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Ghosh G, Neely BA, Bland AM, Whitmer ER, Field CL, Duignan PJ, Janech MG. Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions ( Zalophus californianus). J Proteome Res 2024. [PMID: 38807289 DOI: 10.1021/acs.jproteome.4c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis (DAT) have consistently increased. Outside of direct measurement of domoic acid in bodily fluids at the time of stranding, there are no practical nonlethal clinical tests for the diagnosis of DAT that can be utilized in a rehabilitation facility. Proteomics analysis was conducted to discover candidate protein markers of DAT using cerebrospinal fluid from stranded California sea lions with acute DAT (n = 8), chronic DAT (n = 19), or without DAT (n = 13). A total of 2005 protein families were identified experiment-wide. A total of 83 proteins were significantly different in abundance across the three groups (adj. p < 0.05). MDH1, PLD3, ADAM22, YWHAG, VGF, and CLSTN1 could discriminate California sea lions with or without DAT (AuROC > 0.75). IGKV2D-28, PTRPF, KNG1, F2, and SNCB were able to discriminate acute DAT from chronic DAT (AuROC > 0.75). Proteins involved in alpha synuclein deposition were over-represented as classifiers of DAT, and many of these proteins have been implicated in a variety of neurodegenerative diseases. These proteins should be considered potential markers for DAT in California sea lions and should be prioritized for future validation studies as biomarkers.
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Affiliation(s)
- Gautam Ghosh
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Benjamin A Neely
- National Institute of Standards and Technology (NIST) Charleston, Charleston, South Carolina 29412, United States
| | - Alison M Bland
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Emily R Whitmer
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Cara L Field
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Pádraig J Duignan
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Michael G Janech
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
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Duda HC, von Toerne C, Korbonits L, Didier A, Scholz AM, Märtlbauer E, Hauck SM, Deeg CA. Cathepsin S Is More Abundant in Serum of Mycobacterium avium subsp. paratuberculosis-Infected Dairy Cows. Metabolites 2024; 14:215. [PMID: 38668343 PMCID: PMC11051907 DOI: 10.3390/metabo14040215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of bovine paratuberculosis, a chronic granulomatous enteritis leading to economic losses and posing a risk to human health due to its zoonotic potential. The pathogen cannot reliably be detected by standard methods, and immunological procedures during the infection are not well understood. Therefore, the aim of our study was to explore host-pathogen interactions in MAP-infected dairy cows and to improve diagnostic tests. Serum proteomics analysis using quantitative label-free LC-MS/MS revealed 60 differentially abundant proteins in MAP-infected dairy cows compared to healthy controls from the same infected herd and 90 differentially abundant proteins in comparison to another control group from an uninfected herd. Pathway enrichment analysis provided new insights into the immune response to MAP and susceptibility to the infection. Furthermore, we found a higher abundance of Cathepsin S (CTSS) in the serum of MAP-infected dairy cows, which is involved in multiple enriched pathways associated with the immune system. Confirmed with Western blotting, we identified CTSS as a potential biomarker for bovine paratuberculosis. This study enabled a better understanding of procedures in the host-pathogen response to MAP and improved detection of paratuberculosis-diseased cattle.
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Affiliation(s)
- Heidi C. Duda
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Christine von Toerne
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Lucia Korbonits
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Andrea Didier
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Armin M. Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany;
| | - Erwin Märtlbauer
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
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Guo J, Teymur A, Tang C, Saxena R, Wu T. Advancing Point-of-Care Diagnosis: Digitalizing Combinatorial Biomarker Signals for Lupus Nephritis. BIOSENSORS 2024; 14:147. [PMID: 38534254 DOI: 10.3390/bios14030147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
To improve the efficiency and patient coverage of the current healthcare system, user-friendly novel homecare devices are urgently needed. In this work, we developed a smartphone-based analyzing and reporting system (SBARS) for biomarker detection in lupus nephritis (LN). This system offers a cost-effective alternative to traditional, expensive large equipment in signal detection and quantification. This innovative approach involves using a portable and affordable microscopic reader to capture biomarker signals. Through smartphone-based image processing techniques, the intensity of each biomarker signal is analyzed. This system exhibited comparable performance to a commercial Genepix scanner in the detection of two potential novel biomarkers of LN, VISG4 and TNFRSF1b. Importantly, this smartphone-based analyzing and reporting system allows for discriminating LN patients with active renal disease from healthy controls with the area-under-the-curve (AUC) value = 0.9 for TNFRSF1b and 1.0 for VSIG4, respectively, indicating high predictive accuracy.
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Affiliation(s)
- Jiechang Guo
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
- Department of Computer Science, University of Houston, Houston, TX 77024, USA
| | - Aygun Teymur
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
| | - Chenling Tang
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
| | - Ramesh Saxena
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
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Chen C, Khanthiyong B, Thaweetee-Sukjai B, Charoenlappanit S, Roytrakul S, Thanoi S, Reynolds GP, Nudmamud-Thanoi S. Proteomic association with age-dependent sex differences in Wisconsin Card Sorting Test performance in healthy Thai subjects. Sci Rep 2023; 13:20238. [PMID: 37981639 PMCID: PMC10658079 DOI: 10.1038/s41598-023-46750-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/04/2023] [Indexed: 11/21/2023] Open
Abstract
Sex differences in cognitive function exist, but they are not stable and undergo dynamic change during the lifespan. However, our understanding of how sex-related neural information transmission evolves with age is still in its infancy. This study utilized the Wisconsin Card Sorting Test (WCST) and the label-free proteomics method with bioinformatic analysis to investigate the molecular mechanisms underlying age-related sex differences in cognitive performance in 199 healthy Thai subjects (aged 20-70 years), as well as explore the sex-dependent protein complexes for predicting cognitive aging. The results showed that males outperformed females in two of the five WCST sub-scores: %Corrects and %Errors. Sex differences in these scores were related to aging, becoming noticeable in those over 60. At the molecular level, differently expressed individual proteins and protein complexes between both sexes are associated with the potential N-methyl-D-aspartate type glutamate receptor (NMDAR)-mediated excitotoxicity, with the NMDAR complex being enriched exclusively in elderly female samples. These findings provided a preliminary indication that healthy Thai females might be more susceptible to such neurotoxicity, as evidenced by their cognitive performance. NMDAR protein complex enrichment in serum could be proposed as a potential indication for predicting cognitive aging in healthy Thai females.
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Affiliation(s)
- Chen Chen
- Medical Science Graduate Program, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | | | | | - Sawanya Charoenlappanit
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Samur Thanoi
- School of Medical Sciences, University of Phayao, Phayao, Thailand.
| | - Gavin P Reynolds
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sutisa Nudmamud-Thanoi
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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Ruengket P, Roytrakul S, Tongthainan D, Taruyanon K, Sangkharak B, Limudomporn P, Pongsuchart M, Udom C, Fungfuang W. Serum proteomic profile of wild stump-tailed macaques (Macaca arctoides) infected with malaria parasites in Thailand. PLoS One 2023; 18:e0293579. [PMID: 37910477 PMCID: PMC10619813 DOI: 10.1371/journal.pone.0293579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
The number of patients infected with simian malaria is gradually increasing in many countries of Southeast Asia and South America. The most important risk factor for a zoonotic spillover event of malarial infection is mostly influenced by the interaction between humans, monkeys, and vectors. In this study, we determine the protein expression profile of a wild stump-tailed macaque (Macaca arctoides) from a total of 32 blood samples collected from Prachuap Kiri Khan Province, Thailand. The malarial parasite was analyzed using nested polymerase chain reaction (PCR) assays by dividing the samples into three groups: non-infected, mono-infected, and multiple-infected. The identification and differential proteomic expression profiles were determined using liquid chromatography with tandem mass spectrometry (LC-MS/MS) and bioinformatics tools. A total of 9,532 proteins (total proteins) were identified with the filter-based selection methods analysis, and a subset of 440 proteins were found to be different between each group. Within these proteins, the GhostKOALA functional enrichment analysis indicated that 142 important proteins were associated with either of the organismal system (28.87%), genetic information processing (23.24%), environmental information processing (16.20%), metabolism (13.38%), cellular processes (11.97%), or causing human disease (6.34%). Additionally, using interaction network analysis, nine potential reporter proteins were identified. Here, we report the first study on the protein profiles differentially expressed in the serum of wild stump-tailed macaques between non, mono, and multiple malarial infected living in a natural transmission environment. Our findings demonstrate that differentially expressed proteins implicated in host defense through lipid metabolism, involved with TGF pathway were suppressed, while those with the apoptosis pathway, such as cytokines and proinflammation signals were increased. Including the parasite's response via induced hemolysis and disruption of myeloid cells. A greater understanding of the fundamental processes involved in a malarial infection and host response can be crucial for developing diagnostic tools, medication development, and therapies to improve the health of those affected by the disease.
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Affiliation(s)
- Pakorn Ruengket
- Genetic Engineering and Bioinformatics Program, Graduate School, Kasetsart University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Daraka Tongthainan
- Faculty of Veterinary Medicine, Rajamongala University of Technology Tawan-ok, Chonburi, Thailand
| | - Kanokwan Taruyanon
- Department of National Parks, Wildlife Conservation Division Protected Areas Regional Office, Wildlife and Plant Conservation, Ratchaburi, Thailand
| | - Bencharong Sangkharak
- Department of National Parks, Wildlife Conservation Division, Wildlife and Plant Conservation, Bangkok, Thailand
| | - Paviga Limudomporn
- Faculty of Science, Department of Zoology, Kasetsart University, Bangkok, Thailand
| | - Mongkol Pongsuchart
- Faculty of Science, Department of Zoology, Kasetsart University, Bangkok, Thailand
| | - Chanya Udom
- Faculty of Science, Department of Zoology, Kasetsart University, Bangkok, Thailand
| | - Wirasak Fungfuang
- Faculty of Science, Department of Zoology, Kasetsart University, Bangkok, Thailand
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You Y, Bai C, Wang W, Zhan T, Hu X, Hao F, Xia M, Liu Y, Ma T, Liu Y, Zheng C, Pu T, Zhang Y, Lu Y, Ding N, Li J, Yin Y, Chen Y, Wang L, Zhou J, Niu L, Xiu Y, Lu Y, Jia T, Liu X, Zhang C. Comparative proteomics in captive giant pandas to identify proteins involved in age-related cataract formation. Sci Rep 2023; 13:12722. [PMID: 37543644 PMCID: PMC10404263 DOI: 10.1038/s41598-023-40003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Approximately 20% of aged captive giant pandas (Ailuropoda melanoleuca) have cataracts that impair their quality of life. To identify potential biomarkers of cataract formation, we carried out a quantitative proteomics analysis of 10 giant pandas to find proteins differing in abundance between healthy and cataract-bearing animals. We identified almost 150 proteins exceeding our threshold for differential abundance, most of which were associated with GO categories related to extracellular localization. The most significant differential abundance was associated with components of the proteasome and other proteins with a role in proteolysis or its regulation, most of which were depleted in pandas with cataracts. Other modulated proteins included components of the extracellular matrix or cytoskeleton, as well as associated signaling proteins and regulators, but we did not find any differentially expressed transcription factors. These results indicate that the formation of cataracts involves a complex post-transcriptional network of signaling inside and outside lens cells to drive stress responses as a means to address the accumulation of protein aggregates triggered by oxidative damage. The modulated proteins also indicate that it should be possible to predict the onset of cataracts in captive pandas by taking blood samples and testing them for the presence or absence of specific protein markers.
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Affiliation(s)
- Yuyan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | - Chao Bai
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wei Wang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Tongtong Zhan
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Xin Hu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | | | - Yan Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Tao Ma
- Beijing Zoo, Beijing, China
| | | | | | | | | | | | | | | | | | - Yucun Chen
- Strait (Fuzhou) Giant Panda Research and Exchange Centers, Fuzhou, China
| | | | | | | | - Yunfang Xiu
- Strait (Fuzhou) Giant Panda Research and Exchange Centers, Fuzhou, China
| | - Yan Lu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | | | | | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
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Wang B, Zhang Q, Wu L, Deng C, Luo M, Xie Y, Wu G, Chen W, Sheng Y, Zhu P, Qin G. Data-independent acquisition-based mass spectrometry(DIA-MS) for quantitative analysis of patients with chronic hepatitis B. Proteome Sci 2023; 21:9. [PMID: 37280603 DOI: 10.1186/s12953-023-00209-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/29/2023] [Indexed: 06/08/2023] Open
Abstract
Chronic hepatitis B is a significant public health problem and complex pathologic process, and unraveling the underlying mechanisms and pathophysiology is of great significance. Data independent acquisition mass spectrometry (DIA-MS) is a label-free quantitative proteomics method that has been successfully applied to the study of a wide range of diseases. The aim of this study was to apply DIA-MS for proteomic analysis of patients with chronic hepatitis B. We performed comprehensive proteomics analysis of protein expression in serum samples from HBV patients and healthy controls by using DIA-MS. Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein network analysis were performed on differentially expressed proteins and were further combined with literature analysis. We successfully identified a total of 3786 serum proteins with a high quantitative performance from serum samples in this study. We identified 310 differentially expressed proteins (DEPs) (fold change > 1.5 and P value < 0.05 as the criteria for a significant difference) between HBV and healthy samples. A total of 242 upregulated proteins and 68 downregulated proteins were among the DEPs. Some protein expression levels were significantly elevated or decreased in patients with chronic hepatitis B, indicating a relation to chronic liver disease, which should be further investigated.
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Affiliation(s)
- Bo Wang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Qian Zhang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Lili Wu
- Department of Gastroenterology, Suining First Pepole's Hospital, Suining, 629000, Sichuan, China
| | - Cunliang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Meiyan Luo
- College of Graduate, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yu Xie
- College of Graduate, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Gang Wu
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Wen Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yunjian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Peng Zhu
- Department of Gastroenterology, Suining First Pepole's Hospital, Suining, 629000, Sichuan, China
| | - Gang Qin
- Department of Gastroenterology, Suining First Pepole's Hospital, Suining, 629000, Sichuan, China.
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Back JH, Kim SY, Gu MB, Kim HJ, Lee KN, Lee JE, Park KH. Proteomic analysis of plasma to identify novel biomarkers for intra-amniotic infection and/or inflammation in preterm premature rupture of membranes. Sci Rep 2023; 13:5658. [PMID: 37024561 PMCID: PMC10079851 DOI: 10.1038/s41598-023-32884-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
To identify potential plasma biomarkers associated with microbial invasion of the amniotic cavity (MIAC) and/or intraamniotic inflammation (IAI) in women with preterm premature rupture of membranes (PPROM). This retrospective cohort study included 182 singleton pregnant women with PPROM (23-33 weeks) who underwent amniocentesis. Plasma samples; all subjects were chosen from these participants and were analyzed using label-free liquid chromatography-tandem mass spectrometry for proteome profiling using a nested case-control study design (cases with MIAC/IAI vs. non-MIAC/IAI controls [n = 9 each]). Three identified target molecules for MIAC/IAI were further verified by ELISA in the study cohort (n = 182). Shotgun proteomic analysis revealed 17 differentially expressed proteins (P < 0.05) in the plasma of MIAC/IAI cases. In particular, the levels of FCGR3A and haptoglobin, but not LRP1, were found to be increased in the plasma of patients with MIAC, IAI, and both MIAC/IAI compared with those without these conditions. Moreover, these differences remained significant after adjusting for gestational age at sampling. The area under the curves of plasma FCGR3A and haptoglobin ranged within 0.59-0.65 with respect to each of the three outcome measures. Plasma FCGR3A and haptoglobin were identified as potential independent biomarkers for less-invasively detecting MIAC/IAI in women with PPROM.
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Affiliation(s)
- Ji Hyun Back
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
- Biomedical Research Division, Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, 02792, Korea
| | - So Yeon Kim
- Department of Obstetrics and Gynecology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Man Bock Gu
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Hyeon Ji Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-Ro 173 Beon-Gil, Bundang-Gu, Seongnam, 463-707, Korea
| | - Kyong-No Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-Ro 173 Beon-Gil, Bundang-Gu, Seongnam, 463-707, Korea
| | - Ji Eun Lee
- Biomedical Research Division, Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, 02792, Korea.
| | - Kyo Hoon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-Ro 173 Beon-Gil, Bundang-Gu, Seongnam, 463-707, Korea.
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Deb A, Nalkar GR, Chowdhury D. Biogenic carbon dot-based fluorescence-mediated immunosensor for the detection of disease biomarker. Anal Chim Acta 2023; 1242:340808. [PMID: 36657894 DOI: 10.1016/j.aca.2023.340808] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The dynamic interplay of nanotechnology and immunoassay has unlocked an arena for developing next-generation techniques to contribute to detecting disease biomarkers. Herein, the work establishes the strategic fabrication of an immunosensor by sandwich technique based on the fluorescence phenomenon of carbon dots for the detection of the disease biomarker VEGF (Vascular Endothelial Growth Factor). VEGF, a biomarker for angiogenesis, is considered cancerous if found in elevated levels in the blood, and so is paramount for early detection of disease. Carbon dots derived from a biogenic source were synthesized employing a green microwave-assisted method followed by conjugating with a detection antibody, human immunoglobulin G (IgG), via EDC-NHS amidation reaction. On the other hand, the VEGF biomarker was immobilized onto the capture antibody. The detection antibody tagged with the fluorescent probe is employed as a bridge to connect with the VEGF biomarkers bound to the capture antibody. The response to different concentrations of VEGF biomarkers was recorded in terms of the fluorescence intensity of the carbon dots. The fluorescence immunosensor could exhibit a wide linear range of 0.1 fg/mL to 10 pg/mL with a low detection limit of 5.65 pg/mL towards VEGF. The potentiality of this designed immunosensor was qualitatively assessed with human blood plasma samples, showing promising results, thereby upholding the applicability of carbon dots as fluorescent labels in immunoassay techniques.
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Affiliation(s)
- Ankita Deb
- Material Nanochemistry Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Garchuk, Guwahati, 781035, India
| | - Gaurav Raghunath Nalkar
- Material Nanochemistry Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Garchuk, Guwahati, 781035, India
| | - Devasish Chowdhury
- Material Nanochemistry Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Garchuk, Guwahati, 781035, India.
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Shi T, Bai J, Yang D, Huang L, Fan HF, Zhang DW, Liu T, Lu G. Identification of candidate biomarkers for severe adenovirus community-acquired pneumonia by proteomic approach. Heliyon 2022; 8:e10807. [PMID: 36217477 PMCID: PMC9547224 DOI: 10.1016/j.heliyon.2022.e10807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/19/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction Worldwide, Human adenoviruses (ADV) cause a significant portion of childhood mortality. The severity of ADV Community-acquired Pneumonia (CAP) can be assessed by clinical features, but the rapid and accurate diagnostic biomarkers are still lacking. Candidate biomarkers for severe ADV CAP are to be screened and the different protein expression levels associated with pediatric ADV CAP may help assess the severity of ADV CAP for the pediatricians to make early intervention. Methods In our study, serum samples from healthy controls, patients with ADV CAP, streptococcus pneumonia (SP) and respiratory syncytial virus (RSV) infection were collected. Differently expressed proteins (DEPs) were detected by iTRAQ-based mass spectrometry. Gene Ontology and Pathway Enrichment analysis of DEPs were performed by Cytoscape. The protein interaction network for the identified proteins was constructed by String. Results The results showed that 119 DEPs in mild ADV CAP and 148 DEPs in severe ADV CAP were identified, compared with healthy children. Four proteins (Protein S100-A9 (S100A9), Protein S100-A8 (S100A8), Leucine aminopeptidase III (LAP3), and Apolipoprotein A-IV(APOA4)) were validated by Western blot, and results indicated that the expression levels of these four proteins were consistent with the proteomic analysis. LAP3 was the most significantly up-regulated protein in severe ADV CAP compared to mild group. In addition, LAP3 was the most significantly up-regulated protein in severe ADV CAP comparing with SP CAP infection and RSV CAP infection. Conclusion Our findings identified LAP3 protein as a potential diagnostic biomarker which can assess the severity of ADV CAP.
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Associations of Complete Blood Count Parameters with Disease-Free Survival in Right- and Left-Sided Colorectal Cancer Patients. J Pers Med 2022; 12:jpm12050816. [PMID: 35629238 PMCID: PMC9146340 DOI: 10.3390/jpm12050816] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Some complete blood count (CBC) parameters are found to be associated with CRC prognosis. In this study, ninety-seven pretreated CRC patients were included, and the patients were divided into two groups: left-sided and right-sided, depending on the anatomical location of the tumor. Based on clinicopathologic features including tumor budding, disease stages, and tumor anatomical location, levels of CBC parameters were compared, and disease-free survivals (DFS) were determined. There were differences between patients with different tumor budding scores for only three parameters, including red cell distribution width (RDW), numbers of platelets, and mean platelet volume (MPV). Furthermore, numbers of WBCs, monocytes, and MPV in CRC patients with early disease stages were higher than those with advanced stages. However, levels of eosinophil in CRC patients with advanced stages were higher than those with early stages. Depending on the tumor anatomical location, we observed that numbers of red blood cells (RBCs), hemoglobin (Hgb), and hematocrit (Hct) in CRC patients with left-sided tumors were higher than those with right-sided tumors. We found that low levels of MPV were associated with shorter DFS. However, high levels of eosinophils were associated with shorter DFS in all CRC patients. When patients were divided based on the tumor anatomical location, higher levels of MPV, MCHC, and Hgb were associated with better DFS in the left-sided but not right-sided CRC patients. However, left-sided, but not right-sided, CRC patients with high levels of eosinophil and RDW had shorter DFS. Furthermore, right-sided, but not left-sided, CRC patients with high levels of platelets tended to have a shorter DFS. Our data show that MPV and eosinophils could serve as potential prognostic biomarkers in pre-treatment CRC patients, regardless of the tumor anatomical location. Additionally, lower levels of MPV, MCHC, and Hgb, and high levels of eosinophils and RDW could be negative predictive biomarkers in left-sided CRC patients.
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12
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Dendrimer-Modified Silica Nanoparticles for Efficient Enrichment of Low-Concentration Peptides. Appl Biochem Biotechnol 2022; 194:3419-3434. [PMID: 35366184 DOI: 10.1007/s12010-022-03892-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/14/2022] [Indexed: 11/02/2022]
Abstract
Peptide profiling based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is of particular interest as it can provide physiologically and pathologically related information of the bio-samples. Due to the complexity of real biological samples, MALDI-TOF MS-based peptide mapping methods rely strongly on particular enrichment methods to improve the signal intensity. This paper introduces third-generation dendrimer-modified SBA-15 with the surface functionalization of amino and carboxyl group, respectively (denoted as SBA-15/G3-NH2 and SBA-15/G3-COOH), for the efficient capture of low-abundance peptides. The enrichment ability of the nanocomposites was evaluated by standard peptides digests and real biological samples. The synthesized nanocomposites incorporated the benefit of dendrimers and mesoporous silica nanomaterial SBA-15, showing enhanced peptide enrichment ability. Therefore, this work may provide a new class of nanomaterials for peptide mapping from biological samples.
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13
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Pilar-Orive FJ, Astigarraga I, Azkargorta M, Elortza F, Garcia-Obregon S. A Three-Protein Panel to Support the Diagnosis of Sepsis in Children. J Clin Med 2022; 11:jcm11061563. [PMID: 35329889 PMCID: PMC8955185 DOI: 10.3390/jcm11061563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 02/01/2023] Open
Abstract
Sepsis is a syndrome without a standard validated diagnostic test. Early recognition is crucial. Serum proteome analysis in children with sepsis may identify new biomarkers. This study aimed to find suitable blood biomarkers for an early diagnosis of sepsis. An analytical observational case-control study was carried out in a single center. Children admitted to a Pediatric Intensive Care Unit with clinical diagnosed sepsis were eligible for study. A proteomic analysis conducted by mass spectrometry was performed. Forty patients with sepsis and 24 healthy donors were recruited. Proteomics results revealed 44 proteins differentially expressed between patients and healthy controls. Six proteins were selected to be validated: lactoferrin, serum amyloid-A1 (SAA-1), complement factor B, leucine-rich alpha-2 glycoprotein (LRG1), soluble interleukin-2 alpha chain receptor (sCD25) and soluble haptoglobin−hemoglobin receptor. Our results showed that sCD25, SAA-1, and LRG1 had high levels of specificity and sensitivity, as well as an excellent area under the ROC curve (>0.9). Our study provides a serum proteomic analysis that identifies new diagnostic biomarkers in sepsis. SAA-1, sCD25 and LRG1 were able to separate septic from healthy donor, so they could be used together with other clinical and analytical features to improve sepsis diagnosis in children.
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Affiliation(s)
- Francisco J. Pilar-Orive
- Pediatric Critical Care Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Pediatric Critical Care Service, Hospital Universitario Cruces, 48903 Barakaldo, Spain
- Correspondence: (F.J.P.-O.); (S.G.-O.); Tel.: +34-616958309 (F.J.P.-O.); +34-946006357 (S.G.-O.)
| | - Itziar Astigarraga
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Pediatric Service, Hospital Universitario Cruces, 48903 Barakaldo, Spain
- Pediatric Department, Universidad del País Vasco UPV/EHU, 48940 Leioa, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Susana Garcia-Obregon
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Physiology Department, Universidad del País Vasco UPV/EHU, 48940 Leioa, Spain
- Correspondence: (F.J.P.-O.); (S.G.-O.); Tel.: +34-616958309 (F.J.P.-O.); +34-946006357 (S.G.-O.)
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14
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An Electrochemical and Raman Scattering Dual Detection Biosensor for Rapid Screening and Biomolecular Profiling of Cancer Biomarkers. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10030093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Detecting circulating biomarkers sensitively and quantitatively is paramount for cancer screening, diagnosis, and treatment selection. Particularly, screening of a panel of circulating protein biomarkers followed by mapping of individual biomarkers could assist better diagnosis and understanding of the cancer progression mechanisms. Herein, we present a miniaturized biosensing platform with dual readout schemes (electrochemical and Surface enhanced Raman scattering (SERS)) for rapid cancer screening and specific biomarker expressional profiling to support cancer management. Our approach utilizes a controlled nanomixing phenomena under alternative current electrohydrodynamic condition to improve the isolation of cancer-associated circulating proteins (i.e., Epidermal growth factor receptor (EGFR), BRAF, Programmed death-ligand 1 (PD-L1)) with antibody functionalized sensor surface for rapid and efficient isolation of the targets and subsequent labelling with SERS nanotags. The method employs Differential Pulse Voltammetry (DPV) for rapidly screening for the presence of the circulating proteins on biosensor surface irrespective of their type. Upon positive DPV detection, SERS is applied for sensitive read-out of individual biomarkers biomarker levels. In a proof-of-concept study, we demonstrate the dual detection biosensor for analysing circulating BRAF, EGFR and PDL-1 proteins and successfully screened both ensemble and individual biomarker expressional levels as low as 10 pg (1 ng/mL). Our findings clearly indicate the potential of the proposed method for cancer biomarker analysis which may drive the translation of this dual sensing concept in clinical settings.
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Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
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Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
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16
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Jakšić Ž, Mrljak V, Horvatić A, Gelemanović A, Mičić M. Loggerhead sea turtle Caretta caretta plasma biochemistry and proteome profile modulation during recovery. J Proteomics 2022; 252:104433. [PMID: 34839037 DOI: 10.1016/j.jprot.2021.104433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/26/2022]
Abstract
The aim of the study was to monitor and analyse injured and diseased loggerhead sea turtles (Caretta caretta) plasma proteome profiles and biochemistry parameters during their recovery period in rescue centre within different age and recovery period groups, and determine the potential biomarkers that can be used in diagnostics. The plasma biochemical parameters of total protein and glucose content, accompanied by aspartate aminotransferase (AST) and N-acetyl-cystein-activated creatinine kinase (CK-NAC) are highlighted as valuable and potential biomarkers of turtle's health status and condition. Using high throughput tandem mass tag (TMT)-based proteomic approach we identified 913 plasma proteins, 12 of which shown to be modulated in loggerheads age groups, and identified as a part of (i) platelet degranulation, (ii) neutrophil degranulation, and (iii) innate immune system pathways. The neurofascin (NFASC) is shown to be differentially abundant among all the age groups, and alpha-1-acid glycoprotein 2-like (ORM2) and alpha-1-antitrypsin-like (SERPINA1) proteins were recognized as members of all three above mentioned REACTOME pathways. Furthermore, 29 of plasma proteins were significantly differentially abundant in loggerheads age and recovery period groups. Out of 15 recognized pathways, those proteins were mostly included in three specific REACTOME pathways: (i) post-translational phosphorylation, (ii) regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs), and (iii) platelet degranulation. The alpha-fetoprotein (AFP) was the only protein which showed statistically significant up-regulation patterns in all loggerhead age groups before release from the rescue centre, and the complement component 3 (C3) protein was the only protein modulated in all recovery period groups. Furthermore, C3 protein takes part in 9; and followed up with apolipoprotein A-I (APOA1) in 7; complement component 4 (C4), complement component 5 (C5) and kininogen-1 (KNG1) in 6 REACTOME pathways. Thereby, those proteins are highlighted and recommended as potential biomarkers of turtle's health status. Data are available via ProteomeXchange with identifier PXD029569. Finally, based on our results, we believe that comprehensive omics approach and routine plasma biochemical analysis, accompanied by proteins of acute phase, acid-base status and immune-response indicator analysis may significantly and reliably improve assessment of captive loggerheads rehabilitation and medication. SIGNIFICANCE: Monitoring and comparison of loggerhead sea turtles (C. caretta) blood plasma biochemistry parameters and plasma proteome profiles in relation to the age, and recovery period pointed out significantly differentially abundant proteins, along with certain biochemical parameter contents as potential biomarkers of turtle's fitness, health status and physiology.
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Affiliation(s)
- Ž Jakšić
- Ruđer Bošković Institute, Center for Marine Rresearch Rovinj, G. Paliage 5, HR - 52210 Rovinj, Croatia; Marine Educational Centre Pula, A. Negri 10, HR - 52100 Pula, Croatia.
| | - V Mrljak
- University of Zagreb, Faculty of Veterinary Medicine, Department of Pathophysiology, Heinzelova 55, HR - 10000 Zagreb, Croatia
| | - A Horvatić
- University of Zagreb, Faculty of Veterinary Medicine, Department of Pathophysiology, Heinzelova 55, HR - 10000 Zagreb, Croatia; University of Zagreb, Faculty of Food Technology and Biotechnology, Department of Chemistry and Biochemistry, Pierottieva 6, HR - 10000 Zagreb, Croatia
| | - A Gelemanović
- Mediterranean Institute for Life Sciences (MedILS), Šetalište Ivana Meštrovića 45, HR - 21000 Split, Croatia
| | - M Mičić
- Aquarium Verudela, Verudela bb, HR - 52105 Pula, Croatia; Marine Educational Centre Pula, A. Negri 10, HR - 52100 Pula, Croatia
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17
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Wilson AE, Michaud SA, Jackson AM, Stenhouse G, McClelland CJR, Coops NC, Janz DM. Protein biomarkers in serum as a conservation tool to assess reproduction: a case study on brown bears ( Ursus arctos). CONSERVATION PHYSIOLOGY 2021; 9:coab091. [PMID: 34888057 PMCID: PMC8651255 DOI: 10.1093/conphys/coab091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Monitoring the reproductive characteristics of a species can complement existing conservation strategies by understanding the mechanisms underlying demography. However, methodology to determine important aspects of female reproductive biology is often absent in monitoring programs for large mammals. Protein biomarkers may be a useful tool to detect physiological changes that are indicative of reproductive state. This study aimed to identify protein biomarkers of reproductive status in serum collected from free-ranging female brown bears (Ursus arctos) in Alberta, Canada, from 2001 to 2018. We hypothesized that the expression of proteins related to reproduction in addition to energetics and stress can be used to answer specific management-focused questions: (i) identify when a female is pregnant, (ii) detect if a female is lactating, (iii) determine age of sexual maturity (i.e. primiparity) and (iv) assess female fertility (i.e. reproduction rate). Furthermore, we investigated if silver spoon effects (favourable early life conditions provide fitness benefits through adulthood) could be determined using protein expression. A target panel of 19 proteins with established relationships to physiological function was measured by peptide-based analysis using liquid chromatography and multiple reaction monitoring mass spectrometry and their differential expression was evaluated using a Wilcoxon signed-rank test. We found biomarkers of pregnancy (apolipoprotein B-100 and afamin), lactation (apolipoprotein B-100 and alpha-2-macroglobulin) and sexual maturity (corticosteroid-binding globulin), but there were no statistically significant relationships with protein expression and fertility. The expression of proteins related to reproduction (afamin) and energetics (vitamin-D binding protein) was associated with the nutritional quality of the individual's present habitat rather than their early life habitat. This study highlights potential biomarkers of reproductive status and provides additional methods for monitoring physiological function in wildlife to inform conservation.
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Affiliation(s)
- Abbey E Wilson
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Sarah A Michaud
- The University of Victoria Genome BC Proteomics Centre, 4464 Markham St #3101, Victoria, British Columbia V8Z 7X8, Canada
| | - Angela M Jackson
- The University of Victoria Genome BC Proteomics Centre, 4464 Markham St #3101, Victoria, British Columbia V8Z 7X8, Canada
| | - Gordon Stenhouse
- Grizzly Bear Program, fRI Research, 1176 Switzer Drive, Hinton, Alberta T7V 1V3, Canada
| | | | - Nicholas C Coops
- Department of Forest Resource Management, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - David M Janz
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada
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18
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Dang X, Lin H, Yuan Y, Yang B, Dong J, Zhang Z, Yang K, Li Y, Li X, Chai D, Zuo Y. Quantitative Proteomics Analysis of Differentially Expressed Proteins in Serum of Former Uranium Miners by Isobaric Tags for the Relative and Absolute Quantitation. Dose Response 2021; 19:15593258211056190. [PMID: 34819815 PMCID: PMC8606944 DOI: 10.1177/15593258211056190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022] Open
Abstract
The carcinogenicity of radon has been convincingly documented through epidemiological studies of underground miners. However, there is a lack of early warning indicators for radon radiation damage. In this study, mixed serum samples of 3 groups were collected from 27 underground uranium miners and seven aboveground miners according to the radiation exposure dose. The differentially expressed proteins in the serum were identified using the isobaric tags for the relative and absolute quantitation (iTRAQ)-based method. Some differentially expressed proteins were validated by enzyme-linked immunosorbent assay (ELISA) in 84 underground and 32 aboveground miners. A total of 25 co-differentially expressed proteins in 2 underground miner groups were screened, of which 9 were downregulated and 13 were upregulated. Biological process analysis of these proteins using Metascape showed that 5 GO terms were enriched, such as negative regulation of very-low-density lipoprotein particle clearance, endocytosis, and regulated exocytosis. The results of the ELISA for the expression levels of GCN1, CIP2A, and IGHV1-24 in the serum of 116 miners’ serum showed that the levels of GCN1 and CIP2A were consistent with the iTRAQ results. In conclusion, APOC1, APOC2, APOC3, ORM1, ORM2, ANTXR1, GCN1, and CIP2A may be potential early markers of radon radiation damage.
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Affiliation(s)
- Xuhong Dang
- China Institute for Radiation Protection, Taiyuan, China
| | - Haipeng Lin
- China Institute for Radiation Protection, Taiyuan, China
| | - Yayi Yuan
- China Institute for Radiation Protection, Taiyuan, China
| | - Biao Yang
- China Institute for Radiation Protection, Taiyuan, China
| | - Juancong Dong
- China Institute for Radiation Protection, Taiyuan, China
| | - Zhongxin Zhang
- China Institute for Radiation Protection, Taiyuan, China
| | - Kai Yang
- China Institute for Radiation Protection, Taiyuan, China
| | - Youchen Li
- China Institute for Radiation Protection, Taiyuan, China
| | - Xiaozhen Li
- China Institute for Radiation Protection, Taiyuan, China
| | - Dongliang Chai
- China Institute for Radiation Protection, Taiyuan, China
| | - Yahui Zuo
- China Institute for Radiation Protection, Taiyuan, China
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19
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Martin DR, Sibuyi NR, Dube P, Fadaka AO, Cloete R, Onani M, Madiehe AM, Meyer M. Aptamer-Based Diagnostic Systems for the Rapid Screening of TB at the Point-of-Care. Diagnostics (Basel) 2021; 11:1352. [PMID: 34441287 PMCID: PMC8391981 DOI: 10.3390/diagnostics11081352] [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: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
The transmission of Tuberculosis (TB) is very rapid and the burden it places on health care systems is felt globally. The effective management and prevention of this disease requires that it is detected early. Current TB diagnostic approaches, such as the culture, sputum smear, skin tuberculin, and molecular tests are time-consuming, and some are unaffordable for low-income countries. Rapid tests for disease biomarker detection are mostly based on immunological assays that use antibodies which are costly to produce, have low sensitivity and stability. Aptamers can replace antibodies in these diagnostic tests for the development of new rapid tests that are more cost effective; more stable at high temperatures and therefore have a better shelf life; do not have batch-to-batch variations, and thus more consistently bind to a specific target with similar or higher specificity and selectivity and are therefore more reliable. Advancements in TB research, in particular the application of proteomics to identify TB specific biomarkers, led to the identification of a number of biomarker proteins, that can be used to develop aptamer-based diagnostic assays able to screen individuals at the point-of-care (POC) more efficiently in resource-limited settings.
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Affiliation(s)
- Darius Riziki Martin
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Nicole Remaliah Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Phumuzile Dube
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Adewale Oluwaseun Fadaka
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Martin Onani
- Department of Chemistry, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Abram Madimabe Madiehe
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
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20
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Jafari A, Babajani A, Rezaei-Tavirani M. Multiple Sclerosis Biomarker Discoveries by Proteomics and Metabolomics Approaches. Biomark Insights 2021; 16:11772719211013352. [PMID: 34017167 PMCID: PMC8114757 DOI: 10.1177/11772719211013352] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/05/2021] [Indexed: 12/22/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune inflammatory disorder of the central nervous system (CNS) resulting in demyelination and axonal loss in the brain and spinal cord. The precise pathogenesis and etiology of this complex disease are still a mystery. Despite many studies that have been aimed to identify biomarkers, no protein marker has yet been approved for MS. There is urgently needed for biomarkers, which could clarify pathology, monitor disease progression, response to treatment, and prognosis in MS. Proteomics and metabolomics analysis are powerful tools to identify putative and novel candidate biomarkers. Different human compartments analysis using proteomics, metabolomics, and bioinformatics approaches has generated new information for further clarification of MS pathology, elucidating the mechanisms of the disease, finding new targets, and monitoring treatment response. Overall, omics approaches can develop different therapeutic and diagnostic aspects of complex disorders such as multiple sclerosis, from biomarker discovery to personalized medicine.
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Affiliation(s)
- Ameneh Jafari
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhesam Babajani
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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21
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Reichmuth AM, Kübrich K, Blickenstorfer Y, Frutiger A, Momotenko D, Gatterdam V, Treindl F, Fattinger C, Vörös J. Investigating Complex Samples with Molograms of Low-Affinity Binders. ACS Sens 2021; 6:1067-1076. [PMID: 33629586 DOI: 10.1021/acssensors.0c02346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In vitro diagnostics relies on the quantification of minute amounts of a specific biomolecule, called biomarker, from a biological sample. The majority of clinically relevant biomarkers for conditions beyond infectious diseases are detected by means of binding assays, where target biomarkers bind to a solid phase and are detected by biochemical or physical means. Nonspecifically bound biomolecules, the main source of variation in such assays, need to be washed away in a laborious process, restricting the development of widespread point-of-care diagnostics. Here, we show that a diffractometric assay provides a new, label-free possibility to investigate complex samples, such as blood plasma. A coherently arranged sub-micron pattern, that is, a peptide mologram, is created to demonstrate the insensitivity of this diffractometric assay to the unwanted masking effect of nonspecific interactions. In addition, using an array of low-affinity binders, we also demonstrate the feasibility of molecular profiling of blood plasma in real time and show that individual patients can be differentiated based on the binding kinetics of circulating proteins.
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Affiliation(s)
- Andreas M. Reichmuth
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Katharina Kübrich
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Yves Blickenstorfer
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Volker Gatterdam
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Fridolin Treindl
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Christof Fattinger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
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Deng L, Han Y, Tang C, Liao Q, Li Z. Label-Free Mass Spectrometry-Based Quantitative Proteomics Analysis of Serum Proteins During Early Pregnancy in Jennies ( Equus asinus). Front Vet Sci 2020; 7:569587. [PMID: 33195553 PMCID: PMC7642908 DOI: 10.3389/fvets.2020.569587] [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: 06/04/2020] [Accepted: 09/18/2020] [Indexed: 11/17/2022] Open
Abstract
Early pregnancy in jennies is routinely determined by palpation per rectum or ultrasonography and also by detecting steroid hormone and chorionic gonadotropin levels in the blood, plasma, and serum. Herein we applied label-free mass spectrometry-based quantitative proteomics to identify serum proteins that were differentially expressed between early pregnant (day 45 after ovulation) and non-pregnant jennies. Bioinformatics analysis allowed illustration of pathways potentially involved in early pregnancy. We identified 295 proteins from a total of 2,569 peptides. Twenty-five proteins (22 upregulated and three downregulated) were significantly differentially expressed between the early pregnant and non-pregnant groups. The majority of the differentially expressed proteins were involved in defense response, early embryonic development, and hormone signaling pathways. Furthermore, functional protein analyses suggested that proteins were involved in binding, enzyme inhibitor activity, and enzyme regulator activity. Five serum proteins—granulin precursor/acrogranin, transgelin-2, fibronectin, fibrinogen-like 1, and thrombospondin 1—can be considered as novel, reliable candidates to detect pregnancy in jennies. To the best of our knowledge, this is the first study to use label-free mass spectrometry-based quantitative proteomics to analyze serum proteins during early pregnancy in jennies. Our results should facilitate the identification of valuable pregnancy diagnostic markers in early pregnant jennies.
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Affiliation(s)
- Liang Deng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuwei Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chi Tang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingchao Liao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zheng Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Kumar V, Ray S, Ghantasala S, Srivastava S. An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma. Front Oncol 2020; 10:543997. [PMID: 33072574 PMCID: PMC7538778 DOI: 10.3389/fonc.2020.543997] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Blood plasma is one of the most widely used samples for cancer biomarker discovery research as well as clinical investigations for diagnostic and therapeutic purposes. However, the plasma proteome is extremely complex due to its wide dynamic range of protein concentrations and the presence of high-abundance proteins. Here we have described an optimized, integrated quantitative proteomics pipeline combining the label-free and multiplexed-labeling-based (iTRAQ and TMT) plasma proteome profiling methods for biomarker discovery, followed by the targeted approaches for validation of the identified potential marker proteins. In this workflow, the targeted quantitation of proteins is carried out by multiple-reaction monitoring (MRM) and parallel-reaction monitoring (PRM) mass spectrometry. Thus, our approach enables both unbiased screenings of biomarkers and their subsequent selective validation in human plasma. The overall procedure takes only ~2 days to complete, including the time for data acquisition (excluding database searching). This protocol is quick, flexible, and eliminates the need for a separate immunoassay-based validation workflow in blood cancer biomarker investigations. We anticipate that this plasma proteomics workflow will help to accelerate the cancer biomarker discovery program and provide a valuable resource to the cancer research community.
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Affiliation(s)
- Vipin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Saicharan Ghantasala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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24
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Li W, Sun X, Zhao X, Wang W, Xu S, Luo X. Rapid pattern recognition of different types of sulphur-containing species as well as serum and bacteria discrimination using Au NCs-Cu2+ complexes. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.04.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Bai J, Zhong JY, Liao W, Hu R, Chen L, Wu XJ, Liu SP. iTRAQ‑based proteomic analysis reveals potential regulatory networks in dust mite‑related asthma treated with subcutaneous allergen immunotherapy. Mol Med Rep 2020; 22:3607-3620. [PMID: 32901873 PMCID: PMC7533450 DOI: 10.3892/mmr.2020.11472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 02/24/2020] [Indexed: 12/29/2022] Open
Abstract
Asthma is one of the most common childhood chronic diseases worldwide. Subcutaneous immunotherapy (SCIT) is commonly used in the treatment of house dust mite (HDM)‑related asthma in children. However, the therapeutic mechanism of SCIT in asthma remains unclear. The present study aimed to investigate the molecular biomarkers associated with HDM‑related asthma in asthmatic children prior and subsequent to SCIT treatment compared with those in healthy children via proteomic analysis. The study included a control group (30 healthy children), ‑Treatment group (30 children with HDM‑related allergic asthma) and +Treatment group (30 children with HDM‑related allergic asthma treated with SCIT). An isobaric labeling with relative and absolute quantification‑based method was used to analyze serum proteome changes to detect differentially expressed proteins, while functional enrichment and protein‑protein interaction network analysis were used to select candidate biomarkers. A total of 72 differentially expressed proteins were detected in the ‑Treatment, +Treatment and control groups. A total of 33 and 57 differentially expressed proteins were observed in the ‑Treatment vs. control and +Treatment vs. control groups, respectively. Through bioinformatics analysis, 5 candidate proteins [keratin 1 (KRT1), apolipoprotein B (APOB), fibronectin 1, antithrombin III (SERPINC1) and α‑1‑antitrypsin (SERPINA1)] were selected for validation by western blotting; among them, 4 proteins (KRT1, APOB, SERPINC1 and SERPINA1) showed robust reproducibility in asthma and control samples. This study illustrated the changes in proteome regulation following SCIT treatment for asthma. The 4 identified proteins may serve as potential biomarkers prior and subsequent to SCIT treatment, and help elucidate the molecular regulation mechanisms of SCIT to treat HDM‑related asthma.
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Affiliation(s)
- Jun Bai
- Department of Pediatrics, Foshan Maternal and Children's Hospital Affiliated to Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Jia-Yong Zhong
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, P.R. China
| | - Wang Liao
- Department of Pediatrics, Foshan Maternal and Children's Hospital Affiliated to Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Ruo Hu
- School of Computer Science, Guangdong Polytechnic Normal University, Guangzhou, Guangdong 510000, P.R. China
| | - Liang Chen
- Department of Pediatrics, Foshan Maternal and Children's Hospital Affiliated to Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Xian-Jin Wu
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Key Laboratory of Hunan Higher Education for Western Hunan Medicinal Plant and Ethnobotany, College of Biological and Food Engineering, Huaihua University, Huaihua, Hunan 418008, P.R. China
| | - Shuang-Ping Liu
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
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26
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Palstrøm NB, Rasmussen LM, Beck HC. Affinity Capture Enrichment versus Affinity Depletion: A Comparison of Strategies for Increasing Coverage of Low-Abundant Human Plasma Proteins. Int J Mol Sci 2020; 21:ijms21165903. [PMID: 32824511 PMCID: PMC7460666 DOI: 10.3390/ijms21165903] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/20/2022] Open
Abstract
In the present study, we evaluated four small molecule affinity-based probes based on agarose-immobilized benzamidine (ABA), O-Phospho-L-Tyrosine (pTYR), 8-Amino-hexyl-cAMP (cAMP), or 8-Amino-hexyl-ATP (ATP) for their ability to remove high-abundant proteins such as serum albumin from plasma samples thereby enabling the detection of medium-to-low abundant proteins in plasma samples by mass spectrometry-based proteomics. We compared their performance with the most commonly used immunodepletion method, the Multi Affinity Removal System Human 14 (MARS14) targeting the top 14 most abundant plasma proteins and also the ProteoMiner protein equalization method by label-free quantitative liquid chromatography tandem mass spectrometry (LC-MSMS) analysis. The affinity-based probes demonstrated a high reproducibility for low-abundant plasma proteins, down to picomol per mL levels, compared to the Multi Affinity Removal System (MARS) 14 and the Proteominer methods, and also demonstrated superior removal of the majority of the high-abundant plasma proteins. The ABA-based affinity probe and the Proteominer protein equalization method performed better compared to all other methods in terms of the number of analyzed proteins. All the tested methods were highly reproducible for both high-abundant plasma proteins and low-abundant proteins as measured by correlation analyses of six replicate experiments. In conclusion, our results demonstrated that small-molecule based affinity-based probes are excellent alternatives to the commonly used immune-depletion methods for proteomic biomarker discovery studies in plasma. Data are available via ProteomeXchange with identifier PXD020727.
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Affiliation(s)
- Nicolai Bjødstrup Palstrøm
- Centre of Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, DK-5000 Odense C, Denmark; (N.B.P.); (L.M.R.)
- Centre for Clinical Proteomics, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Lars Melholt Rasmussen
- Centre of Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, DK-5000 Odense C, Denmark; (N.B.P.); (L.M.R.)
- Centre for Clinical Proteomics, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Hans Christian Beck
- Centre of Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, DK-5000 Odense C, Denmark; (N.B.P.); (L.M.R.)
- Centre for Clinical Proteomics, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense C, Denmark
- Correspondence: ; Tel.: +45-29647470
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Elechalawar CK, Hossen MN, McNally L, Bhattacharya R, Mukherjee P. Analysing the nanoparticle-protein corona for potential molecular target identification. J Control Release 2020; 322:122-136. [PMID: 32165239 PMCID: PMC7675788 DOI: 10.1016/j.jconrel.2020.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/18/2022]
Abstract
When nanoparticles are introduced into biological systems, host proteins tend to associate on the particle surface to form a protein layer termed the "protein corona" (PC). Identifying the proteins that constitute the PC can yield useful information about nanoparticle processing, bio-distribution, toxicity and clearance. Similarly, characterizing and identifying proteins within the PC from patient samples provides opportunities to probe disease proteomes and identify molecules that influence the disease process. Thus, nanoparticles represent unique probing tools for discovery of molecular targets for diseases. Here, we report a first review on target identification using nanoparticles in biological samples based on analysing physico chemical interactions. We also summarize the evolution of the PC surrounding various nano-systems, comment on PC signature, address PC complexity in fluids, and outline challenges associated with analysing the PC. In addition, the influence on PC formation of various nanoparticle parameters is summarized; nanoparticle characteristics considered include size, charge, temperature, and surface modifications for both organic and inorganic nanomaterials. We also discuss the advantages of nanotechnology, over other more invasive and laborious methods, for identifying potential diagnostic and therapeutic targets.
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Affiliation(s)
| | - Md Nazir Hossen
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Lacey McNally
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Priyabrata Mukherjee
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Peggy and Charles Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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28
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Babele P, Kumar RB, Rajoria S, Rashid F, Malakar D, Bhagyawant SS, Kamboj DV, Alam SI. Putative serum protein biomarkers for epsilon toxin exposure in mouse model using LC-MS/MS analysis. Anaerobe 2020; 63:102209. [PMID: 32387808 DOI: 10.1016/j.anaerobe.2020.102209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 11/17/2022]
Abstract
Epsilon toxin (ETX), produced by Clostridium perfringens Type B or type D strains, is a potential biological and toxin warfare (BTW) agent, largely for its very high toxicity. The toxin is implicated in several animal diseases. Using LC-MS/MS analysis, we report here elucidation of putative serum maker proteins for ETX exposure with an objective of the early diagnosis of intoxication. Of 166 consensus proteins (488 peptides), showing ETX-induced alterations, 119 proteins exhibited increase and 47 proteins showed decreased abundance in serum, as revealed by SWATH (DIA) acquisition on LC-MS/MS and label free quantitative analysis of control and test samples. Complement and coagulation cascade, nitrogen metabolism, negative regulation of peptidase activity, and response to ROS were among the biological processes and pathways perturbed by the ETX exposure. Interaction network indicated enzyme inhibitor activity, detoxification of ROS, and steroid binding functions were the major interaction networks for the proteins with increased abundance, while, hemostasis and structural molecule activity were the prominent networks for the down-regulated proteins. Validation studies were carried out by immunoprecipitation, ELISA, and Western blot analysis of selected proteins to demonstrate diagnostic potential of the putative marker proteins of ETX exposure.
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Affiliation(s)
- Prabhakar Babele
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ravi Bhushan Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Sakshi Rajoria
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Faraz Rashid
- Sciex, 121 DHR, Udyog Vihar, Gurugram, Haryana, India
| | - Dipankar Malakar
- School of Studies in Biotechnology, Jiwaji University, Gwalior, 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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29
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Harberts E, Liang T, Yoon SH, Opene BN, McFarland MA, Goodlett DR, Ernst RK. Toll-like Receptor 4-Independent Effects of Lipopolysaccharide Identified Using Longitudinal Serum Proteomics. J Proteome Res 2020; 19:1258-1266. [PMID: 32037835 DOI: 10.1021/acs.jproteome.9b00765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Sepsis remains one of the most lethal and costly conditions treated in U.S. hospitals, with approximately 50% of cases caused by Gram-negative bacterial infections. Septic shock is induced when lipopolysaccharide (LPS), the main component of Gram-negative outer bacterial membrane, signals through the Toll-like receptor 4 (TLR4) complex. Lethal endotoxemia, a model for septic shock, was induced in WT C57BL6 and TLR4-/- mice by administration of Escherichia coli LPS. WT LPS treated mice showed high morbidity, while PBS treated LPS and treated TLR4-/- mice did not. ANOVA analysis of label-free quantification of longitudinal serum proteome revealed 182 out of 324 proteins in LPS injected WT mice that were significantly changed across four time points (0, 6, 12, and 18 h). No significant changes were identified in the two control groups. From the 182 identified proteins, examples of known sepsis biomarkers were validated by ELISA, which showed similar trends as MS proteomics data. Longitudinal analysis within individual mice produced 3-fold more significantly changed proteins than pair-wise comparison. A subsequent global analysis of WT and TLR4-/- mice identified pathways activated independent of TLR4. These pathways represent possible compensatory mechanisms that allow for control of Gram-negative bacterial infection regardless of host immune status.
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Affiliation(s)
- Erin Harberts
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Tao Liang
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Sung Hwan Yoon
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Belita N Opene
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Melinda A McFarland
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 21201, United States
| | - David R Goodlett
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States.,University of Gdansk, International Centre for Cancer Vaccine Science, 80-308 Gdansk, Poland, EU
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
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Zhao X, Gao Y, Wang J, Zhan Y, Lu X, Xu S, Luo X. Aggregation-induced emission based one-step “lighting up” sensor array for rapid protein identification. Chem Commun (Camb) 2020; 56:13828-13831. [DOI: 10.1039/d0cc05749e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Based on the distinct fingerprint-like fluorescence responses generated by different electrostatic and hydrophobic interactions, a “lighting up” aggregation-induced emission (AIE) sensor array was developed for rapid protein discrimination.
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Affiliation(s)
- Xuan Zhao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science
- MOE
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Yuhuan Gao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science
- MOE
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Jun Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science
- MOE
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Yating Zhan
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science
- MOE
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xin Lu
- Tianjin Institute for Drug Control
- Tianjin 300070
- P. R. China
| | - Shenghao Xu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science
- MOE
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science
- MOE
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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31
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Zhang L, Huang J, Lin Q, Ma Y, Xia R, Zhu Y, Abudubari S. Serum Proteomic Profiling Analysis of Rats Chronically Exposed to Arsenic. Med Sci Monit 2019; 25:9923-9932. [PMID: 31874112 PMCID: PMC6941779 DOI: 10.12659/msm.918696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Arsenic (As) is an environmental contaminant, and As pollution in water and soil is a public health issue worldwide. As exposure is associated with the incidence of many disorders, such as arteriosclerosis, diabetes, neurodegenerative diseases, and renal dysfunction. However, the mechanism of As toxicity remains unclear. Material/Methods We investigated the changes in serum protein profiles of rats chronically exposed to As. Twenty healthy rats were randomly divided into 4 groups, and sodium arsenite of varying final concentrations (0, 2, 10, and 50 mg/L, respectively) was add into the drinking water for each group. The administration lasted for 3 months. Two proteomic strategies, isobaric tags for relative and absolute quantitation (iTRAQ), and 2-dimensional gel electrophoresis (2-DE), were employed to screen the differential serum proteins between control and arsenite exposure groups. Results We identified a total of 27 differentially-expressed proteins, among which 9 proteins were significantly upregulated and 18 were downregulated by As exposure. Many of the differentially-expressed proteins were related to fat digestion and absorption, including 5 apolipoproteins, which indicated lipid metabolism may be the most affected by As exposure. Conclusions This study revealed the influence of As on lipid metabolism, suggesting an increased potential risk of relevant diseases in subjects chronically exposed to As.
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Affiliation(s)
- Ling Zhang
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Jia Huang
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland).,School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
| | - Qin Lin
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Yan Ma
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
| | - Rongxiang Xia
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Yuming Zhu
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Saimaitikari Abudubari
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
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32
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Erkan EP, Ströbel T, Dorfer C, Sonntagbauer M, Weinhäusel A, Saydam N, Saydam O. Circulating Tumor Biomarkers in Meningiomas Reveal a Signature of Equilibrium Between Tumor Growth and Immune Modulation. Front Oncol 2019; 9:1031. [PMID: 31649887 PMCID: PMC6795693 DOI: 10.3389/fonc.2019.01031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/24/2019] [Indexed: 12/31/2022] Open
Abstract
Meningiomas are primary central nervous system (CNS) tumors that originate from the arachnoid cells of the meninges. Recurrence occurs in higher grade meningiomas and a small subset of Grade I meningiomas with benign histology. Currently, there are no established circulating tumor markers which can be used for diagnostic and prognostic purposes in a non-invasive way for meningiomas. Here, we aimed to identify potential biomarkers of meningioma in patient sera. For this purpose, we collected preoperative (n = 30) serum samples from the meningioma patients classified as Grade I (n = 23), Grade II (n = 4), or Grade III (n = 3). We used a high-throughput, multiplex immunoassay cancer panel comprising of 92 cancer-related protein biomarkers to explore the serum protein profiles of meningioma patients. We detected 14 differentially expressed proteins in the sera of the Grade I meningioma patients in comparison to the age- and gender-matched control subjects (n = 12). Compared to the control group, Grade I meningioma patients showed increased serum levels of amphiregulin (AREG), CCL24, CD69, prolactin, EGF, HB-EGF, caspase-3, and decreased levels of VEGFD, TGF-α, E-Selectin, BAFF, IL-12, CCL9, and GH. For validation studies, we utilized an independent set of meningioma tumor tissue samples (Grade I, n = 20; Grade II, n = 10; Grade III, n = 6), and found that the expressions of amphiregulin and Caspase3 are significantly increased in all grades of meningiomas either at the transcriptional or protein level, respectively. In contrast, the gene expression of VEGF-D was significantly lower in Grade I meningioma tissue samples. Taken together, our study identifies a meningioma-specific protein signature in blood circulation of meningioma patients and highlights the importance of equilibrium between tumor-promoting factors and anti-tumor immunity.
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Affiliation(s)
- Erdogan Pekcan Erkan
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Thomas Ströbel
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Markus Sonntagbauer
- Austrian Institute of Technology, Molecular Diagnostics Center for Health and Bioresources, Vienna, Austria
| | - Andreas Weinhäusel
- Austrian Institute of Technology, Molecular Diagnostics Center for Health and Bioresources, Vienna, Austria
| | - Nurten Saydam
- Department of Biochemistry, Molecular Biology, and Biophysics, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Okay Saydam
- Division of Hematology and Oncology, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, United States
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Xu S, Li W, Zhao X, Wu T, Cui Y, Fan X, Wang W, Luo X. Ultrahighly Efficient and Stable Fluorescent Gold Nanoclusters Coated with Screened Peptides of Unique Sequences for Effective Protein and Serum Discrimination. Anal Chem 2019; 91:13947-13952. [DOI: 10.1021/acs.analchem.9b03463] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Shenghao Xu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Wentao Li
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xuan Zhao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Tong Wu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yanyun Cui
- School of Science, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Xinyue Fan
- Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Wei Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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Yao B, Liu J, Xu D, Pan D, Zhang M, Zhao D, Leng X. Dissection of the molecular targets and signaling pathways of Guzhi Zengsheng Zhitongwan based on the analysis of serum proteomics. Chin Med 2019; 14:29. [PMID: 31485261 PMCID: PMC6712859 DOI: 10.1186/s13020-019-0252-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
Background Guzhi Zengsheng Zhitongwan (GZZSZTW) is an effective formula of traditional Chinese herbal medicine and has been widely applied in the treatment of joint diseases for many years. The aim of this study was to dissect the molecular targets and signaling pathways of Guzhi Zengsheng Zhitongwan based on the analysis of serum proteomics. Methods The Chinese herbs of GZZSZTW were immersed in 5 l distilled water and boiled with reflux extraction method. The extract was filtered, concentrated and freeze-dried. The chemical profile of GZZSZTW extract was determined by high-performance lipid chromatography (HPLC). The 7-week old Sprague-Dawley (SD) rats in GZZSZTW groups were received oral administration at doses of 0.8, 1.05, and 1.3 g/kg per day and the rats in blank group were fed with drinking water. Serum samples were collected from the jugular veins. Primary chondrocyte viability was evaluated by CCK-8 assay. A full spectrum of the molecular targets and signaling pathways of GZZSZTW were investigated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis and a systematic bioinformatics analysis accompanied with parallel reaction monitoring (PRM) and siRNA validation. Results GZZSZTW regulated a series of functional proteins and signaling pathways responsible for cartilage development, growth and repair. Functional classification analysis indicated that these proteins were mainly involved in the process of cell surface dynamics. Pathway analysis mapped these proteins into several signalling pathways involved in chondrogenesis, chondrocyte proliferation and differentiation, and cartilage repair, including hippo signaling pathway, cGMP-PKG signaling pathway, cell cycle and calcium signaling pathway. Protein–protein interaction analysis and siRNA knockdown assay identified an interaction network consisting of TGFB1, RHO GTPases, ILK, FLNA, LYN, DHX15, PKM, RAB15, RAB1B and GIPC1. Conclusions Our results suggest that the effects of GZZSZTW on treating joint diseases might be achieved through the TGFB1/RHO interaction network coupled with other proteins and signaling pathways responsible for cartilage development, growth and repair. Therefore, the present study has greatly expanded our knowledge and provided scientific support for the underlying therapeutic mechanisms of GZZSZTW on treating joint diseases. It also provided possible alternative strategies for the prevention and treatment for joint diseases by using traditional Chinese herbal formulas.
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Affiliation(s)
- Baojin Yao
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Jia Liu
- 2College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Duoduo Xu
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Daian Pan
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Mei Zhang
- 3Innovation Practice Center, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Daqing Zhao
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Xiangyang Leng
- 4The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
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Park HG, Jang KS, Park HM, Song WS, Jeong YY, Ahn DH, Kim SM, Yang YH, Kim YG. MALDI-TOF MS-based total serum protein fingerprinting for liver cancer diagnosis. Analyst 2019; 144:2231-2238. [PMID: 30849133 DOI: 10.1039/c8an02241k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Serum is one of the most commonly used samples in many studies to identify protein biomarkers to diagnose cancer. Although conventional enzyme-linked immunosorbent assay (ELISA) or liquid chromatography-mass spectrometry (LC-MS)-based methods have been applied as clinical tools for diagnosing cancer, there have been troublesome problems, such as inferior multiplexing capabilities, high development costs and long turnaround times, which are inappropriate for high-throughput analytical platforms. Here, we developed a simple and robust cancer diagnostic method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based total serum protein fingerprinting. First, serum samples were simply diluted with distilled water and subsequently spotted onto a MALDI plate without prior chromatographic purification or separation. The sample preparation method was enough to collect reproducible total serum protein fingerprints and would be highly advantageous for high-throughput assay. Each of the integrated main spectrum profiles (MSPs), which are representative of liver cancer patients (n = 40) or healthy controls (n = 80), was automatically generated by the MALDI Biotyper 3 software. The reliability of the integrated MSPs was successfully evaluated in comparison with a blind test set (n = 31), which consisted of 13 liver cancer patients and 18 healthy controls. Additionally, our partial least squares discriminant analysis (PLS-DA) demonstrated a statistically significant difference in MALDI-TOF MS-based total serum protein fingerprints between liver cancer patients and healthy controls. Taken together, this work suggests that this method may be an effective high-throughput platform technology for various cancer diagnoses and disease evaluations.
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Affiliation(s)
- Han-Gyu Park
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Korea.
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Meyfour A, Hosseini M, Sobhanian H, Pahlavan S. Iran's Contribution to Human Proteomic Research. CELL JOURNAL 2019; 21:229-235. [PMID: 31210427 PMCID: PMC6582420 DOI: 10.22074/cellj.2019.6303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/17/2018] [Indexed: 11/04/2022]
Abstract
Proteomics is a powerful approach to study the whole set of proteins expressed in an organism, organ, tissue or cell resulting in valuable information on physiological or pathological state of a biological system. High throughput proteomic data facilitated the understanding of various biological systems with respect to normal and pathological conditions particularly in the instances of human clinical manifestations. The important role of proteins as the functional gene products encouraged scientists to apply this technology to gain a better understanding of extremely complex biological systems. In last two decades, several proteomics teams have been gradually formed in Iran. In this review, we highlight the most important findings of proteomic research groups in Iran at various areas of stem cells, Y chromosome, infertility, infectious disease and biomarker discovery.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mahya Hosseini
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.Electronic Address:
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Proteomics in Human Parkinson’s Disease: Present Scenario and Future Directions. Cell Mol Neurobiol 2019; 39:901-915. [DOI: 10.1007/s10571-019-00700-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022]
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38
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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] [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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Ray P, Steckl AJ. Label-Free Optical Detection of Multiple Biomarkers in Sweat, Plasma, Urine, and Saliva. ACS Sens 2019; 4:1346-1357. [PMID: 30900871 DOI: 10.1021/acssensors.9b00301] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a novel label-free quantitative detection of human performance "stress" biomarkers in different body fluids based on optical absorbance of the biomarkers in the ultraviolet (UV) region. Stress biomarker (hormones and neurotransmitters) concentrations in bodily fluids (blood, sweat, urine, saliva) predict the physical and mental state of the individual. The stress biomarkers primarily focused on in this manuscript are cortisol, serotonin, dopamine, norepinephrine, and neuropeptide Y. UV spectroscopy of stress biomarkers performed in the 190-400 nm range has revealed primary and secondary absorption peaks at near-UV wavelengths depending on their molecular structure. UV characterization of individual and multiple biomarkers is reported in various biofluids. A microfluidic/optoelectronic platform for biomarker detection is reported, with a prime focus toward cortisol evaluation. The current limit of detection of cortisol in sweat is ∼200 ng/mL (∼0.5 μM), which is in the normal (healthy) range. Plasma samples containing both serotonin and cortisol resulted in readily detectable absorption peaks at 203 (serotonin) and 247 (cortisol) nm, confirming feasibility of simultaneous detection of multiple biomarkers in biofluid samples. UV spectroscopy performed on various stress biomarkers shows a similar increasing absorption trend with concentration. The detection mechanism is label free, applicable to a variety of biomarker types, and able to detect multiple biomarkers simultaneously in various biofluids. A microfluidic flow cell has been fabricated on a polymer substrate to enable point-of-use/care UV measurement of target biomarkers. The overall sensor combines sample dispensing and fluid transport to the detection location with optical absorption measurements with a UV light emitting diode (LED) and photodiode. The biomarker concentration is indicated as a function of photocurrent generated at the target wavelength.
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Affiliation(s)
- Prajokta Ray
- Nanoelectronics Laboratory, University of Cincinnati, Cincinnati, Ohio 45221-0030, United States of America
| | - Andrew J. Steckl
- Nanoelectronics Laboratory, University of Cincinnati, Cincinnati, Ohio 45221-0030, United States of America
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Gisbert JP, Chaparro M. Clinical Usefulness of Proteomics in Inflammatory Bowel Disease: A Comprehensive Review. J Crohns Colitis 2019; 13:374-384. [PMID: 30307487 DOI: 10.1093/ecco-jcc/jjy158] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The protein domain is probably the most ubiquitously affected in disease, response and recovery, and therefore proteomics holds special promise for biomarker discovery in general, and particularly in inflammatory bowel disease [IBD], i.e. ulcerative colitis and Crohn's disease. Tremendous progress has been made over the past decade in the development and refinement of proteomics technologies. These advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of IBD. The present review examines the current state of IBD proteomics research and its usefulness in clinical practice. We performed a systematic bibliographic search to identify studies investigating the use of proteomics in patients with IBD, and we then summarized the current 'state of the art' in the applications of proteomic technologies in the study of IBD. In particular, in the present review we provide: [1] a brief introduction to proteomics in health and disease; [2] a review of the different stages from biomarker discovery to clinical application; and [3] a comprehensive review of the clinical usefulness and application of proteomics in IBD, including: [a] screening to differentiate IBD from healthy controls; [b] differentiating Crohn's disease from ulcerative colitis; [c] prediction of the behaviour or the IBD course; [d] prediction of IBD response to biological treatment; and [e] monitoring response to treatment. We also review the importance of the type of sample-blood vs intestinal tissue-for the study of proteomics in IBD patients. Finally, we emphasize the current limitations of proteomic studies in IBD.
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Affiliation(s)
- Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
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Khan NU, Feng Z, He H, Wang Q, Liu X, Li S, Shi X, Wang X, Ge B, Huang F. A facile plasmonic silver needle for fluorescence-enhanced detection of tumor markers. Anal Chim Acta 2018; 1040:120-127. [DOI: 10.1016/j.aca.2018.07.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 11/26/2022]
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Chaubey K, Alam SI, Waghmare CK, Singh L, Srivastava N, Bhattacharya BK. Differential proteome analysis of rat plasma after diisopropyl fluorophosphate (DFP) intoxication, a surrogate of nerve agent sarin. Chem Biol Interact 2018; 298:66-71. [PMID: 30389396 DOI: 10.1016/j.cbi.2018.10.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/22/2018] [Accepted: 10/26/2018] [Indexed: 01/06/2023]
Abstract
Diisopropyl fluorophosphate (DFP), a surrogate of nerve agent sarin, is an organophosphorus (OP) compound which inhibits neuronal enzyme acetylcholinesterase (AChE). Exposure of this compound leads to a wide range of toxic symptoms and survivors may exhibit long term neurotoxicity related to cognitive and memory defects. Due to ease of availability and similar mechanism of action to other highly toxic nerve agent, DFP is widely used as model compound to trace changes associated with nerve agent exposures. Proximal fluids are widely used for the elucidation of biomarkers for exposure to toxic substances and to study the mechanism of toxicity. Using a rat model of OP intoxication, the present study was carried out to elucidate proteomic changes in plasma associated with DFP intoxication. Rats were exposed to a single dose (0.5 LD50) of DFP and their plasma proteome was studied, one day post exposure by two dimensional gel electrophoresis - mass spectrometry (2DE-MS). Some of the milestone changes were validated by Western blot analysis. A total 15 proteins showed significant fold changes in expression with respect to control after 1 day of DFP intoxication. Most of the proteins showing changes in expression at initial stages were related to immunogenic function, acute phase response, blood coagulation, and stress response. Experiments reported here demonstrate that 0.5 LD50 DFP intoxication leads to AChE inhibition, modulation of immunogenic function, and generation of stress at an early stage. Although, some proteins and their putative functional ramifications indicated similarity with those observed in our previous plasma proteome study, neurodegenerative changes were not observed in plasma of 0.5 LD50 DFP treated animals.
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Affiliation(s)
- Kalyani Chaubey
- Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior, MP, 474002, India
| | - Syed Imteyaz Alam
- Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior, MP, 474002, India.
| | - Chandra Kant Waghmare
- Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior, MP, 474002, India
| | - Lokendra Singh
- Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior, MP, 474002, India
| | - Nalini Srivastava
- School of Studies in Biochemistry, Jiwaji University, Gwalior, MP, 474002, India
| | - Bijoy K Bhattacharya
- Defence Research & Development Establishment (DRDE), Jhansi Road, Gwalior, MP, 474002, India.
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Li N, Li H, Cao L, Zhan X. Quantitative analysis of the mitochondrial proteome in human ovarian carcinomas. Endocr Relat Cancer 2018; 25:909-931. [PMID: 29997262 DOI: 10.1530/erc-18-0243] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022]
Abstract
Mitochondria play important roles in growth, signal transduction, division, tumorigenesis and energy metabolism in epithelial ovarian carcinomas (EOCs) without an effective biomarker. To investigate the proteomic profile of EOC mitochondrial proteins, a 6-plex isobaric tag for relative and absolute quantification (iTRAQ) proteomics was used to identify mitochondrial expressed proteins (mtEPs) in EOCs relative to controls, followed by an integrative analysis of the identified mtEPs and the Cancer Genome Atlas (TCGA) data from 419 patients. A total of 5115 quantified proteins were identified from purified mitochondrial samples, and 262 proteins were significantly related to overall survival in EOC patients. Furthermore, 63 proteins were identified as potential biomarkers for the development of an EOC, and our findings were consistent with previous reports on a certain extent. Pathway network analysis identified 70 signaling pathways. Interestingly, the results demonstrated that cancer cells exhibited an increased dependence on mitophagy, such as peroxisome, phagosome, lysosome, valine, leucine and isoleucine degradation and fatty acid degradation pathways, which might play an important role in EOC invasion and metastasis. Five proteins (GLDC, PCK2, IDH2, CPT2 and HMGCS2) located in the mitochondrion and enriched pathways were selected for further analysis in an EOC cell line and tissues, and the results confirmed reliability of iTRAQ proteomics. These findings provide a large-scale mitochondrial proteomic profiling with quantitative information, a certain number of potential protein biomarkers and a novel vision in the mitophagy bio-mechanism of a human ovarian carcinoma.
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Affiliation(s)
- Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of HealthXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug DesignXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- State Local Joint Engineering Laboratory for Anticancer DrugsXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Huanni Li
- Department of Obstetrics and GynecologyXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Lanqin Cao
- Department of Obstetrics and GynecologyXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of HealthXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug DesignXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- State Local Joint Engineering Laboratory for Anticancer DrugsXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- The Laboratory of Medical GeneticsCentral South University, Changsha, Hunan, People's Republic of China
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Ma B, Chen J, Mu Y, Xue B, Zhao A, Wang D, Chang D, Pan Y, Liu J. Proteomic analysis of rat serum revealed the effects of chronic sleep deprivation on metabolic, cardiovascular and nervous system. PLoS One 2018; 13:e0199237. [PMID: 30235220 PMCID: PMC6147403 DOI: 10.1371/journal.pone.0199237] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/28/2018] [Indexed: 12/11/2022] Open
Abstract
Sleep is an essential and fundamental physiological process that plays crucial roles in the balance of psychological and physical health. Sleep disorder may lead to adverse health outcomes. The effects of sleep deprivation were extensively studied, but its mechanism is still not fully understood. The present study aimed to identify the alterations of serum proteins associated with chronic sleep deprivation, and to seek for potential biomarkers of sleep disorder mediated diseases. A label-free quantitative proteomics technology was used to survey the global changes of serum proteins between normal rats and chronic sleep deprivation rats. A total of 309 proteins were detected in the serum samples and among them, 117 proteins showed more than 1.8-folds abundance alterations between the two groups. Functional enrichment and network analyses of the differential proteins revealed a close relationship between chronic sleep deprivation and several biological processes including energy metabolism, cardiovascular function and nervous function. And four proteins including pyruvate kinase M1, clusterin, kininogen1 and profilin-1were identified as potential biomarkers for chronic sleep deprivation. The four candidates were validated via parallel reaction monitoring (PRM) based targeted proteomics. In addition, protein expression alteration of the four proteins was confirmed in myocardium and brain of rat model. In summary, the comprehensive proteomic study revealed the biological impacts of chronic sleep deprivation and discovered several potential biomarkers. This study provides further insight into the pathological and molecular mechanisms underlying sleep disorders at protein level.
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Affiliation(s)
- Bo Ma
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jincheng Chen
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongying Mu
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Bingjie Xue
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Aimei Zhao
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Daoping Wang
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Dennis Chang
- National Institute of Complementary Medicine, Western Sydney University, Penrith, Australia
| | - Yinghong Pan
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Science, Beijing, China
- * E-mail: (JL); (YP)
| | - Jianxun Liu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Complementary Medicine, Western Sydney University, Penrith, Australia
- * E-mail: (JL); (YP)
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Yu CY, Liu GY, Liu XH, Gui YZ, Liu HM, Zheng HC, Gorecki DC, Patel AV, Yu C, Wang YP. Proteomics analysis reveals a potential new target protein for the lipid-lowering effect of Berberine8998. Acta Pharmacol Sin 2018; 39:1473-1482. [PMID: 29645002 DOI: 10.1038/aps.2017.200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/08/2017] [Indexed: 02/07/2023] Open
Abstract
Berberine8998 is a newly synthesized berberine derivative with better lipid-lowering activity and improved absorption. The objective of this study was to investigate the effects of berberine8998 on serum cholesterol and lipid levels in vivo and to examine the mechanisms involved. Hamsters on high-fat diet (HFD) were administered berberine or berberine8998 (50 mg·kg-1·d-1, ig) for 3 weeks. Berberine8998 administration significantly lowered the total cholesterol, triglycerides and LDL-C levels in HFD hamsters. Bioinformatics revealed that berberine and berberine8998 shared similar metabolic pathways and fatty acid metabolism was the predominant pathway. Western blot validation results showed that peroxisomal acyl-coenzyme A oxidase 1 (ACOX1) and long-chain fatty acid-CoA ligase 1 (ACSL1), two proteins involved in fatty acid metabolism, were expressed differently in the berberine8998 group than in the untreated group and the berberine treatment group. Biochemistry results showed that berberine8998 significantly lowered the non-esterified fatty acid (NEFA) levels, which may lead to a reduction in TG levels in the berberine8998 treatment group and the differences observed in proteomics analyses. Pharmacokinetic analysis conducted in rats. After administration of berberine or berberine8998 (50 mg/kg, ig), berberine8998 exhibited a remarkably improved absorption with increasing bioavailability by 6.7 times compared with berberine. These findings suggest that berberine8998 lowers cholesterol and lipid levels via different mechanisms than berberine, and its improved absorption makes it a promising therapeutic candidate for the treatment of hypercholesterolemia and obesity.
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Cao K, Arthurs C, Atta-Ul A, Millar M, Beltran M, Neuhaus J, Horn LC, Henrique R, Ahmed A, Thrasivoulou C. Quantitative Analysis of Seven New Prostate Cancer Biomarkers and the Potential Future of the 'Biomarker Laboratory'. Diagnostics (Basel) 2018; 8:diagnostics8030049. [PMID: 30060509 PMCID: PMC6163663 DOI: 10.3390/diagnostics8030049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/11/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
Prostate cancer is the third highest cause of male mortality in the developed world, with the burden of the disease increasing dramatically with demographic change. There are significant limitations to the current diagnostic regimens and no established effective screening modality. To this end, research has discovered hundreds of potential ‘biomarkers’ that may one day be of use in screening, diagnosis or prognostication. However, the barriers to bringing biomarkers to clinical evaluation and eventually into clinical usage have yet to be realised. This is an operational challenge that requires some new thinking and development of paradigms to increase the efficiency of the laboratory process and add ‘value’ to the clinician. Value comes in various forms, whether it be a process that is seamlessly integrated into the hospital laboratory environment or one that can provide additional ‘information’ for the clinical pathologist in terms of risk profiling. We describe, herein, an efficient and tissue-conserving pipeline that uses Tissue Microarrays in a semi-automated process that could, one day, be integrated into the hospital laboratory domain, using seven putative prostate cancer biomarkers for illustration.
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Affiliation(s)
- Kevin Cao
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London WC2R 2LS, UK.
| | - Callum Arthurs
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London WC2R 2LS, UK.
| | - Ali Atta-Ul
- Prostate Cancer Research Centre, University College London, London WC1E 6BT, UK.
| | - Michael Millar
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH8 9YL, UK.
| | - Mariana Beltran
- Aquila BioMedical, Nine, Edinburgh BioQuarter, 9 Little France Road, Edinburgh EH16 4UX, UK.
| | - Jochen Neuhaus
- Head of Urology Research Laboratories, University of Leipzig, Department of Urology, Research Laboratory, Liebigstr. 19, Building C, 04103 Leipzig, Germany.
| | - Lars-Christian Horn
- Division of Gynecologic, Breast & Perinatal Pathology, University Hospital Leipzig, Liebigstasse 24 D, 04103 Leipzig, Germany.
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Abel Salazar Institute of Biomedical Sciences, University of Porto, 4099-002 Porto, Portugal.
| | - Aamir Ahmed
- Prostate Cancer Research Centre at the Centre for Stem Cells and Regenerative Medicine, King's College London, London WC2R 2LS, UK.
- Prostate Cancer Research Centre, University College London, London WC1E 6BT, UK.
| | - Christopher Thrasivoulou
- Research Department of Cell and Developmental Biology, The Centre for Cell and Molecular Dynamics, Rockefeller Building, University College London, London WC1E 6BT, UK.
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47
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Zhang Z, Li P, Lin D, Wang D, Zhang Y. Proteome analysis of the potential serum biomarkers for chronic benzene poisoning. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2018; 60:157-164. [PMID: 29729575 DOI: 10.1016/j.etap.2018.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
The aim of our study is to seek novel specific biomarkers which could provide clues to the mechanism of chronic benzene poisoning (CBP) and might also be used as specific markers for early detection and diagnosis. In this study, a comparative serological proteome analysis between normal controls and CBP patients at three different levels of poisoning were performed via a 2D-DIGE and MALDI-TOF-MS. As the result a total of 10 proteins were found significantly altered between the normal and the mild, moderate and severe poisoning. The identified differentially expressed proteins were classified according to their molecular functions, biological processes, and protein classes, and three important serum proteins among them, apolipoproteinA-1, alpha-1-antitrypsin and complement C3, were further confirmed by immune turbidimetric analysis for their significant up-regulation in the CBP patients. Our findings suggest that these differential proteins may help elucidate the mechanism of CBP and provide potential biomarkers for diagnosis.
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Affiliation(s)
- Zhimin Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518001, Guangdong, China
| | - Peimao Li
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518001, Guangdong, China
| | - Dafeng Lin
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518001, Guangdong, China
| | - Dianpeng Wang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518001, Guangdong, China
| | - Yanfang Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518001, Guangdong, China.
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48
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Klous G, Smit LAM, Freidl GS, Borlée F, van der Hoek W, IJzermans CJ, Kretzschmar MEE, Heederik DJJ, Coutinho RA, Huss A. Pneumonia risk of people living close to goat and poultry farms - Taking GPS derived mobility patterns into account. ENVIRONMENT INTERNATIONAL 2018; 115:150-160. [PMID: 29573654 DOI: 10.1016/j.envint.2018.03.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
We previously observed an increased incidence of pneumonia in persons living near goat and poultry farms, using animal presence around the home to define exposure. However, it is unclear to what extent individual mobility and time spent outdoors close to home contributes to this increased risk. Therefore, the aim of the current study was to investigate the role of mobility patterns and time spent outdoors in the vicinity of goat or poultry farms in relation to pneumonia risk. In a rural Dutch cohort, 941 members logged their mobility using GPS trackers for 7 days. Pneumonia was diagnosed in 83 subjects (participants reported that pneumonia had been diagnosed by a medical doctor, or recorded in EMR from general practitioners, 2011-2014). We used logistic regression to evaluate pneumonia-risk by presence of goat farms within 500 and 1000 m around the home and around GPS-tracks (only non-motorised mobility), also we evaluated whether more time spent outdoors increased pneumonia-risks. We observed a clearly increased risk of pneumonia among people living in close proximity to goat farms, ORs increased with closer distances of homes to farms (500 m: 6.2 (95% CI 2.2-16.5) 1000 m: 2.5 (1.4-4.3)) The risk increased for individuals who spent more time outdoors close to home, but only if homes were close to goat farms (within 500 m and often outdoors: 12.7 (3.6-45.4) less often: 2.0 (0.3-9.2), no goat farms and often outdoors: 1.0 (0.6-1.6)). For poultry we found no increased risks. Pneumonia-risks increased when people lived near goat farms, especially when they spent more time outdoors, mobility does not seem to add to these risks.
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Affiliation(s)
- Gijs Klous
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, The Netherlands; Institute for Risk Assessment Sciences, Division Environmental Epidemiology and Veterinary Public Health, Utrecht University, The Netherlands.
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Division Environmental Epidemiology and Veterinary Public Health, Utrecht University, The Netherlands.
| | - Gudrun S Freidl
- National Institute for Public Health and the Environment (RIVM), The Netherlands; European Programme for Intervention Epidemiology Training.
| | - Floor Borlée
- Institute for Risk Assessment Sciences, Division Environmental Epidemiology and Veterinary Public Health, Utrecht University, The Netherlands; Netherlands Institute for Health Services Research (NIVEL), The Netherlands.
| | - Wim van der Hoek
- National Institute for Public Health and the Environment (RIVM), The Netherlands.
| | - C Joris IJzermans
- Netherlands Institute for Health Services Research (NIVEL), The Netherlands.
| | - Mirjam E E Kretzschmar
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, The Netherlands; National Institute for Public Health and the Environment (RIVM), The Netherlands.
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Division Environmental Epidemiology and Veterinary Public Health, Utrecht University, The Netherlands.
| | - Roel A Coutinho
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, The Netherlands; Faculty of Veterinary Medicine, Utrecht University, The Netherlands.
| | - Anke Huss
- Institute for Risk Assessment Sciences, Division Environmental Epidemiology and Veterinary Public Health, Utrecht University, The Netherlands.
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49
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Sanctuary MR, Kain JN, Angkustsiri K, German JB. Dietary Considerations in Autism Spectrum Disorders: The Potential Role of Protein Digestion and Microbial Putrefaction in the Gut-Brain Axis. Front Nutr 2018; 5:40. [PMID: 29868601 PMCID: PMC5968124 DOI: 10.3389/fnut.2018.00040] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Children with autism spectrum disorders (ASD), characterized by a range of behavioral abnormalities and social deficits, display high incidence of gastrointestinal (GI) co-morbidities including chronic constipation and diarrhea. Research is now increasingly able to characterize the “fragile gut” in these children and understand the role that impairment of specific GI functions plays in the GI symptoms associated with ASD. This mechanistic understanding is extending to the interactions between diet and ASD, including food structure and protein digestive capacity in exacerbating autistic symptoms. Children with ASD and gut co-morbidities exhibit low digestive enzyme activity, impaired gut barrier integrity and the presence of antibodies specific for dietary proteins in the peripheral circulation. These findings support the hypothesis that entry of dietary peptides from the gut lumen into the vasculature are associated with an aberrant immune response. Furthermore, a subset of children with ASD exhibit high concentrations of metabolites originating from microbial activity on proteinaceous substrates. Taken together, the combination of specific protein intakes poor digestion, gut barrier integrity, microbiota composition and function all on a background of ASD represents a phenotypic pattern. A potential consequence of this pattern of conditions is that the fragile gut of some children with ASD is at risk for GI symptoms that may be amenable to improvement with specific dietary changes. There is growing evidence that shows an association between gut dysfunction and dysbiosis and ASD symptoms. It is therefore urgent to perform more experimental and clinical research on the “fragile gut” in children with ASD in order to move toward advancements in clinical practice. Identifying those factors that are of clinical value will provide an evidence-based path to individual management and targeted solutions; from real time sensing to the design of diets with personalized protein source/processing, all to improve GI function in children with ASD.
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Affiliation(s)
- Megan R Sanctuary
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Jennifer N Kain
- Department of Neurobiology, Physiology and Behavior Department, University of California, Davis, Davis, CA, United States
| | - Kathleen Angkustsiri
- School of Medicine, Department of Pediatrics, University of California, Davis, Sacramento, CA, United States.,Department of Pediatrics, UC Davis MIND Institute, Sacramento, CA, United States
| | - J Bruce German
- Department of Food Science and Technology, University of California, Davis, Davis, CA, United States.,Foods for Health Institute, University of California, Davis, Davis, CA, United States
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50
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Wang W, Wang S, Zhang M. Identification of urine biomarkers associated with lung adenocarcinoma. Oncotarget 2018; 8:38517-38529. [PMID: 28404947 PMCID: PMC5503550 DOI: 10.18632/oncotarget.15870] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/24/2017] [Indexed: 12/16/2022] Open
Abstract
Lung adenocarcinoma (LAC) progression is accompanied by changes in protein levels that may be reflected in body fluids, such as urine. Urine collected from LAC patients (n=34) and healthy controls (n=36) was analyzed via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) combined with weak cationic exchange magnetic beads. The results revealed 76 urinary polypeptides significantly different between LAC patients and normal controls (P<0.05). Twenty-two of these peptides were up-regulated and 54 were down-regulated. Thirteen peptides had average peak intensities >600. Twelve of these 13 peptides were successfully identified using nano-liquid chromatography-tandem MS. Receiver operating characteristic analyses identified seven peptides with superior LAC diagnostic performances. Immunohistochemical staining in 20 paired LAC and adjacent normal tissues showed that IGKC, AAT, SH3BGRL3, osteopontin and gelsolin levels were higher in LAC tissues than in adjacent tissuesand were closely associated with LAC. Urinary peptides assessments may thus provide a novel, noninvasive, repeatable method for detecting and monitoring LAC. New, low-cost detection methods and bioinformatics tools are therefore urgently needed for the analysis of low abundance proteins and peptides in body fluids.
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Affiliation(s)
- Weiwei Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Shanshan Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
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