry. Immunofluorescence staining of γH2AX was used to evaluate DNA damage, respectively. Subsequently, a co-immunoprecipitation assay was used to detect the interaction between CDK1 and KIFC1. The phosphorylated protein of KIFC1 and PI3K/AKT was detected by western blot. Finally, the effect of CDK1 on the tumor formation of EMCA was evaluated in a nude mouse xenograft model. RESULTS CDK1 was highly expressed in EMCA tumor cell lines and tissues, which contributed to cell survival, proliferation, invasion, and migration, inhibited cell apoptosis, and induced DNA damage of EMCA cells dependent on the phosphorylation of KIFC1. Moreover, the CDK1-KIFC1 axis further activated PI3K/AKT pathway. Finally, CDK1 knockdown repressed tumor formation of EMCA in vivo. CONCLUSION We report that increased CDK1 promotes tumor progression and identified it as a potential prognostic marker and therapeutic target of EMCA.
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Affiliation(s)
- Xi Lin
- Department of Gynaecology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Yingying He
- Department of Pathology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Yiming Liu
- Department of Pathology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Huihao Zhou
- Department of Gynaecology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Xiaomin Xu
- Department of Gynaecology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Jingui Xu
- Department of Gynaecology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Kening Zhou
- Department of Gynaecology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China.
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Rojas J, Oz T, Jonak K, Lyzak O, Massaad V, Biriuk O, Zachariae W. Spo13/MEIKIN ensures a Two-Division meiosis by preventing the activation of APC/C Ama1 at meiosis I. EMBO J 2023; 42:e114288. [PMID: 37728253 PMCID: PMC10577557 DOI: 10.15252/embj.2023114288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Genome haploidization at meiosis depends on two consecutive nuclear divisions, which are controlled by an oscillatory system consisting of Cdk1-cyclin B and the APC/C bound to the Cdc20 activator. How the oscillator generates exactly two divisions has been unclear. We have studied this question in yeast where exit from meiosis involves accumulation of the APC/C activator Ama1 at meiosis II. We show that inactivation of the meiosis I-specific protein Spo13/MEIKIN results in a single-division meiosis due to premature activation of APC/CAma1 . In the wild type, Spo13 bound to the polo-like kinase Cdc5 prevents Ama1 synthesis at meiosis I by stabilizing the translational repressor Rim4. In addition, Cdc5-Spo13 inhibits the activity of Ama1 by converting the B-type cyclin Clb1 from a substrate to an inhibitor of Ama1. Cdc20-dependent degradation of Spo13 at anaphase I unleashes a feedback loop that increases Ama1's synthesis and activity, leading to irreversible exit from meiosis at the second division. Thus, by repressing the exit machinery at meiosis I, Cdc5-Spo13 ensures that cells undergo two divisions to produce haploid gametes.
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Affiliation(s)
- Julie Rojas
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Tugce Oz
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Katarzyna Jonak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Oleksii Lyzak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Vinal Massaad
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Olha Biriuk
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Wolfgang Zachariae
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
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5
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Hardt R, Dehghani A, Schoor C, Gödderz M, Cengiz Winter N, Ahmadi S, Sharma R, Schork K, Eisenacher M, Gieselmann V, Winter D. Proteomic investigation of neural stem cell to oligodendrocyte precursor cell differentiation reveals phosphorylation-dependent Dclk1 processing. Cell Mol Life Sci 2023; 80:260. [PMID: 37594553 PMCID: PMC10439241 DOI: 10.1007/s00018-023-04892-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Oligodendrocytes are generated via a two-step mechanism from pluripotent neural stem cells (NSCs): after differentiation of NSCs to oligodendrocyte precursor/NG2 cells (OPCs), they further develop into mature oligodendrocytes. The first step of this differentiation process is only incompletely understood. In this study, we utilized the neurosphere assay to investigate NSC to OPC differentiation in a time course-dependent manner by mass spectrometry-based (phospho-) proteomics. We identify doublecortin-like kinase 1 (Dclk1) as one of the most prominently regulated proteins in both datasets, and show that it undergoes a gradual transition between its short/long isoform during NSC to OPC differentiation. This is regulated by phosphorylation of its SP-rich region, resulting in inhibition of proteolytic Dclk1 long cleavage, and therefore Dclk1 short generation. Through interactome analyses of different Dclk1 isoforms by proximity biotinylation, we characterize their individual putative interaction partners and substrates. All data are available via ProteomeXchange with identifier PXD040652.
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Affiliation(s)
- Robert Hardt
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Alireza Dehghani
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | - Carmen Schoor
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Markus Gödderz
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Nur Cengiz Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Institute of Human Genetics, University Hospital Cologne, 50931, Cologne, Germany
| | - Shiva Ahmadi
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Bayer Pharmaceuticals, 42113, Wuppertal, Germany
| | - Ramesh Sharma
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Volkmar Gieselmann
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany.
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6
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Cosper PF, Hrycyniak LCF, Paracha M, Lee DL, Wan J, Jones K, Bice SA, Nickel K, Mallick S, Taylor AM, Kimple RJ, Lambert PF, Weaver BA. HPV16 E6 induces chromosomal instability due to polar chromosomes caused by E6AP-dependent degradation of the mitotic kinesin CENP-E. Proc Natl Acad Sci U S A 2023; 120:e2216700120. [PMID: 36989302 PMCID: PMC10083562 DOI: 10.1073/pnas.2216700120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/20/2023] [Indexed: 03/30/2023] Open
Abstract
Chromosome segregation during mitosis is highly regulated to ensure production of genetically identical progeny. Recurrent mitotic errors cause chromosomal instability (CIN), a hallmark of tumors. The E6 and E7 oncoproteins of high-risk human papillomavirus (HPV), which causes cervical, anal, and head and neck cancers (HNC), cause mitotic defects consistent with CIN in models of anogenital cancers, but this has not been studied in the context of HNC. Here, we show that HPV16 induces a specific type of CIN in patient HNC tumors, patient-derived xenografts, and cell lines, which is due to defects in chromosome congression. These defects are specifically induced by the HPV16 oncogene E6 rather than E7. We show that HPV16 E6 expression causes degradation of the mitotic kinesin CENP-E, whose depletion produces chromosomes that are chronically misaligned near spindle poles (polar chromosomes) and fail to congress. Though the canonical oncogenic role of E6 is the degradation of the tumor suppressor p53, CENP-E degradation and polar chromosomes occur independently of p53. Instead, E6 directs CENP-E degradation in a proteasome-dependent manner via the E6-associated ubiquitin protein ligase E6AP/UBE3A. This study reveals a mechanism by which HPV induces CIN, which may impact HPV-mediated tumor initiation, progression, and therapeutic response.
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Affiliation(s)
- Pippa F. Cosper
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI53705
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI53705
| | - Laura C. F. Hrycyniak
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin-Madison, Madison, WI53705
| | - Maha Paracha
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI53705
| | - Denis L. Lee
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI53705
| | - Jun Wan
- Physiology Graduate Training Program, University of Wisconsin-Madison, Madison, WI53705
| | - Kathryn Jones
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI53705
| | - Sophie A. Bice
- University of Wisconsin School of Medicine and Public Health, Madison, WI53705
| | - Kwangok Nickel
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI53705
| | - Samyukta Mallick
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY10032
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY10032
| | - Alison M. Taylor
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY10032
| | - Randall J. Kimple
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI53705
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI53705
| | - Paul F. Lambert
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI53705
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI53705
| | - Beth A. Weaver
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI53705
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI53705
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI53705
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7
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Guf1 overexpression improves pancreatic β cell functions in type 2 diabetes mellitus rats with Roux-en-Y gastric bypass (RYGB) surgery. J Physiol Biochem 2023:10.1007/s13105-023-00952-6. [PMID: 36905457 DOI: 10.1007/s13105-023-00952-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
The Roux-en-Y gastric bypass (RYGB) is a one-of-a-kind treatment among contemporary bariatric surgical procedures, and its therapeutic effects for type 2 diabetes mellitus (T2DM) are satisfactory. The present study performed isobaric tags for relative and absolute quantification (iTRAQ) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identifying different proteomics between T2DM rats with or without Roux-en-Y gastric bypass (RYGB) surgery, and GTP binding elongation factor GUF1 (Guf1) was first found to be significantly upregulated in rats from the T2DM plus RYGB group. In the cellular lipotoxicity model induced by palmitic acid stimulation of rat pancreatic beta cell line, INS-1, palmitic acid treatment inhibited cell viability, suppressed GSIS, promoted lipid droplet formation, promoted cell apoptosis, and induced mitochondrial membrane potential loss. The effects of palmitic acid on INS-1 cells mentioned above could be partially eliminated by Guf1 overexpression but aggravated by Guf1 knockdown. Last, under palmitic acid treatment, Guf1 overexpression promotes the PI3K/Akt and NF-κB signaling but inhibits the AMPK activation. Guf1 is upregulated in T2DM rats who received RYGB, and Guf1 overexpression improves cell mitochondrial functions, increases cell proliferation, inhibits cell apoptosis, and promotes cell functions in palmitic acid-treated β cells.
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Abdelbaki A, Ascanelli C, Okoye CN, Akman HB, Janson G, Min M, Marcozzi C, Hagting A, Grant R, De Luca M, Asteriti IA, Guarguaglini G, Paiardini A, Lindon C. Revisiting degron motifs in human AURKA required for its targeting by APC/C FZR1. Life Sci Alliance 2023; 6:6/2/e202201372. [PMID: 36450448 PMCID: PMC9713472 DOI: 10.26508/lsa.202201372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
Mitotic kinase Aurora A (AURKA) diverges from other kinases in its multiple active conformations that may explain its interphase roles and the limited efficacy of drugs targeting the kinase pocket. Regulation of AURKA activity by the cell is critically dependent on destruction mediated by the anaphase-promoting complex (APC/CFZR1) during mitotic exit and G1 phase and requires an atypical N-terminal degron in AURKA called the "A-box" in addition to a reported canonical D-box degron in the C-terminus. Here, we find that the reported C-terminal D-box of AURKA does not act as a degron and instead mediates essential structural features of the protein. In living cells, the N-terminal intrinsically disordered region of AURKA containing the A-box is sufficient to confer FZR1-dependent mitotic degradation. Both in silico and in cellulo assays predict the QRVL short linear interacting motif of the A-box to be a phospho-regulated D-box. We propose that degradation of full-length AURKA also depends on an intact C-terminal domain because of critical conformational parameters permissive for both activity and mitotic degradation of AURKA.
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Affiliation(s)
- Ahmed Abdelbaki
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | | | - Cynthia N Okoye
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - H Begum Akman
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Giacomo Janson
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Mingwei Min
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Chiara Marcozzi
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Anja Hagting
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Rhys Grant
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Maria De Luca
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Italia Anna Asteriti
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Sapienza University of Rome, Rome, Italy
| | - Giulia Guarguaglini
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Sapienza University of Rome, Rome, Italy
| | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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9
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Okoye CN, Rowling PJE, Itzhaki LS, Lindon C. Counting Degrons: Lessons From Multivalent Substrates for Targeted Protein Degradation. Front Physiol 2022; 13:913063. [PMID: 35860655 PMCID: PMC9289945 DOI: 10.3389/fphys.2022.913063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
E3s comprise a structurally diverse group of at least 800 members, most of which target multiple substrates through specific and regulated protein-protein interactions. These interactions typically rely on short linear motifs (SLiMs), called "degrons", in an intrinsically disordered region (IDR) of the substrate, with variable rules of engagement governing different E3-docking events. These rules of engagement are of importance to the field of targeted protein degradation (TPD), where substrate ubiquitination and destruction require tools to effectively harness ubiquitin ligases (E3s). Substrates are often found to contain multiple degrons, or multiple copies of a degron, contributing to the affinity and selectivity of the substrate for its E3. One important paradigm for E3-substrate docking is presented by the Anaphase-Promoting Complex/Cyclosome (APC/C), a multi-subunit E3 ligase that targets hundreds of proteins for destruction during mitotic exit. APC/C substrate targeting takes place in an ordered manner thought to depend on tightly regulated interactions of substrates, with docking sites provided by the substoichiometric APC/C substrate adaptors and coactivators, Cdc20 or Cdh1/FZR1. Both structural and functional studies of individual APC/C substrates indicate that productive ubiquitination usually requires more than one degron, and that degrons are of different types docking to distinct sites on the coactivators. However, the dynamic nature of APC/C substrate recruitment, and the influence of multiple degrons, remains poorly understood. Here we review the significance of multiple degrons in a number of E3-substrate interactions that have been studied in detail, illustrating distinct kinetic effects of multivalency and allovalency, before addressing the role of multiple degrons in APC/C substrates, key to understanding ordered substrate destruction by APC/C. Lastly, we consider how lessons learnt from these studies can be applied in the design of TPD tools.
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Affiliation(s)
| | | | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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11
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Zhang Q, Dai X, Wang H, Wang F, Tang D, Jiang C, Zhang X, Guo W, Lei Y, Ma C, Zhang H, Li P, Zhao Y, Wang Z. Transcriptomic Profiling Provides Molecular Insights Into Hydrogen Peroxide-Enhanced Arabidopsis Growth and Its Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:866063. [PMID: 35463436 PMCID: PMC9019583 DOI: 10.3389/fpls.2022.866063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
Salt stress is an important environmental factor limiting plant growth and crop production. Plant adaptation to salt stress can be improved by chemical pretreatment. This study aims to identify whether hydrogen peroxide (H2O2) pretreatment of seedlings affects the stress tolerance of Arabidopsis thaliana seedlings. The results show that pretreatment with H2O2 at appropriate concentrations enhances the salt tolerance ability of Arabidopsis seedlings, as revealed by lower Na+ levels, greater K+ levels, and improved K+/Na+ ratios in leaves. Furthermore, H2O2 pretreatment improves the membrane properties by reducing the relative membrane permeability (RMP) and malonaldehyde (MDA) content in addition to improving the activities of antioxidant enzymes, including superoxide dismutase, and glutathione peroxidase. Our transcription data show that exogenous H2O2 pretreatment leads to the induced expression of cell cycle, redox regulation, and cell wall organization-related genes in Arabidopsis, which may accelerate cell proliferation, enhance tolerance to osmotic stress, maintain the redox balance, and remodel the cell walls of plants in subsequent high-salt environments.
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Affiliation(s)
- Qikun Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiuru Dai
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, China
| | - Huanpeng Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fanhua Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Dongxue Tang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chunyun Jiang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Xiaoyan Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Wenjing Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yuanyuan Lei
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hui Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, China
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zenglan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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12
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Wei YL, Fan XJ, Diao YY, She ZY, Wang XR. Kinesin-14 KIFC1 modulates spindle assembly and chromosome segregation in mouse spermatocytes. Exp Cell Res 2022; 414:113095. [DOI: 10.1016/j.yexcr.2022.113095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/04/2022]
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13
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Esfandiari Nazzaro E, Sabei FY, Vogel WK, Nazari M, Nicholson KS, Gafken PR, Taratula O, Taratula O, Davare MA, Leid M. Discovery and Validation of a Compound to Target Ewing's Sarcoma. Pharmaceutics 2021; 13:pharmaceutics13101553. [PMID: 34683845 PMCID: PMC8538197 DOI: 10.3390/pharmaceutics13101553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Ewing’s sarcoma, characterized by pathognomonic t (11; 22) (q24; q12) and related chromosomal ETS family translocations, is a rare aggressive cancer of bone and soft tissue. Current protocols that include cytotoxic chemotherapeutic agents effectively treat localized disease; however, these aggressive therapies may result in treatment-related morbidities including second-site cancers in survivors. Moreover, the five-year survival rate in patients with relapsed, recurrent, or metastatic disease is less than 30%, despite intensive therapy with these cytotoxic agents. By using high-throughput phenotypic screening of small molecule libraries, we identified a previously uncharacterized compound (ML111) that inhibited in vitro proliferation of six established Ewing’s sarcoma cell lines with nanomolar potency. Proteomic studies show that ML111 treatment induced prometaphase arrest followed by rapid caspase-dependent apoptotic cell death in Ewing’s sarcoma cell lines. ML111, delivered via methoxypoly(ethylene glycol)-polycaprolactone copolymer nanoparticles, induced dose-dependent inhibition of Ewing’s sarcoma tumor growth in a murine xenograft model and invoked prometaphase arrest in vivo, consistent with in vitro data. These results suggest that ML111 represents a promising new drug lead for further preclinical studies and is a potential clinical development for the treatment of Ewing’s sarcoma.
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Affiliation(s)
- Ellie Esfandiari Nazzaro
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Fahad Y. Sabei
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan 88723, Saudi Arabia
| | - Walter K. Vogel
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Mohamad Nazari
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Katelyn S. Nicholson
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Philip R. Gafken
- Proteomics & Metabolomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Olena Taratula
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
| | - Oleh Taratula
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Correspondence: (O.T.); (M.A.D.)
| | - Monika A. Davare
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA;
- Papé Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Correspondence: (O.T.); (M.A.D.)
| | - Mark Leid
- Departments of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; (E.E.N.); (F.Y.S.); (W.K.V.); (M.N.); (O.T.); (M.L.)
- Department of Integrative Biosciences, Oregon Health & Science University, Portland, OR 97239, USA
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14
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Schweiggert J, Habeck G, Hess S, Mikus F, Beloshistov R, Meese K, Hata S, Knobeloch K, Melchior F. SCF Fbxw5 targets kinesin-13 proteins to facilitate ciliogenesis. EMBO J 2021; 40:e107735. [PMID: 34368969 PMCID: PMC8441365 DOI: 10.15252/embj.2021107735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022] Open
Abstract
Microtubule depolymerases of the kinesin-13 family play important roles in various cellular processes and are frequently overexpressed in different cancer types. Despite the importance of their correct abundance, remarkably little is known about how their levels are regulated in cells. Using comprehensive screening on protein microarrays, we identified 161 candidate substrates of the multi-subunit ubiquitin E3 ligase SCFFbxw5 , including the kinesin-13 member Kif2c/MCAK. In vitro reconstitution assays demonstrate that MCAK and its closely related orthologs Kif2a and Kif2b become efficiently polyubiquitylated by neddylated SCFFbxw5 and Cdc34, without requiring preceding modifications. In cells, SCFFbxw5 targets MCAK for proteasomal degradation predominantly during G2 . While this seems largely dispensable for mitotic progression, loss of Fbxw5 leads to increased MCAK levels at basal bodies and impairs ciliogenesis in the following G1 /G0 , which can be rescued by concomitant knockdown of MCAK, Kif2a or Kif2b. We thus propose a novel regulatory event of ciliogenesis that begins already within the G2 phase of the preceding cell cycle.
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Affiliation(s)
- Jörg Schweiggert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Gregor Habeck
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Sandra Hess
- Institute of NeuropathologyFaculty of MedicineUniversity of FreiburgFreiburgGermany
- Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Felix Mikus
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Roman Beloshistov
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Klaus Meese
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Shoji Hata
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | | | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
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15
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Fan G, Sun L, Meng L, Hu C, Wang X, Shi Z, Hu C, Han Y, Yang Q, Cao L, Zhang X, Zhang Y, Song X, Xia S, He B, Zhang S, Wang C. The ATM and ATR kinases regulate centrosome clustering and tumor recurrence by targeting KIFC1 phosphorylation. Nat Commun 2021; 12:20. [PMID: 33397932 PMCID: PMC7782532 DOI: 10.1038/s41467-020-20208-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 11/18/2020] [Indexed: 12/31/2022] Open
Abstract
Drug resistance and tumor recurrence are major challenges in cancer treatment. Cancer cells often display centrosome amplification. To maintain survival, cancer cells achieve bipolar division by clustering supernumerary centrosomes. Targeting centrosome clustering is therefore considered a promising therapeutic strategy. However, the regulatory mechanisms of centrosome clustering remain unclear. Here we report that KIFC1, a centrosome clustering regulator, is positively associated with tumor recurrence. Under DNA damaging treatments, the ATM and ATR kinases phosphorylate KIFC1 at Ser26 to selectively maintain the survival of cancer cells with amplified centrosomes via centrosome clustering, leading to drug resistance and tumor recurrence. Inhibition of KIFC1 phosphorylation represses centrosome clustering and tumor recurrence. This study identified KIFC1 as a prognostic tumor recurrence marker, and revealed that tumors can acquire therapeutic resistance and recurrence via triggering centrosome clustering under DNA damage stresses, suggesting that blocking KIFC1 phosphorylation may open a new vista for cancer therapy.
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Affiliation(s)
- Guangjian Fan
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Lianhui Sun
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Ling Meng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Shandong First Medical University, 271000, Shandong, China
| | - Chen Hu
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Xing Wang
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Zhan Shi
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Congli Hu
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Yang Han
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Qingqing Yang
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Liu Cao
- Key Laboratory of Medical Cell Biology, College of Translational Medicine, China Medical University, 110000, Shenyang, China
| | - Xiaohong Zhang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R., Detroit, MI, 48201, USA
| | - Yan Zhang
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Xianmin Song
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Shujie Xia
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine; Institute of Urology, Shanghai Jiao Tong University, 200080, Shanghai, China
| | - Baokun He
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China
| | - Shengping Zhang
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China.
| | - Chuangui Wang
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620, Shanghai, China.
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16
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In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators. PLoS Biol 2020; 18:e3000975. [PMID: 33306668 PMCID: PMC7758050 DOI: 10.1371/journal.pbio.3000975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 12/23/2020] [Accepted: 11/05/2020] [Indexed: 01/07/2023] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and critical regulator of cell cycle progression. Despite its vital role, it has remained challenging to globally map APC/C substrates. By combining orthogonal features of known substrates, we predicted APC/C substrates in silico. This analysis identified many known substrates and suggested numerous candidates. Unexpectedly, chromatin regulatory proteins are enriched among putative substrates, and we show experimentally that several chromatin proteins bind APC/C, oscillate during the cell cycle, and are degraded following APC/C activation, consistent with being direct APC/C substrates. Additional analysis revealed detailed mechanisms of ubiquitylation for UHRF1, a key chromatin regulator involved in histone ubiquitylation and DNA methylation maintenance. Disrupting UHRF1 degradation at mitotic exit accelerates G1-phase cell cycle progression and perturbs global DNA methylation patterning in the genome. We conclude that APC/C coordinates crosstalk between cell cycle and chromatin regulatory proteins. This has potential consequences in normal cell physiology, where the chromatin environment changes depending on proliferative state, as well as in disease.
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17
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Schlaffner CN, Kahnert K, Muntel J, Chauhan R, Renard BY, Steen JA, Steen H. FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data. eLife 2020; 9:e58783. [PMID: 33284109 PMCID: PMC7721442 DOI: 10.7554/elife.58783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.
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Affiliation(s)
- Christoph N Schlaffner
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Konstantin Kahnert
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Bioinformatics Unit (MF1), Robert Koch InstituteBerlinGermany
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Jan Muntel
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
| | - Ruchi Chauhan
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Robert Koch InstituteBerlinGermany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of PotsdamPotsdamGermany
| | - Judith A Steen
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Hanno Steen
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
- Precision Vaccines Program, Boston Children’s HospitalBostonUnited States
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18
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Tau PTM Profiles Identify Patient Heterogeneity and Stages of Alzheimer's Disease. Cell 2020; 183:1699-1713.e13. [PMID: 33188775 DOI: 10.1016/j.cell.2020.10.029] [Citation(s) in RCA: 333] [Impact Index Per Article: 83.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/27/2020] [Accepted: 10/16/2020] [Indexed: 01/06/2023]
Abstract
To elucidate the role of Tau isoforms and post-translational modification (PTM) stoichiometry in Alzheimer's disease (AD), we generated a high-resolution quantitative proteomics map of 95 PTMs on multiple isoforms of Tau isolated from postmortem human tissue from 49 AD and 42 control subjects. Although Tau PTM maps reveal heterogeneity across subjects, a subset of PTMs display high occupancy and frequency for AD, suggesting importance in disease. Unsupervised analyses indicate that PTMs occur in an ordered manner, leading to Tau aggregation. The processive addition and minimal set of PTMs associated with seeding activity was further defined by analysis of size-fractionated Tau. To summarize, features in the Tau protein critical for disease intervention at different stages of disease are identified, including enrichment of 0N and 4R isoforms, underrepresentation of the C terminus, an increase in negative charge in the proline-rich region (PRR), and a decrease in positive charge in the microtubule binding domain (MBD).
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19
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Manohar S, Yu Q, Gygi SP, King RW. The Insulin Receptor Adaptor IRS2 is an APC/C Substrate That Promotes Cell Cycle Protein Expression and a Robust Spindle Assembly Checkpoint. Mol Cell Proteomics 2020; 19:1450-1467. [PMID: 32554797 PMCID: PMC8143631 DOI: 10.1074/mcp.ra120.002069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/01/2020] [Indexed: 01/21/2023] Open
Abstract
Insulin receptor substrate 2 (IRS2) is an essential adaptor that mediates signaling downstream of the insulin receptor and other receptor tyrosine kinases. Transduction through IRS2-dependent pathways is important for coordinating metabolic homeostasis, and dysregulation of IRS2 causes systemic insulin signaling defects. Despite the importance of maintaining proper IRS2 abundance, little is known about what factors mediate its protein stability. We conducted an unbiased proteomic screen to uncover novel substrates of the Anaphase Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that controls the abundance of key cell cycle regulators. We found that IRS2 levels are regulated by APC/C activity and that IRS2 is a direct APC/C target in G1 Consistent with the APC/C's role in degrading cell cycle regulators, quantitative proteomic analysis of IRS2-null cells revealed a deficiency in proteins involved in cell cycle progression. We further show that cells lacking IRS2 display a weakened spindle assembly checkpoint in cells treated with microtubule inhibitors. Together, these findings reveal a new pathway for IRS2 turnover and indicate that IRS2 is a component of the cell cycle control system in addition to acting as an essential metabolic regulator.
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Affiliation(s)
- Sandhya Manohar
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Randall W King
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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20
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Feng D, Kumar M, Muntel J, Gurley SB, Birrane G, Stillman IE, Ding L, Wang M, Ahmed S, Schlondorff J, Alper SL, Ferrante T, Marquez SL, Ng CF, Novak R, Ingber DE, Steen H, Pollak MR. Phosphorylation of ACTN4 Leads to Podocyte Vulnerability and Proteinuric Glomerulosclerosis. J Am Soc Nephrol 2020; 31:1479-1495. [PMID: 32540856 PMCID: PMC7351002 DOI: 10.1681/asn.2019101032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/23/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Genetic mutations in α-actinin-4 (ACTN4)-an important actin crosslinking cytoskeletal protein that provides structural support for kidney podocytes-have been linked to proteinuric glomerulosclerosis in humans. However, the effect of post-translational modifications of ACTN4 on podocyte integrity and kidney function is not known. METHODS Using mass spectrometry, we found that ACTN4 is phosphorylated at serine (S) 159 in human podocytes. We used phosphomimetic and nonphosphorylatable ACTN4 to comprehensively study the effects of this phosphorylation in vitro and in vivo. We conducted x-ray crystallography, F-actin binding and bundling assays, and immunofluorescence staining to evaluate F-actin alignment. Microfluidic organ-on-a-chip technology was used to assess for detachment of podocytes simultaneously exposed to fluid flow and cyclic strain. We then used CRISPR/Cas9 to generate mouse models and assessed for renal injury by measuring albuminuria and examining kidney histology. We also performed targeted mass spectrometry to determine whether high extracellular glucose or TGF-β levels increase phosphorylation of ACTN4. RESULTS Compared with the wild type ACTN4, phosphomimetic ACTN4 demonstrated increased binding and bundling activity with F-actin in vitro. Phosphomimetic Actn4 mouse podocytes exhibited more spatially correlated F-actin alignment and a higher rate of detachment under mechanical stress. Phosphomimetic Actn4 mice developed proteinuria and glomerulosclerosis after subtotal nephrectomy. Moreover, we found that exposure to high extracellular glucose or TGF-β stimulates phosphorylation of ACTN4 at S159 in podocytes. CONCLUSIONS These findings suggest that increased phosphorylation of ACTN4 at S159 leads to biochemical, cellular, and renal pathology that is similar to pathology resulting from human disease-causing mutations in ACTN4. ACTN4 may mediate podocyte injury as a consequence of both genetic mutations and signaling events that modulate phosphorylation.
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Affiliation(s)
- Di Feng
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Mukesh Kumar
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children’s Hospital, Boston, Massachusetts
| | | | - Susan B. Gurley
- Division of Nephrology and Hypertension, Oregon Health & Science University, Portland, Oregon
| | - Gabriel Birrane
- Division of Experimental Medicine, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Isaac E. Stillman
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Lai Ding
- NeuroTechnology Studio, Program for Interdisciplinary Neuroscience, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Minxian Wang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Saima Ahmed
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Johannes Schlondorff
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Seth L. Alper
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Tom Ferrante
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Susan L. Marquez
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Carlos F. Ng
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts
| | - Donald E. Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts,Vascular Biology Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, Massachusetts
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Martin R. Pollak
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
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21
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Abdelbaki A, Akman HB, Poteau M, Grant R, Gavet O, Guarguaglini G, Lindon C. AURKA destruction is decoupled from its activity at mitotic exit but is essential to suppress interphase activity. J Cell Sci 2020; 133:jcs243071. [PMID: 32393600 PMCID: PMC7328152 DOI: 10.1242/jcs.243071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/19/2020] [Indexed: 12/22/2022] Open
Abstract
Activity of AURKA is controlled through multiple mechanisms including phosphorylation, ubiquitin-mediated degradation and allosteric interaction with TPX2. Activity peaks at mitosis, before AURKA is degraded during and after mitotic exit in a process strictly dependent on the APC/C coactivator FZR1. We used FZR1 knockout cells (FZR1KO) and a novel FRET-based AURKA biosensor to investigate how AURKA activity is regulated in the absence of destruction. We found that AURKA activity in FZR1KO cells dropped at mitotic exit as rapidly as in parental cells, despite absence of AURKA destruction. Unexpectedly, TPX2 was degraded normally in FZR1KO cells. Overexpression of an N-terminal TPX2 fragment sufficient for AURKA binding, but that is not degraded at mitotic exit, caused delay in AURKA inactivation. We conclude that inactivation of AURKA at mitotic exit is determined not by AURKA degradation but by degradation of TPX2 and therefore is dependent on CDC20 rather than FZR1. The biosensor revealed that FZR1 instead suppresses AURKA activity in interphase and is critically required for assembly of the interphase mitochondrial network after mitosis.This article has an associated First Person interview with the first authors of the paper.
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Affiliation(s)
- Ahmed Abdelbaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - H Begum Akman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Marion Poteau
- Institut Gustave Roussy, UMR9019 - CNRS, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Rhys Grant
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Olivier Gavet
- Institut Gustave Roussy, UMR9019 - CNRS, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Giulia Guarguaglini
- Institute of Molecular Biology and Pathology, CNR, Via degli Apuli 4, 00185 Roma, Italy
| | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
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22
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TRIM8 interacts with KIF11 and KIFC1 and controls bipolar spindle formation and chromosomal stability. Cancer Lett 2020; 473:98-106. [DOI: 10.1016/j.canlet.2019.12.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
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23
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The Cannabis Proteome Draft Map Project. Int J Mol Sci 2020; 21:ijms21030965. [PMID: 32024021 PMCID: PMC7037972 DOI: 10.3390/ijms21030965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources developed from our proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources.
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24
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Wasserman D, Nachum S, Cohen M, Enrico TP, Noach-Hirsh M, Parasol J, Zomer-Polak S, Auerbach N, Sheinberger-Chorni E, Nevenzal H, Levi-Dadon N, Wang X, Lahmi R, Michaely E, Gerber D, Emanuele MJ, Tzur A. Cell cycle oscillators underlying orderly proteolysis of E2F8. Mol Biol Cell 2020; 31:725-740. [PMID: 31995441 PMCID: PMC7185961 DOI: 10.1091/mbc.e19-12-0725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
E2F8 is a transcriptional repressor that antagonizes E2F1 at the crossroads of the cell cycle, apoptosis, and cancer. Previously, we discovered that E2F8 is a direct target of the APC/C ubiquitin ligase. Nevertheless, it remains unknown how E2F8 is dynamically controlled throughout the entirety of the cell cycle. Here, using newly developed human cell-free systems that recapitulate distinct inter-mitotic and G1 phases and a continuous transition from prometaphase to G1, we reveal an interlocking dephosphorylation switch coordinating E2F8 degradation with mitotic exit and the activation of APC/CCdh1. Further, we uncover differential proteolysis rates for E2F8 at different points within G1 phase, accounting for its accumulation in late G1 while APC/CCdh1 is still active. Finally, we demonstrate that the F-box protein Cyclin F regulates E2F8 in G2-phase. Altogether, our data define E2F8 regulation throughout the cell cycle, illuminating an extensive coordination between phosphorylation, ubiquitination and transcription in mammalian cell cycle.
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Affiliation(s)
- Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Meital Cohen
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Taylor P Enrico
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Meirav Noach-Hirsh
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Jasmin Parasol
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sarit Zomer-Polak
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Naomi Auerbach
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Evelin Sheinberger-Chorni
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Hadas Nevenzal
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Nofar Levi-Dadon
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Xianxi Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Roxane Lahmi
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Efrat Michaely
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Doron Gerber
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Michael J Emanuele
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
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25
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Arima N, Sasaki Y, Lee LH, Zhang H, Figueiredo JL, Mlynarchik AK, Qiao J, Yamada I, Higashi H, Ha AH, Halu A, Mizuno K, Singh SA, Yamazaki Y, Aikawa M. Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery. J Proteome Res 2020; 19:129-143. [PMID: 31661273 DOI: 10.1021/acs.jproteome.9b00441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Roux-en-Y gastric bypass (RYGB) surgery reduces weight in obese patients. A marked decrease in blood glucose levels occurs before weight loss; however, key molecules that improve the glycemic profile remain largely unknown. Using a murine RYGB surgery model, we performed multiorgan proteomics and bioinformatics to monitor the proteins and molecular pathways that change in this early glycemic response. Multiplexed proteomic kinetics data analysis revealed that the Roux limb, biliopancreatic limb, liver, and pancreas each exhibited unique temporal and molecular responses to the RYGB surgery. In addition, protein-protein network analysis indicated that the changes to the microbial environment in the intestine may play a crucial role in the beneficial effects of RYGB surgery. Furthermore, insulin-like growth factor binding protein 7 (Igfbp7) was identified as an early induced protein in the Roux limb. Known secretory properties of Igfbp7 prompted us to further investigate its role as a remote organ regulator of glucose metabolism. Igfbp7 overexpression decreased blood glucose levels in diet-induced obese mice and attenuated gluconeogenic gene expression in the liver. Secreted Igfbp7 appeared to mediate these beneficial effects. These results demonstrate that organs responded differentially to RYGB surgery and indicate that Igfbp7 may play an important role in improving blood glucose levels.
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Affiliation(s)
- Naoaki Arima
- Tokyo New Drug Research Laboratories , Kowa Company, Ltd. , Tokyo 189-0022 , Japan
| | - Yusuke Sasaki
- Tokyo New Drug Research Laboratories , Kowa Company, Ltd. , Tokyo 189-0022 , Japan
| | | | | | | | | | | | - Iwao Yamada
- Tokyo New Drug Research Laboratories , Kowa Company, Ltd. , Tokyo 189-0022 , Japan
| | - Hideyuki Higashi
- Tokyo New Drug Research Laboratories , Kowa Company, Ltd. , Tokyo 189-0022 , Japan
| | | | | | - Ken Mizuno
- Tokyo New Drug Research Laboratories , Kowa Company, Ltd. , Tokyo 189-0022 , Japan
| | | | - Yukiyoshi Yamazaki
- Tokyo New Drug Research Laboratories , Kowa Company, Ltd. , Tokyo 189-0022 , Japan
| | - Masanori Aikawa
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health , Moscow , Russian Federation , 119146
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26
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Kustatscher G, Grabowski P, Schrader TA, Passmore JB, Schrader M, Rappsilber J. Co-regulation map of the human proteome enables identification of protein functions. Nat Biotechnol 2019; 37:1361-1371. [PMID: 31690884 DOI: 10.1038/s41587-019-0298-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 09/27/2019] [Indexed: 01/07/2023]
Abstract
Assigning functions to the vast array of proteins present in eukaryotic cells remains challenging. To identify relationships between proteins, and thereby enable functional annotation of proteins, we determined changes in abundance of 10,323 human proteins in response to 294 biological perturbations using isotope-labeling mass spectrometry. We applied the machine learning algorithm treeClust to reveal functional associations between co-regulated human proteins from ProteomeHD, a compilation of our own data and datasets from the Proteomics Identifications database. This produced a co-regulation map of the human proteome. Co-regulation was able to capture relationships between proteins that do not physically interact or colocalize. For example, co-regulation of the peroxisomal membrane protein PEX11β with mitochondrial respiration factors led us to discover an organelle interface between peroxisomes and mitochondria in mammalian cells. We also predicted the functions of microproteins that are difficult to study with traditional methods. The co-regulation map can be explored at www.proteomeHD.net .
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Affiliation(s)
- Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Piotr Grabowski
- Division of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Data Sciences and Artificial Intelligence, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | | | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK. .,Division of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
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27
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Schoor C, Brocke-Ahmadinejad N, Gieselmann V, Winter D. Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics. Proteomics 2019; 19:e1900057. [PMID: 31216117 DOI: 10.1002/pmic.201900057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/02/2019] [Indexed: 01/20/2023]
Abstract
Oligodendrocytes, the myelinating cells of the central nervous system, are essential for correct brain function. They originate from oligodendrocyte precursor cells through a differentiation process which is only incompletely understood and impaired in a variety of demyelinating diseases. Better knowledge of this differentiation holds the promise to develop novel therapies for these disorders. The differentiation of rat oligodendrocyte precursor cells to oligodendrocytes in vitro is investigated. After confirmation of differentiation by immunohistochemical analysis using cell type-specific marker proteins, a quantitative proteomics study using tandem mass tags (TMT) is conducted. Four time points of differentiation covering early, intermediate, and late stages are investigated. Data analysis by Mascot and MaxQuant identified 5259 protein groups of which 471 are not described in the context of cells of the oligodendroglial lineage before. Quantitative analysis of the dataset revealed distinct regulation patterns for proteins of different functional categories including metabolic processes, regulation of the cell cycle, and transcriptional control of protein expression. The present data confirm a significant number of proteins known to play a role in oligodendrocytes and myelination. Furthermore, novel candidate proteins are identified which may play an important role in this differentiation process providing a valuable resource for oligodendrocyte research.
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Affiliation(s)
- Carmen Schoor
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115, Bonn, Germany
| | | | - Volkmar Gieselmann
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115, Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115, Bonn, Germany
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28
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Mitotic Motor KIFC1 Is an Organizer of Microtubules in the Axon. J Neurosci 2019; 39:3792-3811. [PMID: 30804089 DOI: 10.1523/jneurosci.3099-18.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 11/21/2022] Open
Abstract
KIFC1 (also called HSET or kinesin-14a) is best known as a multifunctional motor protein essential for mitosis. The present studies are the first to explore KIFC1 in terminally postmitotic neurons. Using RNA interference to partially deplete KIFC1 from rat neurons (from animals of either gender) in culture, pharmacologic agents that inhibit KIFC1, and expression of mutant KIFC1 constructs, we demonstrate critical roles for KIFC1 in regulating axonal growth and retraction as well as growth cone morphology. Experimental manipulations of KIFC1 elicit morphological changes in the axon as well as changes in the organization, distribution, and polarity orientation of its microtubules. Together, the results indicate a mechanism by which KIFC1 binds to microtubules in the axon and slides them into alignment in an ATP-dependent fashion and then cross-links them in an ATP-independent fashion to oppose their subsequent sliding by other motors.SIGNIFICANCE STATEMENT Here, we establish that KIFC1, a molecular motor well characterized in mitosis, is robustly expressed in neurons, where it has profound influence on the organization of microtubules in a number of different functional contexts. KIFC1 may help answer long-standing questions in cellular neuroscience such as, mechanistically, how growth cones stall and how axonal microtubules resist forces that would otherwise cause the axon to retract. Knowledge about KIFC1 may help researchers to devise strategies for treating disorders of the nervous system involving axonal retraction given that KIFC1 is expressed in adult neurons as well as developing neurons.
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29
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Lee LH, Halu A, Morgan S, Iwata H, Aikawa M, Singh SA. XINA: A Workflow for the Integration of Multiplexed Proteomics Kinetics Data with Network Analysis. J Proteome Res 2019; 18:775-781. [PMID: 30370770 DOI: 10.1021/acs.jproteome.8b00615] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Quantitative proteomics experiments, using for instance isobaric tandem mass tagging approaches, are conducive to measuring changes in protein abundance over multiple time points in response to one or more conditions or stimulations. The aim is often to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with coabundance patterns may have common molecular functions related to a given stimulation. In order to facilitate the identification and analyses of coabundance patterns within and across conditions, we previously developed a software inspired by the isobaric mass tagging method itself. Specifically, multiple data sets are tagged in silico and combined for subsequent subgrouping into multiple clusters within a single output depicting the variation across all conditions, converting a typical inter-data-set comparison into an intra-data-set comparison. An updated version of our software, XINA, not only extracts coabundance profiles within and across experiments but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs. In this report, we compare the kinetics profiles of >5600 unique proteins derived from three macrophage cell culture experiments and demonstrate through intuitive visualizations that XINA identifies key regulators of macrophage activation via their coabundance patterns.
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Affiliation(s)
- Lang Ho Lee
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Arda Halu
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
- Channing Division of Network Medicine , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Stephanie Morgan
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Hiroshi Iwata
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
- Channing Division of Network Medicine , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
- Center for Excellence in Vascular Biology , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division , Brigham and Women's Hospital , Harvard Medical School, Boston , Massachusetts 02115 , United States
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30
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The multiple functions of kinesin-4 family motor protein KIF4 and its clinical potential. Gene 2018; 678:90-99. [DOI: 10.1016/j.gene.2018.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023]
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31
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Bakos G, Yu L, Gak IA, Roumeliotis TI, Liakopoulos D, Choudhary JS, Mansfeld J. An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules. Nat Commun 2018; 9:4776. [PMID: 30429481 PMCID: PMC6235928 DOI: 10.1038/s41467-018-07251-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022] Open
Abstract
Covalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to many biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck in ubiquitin research. Here, we present an E2-thioester-driven identification (E2~dID) method for the targeted identification of substrates of specific E2 and E3 enzyme pairs. E2~dID exploits the central position of E2-conjugating enzymes in the ubiquitination cascade and provides in vitro generated biotinylated E2~ubiquitin thioester conjugates as the sole source for ubiquitination in extracts. This enables purification and mass spectrometry-based identification of modified proteins under stringent conditions independently of the biological source of the extract. We demonstrate the sensitivity and specificity of E2-dID by identifying and validating substrates of APC/C in human cells. Finally, we perform E2~dID with SUMO in S. cerevisiae, showing that this approach can be easily adapted to other ubiquitin-like modifiers and experimental models.
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Affiliation(s)
- Gábor Bakos
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Lu Yu
- Functional Proteomics Group, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Igor A Gak
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | | | - Dimitris Liakopoulos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 34293, Montpellier Cedex 05, France
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany.
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32
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Halu A, Wang JG, Iwata H, Mojcher A, Abib AL, Singh SA, Aikawa M, Sharma A. Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. eLife 2018; 7:37059. [PMID: 30303482 PMCID: PMC6179386 DOI: 10.7554/elife.37059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023] Open
Abstract
The role of pro-inflammatory macrophage activation in cardiovascular disease (CVD) is a complex one amenable to network approaches. While an indispensible tool for elucidating the molecular underpinnings of complex diseases including CVD, the interactome is limited in its utility as it is not specific to any cell type, experimental condition or disease state. We introduced context-specificity to the interactome by combining it with co-abundance networks derived from unbiased proteomics measurements from activated macrophage-like cells. Each macrophage phenotype contributed to certain regions of the interactome. Using a network proximity-based prioritization method on the combined network, we predicted potential regulators of macrophage activation. Prediction performance significantly increased with the addition of co-abundance edges, and the prioritized candidates captured inflammation, immunity and CVD signatures. Integrating the novel network topology with transcriptomics and proteomics revealed top candidate drivers of inflammation. In vitro loss-of-function experiments demonstrated the regulatory role of these proteins in pro-inflammatory signaling. When human cells or tissues are injured, the body triggers a response known as inflammation to repair the damage and protect itself from further harm. However, if the same issue keeps recurring, the tissues become inflamed for longer periods of time, which may ultimately lead to health problems. This is what could be happening in cardiovascular diseases, where long-term inflammation could damage the heart and blood vessels. Many different proteins interact with each other to control inflammation; gaining an insight into the nature of these interactions could help to pinpoint the role of each molecular actor. Researchers have used a combination of unbiased, large-scale experimental and computational approaches to develop the interactome, a map of the known interactions between all proteins in humans. However, interactions between proteins can change between cell types, or during disease. Here, Halu et al. aimed to refine the human interactome and identify new proteins involved in inflammation, especially in the context of cardiovascular disease. Cells called macrophages produce signals that trigger inflammation whey they detect damage in other cells or tissues. The experiments used a technique called proteomics to measure the amounts of all the proteins in human macrophages. Combining these data with the human interactome made it possible to predict new links between proteins known to have a role in inflammation and other proteins in the interactome. Further analysis using other sets of data from macrophages helped identify two new candidate proteins – GBP1 and WARS – that may promote inflammation. Halu et al. then used a genetic approach to deactivate the genes and decrease the levels of these two proteins in macrophages, which caused the signals that encourage inflammation to drop. These findings suggest that GBP1 and WARS regulate the activity of macrophages to promote inflammation. The two proteins could therefore be used as drug targets to treat cardiovascular diseases and other disorders linked to inflammation, but further studies will be needed to precisely dissect how GBP1 and WARS work in humans.
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Affiliation(s)
- Arda Halu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Jian-Guo Wang
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Hiroshi Iwata
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Alexander Mojcher
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Ana Luisa Abib
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
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Abstract
The HTRA1 gene encoding an evolutionary conserved protein quality-control factor can be epigenetically silenced or inactivated by mutation under pathologic conditions such as cancer. Recent evidence suggests that the loss of HTRA1 function causes multiple phenotypes, including the acceleration of cell growth, delayed onset of senescence, centrosome amplification, and polyploidy, suggesting an implication in the regulation of the cell cycle. To address this model, we performed a large-scale proteomics study to correlate the abundance of proteins and HTRA1 levels in various cell cycle phases using label-free-quantification mass spectrometry. These data indicate that the levels of 4723 proteins fluctuated in a cell-cycle-dependent manner, 2872 in a HTRA1-dependent manner, and 1530 in a cell-cycle- and HTRA1-dependent manner. The large number of proteins affected by the modulation of HTRA1 levels supports its general role in protein homeostasis. Moreover, the detected changes in protein abundance, in combination with pull-down data, implicate HTRA1 in various cell cycle events such as DNA replication, chromosome segregation, and cell-cycle-dependent apoptosis. These results highlight the wide implications of HTRA1 in cellular physiology.
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Affiliation(s)
- Jasmin Schillinger
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Katharina Severin
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Farnusch Kaschani
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Markus Kaiser
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Michael Ehrmann
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
- School of Biosciences , Cardiff University , Cardiff CF10 3US , United Kingdom
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34
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Lee HJ, Jedrychowski MP, Vinayagam A, Wu N, Shyh-Chang N, Hu Y, Min-Wen C, Moore JK, Asara JM, Lyssiotis CA, Perrimon N, Gygi SP, Cantley LC, Kirschner MW. Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation. Cell Rep 2018; 20:721-736. [PMID: 28723573 DOI: 10.1016/j.celrep.2017.06.074] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/22/2017] [Accepted: 06/25/2017] [Indexed: 12/28/2022] Open
Abstract
There exist similarities and differences in metabolism and physiology between normal proliferative cells and tumor cells. Once a cell enters the cell cycle, metabolic machinery is engaged to facilitate various processes. The kinetics and regulation of these metabolic changes have not been properly evaluated. To correlate the orchestration of these processes with the cell cycle, we analyzed the transition from quiescence to proliferation of a non-malignant murine pro-B lymphocyte cell line in response to IL-3. Using multiplex mass-spectrometry-based proteomics, we show that the transition to proliferation shares features generally attributed to cancer cells: upregulation of glycolysis, lipid metabolism, amino-acid synthesis, and nucleotide synthesis and downregulation of oxidative phosphorylation and the urea cycle. Furthermore, metabolomic profiling of this transition reveals similarities to cancer-related metabolic pathways. In particular, we find that methionine is consumed at a higher rate than that of other essential amino acids, with a potential link to maintenance of the epigenome.
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Affiliation(s)
- Ho-Joon Lee
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Ning Wu
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ng Shyh-Chang
- Stem Cell & Regenerative Biology, Genome Institute of Singapore, S138672 Singapore, Singapore
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chua Min-Wen
- Stem Cell & Regenerative Biology, Genome Institute of Singapore, S138672 Singapore, Singapore
| | - Jodene K Moore
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
| | - Costas A Lyssiotis
- Division of Gastroenterology, Department of Molecular and Integrative Physiology and Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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35
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SUMO targets the APC/C to regulate transition from metaphase to anaphase. Nat Commun 2018; 9:1119. [PMID: 29549242 PMCID: PMC5856775 DOI: 10.1038/s41467-018-03486-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/15/2018] [Indexed: 01/25/2023] Open
Abstract
Signal transduction by small ubiquitin-like modifier (SUMO) regulates a myriad of nuclear processes. Here we report on the role of SUMO in mitosis in human cell lines. Knocking down the SUMO conjugation machinery results in a delay in mitosis and defects in mitotic chromosome separation. Searching for relevant SUMOylated proteins in mitosis, we identify the anaphase-promoting complex/cyclosome (APC/C), a master regulator of metaphase to anaphase transition. The APC4 subunit is the major SUMO target in the complex, containing SUMO acceptor lysines at positions 772 and 798. SUMOylation is crucial for accurate progression of cells through mitosis and increases APC/C ubiquitylation activity toward a subset of its targets, including the newly identified target KIF18B. Combined, our findings demonstrate the importance of SUMO signal transduction for genome integrity during mitotic progression and reveal how SUMO and ubiquitin cooperate to drive mitosis.
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36
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Lee SH, Joo K, Jung EJ, Hong H, Seo J, Kim J. Export of membrane proteins from the Golgi complex to the primary cilium requires the kinesin motor, KIFC1. FASEB J 2018; 32:957-968. [PMID: 29042452 DOI: 10.1096/fj.201700563r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Microtubule-based motors contribute to the efficiency and selectivity of Golgi exit and post-Golgi transport of membrane proteins that are targeted to distinct compartments. Cytoplasmic dynein moves post-Golgi vesicles that carry rhodopsin toward the base of the connecting cilium in photoreceptor cells; however, the identity of the motors that are involved in the vesicular trafficking of ciliary membrane proteins in nonphotoreceptor cells remains unclear. Here, we demonstrate that the minus end-directed kinesin KIFC1 (kinesin family member C1) is required for both ciliary membrane protein transport and serum starvation-induced ciliogenesis in retinal pigmented epithelial 1 cells. Although KIFC1 is known as a mitotic motor that is sequestered in the nucleus during interphase, KIFC1 immunoreactivity appeared in the Golgi region after serum starvation. Knockdown of KIFC1 inhibited the export of ciliary receptors from the Golgi complex. KIFC1 overexpression affected the Golgi localization of GMAP210 (Golgi microtubule-associated protein 210) and IFT20 (intraflagellar transport 20), which are involved in membrane protein transport to cilia. Moreover, KIFC1 physically interacted with ASAP1 (ADP-ribosylation factor GTPase-activating protein with SH3 domain, ankyrin repeat and PH domain 1), which regulates the budding of rhodopsin transport carriers from the Golgi complex, and KIFC1 depletion caused Golgi accumulation of ASAP1. A decrease in the centrosomal levels of IFT20 and TTBK2 (τ-tubulin kinase 2) was associated with ciliogenesis defects in KIFC1-depleted cells. Our results suggest that KIFC1 plays roles in the Golgi exit of ciliary receptors and in the recruitment of ciliogenesis regulators.-Lee, S.-H., Joo, K., Jung, E. J., Hong, H., Seo, J., Kim, J. Export of membrane proteins from the Golgi complex to the primary cilium requires the kinesin motor, KIFC1.
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Affiliation(s)
- Si-Hyung Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.,Department of Dermatology, Yonsei University College of Medicine, Seoul, Korea
| | - Kwangsic Joo
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.,Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Eun Ji Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Hyowon Hong
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jimyung Seo
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Joon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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37
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Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. Proc Natl Acad Sci U S A 2017; 114:E10838-E10847. [PMID: 29183978 DOI: 10.1073/pnas.1709207114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Fertilization releases the meiotic arrest and initiates the events that prepare the egg for the ensuing developmental program. Protein degradation and phosphorylation are known to regulate protein activity during this process. However, the full extent of protein loss and phosphoregulation is still unknown. We examined absolute protein and phosphosite dynamics of the fertilization response by mass spectrometry-based proteomics in electroactivated eggs. To do this, we developed an approach for calculating the stoichiometry of phosphosites from multiplexed proteomics that is compatible with dynamic, stable, and multisite phosphorylation. Overall, the data suggest that degradation is limited to a few low-abundance proteins. However, this degradation promotes extensive dephosphorylation that occurs over a wide range of abundances during meiotic exit. We also show that eggs release a large amount of protein into the medium just after fertilization, most likely related to the blocks to polyspermy. Concomitantly, there is a substantial increase in phosphorylation likely tied to calcium-activated kinases. We identify putative degradation targets and components of the slow block to polyspermy. The analytical approaches demonstrated here are broadly applicable to studies of dynamic biological systems.
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38
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Tipton AR, Wren JD, Daum JR, Siefert JC, Gorbsky GJ. GTSE1 regulates spindle microtubule dynamics to control Aurora B kinase and Kif4A chromokinesin on chromosome arms. J Cell Biol 2017; 216:3117-3132. [PMID: 28821562 PMCID: PMC5626529 DOI: 10.1083/jcb.201610012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 04/20/2017] [Accepted: 07/12/2017] [Indexed: 12/24/2022] Open
Abstract
In mitosis, the dynamic assembly and disassembly of microtubules are critical for normal chromosome movement and segregation. Microtubule turnover varies among different mitotic spindle microtubules, dictated by their spatial distribution within the spindle. How turnover among the various classes of spindle microtubules is differentially regulated and the resulting significance of differential turnover for chromosome movement remains a mystery. As a new tactic, we used global microarray meta-analysis (GAMMA), a bioinformatic method, to identify novel regulators of mitosis, and in this study, we describe G2- and S phase-expressed protein 1 (GTSE1). GTSE1 is expressed exclusively in late G2 and M phase. From nuclear envelope breakdown until anaphase onset, GTSE1 binds preferentially to the most stable mitotic spindle microtubules and promotes their turnover. Cells depleted of GTSE1 show defects in chromosome alignment at the metaphase plate and in spindle pole integrity. These defects are coupled with an increase in the proportion of stable mitotic spindle microtubules. A consequence of this reduced microtubule turnover is diminished recruitment and activity of Aurora B kinase on chromosome arms. This decrease in Aurora B results in diminished binding of the chromokinesin Kif4A to chromosome arms.
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Affiliation(s)
- Aaron R Tipton
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - John R Daum
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Joseph C Siefert
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
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39
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Üretmen Kagıalı ZC, Şentürk A, Özkan Küçük NE, Qureshi MH, Özlü N. Proteomics in Cell Division. Proteomics 2017; 17. [PMID: 28548456 DOI: 10.1002/pmic.201600100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/07/2017] [Indexed: 11/08/2022]
Abstract
Cell division requires a coordinated action of the cell cycle machinery, cytoskeletal elements, chromosomes, and membranes. Cell division studies have greatly benefitted from the mass spectrometry (MS)-based proteomic approaches for probing the biochemistry of highly dynamic complexes and their coordination with each other as a cell progresses into division. In this review, the authors first summarize a wide-range of proteomic studies that focus on the identification of sub-cellular components/protein complexes of the cell division machinery including kinetochores, mitotic spindle, midzone, and centrosomes. The authors also highlight MS-based large-scale analyses of the cellular components that are largely understudied during cell division such as the cell surface and lipids. Then, the authors focus on posttranslational modification analyses, especially phosphorylation and the resulting crosstalk with other modifications as a cell undergoes cell division. Combining proteomic approaches that probe the biochemistry of cell division components with functional genomic assays will lead to breakthroughs toward a systems-level understanding of cell division.
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Affiliation(s)
| | - Aydanur Şentürk
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - Mohammad Haroon Qureshi
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.,Biomedical Sciences and Engineering, Koç University, Istanbul, Turkey
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
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40
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C-terminal kinesin motor KIFC1 participates in facilitating proper cell division of human seminoma. Oncotarget 2017; 8:61373-61384. [PMID: 28977870 PMCID: PMC5617430 DOI: 10.18632/oncotarget.18139] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/27/2017] [Indexed: 11/25/2022] Open
Abstract
C-terminus kinesin motor KIFC1 is known for centrosome clustering in cancer cells with supernumerary centrosomes. KIFC1 crosslinks and glides on microtubules (MT) to assist normal bipolar spindle formation to avoid multi-polar cell division, which might be fatal. Testis cancer is the most common human cancer among young men. However, the gene expression profiles of testis cancer is still not complete and the expression of the C-terminus kinesin motor KIFC1 in testis cancer has not yet been examined. We found that KIFC1 is enriched in seminoma tissues in both mRNA level and protein level, and is specifically enriched in the cells that divide actively. Cell experiments showed that KIFC1 may be essential in cell division, but not essential in metastasis. Based on subcellular immuno-florescent staining results, we also described the localization of KIFC1 during cell cycle. By expressing ΔC-FLAG peptide in the cells, we found that the tail domain of KIFC1 might be essential for the dynamic disassociation of KIFC1, and the motor domain of KIFC1 might be essential for the degradation of KIFC1. Our work provides a new perspective for seminoma research.
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41
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Xiao YX, Yang WX. KIFC1: a promising chemotherapy target for cancer treatment? Oncotarget 2016; 7:48656-48670. [PMID: 27102297 PMCID: PMC5217046 DOI: 10.18632/oncotarget.8799] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/10/2016] [Indexed: 01/10/2023] Open
Abstract
The kinesin motor KIFC1 has been suggested as a potential chemotherapy target due to its critical role in clustering of the multiple centrosomes found in cancer cells. In this regard, KIFC1 seems to be non-essential in normal somatic cells which usually possess only two centrosomes. Moreover, KIFC1 is also found to initiatively drive tumor malignancy and metastasis by stabilizing a certain degree of genetic instability, delaying cell cycle and protecting cancer cell surviving signals. However, that KIFC1 also plays roles in other specific cell types complicates the question of whether it is a promising chemotherapy target for cancer treatment. For example, KIFC1 is found functionally significant in vesicular and organelle trafficking, spermiogenesis, oocyte development, embryo gestation and double-strand DNA transportation. In this review we summarize a recent collection of information so as to provide a generalized picture of ideas and mechanisms against and in favor of KIFC1 as a chemotherapy target. And we also drew the conclusion that KIFC1 is a promising chemotherapy target for some types of cancers, because the side-effects of inhibiting KIFC1 mentioned in this review are theoretically easy to avoid, while KIFC1 is functionally indispensable during mitosis and malignancy of multi-centrosome cancer cells. Further investigations of how KIFC1 is regulated throughout the mitosis in cancer cells are needed for the understanding of the pathways where KIFC1 is involved and for further exploitation of indirect KIFC1 inhibitors.
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Affiliation(s)
- Yu-Xi Xiao
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, China
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42
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Ghiassian SD, Menche J, Chasman DI, Giulianini F, Wang R, Ricchiuto P, Aikawa M, Iwata H, Müller C, Zeller T, Sharma A, Wild P, Lackner K, Singh S, Ridker PM, Blankenberg S, Barabási AL, Loscalzo J. Endophenotype Network Models: Common Core of Complex Diseases. Sci Rep 2016; 6:27414. [PMID: 27278246 PMCID: PMC4899691 DOI: 10.1038/srep27414] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 05/19/2016] [Indexed: 02/03/2023] Open
Abstract
Historically, human diseases have been differentiated and categorized based on the organ system in which they primarily manifest. Recently, an alternative view is emerging that emphasizes that different diseases often have common underlying mechanisms and shared intermediate pathophenotypes, or endo(pheno)types. Within this framework, a specific disease’s expression is a consequence of the interplay between the relevant endophenotypes and their local, organ-based environment. Important examples of such endophenotypes are inflammation, fibrosis, and thrombosis and their essential roles in many developing diseases. In this study, we construct endophenotype network models and explore their relation to different diseases in general and to cardiovascular diseases in particular. We identify the local neighborhoods (module) within the interconnected map of molecular components, i.e., the subnetworks of the human interactome that represent the inflammasome, thrombosome, and fibrosome. We find that these neighborhoods are highly overlapping and significantly enriched with disease-associated genes. In particular they are also enriched with differentially expressed genes linked to cardiovascular disease (risk). Finally, using proteomic data, we explore how macrophage activation contributes to our understanding of inflammatory processes and responses. The results of our analysis show that inflammatory responses initiate from within the cross-talk of the three identified endophenotypic modules.
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Affiliation(s)
- Susan Dina Ghiassian
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, USA.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jörg Menche
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, USA.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Theoretical Physics, Budapest University of Technology and Economics, Budapest, Hungary
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Ruisheng Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Piero Ricchiuto
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hiroshi Iwata
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian Müller
- University Heart Center Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Lübeck/Kiel, Hamburg, Germany
| | - Tania Zeller
- University Heart Center Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Lübeck/Kiel, Hamburg, Germany
| | - Amitabh Sharma
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, USA.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Philipp Wild
- German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Lübeck/Kiel, Hamburg, Germany.,Preventive Cardiology and Preventive Medicine, Dept. of Medicine 2, University Medical Center Mainz, Mainz, Germany.,Clinical Epidemiology, Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - Karl Lackner
- German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Lübeck/Kiel, Hamburg, Germany.,Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
| | - Sasha Singh
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefan Blankenberg
- University Heart Center Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Lübeck/Kiel, Hamburg, Germany
| | - Albert-László Barabási
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, USA.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Theoretical Physics, Budapest University of Technology and Economics, Budapest, Hungary.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Center for Network Science, Central European University, Budapest, Hungary
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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43
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Zur H, Aviner R, Tuller T. Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. Sci Rep 2016; 6:21635. [PMID: 26898226 PMCID: PMC4761937 DOI: 10.1038/srep21635] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/27/2016] [Indexed: 01/09/2023] Open
Abstract
Two novel approaches were recently suggested for genome-wide identification of protein aspects synthesized at a given time. Ribo-Seq is based on sequencing all the ribosome protected mRNA fragments in a cell, while PUNCH-P is based on mass-spectrometric analysis of only newly synthesized proteins. Here we describe the first Ribo-Seq/PUNCH-P comparison via the analysis of mammalian cells during the cell-cycle for detecting relevant differentially expressed genes between G1 and M phase. Our analyses suggest that the two approaches significantly overlap with each other. However, we demonstrate that there are biologically meaningful proteins/genes that can be detected to be post-transcriptionally regulated during the mammalian cell cycle only by each of the approaches, or their consolidation. Such gene sets are enriched with proteins known to be related to intra-cellular signalling pathways such as central cell cycle processes, central gene expression regulation processes, processes related to chromosome segregation, DNA damage, and replication, that are post-transcriptionally regulated during the mammalian cell cycle. Moreover, we show that combining the approaches better predicts steady state changes in protein abundance. The results reported here support the conjecture that for gaining a full post-transcriptional regulation picture one should integrate the two approaches.
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Affiliation(s)
- Hadas Zur
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Israel
| | - Ranen Aviner
- Department of Cell Research and Immunology, Tel Aviv University, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Israel.,The Sagol School of Neuroscience, Tel Aviv University, Israel
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44
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Guharoy M, Bhowmick P, Tompa P. Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System. J Biol Chem 2016; 291:6723-31. [PMID: 26851277 DOI: 10.1074/jbc.r115.692665] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss post-translational modifications within disordered regions that regulate E3 ligase localization, conformation, and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity. Next we review well studied substrates and discuss that substrate elements (degrons) recognized by E3 ligases are highly disordered: short linear motifs recognized by many E3s constitute an important class of degrons, and these are almost always present in disordered regions. Substrate lysines targeted for ubiquitination are also often located in neighboring regions of the E3 docking motifs and are therefore part of the disordered segment. Finally, biochemical experiments and predictions show that initiation of degradation at the 26S proteasome requires a partially unfolded region to facilitate substrate entry into the proteasomal core.
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Affiliation(s)
- Mainak Guharoy
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Pallab Bhowmick
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Peter Tompa
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and the Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117 Budapest, Hungary
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45
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Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Commun Signal 2015; 13:45. [PMID: 26626130 PMCID: PMC4666095 DOI: 10.1186/s12964-015-0123-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
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46
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Niu B, Wang L, Zhang L, Ren D, Ren R, Copenhaver GP, Ma H, Wang Y. Arabidopsis Cell Division Cycle 20.1 Is Required for Normal Meiotic Spindle Assembly and Chromosome Segregation. THE PLANT CELL 2015; 27:3367-82. [PMID: 26672070 PMCID: PMC4707457 DOI: 10.1105/tpc.15.00834] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/16/2015] [Accepted: 11/22/2015] [Indexed: 05/18/2023]
Abstract
Cell division requires proper spindle assembly; a surveillance pathway, the spindle assembly checkpoint (SAC), monitors whether the spindle is normal and correctly attached to kinetochores. The SAC proteins regulate mitotic chromosome segregation by affecting CDC20 (Cell Division Cycle 20) function. However, it is unclear whether CDC20 regulates meiotic spindle assembly and proper homolog segregation. Here, we show that the Arabidopsis thaliana CDC20.1 gene is indispensable for meiosis and male fertility. We demonstrate that cdc20.1 meiotic chromosomes align asynchronously and segregate unequally and the metaphase I spindle has aberrant morphology. Comparison of the distribution of meiotic stages at different time points between the wild type and cdc20.1 reveals a delay of meiotic progression from diakinesis to anaphase I. Furthermore, cdc20.1 meiocytes exhibit an abnormal distribution of a histone H3 phosphorylation mark mediated by the Aurora kinase, providing evidence that CDC20.1 regulates Aurora localization for meiotic chromosome segregation. Further evidence that CDC20.1 and Aurora are functionally related was provided by meiosis-specific knockdown of At-Aurora1 expression, resulting in meiotic chromosome segregation defects similar to those of cdc20.1. Taken together, these results suggest a critical role for CDC20.1 in SAC-dependent meiotic chromosome segregation.
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Affiliation(s)
- Baixiao Niu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liudan Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ren Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Gregory P Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280 Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-3280
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China Center for Evolutionary Biology, Institutes of Biomedical Sciences School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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47
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Noach-Hirsh M, Nevenzal H, Glick Y, Chorni E, Avrahami D, Barbiro-Michaely E, Gerber D, Tzur A. Integrated Microfluidics for Protein Modification Discovery. Mol Cell Proteomics 2015; 14:2824-32. [PMID: 26276765 DOI: 10.1074/mcp.m115.053512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 12/23/2022] Open
Abstract
Protein post-translational modifications mediate dynamic cellular processes with broad implications in human disease pathogenesis. There is a large demand for high-throughput technologies supporting post-translational modifications research, and both mass spectrometry and protein arrays have been successfully utilized for this purpose. Protein arrays override the major limitation of target protein abundance inherently associated with MS analysis. This technology, however, is typically restricted to pre-purified proteins spotted in a fixed composition on chips with limited life-time and functionality. In addition, the chips are expensive and designed for a single use, making complex experiments cost-prohibitive. Combining microfluidics with in situ protein expression from a cDNA microarray addressed these limitations. Based on this approach, we introduce a modular integrated microfluidic platform for multiple post-translational modifications analysis of freshly synthesized protein arrays (IMPA). The system's potency, specificity and flexibility are demonstrated for tyrosine phosphorylation and ubiquitination in quasicellular environments. Unlimited by design and protein composition, and relying on minute amounts of biological material and cost-effective technology, this unique approach is applicable for a broad range of basic, biomedical and biomarker research.
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Affiliation(s)
- Meirav Noach-Hirsh
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Hadas Nevenzal
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yair Glick
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Evelin Chorni
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Dorit Avrahami
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Efrat Barbiro-Michaely
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Doron Gerber
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amit Tzur
- From the ‡The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
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48
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Ricchiuto P, Iwata H, Yabusaki K, Yamada I, Pieper B, Sharma A, Aikawa M, Singh SA. mIMT-visHTS: A novel method for multiplexing isobaric mass tagged datasets with an accompanying visualization high throughput screening tool for protein profiling. J Proteomics 2015; 128:132-40. [PMID: 26232111 DOI: 10.1016/j.jprot.2015.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 06/26/2015] [Accepted: 07/20/2015] [Indexed: 12/12/2022]
Abstract
Isobaric mass tagging (IMT) methods enable the analysis of thousands of proteins simultaneously. We used tandem mass tagging reagents (TMT™) to monitor the relative changes in the proteome of the mouse macrophage cell line RAW264.7 at the same six time points after no stimulation (baseline phenotype), stimulation with interferon gamma (pro-inflammatory phenotype) or stimulation with interleukin-4 (anti-inflammatory phenotype). The combined TMT datasets yielded nearly 12,000 protein profiles for comparison. To facilitate this large analysis, we developed a novel method that combines or multiplexes the separate IMT (mIMT) datasets into a single super dataset for subsequent model-based clustering and co-regulation analysis. Specially designed visual High Throughput Screening (visHTS) software screened co-regulated proteins. visHTS generates an interactive and visually intuitive color-coded bullseye plot that enables users to browse the cluster outputs and identify co-regulated proteins.
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Affiliation(s)
- Piero Ricchiuto
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hiroshi Iwata
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Katsumi Yabusaki
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Iwao Yamada
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Brett Pieper
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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49
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Belin S, Nawabi H, Wang C, Tang S, Latremoliere A, Warren P, Schorle H, Uncu C, Woolf CJ, He Z, Steen JA. Injury-induced decline of intrinsic regenerative ability revealed by quantitative proteomics. Neuron 2015; 86:1000-1014. [PMID: 25937169 DOI: 10.1016/j.neuron.2015.03.060] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/21/2014] [Accepted: 03/20/2015] [Indexed: 12/28/2022]
Abstract
Neurons differ in their responses to injury, but the underlying mechanisms remain poorly understood. Using quantitative proteomics, we characterized the injury-triggered response from purified intact and axotomized retinal ganglion cells (RGCs). Subsequent informatics analyses revealed a network of injury-response signaling hubs. In addition to confirming known players, such as mTOR, this also identified new candidates, such as c-myc, NFκB, and Huntingtin. Similar to mTOR, c-myc has been implicated as a key regulator of anabolic metabolism and is downregulated by axotomy. Forced expression of c-myc in RGCs, either before or after injury, promotes dramatic RGC survival and axon regeneration after optic nerve injury. Finally, in contrast to RGCs, neither c-myc nor mTOR was downregulated in injured peripheral sensory neurons. Our studies suggest that c-myc and other injury-responsive pathways are critical to the intrinsic regenerative mechanisms and might represent a novel target for developing neural repair strategies in adults.
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Affiliation(s)
- Stephane Belin
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Homaira Nawabi
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Shaojun Tang
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Alban Latremoliere
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Peter Warren
- Department of Urology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Hubert Schorle
- Department of Developmental Pathology, University of Bonn Medical School, Sigmund Freud Strasse 25, 53127 Bonn, Germany
| | - Ceren Uncu
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
| | - Judith A Steen
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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50
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Yang F, Chen Y, Dai W. Sumoylation of Kif18A plays a role in regulating mitotic progression. BMC Cancer 2015; 15:197. [PMID: 25884224 PMCID: PMC4389313 DOI: 10.1186/s12885-015-1226-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kif18A, the kinesin-8 motor protein, plays an essential role in regulating alignment of bi-oriented chromosomes at the midzone during mitosis. Kinesin proteins, including Kif18A, are often deregulated in many types of cancers and are thought to play a critical role in cancer progression. However, little is known about the post-translational modifications of Kif18A and their effects on its biological activity. METHODS Kif18A was identified to be a SUMO2 acceptor by using Ni-IDA resin to precipitate proteins from cells stably expressing His6-SUMO2. To identify the potential lysine residues, multi-site directed mutagenesis together with transient transfection and Ni-IDA pull-down assay were carried out. The confocal time-lapse imaging and immunofluorescent staining were used to study the roles of SUMO2 modification on Kif18A's activity during the cell cycle. RESULTS Kif18A is covalently modified by SUMO2 during the cell cycle, and its sumoylation peaks at metaphase and then rapidly decreases upon anaphase onset. Mutational analysis identifies multiple lysine residues (K148, K442, K533, K660 and K683) as potential SUMO acceptors. The functional studies reveal that sumoylation of Kif18A has little effect on protein stability and subcellular localization. However, compared with the wild-type control, ectopic expression of SUMO-resistant mutants of Kif18A results in a significant delay of mitotic exit. Confocal microscopy shows that cells expressing SUMO-resistant Kif18A display a compromised dissociation of BubR1 from kinetochores after anaphase onset. CONCLUSIONS Our studies reveal that sumoylation functions as an unidentified form of post-translational modification that regulates Kif18A activity during mitotic progression.
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Affiliation(s)
- Feikun Yang
- Department of Environmental Medicine, New York University Langone Medical Center, 57 Old Forge Road, Tuxedo Park, NY, 10987, USA.
| | - Yan Chen
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
| | - Wei Dai
- Department of Environmental Medicine, New York University Langone Medical Center, 57 Old Forge Road, Tuxedo Park, NY, 10987, USA. .,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, 57 Old Forge Road, Tuxedo Park, NY, 10987, USA.
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