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Fan H, Sun Q, Dukenbayev K, Benassi E, Manarbek L, Nurkesh AA, Khamijan M, Mu C, Li G, Razbekova M, Chen Z, Amin A, Xie Y. Carbon nanoparticles induce DNA repair and PARP inhibitor resistance associated with nanozyme activity in cancer cells. Cancer Nanotechnol 2022. [DOI: 10.1186/s12645-022-00144-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Abstract
Background
Quantum nanodots especially carbon nanoparticles (CNPs) have been widely studied in biomedicine in imaging, and drug delivery, but anti-cancer mechanisms remain elusive.
Methods
Here, we investigated a type of cell death induced by food (beet, soybean) derived CNPs in cancer cells and tested whether CNPs induced DNA damage and resistant to anti-cancer agent PARP inhibitor (PARPi) could be overcome by quantum calculations, TEM, AFM, FT-IR, soft agar assay, and cytotoxicity assay.
Results
At high doses, CNPs derived from beet lead to a pop-like apoptosis (Carbopoptosis) in cancer cells. Quantum mechanical calculations confirmed CNPs binding with phosphate groups as well as DNA bases. At low doses, CNPs develop PARPi drug resistance through interactions between CNPs and PARPi. A synergistic drug effect was achieved with the combination of phosphatase inhibitor (PPi), PARPi, and CNPs. This is corroborated by the fact that sulfur modulated CNPs which exhibit super high phosphatase nanozyme activity abrogated the CNPs induced colony formation in anchorage-independent cancer cell growth.
Conclusion
Thus, our data suggest the CNPs intrinsic nanozyme activity of phosphatase may crosstalk with drug resistance, which can be reversed upon modulations.
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Cohen J, Reed W, Foster MW, Kahmke RR, Rocke DJ, Puscas L, Cannon TY, Lee WT. Octreotide may improve pharyngocutaneous fistula healing through downregulation of cystatins: A pilot study. Laryngoscope Investig Otolaryngol 2022; 8:113-119. [PMID: 36846407 PMCID: PMC9948565 DOI: 10.1002/lio2.962] [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: 05/26/2022] [Revised: 07/27/2022] [Accepted: 10/15/2022] [Indexed: 11/30/2022] Open
Abstract
Background Pharyngocutaneous fistula (PCF) and salivary leaks are well known complications of head and neck surgery. The medical management of PCF has included the use of octreotide without a well-defined understanding of its therapeutic mechanism. We hypothesized that octreotide induces alterations in the saliva proteome and that these alterations may provide insight into the mechanism of action underlying improved PCF healing. We undertook an exploratory pilot study in healthy controls that involved collecting saliva before and after a subcutaneous injection of octreotide and performing proteomic analysis to determine the effects of octreotide. Methods Four healthy adult participants provided saliva samples before and after subcutaneous injection of octreotide. A mass-spectrometry based workflow optimized for the quantitative proteomic analysis of biofluids was then employed to analyze changes in salivary protein abundance after octreotide administration. Results There were 3076 human, 332 Streptococcus mitis, 102 G. haemolyans, and 42 Granulicatella adiacens protein groups quantified in saliva samples. A paired statistical analysis was performed using the generalized linear model (glm) function in edgeR. There were and ~300 proteins that had a p < .05 between the pre- and post-octreotide groups ~50 proteins with an FDR-corrected p < .05 between pre- and post-groups. These results were visualized using a volcano plot after filtering on proteins quantified by 2 more or unique precursors. Both human and bacterial proteins were among the proteins altered by octreotide treatment. Notably, four isoforms of the human cystatins, belonging to a family of cysteine proteases, that had significantly lower abundance after treatment. Conclusion This pilot study demonstrated octreotide-induced downregulation of cystatins. By downregulation of cystatins in the saliva, there is decreased inhibition of cysteine proteases such as Cathepsin S. This results in increased cysteine protease activity that has been linked to enhanced angiogenic response, cell proliferation and migration that have resulted in improved wound healing. These insights provide first steps at furthering our understanding of octreotide's effects on saliva and reports of improved PCF healing.
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Affiliation(s)
| | - William Reed
- Department of Head and Neck Surgery and Communication SciencesDuke University Health SystemDurhamNorth CarolinaUSA
| | - Matthew W. Foster
- Department of Medicine, and Duke Proteomics and Metabolomics Core FacilityDuke University Health SystemDurhamNorth CarolinaUSA
| | - Russel R. Kahmke
- Department of Head and Neck Surgery and Communication SciencesDuke University Health SystemDurhamNorth CarolinaUSA
| | - Daniel J. Rocke
- Department of Head and Neck Surgery and Communication SciencesDuke University Health SystemDurhamNorth CarolinaUSA
| | - Liana Puscas
- Department of Head and Neck Surgery and Communication SciencesDuke University Health SystemDurhamNorth CarolinaUSA
| | - Trinitia Y. Cannon
- Department of Head and Neck Surgery and Communication SciencesDuke University Health SystemDurhamNorth CarolinaUSA
| | - Walter T. Lee
- Department of Head and Neck Surgery and Communication SciencesDuke University Health SystemDurhamNorth CarolinaUSA
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Ignatenko O, Malinen S, Rybas S, Vihinen H, Nikkanen J, Kononov A, Jokitalo ES, Ince-Dunn G, Suomalainen A. Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes. J Biophys Biochem Cytol 2022; 222:213692. [PMID: 36383135 PMCID: PMC9674092 DOI: 10.1083/jcb.202203019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/19/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Astrocytes, often considered as secondary responders to neurodegeneration, are emerging as primary drivers of brain disease. Here we show that mitochondrial DNA depletion in astrocytes affects their primary cilium, the signaling organelle of a cell. The progressive oxidative phosphorylation deficiency in astrocytes induces FOXJ1 and RFX transcription factors, known as master regulators of motile ciliogenesis. Consequently, a robust gene expression program involving motile cilia components and multiciliated cell differentiation factors are induced. While the affected astrocytes still retain a single cilium, these organelles elongate and become remarkably distorted. The data suggest that chronic activation of the mitochondrial integrated stress response (ISRmt) in astrocytes drives anabolic metabolism and promotes ciliary elongation. Collectively, our evidence indicates that an active signaling axis involving mitochondria and primary cilia exists and that ciliary signaling is part of ISRmt in astrocytes. We propose that metabolic ciliopathy is a novel pathomechanism for mitochondria-related neurodegenerative diseases.
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Affiliation(s)
- Olesia Ignatenko
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Satu Malinen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sofiia Rybas
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Joni Nikkanen
- Cardiovascular Research Institute, University of California, San Francisco, CA
| | | | - Eija S. Jokitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Gulayse Ince-Dunn
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anu Suomalainen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,HUS Diagnostics, Helsinki University Hospital, Helsinki, Finland
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54
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Zeppillo T, Schulmann A, Macciardi F, Hjelm BE, Föcking M, Sequeira PA, Guella I, Cotter D, Bunney WE, Limon A, Vawter MP. Functional impairment of cortical AMPA receptors in schizophrenia. Schizophr Res 2022; 249:25-37. [PMID: 32513544 PMCID: PMC7718399 DOI: 10.1016/j.schres.2020.03.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
Clinical and preclinical studies suggest that some of the behavioral alterations observed in schizophrenia (SZ) may be mechanistically linked to synaptic dysfunction of glutamatergic signaling. Recent genetic and proteomic studies suggest alterations of cortical glutamate receptors of the AMPA-type (AMPARs), which are the predominant ligand-gated ionic channels of fast transmission at excitatory synapses. The impact of gene and protein alterations on the electrophysiological activity of AMPARs is not known in SZ. In this proof of principle work, using human postmortem brain synaptic membranes isolated from the dorsolateral prefrontal cortex (DLPFC), we combined electrophysiological analysis from microtransplanted synaptic membranes (MSM) with transcriptomic (RNA-Seq) and label-free proteomics data in 10 control and 10 subjects diagnosed with SZ. We observed in SZ a reduction in the amplitude of AMPARs currents elicited by kainate, an agonist of AMPARs that blocks the desensitization of the receptor. This reduction was not associated with protein abundance but with a reduction in kainate's potency to activate AMPARs. Electrophysiologically-anchored dataset analysis (EDA) was used to identify synaptosomal proteins that linearly correlate with the amplitude of the AMPARs responses, gene ontology functional annotations were then used to determine protein-protein interactions. Protein modules associated with positive AMPARs current increases were downregulated in SZ, while protein modules that were upregulated in SZ were associated with decreased AMPARs currents. Our results indicate that transcriptomic and proteomic alterations, frequently observed in the DLPFC in SZ, converge at the synaptic level producing a functional electrophysiological impairment of AMPARs.
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Affiliation(s)
- Tommaso Zeppillo
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, School of Medicine, University of Texas Medical Branch at Galveston, USA; Department of Life Sciences, University of Trieste, B.R.A.I.N., Centre for Neuroscience, Trieste, Italy
| | - Anton Schulmann
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA; Current address: National Institute of Mental Health, Human Genetics Branch, Bethesda, MD, USA
| | - Fabio Macciardi
- Department of Psychiatry & Human Behavior, University of California Irvine, CA 92697, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA, USA
| | | | - P Adolfo Sequeira
- Department of Psychiatry & Human Behavior, University of California Irvine, CA 92697, USA
| | - Ilaria Guella
- Department of Psychiatry & Human Behavior, University of California Irvine, CA 92697, USA
| | - David Cotter
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | - William E Bunney
- Department of Psychiatry & Human Behavior, University of California Irvine, CA 92697, USA
| | - Agenor Limon
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, School of Medicine, University of Texas Medical Branch at Galveston, USA.
| | - Marquis P Vawter
- Department of Psychiatry & Human Behavior, University of California Irvine, CA 92697, USA.
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Pan X, Liu Y, Bao Y, Wei L, Gao Y. Changes in the urinary proteome before and after quadrivalent influenza vaccine and COVID-19 vaccination. Front Immunol 2022; 13:946791. [PMID: 36275736 PMCID: PMC9585259 DOI: 10.3389/fimmu.2022.946791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
The proteome of urine samples from quadrivalent influenza vaccine cohort were analyzed with self-contrasted method. Significantly changed urine protein at 24 hours after vaccination was enriched in immune-related pathways, although each person’s specific pathways varied. We speculate that this may be because different people have different immunological backgrounds associated with influenza. Then, urine samples were collected from several uninfected SARS-CoV-2 young people before and after the first, second, and third doses of the COVID-19 vaccine. The differential proteins compared between after the second dose (24h) and before the second dose were enriched in pathways involving in multicellular organismal process, regulated exocytosis and immune-related pathways, indicating no first exposure to antigen. Surprisingly, the pathways enriched by the differential urinary protein before and after the first dose were similar to those before and after the second dose. It is inferred that although the volunteers were not infected with SARS-CoV-2, they might have been exposed to other coimmunogenic coronaviruses. Two to four hours after the third vaccination, the differentially expressed protein were also enriched in multicellular organismal process, regulated exocytosis and immune-related pathways, indicating that the immune response has been triggered in a short time after vaccination. Multicellular organismal process and regulated exocytosis after vaccination may be a new indicator to evaluate the immune effect of vaccines. Urinary proteome is a terrific window to monitor the changes in human immune function.
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Affiliation(s)
- Xuanzhen Pan
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yongtao Liu
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yijin Bao
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lilong Wei
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Youhe Gao
- Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
- *Correspondence: Youhe Gao,
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56
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Sun X, Li Q, Wang J, Ma Y, Wang M, Qin W. Urinary Proteome Analysis of Global Cerebral Ischemia-Reperfusion Injury Rat Model via Data-Independent Acquisition and Parallel Reaction Monitoring Proteomics. J Mol Neurosci 2022; 72:2020-2029. [PMID: 35920976 PMCID: PMC9392715 DOI: 10.1007/s12031-022-02055-1] [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: 05/24/2022] [Accepted: 07/23/2022] [Indexed: 12/04/2022]
Abstract
Cerebral ischemia–reperfusion (I/R) injury is the leading cause of death in severe hypotension caused by cardiac arrest, drowning, and excessive blood loss. Urine can sensitively reflect pathophysiological changes in the brain even at an early stage. In this study, a rat model of global cerebral I/R injury was established via Pulsinelli’s four-vessel occlusion (4-VO) method. Overall, 164 urinary proteins significantly changed in the 4-VO rat urine samples compared to the control samples by data-independent acquisition (DIA) proteomics technique (1.5-fold change, p < 0.05). Gene Ontology annotation showed that the acute-phase response, the ERK1 and ERK2 cascade, endopeptidase activity, blood coagulation, and angiogenesis were overrepresented. After parallel reaction monitoring (PRM) validation, 15 differential proteins having human orthologs were verified as the potential urinary markers associated with cerebral I/R injury. Of these potential biomarkers, 8 proteins were reported to be closely associated with cerebral I/R injury. Nine differential proteins changed even when there were no clinical manifestations or histopathological cerebral damage, including FGG, COMP, TFF2, HG2A, KNG1, CATZ, PTGDS, PRVA, and HEPC. These 9 proteins are potential biomarkers for early screening of cerebral I/R injury to prevent the development of cerebral injury. KNG1, CATZ, PTGDS, PRVA, and HEPC showed an overall trend of upregulation or downregulation at 12 and 48 h after I/R injury, reflecting the progression of cerebral I/R injury. These 5 proteins may serve as potential biomarkers for prognostic evaluation of cerebral I/R injury. These findings provide important clues to inform the monitoring of cerebral I/R injury and further the current understanding of its molecular biological mechanisms.
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Affiliation(s)
- Xiaopeng Sun
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Qiujie Li
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Jiajia Wang
- Department of Anesthesiology, Qingdao Municipal Hospital, Dalian Medical University, Dalian, 116044, China
| | - Yuan Ma
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China
| | - Mingshan Wang
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China.
| | - Weiwei Qin
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China.
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57
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Suomi T, Elo LL. Statistical and machine learning methods to study human CD4+ T cell proteome profiles. Immunol Lett 2022; 245:8-17. [DOI: 10.1016/j.imlet.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/05/2022]
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Dubois E, Galindo AN, Dayon L, Cominetti O. Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples. Biosystems 2022; 215-216:104661. [PMID: 35247480 DOI: 10.1016/j.biosystems.2022.104661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinical research study, from human biological sample collection and storage, sample preparation, spectral data acquisition, to peptide and protein quantification. In order to remove such diverse and unwanted variability, normalization of the protein data is performed. There have been already several published reviews comparing normalization methods in the -omics field, but reports focusing on proteomic data generated with mass spectrometry (MS) are much fewer. Additionally, most of these reports have only dealt with small datasets. RESULTS As a case study, here we focused on the normalization of a large MS-based proteomic dataset obtained from an overweight and obese pan-European cohort, where different normalization methods were evaluated, namely: center standardize, quantile protein, quantile sample, global standardization, ComBat, median centering, mean centering, single standard and removal of unwanted variation (RUV); some of these are generic normalization methods while others have been specifically created to deal with genomic or metabolomic data. We checked how relationships between proteins and clinical variables (e.g., gender, levels of triglycerides or cholesterol) were improved after normalizing the data with the different methods. CONCLUSIONS Some normalization methods were better adapted for this particular large-scale shotgun proteomic dataset of human plasma samples labeled with isobaric tags and analyzed with liquid chromatography-tandem MS. In particular, quantile sample normalization, RUV, mean and median centering showed very good performance, while quantile protein normalization provided worse results than those obtained with unnormalized data.
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Affiliation(s)
- Etienne Dubois
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland; Chemistry and Chemical Engineering Section, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Ornella Cominetti
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland.
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Qin W, Qin X, Li L, Gao Y. Proteome Analysis of Urinary Biomarkers in a Bovine IRBP-Induced Uveitis Rat Model via Data-Independent Acquisition and Parallel Reaction Monitoring Proteomics. Front Mol Biosci 2022; 9:831632. [PMID: 35274006 PMCID: PMC8901606 DOI: 10.3389/fmolb.2022.831632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Uveitis, a group of intraocular inflammatory diseases, is one of the major causes of severe visual impairment among the working-age population. This study aimed to screen potential urinary biomarkers for uveitis based on proteome analysis. An experimental autoimmune uveitis (EAU) rat model induced by bovine interphotoreceptor retinoid-binding protein (IRBP) was used to mimic uveitis. In discovery phase, a total of 704 urinary proteins were identified via data-independent acquisition (DIA) proteomic technique, of which 76 were significantly changed (34, 36, and 37 on days 5, 8, and 12, respectively, after bovine IRBP immunization). Gene Ontology annotation of the differential proteins indicates that acute-phase response, innate immune response, neutrophil aggregation, and chronic inflammatory response were significantly enriched. Protein-protein interaction network indicates that these differential urinary proteins were biologically connected in EAU, as a group. In validation phase, 17 proteins having human orthologs were verified as the potential markers associated with uveitis by parallel reaction monitoring (PRM) targeted quantitative analysis. Twelve differential proteins changed even when there were no clinical manifestations or histopathological ocular damage. These 12 proteins are potential biomarkers for early diagnosis of uveitis to prevent the development of visual impairment. Five differential proteins changed at three time-points and showed progressive changes as the uveitis progressed, and another five differential proteins changed only on day 12 when EAU severity peaked. These 10 proteins may serve as potential biomarkers for prognostic evaluation of uveitis. Our findings revealed that the urinary proteome could sensitively reflect dynamic pathophysiological changes in EAU, and represent the first step towards the application of urinary protein biomarkers for uveitis.
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Affiliation(s)
- Weiwei Qin
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, China
| | - Xuyan Qin
- Department of Dermatology, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Lujun Li
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, China
- *Correspondence: Youhe Gao,
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Qian YT, Liu XY, Sun HD, Xu JY, Sun JM, Liu W, Chen T, Liu JW, Tan Y, Sun W, Ma DL. Urinary Proteomics Analysis of Active Vitiligo Patients: Biomarkers for Steroid Treatment Efficacy Prediction and Monitoring. Front Mol Biosci 2022; 9:761562. [PMID: 35252347 PMCID: PMC8891126 DOI: 10.3389/fmolb.2022.761562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
Vitiligo is a common acquired skin disorder caused by immune-mediated destruction of epidermal melanocytes. Systemic glucocorticoids (GCs) have been used to prevent the progression of active vitiligo, with 8.2–56.2% of patients insensitive to this therapy. Currently, there is a lack of biomarkers that can accurately predict and evaluate treatment responses. The goal of this study was to identify candidate urinary protein biomarkers to predict the efficacy of GCs treatment in active vitiligo patients and monitor the disease. Fifty-eight non-segmental vitiligo patients were enrolled, and 116 urine samples were collected before and after GCs treatment. Patients were classified into a treatment-effective group (n = 42) and a treatment-resistant group (n = 16). Each group was divided equally into age- and sex-matched experimental and validation groups, and proteomic analyses were performed. Differentially expressed proteins were identified, and Ingenuity Pathway Analysis was conducted for the functional annotation of these proteins. Receiver operating characteristic curves were used to evaluate the diagnostic value. A total of 245 and 341 differentially expressed proteins between the treatment-resistant and treatment-effective groups were found before and after GCs treatment, respectively. Bioinformatic analysis revealed that the urinary proteome reflected the efficacy of GCs in active vitiligo patients. Eighty and fifty-four candidate biomarkers for treatment response prediction and treatment response evaluation were validated, respectively. By ELISA analysis, retinol binding protein-1 and torsin 1A interacting protein 1 were validated to have the potential to predict the efficacy of GCs with AUC value of 1 and 0.875, respectively. Retinol binding protein-1, torsin 1A interacting protein 1 and protein disulfide-isomerase A4 were validated to have the potential to reflect positive treatment effect to GCs treatment in active vitiligo with AUC value of 0.861, 1 and 0.868, respectively. This report is the first to identify urine biomarkers for GCs treatment efficacy prediction in vitiligo patients. These findings might contribute to the application of GCs in treating active vitiligo patients.
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Affiliation(s)
- Yue-Tong Qian
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
| | - Xiao-Yan Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Hai-Dan Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Ji-Yu Xu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jia-Meng Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Liu
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
| | - Tian Chen
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
| | - Jia-Wei Liu
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
| | - Yan Tan
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
| | - Wei Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- *Correspondence: Wei Sun, ; Dong-Lai Ma,
| | - Dong-Lai Ma
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
- *Correspondence: Wei Sun, ; Dong-Lai Ma,
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Budnik B, Straubhaar J, Neveu J, Shvartsman D. In‐depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells. Proteomics 2022; 22:e2100265. [DOI: 10.1002/pmic.202100265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory (MSPRL) FAS Division of Science Harvard University 52 Oxford Street Cambridge MA 02138 USA
| | - Juerg Straubhaar
- Informatics and Scientific Applications Group FAS Center for Systems Biology Harvard University 38 Oxford Street Cambridge MA 02138 USA
| | - John Neveu
- Mass Spectrometry and Proteomics Resource Laboratory (MSPRL) FAS Division of Science Harvard University 52 Oxford Street Cambridge MA 02138 USA
| | - Dmitry Shvartsman
- Department of Stem Cell and Regenerative Biology Harvard Stem Cell Institute Harvard University 7 Divinity Avenue Cambridge MA 02138 USA
- Present address: Cellaria Inc. 9 Audubon Road Wakefield MA 01880 USA
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Zhao Z, Li S, Pan Y, Jiang P, Dong Y, Yang H, Wang X, Guan X, Zhou Z. Proteomics reveals gender differences in physiological characteristics of the gonads and tube feet of the sea cucumber, Apostichopus japonicus. J Proteomics 2022; 251:104396. [PMID: 34673268 DOI: 10.1016/j.jprot.2021.104396] [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: 12/22/2020] [Revised: 04/29/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
The sea cucumber Apostichopus japonicus is an important aquaculture species in China because of its high nutritional and medicinal values. Gender, as a factor affecting the physiology of organisms, is always considered when improving the breeding efficiency of economically important animals. In the present study, protein expression profiles of the gonads and tube feet of male and female A. japonicus were investigated using a comparative proteomics approach. A set of 7499 proteins were identified, which covered a broad range of functions based on function annotations. A significant difference in protein expression profiles was observed between the gonads and tube feet of A. japonicus; gonads showed more apparent gender differences than tube feet. Moreover, the findings revealed that male A. japonicus had more specific functions and most of these functions were associated with energy consumption. Further analyses suggested that the regulation of ERK activity and the capacity of tyrosine production and virus immunity might be more powerful in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. Overall, our study provides new insights into the understanding of molecular mechanisms underlying gender-based physiological differences in A. japonicus. SIGNIFICANCE: The current study aimed to reveal gender differences in the physiological characteristics of gonads and tube feet of the sea cucumber A. japonicus. To the best of our knowledge, this is the first proteomics study to analyze the differences in the protein expression profiles of external organs between male and female A. japonicus. The analysis revealed gender differences in the protein expression profiles of both gonads and tube feet of A. japonicus, and the gender differences in gonads were quite apparent. Moreover, according to the recognition of differentially expressed proteins and the enrichment analyses based on Kyoto Encyclopedia of Genes and Genomes, a draft view of how the physiological functions of A. japonicus were affected by gender was obtained. Male A. japonicus could have more specific functions related to energy consumption than females. The regulation of ERK activity and virus immunity might be more robust in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. The findings presented here will improve the understanding of researchers about the molecular mechanisms underlying gender-based differences in A. japonicus and contribute to the meticulous breeding of A. japonicus.
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Affiliation(s)
- Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shilei Li
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yongjia Pan
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Pingzhe Jiang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Ying Dong
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Huihua Yang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xuda Wang
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
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Fan X, Wu X, Trevisan Franca De Lima L, Stehbens S, Punyadeera C, Webb R, Hamilton B, Ayyapann V, McLauchlan C, Crawford R, Zheng M, Xiao Y, Prasadam I. The deterioration of calcified cartilage integrity reflects the severity of osteoarthritis-A structural, molecular, and biochemical analysis. FASEB J 2022; 36:e22142. [PMID: 35032407 DOI: 10.1096/fj.202101449r] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/03/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022]
Abstract
The calcified cartilage zone (CCZ) is a thin interlayer between the hyaline articular cartilage and the subchondral bone and plays an important role in maintaining the joint homeostasis by providing biological and mechanical support from unmineralized cartilage to the underlying mineralized subchondral bone. The hallmark of CCZ characteristics in osteoarthritis (OA) is less well known. The aim of our study is to evaluate the structural, molecular, and biochemical composition of CCZ in tissues affected by primary knee OA and its relationship with disease severity. We collected osteochondral tissue samples stratified according to disease severity, from 16 knee OA patients who underwent knee replacement surgery. We also used meniscectomy-induced rat samples to confirm the pathophysiologic changes of human samples. We defined the characteristics of the calcified cartilage layer using a combination of morphological, biochemical, proteomic analyses on laser micro-dissected tissue. Our results demonstrated that the Calcium/Phosphate ratio is unchanged during the OA progression, but the calcium-binding protein and cadherin binding protein, as well as carbohydrate metabolism-related proteins, undergo significant changes. These changes were further accompanied by thinning of the CCZ, loss of collagen and proteoglycan content, the occurrence of the endochondral ossification, neovasculature, loss of the elastic module, loss of the collagen direction, and increase of the tortuosity indicating an altered structural and mechanical properties of the CCZ in OA. In conclusion, our results suggest that the calcified cartilage changes can reflect the disease progression.
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Affiliation(s)
- Xiwei Fan
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Xiaoxin Wu
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia.,Department of Orthopaedic Surgery, the Second Xiangya Hospital, Central South University, Changsha, China
| | | | - Samantha Stehbens
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Chamindie Punyadeera
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Brisbane, Queensland, Australia
| | - Richard Webb
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland, Australia
| | - Brett Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland, Australia
| | - Vijay Ayyapann
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Connor McLauchlan
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Ross Crawford
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia.,The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Minghao Zheng
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Yin Xiao
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia.,Australia-China Centre for Tissue Engineering and Regenerative Medicine, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Indira Prasadam
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia
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64
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Geller S, Lieberman H, Belanger AJ, Yew NS, Kloss A, Ivanov AR. Comparison of Microflow and Analytical Flow Liquid Chromatography Coupled to Mass Spectrometry Global Metabolomics Methods Using a Urea Cycle Disorder Mouse Model. J Proteome Res 2022; 21:151-163. [PMID: 34843255 PMCID: PMC8742624 DOI: 10.1021/acs.jproteome.1c00628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microscale-based separations are increasingly being applied in the field of metabolomics for the analysis of small-molecule metabolites. These methods have the potential to provide improved sensitivity, less solvent waste, and reduced sample-size requirements. Ion-pair free microflow-based global metabolomics methods, which we recently reported, were further compared to analytical flow ion-pairing reagent containing methods using a sample set from a urea cycle disorder (UCD) mouse model. Mouse urine and brain homogenate samples representing healthy, diseased, and disease-treated animals were analyzed by both methods. Data processing was performed using univariate and multivariate techniques followed by analyte trend analysis. The microflow methods performed comparably to the analytical flow ion-pairing methods with the ability to separate the three sample groups when analyzed by partial least-squares analysis. The number of detected metabolic features present after each data processing step was similar between the microflow-based methods and the ion-pairing methods in the negative ionization mode. The observed analyte trend and coverage of known UCD biomarkers were the same for both evaluated approaches. The 12.5-fold reduction in sample injection volume required for the microflow-based separations highlights the potential of this method to support studies with sample-size limitations.
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Affiliation(s)
- Sarah Geller
- Sanofi, Waltham, Massachusetts 02451, United States
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | | | | | - Nelson S Yew
- Sanofi, Waltham, Massachusetts 02451, United States
| | - Alla Kloss
- Sanofi, Waltham, Massachusetts 02451, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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65
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Sanford J, Wang Y, Hansen JR, Gritsenko MA, Weitz KK, Sagendorf TJ, Tognon CE, Petyuk VA, Qian WJ, Liu T, Druker BJ, Rodland KD, Piehowski PD. Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:17-30. [PMID: 34813325 PMCID: PMC8739833 DOI: 10.1021/jasms.1c00169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/27/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Global and phosphoproteome profiling has demonstrated great utility for the analysis of clinical specimens. One barrier to the broad clinical application of proteomic profiling is the large amount of biological material required, particularly for phosphoproteomics─currently on the order of 25 mg wet tissue weight. For hematopoietic cancers such as acute myeloid leukemia (AML), the sample requirement is ≥10 million peripheral blood mononuclear cells (PBMCs). Across large study cohorts, this requirement will exceed what is obtainable for many individual patients/time points. For this reason, we were interested in the impact of differential peptide loading across multiplex channels on proteomic data quality. To achieve this, we tested a range of channel loading amounts (approximately the material obtainable from 5E5, 1E6, 2.5E6, 5E6, and 1E7 AML patient cells) to assess proteome coverage, quantification precision, and peptide/phosphopeptide detection in experiments utilizing isobaric tandem mass tag (TMT) labeling. As expected, fewer missing values were observed in TMT channels with higher peptide loading amounts compared to lower loadings. Moreover, channels with a lower loading have greater quantitative variability than channels with higher loadings. A statistical analysis showed that decreased loading amounts result in an increase in the type I error rate. We then examined the impact of differential loading on the detection of known differences between distinct AML cell lines. Similar patterns of increased data missingness and higher quantitative variability were observed as loading was decreased resulting in fewer statistical differences; however, we found good agreement in features identified as differential, demonstrating the value of this approach.
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Affiliation(s)
- James
A. Sanford
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Yang Wang
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Joshua R. Hansen
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Marina A. Gritsenko
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Karl K. Weitz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Tyler J. Sagendorf
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Cristina E. Tognon
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
- Division
of Hematology and Medical Oncology, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Vladislav A. Petyuk
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Wei-Jun Qian
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Tao Liu
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Brian J. Druker
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
- Division
of Hematology and Medical Oncology, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Karin D. Rodland
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Paul D. Piehowski
- Environmental
Molecular Sciences Division, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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66
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Wei J, Huan Y, Heng Z, Zhao C, Jia L, Yu Y, Gao Y. Dynamic urine proteome changes in a rat model of simvastatin-induced skeletal muscle injury. J Proteomics 2022; 254:104477. [PMID: 34990819 DOI: 10.1016/j.jprot.2021.104477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 10/19/2022]
Abstract
Statin-associated muscle symptoms (SAMS) are the main side effects of statins. Currently, there are no effective biomarkers for accurate clinical diagnosis. Urine is not subject to homeostatic control and therefore accumulates early changes, making it an ideal biomarker source. We therefore examined urine proteome changes associated with SAMS. Here, we established a SAMS rat model by intragastric intubation with simvastatin (80 mg/kg). Biochemical analyses and hematoxylin and eosin staining were used to evaluate the degree of muscle injury. The urine proteome on days 3, 6, 9 and 14 was profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Differential proteins on day 14 of SAMS were mainly associated with glycolysis/gluconeogenesis, pyruvate metabolism, metabolism of reactive oxygen species and apoptosis, which were associated with the pathological mechanism of SAMS. Among the 14 differential proteins on day 3, Fibrinogen gamma chain (FIBG), Osteopontin (OSTP) and C-reactive protein (CRP) were associated with muscle damage, while EH domain-containing protein 1(EHD1), Cubilin (CUBN) and Fibronectin (FINC) were associated with the pathogenic mechanisms of SAMS. Our preliminary results indicated that the urine proteome can reflect early changes in the SAMS rat model, providing the potential for monitoring drug side effects in future clinical research. SIGNIFICANCE: This study demonstrate that the early muscle damage caused by simvastatin can be reflected in urinary proteins. The urine proteome also has the potential to reflect the pharmacology and toxicology of drugs in future clinical research.
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Affiliation(s)
- Jing Wei
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China; Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Yuhang Huan
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing 100875, China; Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
| | - Ziqi Heng
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Chenyang Zhao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Lulu Jia
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yuncui Yu
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing 100875, China.
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67
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Pandya NJ, Meier S, Tyanova S, Terrigno M, Wang C, Punt AM, Mientjes EJ, Vautheny A, Distel B, Kremer T, Elgersma Y, Jagasia R. A cross-species spatiotemporal proteomic analysis identifies UBE3A-dependent signaling pathways and targets. Mol Psychiatry 2022; 27:2590-2601. [PMID: 35264729 PMCID: PMC9135630 DOI: 10.1038/s41380-022-01484-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/20/2022] [Accepted: 02/09/2022] [Indexed: 12/19/2022]
Abstract
Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of neuronal E3 ligase UBE3A. Restoring UBE3A levels is a potential disease-modifying therapy for AS and has recently entered clinical trials. There is paucity of data regarding the molecular changes downstream of UBE3A hampering elucidation of disease therapeutics and biomarkers. Notably, UBE3A plays an important role in the nucleus but its targets have yet to be elucidated. Using proteomics, we assessed changes during postnatal cortical development in an AS mouse model. Pathway analysis revealed dysregulation of proteasomal and tRNA synthetase pathways at all postnatal brain developmental stages, while synaptic proteins were altered in adults. We confirmed pathway alterations in an adult AS rat model across multiple brain regions and highlighted region-specific differences. UBE3A reinstatement in AS model mice resulted in near complete and partial rescue of the proteome alterations in adolescence and adults, respectively, supporting the notion that restoration of UBE3A expression provides a promising therapeutic option. We show that the nuclear enriched transketolase (TKT), one of the most abundantly altered proteins, is a novel direct UBE3A substrate and is elevated in the neuronal nucleus of rat brains and human iPSC-derived neurons. Taken together, our study provides a comprehensive map of UBE3A-driven proteome remodeling in AS across development and species, and corroborates an early UBE3A reinstatement as a viable therapeutic option. To support future disease and biomarker research, we present an accessible large-scale multi-species proteomic resource for the AS community ( https://www.angelman-proteome-project.org/ ).
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Affiliation(s)
- Nikhil J. Pandya
- Neuroscience and Rare Diseases Discovery & Translational Area, Basel, Switzerland
| | - Sonja Meier
- Neuroscience and Rare Diseases Discovery & Translational Area, Basel, Switzerland
| | - Stefka Tyanova
- grid.417570.00000 0004 0374 1269pRED Informatics Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Marco Terrigno
- Neuroscience and Rare Diseases Discovery & Translational Area, Basel, Switzerland
| | - Congwei Wang
- Neuroscience and Rare Diseases Discovery & Translational Area, Basel, Switzerland
| | - A. Mattijs Punt
- grid.5645.2000000040459992XDepartment of Clinical Genetics and Department of Neuroscience, The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - E. J. Mientjes
- grid.5645.2000000040459992XDepartment of Clinical Genetics and Department of Neuroscience, The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Audrey Vautheny
- Neuroscience and Rare Diseases Discovery & Translational Area, Basel, Switzerland
| | - Ben Distel
- grid.5645.2000000040459992XDepartment of Clinical Genetics and Department of Neuroscience, The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands ,grid.7177.60000000084992262Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas Kremer
- Neuroscience and Rare Diseases Discovery & Translational Area, Basel, Switzerland
| | - Ype Elgersma
- Department of Clinical Genetics and Department of Neuroscience, The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.
| | - Ravi Jagasia
- Neuroscience and Rare Diseases Discovery & Translational Area, Basel, Switzerland.
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68
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Ma Y, Dammer EB, Felsky D, Duong DM, Klein HU, White CC, Zhou M, Logsdon BA, McCabe C, Xu J, Wang M, Wingo TS, Lah JJ, Zhang B, Schneider J, Allen M, Wang X, Ertekin-Taner N, Seyfried NT, Levey AI, Bennett DA, De Jager PL. Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. Nat Commun 2021; 12:7035. [PMID: 34857756 PMCID: PMC8640037 DOI: 10.1038/s41467-021-27204-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 11/04/2021] [Indexed: 11/09/2022] Open
Abstract
RNA editing is a feature of RNA maturation resulting in the formation of transcripts whose sequence differs from the genome template. Brain RNA editing may be altered in Alzheimer's disease (AD). Here, we analyzed data from 1,865 brain samples covering 9 brain regions from 1,074 unrelated subjects on a transcriptome-wide scale to identify inter-regional differences in RNA editing. We expand the list of known brain editing events by identifying 58,761 previously unreported events. We note that only a small proportion of these editing events are found at the protein level in our proteome-wide validation effort. We also identified the occurrence of editing events associated with AD dementia, neuropathological measures and longitudinal cognitive decline in: SYT11, MCUR1, SOD2, ORAI2, HSDL2, PFKP, and GPRC5B. Thus, we present an extended reference set of brain RNA editing events, identify a subset that are found to be expressed at the protein level, and extend the narrative of transcriptomic perturbation in AD to RNA editing.
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Affiliation(s)
- Yiyi Ma
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA
| | - Charles C White
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA
| | - Maotian Zhou
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Cristin McCabe
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA
| | - Jishu Xu
- Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Julie Schneider
- Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Mariet Allen
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL, 32224, USA
| | - Xue Wang
- Mayo Clinic Florida, Department of Health Sciences Research, Jacksonville, FL, 32224, USA
| | - Nilüfer Ertekin-Taner
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL, 32224, USA
- Mayo Clinic Florida, Department of Neurology, Jacksonville, FL, 32224, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168th street, New York, NY, 10032, USA.
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge, MA, 02142, USA.
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69
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Kim JS, Shah AA, Hummers LK, Zeger SL. Predicting clinical events using Bayesian multivariate linear mixed models with application to scleroderma. BMC Med Res Methodol 2021; 21:249. [PMID: 34773969 PMCID: PMC8590788 DOI: 10.1186/s12874-021-01439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/12/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Scleroderma is a serious chronic autoimmune disease in which a patient's disease state manifests in several irregularly spaced longitudinal measures of lung, heart, skin, and other organ systems. Threshold crossings of pulmonary and cardiac measures indicate potentially life-threatening key clinical events including interstitial lung disease (ILD), cardiomyopathy, and pulmonary hypertension (PH). The statistical challenge is to accurately and precisely predict these events by using all of the clinical history for the patient at hand and for a reference population of patients. METHODS We use a Bayesian mixed model approach to simultaneously characterize each individual's future trajectories for several biomarkers. We estimate this model using a large population of patients from the Johns Hopkins Scleroderma Center Research Registry. The joint probabilities of critical lung and heart events are then calculated as a byproduct of the mixed model. RESULTS The performance of this approach is substantially better than standard, more common alternatives. In order to predict an individual's risks in a clinical setting, we also develop a cross-validated, sequential prediction (CVSP) algorithm. As additional data are observed during a patient's visit, the algorithm sequentially produces updated predictions for the future longitudinal trajectories and for ILD, cardiomyopathy, and PH. The updated prediction distributions with little additional computing, for example within an electronic health record (EHR). CONCLUSIONS This method that generates real-time personalized risk estimates has been implemented within the electronic health record system for clinical testing. To our knowledge, this work represents the first approach to compute personalized risk estimates for multiple scleroderma complications.
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Affiliation(s)
- Ji Soo Kim
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Ami A Shah
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura K Hummers
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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70
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Wang YJ, Downey MA, Choi S, Shoup TM, Elmaleh DR. Cromolyn platform suppresses fibrosis and inflammation, promotes microglial phagocytosis and neurite outgrowth. Sci Rep 2021; 11:22161. [PMID: 34772945 PMCID: PMC8589953 DOI: 10.1038/s41598-021-00465-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/07/2021] [Indexed: 12/18/2022] Open
Abstract
Neurodegenerative diseases are characterized by chronic neuroinflammation and may perpetuate ongoing fibrotic reactions within the central nervous system. Unfortunately, there is no therapeutic available that treats neurodegenerative inflammation and its sequelae. Here we utilize cromolyn, a mast cell inhibitor with anti-inflammatory capabilities, and its fluorinated analogue F-cromolyn to study fibrosis-related protein regulation and secretion downstream of neuroinflammation and their ability to promote microglial phagocytosis and neurite outgrowth. In this report, RNA-seq analysis shows that administration of the pro-inflammatory cytokine TNF-α to HMC3 human microglia results in a robust upregulation of fibrosis-associated genes. Subsequent treatment with cromolyn and F-cromolyn resulted in reduced secretion of collagen XVIII, fibronectin, and tenascin-c. Additionally, we show that cromolyn and F-cromolyn reduce pro-inflammatory proteins PLP1, PELP1, HSP90, IL-2, GRO-α, Eotaxin, and VEGF-Α, while promoting secretion of anti-inflammatory IL-4 in HMC3 microglia. Furthermore, cromolyn and F-cromolyn augment neurite outgrowth in PC12 neuronal cells in concert with nerve growth factor. Treatment also differentially altered secretion of neurogenesis-related proteins TTL, PROX1, Rab35, and CSDE1 in HMC3 microglia. Finally, iPSC-derived human microglia more readily phagocytose Aβ42 with cromolyn and F-cromolyn relative to controls. We propose the cromolyn platform targets multiple proteins upstream of PI3K/Akt/mTOR, NF-κB, and GSK-3β signaling pathways to affect cytokine, chemokine, and fibrosis-related protein expression.
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Affiliation(s)
| | | | - Sungwoon Choi
- Department of New Drug Discovery, Chungnam National University, Daejeon, South Korea
| | - Timothy M Shoup
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02129-2060, USA
| | - David R Elmaleh
- AZTherapies, Inc., Boston, MA, USA.
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02129-2060, USA.
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71
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Nättinen J, Aapola U, Nukareddy P, Uusitalo H. Looking deeper into ocular surface health: an introduction to clinical tear proteomics analysis. Acta Ophthalmol 2021; 100:486-498. [PMID: 34750985 DOI: 10.1111/aos.15059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022]
Abstract
Ocular surface diseases are becoming more prevalent worldwide. Reasons for this include the ongoing population ageing and increasing use of digital displays, although ophthalmologists have a wide selection of tools, which can be implemented in the evaluation of the ocular surface health, methods, which enable the in-depth study of biological functions are gaining more interest. These new approaches are needed, since the individual responses to ocular surface diseases and treatments can vary from person to person, and the correlations between clinical signs and symptoms are often low. Modern mass spectrometry (MS) methods can produce information on hundreds of tear proteins, which in turn can provide valuable information on the biological effects occurring on the ocular surface. In this review article, we will provide an overview of the different aspects, which are part of a successful tear proteomics study design and equip readers with a better understanding of the methods most suited for their MS-based tear proteomics study in the field of ophthalmology and ocular surface.
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Affiliation(s)
- Janika Nättinen
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
| | - Ulla Aapola
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
| | - Praveena Nukareddy
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
| | - Hannu Uusitalo
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
- Tays Eye Centre Tampere University Hospital Tampere Finland
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72
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Correa Rojo A, Heylen D, Aerts J, Thas O, Hooyberghs J, Ertaylan G, Valkenborg D. Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. Front Physiol 2021; 12:723510. [PMID: 34512391 PMCID: PMC8427610 DOI: 10.3389/fphys.2021.723510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
Precision medicine as a framework for disease diagnosis, treatment, and prevention at the molecular level has entered clinical practice. From the start, genetics has been an indispensable tool to understand and stratify the biology of chronic and complex diseases in precision medicine. However, with the advances in biomedical and omics technologies, quantitative proteomics is emerging as a powerful technology complementing genetics. Quantitative proteomics provide insight about the dynamic behaviour of proteins as they represent intermediate phenotypes. They provide direct biological insights into physiological patterns, while genetics accounting for baseline characteristics. Additionally, it opens a wide range of applications in clinical diagnostics, treatment stratification, and drug discovery. In this mini-review, we discuss the current status of quantitative proteomics in precision medicine including the available technologies and common methods to analyze quantitative proteomics data. Furthermore, we highlight the current challenges to put quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data with genomics data for future applications in precision medicine.
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Affiliation(s)
- Alejandro Correa Rojo
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dries Heylen
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Jan Aerts
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Olivier Thas
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), Wollongong, NSW, Australia
| | - Jef Hooyberghs
- Flemish Institute for Technological Research (VITO), Mol, Belgium.,Theoretical Physics, Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Gökhan Ertaylan
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dirk Valkenborg
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
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73
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Proteomic signatures of myeloid derived suppressor cells from liver and lung metastases reveal functional divergence and potential therapeutic targets. Cell Death Discov 2021; 7:232. [PMID: 34482371 PMCID: PMC8418613 DOI: 10.1038/s41420-021-00621-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) promote immunosuppressive activities in the tumor microenvironment (TME), resulting in increased tumor burden and diminishing the anti-tumor response of immunotherapies. While primary and metastatic tumors are typically the focal points of therapeutic development, the immune cells of the TME are differentially programmed by the tissue of the metastatic site. In particular, MDSCs are programmed uniquely within different organs in the context of tumor progression. Given that MDSC plasticity is shaped by the surrounding environment, the proteomes of MDSCs from different metastatic sites are hypothesized to be unique. A bottom-up proteomics approach using sequential window acquisition of all theoretical mass spectra (SWATH-MS) was used to quantify the proteome of CD11b+ cells derived from murine liver metastases (LM) and lung metastases (LuM). A comparative proteomics workflow was employed to compare MDSC proteins from LuM (LuM-MDSC) and LM (LM-MDSC) while also elucidating common signaling pathways, protein function, and possible drug-protein interactions. SWATH-MS identified 2516 proteins from 200 µg of sample. Of the 2516 proteins, 2367 have matching transcriptomic data. Upregulated proteins from lung and liver-derived murine CD11b+ cells with matching mRNA transcriptomic data were categorized based on target knowledge and level of drug development. Comparative proteomic analysis demonstrates that liver and lung tumor-derived MDSCs have distinct proteomes that may be subject to pharmacologic manipulation.
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74
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Tang J, Fu J, Wang Y, Li B, Li Y, Yang Q, Cui X, Hong J, Li X, Chen Y, Xue W, Zhu F. ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. Brief Bioinform 2021; 21:621-636. [PMID: 30649171 PMCID: PMC7299298 DOI: 10.1093/bib/bby127] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/19/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
Label-free quantification (LFQ) with a specific and sequentially integrated workflow of acquisition technique, quantification tool and processing method has emerged as the popular technique employed in metaproteomic research to provide a comprehensive landscape of the adaptive response of microbes to external stimuli and their interactions with other organisms or host cells. The performance of a specific LFQ workflow is highly dependent on the studied data. Hence, it is essential to discover the most appropriate one for a specific data set. However, it is challenging to perform such discovery due to the large number of possible workflows and the multifaceted nature of the evaluation criteria. Herein, a web server ANPELA (https://idrblab.org/anpela/) was developed and validated as the first tool enabling performance assessment of whole LFQ workflow (collective assessment by five well-established criteria with distinct underlying theories), and it enabled the identification of the optimal LFQ workflow(s) by a comprehensive performance ranking. ANPELA not only automatically detects the diverse formats of data generated by all quantification tools but also provides the most complete set of processing methods among the available web servers and stand-alone tools. Systematic validation using metaproteomic benchmarks revealed ANPELA's capabilities in 1 discovering well-performing workflow(s), (2) enabling assessment from multiple perspectives and (3) validating LFQ accuracy using spiked proteins. ANPELA has a unique ability to evaluate the performance of whole LFQ workflow and enables the discovery of the optimal LFQs by the comprehensive performance ranking of all 560 workflows. Therefore, it has great potential for applications in metaproteomic and other studies requiring LFQ techniques, as many features are shared among proteomic studies.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Li
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yinghong Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Xuejiao Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jiajun Hong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
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75
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Nakayasu ES, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, Fillmore TL, Frohnert BI, Rewers M, Krischer JP, Ansong C, Suchy-Dicey AM, Evans-Molina C, Qian WJ, Webb-Robertson BJM, Metz TO. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc 2021; 16:3737-3760. [PMID: 34244696 PMCID: PMC8830262 DOI: 10.1038/s41596-021-00566-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new disease biomarkers. However, certain critical steps of study design such as cohort selection, evaluation of statistical power, sample blinding and randomization, and sample/data quality control are often neglected or underappreciated during experimental design and execution. This tutorial discusses important steps for designing and implementing a liquid-chromatography-mass-spectrometry-based biomarker discovery study. We describe the rationale, considerations and possible failures in each step of such studies, including experimental design, sample collection and processing, and data collection. We also provide guidance for major steps of data processing and final statistical analysis for meaningful biological interpretations along with highlights of several successful biomarker studies. The provided guidelines from study design to implementation to data interpretation serve as a reference for improving rigor and reproducibility of biomarker development studies.
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Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Marina Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brigitte I Frohnert
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Jeffrey P Krischer
- Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Astrid M Suchy-Dicey
- Elson S. Floyd College of Medicine, Washington State University, Seattle, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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76
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Root L, Campo A, MacNiven L, Con P, Cnaani A, Kültz D. Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus modulate epithelial cell turnover. Genomics 2021; 113:3235-3249. [PMID: 34298068 DOI: 10.1016/j.ygeno.2021.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/25/2021] [Accepted: 07/14/2021] [Indexed: 12/27/2022]
Abstract
A data-independent acquisition (DIA) assay library for targeted quantitation of thousands of Oreochromis niloticus gill proteins using a label- and gel-free workflow was generated and used to compare protein and mRNA abundances. This approach generated complimentary rather than redundant data for 1899 unique genes in gills of tilapia acclimated to freshwater and brackish water. Functional enrichment analyses identified mitochondrial energy metabolism, serine protease and immunity-related functions, and cytoskeleton/ extracellular matrix organization as major processes controlled by salinity in O. niloticus gills. Non-linearity in salinity-dependent transcriptome versus proteome regulation was revealed for specific functional groups of genes. The relationship was more linear for other molecular functions/ cellular processes, suggesting that the salinity-dependent regulation of O. niloticus gill function relies on post-transcriptional mechanisms for some functions/ processes more than others. This integrative systems biology approach can be adopted for other tissues and organisms to study cellular dynamics for many changing ecological contexts.
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Affiliation(s)
- Larken Root
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Aurora Campo
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Leah MacNiven
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA.
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77
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Zhao L, Fu G, Cui Y, Xu Z, Cai T, Zhang D. Compensating Complete Loss of Signal Recognition Particle During Co-translational Protein Targeting by the Translation Speed and Accuracy. Front Microbiol 2021; 12:690286. [PMID: 34305852 PMCID: PMC8299109 DOI: 10.3389/fmicb.2021.690286] [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: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 11/23/2022] Open
Abstract
Signal recognition particle (SRP) is critical for delivering co-translational proteins to the bacterial inner membrane. Previously, we identified SRP suppressors in Escherichia coli that inhibit translation initiation and elongation, which provided insights into the mechanism of bypassing the requirement of SRP. Suppressor mutations tended to be located in regions that govern protein translation under evolutionary pressure. To test this hypothesis, we re-executed the suppressor screening of SRP. Here, we isolated a novel SRP suppressor mutation located in the Shine–Dalgarno sequence of the S10 operon, which partially offset the targeting defects of SRP-dependent proteins. We found that the suppressor mutation decreased the protein translation rate, which extended the time window of protein targeting. This increased the possibility of the correct localization of inner membrane proteins. Furthermore, the fidelity of translation was decreased in suppressor cells, suggesting that the quality control of translation was inactivated to provide an advantage in tolerating toxicity caused by the loss of SRP. Our results demonstrated that the inefficient protein targeting due to SRP deletion can be rescued through modulating translational speed and accuracy.
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Affiliation(s)
- Liuqun Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Engineering Laboratory for Industrial Enzymes, Chinese Academy of Sciences, Tianjin, China
| | - Yanyan Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zixiang Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Engineering Laboratory for Industrial Enzymes, Chinese Academy of Sciences, Tianjin, China
| | - Tao Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Engineering Laboratory for Industrial Enzymes, Chinese Academy of Sciences, Tianjin, China
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78
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Rahmatbakhsh M, Gagarinova A, Babu M. Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections. Front Genet 2021; 12:667936. [PMID: 34276775 PMCID: PMC8283032 DOI: 10.3389/fgene.2021.667936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial pathogens have evolved numerous mechanisms to hijack host's systems, thus causing disease. This is mediated by alterations in the combined host-pathogen proteome in time and space. Mass spectrometry-based proteomics approaches have been developed and tailored to map disease progression. The result is complex multidimensional data that pose numerous analytic challenges for downstream interpretation. However, a systematic review of approaches for the downstream analysis of such data has been lacking in the field. In this review, we detail the steps of a typical temporal and spatial analysis, including data pre-processing steps (i.e., quality control, data normalization, the imputation of missing values, and dimensionality reduction), different statistical and machine learning approaches, validation, interpretation, and the extraction of biological information from mass spectrometry data. We also discuss current best practices for these steps based on a collection of independent studies to guide users in selecting the most suitable strategies for their dataset and analysis objectives. Moreover, we also compiled the list of commonly used R software packages for each step of the analysis. These could be easily integrated into one's analysis pipeline. Furthermore, we guide readers through various analysis steps by applying these workflows to mock and host-pathogen interaction data from public datasets. The workflows presented in this review will serve as an introduction for data analysis novices, while also helping established users update their data analysis pipelines. We conclude the review by discussing future directions and developments in temporal and spatial proteomics and data analysis approaches. Data analysis codes, prepared for this review are available from https://github.com/BabuLab-UofR/TempSpac, where guidelines and sample datasets are also offered for testing purposes.
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Affiliation(s)
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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79
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Wang M, Jiang L, Jian R, Chan JY, Liu Q, Snyder MP, Tang H. RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data. Bioinformatics 2021; 37:815-821. [PMID: 33098413 PMCID: PMC8098025 DOI: 10.1093/bioinformatics/btaa904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 10/04/2020] [Accepted: 10/09/2020] [Indexed: 01/15/2023] Open
Abstract
MOTIVATION Data normalization is an important step in processing proteomics data generated in mass spectrometry experiments, which aims to reduce sample-level variation and facilitate comparisons of samples. Previously published methods for normalization primarily depend on the assumption that the distribution of protein expression is similar across all samples. However, this assumption fails when the protein expression data is generated from heterogenous samples, such as from various tissue types. This led us to develop a novel data-driven method for improved normalization to correct the systematic bias meanwhile maintaining underlying biological heterogeneity. RESULTS To robustly correct the systematic bias, we used the density-power-weight method to down-weigh outliers and extended the one-dimensional robust fitting method described in the previous work to our structured data. We then constructed a robustness criterion and developed a new normalization algorithm, called RobNorm.In simulation studies and analysis of real data from the genotype-tissue expression project, we compared and evaluated the performance of RobNorm against other normalization methods. We found that the RobNorm approach exhibits the greatest reduction in systematic bias while maintaining across-tissue variation, especially for datasets from highly heterogeneous samples. AVAILABILITYAND IMPLEMENTATION https://github.com/mwgrassgreen/RobNorm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Meng Wang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joanne Y Chan
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Qing Liu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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80
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Thompson AM, Stratton KG, Bramer LM, Zavoshy NS, McCue LA. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) peak intensity normalization for complex mixture analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9068. [PMID: 33590907 DOI: 10.1002/rcm.9068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/03/2021] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a preferred technique for analyzing complex organic mixtures. Currently, there is no consensus normalization approach, nor an objective method for selecting one, for quantitative analyses of FT-ICR-MS data. We investigate a method to evaluate and score the amount of bias various normalization approaches introduce into the data. METHODS We evaluate the ability of the Statistical Procedure for the Analysis of Normalization Strategies (SPANS) to guide the selection of appropriate normalization approaches for two different FT-ICR-MS data sets. Furthermore, we test the robustness of SPANS results to changes in SPANS parameter values and assess the impact of using various normalization approaches on downstream statistical analyses. RESULTS The normalization approach identified by SPANS differed for the two data sets. Normalization methods impacted the statistical significance of peaks differently, underscoring the importance of carefully evaluating potential methods. More consistent SPANS scores resulted when at least 120 significant peaks are used, where larger sets of peaks were obtained by increasing the p-value threshold. Interestingly, we show that total sum scaling and highest peak normalization, used in previous studies, underperformed relative to SPANS-recommended normalization approaches. CONCLUSIONS Although there is no single, best normalization method for all data sets, SPANS provides a mechanism to identify an appropriate normalization method for analyzing FT-ICR-MS data quantitatively. The number of peaks used in the background distributions of SPANS contributes more significantly to the reproducibility of results than the p-value thresholds used to obtain those peaks.
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Affiliation(s)
- Allison M Thompson
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kelly G Stratton
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lisa M Bramer
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Nicole S Zavoshy
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lee Ann McCue
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
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Important Issues in Planning a Proteomics Experiment: Statistical Considerations of Quantitative Proteomic Data. Methods Mol Biol 2021; 2228:1-20. [PMID: 33950479 DOI: 10.1007/978-1-0716-1024-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Mass spectrometry is frequently used in quantitative proteomics to detect differentially regulated proteins. A very important but unfortunately oftentimes neglected part in detecting differential proteins is the statistical analysis. Data from proteomics experiments are usually high-dimensional and hence require profound statistical methods. It is especially important to already correctly design a proteomic experiment before it is conducted in the laboratory. Only this can ensure that the statistical analysis is capable of detecting truly differential proteins afterward. This chapter thus covers aspects of both statistical planning as well as the actual analysis of quantitative proteomic experiments.
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82
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Stark K, Goncharov T, Varfolomeev E, Xie L, Ngu H, Peng I, Anderson KR, Verschueren E, Choi M, Kirkpatrick DS, Easton A, Webster JD, McKenzie BS, Vucic D, Bingol B. Genetic inactivation of RIP1 kinase activity in rats protects against ischemic brain injury. Cell Death Dis 2021; 12:379. [PMID: 33828080 PMCID: PMC8026634 DOI: 10.1038/s41419-021-03651-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 02/01/2023]
Abstract
RIP1 kinase-mediated inflammatory and cell death pathways have been implicated in the pathology of acute and chronic disorders of the nervous system. Here, we describe a novel animal model of RIP1 kinase deficiency, generated by knock-in of the kinase-inactivating RIP1(D138N) mutation in rats. Homozygous RIP1 kinase-dead (KD) rats had normal development, reproduction and did not show any gross phenotypes at baseline. However, cells derived from RIP1 KD rats displayed resistance to necroptotic cell death. In addition, RIP1 KD rats were resistant to TNF-induced systemic shock. We studied the utility of RIP1 KD rats for neurological disorders by testing the efficacy of the genetic inactivation in the transient middle cerebral artery occlusion/reperfusion model of brain injury. RIP1 KD rats were protected in this model in a battery of behavioral, imaging, and histopathological endpoints. In addition, RIP1 KD rats had reduced inflammation and accumulation of neuronal injury biomarkers. Unbiased proteomics in the plasma identified additional changes that were ameliorated by RIP1 genetic inactivation. Together these data highlight the utility of the RIP1 KD rats for target validation and biomarker studies for neurological disorders.
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Affiliation(s)
- Kimberly Stark
- grid.418158.10000 0004 0534 4718Department of Neuroscience, Genentech, South San Francisco, 94080 CA USA
| | - Tatiana Goncharov
- grid.418158.10000 0004 0534 4718Department of Early Discovery Biochemistry, Genentech, South San Francisco, 94080 CA USA
| | - Eugene Varfolomeev
- grid.418158.10000 0004 0534 4718Department of Early Discovery Biochemistry, Genentech, South San Francisco, 94080 CA USA
| | - Luke Xie
- grid.418158.10000 0004 0534 4718Department of Biomedical Imaging, Genentech, South San Francisco, 94080 CA USA
| | - Hai Ngu
- grid.418158.10000 0004 0534 4718Department of Pathology, Genentech, South San Francisco, 94080 CA USA
| | - Ivan Peng
- grid.418158.10000 0004 0534 4718Department of Translational Immunology, Genentech, South San Francisco, 94080 CA USA
| | - Keith R. Anderson
- grid.418158.10000 0004 0534 4718Department of Molecular Biology, Genentech, South San Francisco, 94080 CA USA
| | - Erik Verschueren
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, 94080 CA USA
| | - Meena Choi
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, 94080 CA USA
| | - Donald S. Kirkpatrick
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, 94080 CA USA
| | - Amy Easton
- grid.418158.10000 0004 0534 4718Department of Neuroscience, Genentech, South San Francisco, 94080 CA USA
| | - Joshua D. Webster
- grid.418158.10000 0004 0534 4718Department of Pathology, Genentech, South San Francisco, 94080 CA USA
| | - Brent S. McKenzie
- grid.418158.10000 0004 0534 4718Department of Translational Immunology, Genentech, South San Francisco, 94080 CA USA
| | - Domagoj Vucic
- grid.418158.10000 0004 0534 4718Department of Early Discovery Biochemistry, Genentech, South San Francisco, 94080 CA USA
| | - Baris Bingol
- grid.418158.10000 0004 0534 4718Department of Neuroscience, Genentech, South San Francisco, 94080 CA USA
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83
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Pomraning KR, Dai Z, Munoz N, Kim YM, Gao Y, Deng S, Kim J, Hofstad BA, Swita MS, Lemmon T, Collett JR, Panisko EA, Webb-Robertson BJM, Zucker JD, Nicora CD, De Paoli H, Baker SE, Burnum-Johnson KE, Hillson NJ, Magnuson JK. Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus. Front Bioeng Biotechnol 2021; 9:603832. [PMID: 33898398 PMCID: PMC8058442 DOI: 10.3389/fbioe.2021.603832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/16/2021] [Indexed: 11/13/2022] Open
Abstract
Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4 × after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.
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Affiliation(s)
- Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ziyu Dai
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nathalie Munoz
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shuang Deng
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joonhoon Kim
- Pacific Northwest National Laboratory, Richland, WA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Beth A Hofstad
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marie S Swita
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Teresa Lemmon
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - James R Collett
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ellen A Panisko
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Jeremy D Zucker
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Nathan J Hillson
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
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84
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Huan Y, Wei J, Su T, Gao Y. Urine proteome changes in a chronic unpredictable mild stress (CUMS) mouse model of major depressive disorder. J Pharm Biomed Anal 2021; 199:114064. [PMID: 33862505 DOI: 10.1016/j.jpba.2021.114064] [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: 11/26/2020] [Revised: 03/29/2021] [Accepted: 04/04/2021] [Indexed: 12/19/2022]
Abstract
Major depressive disorder (MDD) is a prevalent complex psychiatric disorder, and there are no effective biomarkers for clinical diagnosis. Urine is not subjected to homeostatic control, allowing it to reflect the sensitive changes that occur in various diseases. In this study, we examined the urine proteome changes in a chronic unpredictable mild stress mouse model of MDD. Male C57BL/6 mice were subjected to chronic unpredictable mild stress for 5 weeks. The tail suspension test and sucrose consumption test were then applied to evaluate depression-like behaviors. The urine proteomes on day 0 and day 36 in the CUMS group were profiled by liquid chromatography coupled with tandem mass spectrometry (LCMS/MS). A total of 36 differential proteins were identified, 19 of which have been associated with the pathogenic mechanisms of MDD. There was an average of two differential proteins that were identified through 1,048,574 random combination statistical analyses, indicating that at least 95 % of the differential proteins were reliable. The differential proteins were mainly associated with blood coagulation, inflammatory responses and central nervous system development. Our preliminary results indicated that the urine proteome can reflect changes associated with MDD in the CUMS model, which provides potential clues for the diagnosis of MDD.
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Affiliation(s)
- Yuhang Huan
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, 100875, China.
| | - Jing Wei
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, 100875, China.
| | - Tong Su
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences and Peking Union Medical College, Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, 100875, China.
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85
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Orfanou IM, Argyros O, Papapetropoulos A, Tseleni-Balafouta S, Vougas K, Tamvakopoulos C. Discovery and Pharmacological Evaluation of STEAP4 as a Novel Target for HER2 Overexpressing Breast Cancer. Front Oncol 2021; 11:608201. [PMID: 33842315 PMCID: PMC8034292 DOI: 10.3389/fonc.2021.608201] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/08/2021] [Indexed: 01/11/2023] Open
Abstract
Breast cancer (BC) is a highly heterogeneous disease encompassing multiple subtypes with different molecular and histopathological features, disease prognosis, and therapeutic responses. Among these, the Triple Negative BC form (TNBC) is an aggressive subtype with poor prognosis and therapeutic outcome. With respect to HER2 overexpressing BC, although advanced targeted therapies have improved the survival of patients, disease relapse and metastasis remains a challenge for therapeutic efficacy. In this study the aim was to identify key membrane-associated proteins which are overexpressed in these aggressive BC subtypes and can serve as potential biomarkers or drug targets. We leveraged on the development of a membrane enrichment protocol in combination with the global profiling GeLC-MS/MS technique, and compared the proteomic profiles of a HER2 overexpressing (HCC-1954) and a TNBC (MDA-MB-231) cell line with that of a benign control breast cell line (MCF-10A). An average of 2300 proteins were identified from each cell line, of which approximately 600 were membrane-associated proteins. Our global proteomic methodology in tandem with invigoration by Western blot and Immunofluorescence analysis, readily detected several previously-established BC receptors like HER2 and EPHA2, but importantly STEAP4 and CD97 emerged as novel potential candidate markers. This is the first time that the mitochondrial iron reductase STEAP4 protein up-regulation is linked to BC (HER2+ subtype), while for CD97, its role in BC has been previously described, but never before by a global proteomic technology in TNBC. STEAP4 was selected for further detailed evaluation by the employment of Immunohistochemical analysis of BC xenografts and clinical tissue microarray studies. Results showed that STEAP4 expression was evident only in malignant breast tissues whereas all the benign breast cases had no detectable levels. A functional role of STEAP4 intervention was established in HER2 overexpressing BC by pharmacological studies, where blockage of the STEAP4 pathway with an iron chelator (Deferiprone) in combination with the HER2 inhibitor Lapatinib led to a significant reduction in cell growth in vitro. Furthermore, siRNA mediated knockdown of STEAP4 also suppressed cell proliferation and enhanced the inhibition of Lapatinib in HER2 overexpressing BC, confirming its potential oncogenic role in BC. In conclusion, STEAP4 may represent a novel BC related biomarker and a potential pharmacological target for the treatment of HER2 overexpressing BC.
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Affiliation(s)
- Ioanna-Maria Orfanou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Orestis Argyros
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Andreas Papapetropoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Sofia Tseleni-Balafouta
- Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Vougas
- Proteomics Laboratory, Division of Biotechnology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Constantin Tamvakopoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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86
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Jia L, Wu J, Wei J, Du L, Wang P, Zhang Y, Yu Y, Wang X, Yang Y, Gao Y. Proteomic analysis of urine reveals biomarkers for the diagnosis and phenotyping of abdominal-type Henoch-Schonlein purpura. Transl Pediatr 2021; 10:510-524. [PMID: 33850810 PMCID: PMC8039785 DOI: 10.21037/tp-20-317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Abdominal-type Henoch-Schonlein purpura (HSP) is a common refractory disease in children. Currently, no specific diagnostic biomarker is available for HSP. METHODS Children with abdominal type HSP were first diagnosed with three syndromes using Chinese traditional medicine. The urinary proteomes among the three syndromes of patients with abdominal type HSP and healthy controls were compared using two label-free proteomics quantifications, including data-dependent acquisition and data-independent acquisition. RESULTS For the comparison between patients with abdominal type HSP and healthy children, a total of 75 differential urinary proteins were identified by determining the overlap of the two experiments. The ingenuity pathway analysis (IPA) analysis showed that these differential proteins were correlated with the pathogenesis of abdominal type HSP. Of these, 37 proteins were distributed in 13 solid tissues as tissue-enriched proteins. Monitoring changes in these proteins might help us detect uncommon clinical manifestations of HSP. Patients with abdominal type HSP can be further distinguished into three syndromes based on the urine proteome. Finally, a panel of six urinary proteins (P25774, P09417, Q7Z5L0, P60900, P14550 and P09668) was constructed for both the diagnosis and phenotyping of abdominal type HSP. CONCLUSIONS Urinary protein biomarkers for the diagnosis and phenotyping of abdominal type HSP were identified, which will contribute to the personalized treatment of patients with abdominal type HSP.
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Affiliation(s)
- Lulu Jia
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jianqiang Wu
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wei
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
| | - Lina Du
- Department of Chinese Medicine, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Panpan Wang
- Department of Chinese Medicine, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yanju Zhang
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yuncui Yu
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xiaoling Wang
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yan Yang
- Department of Chinese Medicine, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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87
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Barklis E, Alfadhli A, Kyle JE, Bramer LM, Bloodsworth KJ, Barklis RL, Leier HC, Petty RM, Zelnik ID, Metz TO, Futerman AH, Tafesse FG. Ceramide synthase 2 deletion decreases the infectivity of HIV-1. J Biol Chem 2021; 296:100340. [PMID: 33515546 PMCID: PMC7949126 DOI: 10.1016/j.jbc.2021.100340] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/01/2023] Open
Abstract
The lipid composition of HIV-1 virions is enriched in sphingomyelin (SM), but the roles that SM or other sphingolipids (SLs) might play in the HIV-1 replication pathway have not been elucidated. In human cells, SL levels are regulated by ceramide synthase (CerS) enzymes that produce ceramides, which can be converted to SMs, hexosylceramides, and other SLs. In many cell types, CerS2, which catalyzes the synthesis of very long chain ceramides, is the major CerS. We have examined how CerS2 deficiency affects the assembly and infectivity of HIV-1. As expected, we observed that very long chain ceramide, hexosylceramide, and SM were reduced in CerS2 knockout cells. CerS2 deficiency did not affect HIV-1 assembly or the incorporation of the HIV-1 envelope (Env) protein into virus particles, but it reduced the infectivites of viruses produced in the CerS2-deficient cells. The reduced viral infection levels were dependent on HIV-1 Env, since HIV-1 particles that were pseudotyped with the vesicular stomatitis virus glycoprotein did not exhibit reductions in infectivity. Moreover, cell-cell fusion assays demonstrated that the functional defect of HIV-1 Env in CerS2-deficient cells was independent of other viral proteins. Overall, our results indicate that the altered lipid composition of CerS2-deficient cells specifically inhibit the HIV-1 Env receptor binding and/or fusion processes.
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Affiliation(s)
- Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA.
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Lisa M Bramer
- Computing and Analytics Division, National Security Directorate PNNL, Richland, Washington, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Hans C Leier
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - R Max Petty
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Iris D Zelnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA.
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88
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Stavropoulou MI, Termentzi A, Kasiotis KM, Cheilari A, Stathopoulou K, Machera K, Aligiannis N. Untargeted Ultrahigh-Performance Liquid Chromatography-Hybrid Quadrupole-Orbitrap Mass Spectrometry (UHPLC-HRMS) Metabolomics Reveals Propolis Markers of Greek and Chinese Origin. Molecules 2021; 26:molecules26020456. [PMID: 33467182 PMCID: PMC7830967 DOI: 10.3390/molecules26020456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Chemical composition of propolis depends on the plant source and thus on the geographic and climatic characteristics of the site of collection. The aim of this study was to investigate the chemical profile of Greek and Chinese propolis extracts from different regions and suggest similarities and differences between them. Untargeted ultrahigh-performance liquid chromatography coupled to hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-HRMS) method was developed and 22 and 23 propolis samples from Greece and China, respectively, were analyzed. The experimental data led to the observation that there is considerable variability in terms of quality of the distinctive propolis samples. Partial least squares - discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) models were constructed and allowed the identification of significant features for sample discrimination, adding relevant information for the identification of class-determining metabolites. Chinese samples overexpressed compounds that are characteristic of the poplar type propolis, whereas Greek samples overexpress the latter and the diterpenes characteristic of the Mediterranean propolis type.
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Affiliation(s)
- Maria-Ioanna Stavropoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
| | - Aikaterini Termentzi
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (A.T.); (K.M.K.); (K.M.)
| | - Konstantinos M. Kasiotis
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (A.T.); (K.M.K.); (K.M.)
| | - Antigoni Cheilari
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
| | - Konstantina Stathopoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
| | - Kyriaki Machera
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (A.T.); (K.M.K.); (K.M.)
| | - Nektarios Aligiannis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
- Correspondence: ; Tel.: +30-210-727-4524
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89
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Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate. mBio 2021; 12:mBio.02373-20. [PMID: 33436432 PMCID: PMC7844537 DOI: 10.1128/mbio.02373-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The signal recognition particle (SRP) is conserved in all living organisms, and it cotranslationally delivers proteins to the inner membrane or endoplasmic reticulum. Recently, SRP loss was found not to be lethal in either the eukaryote Saccharomyces cerevisiae or the prokaryote Streptococcus mutans In Escherichia coli, the role of SRP in mediating inner membrane protein (IMP) targeting has long been studied. However, the essentiality of SRP remains a controversial topic, partly hindered by the lack of strains in which SRP is completely absent. Here we show that the SRP was nonessential in E. coli by suppressor screening. We identified two classes of extragenic suppressors-two translation initiation factors and a ribosomal protein-all of which are involved in translation initiation. The translation rate and inner membrane proteomic analyses were combined to define the mechanism that compensates for the lack of SRP. The primary factor that contributes to the efficiency of IMP targeting is the extension of the time window for targeting by pausing the initiation of translation, which further reduces translation initiation and elongation rates. Furthermore, we found that easily predictable features in the nascent chain determine the specificity of protein targeting. Our results show why the loss of the SRP pathway does not lead to lethality. We report a new paradigm in which the time delay in translation initiation is beneficial during protein targeting in the absence of SRP.IMPORTANCE Inner membrane proteins (IMPs) are cotranslationally inserted into the inner membrane or endoplasmic reticulum by the signal recognition particle (SRP). Generally, the deletion of SRP can result in protein targeting defects in Escherichia coli Suppressor screening for loss of SRP reveals that pausing at the translation start site is likely to be critical in allowing IMP targeting and avoiding aggregation. In this work, we found for the first time that SRP is nonessential in E. coli The time delay in initiation is different from the previous mechanism that only slows down the elongation rate. It not only maximizes the opportunity for untranslated ribosomes to be near the inner membrane but also extends the time window for targeting translating ribosomes by decreasing the speed of translation. We anticipate that our work will be a starting point for a more delicate regulatory mechanism of protein targeting.
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90
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Cheung HW, Wong KS, To NS, Bond AJ, Farrington AF, Prabhu A, Curl P, Wan TSM, Ho ENM. Label-free proteomics for discovering biomarker candidates of RAD140 administration to castrated horses. Drug Test Anal 2021; 13:1034-1047. [PMID: 33277807 DOI: 10.1002/dta.2988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 12/27/2022]
Abstract
Selective androgen receptor (AR) modulators (SARMs) are potent anabolic agents with a high potential of misuse in horseracing and equestrian sports. In this study, we applied label-free proteomics to discover plasma protein biomarkers in geldings (castrated horses) after administration with a popular SARM named RAD140. Tryptic peptides were prepared from plasma samples and analyzed by nano-flow ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (nano-UHPLC-HRMS/MS) using data-independent acquisition (DIA) method. Orthogonal projection on latent structure-discriminant analysis (OPLS-DA) has led to the development of a predictive model that could discriminate RAD140-administered samples from control samples and could also correctly classify 18 out of 19 in-training horses as control samples. The model comprises 75 proteins with variable importance in projection (VIP) score above 1. Gene Ontology (GO) enrichment analysis and literature review have identified upregulation of AR-regulated clusterin, and proteins associated with inflammation (haptoglobin, cluster of differentiation 14 [CD14], and inter-alpha-trypsin inhibitor heavy chain 4 [ITIH4]) and erythropoiesis (glycosylphosphatidylinositol-specific phospholipase D1 [GPLD1]) after RAD140 administration. Their changes were confirmed by selected reaction monitoring (SRM) experiments. Similar effects have been reported by the use of androgens and other SARMs. This is the first reported study that describes the use of a proteomic biomarker approach to detect horses that have been administered with RAD140 by applying label-free proteomic profiling of plasma samples. These results support the concept of a biomarker-driven approach to enhance the doping control of RAD140 and potentially other SARMs in the future.
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Affiliation(s)
- Hiu Wing Cheung
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Kin-Sing Wong
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Ning Sum To
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Amanda J Bond
- Equestrian Affairs, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Adrian F Farrington
- Department of Veterinary Clinical Services, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Anil Prabhu
- Department of Veterinary Regulation, Welfare and Biosecurity Policy, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Peter Curl
- Department of Veterinary Regulation, Welfare and Biosecurity Policy, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Terence S M Wan
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
| | - Emmie N M Ho
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin, Hong Kong, China
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91
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Abstract
Public databases featuring original, raw data from "Omics" experiments enable researchers to perform meta-analyses by combining either the raw data or the summarized results of several independent studies. In proteomics, high-throughput protein expression data is measured by diverse techniques such as mass spectrometry, 2-D gel electrophoresis or protein arrays yielding data of different scales. Therefore, direct data merging can be problematic, and combining the summarized data of the individual studies can be advantageous. A special form of meta-analysis is network meta-analysis, where studies with different settings of experimental groups can be combined. However, all studies must be linked by one experimental group that has to appear in each study. Usually that is the control group. Then, a study network is formed and indirect statistical inferences can also be made between study groups that appear not in each of the studies.In this chapter, we describe the working principle of and available software for network meta-analysis. The applicability to high-throughput protein expression data is demonstrated in an example from breast cancer research. We also describe the special challenges when applying this method.
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Affiliation(s)
- Christine Winter
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.
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92
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Gao Y, Fillmore TL, Munoz N, Bentley GJ, Johnson CW, Kim J, Meadows JA, Zucker JD, Burnet MC, Lipton AK, Bilbao A, Orton DJ, Kim YM, Moore RJ, Robinson EW, Baker SE, Webb-Robertson BJM, Guss AM, Gladden JM, Beckham GT, Magnuson JK, Burnum-Johnson KE. High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440. Front Bioeng Biotechnol 2020; 8:603488. [PMID: 33425868 PMCID: PMC7793925 DOI: 10.3389/fbioe.2020.603488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/10/2020] [Indexed: 11/13/2022] Open
Abstract
Targeted proteomics is a mass spectrometry-based protein quantification technique with high sensitivity, accuracy, and reproducibility. As a key component in the multi-omics toolbox of systems biology, targeted liquid chromatography-selected reaction monitoring (LC-SRM) measurements are critical for enzyme and pathway identification and design in metabolic engineering. To fulfill the increasing need for analyzing large sample sets with faster turnaround time in systems biology, high-throughput LC-SRM is greatly needed. Even though nanoflow LC-SRM has better sensitivity, it lacks the speed offered by microflow LC-SRM. Recent advancements in mass spectrometry instrumentation significantly enhance the scan speed and sensitivity of LC-SRM, thereby creating opportunities for applying the high speed of microflow LC-SRM without losing peptide multiplexing power or sacrificing sensitivity. Here, we studied the performance of microflow LC-SRM relative to nanoflow LC-SRM by monitoring 339 peptides representing 132 enzymes in Pseudomonas putida KT2440 grown on various carbon sources. The results from the two LC-SRM platforms are highly correlated. In addition, the response curve study of 248 peptides demonstrates that microflow LC-SRM has comparable sensitivity for the majority of detected peptides and better mass spectrometry signal and chromatography stability than nanoflow LC-SRM.
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Affiliation(s)
- Yuqian Gao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Nathalie Munoz
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Gayle J Bentley
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Christopher W Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Joonhoon Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jamie A Meadows
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Jeremy D Zucker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Meagan C Burnet
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anna K Lipton
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Aivett Bilbao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Errol W Robinson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott E Baker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Bobbie-Jo M Webb-Robertson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam M Guss
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - John M Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Gregg T Beckham
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Jon K Magnuson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin E Burnum-Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
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93
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Petrera A, von Toerne C, Behler J, Huth C, Thorand B, Hilgendorff A, Hauck SM. Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling. J Proteome Res 2020; 20:751-762. [PMID: 33253581 DOI: 10.1021/acs.jproteome.0c00641] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The plasma proteome is the ultimate target for biomarker discovery. It stores an endless amount of information on the pathophysiological status of a living organism, which is, however, still difficult to comprehensively access. The high complexity of the plasma proteome can be addressed by either a system-wide and unbiased tool such as mass spectrometry (LC-MS/MS) or a highly sensitive targeted immunoassay such as the proximity extension assay (PEA). To address relevant differences and important shared characteristics, we tested the performance of LC-MS/MS in the data-dependent and data-independent acquisition modes and Olink PEA to measure circulating plasma proteins in 173 human plasma samples from a Southern German population-based cohort. We demonstrated the measurement of more than 300 proteins with both LC-MS/MS approaches applied, mainly including high-abundance plasma proteins. By the use of the PEA technology, we measured 728 plasma proteins, covering a broad dynamic range with high sensitivity down to pg/mL concentrations. Then, we quantified 35 overlapping proteins with all three analytical platforms, verifying the reproducibility of data distributions, measurement correlation, and gender-based differential expression. Our work highlights the limitations and the advantages of both targeted and untargeted approaches and proves their complementary strengths. We demonstrated a significant gain in proteome coverage depth and subsequent biological insight by a combination of platforms-a promising approach for future biomarker and mechanistic studies.
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Affiliation(s)
- Agnese Petrera
- Research Unit Protein Science and Core Facility Proteomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany
| | - Christine von Toerne
- Research Unit Protein Science and Core Facility Proteomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany
| | - Jennifer Behler
- Research Unit Protein Science and Core Facility Proteomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany
| | - Cornelia Huth
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany
| | - Anne Hilgendorff
- Institute for Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Core Facility Proteomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany
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94
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Zegeye EK, Sadler NC, Lomas GX, Attah IK, Jansson JK, Hofmockel KS, Anderton CR, Wright AT. Activity-Based Protein Profiling of Chitin Catabolism. Chembiochem 2020; 22:717-723. [PMID: 33049124 DOI: 10.1002/cbic.202000616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/12/2020] [Indexed: 01/09/2023]
Abstract
The microbial catabolism of chitin, an abundant and ubiquitous environmental organic polymer, is a fundamental cog in terrestrial and aquatic carbon and nitrogen cycles. Despite the importance of this critical bio-geochemical function, there is a limited understanding of the synergy between the various hydrolytic and accessory enzymes involved in chitin catabolism. To address this deficit, we synthesized activity-based probes (ABPs) designed to target active chitinolytic enzymes by modifying the chitin subunits N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. We demonstrate the utility of these ABPs in determining the synergy between various enzymes involved in chitin catabolism. The strategy can be used to gain molecular-level insights that can be used to better understand microbial roles in soil bio-geochemical cycling in the face of a changing climate.
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Affiliation(s)
- Elias K Zegeye
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Natalie C Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Gerard X Lomas
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Isaac K Attah
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
- Department of Ecology, Evolution and Organismal Biology Iowa State University, 251 Bessey Hall, Ames, Iowa (USA) 50011
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Aaron T Wright
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
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95
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Huang T, Choi M, Tzouros M, Golling S, Pandya NJ, Banfai B, Dunkley T, Vitek O. MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures. Mol Cell Proteomics 2020; 19:1706-1723. [PMID: 32680918 PMCID: PMC8015007 DOI: 10.1074/mcp.ra120.002105] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/09/2020] [Indexed: 11/06/2022] Open
Abstract
Tandem mass tag (TMT) is a multiplexing technology widely-used in proteomic research. It enables relative quantification of proteins from multiple biological samples in a single MS run with high efficiency and high throughput. However, experiments often require more biological replicates or conditions than can be accommodated by a single run, and involve multiple TMT mixtures and multiple runs. Such larger-scale experiments combine sources of biological and technical variation in patterns that are complex, unique to TMT-based workflows, and challenging for the downstream statistical analysis. These patterns cannot be adequately characterized by statistical methods designed for other technologies, such as label-free proteomics or transcriptomics. This manuscript proposes a general statistical approach for relative protein quantification in MS- based experiments with TMT labeling. It is applicable to experiments with multiple conditions, multiple biological replicate runs and multiple technical replicate runs, and unbalanced designs. It is based on a flexible family of linear mixed-effects models that handle complex patterns of technical artifacts and missing values. The approach is implemented in MSstatsTMT, a freely available open-source R/Bioconductor package compatible with data processing tools such as Proteome Discoverer, MaxQuant, OpenMS, and SpectroMine. Evaluation on a controlled mixture, simulated datasets, and three biological investigations with diverse designs demonstrated that MSstatsTMT balanced the sensitivity and the specificity of detecting differentially abundant proteins, in large-scale experiments with multiple biological mixtures.
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Affiliation(s)
- Ting Huang
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Meena Choi
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Manuel Tzouros
- Roche Pharma Research and Early Development, Pharmaceutical Sciences-BiOmics and Pathology, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Sabrina Golling
- Roche Pharma Research and Early Development, Pharmaceutical Sciences-BiOmics and Pathology, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Nikhil Janak Pandya
- Roche Pharma Research and Early Development, Pharmaceutical Sciences-BiOmics and Pathology, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Balazs Banfai
- Roche Pharma Research and Early Development, Pharmaceutical Sciences-BiOmics and Pathology, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Tom Dunkley
- Roche Pharma Research and Early Development, Pharmaceutical Sciences-BiOmics and Pathology, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
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96
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Kumar V, Ray S, Ghantasala S, Srivastava S. An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma. Front Oncol 2020; 10:543997. [PMID: 33072574 PMCID: PMC7538778 DOI: 10.3389/fonc.2020.543997] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Blood plasma is one of the most widely used samples for cancer biomarker discovery research as well as clinical investigations for diagnostic and therapeutic purposes. However, the plasma proteome is extremely complex due to its wide dynamic range of protein concentrations and the presence of high-abundance proteins. Here we have described an optimized, integrated quantitative proteomics pipeline combining the label-free and multiplexed-labeling-based (iTRAQ and TMT) plasma proteome profiling methods for biomarker discovery, followed by the targeted approaches for validation of the identified potential marker proteins. In this workflow, the targeted quantitation of proteins is carried out by multiple-reaction monitoring (MRM) and parallel-reaction monitoring (PRM) mass spectrometry. Thus, our approach enables both unbiased screenings of biomarkers and their subsequent selective validation in human plasma. The overall procedure takes only ~2 days to complete, including the time for data acquisition (excluding database searching). This protocol is quick, flexible, and eliminates the need for a separate immunoassay-based validation workflow in blood cancer biomarker investigations. We anticipate that this plasma proteomics workflow will help to accelerate the cancer biomarker discovery program and provide a valuable resource to the cancer research community.
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Affiliation(s)
- Vipin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Saicharan Ghantasala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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97
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Fong S, Handyside B, Sihn CR, Liu S, Zhang L, Xie L, Murphy R, Galicia N, Yates B, Minto WC, Vitelli C, Harmon D, Ru Y, Yu GK, Escher C, Vowinckel J, Woloszynek J, Akeefe H, Mahimkar R, Bullens S, Bunting S. Induction of ER Stress by an AAV5 BDD FVIII Construct Is Dependent on the Strength of the Hepatic-Specific Promoter. Mol Ther Methods Clin Dev 2020; 18:620-630. [PMID: 32775496 PMCID: PMC7397702 DOI: 10.1016/j.omtm.2020.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022]
Abstract
Adeno-associated virus 5 (AAV5)-human factor VIII-SQ (hFVIII-SQ; valoctocogene roxaparvovec) is an AAV-mediated product under evaluation for treatment of severe hemophilia A, which contains a B-domain-deleted hFVIII (hFVIII-SQ) transgene and a hybrid liver-specific promotor (HLP). To increase FVIII-SQ expression and reduce the vector dose required, a stronger promoter may be considered. However, because FVIII-SQ is a protein known to be difficult to fold and secrete, this could potentially induce endoplasmic reticulum (ER) stress. We evaluated the effect of two AAV5-hFVIII-SQ vectors with different liver-specific promoter strength (HLP << 100ATGB) on hepatic ER stress in mice. Five weeks after receiving vehicle or vector, the percentage of transduced hepatocytes and levels of liver hFVIII-SQ DNA and RNA increased dose dependently for both vectors. At lower doses, plasma hFVIII-SQ protein levels were higher for 100ATGB. This difference was attenuated at the highest dose. For 100ATGB, liver hFVIII-SQ protein accumulated dose dependently, with increased expression of ER stress markers at the highest dose, suggesting hepatocytes reached or exceeded their capacity to fold/secrete hFVIII-SQ. These data suggest that weaker promoters may require relatively higher doses to distribute expression load across a greater number of hepatocytes, whereas relatively stronger promoters may produce comparable levels of FVIII in fewer hepatocytes, with potential for ER stress.
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Affiliation(s)
- Sylvia Fong
- BioMarin Pharmaceutical, Inc., Novato, CA, USA
| | | | | | - Su Liu
- BioMarin Pharmaceutical, Inc., Novato, CA, USA
| | | | - Lin Xie
- BioMarin Pharmaceutical, Inc., Novato, CA, USA
| | - Ryan Murphy
- BioMarin Pharmaceutical, Inc., Novato, CA, USA
| | | | | | | | | | | | - Yuanbin Ru
- BioMarin Pharmaceutical, Inc., Novato, CA, USA
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98
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Leier HC, Weinstein JB, Kyle JE, Lee JY, Bramer LM, Stratton KG, Kempthorne D, Navratil AR, Tafesse EG, Hornemann T, Messer WB, Dennis EA, Metz TO, Barklis E, Tafesse FG. A global lipid map defines a network essential for Zika virus replication. Nat Commun 2020; 11:3652. [PMID: 32694525 PMCID: PMC7374707 DOI: 10.1038/s41467-020-17433-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we perform comprehensive lipidomics to create a lipid network map during ZIKV infection. We find that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein results in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocks ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites, and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.
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Affiliation(s)
- Hans C Leier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Jules B Weinstein
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, 99352, USA
| | - Joon-Yong Lee
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, 99352, USA
| | - Lisa M Bramer
- Computing and Analytics Division, National Security Directorate, PNNL, Richland, WA, 99352, USA
| | - Kelly G Stratton
- Computing and Analytics Division, National Security Directorate, PNNL, Richland, WA, 99352, USA
| | - Douglas Kempthorne
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
- Center for Diversity and Inclusion, OHSU, Portland, OR, 97239, USA
| | - Aaron R Navratil
- Departments of Chemistry & Biochemistry and Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Endale G Tafesse
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Thorsten Hornemann
- University Zurich and University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
| | - William B Messer
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
- Department of Medicine, Division of Infectious Diseases, OHSU, Portland, Oregon, 97239, USA
| | - Edward A Dennis
- Departments of Chemistry & Biochemistry and Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, 99352, USA
| | - Eric Barklis
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
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99
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Milivojevic M, Che X, Bateman L, Cheng A, Garcia BA, Hornig M, Huber M, Klimas NG, Lee B, Lee H, Levine S, Montoya JG, Peterson DL, Komaroff AL, Lipkin WI. Plasma proteomic profiling suggests an association between antigen driven clonal B cell expansion and ME/CFS. PLoS One 2020; 15:e0236148. [PMID: 32692761 PMCID: PMC7373296 DOI: 10.1371/journal.pone.0236148] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/30/2020] [Indexed: 02/08/2023] Open
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is an unexplained chronic, debilitating illness characterized by fatigue, sleep disturbances, cognitive dysfunction, orthostatic intolerance and gastrointestinal problems. Using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), we analyzed the plasma proteomes of 39 ME/CFS patients and 41 healthy controls. Logistic regression models, with both linear and quadratic terms of the protein levels as independent variables, revealed a significant association between ME/CFS and the immunoglobulin heavy variable (IGHV) region 3-23/30. Stratifying the ME/CFS group based on self-reported irritable bowel syndrome (sr-IBS) status revealed a significant quadratic effect of immunoglobulin lambda constant region 7 on its association with ME/CFS with sr-IBS whilst IGHV3-23/30 and immunoglobulin kappa variable region 3-11 were significantly associated with ME/CFS without sr-IBS. In addition, we were able to predict ME/CFS status with a high degree of accuracy (AUC = 0.774-0.838) using a panel of proteins selected by 3 different machine learning algorithms: Lasso, Random Forests, and XGBoost. These algorithms also identified proteomic profiles that predicted the status of ME/CFS patients with sr-IBS (AUC = 0.806-0.846) and ME/CFS without sr-IBS (AUC = 0.754-0.780). Our findings are consistent with a significant association of ME/CFS with immune dysregulation and highlight the potential use of the plasma proteome as a source of biomarkers for disease.
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Affiliation(s)
- Milica Milivojevic
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, United States of America
| | - Xiaoyu Che
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, United States of America
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, United States of America
| | - Lucinda Bateman
- Bateman Horne Center, Salt Lake City, UT, United States of America
| | - Aaron Cheng
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, United States of America
| | - Benjamin A. Garcia
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Mady Hornig
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, United States of America
| | - Manuel Huber
- German Research Center for Environmental Health, Institute for Health Economics and Health Care Management, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nancy G. Klimas
- Institute for Neuro Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States of America
- Miami VA Medical Center, Miami, FL, United States of America
| | - Bohyun Lee
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, United States of America
| | - Hyoungjoo Lee
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Susan Levine
- Levine Clinic, New York, NY, United States of America
| | - Jose G. Montoya
- Palo Alto Medical Foundation, Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto, CA, United States of America
| | - Daniel L. Peterson
- Sierra Internal Medicine at Incline Village, Incline Village, NV, United States of America
| | - Anthony L. Komaroff
- Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, United States of America
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100
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Benedetti E, Gerstner N, Pučić-Baković M, Keser T, Reiding KR, Ruhaak LR, Štambuk T, Selman MH, Rudan I, Polašek O, Hayward C, Beekman M, Slagboom E, Wuhrer M, Dunlop MG, Lauc G, Krumsiek J. Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference. Metabolites 2020; 10:E271. [PMID: 32630764 PMCID: PMC7408386 DOI: 10.3390/metabo10070271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 01/15/2023] Open
Abstract
Glycomics measurements, like all other high-throughput technologies, are subject to technical variation due to fluctuations in the experimental conditions. The removal of this non-biological signal from the data is referred to as normalization. Contrary to other omics data types, a systematic evaluation of normalization options for glycomics data has not been published so far. In this paper, we assess the quality of different normalization strategies for glycomics data with an innovative approach. It has been shown previously that Gaussian Graphical Models (GGMs) inferred from glycomics data are able to identify enzymatic steps in the glycan synthesis pathways in a data-driven fashion. Based on this finding, here, we quantify the quality of a given normalization method according to how well a GGM inferred from the respective normalized data reconstructs known synthesis reactions in the glycosylation pathway. The method therefore exploits a biological measure of goodness. We analyzed 23 different normalization combinations applied to six large-scale glycomics cohorts across three experimental platforms: Liquid Chromatography - ElectroSpray Ionization - Mass Spectrometry (LC-ESI-MS), Ultra High Performance Liquid Chromatography with Fluorescence Detection (UHPLC-FLD), and Matrix Assisted Laser Desorption Ionization - Furier Transform Ion Cyclotron Resonance - Mass Spectrometry (MALDI-FTICR-MS). Based on our results, we recommend normalizing glycan data using the 'Probabilistic Quotient' method followed by log-transformation, irrespective of the measurement platform. This recommendation is further supported by an additional analysis, where we ranked normalization methods based on their statistical associations with age, a factor known to associate with glycomics measurements.
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Affiliation(s)
- Elisa Benedetti
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10022, USA;
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Nathalie Gerstner
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
- Max Planck Institute for Psychiatry, 80804 Munich, Germany
| | - Maja Pučić-Baković
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.P.-B.); (G.L.)
| | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (T.Š.)
| | - Karli R. Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands; (K.R.R.); (M.H.J.S.)
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (L.R.R.); (M.W.)
| | - L. Renee Ruhaak
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (L.R.R.); (M.W.)
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Tamara Štambuk
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (T.Š.)
| | - Maurice H.J. Selman
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands; (K.R.R.); (M.H.J.S.)
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH8 9AG, UK;
| | - Ozren Polašek
- Medical School, University of Split, 21000 Split, Croatia;
- Gen-Info Ltd., 10000 Zagreb, Croatia
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK;
| | - Marian Beekman
- Section of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (M.B.); (E.S.)
| | - Eline Slagboom
- Section of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (M.B.); (E.S.)
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (L.R.R.); (M.W.)
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh EH8 9YL, UK;
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.P.-B.); (G.L.)
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (T.Š.)
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10022, USA;
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
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