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Balanced expression of G protein-coupled receptor subtypes in the mouse, macaque, and human cerebral cortex. Neuroscience 2022; 487:107-119. [DOI: 10.1016/j.neuroscience.2022.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/03/2022] [Accepted: 01/31/2022] [Indexed: 12/23/2022]
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102
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Mohd Afandi NS, Habib MAH, Ismail MN. Recent insights on gene expression studies on Hevea Brasiliensis fatal leaf fall diseases. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:471-484. [PMID: 35400887 PMCID: PMC8943083 DOI: 10.1007/s12298-022-01145-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Hevea brasiliensis is one of the most important agricultural commodities globally, heavily cultivated in Southeast Asia. Fatal leaf fall diseases cause aggressive leaf defoliation, linked to lower latex yield and death of crops before maturity. Due to the significant consequences of the disease to H. brasiliensis, the recent gene expression studies from four fall leaf diseases of H. brasiliensis were gathered; South American leaf blight, powdery mildew, Corynespora cassiicola and Phytophthora leaf fall disease. The differential analysis observed the pattern of commonly expressed genes upon fungi triggers using RT-PCR, DDRT-PCR, Real-time qRT-PCR and RNA-Seq. We have observed that RNA-Seq is the best tool to seek novel genes. Among the identified genes with defence-against fungi were pathogenesis-related genes such as β-1,3-glucanase and chitinase, the reactive oxygen species, and the phytoalexin biosynthesis. This manuscript also provided functional elaboration on the responsive genes and predicted possible biosynthetic pathways to identify and characterise novel genes in the future. At the end of the manuscript, the PCR methods and proteomic approaches were presented for future molecular and biochemical studies in the related diseases to H. brasiliensis.
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Affiliation(s)
- Nur Syafiqah Mohd Afandi
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 USM Penang, Malaysia
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103
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Dwivedi P, Rose CM. Understanding the effect of carrier proteomes in single cell proteomic studies - key lessons. Expert Rev Proteomics 2022; 19:5-15. [PMID: 35089822 DOI: 10.1080/14789450.2022.2036126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Mass spectrometry based single cell proteomics (scMS) is experiencing rapid evolution due to the increased sensitivity of mass spectrometers as well as advances in multiplexing and sample preparation. To date, researchers have focused on two general approaches to scMS: label free and isobaric label based multiplexing. While label free analysis provides straightforward sample preparation and a clear path to automation, it currently lacks the throughput necessary to practically analyze thousands of single cells. Multiplexed analysis utilizing isobaric labels requires additional sample manipulation, but increases throughput such that analyzing thousands of cells is currently achievable. A key feature of multiplexed scMS experiments is a 'carrier proteome' - a sample added at 25x-500x the single cell samples that increases the number of proteins that can be identified in an MS analysis. AREAS COVERED Here, we review early examples of carrier proteomes in quantitative proteomics before summarizing advantages and challenges of using a carrier proteome in scMS experiments. EXPERT OPINION We conclude that the addition of carrier proteomes improves depth of identification for scMS, but high levels of carrier proteomes can have adverse effects on quantitative accuracy and precision.
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Affiliation(s)
- Pankaj Dwivedi
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc. 1 DNA Way, South San Francisco CA 94080
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc. 1 DNA Way, South San Francisco CA 94080
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Jackson CA, Vogel C. New horizons in the stormy sea of multimodal single-cell data integration. Mol Cell 2022; 82:248-259. [PMID: 35063095 PMCID: PMC8830781 DOI: 10.1016/j.molcel.2021.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
Abstract
While measurements of RNA expression have dominated the world of single-cell analyses, new single-cell techniques increasingly allow collection of different data modalities, measuring different molecules, structural connections, and intermolecular interactions. Integrating the resulting multimodal single-cell datasets is a new bioinformatics challenge. Equally important, it is a new experimental design challenge for the bench scientist, who is not only choosing from a myriad of techniques for each data modality but also faces new challenges in experimental design. The ultimate goal is to design, execute, and analyze multimodal single-cell experiments that are more than just descriptive but enable the learning of new causal and mechanistic biology. This objective requires strict consideration of the goals behind the analysis, which might range from mapping the heterogeneity of a cellular population to assembling system-wide causal networks that can further our understanding of cellular functions and eventually lead to models of tissues and organs. We review steps and challenges toward this goal. Single-cell transcriptomics is now a mature technology, and methods to measure proteins, lipids, small-molecule metabolites, and other molecular phenotypes at the single-cell level are rapidly developing. Integrating these single-cell readouts so that each cell has measurements of multiple types of data, e.g., transcriptomes, proteomes, and metabolomes, is expected to allow identification of highly specific cellular subpopulations and to provide the basis for inferring causal biological mechanisms.
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Affiliation(s)
- Christopher A Jackson
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
| | - Christine Vogel
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
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105
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Rinnofner C, Felber M, Pichler H. Strains and Molecular Tools for Recombinant Protein Production in Pichia pastoris. Methods Mol Biol 2022; 2513:79-112. [PMID: 35781201 DOI: 10.1007/978-1-0716-2399-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris (Komagataella phaffii) has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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Affiliation(s)
- Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.
- Bisy GmbH, Hofstaetten/Raab, Austria.
| | - Michael Felber
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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106
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Quque M, Villette C, Criscuolo F, Sueur C, Bertile F, Heintz D. Eusociality is linked to caste-specific differences in metabolism, immune system, and somatic maintenance-related processes in an ant species. Cell Mol Life Sci 2021; 79:29. [PMID: 34971425 PMCID: PMC11073003 DOI: 10.1007/s00018-021-04024-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/08/2021] [Accepted: 11/05/2021] [Indexed: 01/08/2023]
Abstract
The social organization of many primate, bird and rodent species and the role of individuals within that organization are associated with specific individual physiological traits. However, this association is perhaps most pronounced in eusocial insects (e.g., termites, ants). In such species, genetically close individuals show significant differences in behavior, physiology, and life expectancy. Studies addressing the metabolic changes according to the social role are still lacking. We aimed at understanding how sociality could influence essential molecular processes in a eusocial insect, the black garden ant (Lasius niger) where queens can live up to ten times longer than workers. Using mass spectrometry-based analysis, we explored the whole metabolome of queens, nest-workers and foraging workers. A former proteomics study done in the same species allowed us to compare the findings of both approaches. Confirming the former results at the proteome level, we showed that queens had fewer metabolites related to immunity. Contrary to our predictions, we did not find any metabolite linked to reproduction in queens. Among the workers, foragers had a metabolic signature reflecting a more stressful environment and a more highly stimulated immune system. We also found that nest-workers had more digestion-related metabolites. Hence, we showed that specific metabolic signatures match specific social roles. Besides, we identified metabolites differently expressed among behavioral castes and involved in nutrient sensing and longevity pathways (e.g., sirtuins, FOXO). The links between such molecular pathways and aging being found in an increasing number of taxa, our results confirm and strengthen their potential universality.
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Affiliation(s)
- Martin Quque
- Université de Strasbourg, CNRS, IPHC UMR 7178, 23 rue du Loess, F-67000, Strasbourg, France.
| | - Claire Villette
- Plant Imaging and Mass Spectrometry (PIMS), Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67000, Strasbourg, France
| | - François Criscuolo
- Université de Strasbourg, CNRS, IPHC UMR 7178, 23 rue du Loess, F-67000, Strasbourg, France
| | - Cédric Sueur
- Université de Strasbourg, CNRS, IPHC UMR 7178, 23 rue du Loess, F-67000, Strasbourg, France
- Institut Universitaire de France, 75005, Paris, France
| | - Fabrice Bertile
- Université de Strasbourg, CNRS, IPHC UMR 7178, 23 rue du Loess, F-67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI, FR2048, Strasbourg, France
| | - Dimitri Heintz
- Plant Imaging and Mass Spectrometry (PIMS), Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67000, Strasbourg, France
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107
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Petrovsky DV, Kopylov AT, Rudnev VR, Stepanov AA, Kulikova LI, Malsagova KA, Kaysheva AL. Managing of Unassigned Mass Spectrometric Data by Neural Network for Cancer Phenotypes Classification. J Pers Med 2021; 11:1288. [PMID: 34945760 PMCID: PMC8707435 DOI: 10.3390/jpm11121288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 11/17/2022] Open
Abstract
Mass spectrometric profiling provides information on the protein and metabolic composition of biological samples. However, the weak efficiency of computational algorithms in correlating tandem spectra to molecular components (proteins and metabolites) dramatically limits the use of "omics" profiling for the classification of nosologies. The development of machine learning methods for the intelligent analysis of raw mass spectrometric (HPLC-MS/MS) measurements without involving the stages of preprocessing and data identification seems promising. In our study, we tested the application of neural networks of two types, a 1D residual convolutional neural network (CNN) and a 3D CNN, for the classification of three cancers by analyzing metabolomic-proteomic HPLC-MS/MS data. In this work, we showed that both neural networks could classify the phenotypes of gender-mixed oncology, kidney cancer, gender-specific oncology, ovarian cancer, and the phenotype of a healthy person by analyzing 'omics' data in 'mgf' data format. The created models effectively recognized oncopathologies with a model accuracy of 0.95. Information was obtained on the remoteness of the studied phenotypes. The closest in the experiment were ovarian cancer, kidney cancer, and prostate cancer/kidney cancer. In contrast, the healthy phenotype was the most distant from cancer phenotypes and ovarian and prostate cancers. The neural network makes it possible to not only classify the studied phenotypes, but also to determine their similarity (distance matrix), thus overcoming algorithmic barriers in identifying HPLC-MS/MS spectra. Neural networks are versatile and can be applied to standard experimental data formats obtained using different analytical platforms.
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Affiliation(s)
- Denis V. Petrovsky
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (D.V.P.); (A.T.K.); (V.R.R.); (A.A.S.); (L.I.K.); (A.L.K.)
| | - Arthur T. Kopylov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (D.V.P.); (A.T.K.); (V.R.R.); (A.A.S.); (L.I.K.); (A.L.K.)
| | - Vladimir R. Rudnev
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (D.V.P.); (A.T.K.); (V.R.R.); (A.A.S.); (L.I.K.); (A.L.K.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Moscow, Russia
| | - Alexander A. Stepanov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (D.V.P.); (A.T.K.); (V.R.R.); (A.A.S.); (L.I.K.); (A.L.K.)
| | - Liudmila I. Kulikova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (D.V.P.); (A.T.K.); (V.R.R.); (A.A.S.); (L.I.K.); (A.L.K.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Moscow, Russia
| | - Kristina A. Malsagova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (D.V.P.); (A.T.K.); (V.R.R.); (A.A.S.); (L.I.K.); (A.L.K.)
| | - Anna L. Kaysheva
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (D.V.P.); (A.T.K.); (V.R.R.); (A.A.S.); (L.I.K.); (A.L.K.)
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108
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Sinha N, van Schothorst EM, Hooiveld GJEJ, Keijer J, Martins Dos Santos VAP, Suarez-Diez M. Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism. BMC Bioinformatics 2021; 22:574. [PMID: 34839828 PMCID: PMC8628452 DOI: 10.1186/s12859-021-04488-8] [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: 04/07/2021] [Accepted: 11/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distributions. Even though existing methods use transcript abundances as a proxy for enzyme activity, each method uses a different hypothesis and assumptions. Most methods implicitly assume a proportionality between transcript levels and flux through the corresponding function, although these proportionality constant(s) are often not explicitly mentioned nor discussed in any of the published methods. E-Flux is one such method and, in this algorithm, flux bounds are related to expression data, so that reactions associated with highly expressed genes are allowed to carry higher flux values. RESULTS Here, we extended E-Flux and systematically evaluated the impact of an assumed proportionality constant on model predictions. We used data from published experiments with Escherichia coli and Saccharomyces cerevisiae and we compared the predictions of the algorithm to measured extracellular and intracellular fluxes. CONCLUSION We showed that detailed modelling using a proportionality constant can greatly impact the outcome of the analysis. This increases accuracy and allows for extraction of better physiological information.
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Affiliation(s)
- Neeraj Sinha
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Human and Animal Physiology, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Evert M van Schothorst
- Human and Animal Physiology, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Guido J E J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,LifeGlimmer GmbH., Markelstrasse 38, 12163, Berlin, Germany.,Bioprocess Engineering Group, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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109
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Maehara T, Fujimori K. Inhibition of Prostaglandin F 2α Receptors Exaggerates HCl-Induced Lung Inflammation in Mice. Int J Mol Sci 2021; 22:ijms222312843. [PMID: 34884648 PMCID: PMC8657597 DOI: 10.3390/ijms222312843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 01/11/2023] Open
Abstract
Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are severe respiratory disorders that are caused by aspiration, sepsis, trauma, and pneumonia. A clinical feature of ALI/ARDS is the acute onset of severe hypoxemia, and the mortality rate, which is estimated at 38-50%, remains high. Although prostaglandins (PGs) are detected in the bronchoalveolar lavage fluid of patients with ALI/ARDS, the role of PGF2α in ALI remains unclear. We aimed to clarify the role of PGF2α/PGF2α receptor (FP) signaling in acid-induced ALI using an FP receptor antagonist, AL8810. Intratracheal injection of hydrochloric acid (HCl) increased neutrophil migration into the lungs, leading to respiratory dysfunction. Pre-administration of AL8810 further increased these features. Moreover, pre-treatment with AL8810 enhanced the HCl-induced expression of pro-inflammatory cytokines and neutrophil migratory factors in the lungs. Administration of HCl decreased the gene expression of lung surfactant proteins, which was further reduced by co-administration of AL8810. Administration of AL8810 also increased lung edema and reduced mRNA expression of epithelial sodium channel in the lungs, indicating that AL8810 reduced fluid clearance. Furthermore, AL8810 also increased lipopolysaccharide-induced expression of adhesion molecules such as intracellular adhesion molecule-1 and E-selectin in human umbilical vein endothelial cells. These results indicate that inhibition of FP receptors by AL8810 exacerbated HCl-induced ALI.
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110
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Huang T, Yu J, Ma Z, Fu Q, Liu S, Luo Z, Liu K, Yu L, Miao W, Yu D, Song Z, Li Y, Zhou L, Xu G. Translatomics Probes Into the Role of Lycopene on Improving Hepatic Steatosis Induced by High-Fat Diet. Front Nutr 2021; 8:727785. [PMID: 34796193 PMCID: PMC8594419 DOI: 10.3389/fnut.2021.727785] [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: 06/19/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Liver is an important organ for fat metabolism. Excessive intake of a high-fat/energy diet is a major cause of hepatic steatosis and its complications such as non-alcoholic fatty liver disease and non-alcoholic steatohepatitis. Supplementation with lycopene, a natural compound, is effective in lowering triglyceride levels in the liver, although the underlying mechanism at the translational level is unclear. In this study, mice were fed a high-fat diet (HFD) to induce hepatic steatosis and treated with or without lycopene. Translation omics and transcriptome sequencing were performed on the liver to explore the regulatory mechanism of lycopene in liver steatosis induced by HFD, and identify differentially expressed genes (DEGs). We identified 1,358 DEGs at the translational level. Through transcriptomics and translatomics joint analysis, we narrowed the range of functional genes to 112 DEGs and found that lycopene may affect lipid metabolism by regulating the expression of LPIN1 at the transcriptional and translational levels. This study provides a powerful tool for translatome and transcriptome integration and a new strategy for the screening of candidate genes.
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Affiliation(s)
- Tengda Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jingsu Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zeqiang Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qinghua Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zupeng Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Kang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lin Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Weiwei Miao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Dongling Yu
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Ziyi Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yixing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Gaoxiao Xu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
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Hunt LC, Graca FA, Pagala V, Wang YD, Li Y, Yuan ZF, Fan Y, Labelle M, Peng J, Demontis F. Integrated genomic and proteomic analyses identify stimulus-dependent molecular changes associated with distinct modes of skeletal muscle atrophy. Cell Rep 2021; 37:109971. [PMID: 34758314 PMCID: PMC8852763 DOI: 10.1016/j.celrep.2021.109971] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/27/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
Skeletal muscle atrophy is a debilitating condition that occurs with aging and disease, but the underlying mechanisms are incompletely understood. Previous work determined that common transcriptional changes occur in muscle during atrophy induced by different stimuli. However, whether this holds true at the proteome level remains largely unexplored. Here, we find that, contrary to this earlier model, distinct atrophic stimuli (corticosteroids, cancer cachexia, and aging) induce largely different mRNA and protein changes during muscle atrophy in mice. Moreover, there is widespread transcriptome-proteome disconnect. Consequently, atrophy markers (atrogenes) identified in earlier microarray-based studies do not emerge from proteomics as generally induced by atrophy. Rather, we identify proteins that are distinctly modulated by different types of atrophy (herein defined as “atroproteins”) such as the myokine CCN1/Cyr61, which regulates myofiber type switching during sarcopenia. Altogether, these integrated analyses indicate that different catabolic stimuli induce muscle atrophy via largely distinct mechanisms. Skeletal muscle wasting is caused by many catabolic stimuli, which were thought to act via shared mechanisms. Hunt et al. now show that distinct catabolic stimuli induce muscle wasting via largely different molecular changes. The authors identify atrophy-associated proteins (“atroproteins”) that may represent diagnostic biomarkers and/or therapeutic targets.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Flavia A Graca
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yuxin Li
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Myriam Labelle
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Chen J, Guo Y, Huang S, Zhan H, Zhang M, Wang J, Shu Y. Integration of transcriptome and proteome reveals molecular mechanisms underlying stress responses of the cutworm, Spodoptera litura, exposed to different levels of lead (Pb). CHEMOSPHERE 2021; 283:131205. [PMID: 34147986 DOI: 10.1016/j.chemosphere.2021.131205] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
Heavy metals are major environmental pollutants that affect organisms across different trophic levels. Herbivorous insects play an important role in the bioaccumulation, and eventually, biomagnification of these metals. Although effects of heavy metal stress on insects have been well-studied, the molecular mechanisms underlying their effects remain poorly understood. Here, we used the RNA-Seq profiling and isobaric tags for relative and absolute quantitation (iTRAQ) approaches to unravel these mechanisms in the polyphagous pest Spodoptera litura exposed to lead (Pb) at two different concentrations (12.5 and 100 mg Pb/kg; PbL and PbH, respectively). Altogether, 1392 and 1630 differentially expressed genes (DEGs) and 58, 114 differentially expressed proteins (DEPs) were identified in larvae exposed to PbL and PbH, respectively. After exposed to PbL, the main up-regulated genes clusters and proteins in S. litura larvae were associated with their metabolic processes, including carbohydrate, protein, and lipid metabolism, but the levels of cytochrome P450 associated with the pathway of xenobiotic biodegradation and metabolism were found to be decreased. In contrast, the main up-regulated genes clusters and proteins in larvae exposed to PbH were enriched in the metabolism of xenobiotic by cytochrome P450, drug metabolism-cytochrome P450, and other drug metabolism enzymes, while the down-regulated genes and proteins were found to be closely related to the lipid (lipase) and protein (serine protease, trypsin) metabolism and growth processes (cuticular protein). These findings indicate that S. litura larvae exposed to PbL could enhance food digestion and absorption to prioritize for growth rather than detoxification, whereas S. litura larvae exposed to PbH reduced food digestion and absorption and channelized the limited energy for detoxification rather than growth. These contrasting results explain the dose-dependent effects of heavy metal stress on insect life-history traits, wherein low levels of heavy metal stress induce stimulation, while high levels of heavy metal stress cause inhibition at the transcriptome and proteome levels.
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Affiliation(s)
- Jin Chen
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Centre for Modern Eco-agriculture, Guangzhou, 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yeshan Guo
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Centre for Modern Eco-agriculture, Guangzhou, 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Shimin Huang
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Centre for Modern Eco-agriculture, Guangzhou, 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Huiru Zhan
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Centre for Modern Eco-agriculture, Guangzhou, 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Meifang Zhang
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Centre for Modern Eco-agriculture, Guangzhou, 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Jianwu Wang
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Centre for Modern Eco-agriculture, Guangzhou, 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Yinghua Shu
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Centre for Modern Eco-agriculture, Guangzhou, 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
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113
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Zhou T, Yang Y, Li T, Liu H, Zhou F, Zhao Y. Sesame β-ketoacyl-acyl carrier protein synthase I regulates pollen development by interacting with an adenosine triphosphate-binding cassette transporter in transgenic Arabidopsis. PHYSIOLOGIA PLANTARUM 2021; 173:1048-1062. [PMID: 34270100 DOI: 10.1111/ppl.13501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Male gametogenesis is an important biological process critical for seed formation and successful breeding. Understanding the molecular mechanisms of male fertility might facilitate hybrid breeding and increase crop yields. Sesame anther development is largely unknown. Here, a sesame β-ketoacyl-[acyl carrier protein] synthase I (SiKASI) was cloned and characterized as being involved in pollen and pollen wall development. Immunohistochemical analysis showed that the spatiotemporal expression of SiKASI protein was altered in sterile sesame anthers compared with fertile anthers. In addition, SiKASI overexpression in Arabidopsis caused male sterility. Cytological observations revealed defective microspore and pollen wall development in SiKASI-overexpressing plants. Aberrant lipid droplets were detected in the tapetal cells of SiKASI-overexpressing plants, and most of the microspores of transgenic plants contained few cytoplasmic inclusions, with irregular pollen wall components embedded on their surfaces. Moreover, the fatty acid metabolism and the expression of a sporopollenin biosynthesis-related gene set were altered in the anthers of SiKASI-overexpressing plants. Additionally, SiKASI interacted with an adenosine triphosphate (ATP)-binding cassette (ABC) transporter. Taken together, our findings suggested that SiKASI was crucial for fatty acid metabolism and might interact with ABCG18 for normal pollen fertility in Arabidopsis.
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Affiliation(s)
- Ting Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuanxiao Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Tianyu Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hongyan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fang Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yingzhong Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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114
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Song I, Lee YK, Kim JW, Lee SW, Park SR, Lee HK, Oh S, Ko K, Kim MK, Park SJ, Kim DH, Kim MS, Kim DS, Ko K. Effect of an Endoplasmic Reticulum Retention Signal Tagged to Human Anti-Rabies mAb SO57 on Its Expression in Arabidopsis and Plant Growth. Mol Cells 2021; 44:770-779. [PMID: 34711693 PMCID: PMC8560589 DOI: 10.14348/molcells.2021.2002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022] Open
Abstract
Transgenic Arabidopsis thaliana expressing an anti-rabies monoclonal antibody (mAb), SO57, was obtained using Agrobacterium-mediated floral dip transformation. The endoplasmic reticulum (ER) retention signal Lys-Asp-Glu-Leu (KDEL) was tagged to the C-terminus of the anti-rabies mAb heavy chain to localize the mAb to the ER and enhance its accumulation. When the inaccurately folded proteins accumulated in the ER exceed its storage capacity, it results in stress that can affect plant development and growth. We generated T1 transformants and obtained homozygous T3 seeds from transgenic Arabidopsis to investigate the effect of KDEL on plant growth. The germination rate did not significantly differ between plants expressing mAb SO57 without KDEL (SO plant) and mAb SO57 with KDEL (SOK plant). The primary roots of SOK agar media grown plants were slightly shorter than those of SO plants. Transcriptomic analysis showed that expression of all 11 ER stress-related genes were not significantly changed in SOK plants relative to SO plants. SOK plants showed approximately three-fold higher mAb expression levels than those of SO plants. Consequently, the purified mAb amount per unit of SOK plant biomass was approximately three times higher than that of SO plants. A neutralization assay revealed that both plants exhibited efficient rapid fluorescent focus inhibition test values against the rabies virus relative to commercially available human rabies immunoglobulins. KDEL did not upregulate ER stress-related genes; therefore, the enhanced production of the mAb did not affect plant growth. Thus, KDEL fusion is recommended for enhancing mAb production in plant systems.
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Affiliation(s)
- Ilchan Song
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Young Koung Lee
- Plasma Technology Research Center, National Fusion Research Institute, Gunsan 54004, Korea
| | - Jin Wook Kim
- Department of Urology, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Seung-Won Lee
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Se Ra Park
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Hae Kyung Lee
- Division of Zoonotic and Vector Borne Diseases Research, Korea National Institute of Health, Osong 28159, Korea
| | - Soyeon Oh
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Kinarm Ko
- Department of Stem Cell Biology, Konkuk University School of Medicine, Seoul 05029, Korea
| | - Mi Kyung Kim
- Department of Pathology, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Soon Ju Park
- Division of Biological Sciences, Wonkwang University, Iksan 54538, Korea
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon 57922, Korea
| | - Moon-Soo Kim
- Department of Chemistry, Western Kentucky University, Bowling Green, KY 42101, USA
| | - Do Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju 55365, Korea
| | - Kisung Ko
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea
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115
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Zhang T, Zhang Y, Xu J, Yan Z, Sun Q, Huang Y, Wang S, Li S, Sun B. Toxic effects of ammonia on the intestine of the Asian clam (Corbicula fluminea). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117617. [PMID: 34174666 DOI: 10.1016/j.envpol.2021.117617] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Intestines contain a large number of microorganisms that collectively play a vital role in regulating physiological and biochemical processes, including digestion, water balance, and immune function. In this study, we explored the effects of ammonia stress on intestinal inflammation, the antioxidant system, and the microbiome of the Asian clam (Corbicula fluminea). Exposure to varying ammonia concentrations (10 and 25 mg N/L) and exposure times (7 and 14 days) resulted in damage to C. fluminea intestinal tissue, according to histological analysis. Furthermore, intestinal inflammatory responses and damage to the antioxidant system were revealed through qPCR, ELISA, and biochemical analysis experiments. Inflammatory responses were more severe in the treatment group exposed to a lower concentration of ammonia. High-throughput 16S rDNA sequencing showed that ammonia stress under different conditions altered intestinal bacterial diversity and microbial community composition, particularly impacting the dominant phylum Proteobacteria and genus Aeromonas. These results indicate that ammonia stress can activate intestinal inflammatory reactions, damage the intestinal antioxidant system, and alter intestinal microbial composition, thereby impeding intestinal physiological function and seriously threatening the health of C. fluminea.
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Affiliation(s)
- Tianxu Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China; Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, PR China.
| | - Yan Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, PR China.
| | - Jiayun Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Qianhang Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Yi Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Shuo Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, PR China.
| | - Binbin Sun
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, PR China.
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116
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Castillo JA, Giraldo DM, Hernandez JC, Smit JM, Rodenhuis-Zybert IA, Urcuqui-Inchima S. Regulation of innate immune responses in macrophages differentiated in the presence of vitamin D and infected with dengue virus 2. PLoS Negl Trop Dis 2021; 15:e0009873. [PMID: 34634046 PMCID: PMC8530315 DOI: 10.1371/journal.pntd.0009873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/21/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022] Open
Abstract
A dysregulated or exacerbated inflammatory response is thought to be the key driver of the pathogenesis of severe disease caused by the mosquito-borne dengue virus (DENV). Compounds that restrict virus replication and modulate the inflammatory response could thus serve as promising therapeutics mitigating the disease pathogenesis. We and others have previously shown that macrophages, which are important cellular targets for DENV replication, differentiated in the presence of bioactive vitamin D (VitD3) are less permissive to viral replication, and produce lower levels of pro-inflammatory cytokines. Therefore, we here evaluated the extent and kinetics of innate immune responses of DENV-2 infected monocytes differentiated into macrophages in the presence (D3-MDMs) or absence of VitD3 (MDMs). We found that D3-MDMs expressed lower levels of RIG I, Toll-like receptor (TLR)3, and TLR7, as well as higher levels of SOCS-1 in response to DENV-2 infection. D3-MDMs produced lower levels of reactive oxygen species, related to a lower expression of TLR9. Moreover, although VitD3 treatment did not modulate either the expression of IFN-α or IFN-β, higher expression of protein kinase R (PKR) and 2'-5'-oligoadenylate synthetase 1 (OAS1) mRNA were found in D3-MDMs. Importantly, the observed effects were independent of reduced infection, highlighting the intrinsic differences between D3-MDMs and MDMs. Taken together, our results suggest that differentiation of MDMs in the presence of VitD3 modulates innate immunity in responses to DENV-2 infection.
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Affiliation(s)
- Jorge Andrés Castillo
- Grupo de Inmunovirología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, (Antioquia), Colombia
- Department of Medical Microbiology and infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Diana M. Giraldo
- Grupo de Inmunovirología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, (Antioquia), Colombia
| | - Juan C. Hernandez
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, (Antioquia), Colombia
| | - Jolanda M. Smit
- Department of Medical Microbiology and infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Silvio Urcuqui-Inchima
- Grupo de Inmunovirología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, (Antioquia), Colombia
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117
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Özenoğlu-Aydınoğlu S, Yıldızhan H, Cansaran-Duman D. A proteomic analysis of Pseudevernia furfuracea after exposure to Cr +6 by MALDI-TOF mass spectrometry. 3 Biotech 2021; 11:444. [PMID: 34631345 DOI: 10.1007/s13205-021-02986-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/04/2021] [Indexed: 10/20/2022] Open
Abstract
The problem of heavy metal pollution in nature has increased rapidly in recent years. Hexavalent chromium (Cr+6) is one of the most toxic heavy metals that cause environmental pollution. Although many studies in the literature that illuminate the stress response mechanisms of biological organisms such as bacteria, algae, and plants against heavy metals, there is limited information about revealing the protein level changes of lichen species in response to heavy metal stress. Here, we used a MALDI-TOF-based proteomic assay to determine protein level changes in Pseudevernia furfuracea after exposure to Cr+6 heavy metal stress at 6, 18 and 24 h. It was determined that expression levels of 26, 149 and 66 proteins changed in P. furfuracea. 6, 18 and 24 h after Cr+6 application compared to the control sample, respectively. We identified 9 common proteins expressed at three different time levels (6, 18, 24 h) and evaluated their protein-protein interaction profiles with the STRING tool. According to the results of the study, it was determined that the expression level of six proteins was up-regulated (OP4, KIP3, BNI5, VSP64, HSP 60, BCK1) and three proteins were down-regulated (MNS1, ABZ2, ATG4) from the expression level of nine proteins in total with Cr+6 exposure. It was determined that nine proteins were also found to be effective in biological processes such as stress signaling, transcription regulation and cellular detoxification metabolisms. To confirm the protein expression level, we analyzed the HSP60 protein by western blot assay. It has been shown that exposure to Cr+6 exposure in P. furfuracea caused an increase in HSP60 protein level compared to the control sample (non-exposed Cr+6). In this study, new knowledge are presented for the use of P. furfuracea as a biosorption agent in the removal of industrial wastes in biotechnological applications.
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118
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Zhao G, Shi Y, Gong C, Liu T, Nan W, Ma L, Wu Z, Da C, Zhou K, Zhang H. Curcumin Exerts Antinociceptive Effects in Cancer-Induced Bone Pain via an Endogenous Opioid Mechanism. Front Neurosci 2021; 15:696861. [PMID: 34539332 PMCID: PMC8446608 DOI: 10.3389/fnins.2021.696861] [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] [Received: 04/18/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Cancer pain is one of the main complications in advanced cancer patients, and its management is still challenging. Therefore, there is an urgent need to develop novel pharmacotherapy for cancer pain. Several natural products have attracted the interest of researchers. In previous studies, curcumin has proved to exhibit antitumor, antiviral, antioxidant, anti-inflammatory, and analgesic effects. However, the analgesic mechanism of curcumin has not been elucidated. Thus, in this study, we aimed to elucidate the antinociceptive potency and analgesic mechanism of curcumin in cancer-induced bone pain. Our results showed that consecutive curcumin treatment (30, 60, 120 mg/kg, i.p., twice daily for 11 days) produced significant analgesic activity, but had no effect on the progress of the bone cancer pain. Notably, pretreatment with naloxone, a non-selective opioid receptor antagonist, markedly reversed the antinociceptive effect induced by curcumin. Moreover, in primary cultured rat dorsal root ganglion (DRG) neurons, curcumin significantly up-regulated the expression of proopiomelanocortin (Pomc) and promoted the release of β-endorphin and enkephalin. Furthermore, pretreatment with the antiserum of β-endorphin or enkephalin markedly attenuated curcumin-induced analgesia in cancer-induced bone pain. Our present study, for the first time, showed that curcumin attenuates cancer-induced bone pain. The results also suggested that stimulation of expression of DRG neurons β-endorphin and enkephalin mediates the antinociceptive effect of curcumin in pain hypersensitivity conditions.
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Affiliation(s)
- Guanghai Zhao
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
| | - Yongqiang Shi
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
| | - Chaoyang Gong
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
| | - Taicong Liu
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
| | - Wei Nan
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Lin Ma
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
| | - Zuolong Wu
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
| | - Chaoming Da
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
| | - Kaisheng Zhou
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Haihong Zhang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Orthopaedics Key Laboratory of Gansu Province, Lanzhou University, Lanzhou, China
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119
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Guo H, Wang L, Deng Y, Ye J. Novel perspectives of environmental proteomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147588. [PMID: 34023612 DOI: 10.1016/j.scitotenv.2021.147588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/08/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
The connection among genome expression, proteome alteration, metabolism regulation and phenotype change under environmental stresses is very vague. It is a tough task for the traditional research approaches to reveal the related scientific mechanisms of the above connection at molecular and systematic levels. Proteomics approach is an insightful tool for revealing the biological functions, metabolic networks and functional protein interaction networks of cells and organisms under stresses at the systematic level. The purpose of this review is to provide an insightful guideline on how to set up a proteomic investigation for revealing biomolecule mechanisms, protein biomarkers and metabolism networks related to stress response, pollutant recognition, transport and biodegradation, and providing an insightful high-throughput approach for screening functional enzymes and effective microbes based on bioinformatics and functional verification method. Furthermore, the toxicity evaluation of pollutants and byproducts by proteomics approaches provides a scientific insight for early diagnosis of ecological risk and determination of the effectiveness of pollutant treatment techniques.
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Affiliation(s)
- Huiying Guo
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Institute of Orthopedic Diseases, Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Lili Wang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ying Deng
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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120
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Perween N, Pekhale K, Haval G, Mittal S, Ghaskadbi S, Ghaskadbi SS. Cloning and characterization of Thioredoxin 1 from the Cnidarian Hydra. J Biochem 2021; 171:41-51. [PMID: 34523686 DOI: 10.1093/jb/mvab092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/11/2021] [Indexed: 11/14/2022] Open
Abstract
Thioredoxins, small disulphide-containing redox proteins, play an important role in the regulation of cellular thiol redox balance through their disulfide reductase activity. In this study, we have identified, cloned, purified and characterized thioredoxin 1 (HvTrx1) from the Cnidarian Hydra vulgaris Ind-Pune. Bioinformatics analysis revealed that HvTrx1 contains an evolutionarily conserved catalytic active site CGPC and shows a closer phylogenetic relationship with vertebrate Trx1. Optimum pH and temperature for enzyme activity of purified HvTrx1 was found to be pH 7.0 and 25 °C respectively. Enzyme activity decreased significantly at acidic or alkaline pH as well as at higher temperatures. HvTrx1 was found to be expressed ubiquitously in whole mount in situ hybridization. Treatment of Hydra with hydrogen peroxide (H2O2), a highly reactive oxidizing agent, led to a significant increase in gene expression and enzyme activity of Trx1. Further experiments using PX12, an inhibitor of Trx1, indicated that Trx1 plays an important role in regeneration in Hydra. Finally, by using growth assay in E. coli and wound healing assay in human colon cancer cells, we demonstrate that HvTrx1 is functionally active in both prokaryotic and eukaryotic heterologous systems.
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Affiliation(s)
- Nusrat Perween
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India.,Department of Zoology, Abeda Inamdar Senior College, Pune 411001, India
| | - Komal Pekhale
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | - Gauri Haval
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India.,Department of Zoology, Abasaheb Garware College, Pune 411004, India
| | - Smriti Mittal
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Surendra Ghaskadbi
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune 411004, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
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Jiang Y, Kang Q, Yin Z, Sun J, Wang B, Zeng XA, Zhao D, Li H, Huang M. Content changes of Jiupei tripeptide Tyr-Gly-Asp during simulated distillation process of baijiu and the potential in vivo antioxidant ability investigation. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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122
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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123
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Marker L, Schjerling P, Mackey AL, Hansen T, Jakobsen J, Kjær M, Krogsgaard MR. Collagens in primary frozen shoulder: expression of collagen mRNA isoforms in the different phases of the disease. Rheumatology (Oxford) 2021; 60:3879-3887. [PMID: 33347577 DOI: 10.1093/rheumatology/keaa802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 09/24/2020] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Primary frozen shoulder (pFS) has three phases that differ in clinical presentation. It is characterized by contracture of the joint capsule. We hypothesized that there is a general upregulation of collagens in pFS, and that this is highest in the first phase of the disease. The aims of this study were to investigate the expression of various collagens and degradation of collagens in patients with primary pFS and relate this to the three phases of the condition. METHODS From twenty-six patients with pFS and eight control patients with subacromial impingement, biopsies were obtained during shoulder arthroscopy from the middle glenohumeral ligament and the anterior capsule, and mRNA levels for collagens, MMP-2 and -14 and TGF-β1, - β2 and -β3 in the tissue were analysed using real-time PCR. RESULTS Genes for collagens type I, III, IV, V, VI and XIV, were activated in pFS, and the total mRNA for all collagens was increased (P < 0.05). This upregulation was independent of disease phases in pFS. In addition, MMP-2, MMP-14, TGF-β1 and TGF-β3 were upregulated in all phases of the disease. CONCLUSION There is a general upregulation and an increased degradation of collagens in pFS in all three phases of the disease. This indicates a constantly increased turnover of the fibrotic tissue in the capsule from pFS. The difference in clinical presentation of pFS observed in the three phases of the disease is not primarily a result of variations in collagen production.
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Affiliation(s)
- Line Marker
- Section for Sports Traumatology M51, Department of Orthopaedic Surgery M, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Peter Schjerling
- Institute of Sports Medicine, Department of Orthopaedic Surgery M, Bispebjerg and Frederiksberg Hospital, Center for Healthy Aging, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Abigail L Mackey
- Institute of Sports Medicine, Department of Orthopaedic Surgery M, Bispebjerg and Frederiksberg Hospital, Center for Healthy Aging, Faculty of Health and Medical Sciences, Copenhagen, Denmark.,Xlab, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Hansen
- Section for Sports Traumatology M51, Department of Orthopaedic Surgery M, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Jens Jakobsen
- Section for Sports Traumatology M51, Department of Orthopaedic Surgery M, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Michael Kjær
- Institute of Sports Medicine, Department of Orthopaedic Surgery M, Bispebjerg and Frederiksberg Hospital, Center for Healthy Aging, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Michael R Krogsgaard
- Section for Sports Traumatology M51, Department of Orthopaedic Surgery M, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
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124
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Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
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125
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Zhang S, Ghatak A, Bazargani MM, Bajaj P, Varshney RK, Chaturvedi P, Jiang D, Weckwerth W. Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:669-687. [PMID: 34227164 PMCID: PMC9291999 DOI: 10.1111/tpj.15410] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Grain filling and grain development are essential biological processes in the plant's life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.
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Affiliation(s)
- Shuang Zhang
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Arindam Ghatak
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | | | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationMurdoch UniversityMurdochWA6150Australia
| | - Palak Chaturvedi
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjing210095China
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Vienna Metabolomics Center (VIME)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
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126
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Eckhardt C, Sbiera I, Krebs M, Sbiera S, Spahn M, Kneitz B, Joniau S, Fassnacht M, Kübler H, Weigand I, Kroiss M. High expression of Sterol-O-Acyl transferase 1 (SOAT1), an enzyme involved in cholesterol metabolism, is associated with earlier biochemical recurrence in high risk prostate cancer. Prostate Cancer Prostatic Dis 2021; 25:484-490. [PMID: 34326474 PMCID: PMC9385470 DOI: 10.1038/s41391-021-00431-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/06/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023]
Abstract
Background Prostate cancer (PCa) is the most frequent cancer in men. The prognosis of PCa is heterogeneous with many clinically indolent tumors and rare highly aggressive cases. Reliable tissue markers of prognosis are lacking. Active cholesteryl ester synthesis has been associated with prostate cancer aggressiveness. Sterol-O-Acyl transferases (SOAT) 1 and 2 catalyze cholesterol esterification in humans. Objective To investigate the value of SOAT1 and SOAT2 tissue expression as prognostic markers in high risk PCa. Patients and methods Formalin-fixed paraffin-embedded tissue samples from 305 high risk PCa cases treated with radical prostatectomy were analyzed for SOAT1 and SOAT2 protein expression by semi-quantitative immunohistochemistry. The Kaplan–Meier method and Cox proportional hazards modeling were used to compare outcome. Main outcome measure Biochemical recurrence (BCR) free survival. Results SOAT1 expression was high in 73 (25%) and low in 219 (75%; not evaluable: 13) tumors. SOAT2 was highly expressed in 40 (14%) and at low levels in 249 (86%) samples (not evaluable: 16). By Kaplan–Meier analysis, we found significantly shorter median BCR free survival of 93 months (95% confidence interval 23.6–123.1) in patients with high SOAT1 vs. 134 months (112.6–220.2, Log-rank p < 0.001) with low SOAT1. SOAT2 expression was not significantly associated with BCR. After adjustment for age, preoperative PSA, tumor stage, Gleason score, resection status, lymph node involvement and year of surgery, high SOAT1 but not SOAT2 expression was associated with shorter BCR free survival with a hazard ratio of 2.40 (95% CI 1.57–3.68, p < 0.001). Time to clinical recurrence and overall survival were not significantly associated with SOAT1 and SOAT2 expression Conclusions SOAT1 expression is strongly associated with BCR free survival alone and after multivariable adjustment in high risk PCa. SOAT1 may serve as a histologic marker of prognosis and holds promise as a future treatment target.
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Affiliation(s)
- Carolin Eckhardt
- University Hospital Würzburg, Department of Internal Medicine I, Division of Endocrinology and Diabetology, Würzburg, Germany
| | - Iuliu Sbiera
- University Hospital Würzburg, Department of Internal Medicine I, Division of Endocrinology and Diabetology, Würzburg, Germany
| | - Markus Krebs
- University Hospital Würzburg, Department of Urology and Pediatric Urology, Würzburg, Germany.,University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Silviu Sbiera
- University Hospital Würzburg, Department of Internal Medicine I, Division of Endocrinology and Diabetology, Würzburg, Germany
| | - Martin Spahn
- Lindenhofspital, Bern, Switzerland.,Department of Urology, University Hospital Essen, Essen, Germany
| | - Burkhard Kneitz
- University Hospital Würzburg, Department of Urology and Pediatric Urology, Würzburg, Germany
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Martin Fassnacht
- University Hospital Würzburg, Department of Internal Medicine I, Division of Endocrinology and Diabetology, Würzburg, Germany.,University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Hubert Kübler
- University Hospital Würzburg, Department of Urology and Pediatric Urology, Würzburg, Germany.,University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Isabel Weigand
- University Hospital Würzburg, Department of Internal Medicine I, Division of Endocrinology and Diabetology, Würzburg, Germany.,Department of Medicine IV, University Hospital Munich, Ludwig-Maximilians-Universität München, München, Germany
| | - Matthias Kroiss
- University Hospital Würzburg, Department of Internal Medicine I, Division of Endocrinology and Diabetology, Würzburg, Germany. .,University of Würzburg, Comprehensive Cancer Center Mainfranken, Würzburg, Germany. .,Department of Medicine IV, University Hospital Munich, Ludwig-Maximilians-Universität München, München, Germany.
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127
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Xiong YM, Pan HT, Ding HG, He Y, Zhang J, Zhang F, Yu B, Zhang T, Huang HF. Proteomic and functional analysis of proteins related to embryonic development of decidua in patients with recurrent pregnancy loss. Biol Reprod 2021; 105:1246-1256. [PMID: 34296254 DOI: 10.1093/biolre/ioab140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/18/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
Recurrent pregnancy loss (RPL) is defined as the loss of two or more consecutive pregnancies before the 20 weeks of gestation. Recurrent pregnancy loss affects about 1-2% of couples trying to conceive; however, the mechanisms leading to this complication are largely unknown. Our previous studies using comparative proteomics identified 314 differentially expressed proteins (DEPs) in the placental villous. In this study, we identified 5479 proteins from a total of 34,157 peptides in decidua of patients with early recurrent pregnancy loss (Data are available via ProteomeXchange with identifier PXD023849). Further analysis identified 311 DEPs in the decidua tissue; and 159 proteins were highly expressed while 152 proteins were lowly expressed. These 311 proteins were further analyzed by using Ingenuity Pathway Analysis (IPA). The results suggested that 50 DEPs played important roles in the embryonic development. Upstream analysis of these DEPs revealed that AGT was the most important upstream regulator. Furthermore, protein - protein interaction (PPI) analysis of the embryonic development DEPs from the placental villous and decidua was performed in the STRING database. This study identified several proteins specifically associated with embryonic development in decidua of patients with early recurrent pregnancy loss. Therefore, these results provide new insights into potential biological mechanisms, that may ultimately inform recurrent pregnancy loss.
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Affiliation(s)
- Yi-Meng Xiong
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Institute of Embryo-Fetal Original Adult Disease, Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, 200030, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Hai-Tao Pan
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China.,Institute of Embryo-Fetal Original Adult Disease, Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, 200030, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Hai-Gang Ding
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yao He
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Juan Zhang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Feng Zhang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Bin Yu
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Tao Zhang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - He-Feng Huang
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, 310058, China.,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,Institute of Embryo-Fetal Original Adult Disease, Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, 200030, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
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White KA, McEntire KD, Buan NR, Robinson L, Barbar E. Charting a New Frontier Integrating Mathematical Modeling in Complex Biological Systems from Molecules to Ecosystems. Integr Comp Biol 2021; 61:2255-2266. [PMID: 34283225 DOI: 10.1093/icb/icab165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Nicole R Buan
- University of Nebraska-Lincoln, Department of Biochemistry
| | | | - Elisar Barbar
- Oregon State University, Department of Biochemistry and Biophysics
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129
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Freitas DF, da Rocha IM, Vieira-da-Motta O, de Paula Santos C. The Role of Melanin in the Biology and Ecology of Nematophagous Fungi. J Chem Ecol 2021; 47:597-613. [PMID: 34232439 DOI: 10.1007/s10886-021-01282-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/03/2021] [Accepted: 05/13/2021] [Indexed: 11/24/2022]
Abstract
Melanin is a heteropolymer formed by the polymerization of phenolic and indolic compounds. It occurs in organisms across all biological kingdoms and has a range different of functions, thus indicating its important evolutionary role. The presence of melanin offers several protective advantages, including against ultraviolet radiation, traumatic damage, oxidative stress, extreme temperatures, and pressure. For many species of fungi, melanin also participates directly in the process of virulence and pathogenicity. These organisms can synthesize melanin in two main ways: using a substrate of endogenous origin, involving 1,8-dihydroxynaphthalene (DHN); alternatively, in an exogenous manner with the addition of L-3, 4-dihydroxyphenylalanine (L-DOPA or levodopa). As melanin is an amorphous and complex substance, its study requires expensive and inaccessible technologies and analyses are often difficult to perform with conventional biochemical techniques. As such, details about its chemical structure are not yet fully understood, particularly for nematophagous fungi that remain poorly studied. Thus, this review presents an overview of the different types of melanin, with an emphasis on fungi, and discusses the role of melanin in the biology and ecology of nematophagous fungi.
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Affiliation(s)
- Deivid França Freitas
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Izabelli Martins da Rocha
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Olney Vieira-da-Motta
- Animal Health Laboratory - Infectious Contagious Diseases Sector, State University of North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Clóvis de Paula Santos
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil.
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Integrated proteomic and transcriptomic profiling identifies aberrant gene and protein expression in the sarcomere, mitochondrial complex I, and the extracellular matrix in Warmblood horses with myofibrillar myopathy. BMC Genomics 2021; 22:438. [PMID: 34112090 PMCID: PMC8194174 DOI: 10.1186/s12864-021-07758-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Background Myofibrillar myopathy in humans causes protein aggregation, degeneration, and weakness of skeletal muscle. In horses, myofibrillar myopathy is a late-onset disease of unknown origin characterized by poor performance, atrophy, myofibrillar disarray, and desmin aggregation in skeletal muscle. This study evaluated molecular and ultrastructural signatures of myofibrillar myopathy in Warmblood horses through gluteal muscle tandem-mass-tag quantitative proteomics (5 affected, 4 control), mRNA-sequencing (8 affected, 8 control), amalgamated gene ontology analyses, and immunofluorescent and electron microscopy. Results We identified 93/1533 proteins and 47/27,690 genes that were significantly differentially expressed. The top significantly differentially expressed protein CSRP3 and three other differentially expressed proteins, including, PDLIM3, SYNPO2, and SYNPOL2, are integrally involved in Z-disc signaling, gene transcription and subsequently sarcomere integrity. Through immunofluorescent staining, both desmin aggregates and CSRP3 were localized to type 2A fibers. The highest differentially expressed gene CHAC1, whose protein product degrades glutathione, is associated with oxidative stress and apoptosis. Amalgamated transcriptomic and proteomic gene ontology analyses identified 3 enriched cellular locations; the sarcomere (Z-disc & I-band), mitochondrial complex I and the extracellular matrix which corresponded to ultrastructural Z-disc disruption and mitochondrial cristae alterations found with electron microscopy. Conclusions A combined proteomic and transcriptomic analysis highlighted three enriched cellular locations that correspond with MFM ultrastructural pathology in Warmblood horses. Aberrant Z-disc mechano-signaling, impaired Z-disc stability, decreased mitochondrial complex I expression, and a pro-oxidative cellular environment are hypothesized to contribute to the development of myofibrillar myopathy in Warmblood horses. These molecular signatures may provide further insight into diagnostic biomarkers, treatments, and the underlying pathophysiology of MFM. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07758-0.
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Huang YH, Chu PY, Chen JL, Huang CT, Huang CC, Tsai YF, Wang YL, Lien PJ, Tseng LM, Liu CY. Expression pattern and prognostic impact of glycoprotein non-metastatic B (GPNMB) in triple-negative breast cancer. Sci Rep 2021; 11:12171. [PMID: 34108545 PMCID: PMC8190094 DOI: 10.1038/s41598-021-91588-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 05/28/2021] [Indexed: 12/31/2022] Open
Abstract
Glycoprotein non-metastatic B (GPNMB) is a transmembrane protein overexpressed in numerous cancers including triple-negative breast cancers (TNBC). It has been linked to promote cancer aggressiveness and implicated as a novel target for GPNMB-expressing cancers. In current study, we aimed to explore the clinical significance of GPNMB in TNBC. Among 759 specimens, immunohistochemistry (IHC) exhibited GPNMB expressions were variable in different subtypes and significantly higher in TNBC. Kaplan-Meier analysis revealed GPNMB overexpression in TNBC was associated with worse prognosis especially distant metastasis (P = 0.020, HR = 2.515, CI 1.154-5.480). Multivariate analysis showed GPNMB expression was an independent prognostic factor in terms of recurrence and distant metastasis (P = 0.008, HR = 3.22, CI 1.36-7.61; P = 0.017, HR = 3.08, CI 1.22-7.74). In silico analysis showed high mRNA expression of GPNMB was associated with distant metastasis and GPNMB was overexpressed in TNBC. Furthermore, GPNMB positively correlated with epithelial-mesenchymal transition (EMT) regulators, mesenchymal marker vimentin, MMP and integrins. The protein levels of Twist and MMP2 were upregulated by GPNMB overexpression in TNBC cells. GPNMB-enhanced cell invasion was attenuated by broad spectrum MMP inhibitor (GM 6001) and the selective inhibitor of MMP-2 (ARP100). In summary, GPNMB expression is prevalent in TNBC and may be implicated as a prognostic biomarker in patients with TNBC.
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Affiliation(s)
- Yu-Hsiang Huang
- School of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Pei-Yi Chu
- Department of Pathology, Show Chwan Memorial Hospital, Changhua City, Taiwan.,School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Ji-Lin Chen
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chun-Teng Huang
- School of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Hematology & Oncology, Department of Medicine, Yang-Ming Branch of Taipei City Hospital, Taipei, Taiwan
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yi-Fang Tsai
- School of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Ling Wang
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Experimental Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Nursing, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ling-Ming Tseng
- School of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Experimental Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chun-Yu Liu
- School of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan. .,Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan. .,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, No. 201, Sec. 2, Shih-Pai Road, Taipei, 112, Taiwan.
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132
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Li X, Xu YC, Tian YQ, Zhang PA, Hu SF, Wang LH, Jiang XH, Xu GY. Downregulation of GRK6 in arcuate nucleus promotes chronic visceral hypersensitivity via NF-κB upregulation in adult rats with neonatal maternal deprivation. Mol Pain 2021; 16:1744806920930858. [PMID: 32484026 PMCID: PMC7268126 DOI: 10.1177/1744806920930858] [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] [Indexed: 01/05/2023] Open
Abstract
AIMS The arcuate nucleus is a vital brain region for coursing of pain command. G protein-coupled kinase 6 (GRK6) accommodates signaling through G protein-coupled receptors. Studies have demonstrated that GRK6 is involved in inflammatory pain and neuropathic pain. The present study was designed to explore the role and the underlying mechanism of GRK6 in arcuate nucleus of chronic visceral pain. METHODS Chronic visceral pain of rats was induced by neonatal maternal deprivation and evaluated by monitoring the threshold of colorectal distension. Western blotting, immunofluorescence, real-time quantitative polymerase chain reaction techniques, and Nissl staining were employed to determine the expression and mutual effect of GRK6 with nuclear factor κB (NF-κB). RESULTS Expression of GRK6 in arcuate nucleus was significantly reduced in neonatal maternal deprivation rats when compared with control rats. GRK6 was mainly expressed in arcuate nucleus neurons, but not in astrocytes, and a little in microglial cells. Neonatal maternal deprivation reduced the percentage of GRK6-positive neurons of arcuate nucleus. Overexpression of GRK6 by Lentiviral injection into arcuate nucleus reversed chronic visceral pain in neonatal maternal deprivation rats. Furthermore, the expression of NF-κB in arcuate nucleus was markedly upregulated in neonatal maternal deprivation rats. NF-κB selective inhibitor pyrrolidine dithiocarbamate suppressed chronic visceral pain in neonatal maternal deprivation rats. GRK6 and NF-κB were expressed in the arcuate nucleus neurons. Importantly, overexpression of GRK6 reversed NF-κB expression at the protein level. In contrast, injection of pyrrolidine dithiocarbamate once daily for seven consecutive days did not alter GRK6 expression in arcuate nucleus of neonatal maternal deprivation rats. CONCLUSIONS Present data suggest that GRK6 might be a pivotal molecule participated in the central mechanisms of chronic visceral pain, which might be mediated by inhibiting NF-κB signal pathway. Overexpression of GRK6 possibly represents a potential strategy for therapy of chronic visceral pain.
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Affiliation(s)
- Xin Li
- Department of Physiology and Neurobiology, Medical College of Soochow University, Suzhou, P. R. China.,Center for Translational Pain Medicine, Institute of Neuroscience, Soochow University, Suzhou, P. R. China
| | - Yu-Cheng Xu
- Center for Translational Pain Medicine, Institute of Neuroscience, Soochow University, Suzhou, P. R. China
| | - Yuan-Qin Tian
- Center for Translational Pain Medicine, Institute of Neuroscience, Soochow University, Suzhou, P. R. China
| | - Ping-An Zhang
- Center for Translational Pain Medicine, Institute of Neuroscience, Soochow University, Suzhou, P. R. China
| | - Shu-Fen Hu
- Center for Translational Pain Medicine, Institute of Neuroscience, Soochow University, Suzhou, P. R. China
| | - Lin-Hui Wang
- Department of Physiology and Neurobiology, Medical College of Soochow University, Suzhou, P. R. China
| | - Xing-Hong Jiang
- Department of Physiology and Neurobiology, Medical College of Soochow University, Suzhou, P. R. China
| | - Guang-Yin Xu
- Department of Physiology and Neurobiology, Medical College of Soochow University, Suzhou, P. R. China.,Center for Translational Pain Medicine, Institute of Neuroscience, Soochow University, Suzhou, P. R. China
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133
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Hadizadeh Tasbiti A, Yari S, Siadat SD, Karimipoor M, Badmasti F, Masoumi M, Abdolrahimi F, Khanipour S, Hassanzadeh SM, Ghalami Nobar M, Yari F. Comparing mRNA expression and protein abundance in MDR Mycobacterium tuberculosis: Novel protein candidates, Rv0443, Rv0379 and Rv0147 as TB potential diagnostic or therapeutic targets. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00641. [PMID: 34189062 PMCID: PMC8220328 DOI: 10.1016/j.btre.2021.e00641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 11/25/2022]
Abstract
Tuberculosis (TB) is a sizable public health threat in the world. This study was conducted to determine the differential protein composition between susceptible and MDRTB strains. Tuberculosis proteins were extracted by Triton™ X-114 and ammonium sulfate. Two-dimensional gel electrophoresis protein spots were selected for identification by mass spectrometry and mRNA expression levels were measured by real- time PCR. 2DE-Western blot and T cell epitope prediction for identified proteins were made by the IEDB server. The result shows at least six protein spots (Rv0147, Rv3597c, Rv0379, Rv3699, Rv1392 and Rv0443) were differentially expressed in MDRTB isolates. However, difference in mRNA gene expression was not found in the six mRNA genes. 2DE-Western blot procedures indicated strong reaction against MDRTB proteins corresponds to 13, 16 and 55 kDa areas that might be used as new diagnostic tools. In conclusion, these MDRTB proteins identified in this study could be reliable TB diagnostic candidates or therapeutic targets.
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Affiliation(s)
- Alireza Hadizadeh Tasbiti
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shamsi Yari
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Morteza Masoumi
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
| | - Farid Abdolrahimi
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
| | - Sharareh Khanipour
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
| | | | - Mostafa Ghalami Nobar
- Reference Health Laboratory, Iran Ministry of Health and Medical Education, Tehran, Iran
| | - Fatemeh Yari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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134
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Zhao H, Zhu S, Zhao Q, Huang B, Liu G, Li Z, Wang L, Dong H, Han H. Molecular characterization and protective efficacy of a new conserved hypothetical protein of Eimeria tenella. ACTA ACUST UNITED AC 2021; 28:40. [PMID: 33944773 PMCID: PMC8095096 DOI: 10.1051/parasite/2021037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/15/2021] [Indexed: 11/14/2022]
Abstract
Eimeria tenella is an obligate intracellular parasite that actively invades cecal epithelial cells of chickens. This parasite encodes a genome of more than 8000 genes. However, more than 70% of the gene models for this species are currently annotated as hypothetical proteins. In this study, a conserved hypothetical protein gene of E. tenella, designated EtCHP18905, was cloned and identified, and its immune protective effects were evaluated. The open reading frame of EtCHP18905 was 1053bp and encoded a protein of 350 amino acids with a molecular weight of 38.7kDa. The recombinant EtCHP18905 protein (rEtCHP18905) was expressed in E. coli. Using western blot, the recombinant protein was successfully recognized by anti GST-Tag monoclonal antibody and anti-sporozoites protein rabbit serum. Real-time quantitative PCR analysis revealed that the EtCHP18905 mRNA levels were higher in sporozoites than in unsporulated oocysts, sporulated oocysts and second-generation merozoites. Western blot analysis showed that EtCHP18905 protein expression levels were lower in sporozoites than in other stages. Immunofluorescence analysis indicated that the EtCHP18905 protein was located on the surface of sporozoites and second-generation merozoites. Inhibition experiments showed that the ability of sporozoites to invade host cells was significantly decreased after treatment with the anti-rEtCHP18905 polyclonal antibody. Vaccination with rEtCHP18905 protein was able to significantly decrease mean lesion scores and oocyst outputs as compared to non-vaccinated controls. The results suggest that the rEtCHP18905 protein can induce partial immune protection against infection with E. tenella and could be an effective candidate for the development of new vaccines.
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Affiliation(s)
- Huanzhi Zhao
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China
| | - Shunhai Zhu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China
| | - Qiping Zhao
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China
| | - Bing Huang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China
| | - Guiling Liu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China - College of Life and Environment Sciences, Shanghai Normal University, 200234 Shanghai, PR China
| | - Zhihang Li
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China - College of Life and Environment Sciences, Shanghai Normal University, 200234 Shanghai, PR China
| | - Lu Wang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China
| | - Hui Dong
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China
| | - Hongyu Han
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, CAAS, 200241 Shanghai, PR China
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135
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Mathew AS, Gorick CM, Thim EA, Garrison WJ, Klibanov AL, Miller GW, Sheybani ND, Price RJ. Transcriptomic response of brain tissue to focused ultrasound-mediated blood-brain barrier disruption depends strongly on anesthesia. Bioeng Transl Med 2021; 6:e10198. [PMID: 34027087 PMCID: PMC8126816 DOI: 10.1002/btm2.10198] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022] Open
Abstract
Focused ultrasound (FUS) mediated blood-brain barrier disruption (BBBD) targets the delivery of systemically-administered therapeutics to the central nervous system. Preclinical investigations of BBBD have been performed on different anesthetic backgrounds; however, the influence of the choice of anesthetic on the molecular response to BBBD is unknown, despite its potential to critically affect interpretation of experimental therapeutic outcomes. Here, using bulk RNA sequencing, we comprehensively examined the transcriptomic response of both normal brain tissue and brain tissue exposed to FUS-induced BBBD in mice anesthetized with either isoflurane with medical air (Iso) or ketamine/dexmedetomidine (KD). In normal murine brain tissue, Iso alone elicited minimal differential gene expression (DGE) and repressed pathways associated with neuronal signaling. KD alone, however, led to massive DGE and enrichment of pathways associated with protein synthesis. In brain tissue exposed to BBBD (1 MHz, 0.5 Hz pulse repetition frequency, 0.4 MPa peak-negative pressure), we systematically evaluated the relative effects of anesthesia, microbubbles, and FUS on the transcriptome. Of particular interest, we observed that gene sets associated with sterile inflammatory responses and cell-cell junctional activity were induced by BBBD, regardless of the choice of anesthesia. Meanwhile, gene sets associated with metabolism, platelet activity, tissue repair, and signaling pathways, were differentially affected by BBBD, with a strong dependence on the anesthetic. We conclude that the underlying transcriptomic response to FUS-mediated BBBD may be powerfully influenced by anesthesia. These findings raise considerations for the translation of FUS-BBBD delivery approaches that impact, in particular, metabolism, tissue repair, and intracellular signaling.
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Affiliation(s)
- Alexander S. Mathew
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Catherine M. Gorick
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - E. Andrew Thim
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - William J. Garrison
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Radiology & Medical ImagingUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Alexander L. Klibanov
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Internal Medicine, Cardiovascular DivisionUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - G. Wilson Miller
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Radiology & Medical ImagingUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Natasha D. Sheybani
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Richard J. Price
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Radiology & Medical ImagingUniversity of VirginiaCharlottesvilleVirginiaUSA
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136
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Xie J, Zhao Y, Dong N, Tian X, Feng J, Liu P, Li M, Wang M, Ying X, Yuan J, Li B, Tian F, Qiu Y, Yan X. Proteomics and transcriptomics jointly identify the key role of oxidative phosphorylation in fluoride-induced myocardial mitochondrial dysfunction in rats. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 218:112271. [PMID: 33932654 DOI: 10.1016/j.ecoenv.2021.112271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
The regulation of mitochondrial function, which is dominated by oxidative phosphorylation (OXPHOs), is important in fluoride induced cardiovascular disease. Based on the previous study of fluoride-induced mitochondrial structure and membrane potential abnormalities, this study integrated ITRAQ protein quantification and RNA-Seq methods to analyze the sequencing data of rat myocardial tissue under fluoride exposure (0, 30, 60 and 90 mg/L). A total of 22 differentially expressed genes associated with the OXPHOs pathway were screened by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis, and were localizated by Interaction Network and calculated inter-genes and inter-omics correlations by Pearson correlation. In general, fluoride exposure can down-regulate genes related OXPHOs, particularly affecting the assembly of the complex I including Ndufa10, resulting in abnormal mitochondrial ATP synthesis and reduced myocardial energy supply. Most importantly, this study shows that the enriched information from the proteomics can explain the change process of energy production, but the specific molecules involved in energy supply cannot be obtained via transcriptomics information alone. Based on the results of transcriptional and protein analysis, our findings contribute to an innovative understanding of the pathways and molecular changes of myocardial injury induced by fluorosis.
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Affiliation(s)
- Jiaxin Xie
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Yannan Zhao
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Nisha Dong
- Heping Hospital Affiliated To Changzhi Medical College, Changzhi 046000, Shanxi, China
| | - Xiaolin Tian
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China; Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Jing Feng
- Laboratory of Cardiovascular Medicine, The Second Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Penghui Liu
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Meng Li
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Meng Wang
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Xiaodong Ying
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Jiyu Yuan
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Ben Li
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Fengjie Tian
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Yulan Qiu
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Xiaoyan Yan
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China.
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137
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Graw S, Chappell K, Washam CL, Gies A, Bird J, Robeson MS, Byrum SD. Multi-omics data integration considerations and study design for biological systems and disease. Mol Omics 2021; 17:170-185. [PMID: 33347526 PMCID: PMC8058243 DOI: 10.1039/d0mo00041h] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. Features such as the transcriptome, methylome, proteome, histone post-translational modifications and the microbiome all influence the host response to various diseases and cancers. Each of these platforms have technological limitations due to sample preparation steps, amount of material needed for sequencing, and sequencing depth requirements. These features provide a snapshot of one level of regulation in a system. The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. In recent years, there has been a push for the development of data integration methods. Each method specifically integrates a subset of omics data using approaches such as conceptual integration, statistical integration, model-based integration, networks, and pathway data integration. In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. The considerations discussed in this review should be regarded when developing new algorithms for integrating multi-omics data.
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Affiliation(s)
- Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Kevin Chappell
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Charity L Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
| | - Allen Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Jordan Bird
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Michael S Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
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138
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Männer L, Schell T, Provataris P, Haase M, Greve C. Inference of DNA methylation patterns in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200166. [PMID: 33813896 DOI: 10.1098/rstb.2020.0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mollusca are the second largest and arguably most diverse phylum of the animal kingdom. This is in sharp contrast to our very limited knowledge concerning epigenetic mechanisms including DNA methylation in this invertebrate group. Here, we inferred DNA methylation patterns by analysing the normalized dinucleotide CG content in protein-coding sequences and identified DNA methyltransferases (DNMT1 and 3) in published transcriptomes and genomes of 140 species across all eight classes of molluscs. Given the evolutionary age and morphological diversity of molluscs, we expected to find evidence for diverse methylation patterns. Our inferences suggest that molluscs possess substantial levels of DNA methylation in gene bodies as a rule. Yet, we found deviations from this general picture with regard to (i) the CpG observed/expected distributions indicating a reduction in DNA methylation in certain groups and (ii) the completeness of the DNMT toolkit. Reductions were evident in Caudofoveata, Solenogastres, Polyplacophora, Monoplacophora, as well as Scaphopoda. Heterobranchia and Oegopsida were remarkable as they lacked DNMT3, usually responsible for de novo methylation, yet showed signs of DNA methylation. Our survey may serve as guidance for direct empirical analyses of DNA methylation in molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Lisa Männer
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Soldmannstraße 23, 17489 Greifswald, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.,Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Martin Haase
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Soldmannstraße 23, 17489 Greifswald, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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139
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Martínez-Matías N, Chorna N, González-Crespo S, Villanueva L, Montes-Rodríguez I, Melendez-Aponte LM, Roche-Lima A, Carrasquillo-Carrión K, Santiago-Cartagena E, Rymond BC, Babu M, Stagljar I, Rodríguez-Medina JR. Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis. Sci Rep 2021; 11:7411. [PMID: 33795741 PMCID: PMC8016984 DOI: 10.1038/s41598-021-86671-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/15/2021] [Indexed: 02/06/2023] Open
Abstract
Functional analysis of the Mtl1 protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI). We observed upregulation of multiple heat shock proteins (HSPs), proteins associated with the formation of stress granules, and the phosphatase subunit of trehalose 6-phosphate synthase which suggests that mtl1Δ strains undergo intrinsic activation of a non-lethal heat stress response. Furthermore, quantitative global proteomic analysis conducted on TMT-labeled proteins combined with metabolome analysis revealed that mtl1Δ strains exhibit decreased levels of metabolites of carboxylic acid metabolism, decreased expression of anabolic enzymes and increased expression of catabolic enzymes involved in the metabolism of amino acids, with enhanced expression of mitochondrial respirasome proteins. These observations support the idea that Mtl1 protein controls the suppression of a non-lethal heat stress response under normal conditions while it plays an important role in metabolic regulatory mechanisms linked to TORC1 signaling that are required to maintain cellular homeostasis and optimal mitochondrial function.
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Affiliation(s)
- Nelson Martínez-Matías
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Nataliya Chorna
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Sahily González-Crespo
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Lilliam Villanueva
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Ingrid Montes-Rodríguez
- Comprehensive Cancer Center, University of Puerto Rico, Puerto Rico Medical Center, Rio Piedras, PR 00936-3027 USA
| | - Loyda M. Melendez-Aponte
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Abiel Roche-Lima
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Kelvin Carrasquillo-Carrión
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Ednalise Santiago-Cartagena
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
| | - Brian C. Rymond
- grid.266539.d0000 0004 1936 8438Department of Biology, University of Kentucky, Lexington, KY 40506 USA
| | - Mohan Babu
- grid.57926.3f0000 0004 1936 9131Department of Biochemistry, University of Regina, Regina, SK S4S 0A2 Canada
| | - Igor Stagljar
- grid.17063.330000 0001 2157 2938Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1 Canada ,grid.482535.d0000 0004 4663 8413Mediterranean Institute for Life Sciences, Split, Croatia
| | - José R. Rodríguez-Medina
- grid.267033.30000 0004 0462 1680Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00936-5067 USA
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140
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Miguel JC, Perez SE, Malek-Ahmadi M, Mufson EJ. Cerebellar Calcium-Binding Protein and Neurotrophin Receptor Defects in Down Syndrome and Alzheimer's Disease. Front Aging Neurosci 2021; 13:645334. [PMID: 33776745 PMCID: PMC7994928 DOI: 10.3389/fnagi.2021.645334] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
Cerebellar hypoplasia is a major characteristic of the Down syndrome (DS) brain. However, the consequences of trisomy upon cerebellar Purkinje cells (PC) and interneurons in DS are unclear. The present study performed a quantitative and qualitative analysis of cerebellar neurons immunostained with antibodies against calbindin D-28k (Calb), parvalbumin (Parv), and calretinin (Calr), phosphorylated and non-phosphorylated intermediate neurofilaments (SMI-34 and SMI-32), and high (TrkA) and low (p75NTR) affinity nerve growth factor (NGF) receptors as well as tau and amyloid in DS (n = 12), Alzheimer's disease (AD) (n = 10), and healthy non-dementia control (HC) (n = 8) cases. Our findings revealed higher Aβ42 plaque load in DS compared to AD and HC but no differences in APP/Aβ plaque load between HC, AD, and DS. The cerebellar cortex neither displayed Aβ40 containing plaques nor pathologic phosphorylated tau in any of the cases examined. The number and optical density (OD) measurements of Calb immunoreactive (-ir) PC soma and dendrites were similar between groups, while the number of PCs positive for Parv and SMI-32 were significantly reduced in AD and DS compared to HC. By contrast, the number of SMI-34-ir PC dystrophic axonal swellings, termed torpedoes, was significantly greater in AD compared to DS. No differences in SMI-32- and Parv-ir PC OD measurements were observed between groups. Conversely, total number of Parv- (stellate/basket) and Calr (Lugaro, brush, and Golgi)-positive interneurons were significantly reduced in DS compared to AD and HC. A strong negative correlation was found between counts for Parv-ir interneurons, Calr-ir Golgi and brush cells, and Aβ42 plaque load. Number of TrkA and p75NTR positive PCs were reduced in AD compared to HC. These findings suggest that disturbances in calcium binding proteins play a critical role in cerebellar neuronal dysfunction in adults with DS.
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Affiliation(s)
- Jennifer C. Miguel
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, United States
| | - Sylvia E. Perez
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, United States
| | - Michael Malek-Ahmadi
- Department of Biomedical Informatics, Banner Alzheimer's Institute, Phoenix, AZ, United States
| | - Elliott J. Mufson
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, United States
- Department of Neurology, Barrow Neurological Institute, Phoenix, AZ, United States
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141
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Dail ME, Brino MLM, Chambers JE. Effects of novel brain-penetrating oxime acetylcholinesterase reactivators on sarin surrogate-induced changes in rat brain gene expression. J Biochem Mol Toxicol 2021; 35:1-10. [PMID: 33682265 DOI: 10.1002/jbt.22755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/28/2021] [Accepted: 02/24/2021] [Indexed: 11/11/2022]
Abstract
Past assassinations and terrorist attacks demonstrate the need for a more effective antidote against nerve agents and other organophosphates (OP) that cause brain damage through inhibition of acetylcholinesterase (AChE). Our lab has invented a platform of phenoxyalkyl pyridinium oximes (US patent 9,277,937) that demonstrate the ability to cross the blood-brain barrier in in vivo rat tests with a sarin surrogate nitrophenyl isopropyl methylphosphonate (NIMP) and provide evidence of brain penetration by reducing cessation time of seizure-like behaviors, accumulation of glial fibrillary acidic protein (GFAP), and hippocampal neuropathology, as opposed to the currently approved oxime, 2-pyridine aldoxime methyl chloride (2-PAM). Using two of the novel oximes (Oximes 1 and 20), this project examined whether gene expression changes might help explain this protection. Expression changes in the piriform cortex were examined using polymerase chain reaction arrays for inflammatory cytokines and receptors. The hippocampus was examined via quantitative polymerase chain reaction for the expression of immediate-early genes involved in brain repair (Bdnf), increasing neurotoxicity (Fos), and apoptosis control (Jdp2, Bcl2l1, Bcl2l11). In the piriform cortex, NIMP significantly stimulated expression for the macrophage inflammatory proteins CCL4, IL-1A, and IL-1B. Oxime 20 by itself elicited the most changes. When it was given therapeutically post-NIMP, the largest change occurred: a 310-fold repression of the inflammatory cytokine, CCL12. In the hippocampus, NIMP increased the expression of the neurotoxicity marker Fos and decreased the expression of neuroprotective Bdnf and antiapoptotic Bcl2l1. Compared with 2-PAM, Oxime 20 stimulated Bcl2l1 expression more and returned expression closer to the vehicle control values.
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Affiliation(s)
- Mary E Dail
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, Mississippi State University, College of Veterinary Medicine, Mississippi State, United States, USA
| | - Meghan L M Brino
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, Mississippi State University, College of Veterinary Medicine, Mississippi State, United States, USA
| | - Janice E Chambers
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, Mississippi State University, College of Veterinary Medicine, Mississippi State, United States, USA
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142
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Lu G, Shan S, Zainab B, Ayaz Z, He J, Xie Z, Rashid U, Zhang D, Mehmood Abbasi A. Novel vaccine design based on genomics data analysis: A review. Scand J Immunol 2021; 93:e12986. [PMID: 33043473 DOI: 10.1111/sji.12986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/04/2020] [Accepted: 10/05/2020] [Indexed: 12/28/2022]
Abstract
Modification of pathogenic strains with the passage of time is responsible for evolution in the timeline of vaccine development for last 30 years. Recent advancements in computational vaccinology on the one hand and genome sequencing approaches on the other have generated new hopes in vaccine development. The aim of this review was to discuss the evolution of vaccines, their characteristics and limitations. In this review, we highlighted the evolution of vaccines, from first generation to the current status, pointing out how different vaccines have emerged and different approaches that are being followed up in the development of more rational vaccines against a wide range of diseases. Data were collected using Google Scholar, Web of Science, Science Direct, Web of Knowledge, Scopus and Science Hub, whereas computational tools such as NCBI, GeneMANIA and STRING were used to analyse the pathways of vaccine action. Innovative tools, such as computational tools, recombinant technologies and intra-dermal devices, are currently being investigated in order to improve the immunological response. New technologies enlightened the interactions of host proteins with pathogenic proteins for vaccine candidate development, but still there is a need of integrating transcriptomic and proteomic approaches. Although immunization with genomics data is a successful approach, its advantages must be assessed case by case and its applicability depends on the nature of the agent to be immunized, the nature of the antigen and the type of immune response required to achieve effective protection.
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Affiliation(s)
- Guangli Lu
- Institute of Business, School of Business, Henan University, Henan, China
| | - Sharui Shan
- The First Affiliated Hospital of Jinan University (Guangzhou Overseas Chinese Hospital), Guangzhou, China
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Bibi Zainab
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zainab Ayaz
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Jialiang He
- School of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Zhenxing Xie
- Basic School of Medicine, Henan University, Kaifeng, China
| | - Umer Rashid
- Department of Chemistry, COMSATS University Islamabad, Islamabad, Pakistan
| | - Dalin Zhang
- Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Arshad Mehmood Abbasi
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
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143
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Pereiro I, Aubert J, Kaigala GV. Micro-scale technologies propel biology and medicine. BIOMICROFLUIDICS 2021; 15:021302. [PMID: 33948133 PMCID: PMC8081554 DOI: 10.1063/5.0047196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/05/2021] [Indexed: 05/05/2023]
Abstract
Historically, technology has been central to new discoveries in biology and progress in medicine. Among various technologies, microtechnologies, in particular, have had a prominent role in the revolution experienced by the life sciences in the last few decades, which will surely continue in the years to come. In this Perspective, we illustrate how microtechnologies, with a focus on microfluidics, have evolved in trends/waves to tackle the boundary of knowledge in the life sciences. We provide illustrative examples of technology-enabled biological breakthroughs and their current and future use in clinics. Finally, we take a closer look at the translational process to understand why the incorporation of new micro-scale technologies in medicine has been comparatively slow so far.
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144
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Chiou AE, Liu C, Moreno-Jiménez I, Tang T, Wagermaier W, Dean MN, Fischbach C, Fratzl P. Breast cancer-secreted factors perturb murine bone growth in regions prone to metastasis. SCIENCE ADVANCES 2021; 7:eabf2283. [PMID: 33731354 PMCID: PMC7968847 DOI: 10.1126/sciadv.abf2283] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/27/2021] [Indexed: 05/03/2023]
Abstract
Breast cancer frequently metastasizes to bone, causing osteolytic lesions. However, how factors secreted by primary tumors affect the bone microenvironment before the osteolytic phase of metastatic tumor growth remains unclear. Understanding these changes is critical as they may regulate metastatic dissemination and progression. To mimic premetastatic bone adaptation, immunocompromised mice were injected with MDA-MB-231-conditioned medium [tumor-conditioned media (TCM)]. Subsequently, the bones of these mice were subjected to multiscale, correlative analysis including RNA sequencing, histology, micro-computed tomography, x-ray scattering analysis, and Raman imaging. In contrast to overt metastasis causing osteolysis, TCM treatment induced new bone formation that was characterized by increased mineral apposition rate relative to control bones, altered bone quality with less matrix and more carbonate substitution, and the deposition of disoriented mineral near the growth plate. Our study suggests that breast cancer-secreted factors may promote perturbed bone growth before metastasis, which could affect initial seeding of tumor cells.
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Affiliation(s)
- Aaron E Chiou
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Chuang Liu
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Inés Moreno-Jiménez
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Tengteng Tang
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Wolfgang Wagermaier
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Mason N Dean
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - Peter Fratzl
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.
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145
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Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields. Genes (Basel) 2021; 12:genes12020299. [PMID: 33672614 PMCID: PMC7924190 DOI: 10.3390/genes12020299] [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: 01/27/2021] [Revised: 02/10/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
In cells, intrinsic endogenous direct current (DC) electric fields (EFs) serve as morphogenetic cues and are necessary for several important cellular responses including activation of multiple signaling pathways, cell migration, tissue regeneration and wound healing. Endogenous DC EFs, generated spontaneously following injury in physiological conditions, directly correlate with wound healing rate, and different cell types respond to these EFs via directional orientation and migration. Application of external DC EFs results in electrode polarity and is known to activate intracellular signaling events in specific direction. In contrast, alternating current (AC) EFs are known to induce continuous bidirectional flow of charged particles without electrode polarity and also minimize electrode corrosion. In this context, the present study is designed to study effects of AC EFs on corneal epithelial cell gene and protein expression profiles in vitro. We performed gene and antibody arrays, analyzed the data to study specific influence of AC EFs, and report that AC EFs has no deleterious effect on epithelial cell function. Gene Ontology results, following gene and protein array data analysis, showed that AC EFs influence similar biological processes that are predominantly responsive to organic substance, chemical, or external stimuli. Both arrays activate cytokine–cytokine receptor interaction, MAPK and IL-17 signaling pathways. Further, in comparison to the gene array data, the protein array data show enrichment of diverse activated signaling pathways through several interconnecting networks.
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146
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Asai M, Sheehan G, Li Y, Robertson BD, Kavanagh K, Langford PR, Newton SM. Innate Immune Responses of Galleria mellonella to Mycobacterium bovis BCG Challenge Identified Using Proteomic and Molecular Approaches. Front Cell Infect Microbiol 2021; 11:619981. [PMID: 33634038 PMCID: PMC7900627 DOI: 10.3389/fcimb.2021.619981] [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: 10/22/2020] [Accepted: 01/04/2021] [Indexed: 01/10/2023] Open
Abstract
The larvae of the insect Galleria mellonella, have recently been established as a non-mammalian infection model for the Mycobacterium tuberculosis complex (MTBC). To gain further insight into the potential of this model, we applied proteomic (label-free quantification) and transcriptomic (gene expression) approaches to characterise the innate immune response of G. mellonella to infection with Mycobacterium bovis BCG lux over a 168 h time course. Proteomic analysis of the haemolymph from infected larvae revealed distinct changes in the proteome at all time points (4, 48, 168 h). Reverse transcriptase quantitative PCR confirmed induction of five genes (gloverin, cecropin, IMPI, hemolin, and Hdd11), which encoded proteins found to be differentially abundant from the proteomic analysis. However, the trend between gene expression and protein abundance were largely inconsistent (20%). Overall, the data are in agreement with previous phenotypic observations such as haemocyte internalization of mycobacterial bacilli (hemolin/β-actin), formation of granuloma-like structures (Hdd11), and melanization (phenoloxidase activating enzyme 3 and serpins). Furthermore, similarities in immune expression in G. mellonella, mouse, zebrafish and in vitro cell-line models of tuberculosis infection were also identified for the mechanism of phagocytosis (β-actin). Cecropins (antimicrobial peptides), which share the same α-helical motif as a highly potent peptide expressed in humans (h-CAP-18), were induced in G. mellonella in response to infection, giving insight into a potential starting point for novel antimycobacterial agents. We believe that these novel insights into the innate immune response further contribute to the validation of this cost-effective and ethically acceptable insect model to study members of the MTBC.
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Affiliation(s)
- Masanori Asai
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gerard Sheehan
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Ireland.,Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Yanwen Li
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Kevin Kavanagh
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Ireland
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sandra M Newton
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
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147
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Kochanowski M, Dąbrowska J, Różycki M, Karamon J, Sroka J, Cencek T. Proteomic Profiling Reveals New Insights into the Allergomes of Anisakis simplex, Pseudoterranova decipiens, and Contracaecum osculatum. J Parasitol 2021; 106:572-588. [PMID: 32906150 DOI: 10.1645/19-75] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Anisakis simplex, Pseudoterranova decipiens, and Contracaecum osculatum third-stage larvae (L3) are fish-borne nematodes that can cause human anisakidosis. Although A. simplex is a known source of allergens, knowledge about the allergic potential of P. decipiens and C. osculatum is limited. Therefore, we performed comparative proteomic profiling of A. simplex, P. decipiens, and C. osculatum L3 larvae using liquid chromatography-tandem mass spectrometry. In total, 645, 397, and 261 proteins were detected in A. simplex, P. decipiens, and C. osculatum L3 larvae, respectively. Western blot analysis confirmed the cross-reactivity of anti-A. simplex immunoglobulin (Ig)G antibodies with protein extracts from P. decipiens and C. osculatum L3 larvae. The identified proteins of the Anisakidae proteomes were characterized by label-free quantification and functional analysis, and proteins involved in many essential biological mechanisms, such as parasite survival, were identified. In the proteome of A. simplex 14, the following allergens were identified: Ani s 1, Ani s 2 (2 isomers), Ani s 3 (2 isomers), Ani s 4, Ani s 8, Ani s 9, Ani s 10, Ani s 11-like, Ani s 13, Ani s fructose 1,6-bisphosphatase, Ani s phosphatidylethanolamine-binding protein (PEPB), and Thu a 3.0101. The following 8 allergens were detected in P. decipiens: Ani s 2, Ani s 3 (2 isomers), Ani s 5, Ani s 8, Ani s 9, Ani s PEPB, and Ani s troponin. In C. osculatum 4, the following allergens were identified: Ani s 2, Ani s 5, Ani s 13, and Asc l 3. Furthermore, 28 probable allergens were predicted in A. simplex and P. decipiens, whereas in C. osculatum, 25 possible allergens were identified. Among the putative allergens, heat shock proteins were most frequently detected, followed by paramyosin, peptidyl-prolyl cis-trans isomerase, enolase, and tropomyosin. We provide a new proteomic data set that could be beneficial for the discovery of biomarkers or drug target candidates. Furthermore, our findings showed that in addition to A. simplex, P. decipiens and C. osculatum should also be considered as potential sources of allergens that could lead to IgE-mediated hypersensitivity.
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Affiliation(s)
- Maciej Kochanowski
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 Puławy, Poland
| | - Joanna Dąbrowska
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 Puławy, Poland
| | - Mirosław Różycki
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 Puławy, Poland
| | - Jacek Karamon
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 Puławy, Poland
| | - Jacek Sroka
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 Puławy, Poland
| | - Tomasz Cencek
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 Puławy, Poland
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148
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Tsamir-Rimon M, Ben-Dor S, Feldmesser E, Oppenhimer-Shaanan Y, David-Schwartz R, Samach A, Klein T. Rapid starch degradation in the wood of olive trees under heat and drought is permitted by three stress-specific beta amylases. THE NEW PHYTOLOGIST 2021; 229:1398-1414. [PMID: 32880972 DOI: 10.1111/nph.16907] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Carbon reserve use is a major drought response in trees, enabling tree survival in conditions prohibiting photosynthesis. However, regulation of starch metabolism under drought at the whole-tree scale is still poorly understood. To this end, we combined measurements of nonstructural carbohydrates (NSCs), tree physiology and gene expression. The experiment was conducted outside on olive trees in pots under 90 d of seasonal spring to summer warming. Half of the trees were also subjected to limited water conditions for 28 d. Photosynthesis decreased in dehydrating trees from 19 to 0.5 µmol m-2 s-1 during the drought period. Starch degradation and mannitol production were a major drought response, with mannitol increasing to 71% and 41% out of total NSCs in shoots and roots, respectively. We identified the gene family members potentially relevant either to long-term or stress-induced carbon storage. Partitioning of expression patterns among β amylase and starch synthase family members was observed, with three β amylases possibly facilitating the rapid starch degradation under heat and drought. Our results suggest a group of stress-related, starch metabolism genes, correlated with NSC fluctuations during drought and recovery. The daily starch metabolism gene expression was different from the stress-mode starch metabolism pattern, where some genes are uniquely expressed during the stress-mode response.
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Affiliation(s)
- Mor Tsamir-Rimon
- Plant & Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Shifra Ben-Dor
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ester Feldmesser
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yaara Oppenhimer-Shaanan
- Plant & Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rakefet David-Schwartz
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7505101, Israel
| | - Alon Samach
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Tamir Klein
- Plant & Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel
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149
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Gautam S, Sharma D, Goel A, Patil SA, Bisht D. Insights into Mycobacterium leprae Proteomics and Biomarkers-An Overview. Proteomes 2021; 9:7. [PMID: 33573064 PMCID: PMC7931084 DOI: 10.3390/proteomes9010007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Although leprosy is curable, the identification of biomarkers for the early diagnosis of leprosy would play a pivotal role in reducing transmission and the overall prevalence of the disease. Leprosy-specific biomarkers for diagnosis, particularly for the paucibacillary disease, are not well defined. Therefore, the identification of new biomarkers for leprosy is one of the prime themes of leprosy research. Studying Mycobacterium leprae, the causative agent of leprosy, at the proteomic level may facilitate the identification, quantification, and characterization of proteins that could be potential diagnostics or targets for drugs and can help in better understanding the pathogenesis. This review aims to shed light on the knowledge gained to understand leprosy or its pathogen employing proteomics and its role in diagnosis.
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Affiliation(s)
- Sakshi Gautam
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
- Department of Biotechnology, GLA University, NH-2, Mathura-Delhi Road, Mathura 281406, India;
| | - Devesh Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
| | - Anjana Goel
- Department of Biotechnology, GLA University, NH-2, Mathura-Delhi Road, Mathura 281406, India;
| | - Shripad A. Patil
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
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150
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Wang Y, Sang Z, Xu S, Xu Q, Zeng X, Jabu D, Yuan H. Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry. Gigascience 2021; 9:5775614. [PMID: 32126136 PMCID: PMC7053489 DOI: 10.1093/gigascience/giaa019] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/18/2020] [Accepted: 02/12/2020] [Indexed: 12/25/2022] Open
Abstract
Background Tibetan hull-less barley (Hordeum vulgare L. var. nudum) is one of the primary crops cultivated in the mountains of Tibet and encounters low temperature, high salinity, and drought. Specifically, drought is one of the major abiotic stresses that affect and limit Tibetan barley growth. Osmotic stress is often simultaneously accompanied by drought conditions. Thus, to improve crop yield, it is critical to explore the molecular mechanism governing the responses of hull-less barley to osmotic/drought stress conditions. Findings In this study, we used quantitative proteomics by data-independent acquisition mass spectrometry to investigate protein abundance changes in tolerant (XL) and sensitive (DQ) cultivars. A total of 6,921 proteins were identified and quantified in all samples. Two distinct strategies based on pairwise and time-course comparisons were utilized in the comprehensive analysis of differentially abundant proteins. Further functional analysis of differentially abundant proteins revealed that some hormone metabolism–associated and phytohormone abscisic acid–induced genes are primarily affected by osmotic stress. Enhanced regulation of reactive oxygen species (may promote the tolerance of hull-less barley under osmotic stress. Moreover, we found that some regulators, such as GRF, PR10, MAPK, and AMPK, were centrally positioned in the gene regulatory network, suggesting that they may have a dominant role in the osmotic stress response of Tibetan barley. Conclusions Our findings highlight a subset of proteins and processes that are involved in the alleviation of osmotic stress. In addition, this study provides a large-scale and multidimensional proteomic data resource for the further investigation and improvement of osmotic/drought stress tolerance in hull-less barley or other plant species.
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Affiliation(s)
- Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China.,Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China
| | - Zha Sang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China.,Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China
| | - Shaohang Xu
- Deepxomics Co., Ltd, No.2082 Shenyan Road, Yantian District., Shenzhen 518000, Guangdong, China
| | - Qijun Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China.,Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China.,Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China
| | - Dunzhu Jabu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China.,Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China.,Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, No.130 Jinzhu West Road, Chengguan District, Lhasa 850002, Tibet, China
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