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Bhardwaj S, Bulluss M, D'Aubeterre A, Derakhshani A, Penner R, Mahajan M, Mahajan VB, Dufour A. Integrating the analysis of human biopsies using post-translational modifications proteomics. Protein Sci 2024; 33:e4979. [PMID: 38533548 DOI: 10.1002/pro.4979] [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: 01/05/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.
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Affiliation(s)
- Sonali Bhardwaj
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mitchell Bulluss
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ana D'Aubeterre
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Afshin Derakhshani
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Regan Penner
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - MaryAnn Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Antoine Dufour
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Demeulemeester N, Gébelin M, Caldi Gomes L, Lingor P, Carapito C, Martens L, Clement L. msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level. Mol Cell Proteomics 2024; 23:100708. [PMID: 38154689 PMCID: PMC10875266 DOI: 10.1016/j.mcpro.2023.100708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/19/2023] [Accepted: 12/24/2023] [Indexed: 12/30/2023] Open
Abstract
In the era of open-modification search engines, more posttranslational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, metastasis, and aging. However, despite these advances in modification identification, statistical methods for PTM-level quantification and differential analysis have yet to catch up. This absence can partly be explained by statistical challenges inherent to the data, such as the confounding of PTM intensities with its parent protein abundance. Therefore, we have developed msqrob2PTM, a new workflow in the msqrob2 universe capable of differential abundance analysis at the PTM and at the peptidoform level. The latter is important for validating PTMs found as significantly differential. Indeed, as our method can deal with multiple PTMs per peptidoform, there is a possibility that significant PTMs stem from one significant peptidoform carrying another PTM, hinting that it might be the other PTM driving the perceived differential abundance. Our workflows can flag both differential peptidoform abundance (DPA) and differential peptidoform usage (DPU). This enables a distinction between direct assessment of differential abundance of peptidoforms (DPA) and differences in the relative usage of peptidoforms corrected for corresponding protein abundances (DPU). For DPA, we directly model the log2-transformed peptidoform intensities, while for DPU, we correct for parent protein abundance by an intermediate normalization step which calculates the log2-ratio of the peptidoform intensities to their summarized parent protein intensities. We demonstrated the utility and performance of msqrob2PTM by applying it to datasets with known ground truth, as well as to biological PTM-rich datasets. Our results show that msqrob2PTM is on par with, or surpassing the performance of, the current state-of-the-art methods. Moreover, msqrob2PTM is currently unique in providing output at the peptidoform level.
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Affiliation(s)
- Nina Demeulemeester
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Marie Gébelin
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Infrastructure Nationale de Protéomique ProFI - FR2048, Université de Strasbourg, Strasbourg, France
| | - Lucas Caldi Gomes
- Department of Neurology, Technical University Munich, Munich, Germany
| | - Paul Lingor
- Department of Neurology, Technical University Munich, Munich, Germany
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Infrastructure Nationale de Protéomique ProFI - FR2048, Université de Strasbourg, Strasbourg, France
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
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Dong J, Xu Q, Chen S, Lei H, Wang J, Yan S, Qian C, Wang X. Comparative Proteomic and Phospho-proteomic Analysis of Mouse Placentas Generated via In Vivo and In Vitro Fertilization. Reprod Sci 2023; 30:1143-1156. [PMID: 36280645 DOI: 10.1007/s43032-022-01109-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/13/2022] [Indexed: 10/31/2022]
Abstract
Offspring conceived by assisted reproductive technologies (ART) have increased risk of suffering from gestational complications, and placental dysfunction is related with the adverse outcomes. Studies have revealed that abnormal or adaptive changes can occur in ART placentas, but the potential reasons are not fully understood. Hereby, we tried to use proteomics and phospho-proteomics to find the underlying mechanisms responsible for the changes of ART placentas. Liquid chromatography-tandem mass spectrometry was utilized to perform proteome and phospho-proteome detection on mouse placentas. The differential expressed proteins (DEPs) or phospho-proteins (DEPPs) were analyzed based on subcellular localization, functional classification, and enrichment. Western blot was used to verify the DEPs (Afadin, ZO-1, Ace2, Agt, Slc7a5, and Slc38a10) and measure mTOR signaling activities (mTOR, Rps6, and 4Ebp1). The data showed that 161 DEPs and 304 DEPPs were found in proteome and phospho-proteome, respectively. Multiple biological processes were enriched based on those DEPs and DEPPs, and renin-angiotensin system, cell junction, and PI3K-Akt pathway were investigated. By protein expression identification, two key proteins associated with renin-angiotensin system (Ace2 and Agt) were down-regulated, and the levels of Afadin and ZO-1 (related with cell junction) as well as Slc38a10 were increased in IVF placentas. In addition, mTOR downstream activities were increased as shown by p-Rps6 and p-4Ebp1 in IVF placentas. In conclusion, IVF leads to the changes of cell junction, renin-angiotensin system, amino acid transport, and increased mTOR signaling in mouse placentas, which may be associated with the altered structure and function of IVF placentas.
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Affiliation(s)
- Jie Dong
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China
| | - Qian Xu
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China
| | - Shuqiang Chen
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China
| | - Hui Lei
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China
| | - Jingjing Wang
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China
| | - Song Yan
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China
| | - Chenxi Qian
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China
| | - Xiaohong Wang
- Department of Obstetrics and Gynaecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi Province, China.
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Pongprayoon W, Panya A, Jaresitthikunchai J, Phaonakrop N, Roytrakul S. Phosphoprotein Profile of Rice ( Oryza sativa L.) Seedlings under Osmotic Stress after Pretreatment with Chitosan. PLANTS (BASEL, SWITZERLAND) 2022; 11:2729. [PMID: 36297750 PMCID: PMC9611960 DOI: 10.3390/plants11202729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
This study aims to identify novel chitosan (CTS)-responsive phosphoproteins in Leung Pratew 123 (LPT123) and Khao Dawk Mali 105 (KDML105) as drought-sensitive rice cultivars and differences in the CTS response. Rice seeds were soaked in CTS solution before germination, and 2- and 4-week-old rice seedlings sprayed with CTS before osmotic stress comprised the following four groups: (1) seedlings treated with distilled water; (2) seedlings treated with CTS; (3) seedlings pretreated with distilled water and subjected to osmotic stress; and (4) seedlings pretreated with CTS and subjected to osmotic stress. Phosphoproteins of leaf tissues were enriched using immobilized metal affinity chromatography (IMAC) before tryptic digestion and analysis via LC-MS. Phosphoprotein profiling analyses led to the identification of 4721 phosphoproteins representing 1052 and 1040 unique phosphoproteins in the LPT123 and KDML105 seedlings, respectively. In response to CTS pretreatment before osmotic stress, 22 differently expressed proteins were discovered, of which 10 and 12 were identified in the LPT123 and KDML105, respectively. These proteins are typically involved in signaling, transport, protein folding, protein degradation, and metabolism. This study provides fruitful data to understand the signal transduction mechanisms of rice seedlings pretreated with CTS before exposure to osmotic stress.
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Affiliation(s)
- Wasinee Pongprayoon
- Department of Biology, Faculty of Science, Burapha University, 169 Longhaad Bangsaen Rd, Saensook, Mueang, Chonburi 20131, Thailand
| | - Atikorn Panya
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Janthima Jaresitthikunchai
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Narumon Phaonakrop
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
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Hegde M, Daimary UD, Jose S, Sajeev A, Chinnathambi A, Alharbi SA, Shakibaei M, Kunnumakkara AB. Differential Expression of Genes Regulating Store-operated Calcium Entry in Conjunction With Mitochondrial Dynamics as Potential Biomarkers for Cancer: A Single-Cell RNA Analysis. Front Genet 2022; 13:866473. [PMID: 35711942 PMCID: PMC9197647 DOI: 10.3389/fgene.2022.866473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of intracellular concentration of calcium levels is crucial for cell signaling, homeostasis, and in the pathology of diseases including cancer. Agonist-induced entry of calcium ions into the non-excitable cells is mediated by store-operated calcium channels (SOCs). This pathway is activated by the release of calcium ions from the endoplasmic reticulum and further regulated by the calcium uptake through mitochondria leading to calcium-dependent inactivation of calcium-release activated calcium channels (CARC). SOCs including stromal interaction molecules (STIM) and ORAI proteins have been implicated in tumor growth, progression, and metastasis. In the present study, we analyzed the mRNA and protein expression of genes mediating SOCs-STIM1, STIM2, ORAI1, ORAI2, ORAI3, TRPC1, TRPC3, TRPC4, TRPC5, TRPC6, TRPC7, TRPV1, TRPV2, TRPM1, and TRPM7 in head and neck squamous cell cancer (HNSC) patients using TCGA and CPTAC analysis. Further, our in silico analysis showed a significant correlation between the expression of SOCs and genes involved in the mitochondrial dynamics (MDGs) both at mRNA and protein levels. Protein-protein docking results showed lower binding energy for SOCs with MDGs. Subsequently, we validated these results using gene expression and single-cell RNA sequencing datasets retrieved from Gene Expression Omnibus (GEO). Single-cell gene expression analysis of HNSC tumor tissues revealed that SOCs expression is remarkably associated with the MDGs expression in both cancer and fibroblast cells.
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Affiliation(s)
- Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India.,DBT-AIST International Center for Translational and Environmental Research, Indian Institute of Technology-Guwahati, Guwahati, India
| | - Uzini Devi Daimary
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India.,DBT-AIST International Center for Translational and Environmental Research, Indian Institute of Technology-Guwahati, Guwahati, India
| | - Sandra Jose
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India.,DBT-AIST International Center for Translational and Environmental Research, Indian Institute of Technology-Guwahati, Guwahati, India
| | - Anjana Sajeev
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India.,DBT-AIST International Center for Translational and Environmental Research, Indian Institute of Technology-Guwahati, Guwahati, India
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sulaiman Ali Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mehdi Shakibaei
- Musculoskeletal Research Group and Tumor Biology, Faculty of Medicine, Institute of Anatomy, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India.,DBT-AIST International Center for Translational and Environmental Research, Indian Institute of Technology-Guwahati, Guwahati, India
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Perron N, Tan B, Dufresne C, Chen S. Proteomics and phosphoproteomics of C3 to CAM transition in the common ice plant. Methods Enzymol 2022; 676:347-368. [DOI: 10.1016/bs.mie.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Babu N, Bhat MY, John AE, Chatterjee A. The role of proteomics in the multiplexed analysis of gene alterations in human cancer. Expert Rev Proteomics 2021; 18:737-756. [PMID: 34602018 DOI: 10.1080/14789450.2021.1984884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Proteomics has played a pivotal role in identifying proteins perturbed in disease conditions when compared with healthy samples. Study of dysregulated proteins aids in identifying diagnostic markers and potential therapeutic targets. Cancer is an outcome of interplay of several such disarrayed proteins and molecular pathways which perturb cellular homeostasis, resulting in transformation. In this review, we discuss various facets of proteomic approaches, including tools and technological advancements, aiding in understanding differentially expressed molecules and signaling mechanisms. AREAS COVERED In this review, we have taken the approach of documenting the different methods of proteomic studies, ranging from labeling techniques, data analysis methods, and the nature of molecule detected. We summarize each technique and provide a glimpse of cancer research carried out using them, highlighting the advantages and drawbacks in comparison with others. Literature search using online resources, such as PubMed and Google Scholar were carried out for this approach. EXPERT OPINION Technological advancements in proteomics studies have come a long way from the study of two-dimensional mapping of proteins separated on gels in the early 1970s. Higher precision in molecular identification and quantification (high throughput), and greater number of samples analyzed have been the focus of researchers.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Mohd Younis Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
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Hallal M, Braga-Lagache S, Jankovic J, Simillion C, Bruggmann R, Uldry AC, Allam R, Heller M, Bonadies N. Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA). BMC Cancer 2021; 21:789. [PMID: 34238254 PMCID: PMC8268341 DOI: 10.1186/s12885-021-08479-z] [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: 12/08/2020] [Accepted: 06/10/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Despite the introduction of targeted therapies, most patients with myeloid malignancies will not be cured and progress. Genomics is useful to elucidate the mutational landscape but remains limited in the prediction of therapeutic outcome and identification of targets for resistance. Dysregulation of phosphorylation-based signaling pathways is a hallmark of cancer, and therefore, kinase-inhibitors are playing an increasingly important role as targeted treatments. Untargeted phosphoproteomics analysis pipelines have been published but show limitations in inferring kinase-activities and identifying potential biomarkers of response and resistance. METHODS We developed a phosphoproteomics workflow based on titanium dioxide phosphopeptide enrichment with subsequent analysis by liquid chromatography tandem mass spectrometry (LC-MS). We applied a novel Kinase-Activity Enrichment Analysis (KAEA) pipeline on differential phosphoproteomics profiles, which is based on the recently published SetRank enrichment algorithm with reduced false positive rates. Kinase activities were inferred by this algorithm using an extensive reference database comprising five experimentally validated kinase-substrate meta-databases complemented with the NetworKIN in-silico prediction tool. For the proof of concept, we used human myeloid cell lines (K562, NB4, THP1, OCI-AML3, MOLM13 and MV4-11) with known oncogenic drivers and exposed them to clinically established kinase-inhibitors. RESULTS Biologically meaningful over- and under-active kinases were identified by KAEA in the unperturbed human myeloid cell lines (K562, NB4, THP1, OCI-AML3 and MOLM13). To increase the inhibition signal of the driving oncogenic kinases, we exposed the K562 (BCR-ABL1) and MOLM13/MV4-11 (FLT3-ITD) cell lines to either Nilotinib or Midostaurin kinase inhibitors, respectively. We observed correct detection of expected direct (ABL, KIT, SRC) and indirect (MAPK) targets of Nilotinib in K562 as well as indirect (PRKC, MAPK, AKT, RPS6K) targets of Midostaurin in MOLM13/MV4-11, respectively. Moreover, our pipeline was able to characterize unexplored kinase-activities within the corresponding signaling networks. CONCLUSIONS We developed and validated a novel KAEA pipeline for the analysis of differential phosphoproteomics MS profiling data. We provide translational researchers with an improved instrument to characterize the biological behavior of kinases in response or resistance to targeted treatment. Further investigations are warranted to determine the utility of KAEA to characterize mechanisms of disease progression and treatment failure using primary patient samples.
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Affiliation(s)
- Mahmoud Hallal
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sophie Braga-Lagache
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Jovana Jankovic
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cedric Simillion
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ramanjaneyulu Allam
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Manfred Heller
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Nicolas Bonadies
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.
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Wang Y, Wang F. Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code. Front Pharmacol 2021; 12:685011. [PMID: 34177595 PMCID: PMC8224227 DOI: 10.3389/fphar.2021.685011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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Fatangare A, Glässner A, Sachs B, Sickmann A. Future perspectives on in-vitro diagnosis of drug allergy by the lymphocyte transformation test. J Immunol Methods 2021; 495:113072. [PMID: 34000289 DOI: 10.1016/j.jim.2021.113072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/22/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022]
Abstract
This article aims to envisage future perspectives of the lymphocyte transformation test (LTT). We describe the select innovative techniques, which can be integrated at different stages of the LTT to potentially improve the sensitivity, specificity, or practicability of the LTT. We first focus upon the cell sorting techniques comprising immunomagnetic cell separation and flow cytometry, which can be implemented prior and after the LTT culturing step to concentrate and quantify specific immune cell types. Further, we elaborate upon three important omics techniques such as transcriptomics, proteomics, and metabolomics, which can be integrated downstream of the LTT to analyze molecular changes in specific immune cells following drug induced activation and proliferation. We also develop visions, how state of the art techniques used in other scientific fields, can be transferred and applied in the context of in-vitro detection of drug allergy.
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Affiliation(s)
- Amol Fatangare
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany
| | - Andreas Glässner
- Federal Institute for Drugs and Medical Devices, Research Division, Bonn, Germany
| | - Bernhardt Sachs
- Federal Institute for Drugs and Medical Devices, Research Division, Bonn, Germany; Department for Dermatology and Allergology, University Hospital Aachen, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany; Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, 44801 Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB243FX, Scotland, UK.
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11
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Ondrej M, Rehulka P, Rehulkova H, Kupcik R, Tichy A. Fractionation of Enriched Phosphopeptides Using pH/Acetonitrile-Gradient-Reversed-Phase Microcolumn Separation in Combination with LC-MS/MS Analysis. Int J Mol Sci 2020; 21:ijms21113971. [PMID: 32492839 PMCID: PMC7312998 DOI: 10.3390/ijms21113971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry (MS) is a powerful and sensitive method often used for the identification of phosphoproteins. However, in phosphoproteomics, there is an identified need to compensate for the low abundance, insufficient ionization, and suppression effects of non-phosphorylated peptides. These may hamper the subsequent liquid chromatography–mass spectrometry/mass spectrometry (LC–MS/MS) analysis, resulting in incomplete phosphoproteome characterization, even when using high-resolution instruments. To overcome these drawbacks, we present here an effective microgradient chromatographic technique that yields specific fractions of enriched phosphopeptides compatible with LC–MS/MS analysis. The purpose of our study was to increase the number of identified phosphopeptides, and thus, the coverage of the sample phosphoproteome using the reproducible and straightforward fractionation method. This protocol includes a phosphopeptide enrichment step followed by the optimized microgradient fractionation of enriched phosphopeptides and final LC–MS/MS analysis of the obtained fractions. The simple fractionation system consists of a gas-tight microsyringe delivering the optimized gradient mobile phase to reversed-phase microcolumn. Our data indicate that combining the phosphopeptide enrichment with the microgradient separation is a promising technique for in-depth phosphoproteomic analysis due to moderate input material requirements and more than 3-fold enhanced protein identification.
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Affiliation(s)
- Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Pavel Rehulka
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic;
| | - Helena Rehulkova
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Rudolf Kupcik
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, 532 10 Pardubice, Czech Republic;
| | - Ales Tichy
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
- Correspondence: ; Tel.: +420-973-253-216
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12
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Robichon A. Protein Phosphorylation Dynamics: Unexplored Because of Current Methodological Limitations: Dynamics of Processive Phosphorylation. Bioessays 2020; 42:e1900149. [PMID: 32103519 DOI: 10.1002/bies.201900149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/21/2020] [Indexed: 12/30/2022]
Abstract
The study of intrinsic phosphorylation dynamics and kinetics in the context of complex protein architecture in vivo has been challenging: Method limitations have prevented significant advances in the understanding of the highly variable turnover of phosphate groups, synergy, and cooperativity between P-sites. However, over the last decade, powerful analytical technologies have been developed to determine the full catalog of the phosphoproteome for many species. The curated databases of phospho sites found by mass spectrometry analysis and the computationally predicted sites based on the linear sequence of kinase motifs are valuable tools. They allow investigation of the complexity of phosphorylation in vivo, albeit with strong discrepancies between different methods. A series of hypothetical scenarios on combinatorial processive phosphorylation is proposed that are likely unverifiable with current methodologies. These proposed a priori postulates could be considered as possible extensions of the known schemes of the activation/inhibition signaling process in vivo.
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Affiliation(s)
- Alain Robichon
- Université Côte d'Azur (UCA), Agrobiotech Institute, INRA, CNRS, ISA, 06270, France
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13
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Atakay M, Çelikbıçak Ö, Salih B. Use of Sulfonates as Desorption Agents for Phosphopeptide Elution from an Anion-exchange Material. ANAL LETT 2017. [DOI: 10.1080/00032719.2017.1355376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mehmet Atakay
- Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Ömür Çelikbıçak
- Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Bekir Salih
- Department of Chemistry, Hacettepe University, Ankara, Turkey
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14
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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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15
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Naik E, Dixit VM. Usp9X Is Required for Lymphocyte Activation and Homeostasis through Its Control of ZAP70 Ubiquitination and PKCβ Kinase Activity. THE JOURNAL OF IMMUNOLOGY 2016; 196:3438-51. [PMID: 26936881 DOI: 10.4049/jimmunol.1403165] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/09/2016] [Indexed: 11/19/2022]
Abstract
To achieve a durable adaptive immune response, lymphocytes must undergo clonal expansion and induce a survival program that enables the persistence of Ag-experienced cells and the development of memory. During the priming phase of this response, CD4(+)T lymphocytes either remain tolerized or undergo clonal expansion. In this article, we show that Usp9X functions as a positive regulatory switch during T lymphocyte priming through removal of inhibitory monoubiquitination from ZAP70. In the absence of Usp9X, an increased amount of ZAP70 localized to early endosomes consistent with the role of monoubiquitin in endocytic sorting. Usp9X becomes competent to deubiquitinate ZAP70 through TCR-dependent phosphorylation and enhancement of its catalytic activity and association with the LAT signalosome. In B lymphocytes, Usp9X is required for the induction of PKCβ kinase activity after BCR-dependent activation. Accordingly, inUsp9Xknockout B cells, there was a significant reduction in phospho-CARMA1 levels that resulted in reduced CARMA1/Bcl-10/MALT-1 complex formation and NF-κB-dependent cell survival. The pleiotropic effect of Usp9X during Ag-receptor signaling highlights its importance for the development of an effective and durable adaptive immune response.
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Affiliation(s)
- Edwina Naik
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, CA 94080
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, CA 94080
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16
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Monitoring Protein Kinase Expression and Phosphorylation in Cell Lysates with Antibody Microarrays. Methods Mol Biol 2016; 1360:107-22. [PMID: 26501906 DOI: 10.1007/978-1-4939-3073-9_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Fuelled by advances in our understanding of the human kinome and phosphoproteome and the increasing availability of pan- and phosphosite-specific antibodies, antibody microarrays have emerged as powerful tools for interrogating protein phosphorylation-mediated signaling systems in ex vivo studies. This economical platform permits ultra-sensitive, semiquantitative measurements of the levels of hundreds of protein kinases and their substrates along with their phosphorylation status simultaneously with minute amounts of specimens. Recent technological innovations in the design and fabrication of antibody microarrays and sample preparation have permitted further refinements of the technology to yield improvements in data quality. In this chapter, we describe a detailed protocol that we have developed for tracking the expression and phosphorylation of protein kinases and their substrates in crude cell lysate samples using a high-content antibody microarray.
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17
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Canto AC, Suman SP, Nair MN, Li S, Rentfrow G, Beach CM, Silva TJ, Wheeler TL, Shackelford SD, Grayson A, McKeith RO, King DA. Differential abundance of sarcoplasmic proteome explains animal effect on beef Longissimus lumborum color stability. Meat Sci 2015; 102:90-8. [DOI: 10.1016/j.meatsci.2014.11.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
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18
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Jouy F, Müller SA, Wagner J, Otto W, von Bergen M, Tomm JM. Integration of conventional quantitative and phospho-proteomics reveals new elements in activated Jurkat T-cell receptor pathway maintenance. Proteomics 2014; 15:25-33. [DOI: 10.1002/pmic.201400119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 09/23/2014] [Accepted: 10/21/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Florent Jouy
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Stephan A. Müller
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Juliane Wagner
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Wolfgang Otto
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Martin von Bergen
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
- Department of Metabolomics; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
- Department of Biotechnology and Environmental Engineering; University of Aalborg; Aalborg Denmark
| | - Janina M. Tomm
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
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19
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Kwak JW, Jeong H, Han SH, Kim Y, Son SM, Mook-Jung I, Hwang D, Park JW. Phosphokinase antibody arrays on dendron-coated surface. PLoS One 2014; 9:e96456. [PMID: 24802362 PMCID: PMC4011796 DOI: 10.1371/journal.pone.0096456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 04/08/2014] [Indexed: 12/04/2022] Open
Abstract
Monitoring protein phosphorylation at the cellular level is important to understand the intracellular signaling. Among the phosphoproteomics methods, phosphokinase antibody arrays have emerged as preferred tools to measure well-characterized phosphorylation in the intracellular signaling. Here, we present a dendron-coated phosphokinase antibody array (DPA) in which the antibodies are immobilized on a dendron-coated glass slide. Self-assembly of conically shaped dendrons well-controlled in size and structure resulted in precisely controlled lateral spacing between the immobilized phosphosite-specific antibodies, leading to minimized steric hindrance and improved antigen-antibody binding kinetics. These features increased sensitivity, selectivity, and reproducibility in measured amounts of protein phosphorylation. To demonstrate the utility of the DPA, we generated the phosphorylation profiles of brain tissue samples obtained from Alzheimer's disease (AD) model mice. The analysis of the profiles revealed signaling pathways deregulated during the course of AD progression.
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Affiliation(s)
- Ju-Won Kwak
- Department of Chemistry, POSTECH, Pohang, Republic of Korea
| | - Hyobin Jeong
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea
| | - Sun-Ho Han
- Department of Biochemistry and Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Youngkyu Kim
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea
| | - Sung Min Son
- Department of Biochemistry and Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail: (IM-J); (DH); (JWP)
| | - Daehee Hwang
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea
- Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu, Republic of Korea
- * E-mail: (IM-J); (DH); (JWP)
| | - Joon Won Park
- Department of Chemistry, POSTECH, Pohang, Republic of Korea
- * E-mail: (IM-J); (DH); (JWP)
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20
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Korrodi-Gregório L, Abrantes J, Muller T, Melo-Ferreira J, Marcus K, da Cruz e Silva OAB, Fardilha M, Esteves PJ. Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes. BMC Evol Biol 2013; 13:242. [PMID: 24195737 PMCID: PMC3840573 DOI: 10.1186/1471-2148-13-242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/29/2013] [Indexed: 01/23/2023] Open
Abstract
Background Pseudogenes are traditionally considered “dead” genes, therefore lacking biological functions. This view has however been challenged during the last decade. This is the case of the Protein phosphatase 1 regulatory subunit 2 (PPP1R2) or inhibitor-2 gene family, for which several incomplete copies exist scattered throughout the genome. Results In this study, the pseudogenization process of PPP1R2 was analyzed. Ten PPP1R2-related pseudogenes (PPP1R2P1-P10), highly similar to PPP1R2, were retrieved from the human genome assembly present in the databases. The phylogenetic analysis of mammalian PPP1R2 and related pseudogenes suggested that PPP1R2P7 and PPP1R2P9 retroposons appeared before the great mammalian radiation, while the remaining pseudogenes are primate-specific and retroposed at different times during Primate evolution. Although considered inactive, four of these pseudogenes seem to be transcribed and possibly possess biological functions. Given the role of PPP1R2 in sperm motility, the presence of these proteins was assessed in human sperm, and two PPP1R2-related proteins were detected, PPP1R2P3 and PPP1R2P9. Signatures of negative and positive selection were also detected in PPP1R2P9, further suggesting a role as a functional protein. Conclusions The results show that contrary to initial observations PPP1R2-related pseudogenes are not simple bystanders of the evolutionary process but may rather be at the origin of genes with novel functions.
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Affiliation(s)
| | | | | | | | | | | | | | - Pedro J Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal.
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21
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El'skaya AV, Negrutskii BS, Shalak VF, Vislovukh AA, Vlasenko DO, Novosylna AV, Lukash TO, Veremieva MV. Specific features of protein biosynthesis in higher eukaryotes. ACTA ACUST UNITED AC 2013. [DOI: 10.7124/bc.000818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- A. V. El'skaya
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - B. S. Negrutskii
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - V. F. Shalak
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. A. Vislovukh
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - D. O. Vlasenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. V. Novosylna
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - T. O. Lukash
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - M. V. Veremieva
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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22
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Korrodi-Gregório L, Ferreira M, Vintém AP, Wu W, Muller T, Marcus K, Vijayaraghavan S, Brautigan DL, da Cruz E Silva OAB, Fardilha M, da Cruz E Silva EF. Identification and characterization of two distinct PPP1R2 isoforms in human spermatozoa. BMC Cell Biol 2013; 14:15. [PMID: 23506001 PMCID: PMC3606321 DOI: 10.1186/1471-2121-14-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 03/11/2013] [Indexed: 11/29/2022] Open
Abstract
Background Protein Ser/Thr Phosphatase PPP1CC2 is an alternatively spliced isoform of PPP1C that is highly enriched in testis and selectively expressed in sperm. Addition of the phosphatase inhibitor toxins okadaic acid or calyculin A to caput and caudal sperm triggers and stimulates motility, respectively. Thus, the endogenous mechanisms of phosphatase inhibition are fundamental for controlling sperm function and should be characterized. Preliminary results have shown a protein phosphatase inhibitor activity resembling PPP1R2 in bovine and primate spermatozoa. Results Here we show conclusively, for the first time, that PPP1R2 is present in sperm. In addition, we have also identified a novel protein, PPP1R2P3. The latter was previously thought to be an intron-less pseudogene. We show that the protein corresponding to the pseudogene is expressed. It has PPP1 inhibitory potency similar to PPP1R2. The potential phosphosites in PPP1R2 are substituted by non-phosphorylable residues, T73P and S87R, in PPP1R2P3. We also confirm that PPP1R2/PPP1R2P3 are phosphorylated at Ser121 and Ser122, and report a novel phosphorylation site, Ser127. Subfractionation of sperm structures show that PPP1CC2, PPP1R2/PPP1R2P3 are located in the head and tail structures. Conclusions The conclusive identification and localization of sperm PPP1R2 and PPP1R2P3 lays the basis for future studies on their roles in acrosome reaction, sperm motility and hyperactivation. An intriguing possibility is that a switch in PPP1CC2 inhibitory subunits could be the trigger for sperm motility in the epididymis and/or sperm hyperactivation in the female reproductive tract.
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Affiliation(s)
- Luis Korrodi-Gregório
- Laboratory of Signal Transduction, Centre for Cell Biology, Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal
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23
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Bienvenut WV, Sumpton D, Lilla S, Martinez A, Meinnel T, Giglione C. Influence of various endogenous and artefact modifications on large-scale proteomics analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:443-450. [PMID: 23280976 DOI: 10.1002/rcm.6474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 11/16/2012] [Accepted: 11/18/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE Some large-scale proteomics studies in which strong cation exchange chromatography has been applied are used to determine proteomes and post-translational modification dynamics. Although such datasets favour the characterisation of thousands of modified peptides, e.g., phosphorylated and N-α-acetylated, a large fraction of the acquired spectra remain unexplained by standard proteomics approaches. Thus, advanced data processing allows characterisation of a significant part of these unassigned spectra. METHODS Our recent investigation of the N-α-acetylation status of plant proteins gave a dataset of choice to investigate further the in-depth characterisation of peptide modifications using Mascot tools associated with relevant validation processes. Such an approach allows to target frequently occurring modifications such as methionine oxidation, phosphorylation or N-α-acetylation, but also the less usual peptide cationisation. Finally, this dataset offers the unique opportunity to determine the overall influence of some of these modifications on the identification score. RESULTS Although methionine oxidation has no influence and tends to favour the characterisation of protein N-terminal peptides, peptide alkalinisation shows an adverse effect on peptide average score. Nevertheless, peptide cationisation appears to favour the characterisation of protein C-terminal peptides with a limited to no direct influence on the identification score. Unexpectedly, our investigation reveals the unfortunate combination of the molecular weight of N-α-acetylation and potassium cation that mimics the mass increment of a phosphorylation group. CONCLUSIONS Since these characterisations rely upon computational treatment associated with statistical validation approaches such as 'False discovery rates' calculation or post-translational modification position validation, our investigation highlights the limitation of such treatment which is biased by the initial searched hypotheses.
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Affiliation(s)
- Willy V Bienvenut
- CNRS, ISV, UPR2355, Bâtiment 23A, 1 avenue de la Terrasse, F-91198, Gif-sur-Yvette Cedex, France.
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24
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Abstract
In the human genome, 43 different genes are found that encode proteins belonging to the family of the POK (poxvirus and zinc finger and Krüppel)/ZBTB (zinc finger and broad complex, tramtrack, and bric à brac) factors. Generally considered transcriptional repressors, several of these genes play fundamental roles in cell lineage fate decision in various tissues, programming specific tasks throughout the life of the organism. Here, we focus on functions of leukemia/lymphoma-related factor/POK erythroid myeloid ontogenic factor, which is probably one of the most exciting and yet enigmatic members of the POK/ZBTB family.
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26
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Zhang H, Pelech S. Using protein microarrays to study phosphorylation-mediated signal transduction. Semin Cell Dev Biol 2012; 23:872-82. [DOI: 10.1016/j.semcdb.2012.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 01/18/2023]
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27
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Tian T, Song J. Mathematical modelling of the MAP kinase pathway using proteomic datasets. PLoS One 2012; 7:e42230. [PMID: 22905119 PMCID: PMC3414524 DOI: 10.1371/journal.pone.0042230] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 07/04/2012] [Indexed: 12/29/2022] Open
Abstract
The advances in proteomics technologies offer an unprecedented opportunity and valuable resources to understand how living organisms execute necessary functions at systems levels. However, little work has been done up to date to utilize the highly accurate spatio-temporal dynamic proteome data generated by phosphoprotemics for mathematical modeling of complex cell signaling pathways. This work proposed a novel computational framework to develop mathematical models based on proteomic datasets. Using the MAP kinase pathway as the test system, we developed a mathematical model including the cytosolic and nuclear subsystems; and applied the genetic algorithm to infer unknown model parameters. Robustness property of the mathematical model was used as a criterion to select the appropriate rate constants from the estimated candidates. Quantitative information regarding the absolute protein concentrations was used to refine the mathematical model. We have demonstrated that the incorporation of more experimental data could significantly enhance both the simulation accuracy and robustness property of the proposed model. In addition, we used the MAP kinase pathway inhibited by phosphatases with different concentrations to predict the signal output influenced by different cellular conditions. Our predictions are in good agreement with the experimental observations when the MAP kinase pathway was inhibited by phosphatase PP2A and MKP3. The successful application of the proposed modeling framework to the MAP kinase pathway suggests that our method is very promising for developing accurate mathematical models and yielding insights into the regulatory mechanisms of complex cell signaling pathways.
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Affiliation(s)
- Tianhai Tian
- School of Mathematical Sciences, Faculty of Science, Monash University, Clayton, Victoria, Australia.
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28
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West JD, Wang Y, Morano KA. Small molecule activators of the heat shock response: chemical properties, molecular targets, and therapeutic promise. Chem Res Toxicol 2012; 25:2036-53. [PMID: 22799889 DOI: 10.1021/tx300264x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
All cells have developed various mechanisms to respond and adapt to a variety of environmental challenges, including stresses that damage cellular proteins. One such response, the heat shock response (HSR), leads to the transcriptional activation of a family of molecular chaperone proteins that promote proper folding or clearance of damaged proteins within the cytosol. In addition to its role in protection against acute insults, the HSR also regulates lifespan and protects against protein misfolding that is associated with degenerative diseases of aging. As a result, identifying pharmacological regulators of the HSR has become an active area of research in recent years. Here, we review progress made in identifying small molecule activators of the HSR, what cellular targets these compounds interact with to drive response activation, and how such molecules may ultimately be employed to delay or reverse protein misfolding events that contribute to a number of diseases.
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Affiliation(s)
- James D West
- Biochemistry and Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, Ohio 44691, USA.
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29
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Lam HM, Babu CS, Wang J, Yuan Y, Lam YW, Ho SM, Leung YK. Phosphorylation of human estrogen receptor-beta at serine 105 inhibits breast cancer cell migration and invasion. Mol Cell Endocrinol 2012; 358:27-35. [PMID: 22370157 PMCID: PMC3348253 DOI: 10.1016/j.mce.2012.02.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 01/20/2012] [Accepted: 02/10/2012] [Indexed: 12/30/2022]
Abstract
Multiple phosphorylation sites on the human estrogen receptor (hER)α were identified and shown to influence mammary carcinogenesis. In contrast, functional phosphorylation sites of hERβ have yet to be experimentally identified and validated. Here, using mass spectrometry, we uncovered three serines (S75, S87, and S105) in the N-terminus of hERβ as targets of ERK1/2 and p38 kinases. We raised a specific antibody against phosphorylated S105 (pS105) and demonstrated that this site was endogenously phosphorylated in MDA-MB-231 and BT-474 cells. A phospho-mimetic mutant generated from hERβ1 was found to exhibit higher transactivation activity than hERβ1. Ectopic expression of this mutant inhibited cell migration and invasion, but did not affect cell growth and cell-cycle progression in these cell models. In breast cancer specimens, pS105-hERβ immunoreactivity was detected with a higher prevalence and intensity than that of hERβ1. These results underscore the functional importance of the first experimentally identified hERβ-phosphorylation site in breast cancer.
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Affiliation(s)
- Hung-Ming Lam
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267
| | - C.V. Suresh Babu
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267
| | - Jiang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267
| | - Yong Yuan
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267
| | - Ying-Wai Lam
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267
- Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH 45267
| | - Shuk-Mei Ho
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267
- Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH 45267
- Cincinnati Cancer Center, University of Cincinnati Medical Center, Cincinnati, OH 45267
- Cincinnati Veteran Affairs Medical Center, Cincinnati, OH 45220
- To whom correspondence should be addressed (co-corresponding authors): Yuet-Kin Leung, Ph.D., Division of Environmental Genetics and Molecular Toxicology, Kettering Complex, Room 331, 3223 Eden Avenue, Department of Environmental Health, College of Medicine, University of Cincinnati Medical Center, PO Box 670056, Cincinnati, OH 45267, Tel: 513- 558-5181, Fax: 513-558-5155, , Shuk-Mei Ho, Ph.D., Kettering Complex, Room 128, 3223 Eden Avenue, Department of Environmental Health, College of Medicine, University of Cincinnati Medical Center, PO Box 670056, Cincinnati, OH 45267, Tel: 513- 558-5701, Fax: 513-558-5155,
| | - Yuet-Kin Leung
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267
- Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH 45267
- Cincinnati Cancer Center, University of Cincinnati Medical Center, Cincinnati, OH 45267
- To whom correspondence should be addressed (co-corresponding authors): Yuet-Kin Leung, Ph.D., Division of Environmental Genetics and Molecular Toxicology, Kettering Complex, Room 331, 3223 Eden Avenue, Department of Environmental Health, College of Medicine, University of Cincinnati Medical Center, PO Box 670056, Cincinnati, OH 45267, Tel: 513- 558-5181, Fax: 513-558-5155, , Shuk-Mei Ho, Ph.D., Kettering Complex, Room 128, 3223 Eden Avenue, Department of Environmental Health, College of Medicine, University of Cincinnati Medical Center, PO Box 670056, Cincinnati, OH 45267, Tel: 513- 558-5701, Fax: 513-558-5155,
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30
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Li X, Rao V, Jin J, Guan B, Anderes KL, Bieberich CJ. Identification and validation of inhibitor-responsive kinase substrates using a new paradigm to measure kinase-specific protein phosphorylation index. J Proteome Res 2012; 11:3637-49. [PMID: 22663298 DOI: 10.1021/pr3000514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Regulation of all cellular processes requires dynamic regulation of protein phosphorylation. We have developed an unbiased system to globally quantify the phosphorylation index for substrates of a specific kinase by independently quantifying phosphorylated and total substrate molecules in a reverse in-gel kinase assay. Non-phosphorylated substrate molecules are first quantified in the presence and absence of a specific stimulus. Total substrate molecules are then measured after complete chemical dephosphorylation, and a ratio of phosphorylated to total substrate is derived. To demonstrate the utility of this approach, we profiled and quantified changes in phosphorylation index for Protein Kinase CK2 substrates that respond to a small-molecule inhibitor. A broad range of inhibitor-induced changes in phosphorylation was observed in cultured cells. Differences among substrates in the kinetics of phosphorylation change were also revealed. Comparison of CK2 inhibitor-induced changes in phosphorylation in cultured cells and in mouse peripheral blood lymphocytes in vivo revealed distinct kinetic and depth-of-response profiles. This technology provides a new approach to facilitate functional analyses of kinase-specific phosphorylation events. This strategy can be used to dissect the role of phosphorylation in cellular events, to facilitate kinase inhibitor target validation studies, and to inform in vivo analyses of kinase inhibitor drug efficacy.
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Affiliation(s)
- Xiang Li
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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31
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Negrutskii B, Vlasenko D, El'skaya A. From global phosphoproteomics to individual proteins: the case of translation elongation factor eEF1A. Expert Rev Proteomics 2012; 9:71-83. [PMID: 22292825 DOI: 10.1586/epr.11.71] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Phosphoproteomics is often aimed at deciphering the modified components of signaling pathways in certain organisms, tissues and pathologies. Phosphorylation of housekeeping proteins, albeit important, usually attracts less attention. Here, we provide targeted analysis of eukaryotic translation elongation factor 1A (eEF1A), which is the main element of peptide elongation machinery. There are 97% homologous A1 and A2 isoforms of eEF1A; their expression in mammalian tissues is mutually exclusive and differentially regulated in development. The A2 isoform reveals proto-oncogenic properties and specifically interacts with some cellular proteins. Several tyrosine residues shown experimentally to be phosphorylated in eEF1A1 are hardly solution accessible, so their phosphorylation could be linked with structural rearrangement of the protein molecule. The possible role of tyrosine phosphorylation in providing the background for structural differences between the 'extended' A1 isoform and the compact oncogenic A2 isoform is discussed. The 'road map' for targeted analysis of any protein of interest using phosphoproteomics data is presented.
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Affiliation(s)
- Boris Negrutskii
- Institute of Molecular Biology & Genetics, National Academy of Sciences of Ukraine, Kiev, 03680, Ukraine.
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32
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Nesvizhskii AI. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 2010; 73:2092-123. [PMID: 20816881 DOI: 10.1016/j.jprot.2010.08.009] [Citation(s) in RCA: 358] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/25/2010] [Accepted: 08/25/2010] [Indexed: 12/18/2022]
Abstract
This manuscript provides a comprehensive review of the peptide and protein identification process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic experiments. The commonly used methods for assigning peptide sequences to MS/MS spectra are critically discussed and compared, from basic strategies to advanced multi-stage approaches. A particular attention is paid to the problem of false-positive identifications. Existing statistical approaches for assessing the significance of peptide to spectrum matches are surveyed, ranging from single-spectrum approaches such as expectation values to global error rate estimation procedures such as false discovery rates and posterior probabilities. The importance of using auxiliary discriminant information (mass accuracy, peptide separation coordinates, digestion properties, and etc.) is discussed, and advanced computational approaches for joint modeling of multiple sources of information are presented. This review also includes a detailed analysis of the issues affecting the interpretation of data at the protein level, including the amplification of error rates when going from peptide to protein level, and the ambiguities in inferring the identifies of sample proteins in the presence of shared peptides. Commonly used methods for computing protein-level confidence scores are discussed in detail. The review concludes with a discussion of several outstanding computational issues.
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33
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Abstract
Advances in the generation and interpretation of proteomics data have spurred a transition from focusing on protein identification to functional analysis. Here we review recent proteomics results that have elucidated new aspects of the roles and regulation of signal transduction pathways in cancer using the epidermal growth factor receptor (EGFR), ERK and breakpoint cluster region (BCR)-ABL1 networks as examples. The emerging theme is to understand cancer signalling as networks of multiprotein machines which process information in a highly dynamic environment that is shaped by changing protein interactions and post-translational modifications (PTMs). Cancerous genetic mutations derange these protein networks in complex ways that are tractable by proteomics.
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Affiliation(s)
- Walter Kolch
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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