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Saini A, Kumar V, Tomar AK, Sharma A, Yadav S. Multimerin 1 aids in the progression of ovarian cancer possibly via modulation of DNA damage response and repair pathways. Mol Cell Biochem 2023; 478:2395-2403. [PMID: 36723821 DOI: 10.1007/s11010-023-04668-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/16/2023] [Indexed: 02/02/2023]
Abstract
Ovarian cancer is one of the leading causes of deaths among women. Despite advances in the treatment regimes, a high rate of diagnosis in the advanced stage makes it almost an incurable malignancy. Thus, more research efforts are required to identify potential molecular markers for early detection of the disease and therapeutic targets to augment the survival rate of ovarian cancer patients. Previously, in this context, we identified dysregulated expression of multimerin 1 (MMRN1) in ovarian cancer. To elucidate the relationship between MMRN1 expression and ovarian cancer progression, siRNA-based MMRN1 knockdown was employed and various cell assays were performed to study its effect on ovarian cancer cells. In addition, network of dysregulated proteins was identified by quantitative proteomics and associated pathways were explored by bioinformatics analysis. MMRN1 silencing showed a significant reduction in cell viability, adhesion, migration, and invasion and a high frequency of cell apoptosis. Label-free quantitative proteomics and in-depth statistical analysis identified 448 dysregulated proteins, majority of which were overexpressed in MMRN1 knockdown cells. The pathways overrepresented in ovarian cancer were DNA replication, mismatch repair, nucleotide excision repair, and cell cycle regulation. Conclusively, the findings of this study suggest that MMRN1 aids in the progression of ovarian cancer via modulation of DNA damage response and repair pathways.
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Affiliation(s)
- Abhinav Saini
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 11029, India
| | - Vikrant Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 11029, India
| | - Anil Kumar Tomar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 11029, India
| | - Alpana Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 11029, India
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 11029, India.
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2
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Safi AUR, Bendixen E, Rahman H, Khattak B, Wu W, Ullah W, Khan N, Ali F, Yasin N, Qasim M. Molecular identification and differential proteomics of drug resistant Salmonella Typhi. Diagn Microbiol Infect Dis 2023; 105:115883. [PMID: 36731197 DOI: 10.1016/j.diagmicrobio.2022.115883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 12/04/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
This study aimed to elucidate differentially expressed proteins in drug resistant Salmonella Typhi. Among 100 samples, S. typhi were identified in 43 samples. In drug susceptibility profile, 95.3% (41/43), 80% (35/43) and 70% (30/43) resistances were observed against Nalidixic acid, Ampicillin, and Chloramphenicol respectively. No resistance was observed against Imipenum and Azithromycin while only 11% (5/43) isolates were found resistant to Ceftriaxone. Mass spectrometric differential analysis resulted in 23 up-regulated proteins in drug resistant isolates. Proteins found up-regulated are involved in virulence (vipB, galU, tufA, and lpp1), translation (rpsF, rpsG, rplJ, and rplR), antibiotic resistance (zwf, phoP, and ompX), cell metabolism (metK, ftsZ, pepD, and secB), stress response (ridA, rbfA, and dps), housekeeping (gapA and eno) and hypothetical proteins including ydfZ, t1802, and yajQ. These proteins are of diverse nature and functions but highly interconnected. Further characterization may be helpful for elucidation of new biomarker proteins and therapeutic drug targets.
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Affiliation(s)
- Aziz Ur Rehman Safi
- Department of Microbiology, Kohat University of Science and Technology, Kohat Pakistan
| | - Emoke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C Denmark
| | - Hazir Rahman
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan Pakistan
| | - Baharullah Khattak
- Department of Microbiology, Kohat University of Science and Technology, Kohat Pakistan
| | - Wei Wu
- College of Animal Sciences and Technology, Southwest University, Chongqing China
| | - Waheed Ullah
- Department of Microbiology, Kohat University of Science and Technology, Kohat Pakistan
| | - Nasar Khan
- Department of Microbiology, Kohsar University Murree, Kashmir Point, Punjab, Pakistan
| | - Farhad Ali
- Department of Microbiology, Kohat University of Science and Technology, Kohat Pakistan
| | - Nusrat Yasin
- Department of Microbiology, Kohat University of Science and Technology, Kohat Pakistan
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology, Kohat Pakistan.
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Wang B, Pan X, Wang F, Liu L, Jia J. Photoprotective carbon redistribution in mixotrophic Haematococcus pluvialis under high light stress. Bioresour Technol 2022; 362:127761. [PMID: 35961507 DOI: 10.1016/j.biortech.2022.127761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
Mixotrophy of Haematococcus pluvialis is a potential strategy for producing astaxanthin. However, this strategy has not been extensively commercialized because the mixotrophic mechanisms by which H. pluvialis overcomes high light stress are unclear. This study analyzed the biochemical compositions and differential proteomics of mixotrophic H. pluvialis under different light conditions. High light exposure substantially increased astaxanthin, carbohydrate, and fatty acid contents. A total of 119 and 81 proteins were significantly up- and down-regulated after two days of high light exposure. These proteins mainly enriched pathways for photosynthetic metabolism, glyoxylate cycle, and biosynthesis of secondary metabolites. This study proposed a regulatory model through which mixotrophic H. pluvialis copes with high light stress. The model includes pathways for modulating photosynthetic apparatus, increasing astaxanthin accumulation by enhancing photorespiration, pentose phosphate and Embden-Meyerhof-Parna pathways, while thickening the cell wall by malate-oxaloacetate shuttle.
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Affiliation(s)
- Baobei Wang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou 362000, China; Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou 362000, China; Key Laboratory of Inshore Resources and Biotechnology, Fujian Province University, Quanzhou 362000, China
| | - Xueshan Pan
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Bengbu 233030, China
| | - Fang Wang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lulu Liu
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou 362000, China; College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jing Jia
- SDIC Microalgae Biotechnology Center, SDIC Biotechnology Investment Co. Ltd., State Development and Investment Corporation, Beijing 100034, China; Beijing Key Laboratory of Microalgae Bioenergy and Bioresource, Beijing 100142, China.
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Zhan X, Li J, Guo Y, Golubnitschaja O. Mass spectrometry analysis of human tear fluid biomarkers specific for ocular and systemic diseases in the context of 3P medicine. EPMA J 2021; 12:449-475. [PMID: 34876936 PMCID: PMC8639411 DOI: 10.1007/s13167-021-00265-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/03/2021] [Indexed: 12/23/2022]
Abstract
Over the last two decades, a large number of non-communicable/chronic disorders reached an epidemic level on a global scale such as diabetes mellitus type 2, cardio-vascular disease, several types of malignancies, neurological and eye pathologies-all exerted system's enormous socio-economic burden to primary, secondary, and tertiary healthcare. The paradigm change from reactive to predictive, preventive, and personalized medicine (3PM/PPPM) has been declared as an essential transformation of the overall healthcare approach to benefit the patient and society at large. To this end, specific biomarker panels are instrumental for a cost-effective predictive approach of individualized prevention and treatments tailored to the person. The source of biomarkers is crucial for specificity and reliability of diagnostic tests and treatment targets. Furthermore, any diagnostic approach preferentially should be noninvasive to increase availability of the biomaterial, and to decrease risks of potential complications as well as concomitant costs. These requirements are clearly fulfilled by tear fluid, which represents a precious source of biomarker panels. The well-justified principle of a "sick eye in a sick body" makes comprehensive tear fluid biomarker profiling highly relevant not only for diagnostics of eye pathologies but also for prediction, prognosis, and treatment monitoring of systemic diseases. One prominent example is the Sicca syndrome linked to a cascade of severe complications that include dry eye, neurologic, and oncologic diseases. In this review, protein profiles in tear fluid are highlighted and corresponding biomarkers are exemplified for several relevant pathologies, including dry eye disease, diabetic retinopathy, cancers, and neurological disorders. Corresponding analytical approaches such as sample pre-processing, differential proteomics, electrophoretic techniques, high-performance liquid chromatography (HPLC), enzyme-linked immuno-sorbent assay (ELISA), microarrays, and mass spectrometry (MS) methodology are detailed. Consequently, we proposed the overall strategies based on the tear fluid biomarkers application for 3P medicine practice. In the context of 3P medicine, tear fluid analytical pathways are considered to predict disease development, to target preventive measures, and to create treatment algorithms tailored to individual patient profiles.
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Affiliation(s)
- Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, 250117 Shandong China
- Medical Science and Technology Innovation Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, 250117 Shandong China
- Gastroenterology Research Institute and Clinical Center, Shandong First Medical University, 38 Wuying Shan Road, Jinan, Shandong 250031 People’s Republic of China
| | - Jiajia Li
- Medical Science and Technology Innovation Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, 250117 Shandong China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan China
| | - Yuna Guo
- Medical Science and Technology Innovation Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, 250117 Shandong China
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-University of Bonn, Sigmund-Freud-Str 25, 53105 Bonn, Germany
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Schnaars V, Wöhlbrand L, Scheve S, Hinrichs C, Reinhardt R, Rabus R. Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. Microb Physiol 2021; 31:1-20. [PMID: 33611323 PMCID: PMC8315694 DOI: 10.1159/000513383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/19/2022]
Abstract
The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.
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Affiliation(s)
- Vanessa Schnaars
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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Lin W, Xu X, Lv R, Huang W, Ul Haq H, Gao Y, Ren H, Lan C, Tian B. Differential proteomics reveals main determinants for the improved pectinase activity in UV-mutagenized Aspergillus niger strain. Biotechnol Lett 2021; 43:909-918. [PMID: 33449253 DOI: 10.1007/s10529-020-03075-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/26/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES To reveal the potential mechanism and key determinants that contributed to the improved pectinase activity in Aspergillus niger mutant EIMU2, which was previously obtained by UV-mutagenesis from the wild-type A. niger EIM-6. RESULTS Proteomic analysis for Aspergillus niger EIMU2 by two-dimensional electrophoresis demonstrated that mutant EIMU2 harbored a multiple enzyme system for the degradation of pectin, mainly constituting by main-chain-cleaving enzymes polygalacturonase, pectate lyase, pectinesterase, and some accessory enzymes rhamnogalacturonan lyase and arabinofuranosidase. Further quantitatively differential proteomic analysis revealed that the quantities of four proteins, pectinesterase, rhamnogalacturonan lyase A, DNA-directed RNA polymerase A, and a hypothetical protein in strain EIMU2 were much higher than those in EIM-6. PCR amplification, sequencing and alignment analysis of genes for the two main members of pectin-degrading enzymes, pectate lyase and polygalacturonase showed that their sequences were completely consistent in A. niger EIM-6 and mutant EIMU2. CONCLUSIONS The result demonstrated that the improved pectinase activity by UV-mutagenesis in A. niger EIMU2 was probably contributed to the up-regulated expression of rhamnogalacturonan lyase, or pectinesterase, which resulted in the optimization of synergy amongst different components of pectin-degrading enzymes.
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Affiliation(s)
- Weiling Lin
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China.,Fujian Health College, Fuzhou, 350101, Fujian, China
| | - Xiaohong Xu
- Library, Fujian Normal University, Fuzhou, 350108, Fujian, China
| | - Ruirui Lv
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China
| | - Wei Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China.,Institute of Agricultural Quality Standards and Testing Technology Research, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Hafeez Ul Haq
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China
| | - Yuanyuan Gao
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China
| | - Hongli Ren
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China
| | - Canhua Lan
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China
| | - Baoyu Tian
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, No.8, Shangsan Road, Cangshan District, Fuzhou, 350108, Fujian, China.
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7
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Niada S, Giannasi C, Magagnotti C, Andolfo A, Brini AT. Proteomic analysis of extracellular vesicles and conditioned medium from human adipose-derived stem/stromal cells and dermal fibroblasts. J Proteomics 2020; 232:104069. [PMID: 33309826 DOI: 10.1016/j.jprot.2020.104069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/23/2020] [Accepted: 11/29/2020] [Indexed: 12/19/2022]
Abstract
Conditioned medium (CM) and extracellular vesicles (EV) from Adipose-derived Stem/stromal cells (ASC) and Dermal fibroblasts (DF) represent promising tools for therapeutic applications. Which one should be preferred is still under debate and no direct comparison of their proteome has been reported yet. Here, we apply quantitative proteomics to explore the protein composition of CM and EV from the two cell types. Data are available via ProteomeXchange (identifier PXD020219). We identified 1977 proteins by LC-MS/MS proteomic analysis. Unsupervised clustering analysis and PCA recognized CM and EV as separate groups. We identified 68 and 201 CM and EV specific factors. CM were enriched in proteins of endoplasmic reticulum, Golgi apparatus and lysosomes, whereas EV contained a large amount of GTPases, ribosome and translation factors. The analysis of ASC and DF secretomes revealed the presence of cell type-specific proteins. ASC-CM and -EV carried factors involved in ECM organization and immunological regulation, respectively. Conversely, DF-CM and -EV were enriched in epithelium development associated factors and -EV in Wnt signaling factors. In conclusion, this analysis provides evidence of a different protein composition between CM and EV and of the presence of cell type-specific bioactive mediators suggesting their specific future use as advanced therapy medicinal products. SIGNIFICANCE: The use of cell secretome presents several advantages over cell therapy such as the lower risks associated to the administration step and the avoidance of any potential risk of malignant transformation. The main secretome preparations consist in concentrated conditioned medium (CM) and extracellular vesicles (EV). Both of them showed well-documented therapeutic potentials. However, it is still not clear in which case it should be better to use one preparation over the other and an exhaustive comparison between their proteome has not been performed yet. The choice of the cell source is another relevant aspect that still needs to be addressed. In order to shed light on these questions we explored the protein composition of CM and EV obtained from Adipose-derived Stem/stromal Cells (ASC) and Dermal Fibroblasts (DF), by a comprehensive quantitative proteomics approach. The analysis showed a clear distinction between CM and EV proteome. CM were enriched in proteins of endoplasmic reticulum, Golgi apparatus and lysosomes, whereas EV contained a large amount of GTPases, ribosome and translation-related factors. Furthermore, the analysis of ASC and DF secretomes revealed specific biological processes for the different cell products. ASC secretome presented factors involved in ECM organization (hyaluronan and glycosaminoglycan metabolism) and immunological regulation (e.g. macrophage and IkB/NFkB signaling regulation), respectively. On the other hand, DF-CM and -EV were both enriched in epithelium development associated factors, whilst DF-CM in proteins involved in cellular processes regulation and -EV in Wnt signaling factors. In conclusion, our study shed a light on the different protein composition of CM and EV of two promising cell types, spanning from basic processes involved in secretion to specific pathways supporting their therapeutic potential and their possible future use as advanced therapy medicinal products.
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Affiliation(s)
| | | | - Cinzia Magagnotti
- Proteomics and Metabolomics Facility (ProMeFa), IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Annapaola Andolfo
- Proteomics and Metabolomics Facility (ProMeFa), IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Anna Teresa Brini
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy; Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy.
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8
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Jain P, Ojha SK, Kumar V, Bakhshi S, Singh S, Yadav S. Differential seminal plasma proteome signatures of acute lymphoblastic leukemia survivors. Reprod Biol 2019; 19:322-328. [PMID: 31711845 DOI: 10.1016/j.repbio.2019.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 02/07/2023]
Abstract
With advances in therapeutic methods, there is a high survival rate among leukemia patients, of an extent more than 80%. However, chemotherapeutic drugs used to treat these patients have adverse effects on their overall health profile including fertility. The primary aim of this study was to identify differentially expressed proteins in seminal plasma of acute lymphoblastic leukemia (ALL) survivors compared to age-matched healthy controls, which can provide molecular basis of idiopathic infertility in such survivors. Differential proteome profiling was performed by 2D-differential in-gel electrophoresis, protein spots were identified by mass spectrometry and selective differentially expressed proteins (DEPs) were validated by western blotting and ELISA method. Out of eight DEPs identified, five proteins (isocitrate dehydrogenase 1, semenogelin 1, lactoferrin, prolactin-inducible protein, and human serum albumin) were upregulated and three (pepsinogen, prostate specific antigen and prostatic acid phosphatase) were downregulated. Expression profiles of these proteins are suggestive of reduction in semen quality in ALL survivors and can further be explored to determine their fertility status.
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Affiliation(s)
- Paras Jain
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sanjay Kumar Ojha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Vikrant Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sameer Bakhshi
- Department of Medical Oncology, IRCH, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sarman Singh
- Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India; All India Institute of Medical Sciences, Bhopal, 462020, India
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Santos MDM, Lima DB, Silva ARF, Kurt LU, Clasen MA, Pinto AFM, Moresco JJ, Yates JR, Aquino P, Barbosa VC, Fischer JSG, Carvalho PC. A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics. J Proteomics 2019; 202:103371. [PMID: 31034900 DOI: 10.1016/j.jprot.2019.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 10/26/2022]
Abstract
We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.
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Affiliation(s)
- Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
| | - Diogo B Lima
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil; Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur, Paris, France
| | - André R F Silva
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Louise U Kurt
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Milan A Clasen
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Antônio F M Pinto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Priscila Aquino
- Leônidas and Maria Deane Institute, Fiocruz, Amazonas, Brazil
| | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S G Fischer
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Paulo C Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
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10
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Babele P, Verma S, Kumar RB, Bhagyawant SS, Kamboj DV, Alam SI. Elucidation of protein biomarkers in plasma and urine for epsilon toxin exposure in mouse model. Anaerobe 2019; 59:76-91. [PMID: 31145997 DOI: 10.1016/j.anaerobe.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/02/2019] [Accepted: 05/22/2019] [Indexed: 01/09/2023]
Abstract
Epsilon toxin (ETX) is the major virulence determinant of C. perfringens type B or type D strains, causing diseases in animals, besides being a listed biological and toxin warfare (BTW) agent. Keeping in mind the high lethality and the rapid onset of clinical manifestations, early diagnosis of epsilon toxin exposure is of paramount importance for implementation of appropriate medical countermeasures. Using a 2DE-MS approach, the present study is the first comprehensive proteomic elucidation of ETX-induced protein markers in the mouse model, providing putative targets for early diagnosis of ETX exposure. A total of 52 unique proteins showing ETX-induced modulations were identified in plasma and urine samples. Fibrinogen, apolipoprotein, serum amyloid protein, plasminogen, serum albumin, glutathione peroxidase, transferrin, major urinary protein 2, haptoglobin, transthyretin, and vitamin D-binding protein were among the proteins observed in more than one dataset with altered abundance after the ETX-intoxication. The predicted localization, function, and interaction of the ETX-modulated proteins in the plasma and urine indicated involvement of multiple pathways; extracellular proteins, followed by macromolecular complexes associated with blood coagulation and plasminogen activating cascade, being the most prominent among others. The putative markers elucidated here warrants further validation and can be of immense value for the early diagnosis of ETX exposure.
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Affiliation(s)
- Prabhakar Babele
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Smarti Verma
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ravi Bhushan Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | | | - Dev Vrat Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Syed Imteyaz Alam
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India.
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11
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Abstract
Differential proteomics, which has been widely used in studying of traditional Chinese medicines (TCMs) during the past 10 years, is a powerful tool to visualize differentially expressed proteins and analyzes their functions. In this paper, the applications of differential proteomics in exploring the action mechanisms of TCMs on various diseases including cancers, cardiovascular diseases, diabetes, liver diseases, kidney disorders and obesity, etc. were reviewed. Furthermore, differential proteomics in studying of TCMs identification, toxicity, processing and compatibility mechanisms were also included. This review will provide information for the further applications of differential proteomics in TCMs studies.
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Affiliation(s)
- Yi-Yao Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People’s Republic of China
| | - Feng-Qing Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People’s Republic of China
| | - Jian-Li Gao
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053 Zhejiang People’s Republic of China
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12
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Tavares de Oliveira M, Taciana Santos Silva K, Xavier Neves L, de Ornelas Toledo MJ, Castro-Borges W, de Lana M. Differential expression of proteins in genetically distinct Trypanosoma cruzi samples (TcI and TcII DTUs) isolated from chronic Chagas disease cardiac patients. Parasit Vectors 2018; 11:611. [PMID: 30497493 PMCID: PMC6267078 DOI: 10.1186/s13071-018-3181-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi, a hemoflagellate protozoan parasite and the etiological agent of Chagas disease (CD), exhibits great genetic and biological diversity. Infected individuals may present clinical manifestations with different levels of severity. Several hypotheses have been proposed to attempt to correlate the diversity of clinical signs and symptoms to the genetic variability of T. cruzi. This work aimed to investigate the differential expression of proteins from two distinct genetic groups of T. cruzi (discrete typing units TcI and TcII), isolated from chronically infected individuals displaying the cardiac form of CD. For this purpose, epimastigote forms of the two isolates were cultured in vitro and the cells recovered for protein extraction. Comparative two-dimensional (2D) gel electrophoreses were performed and differentially expressed spots selected for identification by mass spectrometry, followed by database searching and protein categorization. RESULTS The 2D electrophoretic profiles revealed the complex composition of the T. cruzi extracted proteome. Protein spots were distributed along the entire pH and molecular mass ranges attesting for the integrity of the protein preparations. In total, 46 differentially expressed proteins were identified present in 40 distinct spots found in the comparative gel analyses. Of these, 16 displayed upregulation in the gel from TcI-typed parasites and 24 appeared overexpressed in the gel from TcII-typed parasites. Functional characterization of differentially expressed proteins revealed major alterations associated with stress response, lipid and amino acid metabolism in parasites of the TcII isolate, whilst those proteins upregulated in the TcI sample were primarily linked to central metabolic pathways. CONCLUSIONS The comparative 2D-gel electrophoresis allowed detection of major differences in protein expression between two T. cruzi isolates, belonging to the TcI and TcII genotypes. Our findings suggest that patients displaying the cardiac form of the disease harbor parasites capable of exhibiting distinct proteomic profiles. This should be of relevance to disease prognosis and treatment.
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Affiliation(s)
- Maykon Tavares de Oliveira
- Programa de Pós-Graduação em Ciências Biológicas do Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP, Ouro Preto, MG 35400-000 Brazil
| | - Karina Taciana Santos Silva
- Departamento de Farmácia, Escola de Farmácia, Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP, Ouro Preto, MG 35400-000 Brazil
| | - Leandro Xavier Neves
- Programa de Pós-Graduação em Biotecnologia do Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP: 35400-000, Ouro Preto, MG Brazil
| | - Max Jean de Ornelas Toledo
- Departamento de Ciências Básicas da Saúde – Parasitologia, Universidade Estadual de Maringá, CEP: 87020-900, Maringá, Paraná, PR Brazil
| | - William Castro-Borges
- Programa de Pós-Graduação em Ciências Biológicas do Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP, Ouro Preto, MG 35400-000 Brazil
- Programa de Pós-Graduação em Biotecnologia do Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP: 35400-000, Ouro Preto, MG Brazil
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP: 35400-000, Ouro Preto, MG Brazil
| | - Marta de Lana
- Programa de Pós-Graduação em Ciências Biológicas do Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP, Ouro Preto, MG 35400-000 Brazil
- Departamento de Análises Clínicas, Escola de Farmácia, Campus Universitário Morro do Cruzeiro, Universidade Federal de Ouro Preto, CEP: 35400-000, Ouro Preto, MG Brazil
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13
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Sohail W, Majeed F, Afroz A. Differential proteome analysis of diabetes mellitus type 2 and its pathophysiological complications. Diabetes Metab Syndr 2018; 12:1125-1131. [PMID: 29907545 DOI: 10.1016/j.dsx.2018.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 06/05/2018] [Indexed: 01/18/2023]
Abstract
The prevalence of Diabetes Mellitus Type 2 (DM 2) is increasing every passing year due to some global changes in lifestyles of people. The exact underlying mechanisms of the progression of this disease are not yet known. However recent advances in the combined omics more particularly in proteomics and genomics have opened a gateway towards the understanding of predetermined genetic factors, progression, complications and treatment of this disease. Here we shall review the recent advances in proteomics that have led to an early and better diagnostic approaches in controlling DM 2 more importantly the comparison of structural and functional protein biomarkers that are modified in the diseased state. By applying these advanced and promising proteomic strategies with bioinformatics applications and bio-statistical tools the prevalence of DM 2 and its associated disorders i-e nephropathy and retinopathy are expected to be controlled.
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Affiliation(s)
- Waleed Sohail
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan.
| | - Fatimah Majeed
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan
| | - Amber Afroz
- Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan
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14
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Trautwein K, Rabus R. Applications of Difference Gel Electrophoresis (DIGE) in the Study of Microorganisms. Methods Mol Biol 2018; 1841:95-112. [PMID: 30259482 DOI: 10.1007/978-1-4939-8695-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
OMICs-based investigations of microorganisms are becoming more and more widespread in the upcoming era of systems and synthetic biology. Here, proteomics plays a key role and two-dimensional difference gel electrophoresis (2D DIGE) remains the "gold-standard" for globally determining protein abundance changes on a quantitative and statistically confident level-in particular also for laboratories not having full-cycle proteomic facilities at their disposal. In this contribution we summarize our methodological procedures and experiences with 2D DIGE accumulated over the past 15 years.
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15
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Suyal DC, Kumar S, Joshi D, Soni R, Goel R. Quantitative proteomics of psychotrophic diazotroph in response to nitrogen deficiency and cold stress. J Proteomics 2018; 187:235-242. [PMID: 30092381 DOI: 10.1016/j.jprot.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 07/20/2018] [Accepted: 08/04/2018] [Indexed: 12/11/2022]
Abstract
Effective protocols and novel biomarkers are the need of this hour to screen potential cold adapted diazotrophs for sustainable mountain agricultural plans. LC-MS/MS based gel less quantitative proteomics was employed to investigate the metabolic response of Himalayan cold adapted diazotroph Pseudomonas palleroniana N26 (JN055435) for nitrogen deficiency and cold stress. More than 5000 proteins were identified, and 125 of them showed significant difference with a 2-fold or greater change (p < .05) between normal and stress conditions, including 29 up-regulated proteins and 35 down-regulated proteins. Expression of nifA, nifL, nifH, nifB, nifD, and nifK during N2 fixing conditions reveals that nitrogenase system was successfully activated. Further, 8% of the upregulated proteins showed similarity with uncharacterized proteins of several nitrogen fixing genera which suggests their in-depth investigation. Additionally, as per earlier studies, cowN was differentially expressed under nitrogen fixing conditions; thereby, confirming its potential to be a potent biomarker for monitoring the nitrogen fixation in cold niches. BIOLOGICAL SIGNIFICANCE Understanding of nitrogenase expression and regulation is essential to employ potential diazotrophs under diverse ecological niches to achieve agricultural as well as environmental sustainability. The molecular mechanisms of cold adapted diazotrophy are still unaddressed. In this scenario, present study, besides characterizing diazotrophic proteins, is helpful in identifying the protein(s) or a biomarker viz. CowN to facilitate the monitoring of nitrogen fixation in cold niches. To the best of our knowledge, this is the first gel-less quantitative free-living diazotrophic proteome study using label free mass spectrometry having high mass accuracy in both MS and MS/MS scans. It enriches the diazotrophic proteome database and will complement the other "omics" technologies for improved crop protection and sustainability strategies.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Saurabh Kumar
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Divya Joshi
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Viswavidyalaya, Raipur, C.G., India
| | - Reeta Goel
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India.
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16
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Wang S, Chen W, Yang C, Yao J, Xiao W, Xin Y, Qiu J, Hu W, Yao H, Ying W, Fu Y, Tong J, Chen Z, Ruan S, Ma H. Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice. BMC Plant Biol 2016; 16:199. [PMID: 27619227 PMCID: PMC5020550 DOI: 10.1186/s12870-016-0891-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/06/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Polyploidy has pivotal influences on rice (Oryza sativa L.) morphology and physiology, and is very important for understanding rice domestication and improving agricultural traits. Diploid (DP) and triploid (TP) rice shows differences in morphological parameters, such as plant height, leaf length, leaf width and the physiological index of chlorophyll content. However, the underlying mechanisms determining these morphological differences are remain to be defined. To better understand the proteomic changes between DP and TP, tandem mass tags (TMT) mass spectrometry (MS)/MS was used to detect the significant changes to protein expression between DP and TP. RESULTS Results indicated that both photosynthesis and metabolic pathways were highly significantly associated with proteomic alteration between DP and TP based on biological process and pathway enrichment analysis, and 13 higher abundance chloroplast proteins involving in these two pathways were identified in TP. Quantitative real-time PCR analysis demonstrated that 5 of the 13 chloroplast proteins ATPF, PSAA, PSAB, PSBB and RBL in TP were higher abundance compared with those in DP. CONCLUSIONS This study integrates morphology, physiology and proteomic profiling alteration of DP and TP to address their underlying different molecular mechanisms. Our finding revealed that ATPF, PSAA, PSAB, PSBB and RBL can induce considerable expression changes in TP and may affect the development and growth of rice through photosynthesis and metabolic pathways.
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Affiliation(s)
- Shuzhen Wang
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016 China
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310012 China
| | - Wenyue Chen
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Changdeng Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Jian Yao
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016 China
| | - Wenfei Xiao
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Ya Xin
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Jieren Qiu
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Weimin Hu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310012 China
| | - Haigen Yao
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016 China
| | - Wu Ying
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Yaping Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Jianxin Tong
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Zhongzhong Chen
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Songlin Ruan
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
| | - Huasheng Ma
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 China
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Xing M, Wang Y, Xu T, Yang J. Highlighting earthworm contribution in uplifting biochemical response for organic matter decomposition during vermifiltration processing sewage sludge: Insights from proteomics. Bioresour Technol 2016; 216:1088-1092. [PMID: 27287202 DOI: 10.1016/j.biortech.2016.05.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/20/2016] [Accepted: 05/24/2016] [Indexed: 06/06/2023]
Abstract
A vermifilter (VF) was steadily operated to explore the mechanism of lower microbial biomass and higher enzymatic activities due to the presence of earthworms, with a conventional biofilter (BF) as a control. The analysis of 2-DE indicated that 432 spots and 488 spots were clearly detected in the VF and BF biofilm. Furthermore, MALDI-TOF/TOF MS revealed that six differential up-regulated proteins, namely Aldehyde Dehydrogenase, Molecular chaperone GroEL, ATP synthase subunit alpha, Flagellin, Chaperone protein HtpG and ATP synthase subunit beta, changed progressively. Based on Gene Ontology annotation, these differential proteins mainly performed 71.38% ATP binding and 16.23% response to stress functions. Taken the VF process performance merits into considerations, it was addressed that earthworm activities biochemically strengthened energy releasing of the microbial metabolism in an uncoupled manner.
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Affiliation(s)
- Meiyan Xing
- The Institute of Biofilm Technology, Key Laboratory of Yangtze Water Environment for Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Yin Wang
- The Institute of Biofilm Technology, Key Laboratory of Yangtze Water Environment for Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ting Xu
- The Institute of Biofilm Technology, Key Laboratory of Yangtze Water Environment for Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jian Yang
- The Institute of Biofilm Technology, Key Laboratory of Yangtze Water Environment for Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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18
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Xu L, Ge J, Huo X, Zhang Y, Lau ATY, Xu X. Differential proteomic expression of human placenta and fetal development following e-waste lead and cadmium exposure in utero. Science of The Total Environment 2016; 550:1163-1170. [PMID: 26895036 DOI: 10.1016/j.scitotenv.2015.11.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/17/2015] [Accepted: 11/17/2015] [Indexed: 02/05/2023]
Abstract
Prenatal exposure to lead (Pb) and cadmium (Cd) has been associated with a series of physiological problems resulting in fetal growth restriction. We aimed to investigate the effects of Pb and Cd exposure on placental function and the potential mechanisms involved in fetal development. Placental specimens and questionnaires were collected from an e-waste area and a reference area in China. Two-dimensional electrophoresis combined with MALDI-TOF-MS/MS and molecular network relationship were performed to analyze differentially expressed proteins using a compositing sample pool. Compared with the reference group, the exposed group exhibited significantly higher levels of placental Pb and Cd (p<0.01), shorter body length and higher gestational age (p<0.01). After bivariate adjustment in a linear regression model, decreases of 205.05g in weight and 0.44cm in body length were associated with a 10ng/g wt increase in placental Cd. Pb showed a negative trend but lacked statistical significance. Proteomic analysis showed 32 differentially-expressed proteins and were predominantly involved in protein translocation, cytoskeletal structure, and energy metabolism. Fumarate hydratase was down-regulated in the exposed placenta tissues and validated by ELISA. Alterations in placental proteome suggest that imbalances in placental mitochondria respiration might be a vital pathway targeting fetal growth restriction induced by exposure to Cd.
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Affiliation(s)
- Long Xu
- Laboratory of Environmental Medicine and Developmental Toxicology, Shantou University Medical College, Shantou 515041, PR China
| | - Jingjing Ge
- Laboratory of Environmental Medicine and Developmental Toxicology, Shantou University Medical College, Shantou 515041, PR China
| | - Xia Huo
- Laboratory of Environmental Medicine and Developmental Toxicology, Shantou University Medical College, Shantou 515041, PR China
| | - Yuling Zhang
- Laboratory of Environmental Medicine and Developmental Toxicology, Shantou University Medical College, Shantou 515041, PR China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Shantou University Medical College, Shantou 515041, PR China; Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, PR China
| | - Xijin Xu
- Laboratory of Environmental Medicine and Developmental Toxicology, Shantou University Medical College, Shantou 515041, PR China; Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, PR China.
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19
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Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJC, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. J Proteome Res 2015; 15:691-706. [PMID: 26653538 PMCID: PMC4779376 DOI: 10.1021/acs.jproteome.5b00859] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm ). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.
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Affiliation(s)
| | - Xia Wang
- Department of Mathematical Sciences, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Karl R Clauser
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Philipp Mertins
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | | | | | | | | | | | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Sherri R Davies
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Matthew J C Ellis
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Shunqiang Li
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - R Reid Townsend
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Karen A Ketchum
- Enterprise Science and Computing, Inc. , Rockville, Maryland 20850, United States
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Tao Liu
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Sangtae Kim
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Jason E McDermott
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Samuel H Payne
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Vladislav A Petyuk
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Karin D Rodland
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Richard D Smith
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Feng Yang
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Daniel W Chan
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Bai Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Hui Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Zhen Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Jian-Ying Zhou
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
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20
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Jang S, Yu LR, Abdelmegeed MA, Gao Y, Banerjee A, Song BJ. Critical role of c-jun N-terminal protein kinase in promoting mitochondrial dysfunction and acute liver injury. Redox Biol 2015; 6:552-64. [PMID: 26491845 DOI: 10.1016/j.redox.2015.09.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 09/29/2015] [Indexed: 12/11/2022] Open
Abstract
The mechanism by which c-Jun N-terminal protein kinase (JNK) promotes tissue injury is poorly understood. Thus we aimed at studying the roles of JNK and its phospho-target proteins in mouse models of acute liver injury. Young male mice were exposed to a single dose of CCl4 (50 mg/kg, IP) and euthanized at different time points. Liver histology, blood alanine aminotransferase, and other enzyme activities were measured in CCl4-exposed mice without or with the highly-specific JNK inhibitors. Phosphoproteins were purified from control or CCl4-exposed mice and analyzed by differential mass-spectrometry followed by further characterizations of immunoprecipitation and activity measurements. JNK was activated within 1 h while liver damage was maximal at 24 h post-CCl4 injection. Markedly increased phosphorylation of many mitochondrial proteins was observed between 1 and 8 h following CCl4 exposure. Pretreatment with the selective JNK inhibitor SU3327 or the mitochondria-targeted antioxidant mito-TEMPO markedly reduced the levels of p-JNK, mitochondrial phosphoproteins and liver damage in CCl4-exposed mice. Differential proteomic analysis identified many phosphorylated mitochondrial proteins involved in anti-oxidant defense, electron transfer, energy supply, fatty acid oxidation, etc. Aldehyde dehydrogenase, NADH-ubiquinone oxidoreductase, and α-ketoglutarate dehydrogenase were phosphorylated in CCl4-exposed mice but dephosphorylated after SU3327 pretreatment. Consistently, the suppressed activities of these enzymes were restored by SU3327 pretreatment in CCl4-exposed mice. These data provide a novel mechanism by which JNK, rapidly activated by CCl4, promotes mitochondrial dysfunction and acute hepatotoxicity through robust phosphorylation of numerous mitochondrial proteins. JNK was rapidly activated after carbon tetrachloride (CCl4) exposure. Activated JNK was translocated to mitochondria and phosphorylated many proteins. Many mitochondrial phosphoproteins were identified by mass-spec analysis. Mitochondrial ALDH2, α-KGDH, and complex I were inactivated by phosphorylation. JNK inhibition reduced phosphorylation of mitochondrial proteins and hepatotoxicity.
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Romanello M, Piatkowska E, Antoniali G, Cesaratto L, Vascotto C, Iozzo RV, Delneri D, Brancia FL. Osteoblastic cell secretome: a novel role for progranulin during risedronate treatment. Bone 2014; 58:81-91. [PMID: 24120669 PMCID: PMC5072534 DOI: 10.1016/j.bone.2013.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/19/2013] [Accepted: 10/01/2013] [Indexed: 11/25/2022]
Abstract
It is well established that osteoblasts, the key cells involved in bone formation during development and in adult life, secrete a number of glycoproteins harboring autocrine and paracrine functions. Thus, investigating the osteoblastic secretome could yield important information for the pathophysiology of bone. In the present study, we characterized for the first time the secretome of human Hobit osteoblastic cells. We discovered that the secretome comprised 89 protein species including the powerful growth factor progranulin. Recombinant human progranulin (6nM) induced phosphorylation of mitogen-activated protein kinase in both Hobit and osteocytic cells and induced cell proliferation and survival. Notably, risedronate, a nitrogen-containing bisphosphonate widely used in the treatment of osteoporosis, induced the expression and secretion of progranulin in the Hobit secretome. In addition, our proteomic study of the Hobit secretome revealed that risedronate induced the expression of ERp57, HSP60 and HSC70, three proteins already shown to be associated with the prevention of bone loss in osteoporosis. Collectively, our findings unveil novel targets of risedronate-evoked biological effects on osteoblast-like cells and further our understanding of the mechanisms of action of this currently used compound.
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Affiliation(s)
- Milena Romanello
- Laboratory of Regional Centre for Rare Diseases, University Hospital, Santa Maria della Misericordia, 33100 Udine, Italy.
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Zhang M, Zheng X, Wu Y, Gan M, He A, Li Z, Zhang D, Wu X, Zhan X. Differential proteomics of Aedes albopictus salivary gland, midgut and C6/36 cell induced by dengue virus infection. Virology 2013; 444:109-18. [PMID: 23816433 DOI: 10.1016/j.virol.2013.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/04/2013] [Accepted: 06/03/2013] [Indexed: 11/26/2022]
Abstract
The interaction between dengue virus (DENV) and vector mosquitoes are still poorly understood at present. In this study, 2-D DIGE combined with MS was used to analyze the differential proteomes of Aedes albopictus salivary gland, midgut and C6/36 cells induced by DENV-2. Our results indicated that the virus infection regulated several functional classes of proteins. Among them, 26 were successfully analyzed by real-time RT-PCR. The mRNA levels of 15 were the highest in salivary gland, 2 in midgut and none in C6/36 cells, however, 18 were the least in fat body compared to other organs. Interestingly, the changes of differential proteins mRNA were the most obvious in fat body post-infection. Chaperone, cytoskeleton and energy metabolism enzyme were the most down- or up- regulated proteins after DENV-2 infection. The abundant expression of these proteins in salivary gland may relate to its high susceptibility.
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Affiliation(s)
- Meichun Zhang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China
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Sinha R, Bhattacharyya D, Majumdar AB, Datta R, Hazra S, Chattopadhyay S. Leaf proteome profiling of transgenic mint infected with Alternaria alternata. J Proteomics 2013; 93:117-32. [PMID: 23369890 DOI: 10.1016/j.jprot.2013.01.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 01/14/2013] [Accepted: 01/20/2013] [Indexed: 10/27/2022]
Abstract
UNLABELLED The genus Mentha has been widely used in food, flavor, culinary, cosmetic and pharmaceutical industries. Substantial damage to this crop happened regularly due to environmental stresses like metal toxicity and pathogen attack. Here, an approach has been taken to raise transgenic mint over-expressing γ-glutamyl-cysteine synthetase (γ-ECS), the rate-limiting enzyme of GSH biosynthesis, resulted enhanced GSH content and its in planta expression confers significant tolerance towards abiotic/biotic stresses viz. metal toxicity - Cd, Zn as well as against infection of Alternaria alternata and Rhizoctonia solani. A differential proteomic analysis through 2-DE and MALDI TOF-TOF MSMS was performed to focus on the altered abundance of functionally important protein species in control and infected transgenic mint. Results showed a significant variation in the protein profile of the infected transgenic plant as compared to the wild/control transgenic counterpart. In addition to protein species related to stress and defense, redox regulation, transcription factors and energy & metabolism, protein species related to signaling and gene regulation as well as cell division also showed differential accumulation in infected transgenic. Hence, proteomics can be used as a tool to decipher the mechanism of action of GSH in providing tolerance against a necrotrophic fungus, A. alternata in transgenic mint. BIOLOGICAL SIGNIFICANCE The reported work describes a comparative proteomics of non-model unsequenced plants like Mentha. There is a comparative protein profile between transgenic and its wild counterparts under control and infected condition. The work has an impact in crop proteomics and also tries to explain the application of proteomic approach to decipher the mechanism by which a foreign metabolite mediates stress tolerance in plant under control and infected condition. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Ragini Sinha
- Plant Biology Laboratory, Drug Development/Diagnostics & Biotechnology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C.Mullick Road, Kolkata 700 032, India
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