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Wang X, Wang Q, Zhao J, Chen J, Wu R, Pan J, Li J, Wang Z, Chen Y, Guo W, Li Y. RCDdb: A manually curated database and analysis platform for regulated cell death. Comput Struct Biotechnol J 2024; 23:3211-3221. [PMID: 39257527 PMCID: PMC11384979 DOI: 10.1016/j.csbj.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/11/2024] [Accepted: 08/11/2024] [Indexed: 09/12/2024] Open
Abstract
Regulated cell death is a pivotal regulatory mechanism governing the development and homeostasis of multicellular organisms. A comprehensive understanding of RCD's regulatory mechanisms is crucial for developing novel therapeutic strategies against diseases associated with cell death, such as cancer and neurodegenerative diseases. However, existing data repositories support limited types of cell death data and lack comprehensive annotation and analytical functionalities. Thus, establishing an extensive cell death database is an urgent imperative. To address this gap, we developed the Regulated Cell Death Database (RCDdb, chenyclab.com/RCDdb), the first comprehensively manually annotated database designed to support annotations and analytical capabilities across all RCD types. We compiled 3090 marker gene annotations associated with 15 RCD types from 2180 relevant articles. The RCDdb includes annotation data on these marker genes concerning diseases, drugs, pathways, proteins, and gene expressions. Furthermore, it provides 49 diverse visualization methods to present this information. More importantly, the RCDdb features three online analysis tools for identifying and analyzing RCD-related features within user-submitted data. Furthermore, the RCDdb offers a user-friendly interface for querying, browsing, analysis, and visualization of detailed information associated with each RCD category. This resource promises to significantly aid researchers in better understanding the mechanisms of cell death, thereby accelerating progress in research and therapeutic strategies aimed at combating RCD-related diseases.
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Affiliation(s)
- Xiaopeng Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
- Southwest United Graduate School, Kunming 650092, China
| | - Qing Wang
- College of Bioengineering, Graduate School, Chongqing University, Chongqing 400044, China
| | - Jun Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jiaxin Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruo Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
| | - Juanjuan Pan
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Jiaxin Li
- Graduate School of Zunyi Medical University, Zunyi 563000, China
| | - Zechang Wang
- Economics and Management School of Wuhan University, Wuhan 430060, China
| | - Yongchang Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
- Southwest United Graduate School, Kunming 650092, China
| | - Wenting Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
| | - Yuanyuan Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
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Van Berkel AA, Koopmans F, Gonzalez-Lozano MA, Lammertse HCA, Feringa F, Bryois J, Sullivan PF, Smit AB, Toonen RF, Verhage M. Dysregulation of synaptic and developmental transcriptomic/proteomic profiles upon depletion of MUNC18-1. eNeuro 2022; 9:ENEURO.0186-22.2022. [PMID: 36257704 PMCID: PMC9668351 DOI: 10.1523/eneuro.0186-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/27/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Absence of presynaptic protein MUNC18-1 (gene: Stxbp1) leads to neuronal cell death at an immature stage before synapse formation. Here, we performed transcriptomic and proteomic profiling of immature Stxbp1 knockout (KO) cells to discover which cellular processes depend on MUNC18-1. Hippocampi of Stxbp1 KO mice showed cell-type specific dysregulation of 2123 transcripts primarily related to synaptic transmission and immune response. To further investigate direct, neuron-specific effects of MUNC18-1 depletion, a proteomic screen was performed on murine neuronal cultures at two developmental timepoints prior to onset of neuron degeneration. 399 proteins were differentially expressed, which were primarily involved in synaptic function (especially synaptic vesicle exocytosis) and neuron development. We further show that many of the downregulated proteins upon loss of MUNC18-1 are normally upregulated during this developmental stage. Thus, absence of MUNC18-1 extensively dysregulates the transcriptome and proteome, primarily affecting synaptic and developmental profiles. Lack of synaptic activity is unlikely to underlie these effects, as the changes were observed in immature neurons without functional synapses, and minimal overlap was found to activity-dependent proteins. We hypothesize that presence of MUNC18-1 is essential to advance neuron development, serving as a 'checkpoint' for neurons to initiate cell death in its absence.Significance StatementPresynaptic protein MUNC18-1 is essential for neuronal functioning. Pathogenic variants in its gene, STXBP1, are among the most common found in patients with developmental delay and epilepsy. To discern the pathogenesis in these patients, a thorough understanding of MUNC18-1's function in neurons is required. Here, we show that loss of MUNC18-1 results in extensive dysregulation of synaptic and developmental proteins in immature neurons before synapse formation. Many of the downregulated proteins are normally upregulated during this developmental stage. This indicates that MUNC18-1 is a critical regulator of neuronal development, which could play an important role in the pathogenesis of STXBP1 variant carriers.
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Affiliation(s)
- A A Van Berkel
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - F Koopmans
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - M A Gonzalez-Lozano
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - H C A Lammertse
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - F Feringa
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - J Bryois
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Nobels vag 12A, 171 77 Stockholm, Sweden
| | - P F Sullivan
- UNC Center for Psychiatric Genomics, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599-7160, USA
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Nobels vag 12A, 171 77 Stockholm, Sweden
| | - A B Smit
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - R F Toonen
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - M Verhage
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
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3
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iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death. Cells 2022; 11:cells11132018. [PMID: 35805101 PMCID: PMC9265749 DOI: 10.3390/cells11132018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Programmed cell death (PCD) is an essential biological process involved in many human pathologies. According to the continuous discovery of new PCD forms, a large number of proteins have been found to regulate PCD. Notably, post-translational modifications play critical roles in PCD process and the rapid advances in proteomics have facilitated the discovery of new PCD proteins. However, an integrative resource has yet to be established for maintaining these regulatory proteins. Here, we briefly summarize the mainstream PCD forms, as well as the current progress in the development of public databases to collect, curate and annotate PCD proteins. Further, we developed a comprehensive database, with integrated annotations for programmed cell death (iPCD), which contained 1,091,014 regulatory proteins involved in 30 PCD forms across 562 eukaryotic species. From the scientific literature, we manually collected 6493 experimentally identified PCD proteins, and an orthologous search was then conducted to computationally identify more potential PCD proteins. Additionally, we provided an in-depth annotation of PCD proteins in eight model organisms, by integrating the knowledge from 102 additional resources that covered 16 aspects, including post-translational modification, protein expression/proteomics, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein–protein interaction, drug–target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, subcellular localization and DNA and RNA element. With a data volume of 125 GB, we anticipate that iPCD can serve as a highly useful resource for further analysis of PCD in eukaryotes.
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Abstract
The potential therapeutic uses of electromagnetic fields (EMF), part of the nonionizing radiation spectrum, increase with time. Among them, those considering the potential antitumor effects exerted by the Magnetic Fields (MFs), part of the EMF entity, have gained more and more interest. A recent review on this subject reports the MFs' effect on apoptosis of tumor cells as one of the most important breakthroughs. Apoptosis is considered a key mechanism regulating the genetic stability of cells and as such is considered of fundamental importance in cancer initiation and development. According to an atomic/sub-atomic analysis, based on quantum physics, of the complexity of biological life and the role played by oxygen and its radicals in cancer biology, a possible biophysical mechanism is described. The mechanism considers the influence of MFs on apoptosis through an effect on electron spin that is able to increase reactive oxygen species (ROS) concentration. Impacting on the delicate balance between ROS production and ROS elimination in tumor cells is considered a promising cancer therapy, affecting different biological processes, such as apoptosis and metastasis. An analysis in the literature, which allows correlation between MFs exposure characteristics and their influence on apoptosis and ROS concentration, supports the validity of the mechanism.
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Affiliation(s)
- Santi Tofani
- Department of Medical Physics, Ivrea Hospital - ASL Torino Nord-Ovest TO4, Ivrea Torino, Italy.,Department of Public Health Science, School of Medicine, University of Turin, Ivrea Torino, Italy
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Gadepalli VS, Kim H, Liu Y, Han T, Cheng L. XDeathDB: a visualization platform for cell death molecular interactions. Cell Death Dis 2021; 12:1156. [PMID: 34907160 PMCID: PMC8669630 DOI: 10.1038/s41419-021-04397-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/07/2021] [Accepted: 11/09/2021] [Indexed: 12/23/2022]
Abstract
Lots of cell death initiator and effector molecules, signalling pathways and subcellular sites have been identified as key mediators in both cell death processes in cancer. The XDeathDB visualization platform provides a comprehensive cell death and their crosstalk resource for deciphering the signaling network organization of interactions among different cell death modes associated with 1461 cancer types and COVID-19, with an aim to understand the molecular mechanisms of physiological cell death in disease and facilitate systems-oriented novel drug discovery in inducing cell deaths properly. Apoptosis, autosis, efferocytosis, ferroptosis, immunogenic cell death, intrinsic apoptosis, lysosomal cell death, mitotic cell death, mitochondrial permeability transition, necroptosis, parthanatos, and pyroptosis related to 12 cell deaths and their crosstalk can be observed systematically by the platform. Big data for cell death gene-disease associations, gene-cell death pathway associations, pathway-cell death mode associations, and cell death-cell death associations is collected by literature review articles and public database from iRefIndex, STRING, BioGRID, Reactom, Pathway's commons, DisGeNET, DrugBank, and Therapeutic Target Database (TTD). An interactive webtool, XDeathDB, is built by web applications with R-Shiny, JavaScript (JS) and Shiny Server Iso. With this platform, users can search specific interactions from vast interdependent networks that occur in the realm of cell death. A multilayer spectral graph clustering method that performs convex layer aggregation to identify crosstalk function among cell death modes for a specific cancer. 147 hallmark genes of cell death could be observed in detail in these networks. These potential druggable targets are displayed systematically and tailoring networks to visualize specified relations is available to fulfil user-specific needs. Users can access XDeathDB for free at https://pcm2019.shinyapps.io/XDeathDB/ .
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Affiliation(s)
- Venkat Sundar Gadepalli
- Research Information Technology, College of Medicine, Ohio State University, 1585 Neil Ave, Columbus, OH, 43210, USA
| | - Hangil Kim
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yueze Liu
- The Grainger College of Engineering, The University of Illinois-Urbana-Champaign, Urbana and Champaign, Champaign, IL, 61801, USA
| | - Tao Han
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Lijun Cheng
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
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6
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Kassem S, van der Pan K, de Jager AL, Naber BAE, de Laat IF, Louis A, van Dongen JJM, Teodosio C, Díez P. Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis. J Proteome Res 2021; 20:4217-4230. [PMID: 34328739 PMCID: PMC8419858 DOI: 10.1021/acs.jproteome.1c00321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Nowadays, massive genomics and transcriptomics data can be generated at the single-cell level. However, proteomics in this setting is still a big challenge. Despite the great improvements in sensitivity and performance of mass spectrometry instruments and the better knowledge on sample preparation processing, it is widely acknowledged that multistep proteomics workflows may lead to substantial sample loss, especially when working with paucicellular samples. Still, in clinical fields, frequently limited sample amounts are available for downstream analysis, thereby hampering comprehensive characterization at protein level. To aim at better protein and peptide recoveries, we compare existing and novel approaches in the multistep sample preparation protocols for mass spectrometry studies, from sample collection, cell lysis, protein quantification, and electrophoresis/staining to protein digestion, peptide recovery, and LC-MS/MS instruments. From this critical evaluation, we conclude that the recent innovations and technologies, together with high quality management of samples, make proteomics on paucicellular samples possible, which will have immediate impact for the proteomics community.
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Affiliation(s)
- Sara Kassem
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Kyra van der Pan
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Anniek L. de Jager
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Inge F. de Laat
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Alesha Louis
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Jacques J. M. van Dongen
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Cristina Teodosio
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Paula Díez
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
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7
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Bose RJC, Tharmalingam N, Garcia Marques FJ, Sukumar UK, Natarajan A, Zeng Y, Robinson E, Bermudez A, Chang E, Habte F, Pitteri SJ, McCarthy JR, Gambhir SS, Massoud TF, Mylonakis E, Paulmurugan R. Reconstructed Apoptotic Bodies as Targeted "Nano Decoys" to Treat Intracellular Bacterial Infections within Macrophages and Cancer Cells. ACS NANO 2020; 14:5818-5835. [PMID: 32347709 PMCID: PMC9116903 DOI: 10.1021/acsnano.0c00921] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Staphylococcus aureus (S. aureus) is a highly pathogenic facultative anaerobe that in some instances resides as an intracellular bacterium within macrophages and cancer cells. This pathogen can establish secondary infection foci, resulting in recurrent systemic infections that are difficult to treat using systemic antibiotics. Here, we use reconstructed apoptotic bodies (ReApoBds) derived from cancer cells as "nano decoys" to deliver vancomycin intracellularly to kill S. aureus by targeting inherent "eat me" signaling of ApoBds. We prepared ReApoBds from different cancer cells (SKBR3, MDA-MB-231, HepG2, U87-MG, and LN229) and used them for vancomycin delivery. Physicochemical characterization showed ReApoBds size ranges from 80 to 150 nm and vancomycin encapsulation efficiency of 60 ± 2.56%. We demonstrate that the loaded vancomycin was able to kill intracellular S. aureus efficiently in an in vitro model of S. aureus infected RAW-264.7 macrophage cells, and U87-MG (p53-wt) and LN229 (p53-mt) cancer cells, compared to free-vancomycin treatment (P < 0.001). The vancomycin loaded ReApoBds treatment in S. aureus infected macrophages showed a two-log-order higher CFU reduction than the free-vancomycin treatment group. In vivo studies revealed that ReApoBds can specifically target macrophages and cancer cells. Vancomycin loaded ReApoBds have the potential to kill intracellular S. aureus infection in vivo in macrophages and cancer cells.
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Affiliation(s)
- Rajendran J C Bose
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Nagendran Tharmalingam
- Infectious Disease Division, Department of Medicine, Rhode Island Hospital and Alpert Medical School of Brown University, Brown University, Providence, Rhode Island 02903, United States
| | - Fernando J Garcia Marques
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Uday Kumar Sukumar
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Arutselvan Natarajan
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Yitian Zeng
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Elise Robinson
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Abel Bermudez
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Edwin Chang
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Frezghi Habte
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Jason R McCarthy
- Masonic Medical Research Institute, 2150 Bleecker Street, Utica, New York 13501, United States
| | - Sanjiv S Gambhir
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Tarik F Massoud
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
| | - Eleftherios Mylonakis
- Infectious Disease Division, Department of Medicine, Rhode Island Hospital and Alpert Medical School of Brown University, Brown University, Providence, Rhode Island 02903, United States
| | - Ramasamy Paulmurugan
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford University, 3155 Porter Drive, Palo Alto, California 94305, United States
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8
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Ravel JM, Monraz Gomez LC, Sompairac N, Calzone L, Zhivotovsky B, Kroemer G, Barillot E, Zinovyev A, Kuperstein I. Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. Cancers (Basel) 2020; 12:E990. [PMID: 32316560 PMCID: PMC7226067 DOI: 10.3390/cancers12040990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022] Open
Abstract
The processes leading to, or avoiding cell death are widely studied, because of their frequent perturbation in various diseases. Cell death occurs in three highly interconnected steps: Initiation, signaling and execution. We used a systems biology approach to gather information about all known modes of regulated cell death (RCD). Based on the experimental data retrieved from literature by manual curation, we graphically depicted the biological processes involved in RCD in the form of a seamless comprehensive signaling network map. The molecular mechanisms of each RCD mode are represented in detail. The RCD network map is divided into 26 functional modules that can be visualized contextually in the whole seamless network, as well as in individual diagrams. The resource is freely available and accessible via several web platforms for map navigation, data integration, and analysis. The RCD network map was employed for interpreting the functional differences in cell death regulation between Alzheimer's disease and non-small cell lung cancer based on gene expression data that allowed emphasizing the molecular mechanisms underlying the inverse comorbidity between the two pathologies. In addition, the map was used for the analysis of genomic and transcriptomic data from ovarian cancer patients that provided RCD map-based signatures of four distinct tumor subtypes and highlighted the difference in regulations of cell death molecular mechanisms.
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Affiliation(s)
- Jean-Marie Ravel
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
- Laboratoire de génétique médicale, CHRU-Nancy, F-54000 Nancy, France
- Inserm, NGERE, Université de Lorraine, F-54000 Nancy, France
| | - L. Cristobal Monraz Gomez
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Nicolas Sompairac
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
- Centre de Recherches Interdisciplinaires, Université Paris Descartes, 75006 Paris, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Boris Zhivotovsky
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France;
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou 215163, China
- Karolinska Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, 171 77 Stockholm, Sweden
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Inna Kuperstein
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
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9
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Morak-Młodawska B, Pluta K, Latocha M, Jeleń M, Kuśmierz D, Suwińska K, Shkurenko A, Czuba Z, Jurzak M. 10 H-1,9-diazaphenothiazine and its 10-derivatives: synthesis, characterisation and biological evaluation as potential anticancer agents. J Enzyme Inhib Med Chem 2019; 34:1298-1306. [PMID: 31307242 PMCID: PMC6691808 DOI: 10.1080/14756366.2019.1639695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
10H-1,9-diazaphenothiazine was obtained in the sulphurisation reaction of diphenylamine with elemental sulphur and transformed into new 10-substituted derivatives, containing alkyl and dialkylaminoalkyl groups at the thiazine nitrogen atom. The 1,9-diazaphenothiazine ring system was identified with advanced 1H and 13C NMR techniques (COSY, NOESY, HSQC and HMBC) and confirmed by X-ray diffraction analysis of the methyl derivative. The compounds exhibited significant anticancer activities against the human glioblastoma SNB-19, melanoma C-32 and breast cancer MDA-MB-231 cell lines. The most active 1,9-diazaphenothiazines were the derivatives with the propynyl and N, N-diethylaminoethyl groups being more potent than cisplatin. For those two compounds, the expression of H3, TP53, CDKN1A, BCL-2 and BAX genes was detected by the RT-QPCR method. The proteome profiling study showed the most probable compound action on SNB-19 cells through the intrinsic mitochondrial pathway of apoptosis. The 1,9-diazaphenotiazine system seems to be more potent than known isomeric ones (1,6-diaza-, 1,8-diaza-, 2,7-diaza- and 3,6-diazaphenothiazine).
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Affiliation(s)
- Beata Morak-Młodawska
- Department of Organic Chemistry, School of Pharmacy with the Division of Laboratory Medicine, The Medical University of Silesia, Sosnowiec, Poland
| | - Krystian Pluta
- Department of Organic Chemistry, School of Pharmacy with the Division of Laboratory Medicine, The Medical University of Silesia, Sosnowiec, Poland
| | - Małgorzata Latocha
- Department of Cell Biology, School of Pharmacy with the Division of Laboratory Medicine, The Medical University of Silesia, Sosnowiec, Poland
| | - Małgorzata Jeleń
- Department of Organic Chemistry, School of Pharmacy with the Division of Laboratory Medicine, The Medical University of Silesia, Sosnowiec, Poland
| | - Dariusz Kuśmierz
- Department of Cell Biology, School of Pharmacy with the Division of Laboratory Medicine, The Medical University of Silesia, Sosnowiec, Poland
| | - Kinga Suwińska
- Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszyński University, Warszawa, Poland
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | - Aleksander Shkurenko
- Division of Physical Functional Materials Design, Discovery & Development Research Group (FMD3), Sciences and Engineering Advanced Membranes & Porous Materials (AMPM), King Abdullah University of Science and Technology (KAU ST), Thuwal, Kingdom of Saudi Arabia
| | - Zenon Czuba
- Department of Microbiology and Immunology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Magdalena Jurzak
- Department of Cell Biology, School of Pharmacy with the Division of Laboratory Medicine, The Medical University of Silesia, Sosnowiec, Poland
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10
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Deng W, Ma L, Zhang Y, Zhou J, Wang Y, Liu Z, Xue Y. THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. Autophagy 2019; 14:296-310. [PMID: 29157087 DOI: 10.1080/15548627.2017.1402990] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org ), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of ATG genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.
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Affiliation(s)
- Wankun Deng
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Lili Ma
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Ying Zhang
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Jiaqi Zhou
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Yongbo Wang
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Zexian Liu
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China.,b State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine , Sun Yat-sen University Cancer Center , 651 Dongfeng Road East, 510060 , Guangzhou , Guangdong , P. R. China
| | - Yu Xue
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
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11
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Aouacheria A, Navratil V, Combet C. Database and Bioinformatic Analysis of BCL-2 Family Proteins and BH3-Only Proteins. Methods Mol Biol 2019; 1877:23-43. [PMID: 30535996 DOI: 10.1007/978-1-4939-8861-7_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BCL-2 proteins correspond to a structurally, functionally, and phylogenetically heterogeneous group of regulators that play crucial roles in the life and death of animal cells. Some of these regulators also represent therapeutic targets in human diseases including cancer. In the omics era, there is great need for easy data retrieval and fast analysis of the molecular players involved in cell death. In this chapter, we present generic and specific computational resources (such as the reference database BCL2DB) as well as bioinformatics tools that can be used to investigate BCL-2 homologs and BH3-only proteins.
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Affiliation(s)
- Abdel Aouacheria
- ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, UMR 5554, CNRS, IRD, EPHE, Montpellier, France.
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Christophe Combet
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm U1052, CNRS 5286, Université Claude Bernard Lyon 1, Centre Léon Bérard, Lyon, France
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12
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Rybczynska AA, Boersma HH, de Jong S, Gietema JA, Noordzij W, Dierckx RAJO, Elsinga PH, van Waarde A. Avenues to molecular imaging of dying cells: Focus on cancer. Med Res Rev 2018. [PMID: 29528513 PMCID: PMC6220832 DOI: 10.1002/med.21495] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Successful treatment of cancer patients requires balancing of the dose, timing, and type of therapeutic regimen. Detection of increased cell death may serve as a predictor of the eventual therapeutic success. Imaging of cell death may thus lead to early identification of treatment responders and nonresponders, and to “patient‐tailored therapy.” Cell death in organs and tissues of the human body can be visualized, using positron emission tomography or single‐photon emission computed tomography, although unsolved problems remain concerning target selection, tracer pharmacokinetics, target‐to‐nontarget ratio, and spatial and temporal resolution of the scans. Phosphatidylserine exposure by dying cells has been the most extensively studied imaging target. However, visualization of this process with radiolabeled Annexin A5 has not become routine in the clinical setting. Classification of death modes is no longer based only on cell morphology but also on biochemistry, and apoptosis is no longer found to be the preponderant mechanism of cell death after antitumor therapy, as was earlier believed. These conceptual changes have affected radiochemical efforts. Novel probes targeting changes in membrane permeability, cytoplasmic pH, mitochondrial membrane potential, or caspase activation have recently been explored. In this review, we discuss molecular changes in tumors which can be targeted to visualize cell death and we propose promising biomarkers for future exploration.
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Affiliation(s)
- Anna A Rybczynska
- Molecular Imaging Center, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Genetics, University of Groningen, Groningen, the Netherlands
| | - Hendrikus H Boersma
- Molecular Imaging Center, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Clinical Pharmacy & Pharmacology, University of Groningen, Groningen, the Netherlands
| | - Steven de Jong
- Department of Medical Oncology, University of Groningen, Groningen, the Netherlands
| | - Jourik A Gietema
- Department of Medical Oncology, University of Groningen, Groningen, the Netherlands
| | - Walter Noordzij
- Molecular Imaging Center, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rudi A J O Dierckx
- Molecular Imaging Center, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Nuclear Medicine, Ghent University, Ghent, Belgium
| | - Philip H Elsinga
- Molecular Imaging Center, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Aren van Waarde
- Molecular Imaging Center, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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13
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Kumar S, Cieplak P. Effect of phosphorylation and single nucleotide polymorphisms on caspase substrates processing. Apoptosis 2018; 23:194-200. [DOI: 10.1007/s10495-018-1442-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Imperlini E, Gnecchi M, Rognoni P, Sabidò E, Ciuffreda MC, Palladini G, Espadas G, Mancuso FM, Bozzola M, Malpasso G, Valentini V, Palladini G, Orrù S, Ferraro G, Milani P, Perlini S, Salvatore F, Merlini G, Lavatelli F. Proteotoxicity in cardiac amyloidosis: amyloidogenic light chains affect the levels of intracellular proteins in human heart cells. Sci Rep 2017; 7:15661. [PMID: 29142197 PMCID: PMC5688098 DOI: 10.1038/s41598-017-15424-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022] Open
Abstract
AL amyloidosis is characterized by widespread deposition of immunoglobulin light chains (LCs) as amyloid fibrils. Cardiac involvement is frequent and leads to life-threatening cardiomyopathy. Besides the tissue alteration caused by fibrils, clinical and experimental evidence indicates that cardiac damage is also caused by proteotoxicity of prefibrillar amyloidogenic species. As in other amyloidoses, the damage mechanisms at cellular level are complex and largely undefined. We have characterized the molecular changes in primary human cardiac fibroblasts (hCFs) exposed in vitro to soluble amyloidogenic cardiotoxic LCs from AL cardiomyopathy patients. To evaluate proteome alterations caused by a representative cardiotropic LC, we combined gel-based with label-free shotgun analysis and performed bioinformatics and data validation studies. To assess the generalizability of our results we explored the effects of multiple LCs on hCF viability and on levels of a subset of cellular proteins. Our results indicate that exposure of hCFs to cardiotropic LCs translates into proteome remodeling, associated with apoptosis activation and oxidative stress. The proteome alterations affect proteins involved in cytoskeletal organization, protein synthesis and quality control, mitochondrial activity and metabolism, signal transduction and molecular trafficking. These results support and expand the concept that soluble amyloidogenic cardiotropic LCs exert toxic effects on cardiac cells.
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Affiliation(s)
- Esther Imperlini
- IRCCS SDN, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Massimiliano Gnecchi
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Molecular Medicine, Unit of Cardiology, University of Pavia, Pavia, Italy.,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Paola Rognoni
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Eduard Sabidò
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maria Chiara Ciuffreda
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giovanni Palladini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Mattia Mancuso
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Margherita Bozzola
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giuseppe Malpasso
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Veronica Valentini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giuseppina Palladini
- Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Stefania Orrù
- IRCCS SDN, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy.,Department of Movement Sciences, "Parthenope" University, Naples, Italy
| | - Giovanni Ferraro
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Paolo Milani
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Stefano Perlini
- Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy. .,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Pavia, Italy.
| | - Giampaolo Merlini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy.
| | - Francesca Lavatelli
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
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15
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Tran TT, Strozynski M, Thiede B. Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/12/2017] [Accepted: 04/27/2017] [Indexed: 01/06/2023]
Affiliation(s)
- The Trung Tran
- Department of Biosciences; University of Oslo; Oslo Norway
| | | | - Bernd Thiede
- Department of Biosciences; University of Oslo; Oslo Norway
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16
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Tran TT, Bollineni RC, Strozynski M, Koehler CJ, Thiede B. Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches. J Proteome Res 2017; 16:2571-2578. [PMID: 28508642 DOI: 10.1021/acs.jproteome.7b00126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies were analyzed using these two databases. Several nonalternative splice variant-1-specific peptides were found in both cell lines, and some of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several nonalternative splice variant-1-specific peptides, and some of them showed clear quantitative differences between the two states.
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Affiliation(s)
- Trung T Tran
- Department of Biosciences, University of Oslo , Oslo 0316, Norway
| | - Ravi C Bollineni
- Department of Biosciences, University of Oslo , Oslo 0316, Norway
| | | | | | - Bernd Thiede
- Department of Biosciences, University of Oslo , Oslo 0316, Norway
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17
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Helander L, Sharma A, Krokan HE, Plaetzer K, Krammer B, Tortik N, Gederaas OA, Slupphaug G, Hagen L. Photodynamic treatment with hexyl-aminolevulinate mediates reversible thiol oxidation in core oxidative stress signaling proteins. MOLECULAR BIOSYSTEMS 2016; 12:796-805. [DOI: 10.1039/c5mb00744e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
HAL-PDT mediates reversible cysteine oxidation in core proteins involved in oxidative stress and apoptotic signalling.
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Affiliation(s)
- Linda Helander
- Department of Cancer Research and Molecular Medicine
- Norwegian University of Science and Technology
- Norway
| | - Animesh Sharma
- Department of Cancer Research and Molecular Medicine
- Norwegian University of Science and Technology
- Norway
- PROMEC Core Facility for Proteomics and Metabolomics
- Norwegian University of Science and Technology
| | - Hans E. Krokan
- Department of Cancer Research and Molecular Medicine
- Norwegian University of Science and Technology
- Norway
| | - Kristjan Plaetzer
- Laboratory of Photodynamic Inactivation of Microorganisms
- Department of Materials Science and Physics
- University of Salzburg
- Austria
| | - Barbara Krammer
- Division of Molecular Tumor Biology
- Department of Molecular Biology
- University of Salzburg
- Austria
| | - Nicole Tortik
- Laboratory of Photodynamic Inactivation of Microorganisms
- Department of Materials Science and Physics
- University of Salzburg
- Austria
| | - Odrun A. Gederaas
- Department of Cancer Research and Molecular Medicine
- Norwegian University of Science and Technology
- Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine
- Norwegian University of Science and Technology
- Norway
- PROMEC Core Facility for Proteomics and Metabolomics
- Norwegian University of Science and Technology
| | - Lars Hagen
- Department of Cancer Research and Molecular Medicine
- Norwegian University of Science and Technology
- Norway
- PROMEC Core Facility for Proteomics and Metabolomics
- Norwegian University of Science and Technology
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18
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Tebbi A, Guittet O, Tuphile K, Cabrié A, Lepoivre M. Caspase-dependent Proteolysis of Human Ribonucleotide Reductase Small Subunits R2 and p53R2 during Apoptosis. J Biol Chem 2015; 290:14077-90. [PMID: 25878246 DOI: 10.1074/jbc.m115.649640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductase (RnR) is a key enzyme synthesizing deoxyribonucleotides for DNA replication and repair. In mammals, the R1 catalytic subunit forms an active complex with either one of the two small subunits R2 and p53R2. Expression of R2 is S phase-specific and required for DNA replication. The p53R2 protein is expressed throughout the cell cycle and in quiescent cells where it provides dNTPs for mitochondrial DNA synthesis. Participation of R2 and p53R2 in DNA repair has also been suggested. In this study, we investigated the fate of the RnR subunits during apoptosis. The p53R2 protein was cleaved in a caspase-dependent manner in K-562 cells treated with inhibitors of the Bcr-Abl oncogenic kinase and in HeLa 229 cells incubated with TNF-α and cycloheximide. The cleavage site was mapped between Asp(342) and Asn(343). Caspase attack released a C-terminal p53R2 peptide of nine residues containing the conserved heptapeptide essential for R1 binding. As a consequence, the cleaved p53R2 protein was inactive. In vitro, purified caspase-3 and -8 could release the C-terminal tail of p53R2. Knocking down these caspases, but not caspase-2, -7, and -10, also inhibited p53R2 cleavage in cells committed to die via the extrinsic death receptor pathway. The R2 subunit was subjected to caspase- and proteasome-dependent proteolysis, which was prevented by siRNA targeting caspase-8. Knocking down caspase-3 was ineffective. Protein R1 was not subjected to degradation. Adding deoxyribonucleosides to restore dNTP pools transiently protected cells from apoptosis. These data identify RnR activity as a prosurvival function inactivated by proteolysis during apoptosis.
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Affiliation(s)
- Ali Tebbi
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and Department of Virology, Institut Pasteur, Pathogenesis of Hepatitis B Virus, 75015 Paris, France
| | - Olivier Guittet
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Karine Tuphile
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Aimeric Cabrié
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Michel Lepoivre
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
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19
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Fridman A, Pak I, Butts BD, Hoek M, Nicholson DW, Mehmet H. MerCASBA: an updated and refined database of caspase substrates. Apoptosis 2013; 18:369-71. [PMID: 23334582 DOI: 10.1007/s10495-012-0789-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Størvold GL, Landskron J, Strozynski M, Arntzen MØ, Koehler CJ, Kalland ME, Taskén K, Thiede B. Quantitative profiling of tyrosine phosphorylation revealed changes in the activity of the T cell receptor signaling pathway upon cisplatin-induced apoptosis. J Proteomics 2013; 91:344-57. [DOI: 10.1016/j.jprot.2013.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/08/2013] [Accepted: 07/22/2013] [Indexed: 12/18/2022]
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21
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Arntzen MØ, Bull VH, Thiede B. Cell death proteomics database: consolidating proteomics data on cell death. J Proteome Res 2013; 12:2206-13. [PMID: 23537399 DOI: 10.1021/pr4000703] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Programmed cell death is a ubiquitous process of utmost importance for the development and maintenance of multicellular organisms. More than 10 different types of programmed cell death forms have been discovered. Several proteomics analyses have been performed to gain insight in proteins involved in the different forms of programmed cell death. To consolidate these studies, we have developed the cell death proteomics (CDP) database, which comprehends data from apoptosis, autophagy, cytotoxic granule-mediated cell death, excitotoxicity, mitotic catastrophe, paraptosis, pyroptosis, and Wallerian degeneration. The CDP database is available as a web-based database to compare protein identifications and quantitative information across different experimental setups. The proteomics data of 73 publications were integrated and unified with protein annotations from UniProt-KB and gene ontology (GO). Currently, more than 6,500 records of more than 3,700 proteins are included in the CDP. Comparing apoptosis and autophagy using overrepresentation analysis of GO terms, the majority of enriched processes were found in both, but also some clear differences were perceived. Furthermore, the analysis revealed differences and similarities of the proteome between autophagosomal and overall autophagy. The CDP database represents a useful tool to consolidate data from proteome analyses of programmed cell death and is available at http://celldeathproteomics.uio.no.
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Affiliation(s)
- Magnus Ø Arntzen
- The Biotechnology Centre of Oslo, University of Oslo, 0317 Oslo, Norway.
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22
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Koehler CJ, Arntzen MØ, de Souza GA, Thiede B. An Approach for Triplex-Isobaric Peptide Termini Labeling (Triplex-IPTL). Anal Chem 2013; 85:2478-85. [DOI: 10.1021/ac3035508] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Christian J. Koehler
- The Biotechnology
Centre of
Oslo, University of Oslo, P.O. Box 1125
Blindern, 0317 Oslo, Norway
| | - Magnus Ø. Arntzen
- The Biotechnology
Centre of
Oslo, University of Oslo, P.O. Box 1125
Blindern, 0317 Oslo, Norway
| | - Gustavo Antonio de Souza
- Department
of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, 0424 Oslo, Norway
| | - Bernd Thiede
- The Biotechnology
Centre of
Oslo, University of Oslo, P.O. Box 1125
Blindern, 0317 Oslo, Norway
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23
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Crawford ED, Seaman JE, Agard N, Hsu GW, Julien O, Mahrus S, Nguyen H, Shimbo K, Yoshihara HAI, Zhuang M, Chalkley RJ, Wells JA. The DegraBase: a database of proteolysis in healthy and apoptotic human cells. Mol Cell Proteomics 2012; 12:813-24. [PMID: 23264352 DOI: 10.1074/mcp.o112.024372] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteolysis is a critical post-translational modification for regulation of cellular processes. Our lab has previously developed a technique for specifically labeling unmodified protein N termini, the α-aminome, using the engineered enzyme, subtiligase. Here we present a database, called the DegraBase (http://wellslab.ucsf.edu/degrabase/), which compiles 8090 unique N termini from 3206 proteins directly identified in subtiligase-based positive enrichment mass spectrometry experiments in healthy and apoptotic human cell lines. We include both previously published and unpublished data in our analysis, resulting in a total of 2144 unique α-amines identified in healthy cells, and 6990 in cells undergoing apoptosis. The N termini derive from three general categories of proteolysis with respect to cleavage location and functional role: translational N-terminal methionine processing (∼10% of total proteolysis), sites close to the translational N terminus that likely represent removal of transit or signal peptides (∼25% of total), and finally, other endoproteolytic cuts (∼65% of total). Induction of apoptosis causes relatively little change in the first two proteolytic categories, but dramatic changes are seen in endoproteolysis. For example, we observed 1706 putative apoptotic caspase cuts, more than double the total annotated sites in the CASBAH and MEROPS databases. In the endoproteolysis category, there are a total of nearly 3000 noncaspase nontryptic cleavages that are not currently reported in the MEROPS database. These studies significantly increase the annotation for all categories of proteolysis in human cells and allow public access for investigators to explore interesting proteolytic events in healthy and apoptotic human cells.
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Affiliation(s)
- Emily D Crawford
- Department of Pharmaceutical Chemistry, University of California-San Francisco, CA 94158, USA
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Colaert N, Maddelein D, Impens F, Van Damme P, Plasman K, Helsens K, Hulstaert N, Vandekerckhove J, Gevaert K, Martens L. The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events. Nucleic Acids Res 2012; 41:D333-7. [PMID: 23093603 PMCID: PMC3531153 DOI: 10.1093/nar/gks998] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We here present The Online Protein Processing Resource (TOPPR; http://iomics.ugent.be/toppr/), an online database that contains thousands of published proteolytically processed sites in human and mouse proteins. These cleavage events were identified with COmbinded FRActional DIagonal Chromatography proteomics technologies, and the resulting database is provided with full data provenance. Indeed, TOPPR provides an interactive visual display of the actual fragmentation mass spectrum that led to each identification of a reported processed site, complete with fragment ion annotations and search engine scores. Apart from warehousing and disseminating these data in an intuitive manner, TOPPR also provides an online analysis platform, including methods to analyze protease specificity and substrate-centric analyses. Concretely, TOPPR supports three ways to retrieve data: (i) the retrieval of all substrates for one or more cellular stimuli or assays; (ii) a substrate search by UniProtKB/Swiss-Prot accession number, entry name or description; and (iii) a motif search that retrieves substrates matching a user-defined protease specificity profile. The analysis of the substrates is supported through the presence of a variety of annotations, including predicted secondary structure, known domains and experimentally obtained 3D structure where available. Across substrates, substrate orthologs and conserved sequence stretches can also be shown, with iceLogo visualization provided for the latter.
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Affiliation(s)
- Niklaas Colaert
- Department of Medical Protein Research, VIB, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium
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25
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Dix MM, Simon GM, Wang C, Okerberg E, Patricelli MP, Cravatt BF. Functional interplay between caspase cleavage and phosphorylation sculpts the apoptotic proteome. Cell 2012; 150:426-40. [PMID: 22817901 DOI: 10.1016/j.cell.2012.05.040] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/26/2012] [Accepted: 05/16/2012] [Indexed: 12/14/2022]
Abstract
Caspase proteases are principal mediators of apoptosis, where they cleave hundreds of proteins. Phosphorylation also plays an important role in apoptosis, although the extent to which proteolytic and phosphorylation pathways crosstalk during programmed cell death remains poorly understood. Using a quantitative proteomic platform that integrates phosphorylation sites into the topographical maps of proteins, we identify a cohort of over 500 apoptosis-specific phosphorylation events and show that they are enriched on cleaved proteins and clustered around sites of caspase proteolysis. We find that caspase cleavage can expose new sites for phosphorylation, and, conversely, that phosphorylation at the +3 position of cleavage sites can directly promote substrate proteolysis by caspase-8. This study provides a global portrait of the apoptotic phosphoproteome, revealing heretofore unrecognized forms of functional crosstalk between phosphorylation and caspase proteolytic pathways that lead to enhanced rates of protein cleavage and the unveiling of new sites for phosphorylation.
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Affiliation(s)
- Melissa M Dix
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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26
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Thiede B, Koehler CJ, Strozynski M, Treumann A, Stein R, Zimny-Arndt U, Schmid M, Jungblut PR. High resolution quantitative proteomics of HeLa cells protein species using stable isotope labeling with amino acids in cell culture(SILAC), two-dimensional gel electrophoresis(2DE) and nano-liquid chromatograpohy coupled to an LTQ-OrbitrapMass spectrometer. Mol Cell Proteomics 2012; 12:529-38. [PMID: 23033477 DOI: 10.1074/mcp.m112.019372] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proteomics field has shifted over recent years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel-free workflows because of the tremendous developments in isotopic labeling techniques, nano-liquid chromatography, and high-resolution mass spectrometry. However, 2-DE still offers the highest resolution in protein separation. Therefore, we combined stable isotope labeling with amino acids in cell culture of controls and apoptotic HeLa cells with 2-DE and the subsequent analysis of tryptic peptides via nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer to obtain quantitative data using the methods with the highest resolving power on all levels of the proteomics workflow. More than 1,200 proteins with more than 2,700 protein species were identified and quantified from 816 Coomassie Brilliant Blue G-250 stained 2-DE spots. About half of the proteins were identified and quantified only in single 2-DE spots. The majority of spots revealed one to five proteins; however, in one 2-DE spot, up to 23 proteins were identified. Only half of the 2-DE spots represented a dominant protein with more than 90% of the whole protein amount. Consequently, quantification based on staining intensities in 2-DE gels would in approximately half of the spots be imprecise, and minor components could not be quantified. These problems are circumvented by quantification using stable isotope labeling with amino acids in cell culture. Despite challenges, as shown in detail for lamin A/C and vimentin, the quantitative changes of protein species can be detected. The combination of 2-DE with high-resolution nano-liquid chromatography-mass spectrometry allowed us to identify proteomic changes in apoptotic cells that would be unobservable using any of the other previously employed proteomic workflows.
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Affiliation(s)
- Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, Gaustadalleen 21, 0349 Oslo, Norway.
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McPhee CK, Balgley BM, Nelson C, Hill JH, Batlevi Y, Fang X, Lee CS, Baehrecke EH. Identification of factors that function in Drosophila salivary gland cell death during development using proteomics. Cell Death Differ 2012; 20:218-25. [PMID: 22935612 DOI: 10.1038/cdd.2012.110] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Proteasome inhibitors induce cell death and are used in cancer therapy, but little is known about the relationship between proteasome impairment and cell death under normal physiological conditions. Here, we investigate the relationship between proteasome function and larval salivary gland cell death during development in Drosophila. Drosophila larval salivary gland cells undergo synchronized programmed cell death requiring both caspases and autophagy (Atg) genes during development. Here, we show that ubiquitin proteasome system (UPS) function is reduced during normal salivary gland cell death, and that ectopic proteasome impairment in salivary gland cells leads to early DNA fragmentation and salivary gland condensation in vivo. Shotgun proteomic analyses of purified dying salivary glands identified the UPS as the top category of proteins enriched, suggesting a possible compensatory induction of these factors to maintain proteolysis during cell death. We compared the proteome following ectopic proteasome impairment to the proteome during developmental cell death in salivary gland cells. Proteins that were enriched in both populations of cells were screened for their function in salivary gland degradation using RNAi knockdown. We identified several factors, including trol, a novel gene CG11880, and the cop9 signalsome component cop9 signalsome 6, as required for Drosophila larval salivary gland degradation.
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Affiliation(s)
- C K McPhee
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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28
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Tomazella GG, Kassahun H, Nilsen H, Thiede B. Quantitative proteome analysis reveals RNA processing factors as modulators of ionizing radiation-induced apoptosis in the C. elegans germline. J Proteome Res 2012; 11:4277-88. [PMID: 22757771 DOI: 10.1021/pr300386z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nematode Caenorhabditis elegans is an organism most recognized for forward and reverse genetic and functional genomic approaches. Proteomic analyses of DNA damage-induced apoptosis have not been shown because of a limited number of cells undergoing apoptosis. We applied mass spectrometry-based quantitative proteomics to evaluate protein changes induced by ionizing radiation (IR) in isolated C. elegans germlines. For this purpose, we used isobaric peptide termini labeling (IPTL) combined with the data analysis tool IsobariQ, which utilizes MS/MS spectra for relative quantification of peak pairs formed during fragmentation. Using stringent statistical critera, we identified 48 proteins to be significantly up- or down-regulated, most of which are part of a highly interconnected protein-protein interaction network dominated by proteins involved in translational control. RNA-mediated depletion of a selection of the IR-regulated proteins revealed that the conserved CAR-1/CGH-1/CEY-3 germline RNP complex acts as a novel negative regulator of DNA-damage induced apoptosis. Finally, a central role of nucleolar proteins in orchestrating these responses was confirmed as the H/ACA snRNP protein GAR-1 was required for IR-induced apoptosis in the C. elegans germline.
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Hanash S, Schliekelman M, Zhang Q, Taguchi A. Integration of proteomics into systems biology of cancer. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:327-37. [PMID: 22407608 DOI: 10.1002/wsbm.1169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Deciphering the complexity and heterogeneity of cancer, benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date, and the challenges involved in integrating diverse datasets are addressed in this review.
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Affiliation(s)
- S Hanash
- Molecular Diagnostics Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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