1
|
Sulaj E, Schwaigerlehner L, Sandell FL, Dohm JC, Marzban G, Kunert R. Quantitative proteomics reveals cellular responses to individual mAb expression and tunicamycin in CHO cells. Appl Microbiol Biotechnol 2024; 108:381. [PMID: 38896138 PMCID: PMC11186912 DOI: 10.1007/s00253-024-13223-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Chinese hamster ovary (CHO) cells are popular in the pharmaceutical industry for their ability to produce high concentrations of antibodies and their resemblance to human cells in terms of protein glycosylation patterns. Current data indicate the relevance of CHO cells in the biopharmaceutical industry, with a high number of product commendations and a significant market share for monoclonal antibodies. To enhance the production capabilities of CHO cells, a deep understanding of their cellular and molecular composition is crucial. Genome sequencing and proteomic analysis have provided valuable insights into the impact of the bioprocessing conditions, productivity, and product quality. In our investigation, we conducted a comparative analysis of proteomic profiles in high and low monoclonal antibody-producing cell lines and studied the impact of tunicamycin (TM)-induced endoplasmic reticulum (ER) stress. We examined the expression levels of different proteins including unfolded protein response (UPR) target genes by using label-free quantification techniques for protein abundance. Our results show the upregulation of proteins associated with protein folding mechanisms in low producer vs. high producer cell line suggesting a form of ER stress related to specific protein production. Further, Hspa9 and Dnaja3 are notable candidates activated by the mitochondria UPR and play important roles in protein folding processes in mitochondria. We identified significant upregulation of Nedd8 and Lgmn proteins in similar levels which may contribute to UPR stress. Interestingly, the downregulation of Hspa5/Bip and Pdia4 in response to tunicamycin treatment suggests a low-level UPR activation. KEY POINTS: • Proteome profiling of recombinant CHO cells under mild TM treatment. • Identified protein clusters are associated with the unfolded protein response (UPR). • The compared cell lines revealed noticeable disparities in protein expression levels.
Collapse
Affiliation(s)
- Eldi Sulaj
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Linda Schwaigerlehner
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Felix L Sandell
- Department of Biotechnology, Institute of Computational Biology (ICB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology (ICB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| | - Gorji Marzban
- Department of Biotechnology, Institute of Bioprocess Science and Engineering (IBSE), BOKU University, Muthgasse 18, 1190, Vienna, Austria.
| | - Renate Kunert
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190, Vienna, Austria
| |
Collapse
|
2
|
Doshi TL, Dorsey SG, Huang W, Kane MA, Lim M. Proteomic Analysis to Identify Prospective Biomarkers of Treatment Outcome After Microvascular Decompression for Trigeminal Neuralgia: A Preliminary Study. THE JOURNAL OF PAIN 2024; 25:781-790. [PMID: 37838347 PMCID: PMC10922145 DOI: 10.1016/j.jpain.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Trigeminal neuralgia (TN) is a severe neuropathic facial pain disorder, often caused by vascular or neuronal compression of the trigeminal nerve. In such cases, microvascular decompression (MVD) surgery can be used to treat TN, but pain relief is not guaranteed. The molecular mechanisms that affect treatment response to MVD are not well understood. In this exploratory study, we performed label-free quantitative proteomic profiling of plasma and cerebrospinal fluid samples from patients undergoing MVD for TN, then compared the proteomic profiles of patients graded as responders (n = 7) versus non-responders (n = 9). We quantified 1,090 proteins in plasma and 1,087 proteins in the cerebrospinal fluid, of which 12 were differentially regulated in the same direction in both sample types. Functional analyses of differentially regulated proteins in protein-protein interaction networks suggested pathways of the immune system, axon guidance, and cellular stress response to be associated with response to MVD. These findings suggest potential biomarkers of response to MVD, as well as possible mechanisms of variable treatment success in TN patients. PERSPECTIVE: This exploratory study evaluates proteomic profiles in plasma and cerebrospinal fluid of patients undergoing microvascular decompression surgery for trigeminal neuralgia. Differential expression of proteins between surgery responders versus non-responders may serve as biomarkers to predict surgical success and provide insight into surgical mechanisms of pain relief in trigeminal neuralgia.
Collapse
Affiliation(s)
- Tina L. Doshi
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Susan G. Dorsey
- Department of Pain and Translational Symptom Science, University of Maryland, Baltimore, MD
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Michael Lim
- Department of Neurosurgery, Stanford University, Palo Alto, CA
| |
Collapse
|
3
|
Weiner AK, Radaoui AB, Tsang M, Martinez D, Sidoli S, Conkrite KL, Delaidelli A, Modi A, Rokita JL, Patel K, Lane MV, Zhang B, Zhong C, Ennis B, Miller DP, Brown MA, Rathi KS, Raman P, Pogoriler J, Bhatti T, Pawel B, Glisovic-Aplenc T, Teicher B, Erickson SW, Earley EJ, Bosse KR, Sorensen PH, Krytska K, Mosse YP, Havenith KE, Zammarchi F, van Berkel PH, Smith MA, Garcia BA, Maris JM, Diskin SJ. A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.06.570390. [PMID: 38106022 PMCID: PMC10723418 DOI: 10.1101/2023.12.06.570390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, an often-fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 60 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Moreover, DLK1 is highly expressed in several adult cancer types, including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG), hepatoblastoma, and small cell lung cancer (SCLC), suggesting potential clinical benefit beyond neuroblastoma. Taken together, our study demonstrates the utility of comprehensive cancer surfaceome characterization and credentials DLK1 as an immunotherapeutic target. Highlights Plasma membrane enriched proteomics defines surfaceome of neuroblastomaMulti-omic data integration prioritizes DLK1 as a candidate immunotherapeutic target in neuroblastoma and other cancersDLK1 expression is driven by a super-enhancer DLK1 silencing in neuroblastoma cells results in cellular differentiation ADCT-701, a DLK1-targeting antibody-drug conjugate, shows potent and specific cytotoxicity in DLK1-expressing neuroblastoma preclinical models.
Collapse
|
4
|
Smith E, Lewis A, Narine SS, Emery RJN. Unlocking Potentially Therapeutic Phytochemicals in Capadulla ( Doliocarpus dentatus) from Guyana Using Untargeted Mass Spectrometry-Based Metabolomics. Metabolites 2023; 13:1050. [PMID: 37887375 PMCID: PMC10608729 DOI: 10.3390/metabo13101050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Doliocarpus dentatus is thought to have a wide variety of therapeutic phytochemicals that allegedly improve libido and cure impotence. Although a few biomarkers have been identified with potential antinociceptive and cytotoxic properties, an untargeted mass spectrometry-based metabolomics approach has never been undertaken to identify therapeutic biofingerprints for conditions, such as erectile dysfunction, in men. This study executes a preliminary phytochemical screening of the woody vine of two ecotypes of D. dentatus with renowned differences in therapeutic potential for erectile dysfunction. Liquid chromatography-mass spectrometry-based metabolomics was used to screen for flavonoids, terpenoids, and other chemical classes found to contrast between red and white ecotypes. Among the metabolite chemodiversity found in the ecotype screens, using a combination of GNPS, MS-DIAL, and SIRIUS, approximately 847 compounds were annotated at levels 2 to 4, with the majority of compounds falling under lipid and lipid-like molecules, benzenoids and phenylpropanoids, and polyketides, indicative of the contributions of the flavonoid, shikimic acid, and terpenoid biosynthesis pathways. Despite the extensive annotation, we report on 138 tentative compound identifications of potentially therapeutic compounds, with 55 selected compounds at a level-2 annotation, and 22 statistically significant therapeutic biomarkers, the majority of which were polyphenols. Epicatechin methyl gallate, catechin gallate, and proanthocyanidin A2 had the greatest significant differences and were also relatively abundant among the red and white ecotypes. These putatively identified compounds reportedly act as antioxidants, neutralizing damaging free radicals, and lowering cell oxidative stress, thus aiding in potentially preventing cellular damage and promoting overall well-being, especially for treating erectile dysfunction (ED).
Collapse
Affiliation(s)
- Ewart Smith
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 0G2, Canada
| | - Ainsely Lewis
- Department of Biology, Trent University, Peterborough, ON K9J 0G2, Canada
| | - Suresh S. Narine
- Trent Centre for Biomaterials Research, Trent University, Peterborough, ON K9J 0G2, Canada
- Departments of Physics & Astronomy and Chemistry, Trent University, Peterborough, ON K9J 0G2, Canada
| | - R. J. Neil Emery
- Department of Biology, Trent University, Peterborough, ON K9J 0G2, Canada
| |
Collapse
|
5
|
Kaczmarek M, Zhang N, Buzhansky L, Gilead S, Gazit E. Optimization Strategies for Mass Spectrometry-Based Untargeted Metabolomics Analysis of Small Polar Molecules in Human Plasma. Metabolites 2023; 13:923. [PMID: 37623867 PMCID: PMC10456887 DOI: 10.3390/metabo13080923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023] Open
Abstract
The untargeted approach to mass spectrometry-based metabolomics has a wide potential to investigate health and disease states, identify new biomarkers for diseases, and elucidate metabolic pathways. All this holds great promise for many applications in biological and chemical research. However, the complexity of instrumental parameters on advanced hybrid mass spectrometers can make the optimization of the analytical method immensely challenging. Here, we report a strategy to optimize the selected settings of a hydrophilic interaction liquid chromatography-tandem mass spectrometry method for untargeted metabolomics studies of human plasma, as a sample matrix. Specifically, we evaluated the effects of the reconstitution solvent in the sample preparation procedure, the injection volume employed, and different mass spectrometry-related operating parameters including mass range, the number of data-dependent fragmentation scans, collision energy mode, duration of dynamic exclusion time, and mass resolution settings on the metabolomics data quality and output. This study highlights key instrumental variables influencing the detection of metabolites along with suggested settings for the IQ-X tribrid system and proposes a new methodological framework to ensure increased metabolome coverage.
Collapse
Affiliation(s)
- Michał Kaczmarek
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Nanyun Zhang
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Ludmila Buzhansky
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Sharon Gilead
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Ehud Gazit
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
6
|
Gräwe C, Hernandez-Quiles M, Jansen PWTC, Brimmers A, Vermeulen M. Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy. J Proteome Res 2023; 22:2683-2693. [PMID: 37466164 PMCID: PMC10407929 DOI: 10.1021/acs.jproteome.3c00248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 07/20/2023]
Abstract
In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS1-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and determination of apparent binding affinities. We benchmarked PASMAN using the SP/KLF motif and further applied it to gain insights into two CGCG-containing consensus DNA motifs. These motifs are recognized by two BEN domain-containing proteins, BANP and BEND3, which we find to interact with these motifs with distinct affinities. Finally, we profiled the BEND3 proximal proteome, revealing the NuRD complex as the major BEND3 proximal protein complex in vivo. In summary, PASMAN represents, to our knowledge, the first higher-order multiplexing-based interaction proteomics method that can be used to decipher specific DNA-protein interactions and their apparent affinities in various biological and pathological contexts.
Collapse
Affiliation(s)
- Cathrin Gräwe
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Miguel Hernandez-Quiles
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
| | - Pascal W. T. C. Jansen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Annika Brimmers
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
| |
Collapse
|
7
|
Grogan A, Huang W, Brong A, Kane MA, Kontrogianni-Konstantopoulos A. Alterations in cytoskeletal and Ca 2+ cycling regulators in atria lacking the obscurin Ig58/59 module. Front Cardiovasc Med 2023; 10:1085840. [PMID: 37304957 PMCID: PMC10251194 DOI: 10.3389/fcvm.2023.1085840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/26/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Obscurin (720-870 kDa) is a giant cytoskeletal and signaling protein that possesses both structural and regulatory functions in striated muscles. Immunoglobulin domains 58/59 (Ig58/59) of obscurin bind to a diverse set of proteins that are essential for the proper structure and function of the heart, including giant titin, novex-3, and phospholamban (PLN). Importantly, the pathophysiological significance of the Ig58/59 module has been further underscored by the discovery of several mutations within Ig58/59 that are linked to various forms of myopathy in humans. We previously generated a constitutive deletion mouse model, Obscn-ΔIg58/59, that expresses obscurin lacking Ig58/59, and characterized the effects of this deletion on cardiac morphology and function through aging. Our findings demonstrated that Obscn-ΔIg58/59 male animals develop severe arrhythmia, primarily manifesting as episodes of junctional escape and spontaneous loss of regular p-waves, reminiscent of human atrial fibrillation, accompanied by significant atrial enlargement that progresses in severity with aging. Methods and Results To comprehensively characterize the molecular alterations responsible for these pathologies, we performed proteomic and phospho-proteomic analyses in aging Obscn-ΔIg58/59 atria. Our studies revealed extensive and novel alterations in the expression and phosphorylation profile of major cytoskeletal proteins, Ca2+ regulators, and Z-disk associated protein complexes in the Obscn-ΔIg58/59 atria through aging. Discussion These studies implicate obscurin, particularly the Ig58/59 module, as an essential regulator of the Z-disk associated cytoskeleton and Ca2+ cycling in the atria and provide new molecular insights into the development of atrial fibrillation and remodeling.
Collapse
Affiliation(s)
- Alyssa Grogan
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, United States
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Annie Brong
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, United States
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | | |
Collapse
|
8
|
Hitefield NL, Mackay S, Hays LE, Chen S, Oduor IO, Troyer DA, Nyalwidhe JO. Differential Activation of NRF2 Signaling Pathway in Renal-Cell Carcinoma Caki Cell Lines. Biomedicines 2023; 11:biomedicines11041010. [PMID: 37189628 DOI: 10.3390/biomedicines11041010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Renal-cell carcinoma (RCC) is a heterogeneous disease consisting of several subtypes based on specific genomic profiles and histological and clinical characteristics. The subtype with the highest prevalence is clear-cell RCC (ccRCC), next is papillary RCC (pRCC), and then chromophobe RCC (chRCC). The ccRCC cell lines are further subdivided into prognostic expression-based subtypes ccA or ccB. This heterogeneity necessitates the development, availability, and utilization of cell line models with the correct disease phenotypic characteristics for RCC research. In this study, we focused on characterizing proteomic differences between the Caki-1 and Caki-2 cell lines that are commonly used in ccRCC research. Both cells are primarily defined as human ccRCC cell lines. Caki-1 cell lines are metastatic, harboring wild-type VHL, whereas Caki-2 are considered as the primary ccRCC cell lines expressing wild-type von Hippel–Lindau protein (pVHL). Here, we performed a comprehensive comparative proteomic analysis of Caki-1 and Caki-2 cells using tandem mass-tag reagents together with liquid chromatography mass spectrometry (LC/MS) for the identification and quantitation of proteins in the two cell lines. Differential regulation of a subset of the proteins identified was validated using orthogonal methods including western blot, q-PCR, and immunofluorescence assays. Integrative bioinformatic analysis identifies the activation/inhibition of specific molecular pathways, upstream regulators, and causal networks that are uniquely regulated and associated with the two cell lines and RCC subtypes, and potentially the disease stage. Altogether, we have identified multiple molecular pathways, including NRF2 signaling, which is the most significantly activated pathway in Caki-2 versus Caki-1 cells. Some of the differentially regulated molecules and signaling pathways could serve as potential diagnostic and prognostic biomarkers and therapeutic targets amongst ccRCC subtypes.
Collapse
|
9
|
Klinedinst NJ, Huang W, Nelson AK, Resnick B, Renn C, Kane MA, Dorsey SG. Protein Changes After 6 weeks of Walking and the Relationship to Pain in Adults with Knee Osteoarthritis. Biol Res Nurs 2023; 25:65-75. [PMID: 36050838 DOI: 10.1177/10998004221117179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: Knee osteoarthritis (KOA) affects 22.9% of individuals over the age of 40 and causes significant pain and disability. Pain is the most prevalent and troublesome symptom of KOA leading patients to seek medical interventions for relief. Knee osteoarthritis pain has both peripheral and central mechanisms that vary by individual. Non-pharmacological pain management strategies such as walking is the first step in reducing KOA pain. However, initiation of a walking regime can induce knee pain for some and the mechanism by which habitual walking reduces KOA pain is unclear. Purpose: The purpose of this study was to use a discovery proteomics approach and quantitative sensory testing (QST) to determine the molecular changes that occur after habitual walking and their relationship to pain sensitivity. Research Design and Study Sample: We conducted a pre-test/post-test study using QST to measure neurophysiological parameters at the knee and contralateral forearm and examined platelet protein signatures before and after 6 weeks of walking 3 days per week for 30 minutes among six adults with KOA and six healthy controls. Results: Knee pain sensitivity did not change significantly after 6 weeks of walking among either KOA or healthy participants. However, forearm pressure pain sensitivity decreased for both groups after walking, indicating reduction in central pain pathways. Protein signatures showed downregulation of immune and inflammatory, pathways among KOA participants after walking which were upregulated in healthy controls. Conclusion: These differences may contribute differences in centralized pain thresholds seen between KOA and healthy participants.
Collapse
Affiliation(s)
| | - Weiliang Huang
- 15513University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Amy K Nelson
- 16112University of Maryland School of Nursing, Baltimore, MD, USA
| | - Barbara Resnick
- 16112University of Maryland School of Nursing, Baltimore, MD, USA
| | - Cynthia Renn
- 16112University of Maryland School of Nursing, Baltimore, MD, USA
| | - Maureen A Kane
- 15513University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Susan G Dorsey
- 16112University of Maryland School of Nursing, Baltimore, MD, USA
| |
Collapse
|
10
|
Zhu JY, Wang G, Huang X, Lee H, Lee JG, Yang P, van de Leemput J, Huang W, Kane MA, Yang P, Han Z. SARS-CoV-2 Nsp6 damages Drosophila heart and mouse cardiomyocytes through MGA/MAX complex-mediated increased glycolysis. Commun Biol 2022; 5:1039. [PMID: 36180527 PMCID: PMC9523645 DOI: 10.1038/s42003-022-03986-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/13/2022] [Indexed: 12/01/2022] Open
Abstract
SARS-CoV-2 infection causes COVID-19, a severe acute respiratory disease associated with cardiovascular complications including long-term outcomes. The presence of virus in cardiac tissue of patients with COVID-19 suggests this is a direct, rather than secondary, effect of infection. Here, by expressing individual SARS-CoV-2 proteins in the Drosophila heart, we demonstrate interaction of virus Nsp6 with host proteins of the MGA/MAX complex (MGA, PCGF6 and TFDP1). Complementing transcriptomic data from the fly heart reveal that this interaction blocks the antagonistic MGA/MAX complex, which shifts the balance towards MYC/MAX and activates glycolysis-with similar findings in mouse cardiomyocytes. Further, the Nsp6-induced glycolysis disrupts cardiac mitochondrial function, known to increase reactive oxygen species (ROS) in heart failure; this could explain COVID-19-associated cardiac pathology. Inhibiting the glycolysis pathway by 2-deoxy-D-glucose (2DG) treatment attenuates the Nsp6-induced cardiac phenotype in flies and mice. These findings point to glycolysis as a potential pharmacological target for treating COVID-19-associated heart failure.
Collapse
Affiliation(s)
- Jun-Yi Zhu
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Guanglei Wang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Xiaohu Huang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Hangnoh Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Jin-Gu Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Penghua Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
- University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Peixin Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
| |
Collapse
|
11
|
Klinedinst NJ, Huang W, Nelson AK, Resnick B, Renn C, Kane MA, Dorsey SG. Inflammatory and Immune Protein Pathways Possible Mechanisms for Pain Following Walking in Knee Osteoarthritis. Nurs Res 2022; 71:328-335. [PMID: 35302959 PMCID: PMC9246935 DOI: 10.1097/nnr.0000000000000593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Knee osteoarthritis affects nearly 30% of adults aged 60 years or older and causes significant pain and disability. Walking is considered a "gold standard" treatment option for reducing knee osteoarthritis pain and maintaining joint mobility but does not reduce pain for all adults with knee osteoarthritis pain and may induce pain-particularly when starting a walking routine. The mechanism by which walking is helpful for knee osteoarthritis pain is unclear. Quantitative sensory testing has revealed that knee osteoarthritis pain has both peripheral and central components, which vary by individual. OBJECTIVE The purpose of this study was to better understand the mechanisms underlying the value of walking for knee pain. METHODS We conducted a pretest/posttest study using quantitative sensory testing to measure neurophysiological parameters and examined systemic protein signatures. Adults with knee osteoarthritis and healthy controls underwent quantitative sensory testing and blood draw for platelet proteomics before and after a 30-minute walk at 100 steps per minute. RESULTS A single 30-minute walk moderately increased pressure pain sensitivity at the affected knee among persons with knee osteoarthritis. Healthy adults showed no difference in pain sensitivity. Protein signatures among participants with knee osteoarthritis indicated changes in inflammatory and immune pathways, including the complement system and SAA1 protein that coincided with changes in pain with walking and differed from healthy participants. DISCUSSION One goal of developing individualized interventions for knee osteoarthritis pain is to elucidate the mechanisms by which self-management interventions affect pain. The addition of therapies that target the complement system or SAA1 expression may improve the pain sensitivity after a moderate walk for adults with knee osteoarthritis.
Collapse
|
12
|
Shimada BK, Boyman L, Huang W, Zhu J, Yang Y, Chen F, Kane MA, Yadava N, Zou L, Lederer WJ, Polster BM, Chao W. Pyruvate-Driven Oxidative Phosphorylation is Downregulated in Sepsis-Induced Cardiomyopathy: A Study of Mitochondrial Proteome. Shock 2022; 57:553-564. [PMID: 34506367 PMCID: PMC8904652 DOI: 10.1097/shk.0000000000001858] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Sepsis-induced cardiomyopathy (SIC) is a major contributing factor for morbidity and mortality in sepsis. Accumulative evidence has suggested that cardiac mitochondrial oxidative phosphorylation is attenuated in sepsis, but the underlying molecular mechanisms remain incompletely understood. METHODS Adult male mice of 9 to 12 weeks old were subjected to sham or cecal ligation and puncture procedure. Echocardiography in vivo and Langendorff-perfused hearts were used to assess cardiac function 24 h after the procedures. Unbiased proteomics analysis was performed to profile mitochondrial proteins in the hearts of both sham and SIC mice. Seahorse respirator technology was used to evaluate oxygen consumption in purified mitochondria. RESULTS Of the 665 mitochondrial proteins identified in the proteomics assay, 35 were altered in septic mice. The mitochondrial remodeling involved various energy metabolism pathways including subunits of the electron transport chain, fatty acid catabolism, and carbohydrate oxidative metabolism. We also identified a significant increase of pyruvate dehydrogenase (PDH) kinase 4 (PDK4) and inhibition of PDH activity in septic hearts. Furthermore, compared to sham mice, mitochondrial oxygen consumption of septic mice was significantly reduced when pyruvate was provided as a substrate. However, it was unchanged when PDH was bypassed by directly supplying the Complex I substrate NADH, or by using the Complex II substrate succinate, or using Complex IV substrate, or by providing the beta-oxidation substrate palmitoylcarnitine, neither of which require PDH for mitochondrial oxygen consumption. CONCLUSIONS These data demonstrate a broad mitochondrial protein remodeling, PDH inactivation and impaired pyruvate-fueled oxidative phosphorylation during SIC, and provide a molecular framework for further exploration.
Collapse
Affiliation(s)
- Briana K. Shimada
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| | - Liron Boyman
- The Department of Physiology and Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Jing Zhu
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| | - Yang Yang
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| | - Fengqian Chen
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Nagendra Yadava
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| | - Lin Zou
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| | - W. Jonathan Lederer
- The Department of Physiology and Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Brian M. Polster
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| | - Wei Chao
- Translational Research Program, Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, Baltimore, Maryland
| |
Collapse
|
13
|
Zhong P, Wei X, Li X, Wei X, Wu S, Huang W, Koidis A, Xu Z, Lei H. Untargeted metabolomics by liquid chromatography‐mass spectrometry for food authentication: A review. Compr Rev Food Sci Food Saf 2022; 21:2455-2488. [DOI: 10.1111/1541-4337.12938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Peng Zhong
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
| | - Xiaoqun Wei
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
| | - Xiangmei Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
| | - Xiaoyi Wei
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
| | - Shaozong Wu
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
| | - Weijuan Huang
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
| | - Anastasios Koidis
- Institute for Global Food Security Queen's University Belfast Belfast UK
| | - Zhenlin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety / National–Local Joint Engineering Research Center for Precision Machining and Safety of Livestock and Poultry Products, College of Food Science South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural University Guangzhou 510642 China
| |
Collapse
|
14
|
Morrison KE, Stenson AF, Marx-Rattner R, Carter S, Michopoulos V, Gillespie CF, Powers A, Huang W, Kane MA, Jovanovic T, Bale TL. Developmental Timing of Trauma in Women Predicts Unique Extracellular Vesicle Proteome Signatures. Biol Psychiatry 2022; 91:273-282. [PMID: 34715991 PMCID: PMC9219961 DOI: 10.1016/j.biopsych.2021.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Exposure to traumatic events is a risk factor for negative physical and mental health outcomes. However, the underlying biological mechanisms that perpetuate these lasting effects are not known. METHODS We investigated the impact and timing of sexual trauma, a specific type of interpersonal violence, experienced during key developmental windows of childhood, adolescence, or adulthood on adult health outcomes and associated biomarkers, including circulating cell-free mitochondrial DNA levels and extracellular vesicles (EVs), in a predominantly Black cohort of women (N = 101). RESULTS Significant changes in both biomarkers examined, circulating cell-free mitochondrial DNA levels and EV proteome, were specific to developmental timing of sexual trauma. Specifically, we identified a large number of keratin-related proteins from EVs unique to the adolescent sexual trauma group. Remarkably, the majority of these keratin proteins belong to a 17q21 gene cluster, which suggests a potential local epigenetic regulatory mechanism altered by adolescent trauma to impact keratinocyte EV secretion or its protein cargo. These results, along with changes in fear-potentiated startle and skin conductance detected in these women, suggest that sexual violence experienced during the specific developmental window of adolescence may involve unique programming of the skin, the body's largest stress organ. CONCLUSIONS Together, these descriptive studies provide novel insight into distinct biological processes altered by trauma experienced during specific developmental windows. Future studies will be required to mechanistically link these biological processes to health outcomes.
Collapse
Affiliation(s)
- Kathleen E Morrison
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, Maryland
| | - Anaïs F Stenson
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, Michigan
| | - Ruth Marx-Rattner
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, Maryland
| | - Sierra Carter
- Department of Psychology, Georgia State University, Atlanta, Georgia
| | - Vasiliki Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, Georgia
| | - Charles F Gillespie
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, Georgia
| | - Abigail Powers
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, Georgia
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, Michigan
| | - Tracy L Bale
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, Maryland.
| |
Collapse
|
15
|
Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas ME, Macek B. An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. Gut Microbes 2022; 13:1994836. [PMID: 34763597 PMCID: PMC8726736 DOI: 10.1080/19490976.2021.1994836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behavior. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomics is well suited for analysis of individual microbes, metaproteomics of fecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of taxa. Furthermore, there is a lack of consensus regarding preparation of fecal samples, as well as downstream bioinformatic analyses following metaproteomics data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse feces in a typical mass spectrometry-based metaproteomic experiment. We show that subtle changes in sample preparation protocols may influence interpretation of biological findings. Two-step database search strategies led to significant underestimation of false positive protein identifications. Unipept software provided the highest sensitivity and specificity in taxonomic annotation of the identified peptides of unknown origin. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomics when studying complex microbiome samples.
Collapse
Affiliation(s)
- Nicolas Nalpas
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Lesley Hoyles
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Viktoria Anselm
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Tariq Ganief
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Laura Martinez-Gili
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Cristina Grau
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain
| | | | | | - Xavier Altafaj
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain,Neurophysiology Unit, University of Barcelona – Idibaps, Barcelona, Spain
| | - Marc-Emmanuel Dumas
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Genomic and Environmental Medicine, National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, UK,European Genomic Institute for Diabetes, Inserm Umr 1283, Cnrs Umr 8199, Institut Pasteur De Lille, Lille University Hospital, University of Lille, Lille, France
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany,CONTACT Boris Macek Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, Auf Der Morgenstelle 15, Tuebingen72076, Germany
| |
Collapse
|
16
|
Chen X, Sun Y, Zhang T, Shu L, Roepstorff P, Yang F. Quantitative Proteomics Using Isobaric Labeling: A Practical Guide. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:689-706. [PMID: 35007772 PMCID: PMC9170757 DOI: 10.1016/j.gpb.2021.08.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 05/19/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023]
Abstract
In the past decade, relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples. Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions, its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results. Here, we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method. We also discuss which precautions should be taken at each step of the isobaric labeling workflow, to obtain reliable quantification results in large-scale quantitative proteomics experiments. In the last section, we discuss the broad applications of the isobaric labeling technology in biological and clinical studies, with an emphasis on thermal proteome profiling and proteogenomics.
Collapse
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Lian Shu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
| |
Collapse
|
17
|
Zalesak-Kravec S, Huang W, Wang P, Yu J, Liu T, Defnet AE, Moise AR, Farese AM, MacVittie TJ, Kane MA. Multi-omic Analysis of Non-human Primate Heart after Partial-body Radiation with Minimal Bone Marrow Sparing. HEALTH PHYSICS 2021; 121:352-371. [PMID: 34546217 PMCID: PMC8554778 DOI: 10.1097/hp.0000000000001478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
ABSTRACT High-dose radiation exposure results in hematopoietic and gastrointestinal acute radiation syndromes followed by delayed effects of acute radiation exposure, which encompasses multiple organs, including heart, kidney, and lung. Here we sought to further characterize the natural history of radiation-induced heart injury via determination of differential protein and metabolite expression in the heart. We quantitatively profiled the proteome and metabolome of left and right ventricle from non-human primates following 12 Gy partial body irradiation with 2.5% bone marrow sparing over a time period of 3 wk. Global proteome profiling identified more than 2,200 unique proteins, with 220 and 286 in the left and right ventricles, respectively, showing significant responses across at least three time points compared to baseline levels. High-throughput targeted metabolomics analyzed a total of 229 metabolites and metabolite combinations, with 18 and 22 in the left and right ventricles, respectively, showing significant responses compared to baseline levels. Bioinformatic analysis performed on metabolomic and proteomic data revealed pathways related to inflammation, energy metabolism, and myocardial remodeling were dysregulated. Additionally, we observed dysregulation of the retinoid homeostasis pathway, including significant post-radiation decreases in retinoic acid, an active metabolite of vitamin A. Significant differences between left and right ventricles in the pathology of radiation-induced injury were identified. This multi-omic study characterizes the natural history and molecular mechanisms of radiation-induced heart injury in NHP exposed to PBI with minimal bone marrow sparing.
Collapse
Affiliation(s)
- Stephanie Zalesak-Kravec
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Weiliang Huang
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Pengcheng Wang
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Jianshi Yu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Tian Liu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Amy E. Defnet
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Alexander R. Moise
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON, Canada; Departments of Chemistry and Biochemistry, and Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada
| | - Ann M. Farese
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD
| | - Thomas J. MacVittie
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD
| | - Maureen A. Kane
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| |
Collapse
|
18
|
Stokum JA, Shim B, Huang W, Kane M, Smith JA, Gerzanich V, Simard JM. A large portion of the astrocyte proteome is dedicated to perivascular endfeet, including critical components of the electron transport chain. J Cereb Blood Flow Metab 2021; 41:2546-2560. [PMID: 33818185 PMCID: PMC8504955 DOI: 10.1177/0271678x211004182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The perivascular astrocyte endfoot is a specialized and diffusion-limited subcellular compartment that fully ensheathes the cerebral vasculature. Despite their ubiquitous presence, a detailed understanding of endfoot physiology remains elusive, in part due to a limited understanding of the proteins that distinguish the endfoot from the greater astrocyte body. Here, we developed a technique to isolate astrocyte endfeet from brain tissue, which was used to study the endfoot proteome in comparison to the astrocyte somata. In our approach, brain microvessels, which retain their endfoot processes, were isolated from mouse brain and dissociated, whereupon endfeet were recovered using an antibody-based column astrocyte isolation kit. Our findings expand the known set of proteins enriched at the endfoot from 10 to 516, which comprised more than 1/5th of the entire detected astrocyte proteome. Numerous critical electron transport chain proteins were expressed only at the endfeet, while enzymes involved in glycogen storage were distributed to the somata, indicating subcellular metabolic compartmentalization. The endfoot proteome also included numerous proteins that, while known to have important contributions to blood-brain barrier function, were not previously known to localize to the endfoot. Our findings highlight the importance of the endfoot and suggest new routes of investigation into endfoot function.
Collapse
Affiliation(s)
- Jesse A Stokum
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bosung Shim
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Maureen Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Jesse A Smith
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Volodymyr Gerzanich
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - J Marc Simard
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
19
|
Machata S, Müller MM, Lehmann R, Sieber P, Panagiotou G, Carvalho A, Cunha C, Lagrou K, Maertens J, Slevogt H, Jacobsen ID. Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans. Virulence 2021; 11:1337-1351. [PMID: 33043780 PMCID: PMC7549978 DOI: 10.1080/21505594.2020.1824960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Invasive pulmonary aspergillosis (IPA) is a severe infection that is difficult to diagnose due to the ubiquitous presence of fungal spores, the underlying diseases of risk patients, and limitations of currently available markers. In this study, we performed a comprehensive liquid chromatography tandem mass spectrometry (LC-MS/MS)-based identification of host and fungal proteins expressed during IPA in mice and humans. The proteomic analysis of bronchoalveolar lavage samples of individual IPA and control cases allowed the description of common host factors that had significantly increased abundance in both infected animals and IPA patients compared to their controls. Although increased levels of these individual host proteins might not be sufficient to distinguish bacterial from fungal infection, a combination of these markers might be beneficial to improve diagnosis. We also identified 16 fungal proteins that were specifically detected during infection and may be valuable candidates for biomarker evaluation.
Collapse
Affiliation(s)
- Silke Machata
- Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany
| | - Mario M Müller
- Septomics Research Centre, Jena University Hospital , Jena, Germany
| | - Roland Lehmann
- Septomics Research Centre, Jena University Hospital , Jena, Germany
| | - Patricia Sieber
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany.,School of the Biological Sciences, Faculty of Sciences, The University of Hong Kong , Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong , Hong Kong, China
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven , Leuven, Belgium.,Clinical Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven , Leuven, Belgium
| | - Johan Maertens
- Department of Microbiology, Immunology and Transplantation, KU Leuven , Leuven, Belgium.,Department of Hematology, University Hospitals Leuven , Leuven, Belgium
| | - Hortense Slevogt
- Septomics Research Centre, Jena University Hospital , Jena, Germany
| | - Ilse D Jacobsen
- Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany.,Institute for Microbiology, Friedrich-Schiller-University Jena , Jena, Germany
| |
Collapse
|
20
|
Pfammatter S, Wu Z, Bonneil E, Bailey DJ, Prasad S, Belford M, Rochon J, Picard P, Lacoursière J, Dunyach JJ, Thibault P. Integration of Segmented Ion Fractionation and Differential Ion Mobility on a Q-Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer. Anal Chem 2021; 93:9817-9825. [PMID: 34213903 DOI: 10.1021/acs.analchem.1c01376] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-field asymmetric waveform ion mobility spectrometry (FAIMS) has gained popularity in the proteomics field for its capability to improve mass spectrometry sensitivity and to decrease peptide co-fragmentation. The recent implementation of FAIMS on Tribrid Orbitrap instruments enhanced proteome coverage and increased the precision of quantitative measurements. However, the FAIMS interface has not been available on older generation Orbitrap mass spectrometers such as the Q-Exactive. Here, we report the integration of the FAIMS Pro device with embedded electrical and gas connections to a Q-Exactive HF mass spectrometer. Proteomic experiments performed on HeLa tryptic digests with the modified mass spectrometer improved signal to noise and reduced interfering ions, resulting in an increase of 42% in peptide identification. FAIMS was also combined with segmented ion fractionation where 100 m/z windows were obtained in turn to further increase the depth of proteome analysis by reducing the proportion of chimeric MS/MS spectra from 50 to 27%. We also demonstrate the application of FAIMS to improve quantitative measurements when using isobaric peptide labeling. FAIMS experiments performed on a two-proteome model revealed that FAIMS Pro provided a 65% improvement in quantification accuracy compared to conventional LC-MS/MS experiments.
Collapse
Affiliation(s)
- Sibylle Pfammatter
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Zhaoguan Wu
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Derek J Bailey
- ThermoFisher Scientific, San Jose, California 95134, United States
| | - Satendra Prasad
- ThermoFisher Scientific, San Jose, California 95134, United States
| | - Michael Belford
- ThermoFisher Scientific, San Jose, California 95134, United States
| | | | - Pierre Picard
- Phytronix Technologies, Québec, Quebec G1P 2J7, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC)Université de Montréal, Montréal, Quebec H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| |
Collapse
|
21
|
Strasser L, Farrell A, Ho JTC, Scheffler K, Cook K, Pankert P, Mowlds P, Viner R, Karger BL, Bones J. Proteomic Profiling of IgG1 Producing CHO Cells Using LC/LC-SPS-MS 3: The Effects of Bioprocessing Conditions on Productivity and Product Quality. Front Bioeng Biotechnol 2021; 9:569045. [PMID: 33898396 PMCID: PMC8062983 DOI: 10.3389/fbioe.2021.569045] [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: 06/02/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
The biopharmaceutical market is dominated by monoclonal antibodies, the majority of which are produced in Chinese hamster ovary (CHO) cell lines. Intense cell engineering, in combination with optimization of various process parameters results in increasing product titers. To enable further improvements in manufacturing processes, detailed information about how certain parameters affect cellular mechanisms in the production cells, and thereby also the expressed drug substance, is required. Therefore, in this study the effects of commonly applied changes in bioprocessing parameters on an anti-IL8 IgG1 producing CHO DP-12 cell line were investigated on the level of host cell proteome expression combined with product quality assessment of the expressed IgG1 monoclonal antibody. Applying shifts in temperature, pH and dissolved oxygen concentration, respectively, resulted in altered productivity and product quality. Furthermore, analysis of the cells using two-dimensional liquid chromatography-mass spectrometry employing tandem mass tag based isotopic quantitation and synchronous precursor selection-MS3 detection revealed substantial changes in the protein expression profiles of CHO cells. Pathway analysis indicated that applied bioprocessing conditions resulted in differential activation of oxidative phosphorylation. Additionally, activation of ERK5 and TNFR1 signaling suggested an affected cell cycle. Moreover, in-depth product characterization by means of charge variant analysis, peptide mapping, as well as structural and functional analysis, revealed posttranslational and structural changes in the expressed drug substance. Taken together, the present study allows the conclusion that, in anti-IL8 IgG1 producing CHO DP-12 cells, an improved energy metabolism achieved by lowering the cell culture pH is favorable when aiming towards high antibody production rates while maintaining product quality.
Collapse
Affiliation(s)
- Lisa Strasser
- Characterization and Comparability Laboratory, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Amy Farrell
- Characterization and Comparability Laboratory, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Jenny T C Ho
- Thermo Fisher Scientific, Hemel Hempstead, United Kingdom
| | | | - Ken Cook
- Thermo Fisher Scientific, Hemel Hempstead, United Kingdom
| | | | - Peter Mowlds
- Thermo Fisher Scientific, Hemel Hempstead, United Kingdom
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, United States
| | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, United States
| | - Jonathan Bones
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| |
Collapse
|
22
|
Lee JG, Huang W, Lee H, van de Leemput J, Kane MA, Han Z. Characterization of SARS-CoV-2 proteins reveals Orf6 pathogenicity, subcellular localization, host interactions and attenuation by Selinexor. Cell Biosci 2021; 11:58. [PMID: 33766124 PMCID: PMC7993076 DOI: 10.1186/s13578-021-00568-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 causes COVID-19 which has a widely diverse disease profile. The mechanisms underlying its pathogenicity remain unclear. We set out to identify the SARS-CoV-2 pathogenic proteins that through host interactions cause the cellular damages underlying COVID-19 symptomatology. METHODS We examined each of the individual SARS-CoV-2 proteins for their cytotoxicity in HEK 293 T cells and their subcellular localization in COS-7 cells. We also used Mass-Spec Affinity purification to identify the host proteins interacting with SARS-CoV-2 Orf6 protein and tested a drug that could inhibit a specific Orf6 and host protein interaction. RESULTS We found that Orf6, Nsp6 and Orf7a induced the highest toxicity when over-expressed in human 293 T cells. All three proteins showed membrane localization in COS-7 cells. We focused on Orf6, which was most cytotoxic and localized to the endoplasmic reticulum, autophagosome and lysosomal membranes. Proteomics revealed Orf6 interacts with nucleopore proteins (RAE1, XPO1, RANBP2 and nucleoporins). Treatment with Selinexor, an FDA-approved inhibitor for XPO1, attenuated Orf6-induced cellular toxicity in human 293 T cells. CONCLUSIONS Our study revealed Orf6 as a highly pathogenic protein from the SARS-CoV-2 genome, identified its key host interacting proteins, and Selinexor as a drug candidate for directly targeting Orf6 host protein interaction that leads to cytotoxicity.
Collapse
Affiliation(s)
- Jin-Gu Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Hangnoh Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
23
|
Taverna D, Gaspari M. A critical comparison of three MS-based approaches for quantitative proteomics analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4669. [PMID: 33128495 DOI: 10.1002/jms.4669] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/07/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
MS-based proteomics is expanding its role as a routine tool for biological discovery. Nevertheless, the task of accurately and precisely quantifying thousands of analytes in a single experiment remains challenging. In this study, the diagnostic accuracy of three popular data-dependent methods for protein relative quantification (label-free [LF], dimethyl labelling [DML] and tandem mass tags [TMT]) has been assessed using a mixed species proteome (three species) and five experimental replicates per condition. Data were produced using a quadrupole-Orbitrap mass spectrometer and analysed using a single platform (the MaxQuant/Perseus software suite). The whole comparative analysis was repeated three times over a period of 6 months, in order to assess the consistency of the reported findings. As expected, label-based methods reproducibly provided a lower false positives rate, whereas TMT and LF performed similarly, and significantly better than DML, in terms of proteome coverage using the same instrument time. Although parameters like proteome coverage and precision were consistent in between replicates, other parameters like sensitivity, intended as the capacity of correctly classifying true positives (regulated proteins), were found to be less reproducible, especially at challenging fold-changes (1.5). Collectively, data suggest that an increased interest in data reproducibility would be desirable in the quantitative proteomics field.
Collapse
Affiliation(s)
- Domenico Taverna
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| |
Collapse
|
24
|
Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease. Int J Mol Sci 2020; 21:ijms21239088. [PMID: 33260377 PMCID: PMC7730581 DOI: 10.3390/ijms21239088] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
We previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation of LpxC, providing the first alternative pathway of LpxC degradation. Isolation and characterization of an extragenic suppressor mutation that prevents lethality of ΔlapB by restoration of normal LPS synthesis identified a frame-shift mutation after 377 aa in the essential gene designated lapC, suggesting LapB and LapC act antagonistically. The same lapC gene was identified during selection for mutations that induce transcription from LPS defects-responsive rpoEP3 promoter, confer sensitivity to LpxC inhibitor CHIR090 and a temperature-sensitive phenotype. Suppressors of lapC mutants that restored growth at elevated temperatures mapped to lapA/lapB, lpxC and ftsH genes. Such suppressor mutations restored normal levels of LPS and prevented proteolysis of LpxC in lapC mutants. Interestingly, a lapC deletion could be constructed in strains either overproducing LpxC or in the absence of LapB, revealing that FtsH, LapB and LapC together regulate LPS synthesis by controlling LpxC amounts.
Collapse
|
25
|
Huang W, Yu J, Liu T, Defnet AE, Zalesak S, Farese AM, MacVittie TJ, Kane MA. Proteomics of Non-human Primate Plasma after Partial-body Radiation with Minimal Bone Marrow Sparing. HEALTH PHYSICS 2020; 119:621-632. [PMID: 32947488 PMCID: PMC7541796 DOI: 10.1097/hp.0000000000001350] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
High-dose radiation exposure results in organ-specific sequelae that occurs in a time- and dose-dependent manner. The partial body irradiation with minimal bone marrow sparing model was developed to mimic intentional or accidental radiation exposures in humans where bone marrow sparing is likely and permits the concurrent analysis of coincident short- and long-term damage to organ systems. To help inform on the natural history of the radiation-induced injury of the partial body irradiation model, we quantitatively profiled the plasma proteome of non-human primates following 12 Gy partial body irradiation with 2.5% bone marrow sparing with 6 MV LINAC-derived photons at 0.80 Gy min over a time period of 3 wk. The plasma proteome was analyzed by liquid chromatography-tandem mass spectrometry. A number of trends were identified in the proteomic data including pronounced protein changes as well as protein changes that were consistently upregulated or downregulated at all time points and dose levels interrogated. Pathway and gene ontology analysis were performed; bioinformatic analysis revealed significant pathway and biological process perturbations post high-dose irradiation and shed light on underlying mechanisms of radiation damage. Additionally, proteins were identified that had the greatest potential to serve as biomarkers for radiation exposure.
Collapse
Affiliation(s)
- Weiliang Huang
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Jianshi Yu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Tian Liu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Amy E. Defnet
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Stephanie Zalesak
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
| | - Ann M. Farese
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD
| | - Thomas J. MacVittie
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD
| | - Maureen A. Kane
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD
- Correspondence: Maureen A. Kane, University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 20 N. Pine Street, Room N731, Baltimore, MD 21201, Phone: (410) 706-5097, Fax: (410) 706-0886,
| |
Collapse
|
26
|
Huang W, Yu J, Liu T, Tudor G, Defnet AE, Zalesak S, Kumar P, Booth C, Farese AM, MacVittie TJ, Kane MA. Proteomic Evaluation of the Natural History of the Acute Radiation Syndrome of the Gastrointestinal Tract in a Non-human Primate Model of Partial-body Irradiation with Minimal Bone Marrow Sparing Includes Dysregulation of the Retinoid Pathway. HEALTH PHYSICS 2020; 119:604-620. [PMID: 32947489 PMCID: PMC7541663 DOI: 10.1097/hp.0000000000001351] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Exposure to ionizing radiation results in injuries of the hematopoietic, gastrointestinal, and respiratory systems, which are the leading causes responsible for morbidity and mortality. Gastrointestinal injury occurs as an acute radiation syndrome. To help inform on the natural history of the radiation-induced injury of the partial body irradiation model, we quantitatively profiled the proteome of jejunum from non-human primates following 12 Gy partial body irradiation with 2.5% bone marrow sparing over a time period of 3 wk. Jejunum was analyzed by liquid chromatography-tandem mass spectrometry, and pathway and gene ontology analysis were performed. A total of 3,245 unique proteins were quantified out of more than 3,700 proteins identified in this study. Also a total of 289 proteins of the quantified proteins showed significant and consistent responses across at least three time points post-irradiation, of which 263 proteins showed strong upregulations while 26 proteins showed downregulations. Bioinformatic analysis suggests significant pathway and upstream regulator perturbations post-high dose irradiation and shed light on underlying mechanisms of radiation damage. Canonical pathways altered by radiation included GP6 signaling pathway, acute phase response signaling, LXR/RXR activation, and intrinsic prothrombin activation pathway. Additionally, we observed dysregulation of proteins of the retinoid pathway and retinoic acid, an active metabolite of vitamin A, as quantified by liquid chromatography-tandem mass spectrometry. Correlation of changes in protein abundance with a well-characterized histological endpoint, corrected crypt number, was used to evaluate biomarker potential. These data further define the natural history of the gastrointestinal acute radiation syndrome in a non-human primate model of partial body irradiation with minimal bone marrow sparing.
Collapse
Affiliation(s)
- Weiliang Huang
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
| | - Jianshi Yu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
| | - Tian Liu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
| | | | - Amy E Defnet
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
| | - Stephanie Zalesak
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
| | - Praveen Kumar
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
| | | | - Ann M. Farese
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Thomas J. MacVittie
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Maureen A Kane
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
- Correspondence: Maureen A. Kane, University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 20 N. Pine Street, Room N731, Baltimore, MD 21201, Phone: (410) 706-5097, Fax: (410) 706-0886,
| |
Collapse
|
27
|
Martinez R, Huang W, Samadani R, Mackowiak B, Centola G, Chen L, Conlon IL, Hom K, Kane MA, Fletcher S, Shapiro P. Mechanistic Analysis of an Extracellular Signal-Regulated Kinase 2-Interacting Compound that Inhibits Mutant BRAF-Expressing Melanoma Cells by Inducing Oxidative Stress. J Pharmacol Exp Ther 2020; 376:84-97. [PMID: 33109619 PMCID: PMC7788356 DOI: 10.1124/jpet.120.000266] [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: 08/03/2020] [Accepted: 10/06/2020] [Indexed: 11/22/2022] Open
Abstract
Constitutively active extracellular signal–regulated kinase (ERK) 1/2 signaling promotes cancer cell proliferation and survival. We previously described a class of compounds containing a 1,1-dioxido-2,5-dihydrothiophen-3-yl 4-benzenesulfonate scaffold that targeted ERK2 substrate docking sites and selectively inhibited ERK1/2-dependent functions, including activator protein-1–mediated transcription and growth of cancer cells containing active ERK1/2 due to mutations in Ras G-proteins or BRAF, Proto-oncogene B-RAF (Rapidly Acclerated Fibrosarcoma) kinase. The current study identified chemical features required for biologic activity and global effects on gene and protein levels in A375 melanoma cells containing mutant BRAF (V600E). Saturation transfer difference-NMR and mass spectrometry analyses revealed interactions between a lead compound (SF-3-030) and ERK2, including the formation of a covalent adduct on cysteine 252 that is located near the docking site for ERK/FXF (DEF) motif for substrate recruitment. Cells treated with SF-3-030 showed rapid changes in immediate early gene levels, including DEF motif–containing ERK1/2 substrates in the Fos family. Analysis of transcriptome and proteome changes showed that the SF-3-030 effects overlapped with ATP-competitive or catalytic site inhibitors of MAPK/ERK Kinase 1/2 (MEK1/2) or ERK1/2. Like other ERK1/2 pathway inhibitors, SF-3-030 induced reactive oxygen species (ROS) and genes associated with oxidative stress, including nuclear factor erythroid 2–related factor 2 (NRF2). Whereas the addition of the ROS inhibitor N-acetyl cysteine reversed SF-3-030–induced ROS and inhibition of A375 cell proliferation, the addition of NRF2 inhibitors has little effect on cell proliferation. These studies provide mechanistic information on a novel chemical scaffold that selectively regulates ERK1/2-targeted transcription factors and inhibits the proliferation of A375 melanoma cells through a ROS-dependent mechanism.
Collapse
Affiliation(s)
- Ramon Martinez
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Ramin Samadani
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Bryan Mackowiak
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Garrick Centola
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Lijia Chen
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Ivie L Conlon
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| |
Collapse
|
28
|
Yan XT, Zhang Y, Zhou Y, Li GH, Feng XS. Technical Overview of Orbitrap High Resolution Mass Spectrometry and Its Application to the Detection of Small Molecules in Food (Update Since 2012). Crit Rev Anal Chem 2020; 52:593-626. [PMID: 32880479 DOI: 10.1080/10408347.2020.1815168] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Food safety and quality issues are becoming increasingly important and attract much attention, requiring the development of better analytical platforms. For example, high-resolution (especially Orbitrap) mass spectrometry simultaneously offers versatile functions such as targeted/non-targeted screening while providing qualitative and quantitative information on an almost unlimited number of analytes to facilitate routine analysis and even allows for official surveillance in the food field. This review covers the current state of Orbitrap mass spectrometry (OMS) usage in food analysis based on research reported in 2012-2019, particularly highlighting the technical aspects of OMS application and the achievement of OMS-based screening and quantitative analysis in the food field. The gained insights enhance our understanding of state-of-the-art high-resolution mass spectrometry and highlight the challenges and directions of future research.
Collapse
Affiliation(s)
- Xiao-Ting Yan
- School of Pharmacy, China Medical University, Shenyang, China
| | - Yuan Zhang
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Zhou
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guo-Hui Li
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue-Song Feng
- School of Pharmacy, China Medical University, Shenyang, China
| |
Collapse
|
29
|
Moroni L, Barbaro F, Caiment F, Coleman O, Costagliola S, Di Conza G, Elviri L, Giselbrecht S, Krause C, Mota C, Nazzari M, Pennington SR, Ringwald A, Sandri M, Thomas S, Waddington J, Toni R. SCREENED: A Multistage Model of Thyroid Gland Function for Screening Endocrine-Disrupting Chemicals in a Biologically Sex-Specific Manner. Int J Mol Sci 2020; 21:E3648. [PMID: 32455722 PMCID: PMC7279272 DOI: 10.3390/ijms21103648] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/04/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Abstract
Endocrine disruptors (EDs) are chemicals that contribute to health problems by interfering with the physiological production and target effects of hormones, with proven impacts on a number of endocrine systems including the thyroid gland. Exposure to EDs has also been associated with impairment of the reproductive system and incidence in occurrence of obesity, type 2 diabetes, and cardiovascular diseases during ageing. SCREENED aims at developing in vitro assays based on rodent and human thyroid cells organized in three different three-dimensional (3D) constructs. Due to different levels of anatomical complexity, each of these constructs has the potential to increasingly mimic the structure and function of the native thyroid gland, ultimately achieving relevant features of its 3D organization including: 1) a 3D organoid based on stem cell-derived thyrocytes, 2) a 3D organoid based on a decellularized thyroid lobe stromal matrix repopulated with stem cell-derived thyrocytes, and 3) a bioprinted organoid based on stem cell-derived thyrocytes able to mimic the spatial and geometrical features of a native thyroid gland. These 3D constructs will be hosted in a modular microbioreactor equipped with innovative sensing technology and enabling precise control of cell culture conditions. New superparamagnetic biocompatible and biomimetic particles will be used to produce "magnetic cells" to support precise spatiotemporal homing of the cells in the 3D decellularized and bioprinted constructs. Finally, these 3D constructs will be used to screen the effect of EDs on the thyroid function in a unique biological sex-specific manner. Their performance will be assessed individually, in comparison with each other, and against in vivo studies. The resulting 3D assays are expected to yield responses to low doses of different EDs, with sensitivity and specificity higher than that of classical 2D in vitro assays and animal models. Supporting the "Adverse Outcome Pathway" concept, proteogenomic analysis and biological computational modelling of the underlying mode of action of the tested EDs will be pursued to gain a mechanistic understanding of the chain of events from exposure to adverse toxic effects on thyroid function. For future uptake, SCREENED will engage discussion with relevant stakeholder groups, including regulatory bodies and industry, to ensure that the assays will fit with purposes of ED safety assessment. In this project review, we will briefly discuss the current state of the art in cellular assays of EDs and how our project aims at further advancing the field of cellular assays for EDs interfering with the thyroid gland.
Collapse
Affiliation(s)
- Lorenzo Moroni
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Complex Tissue Regeneration, Maastricht University, 6229ET Maastricht, The Netherlands;
| | - Fulvio Barbaro
- Department of Medicine and Surgery—DIMEC, Unit of Biomedical, Biotechnological and Translational Sciences (S.BI.BI.T.), Laboratory of Regenerative Morphology and Bioartificial Structures (Re.Mo.Bio.S. Lab.), University of Parma, 43121 Parma, Italy; (F.B.); (G.D.C.); (R.T.)
| | - Florian Caiment
- Toxicogenomics, Maastricht University, 6229ET Maastricht, The Netherlands; (F.C.); (M.N.)
| | - Orla Coleman
- Atturos Ltd., c/o Conway Research Institute, University College Dublin, Dublin 4, Ireland; (O.C.); (S.R.P.)
| | - Sabine Costagliola
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, 1050 Brussels, Belgium;
| | - Giusy Di Conza
- Department of Medicine and Surgery—DIMEC, Unit of Biomedical, Biotechnological and Translational Sciences (S.BI.BI.T.), Laboratory of Regenerative Morphology and Bioartificial Structures (Re.Mo.Bio.S. Lab.), University of Parma, 43121 Parma, Italy; (F.B.); (G.D.C.); (R.T.)
| | - Lisa Elviri
- Food and Drug Department, University of Parma, 43121 Parma, Italy;
| | - Stefan Giselbrecht
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Instruct Biomaterials Engineering, Maastricht University, 6229ET Maastricht, The Netherlands;
| | | | - Carlos Mota
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Complex Tissue Regeneration, Maastricht University, 6229ET Maastricht, The Netherlands;
| | - Marta Nazzari
- Toxicogenomics, Maastricht University, 6229ET Maastricht, The Netherlands; (F.C.); (M.N.)
| | - Stephen R. Pennington
- Atturos Ltd., c/o Conway Research Institute, University College Dublin, Dublin 4, Ireland; (O.C.); (S.R.P.)
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland;
| | | | - Monica Sandri
- Institute of Science and Technology for Ceramics, National Research Council of Italy (ISTEC-CNR), 48018 Faenza, Italy;
| | - Simon Thomas
- Cyprotex Discovery Ltd., No. 24 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK;
| | - James Waddington
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Roberto Toni
- Department of Medicine and Surgery—DIMEC, Unit of Biomedical, Biotechnological and Translational Sciences (S.BI.BI.T.), Laboratory of Regenerative Morphology and Bioartificial Structures (Re.Mo.Bio.S. Lab.), University of Parma, 43121 Parma, Italy; (F.B.); (G.D.C.); (R.T.)
- Division of Endocrinology, Diabetes, and Metabolism, Tufts Medical Center - Tufts University School of Medicine, Boston, MA 02111, USA
| |
Collapse
|
30
|
Choi H, Simpson D, Wang D, Prescott M, Pitsillides AA, Dudhia J, Clegg PD, Ping P, Thorpe CT. Heterogeneity of proteome dynamics between connective tissue phases of adult tendon. eLife 2020; 9:e55262. [PMID: 32393437 PMCID: PMC7217697 DOI: 10.7554/elife.55262] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/16/2020] [Indexed: 12/29/2022] Open
Abstract
Maintenance of connective tissue integrity is fundamental to sustain function, requiring protein turnover to repair damaged tissue. However, connective tissue proteome dynamics remain largely undefined, as do differences in turnover rates of individual proteins in the collagen and glycoprotein phases of connective tissue extracellular matrix (ECM). Here, we investigate proteome dynamics in the collagen and glycoprotein phases of connective tissues by exploiting the spatially distinct fascicular (collagen-rich) and interfascicular (glycoprotein-rich) ECM phases of tendon. Using isotope labelling, mass spectrometry and bioinformatics, we calculate turnover rates of individual proteins within rat Achilles tendon and its ECM phases. Our results demonstrate complex proteome dynamics in tendon, with ~1000 fold differences in protein turnover rates, and overall faster protein turnover within the glycoprotein-rich interfascicular matrix compared to the collagen-rich fascicular matrix. These data provide insights into the complexity of proteome dynamics in tendon, likely required to maintain tissue homeostasis.
Collapse
Affiliation(s)
- Howard Choi
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Deborah Simpson
- Centre for Proteome Research, Biosciences Building, Institute of Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Ding Wang
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Mark Prescott
- Centre for Proteome Research, Biosciences Building, Institute of Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew A Pitsillides
- Department of Comparative Biomedical Sciences, Royal Veterinary CollegeLondonUnited Kingdom
| | - Jayesh Dudhia
- Department of Clinical Sciences and Services, Royal Veterinary CollegeHatfieldUnited Kingdom
| | - Peter D Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of LiverpoolLiverpoolUnited Kingdom
| | - Peipei Ping
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Chavaunne T Thorpe
- Department of Comparative Biomedical Sciences, Royal Veterinary CollegeLondonUnited Kingdom
| |
Collapse
|
31
|
Mortensen LA, Svane AM, Burton M, Bistrup C, Thiesson HC, Marcussen N, Beck HC. Proteomic Analysis of Renal Biomarkers of Kidney Allograft Fibrosis-A Study in Renal Transplant Patients. Int J Mol Sci 2020; 21:ijms21072371. [PMID: 32235494 PMCID: PMC7177439 DOI: 10.3390/ijms21072371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/12/2020] [Accepted: 03/25/2020] [Indexed: 12/20/2022] Open
Abstract
Renal transplantation is the preferred treatment of end stage renal disease, but allograft survival is limited by the development of interstitial fibrosis and tubular atrophy in response to various stimuli. Much effort has been put into identifying new protein markers of fibrosis to support the diagnosis. In the present work, we performed an in-depth quantitative proteomics analysis of allograft biopsies from 31 prevalent renal transplant patients and correlated the quantified proteins with the volume fraction of fibrosis as determined by a morphometric method. Linear regression analysis identified four proteins that were highly associated with the degree of interstitial fibrosis, namely Coagulation Factor XIII A chain (estimate 18.7, adjusted p < 0.03), Uridine Phosphorylase 1 (estimate 19.4, adjusted p < 0.001), Actin-related protein 2/3 subunit 2 (estimate 34.2, adjusted p < 0.05) and Cytochrome C Oxidase Assembly Factor 6 homolog (estimate -44.9, adjusted p < 0.002), even after multiple testing. Proteins that were negatively associated with fibrosis (p < 0.005) were primarily related to normal metabolic processes and respiration, whereas proteins that were positively associated with fibrosis (p < 0.005) were involved in catabolic processes, cytoskeleton organization and the immune response. The identified proteins may be candidates for further validation with regards to renal fibrosis. The results support the notion that cytoskeleton organization and immune responses are prevalent processes in renal allograft fibrosis.
Collapse
Affiliation(s)
- Line Aas Mortensen
- Department of Nephrology, Odense University Hospital, DK-5000 Odense, Denmark; (L.A.M.); (C.B.); (H.C.T.)
| | - Anne Marie Svane
- Department of Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, DK-5000 Odense, Denmark;
| | - Mark Burton
- Department of Clinical Genetics, Odense University Hospital, DK-5000 Odense, Denmark;
| | - Claus Bistrup
- Department of Nephrology, Odense University Hospital, DK-5000 Odense, Denmark; (L.A.M.); (C.B.); (H.C.T.)
| | - Helle Charlotte Thiesson
- Department of Nephrology, Odense University Hospital, DK-5000 Odense, Denmark; (L.A.M.); (C.B.); (H.C.T.)
| | - Niels Marcussen
- Department of Pathology, Odense University Hospital, DK-5000 Odense, Denmark;
| | - Hans Christian Beck
- Department of Clinical Biochemistry and Pharmacology, Centre for Clinical Proteomics, Odense University Hospital, DK-5000 Odense, Denmark
- Correspondence:
| |
Collapse
|
32
|
Chan JC, Morgan CP, Adrian Leu N, Shetty A, Cisse YM, Nugent BM, Morrison KE, Jašarević E, Huang W, Kanyuch N, Rodgers AB, Bhanu NV, Berger DS, Garcia BA, Ament S, Kane M, Neill Epperson C, Bale TL. Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment. Nat Commun 2020; 11:1499. [PMID: 32198406 PMCID: PMC7083921 DOI: 10.1038/s41467-020-15305-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 02/27/2020] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) are a unique mode of intercellular communication capable of incredible specificity in transmitting signals involved in cellular function, including germ cell maturation. Spermatogenesis occurs in the testes, behind a protective barrier to ensure safeguarding of germline DNA from environmental insults. Following DNA compaction, further sperm maturation occurs in the epididymis. Here, we report reproductive tract EVs transmit information regarding stress in the paternal environment to sperm, potentially altering fetal development. Using intracytoplasmic sperm injection, we found that sperm incubated with EVs collected from stress-treated epididymal epithelial cells produced offspring with altered neurodevelopment and adult stress reactivity. Proteomic and transcriptomic assessment of these EVs showed dramatic changes in protein and miRNA content long after stress treatment had ended, supporting a lasting programmatic change in response to chronic stress. Thus, EVs as a normal process in sperm maturation, can also perform roles in intergenerational transmission of paternal environmental experience.
Collapse
Affiliation(s)
- Jennifer C Chan
- Department of Biomedical Sciences, School of Veterinary Medicine and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Christopher P Morgan
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, School of Veterinary Medicine and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amol Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yasmine M Cisse
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Bridget M Nugent
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Kathleen E Morrison
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Eldin Jašarević
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- Department of Pharmaceutical Science, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Nickole Kanyuch
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ali B Rodgers
- Department of Biomedical Sciences, School of Veterinary Medicine and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dara S Berger
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Seth Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Maureen Kane
- Department of Pharmaceutical Science, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - C Neill Epperson
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tracy L Bale
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| |
Collapse
|
33
|
Tannous A, Boonen M, Zheng H, Zhao C, Germain CJ, Moore DF, Sleat DE, Jadot M, Lobel P. Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. J Proteome Res 2020; 19:1718-1730. [PMID: 32134668 DOI: 10.1021/acs.jproteome.9b00862] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Knowledge of intracellular location can provide important insights into the function of proteins and their respective organelles, and there is interest in combining classical subcellular fractionation with quantitative mass spectrometry to create global cellular maps. To evaluate mass spectrometric approaches specifically for this application, we analyzed rat liver differential centrifugation and Nycodenz density gradient subcellular fractions by tandem mass tag (TMT) isobaric labeling with reporter ion measurement at the MS2 and MS3 level and with two different label-free peak integration approaches, MS1 and data independent acquisition (DIA). TMT-MS2 provided the greatest proteome coverage, but ratio compression from contaminating background ions resulted in a narrower accurate dynamic range compared to TMT-MS3, MS1, and DIA, which were similar. Using a protein clustering approach to evaluate data quality by assignment of reference proteins to their correct compartments, all methods performed well, with isobaric labeling approaches providing the highest quality localization. Finally, TMT-MS2 gave the lowest percentage of missing quantifiable data when analyzing orthogonal fractionation methods containing overlapping proteomes. In summary, despite inaccuracies resulting from ratio compression, data obtained by TMT-MS2 assigned protein localization as well as other methods but achieved the highest proteome coverage with the lowest proportion of missing values.
Collapse
Affiliation(s)
- Abla Tannous
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Marielle Boonen
- URPhyM-Intracellular Trafficking Biology, NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000, Belgium
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Colin J Germain
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Dirk F Moore
- Department of Biostatistics, School of Public Health, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - David E Sleat
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Michel Jadot
- URPhyM-Physiological Chemistry, NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000, Belgium
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| |
Collapse
|
34
|
Defnet AE, Huang W, Polischak S, Yadav SK, Kane MA, Shapiro P, Deshpande DA. Effects of ATP-competitive and function-selective ERK inhibitors on airway smooth muscle cell proliferation. FASEB J 2019; 33:10833-10843. [PMID: 31266368 PMCID: PMC6766654 DOI: 10.1096/fj.201900680r] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/04/2019] [Indexed: 12/14/2022]
Abstract
Increased airway smooth muscle (ASM) cell mass and secretory functions are characteristics of airway inflammatory diseases, such as asthma. To date, there are no effective therapies to combat ASM cell proliferation, which contributes to bronchoconstriction and airway obstruction. Growth factors such as platelet-derived growth factor (PDGF) and the activation of the ERK1/2 are major regulators of ASM cell proliferation and airway remodeling in asthma. However, given the ubiquitous expression and multiple functions of ERK1/2, complete inhibition of ERK1/2 using ATP-competitive inhibitors may lead to unwanted off-target effects. Alternatively, we have identified compounds that are designed to target substrate docking sites and act as function-selective inhibitors of ERK1/2 signaling. Here, we show that both function-selective and ATP-competitive ERK1/2 inhibitors are effective at inhibiting PDGF-mediated proliferation, collagen production, and IL-6 secretion in ASM cells. Proteomic analysis revealed that both types of inhibitors had similar effects on reducing proteins related to TGF-β and IL-6 signaling that are relevant to airway remodeling. However, function-selective ERK1/2 inhibitors caused fewer changes in protein expression compared with ATP-competitive inhibitors. These studies provide a molecular basis for the development of function-selective ERK1/2 inhibitors to mitigate airway remodeling in asthma with defined regulation of ERK1/2 signaling.-Defnet, A. E., Huang, W., Polischak, S., Yadav, S. K., Kane, M. A., Shapiro, P., Deshpande, D. A. Effects of ATP-competitive and function-selective ERK inhibitors on airway smooth muscle cell proliferation.
Collapse
Affiliation(s)
- Amy E. Defnet
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Steven Polischak
- Department of Medicine, Jefferson University, Philadelphia, Pennsylvania, USA
| | - Santosh Kumar Yadav
- Department of Medicine, Jefferson University, Philadelphia, Pennsylvania, USA
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Deepak A. Deshpande
- Department of Medicine, Jefferson University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
35
|
Giardina BJ, Shahzad S, Huang W, Wilks A. Heme uptake and utilization by hypervirulent Acinetobacter baumannii LAC-4 is dependent on a canonical heme oxygenase (abHemO). Arch Biochem Biophys 2019; 672:108066. [PMID: 31398314 DOI: 10.1016/j.abb.2019.108066] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023]
Abstract
Acinetobacter baumannii is an opportunistic pathogen that causes serious infections in critically ill and immune compromised patients. The ability to acquire iron from the hosts iron and heme containing proteins is critical to their survival and virulence. The majority of A. baumannii hypervirulent strains encode a heme uptake system that includes a putative heme oxygenase (hemO). Despite reports indicating A. baumannii can grow on heme direct evidence of extracellular heme uptake and metabolism has not been shown. Through isotopic labeling (13C-heme) we show the hypervirulent A. baumannii LAC-4 metabolizes heme to biliverdin IXα (BVIXα), whereas ATC 17978 that lacks the hemO gene cluster cannot efficiently utilize heme. Expression and purification of the protein encoded by the A. baumannii LAC-4 hemO gene confirmed catalytic conversion of heme to BVIX. We further show inhibition of abHemO with previously characterized P. aeruginosa HemO inhibitors in a fluorescence based assay that couples HemO catalytic activity to the BVIXα binding phytochrome IFP1.4. Furthermore, the hemO gene cluster encodes genes with homology to heme-dependent extra cytoplasmic function (ECF) σ factor systems. The hemophore-dependent ECF system in Pseudomonas aeruginosa has been shown to play a critical role in heme sensing and virulence within the host. The prevalence of a hemO gene cluster in A. baumannii LAC4 and other hypervirulent strains suggests it is required within the host to adapt and utilize heme and is a major contributor to virulence.
Collapse
Affiliation(s)
- Bennett J Giardina
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Saba Shahzad
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA.
| |
Collapse
|
36
|
Noncoding dsRNA induces retinoic acid synthesis to stimulate hair follicle regeneration via TLR3. Nat Commun 2019; 10:2811. [PMID: 31243280 PMCID: PMC6594970 DOI: 10.1038/s41467-019-10811-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
How developmental programs reactivate in regeneration is a fundamental question in biology. We addressed this question through the study of Wound Induced Hair follicle Neogenesis (WIHN), an adult organogenesis model where stem cells regenerate de novo hair follicles following deep wounding. The exact mechanism is uncertain. Here we show that self-noncoding dsRNA activates the anti-viral receptor toll like receptor 3 (TLR3) to induce intrinsic retinoic acid (RA) synthesis in a pattern that predicts new hair follicle formation after wounding in mice. Additionally, in humans, rejuvenation lasers induce gene expression signatures for dsRNA and RA, with measurable increases in intrinsic RA synthesis. These results demonstrate a potent stimulus for RA synthesis by non-coding dsRNA, relevant to their broad functions in development and immunity. During wound induced hair follicle neogenesis (WIHN), stem cells regenerate hair follicles but how this arises is unclear. Here, the authors show that self-noncoding dsRNA activates the antiviral receptor TLR3 to induce intrinsic retinoic acid, which stimulates WIHN in mice, and in isolated human keratinocyte cells.
Collapse
|
37
|
Dai L, Prabhu N, Yu LY, Bacanu S, Ramos AD, Nordlund P. Horizontal Cell Biology: Monitoring Global Changes of Protein Interaction States with the Proteome-Wide Cellular Thermal Shift Assay (CETSA). Annu Rev Biochem 2019; 88:383-408. [DOI: 10.1146/annurev-biochem-062917-012837] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cellular thermal shift assay (CETSA) is a biophysical technique allowing direct studies of ligand binding to proteins in cells and tissues. The proteome-wide implementation of CETSA with mass spectrometry detection (MS-CETSA) has now been successfully applied to discover targets for orphan clinical drugs and hits from phenotypic screens, to identify off-targets, and to explain poly-pharmacology and drug toxicity. Highly sensitive multidimensional MS-CETSA implementations can now also access binding of physiological ligands to proteins, such as metabolites, nucleic acids, and other proteins. MS-CETSA can thereby provide comprehensive information on modulations of protein interaction states in cellular processes, including downstream effects of drugs and transitions between different physiological cell states. Such horizontal information on ligandmodulation in cells is largely orthogonal to vertical information on the levels of different proteins and therefore opens novel opportunities to understand operational aspects of cellular proteomes.
Collapse
Affiliation(s)
- Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, Singapore 138673;, ,
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, Singapore 138673;, ,
| | - Liang Ying Yu
- School of Biological Sciences, Nanyang Technological University, Singapore 138673;, ,
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;, ,
| | - Smaranda Bacanu
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;, ,
| | - Anderson Daniel Ramos
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;, ,
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore 138673;, ,
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;, ,
- Institute of Molecular and Cellular Biology, A*STAR, Singapore 138673
| |
Collapse
|
38
|
Al-Mohanna T, Ahsan N, Bokros NT, Dimlioglu G, Reddy KR, Shankle M, Popescu GV, Popescu SC. Proteomics and Proteogenomics Analysis of Sweetpotato (Ipomoea batatas) Leaf and Root. J Proteome Res 2019; 18:2719-2734. [DOI: 10.1021/acs.jproteome.8b00943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island, USA Hospital, Providence, Rhode Island 02903, United States
- Division of Biology and Medicine, Brown University, Providence, Rhode Island 02903, United States
| | - Norbert T. Bokros
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Gizem Dimlioglu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Kambham R. Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Mark Shankle
- Pontotoc Experimental Station, Mississippi State University, Pontotoc, Mississippi 38863, United States
| | - George V. Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39759, United States
- The National Institute for Laser, Plasma and Radiation Physics, Bucharest RO-077125, Romania
| | - Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| |
Collapse
|
39
|
Zhang Y, Wen Z, Washburn MP, Florens L. Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems. J Proteome Res 2019; 18:1857-1869. [PMID: 30884231 DOI: 10.1021/acs.jproteome.9b00036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Orbitrap is now a core component of several different instruments. However, evaluating the capabilities of each system is lacking in the field. Here, we compared the performance of multidimensional protein identification (MudPIT) on Velos Pro Orbitrap and Velos Orbitrap Elite mass spectrometers to reversed phase liquid chromatography (RPLC) on a Q-Exactive Plus and an Orbitrap Fusion Lumos. Using HeLa cell protein digests, we carried out triplicate analyses of 16 different chromatography conditions on four different instrumentation platforms. We first optimized RPLC conditions by varying column lengths, inner diameters, and particle sizes. We found that smaller particle sizes improve results but only with smaller inner diameter microcapillary columns. We then selected one chromatography condition on each system and varied gradient lengths. We used distributed normalized spectral abundance factor (dNSAF) values to determine quantitative reproducibility. With Pearson product-moment correlation coefficient r values routinely above 0.96, single RPLC on both the QE+ and Orbitrap Lumos outperformed MudPIT on the Orbitrap Elite mass spectrometer. In addition, when comparing dNSAF values measured for the same proteins across the different platforms, RPLC on the Orbitrap Lumos had greater sensitivity than MudPIT, as demonstrated by the detection and quantification of histone deacetylase complex components. Data are available via ProteomeXchange with identifier 10.6019/PXD009875.
Collapse
Affiliation(s)
- Ying Zhang
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Zhihui Wen
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Michael P Washburn
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States.,Department of Pathology and Laboratory Medicine , University of Kansas Medical Center , Kansas City , Kansas 66160 , United States
| | - Laurence Florens
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| |
Collapse
|
40
|
Lee KJ, Comerford EJ, Simpson DM, Clegg PD, Canty-Laird EG. Identification and Characterization of Canine Ligament Progenitor Cells and Their Extracellular Matrix Niche. J Proteome Res 2019; 18:1328-1339. [DOI: 10.1021/acs.jproteome.8b00933] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Katie J Lee
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, United Kingdom
| | - Eithne J Comerford
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, United Kingdom
- School of Veterinary Science, Leahurst Campus, University of Liverpool, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - Deborah M Simpson
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Peter D Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, United Kingdom
- School of Veterinary Science, Leahurst Campus, University of Liverpool, Chester High Road, Neston, CH64 7TE, United Kingdom
- The MRC-Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool L7 8TX, United Kingdom
| | - Elizabeth G Canty-Laird
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, United Kingdom
- The MRC-Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool L7 8TX, United Kingdom
| |
Collapse
|
41
|
Zhang L, Lu Y, Ye YH, Yang SH, Tu ZC, Chen J, Wang H, Wang HH, Yuan T. Insights into the Mechanism of Quercetin against BSA-Fructose Glycation by Spectroscopy and High-Resolution Mass Spectrometry: Effect on Physicochemical Properties. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:236-246. [PMID: 30567433 DOI: 10.1021/acs.jafc.8b06075] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quercetin has been reported to suppress protein glycation or the formation of advanced glycation end-products (AGEs), but the inhibition mechanism related to protein structure and glycation sites and the influence on physicochemical properties remain unclear. The aim of the current research was to investigate the mechanism of quercetin against glycation with BSA-fructose as model by spectroscopic and spectrometric techniques. Changes in physicochemical properties were evaluated by antioxidant activity and emulsifying properties. The results indicated that quercetin dose-dependently inhibited the glycation of BSA by attenuating the alteration of conformational structure and microenvironment induced by glycation. It could also suppress the cross-linking or aggregation of glycated BSA, which reflected in the decreased molecular weight determined by SDS-PAGE and MALDI-TOF. Nanoliquid chromatography coupled to Q-Exactive tandem mass spectrometry analysis revealed the mapping of 20, 23, 19, and 19 glycation sites in glycated BSA with 0, 0.5, 1.5, and 3.0 mM quercetin, respectively. Quercetin changed the glycation sites of BSA, but it could not reduce the number greatly. In addition, quercetin reduced the antioxidant ability and increased the emulsifying properties of BSA, while negligible efficiency was observed on the antioxidant activity and emulsifying activity index of glycated BSA.
Collapse
Affiliation(s)
- Lu Zhang
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
| | - Yu Lu
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
| | - Yun-Hua Ye
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
| | - Si-Hang Yang
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
| | - Zong-Cai Tu
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
- State Key Laboratory of Food Science and Technology , Nanchang University , Nanchang , Jiangxi 330047 , China
| | - Juan Chen
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
| | - Hui Wang
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
- State Key Laboratory of Food Science and Technology , Nanchang University , Nanchang , Jiangxi 330047 , China
| | - Hong-Hong Wang
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
| | - Tao Yuan
- National R&D Center for Freshwater Fish Processing, and Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, College of Life Science , Jiangxi Normal University , Nanchang , Jiangxi 330022 , China
- The Key Laboratory of Plant Resources and Chemistry of Arid Zone, and State Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry , Chinese Academy of Sciences , Urumqi 830011 , China
| |
Collapse
|
42
|
Wang S, Huang W, Castillo HA, Kane MA, Xavier-Neto J, Trainor PA, Moise AR. Alterations in retinoic acid signaling affect the development of the mouse coronary vasculature. Dev Dyn 2018; 247:976-991. [PMID: 29806219 DOI: 10.1002/dvdy.24639] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND During the final stages of heart development the myocardium grows and becomes vascularized by means of paracrine factors and cell progenitors derived from the epicardium. There is evidence to suggest that retinoic acid (RA), a metabolite of vitamin A, plays an important role in epicardial-based developmental programming. However, the consequences of altered RA-signaling in coronary development have not been systematically investigated. RESULTS We explored the developmental consequences of altered RA-signaling in late cardiogenic events that involve the epicardium. For this, we used a model of embryonic RA excess based on mouse embryos deficient in the retinaldehyde reductase DHRS3, and a complementary model of embryonic RA deficiency based on pharmacological inhibition of RA synthesis. We found that alterations in embryonic RA signaling led to a thin myocardium and aberrant coronary vessel formation and remodeling. Both excess, and deficient RA-signaling are associated with reductions in ventricular coverage and density of coronary vessels, altered vessel morphology, and impaired recruitment of epicardial-derived mural cells. Using a combined transcriptome and proteome profiling approach, we found that RA treatment of epicardial cells influenced key signaling pathways relevant for cardiac development. CONCLUSIONS Epicardial RA-signaling plays critical roles in the development of the coronary vasculature needed to support myocardial growth. Developmental Dynamics 247:976-991, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Suya Wang
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Hozana A Castillo
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - José Xavier-Neto
- Conselho Nacional do Desenvolvimnto Científico e Tecnológico (Cnpq) CEP 01414000 Cerqueira Cesar Sao Paulo, Sao Paulo, Brazil
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Alexander R Moise
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas.,Northern Ontario School of Medicine, Biomolecular Sciences Program and Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| |
Collapse
|
43
|
Rioseras B, Shliaha PV, Gorshkov V, Yagüe P, López-García MT, Gonzalez-Quiñonez N, Kovalchuk S, Rogowska-Wrzesinska A, Jensen ON, Manteca A. Quantitative Proteome and Phosphoproteome Analyses of Streptomyces coelicolor Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism. Mol Cell Proteomics 2018; 17:1591-1611. [PMID: 29784711 PMCID: PMC6072539 DOI: 10.1074/mcp.ra117.000515] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/15/2018] [Indexed: 02/03/2023] Open
Abstract
Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode many Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor We identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (first mycelium); secondary metabolite producing hyphae (second mycelium); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signaling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism. Phosphoproteomics revealed 85 unique protein phosphorylation sites, 58 of them differentially phosphorylated during differentiation. Computational analysis suggested that these regulated protein phosphorylation events are implicated in important cellular processes, including cell division, differentiation, regulation of secondary metabolism, transcription, protein synthesis, protein folding and stress responses. We discovered a novel regulated phosphorylation site in the key bacterial cell division protein FtsZ (pSer319) that modulates sporulation and regulates actinorhodin antibiotic production. We conclude that manipulation of distinct protein phosphorylation events may improve secondary metabolite production in industrial streptomycetes, including the activation of cryptic pathways during the screening for new secondary metabolites from streptomycetes.
Collapse
Affiliation(s)
- Beatriz Rioseras
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Pavel V Shliaha
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Vladimir Gorshkov
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Paula Yagüe
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - María T López-García
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Nathaly Gonzalez-Quiñonez
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Sergey Kovalchuk
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Adelina Rogowska-Wrzesinska
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Ole N Jensen
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Angel Manteca
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain;
| |
Collapse
|
44
|
Multiclass screening of >200 pharmaceutical and other residues in aquatic foods by ultrahigh-performance liquid chromatography-quadrupole-Orbitrap mass spectrometry. Anal Bioanal Chem 2018; 410:5545-5553. [PMID: 29748759 DOI: 10.1007/s00216-018-1124-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 01/21/2023]
Abstract
A quick screening method of more than 200 pharmaceutical and other residues in aquatic foods based on ultrahigh-performance liquid chromatography-quadrupole-Orbitrap mass spectrometry (UHPLC-Q/Orbitrap MS) was established. In this method, after the addition of 200 μL of 1 M EDTA-Na2, 2 g of each sample homogenate was extracted successively with 10 mL of acetonitrile and 10 mL of ethyl acetate. The extracts were combined, dried under nitrogen flow, and redissolved in 0.1% formic acid in acetonitrile/water (4:6, v/v) for analysis. The prepared samples were analyzed by UHPLC- Q/Orbitrap MS system in Full MS/ddMS2 (full-scan data-dependent MS/MS) mode. Compound identification was performed through comparison of the sample data with the database for standard chemicals, including the retention time, precursor ion, product ions, and isotope pattern for all 206 compounds. Five different aquatic food matrices (carp, shrimp, crab, eel, and mussel) spiked with the analytes at 1, 10, and 50 ng/g were evaluated to assess recoveries, precision, matrix effects, stability, and detection limits using the method. UHPLC analyses required 25 min, and 178-200 analytes met identification criteria at 50 ng/g depending on the matrix. Furthermore, practical application of this method for real samples displayed strong screening capability. Graphical abstract A quick screening method of >200 pharmaceutical and other residues in aquatic foods based on ultrahighperformance liquid chromatography-quadrupole-Orbitrap mass spectrometer was established. Fivedifferent aquatic food matrices, including carp, shrimp, crab, eel and mussel, were studied to evaluatescreen limit at 1, 10 and 50 μg·kg-1 level. Results suggest the high reliability, high time-efficiency and goodsimplicity of the method.
Collapse
|
45
|
Makar T, Nimmagadda VK, Guda PR, Hampton B, Huang W, Kane MA, Fishman PS, Pessac B, Bever CT, Trisler D. A subset of mobilized human hematopoietic stem cells express germ layer lineage genes which can be modulated by culture conditions. Stem Cell Res Ther 2018; 9:127. [PMID: 29720239 PMCID: PMC5930965 DOI: 10.1186/s13287-018-0858-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/20/2018] [Accepted: 04/02/2018] [Indexed: 12/15/2022] Open
Abstract
Background Adult bone marrow contains stem cells that replenish the myeloid and lymphoid lineages. A subset of human and mouse CD34+ bone marrow stem cells can be propagated in culture to autonomously express embryonic stem cell genes and embryonic germ layer lineage genes. The current study was undertaken to determine whether these CD34+ stem cells could be obtained from human blood, whether gene expression could be modulated by culture conditions and whether the cells produce insulin. Methods Human peripheral blood buffy coat cells and mobilized CD34+ cells from human blood and from blood from C57Bl/6 J mice were cultured in hybridoma medium or neural stem cell induction medium supplemented with interleukin (IL)-3, IL-6, and stem cell factor (SCF). Changes in mRNA and protein expression were assessed by Western blot analysis and by immunohistochemistry. Mass spectrometry was used to assess insulin production. Results We were able to culture CD34+ cells expressing embryonic stem cell and embryonic germ layer lineage genes from adult human peripheral blood after standard mobilization procedures and from mouse peripheral blood. Gene expression could be modulated by culture conditions, and the cells produced insulin in culture. Conclusion These results suggest a practical method for obtaining large numbers of CD34+ cells from humans to allow studies on their potential to differentiate into other cell types. Electronic supplementary material The online version of this article (10.1186/s13287-018-0858-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tapas Makar
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Multiple Sclerosis Center of Excellence, East VA Maryland Health Care System, Baltimore, MD, 21201, USA.,VA Maryland Health Care System, Baltimore, 21201, USA
| | - Vamshi K Nimmagadda
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,VA Maryland Health Care System, Baltimore, 21201, USA
| | - Poornachander R Guda
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,VA Maryland Health Care System, Baltimore, 21201, USA
| | - Brian Hampton
- Protein Analysis Laboratory, Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, 21201, USA.,Mass Spectrometry Center, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Maureen A Kane
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, 21201, USA.,Mass Spectrometry Center, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Paul S Fishman
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,VA Maryland Health Care System, Baltimore, 21201, USA
| | - Bernard Pessac
- CNRS UMR 8118, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France.,Académie Nationale de Médecine, 16 rue Bonaparte, 75006, Paris, France
| | - Christopher T Bever
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Multiple Sclerosis Center of Excellence, East VA Maryland Health Care System, Baltimore, MD, 21201, USA. .,VA Maryland Health Care System, Baltimore, 21201, USA.
| | - David Trisler
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Multiple Sclerosis Center of Excellence, East VA Maryland Health Care System, Baltimore, MD, 21201, USA.,VA Maryland Health Care System, Baltimore, 21201, USA
| |
Collapse
|
46
|
Hogrebe A, von Stechow L, Bekker-Jensen DB, Weinert BT, Kelstrup CD, Olsen JV. Benchmarking common quantification strategies for large-scale phosphoproteomics. Nat Commun 2018. [PMID: 29535314 PMCID: PMC5849679 DOI: 10.1038/s41467-018-03309-6] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2- and MS3-measured tandem mass tags (TMT). In a mixed species comparison with fixed phosphopeptide ratios, we find LFQ and SILAC to be the most accurate techniques. MS2-based TMT yields the highest precision but lowest accuracy due to ratio compression, which MS3-based TMT can partly rescue. However, MS2-based TMT outperforms MS3-based TMT when analyzing phosphoproteome changes in the DNA damage response, since its higher precision and larger identification numbers allow detection of a greater number of significantly regulated phosphopeptides. Finally, we utilize the TMT multiplexing capabilities to develop an algorithm for determining phosphorylation site stoichiometry, showing that such applications benefit from the high accuracy of MS3-based TMT. Quantitative phosphoproteomics has become a standard method in molecular and cell biology. Here, the authors compare performance and parameters of phosphoproteome quantification by LFQ, SILAC, and MS2-/MS3-based TMT and introduce a TMT-adapted algorithm for calculating phosphorylation site stoichiometry.
Collapse
Affiliation(s)
- Alexander Hogrebe
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Louise von Stechow
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Brian T Weinert
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark.
| |
Collapse
|
47
|
Thygesen C, Boll I, Finsen B, Modzel M, Larsen MR. Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev Proteomics 2018; 15:245-258. [DOI: 10.1080/14789450.2018.1433036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Camilla Thygesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
48
|
Stolfa G, Smonskey MT, Boniface R, Hachmann AB, Gulde P, Joshi AD, Pierce AP, Jacobia SJ, Campbell A. CHO-Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction. Biotechnol J 2017; 13:e1700227. [PMID: 29072373 DOI: 10.1002/biot.201700227] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 01/07/2023]
Abstract
CHO cells are the most prevalent platform for modern bio-therapeutic production. Currently, there are several CHO cell lines used in bioproduction with distinct characteristics and unique genotypes and phenotypes. These differences limit advances in productivity and quality that can be achieved by the most common approaches to bioprocess optimization and cell line engineering. Incorporating omics-based approaches into current bioproduction processes will complement traditional methodologies to maximize gains from CHO engineering and bioprocess improvements. In order to highlight the utility of omics technologies in CHO bioproduction, the authors discuss current applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, lipidomics, fluxomics, glycomics, and multi-omics approaches and the potential they hold for the future of bioproduction. Multiple omics approaches are currently being used to improve CHO bioprocesses; however, the application of these technologies is still limited. As more CHO-omic datasets become available and integrated into systems models, the authors expect significant gains in product yield and quality. While individual omics technologies provide incremental improvements in bioproduction, the authors will likely see the most significant gains by applying multi-omics and systems biology approaches to individual CHO cell lines.
Collapse
Affiliation(s)
- Gino Stolfa
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Ryan Boniface
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Paul Gulde
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Atul D Joshi
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Anson P Pierce
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Scott J Jacobia
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Andrew Campbell
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| |
Collapse
|
49
|
Weiner AK, Sidoli S, Diskin SJ, Garcia BA. Graphical Interpretation and Analysis of Proteins and their Ontologies (GiaPronto): A One-Click Graph Visualization Software for Proteomics Data Sets. Mol Cell Proteomics 2017; 17:1426-1431. [PMID: 29118029 DOI: 10.1074/mcp.tir117.000438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Indexed: 01/09/2023] Open
Abstract
Here we present a free interactive web tool to process and visualize proteomics data sets with a single click. GiaPronto can process all proteomics quantification methods, i.e. label-free, SILAC and isobaric labeling, and analyze post-translational modifications (PTMs). The software performs normalization and statistics, assists determination of regulated proteins, biomarkers and Gene Ontology (GO) enrichment, and provides high resolution images and tables for further data analysis. We foresee that GiaPronto will become the most rapid and simple tool for assessing data quality and determining most relevant features of proteomic data sets. GiaPronto is available at giapronto.diskinlab.org.
Collapse
Affiliation(s)
- Amber K Weiner
- From the ‡Genomics and Computational Biology, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,§Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,¶Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Simone Sidoli
- ¶Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sharon J Diskin
- From the ‡Genomics and Computational Biology, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,§Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Benjamin A Garcia
- From the ‡Genomics and Computational Biology, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; .,¶Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
50
|
Luo X, Zhang L, Niu Z, Ye X, Tang Z, Xia S. Liquid chromatography coupled to quadrupole-Orbitrap high resolution mass spectrometry based method for target analysis and suspect screening of non-ionic surfactants in textiles. J Chromatogr A 2017; 1530:80-89. [PMID: 29153579 DOI: 10.1016/j.chroma.2017.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 10/18/2022]
Abstract
In this study, we describe a high-throughput and sensitive method for textiles analysis, using liquid chromatography coupled to quadrupole-Orbitrap high resolution mass spectrometry (LC-Q-Orbitrap HRMS), for the simultaneously quantitative analysis of 40 target alkylphenol polyethoxylates (APEO) oligomers with reference standards and screening of 160 alcohol polyethoxylates (AEO) oligomers without standards in textiles. The APEOs contain nonylphenol ethoxylates (NPEOs) and octylphenol ethoxylates (OPEOs) with an EO number of ethylene oxide of 1-20, while AEOs focus on C11EOs-C18EOs with an EO number of 1-20. After ultrasonic extraction in methanol, the extract was directly separated using a core-shell CORTECS C18+ column and analyzed by Full MS/dd-MS2 (data dependent acquisition) scan in ESI positive mode. Two best sensitivity experimental conditions for APEOs with short EO chains (AP(EO)1-2) and long EO chains (AP(EO)3-20) were investigated, respectively. Most APEO oligomers had wide concentration ranges and the correlation coefficients (R2) were higher than 0.999. The limit of quantitation (LOQ) values for NP(EO)3-20 oligomers ranges from 16.00 to 52.80μg/kg and for OP(EO)3-20 oligomers is from 2.40 to 8.00μg/kg. LOQ for NP(EO)1 and NP(EO)2, OP(EO)1 and OP(EO)2 was 2.40mg/kg and 0.24mg/kg, 1.20mg/kg and 0.16mg/kg, respectively. The average recovery for each APEO oligomer in cotton and polyester matrix was between 78% and 110% at three spiked levels and the relative standard deviation (RSD%) was below 10%. As to AEOs suspects, a HRMS compound database containing 160 AEO oligomers was built and several parameters such as exact m/z, isotopic patterns, predicted product ions and predicted retention time were used for screening and confirmation. The established method was successfully applied for analysis of 40 commercial textile samples. Compared with OPEOs, NPEOs, especially NP(EO)3-15 oligomers, were widely detected in samples and the total concentration ranged from 1.56 to 1376.31mg/kg. AEOs were also found in most samples, among which C12-14, C16 and C18 compounds appeared more frequently and the EO chains mainly ranged from 3 to 15.
Collapse
Affiliation(s)
- Xin Luo
- Inspection and Quarantine Technical Center, Shandong Entry-Exit Inspection and Quarantine Bureau, Qingdao 266002, China
| | - Li Zhang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Zengyuan Niu
- Inspection and Quarantine Technical Center, Shandong Entry-Exit Inspection and Quarantine Bureau, Qingdao 266002, China.
| | - Xiwen Ye
- Inspection and Quarantine Technical Center, Shandong Entry-Exit Inspection and Quarantine Bureau, Qingdao 266002, China
| | - Zhixu Tang
- Inspection and Quarantine Technical Center, Shandong Entry-Exit Inspection and Quarantine Bureau, Qingdao 266002, China
| | - Shuwei Xia
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| |
Collapse
|