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Peng M, Zhou Y, Wan C. Identification of phosphorylated small ORF-encoded peptides in Hep3B cells by LC/MS/MS. J Proteomics 2024; 303:105214. [PMID: 38823442 DOI: 10.1016/j.jprot.2024.105214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Small ORF-encoded peptides (SEPs) are a class of low molecular weight proteins and peptides comprising <100 amino acids with important functions in various life activities. Although the sequence length is short, SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. In this work, we enriched phosphopeptides with IMAC and TiO2 materials and analyzed the phosphorylated SEPs in Hep3B cells. A total of 24 phosphorylated SEPs were identified, and 11 SEPs were coded by ncRNA. For the sequence analysis, we found that the general characteristics of phosphorylated SEPs are roughly the same as canonical proteins. Besides, two phosphorylation SEPs have the Stathmin family signature 2 motif, which can regulate the microtubule cytoskeleton. Some SEPs have domains or signal peptides, indicating their specific functions and subcellular locations. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of some SEPs. However, only one-fifth of the predicted phosphorylation sites were identified by LC/MS/MS, indicating that many SEP PTMs are hidden in the dark, waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation. SIGNIFICANCE: Small ORF-encoded peptides (SEPs) are important in various life activities. Although the sequence length is short (<100AA), SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. We enriched phosphopeptides and analyzed the phosphorylated SEPs in Hep3B cells. That is the first time to explore the PTM of SPEs systematically. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of SEPs. More SEP PTMs are hidden in the dark and waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation.
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Affiliation(s)
- Mingbo Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yutian Zhou
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.
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2
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Zhao Y, Shen H, Wu J, Yu J, Yuan Y, Zhong C. Discovery, identification and mechanism of chemosensitivity-relate biomarker inter-α-trypsin inhibitor heavy chain 4 in metastatic colorectal cancer. Heliyon 2024; 10:e33571. [PMID: 39040328 PMCID: PMC11260961 DOI: 10.1016/j.heliyon.2024.e33571] [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: 03/19/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Predictive biomarkers of response to chemotherapy in patients with metastatic colorectal cancer (mCRC) are needed to better characterize tumors and enable more tailored therapies. Here we used serum proteomics to screen for chemotherapy predictive markers. We found that higher baseline serum inter-α-trypsin inhibitor Heavy Chain 4 (ITIH4) expression in newly diagnosed mCRC patients was associated with poorer response to standard first-line chemotherapy. In addition, the higher expression of ITIH4 in CRC tissue also suggested poorer prognosis mCRC patients. Moreover, the overexpression of ITIH4 could promote the proliferation of CRC cells and reduce the sensitivity of CRC cells to 5-fluorouracil (5-FU) by inhibiting apoptosis in vivo and vitro. Through RNA-seq combined with bioinformatics analysis, we speculated that ITIH4 may activate phosphatidyl 3-kinase-protein kinase B (PI3K-AKT) pathway to inhibit apoptosis, thereby reducing the sensitivity of CRC cells to 5-FU. In conclusion, our findings unveil that ITIH4 is associated with CRC resistance to 5-FU, and may serve as a potential predictive biomarker for the sensitivity of advanced CRC patients to standard first-line chemotherapy regimens, and also provide a potential therapeutic target to render 5-FU resistance in CRC patients.
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Affiliation(s)
- Yingxin Zhao
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Hong Shen
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Jianmin Wu
- Institute of Microanalytical System Department of Chemistry, Zhejiang University Hangzhou, Zhejiang, 310058, China
| | - Jiekai Yu
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou, Zhejiang, 310009, China
| | - Chenhan Zhong
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
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Steel R, Timms M, Bamford N, Spence R, Sillence M. The detection of ACTH and insulin in equine plasma by solid-phase extraction and micro-flow LC/MSMS. Drug Test Anal 2024. [PMID: 38978168 DOI: 10.1002/dta.3762] [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: 04/15/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024]
Abstract
Previous liquid chromatography/mass spectrometry (LC/MS) methods for the detection of insulin and other similar peptide hormones in equine plasma relied on the use of antibody affinity extraction. As a result, these methods were not suitable for routine high-throughput analysis. A solid-phase extraction (SPE) method incorporating size exclusion as well as reversed-phase interactions allows the selective extraction of peptide hormones such as adrenocorticotropic hormone (ACTH), insulin and their synthetic analogues from equine plasma with approximately 80% extraction efficiencies. This extraction was combined with on-column derivatisation with acetic anhydride, followed by tryptic digestion and analysis by micro-LC/MSMS for high-sensitivity peptide hormone detection. The analysis of tryptic peptides provides greater sensitivity and more robust chromatography compared with the analysis of intact insulin and ACTH. For quantitative analysis, isotopically labelled internal standards of target peptides can be prepared in the laboratory through the use of deuterated acetic anhydride. The utility of the method was assessed for the analysis of ACTH and insulin in samples from horses suffering from pituitary pars intermedia dysfunction (PPID).
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Affiliation(s)
- Rohan Steel
- Biological Research Unit, Racing Analytical Services Ltd, Flemington, Australia
| | - Mark Timms
- Biological Research Unit, Racing Analytical Services Ltd, Flemington, Australia
| | - Nicholas Bamford
- Veterinary Biosciences, Melbourne University, Parkville, Australia
| | - Robert Spence
- Department of Biological and Environmental Sciences, Queensland University of Technology, Brisbane, Australia
| | - Martin Sillence
- Department of Biological and Environmental Sciences, Queensland University of Technology, Brisbane, Australia
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Uzelac T, Takić M, Stevanović V, Vidović N, Pantović A, Jovanović P, Jovanović V. The Potential Benefits of Acute Aronia Juice Supplementation on Physical Activity Induced Alterations of the Serum Protein Profiles in Recreational Runners: A Pilot Study. Healthcare (Basel) 2024; 12:1276. [PMID: 38998811 PMCID: PMC11240927 DOI: 10.3390/healthcare12131276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/15/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Intensive physical activity (PA) can lead to proteinuria and, consequently, serum protein profiles in athletes. Therefore, the aim of this study was to investigate the effects of acute aronia juice consumption before a simulated half-marathon race on serum protein profiles in recreational runners. The pilot study was designed as a single-blind, placebo-controlled, crossover study, with 10 male participants who consumed aronia juice (containing 1.3 g polyphenols) or placebo before the race. The blood levels of total proteins, albumin, the non-albumin fractions gamma, beta, alpha2 and alpha1, as well as renal function parameters, were determined before and 15 min, 1 h and 24 h after the race. The significant changes in urea, creatinine and uric acid levels were noticed at selected time points in both groups. In the placebo group, a significant decrease in total proteins (p < 0.05) was observed 24 h after the race, along with an increase in gamma fraction abundance (p < 0.05). In addition, urea and uric acid levels returned to baseline only in the aronia group 24 h after the race. Thus, according to the results obtained, acute aronia juice supplementation before intensive PA could influence the transient change in renal function and PA-induced protein loss in recreational runners.
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Affiliation(s)
- Tamara Uzelac
- Department of Biochemistry and Centre of Excellence for Molecular Food Sciences, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Marija Takić
- Institute for Medical Research, National Institute of Republic of Serbia, Group for Nutrition and Metabolism, Centre of Research Excellence in Nutrition and Metabolism, University of Belgrade, Tadeuša Košćuškog 1, 11000 Belgrade, Serbia
| | - Vuk Stevanović
- Institute for Medical Research, National Institute of Republic of Serbia, Group for Nutrition and Metabolism, Centre of Research Excellence in Nutrition and Metabolism, University of Belgrade, Tadeuša Košćuškog 1, 11000 Belgrade, Serbia
| | - Nevena Vidović
- Institute for Medical Research, National Institute of Republic of Serbia, Group for Nutrition and Metabolism, Centre of Research Excellence in Nutrition and Metabolism, University of Belgrade, Tadeuša Košćuškog 1, 11000 Belgrade, Serbia
| | - Ana Pantović
- Institute for Medical Research, National Institute of Republic of Serbia, Group for Nutrition and Metabolism, Centre of Research Excellence in Nutrition and Metabolism, University of Belgrade, Tadeuša Košćuškog 1, 11000 Belgrade, Serbia
| | - Petar Jovanović
- Department of Biochemistry and Centre of Excellence for Molecular Food Sciences, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
- Institute for Medical Research, National Institute of Republic of Serbia, Group for Nutrition and Metabolism, Centre of Research Excellence in Nutrition and Metabolism, University of Belgrade, Tadeuša Košćuškog 1, 11000 Belgrade, Serbia
| | - Vesna Jovanović
- Department of Biochemistry and Centre of Excellence for Molecular Food Sciences, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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Darmayanti S, Lesmana R, Meiliana A, Abdulah R. V-ATPase subunit C 1 and IKBIP as tandem prospective biomarkers for diabetic nephropathy. Diabetes Res Clin Pract 2023; 203:110887. [PMID: 37604283 DOI: 10.1016/j.diabres.2023.110887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
AIMS The appearance of low-molecular-weight (LMW) protein in the urine indicates any disruption in the structural integrity of the glomerular capillary wall; therefore, the presence of LMW protein may be a potential predictive marker for DN. METHODS The urine proteomic profiling of T2DM patients (n = 94) and control group (n = 32) was compared by liquid chromatography-tandem mass spectrometry, and the untargeted LMW protein was identified by Progenesis Q1 For Proteomics v4.2. RESULTS A total of 73 LMW proteins were identified and quantified, of which, 32 proteins were found to be altered significantly (p < 0.05). Further analysis with heat maps identified two potential proteins with the highest folding alterations in urine. V-ATPase subunit C 1 abundance was significantly inversely correlated with microalbumin and significantly decreased in urine, whereas increased IKBIP was positively correlated with microalbumin. The level of those proteins was significantly different among the control, T2DM, and DN groups, implying an association with the progression of DN. CONCLUSIONS The present findings of our study indicate that the decreasing V-ATPase subunit C 1 together with increasing IKBIP in urine, were found to be closely associated with DN complications and signifying their value as biomarkers for predicting the risk of DN at initial diagnosis.
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Affiliation(s)
- Siska Darmayanti
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia; Prodia Clinical Laboratory, Jakarta, Indonesia
| | - Ronny Lesmana
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Jatinangor, Indonesia; Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Jatinangor, Indonesia.
| | - Anna Meiliana
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia; Prodia Clinical Laboratory, Jakarta, Indonesia
| | - Rizky Abdulah
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia; Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Jatinangor, Indonesia
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Rejeeth C, Varukattu NB, Kumar RS, Almansour AI, Arumugam N. A novel device for swift and efficient CD44 protein digestion of pipette tips in human serum. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1227:123840. [PMID: 37494752 DOI: 10.1016/j.jchromb.2023.123840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/12/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
For molecular diagnostics in modern biomedical research, electrospray ionisation mass spectrometry (ESI-MS) based on proteome profiling is important. Now a days, sample preparation such as proteolysis and protein extraction remain incredibly challenging and inefficient. Recent sample-preparation methods based on micro tips show promising results toward the aim "a proteome in an hour". Proteolysis at the tip, is still infrequently observed and does not represent the processing of complex bio-samples. In this study, we outline a unique technique for detecting and extracting human serum CD44 biomarkers by ligand-protein interactions. This method employs macropores silica particles (MPSP) or (MOSF) modified with hyaluronic acid (HA). In order to assist in the profile of the human serum proteome, we limitations of immunoassays for rapid and multimodal proteolysis. For effective in situ proteolysis, in micropipette tips, MPSP were designed as nanoreactors with variable pore size and surface chemistry. In MS-based bottom-up proteome analysis, the device as-built demonstrated favourable sensitivity (LOD of 0.304 ± 0.007 ng/mL and LOQ of 0.973 ± 0.054 ng/mL), selectivity, durability (at -20 °C for 2 months), reuse (at least 10 times), and minimal memory impact. In addition, we examined into specific surface chemistries of nanoparticles for the absorption of proteins in serum and profiled the HA-binding serum proteome, setting a new preliminary benchmark for future databases. Our study not only helped establish a new platform for extracting/detection of CD44 and identifying the HA-binding proteome, but it also offered design recommendations for ligand affinity-based techniques for the antibody-free study of serum biomarkers with a view towards diagnostic applications.
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Affiliation(s)
- Chandrababu Rejeeth
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu 636011, India.
| | - Nipun Babu Varukattu
- Department of Nutrition and Health Sciences, The University of Nebraska Lincoln, Lincoln, NE 68583-0806, USA
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Tian J, Zhu X, Wu H, Wang Y, Hu X. Serum metabolic profile and metabolome genome-wide association study in chicken. J Anim Sci Biotechnol 2023; 14:69. [PMID: 37138301 PMCID: PMC10158329 DOI: 10.1186/s40104-023-00868-7] [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: 12/12/2022] [Accepted: 03/09/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Chickens provide globally important livestock products. Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding. Influenced by a combination of genetic and environmental factors, metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits. However, the serum metabolite profile and genetic architecture of the metabolome in chickens have not been well studied. RESULTS Here, comprehensive metabolome detection was performed using non-targeted LC-MS/MS on serum from a chicken advanced intercross line (AIL). In total, 7,191 metabolites were used to construct a chicken serum metabolomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population. Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. Many functional genes affect metabolite synthesis, metabolism, and regulation. We highlight the key roles of TDH and AASS in amino acids, and ABCB1 and CD36 in lipids. CONCLUSIONS We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a reference for future chicken metabolome characterization work. Meanwhile, we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.
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Affiliation(s)
- Jing Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hanyu Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
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Tian F, de Carvalho LFDCES, Casey A, Nogueira MS, Byrne HJ. Surface-Enhanced Raman Analysis of Uric Acid and Hypoxanthine Analysis in Fractionated Bodily Fluids. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1216. [PMID: 37049309 PMCID: PMC10097234 DOI: 10.3390/nano13071216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
In recent years, the disease burden of hyperuricemia has been increasing, especially in high-income countries and the economically developing world with a Western lifestyle. Abnormal levels of uric acid and hypoxanthine are associated with many diseases, and therefore, to demonstrate improved methods of uric acid and hypoxanthine detection, three different bodily fluids were analysed using surface-enhanced Raman spectroscopy (SERS) and high-performance liquid chromatography (HPLC). Gold nanostar suspensions were mixed with series dilutions of uric acid and hypoxanthine, 3 kDa centrifugally filtered human blood serum, urine and saliva. The results show that gold nanostars enable the quantitative detection of the concentration of uric acid and hypoxanthine in the range 5-50 μg/mL and 50-250 ng/mL, respectively. The peak areas of HPLC and maximum peak intensity of SERS have strongly correlated, notably with the peaks of uric acid and hypoxanthine at 1000 and 640 cm-1, respectively. The r2 is 0.975 and 0.959 for uric acid and hypoxanthine, respectively. Each of the three body fluids has a number of spectral features in common with uric acid and hypoxanthine. The large overlap of the spectral bands of the SERS of uric acid against three body fluids at spectra peaks were at 442, 712, 802, 1000, 1086, 1206, 1343, 1436 and 1560 cm-1. The features at 560, 640, 803, 1206, 1290 and 1620 cm-1 from hypoxanthine were common to serum, saliva and urine. There is no statistical difference between HPLC and SERS for determination of the concentration of uric acid and hypoxanthine (p > 0.05). For clinical applications, 3 kDa centrifugal filtration followed by SERS can be used for uric acid and hypoxanthine screening is, which can be used to reveal the subtle abnormalities enhancing the great potential of vibrational spectroscopy as an analytical tool. Our work supports the hypnosis that it is possible to obtain the specific concentration of uric acid and hypoxanthine by comparing the SER signals of serum, saliva and urine. In the future, the analysis of other biofluids can be employed to detect biomarkers for the diagnosis of systemic pathologies.
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Affiliation(s)
- Furong Tian
- FOCAS Research Institute, Technological University Dublin Camden Row, D08CKP1 Dublin, Ireland; (A.C.)
| | - Luis Felipe das Chagas e Silva de Carvalho
- FOCAS Research Institute, Technological University Dublin Camden Row, D08CKP1 Dublin, Ireland; (A.C.)
- Centro Universitario Braz Cubas, Mogi das Cruzes 08773-380, Brazil
- Universidade de Taubate, Taubate 12080-000, Brazil
| | - Alan Casey
- FOCAS Research Institute, Technological University Dublin Camden Row, D08CKP1 Dublin, Ireland; (A.C.)
| | - Marcelo Saito Nogueira
- Tyndall National Institute, Lee Maltings Complex, Dyke Parade, T12R5CP Cork, Ireland;
- Department of Physics, University College Cork, College Road, T12K8AF Cork, Ireland
| | - Hugh J. Byrne
- FOCAS Research Institute, Technological University Dublin Camden Row, D08CKP1 Dublin, Ireland; (A.C.)
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Kim H, Cheon DH, Yang WS, Baek JH. Simultaneous Quantification of Apolipoprotein C-III O-Glycoforms by Protein-MRM. J Proteome Res 2023; 22:91-100. [PMID: 36412001 DOI: 10.1021/acs.jproteome.2c00490] [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: 11/23/2022]
Abstract
Apolipoprotein C-III (APOC-III) regulates triglyceride levels, associated with a risk of cardiovascular disease. One gene generates several proteoforms, each with a different molecular mass and a unique function. Unlike peptide multiple reaction monitoring (MRM), protein-MRM without digestion is required to analyze clinically relevant individual proteoforms. We developed a protein-MRM method without digestion to individually quantify APOC-III proteoforms in human serum. We optimized the protein-MRM method following 60% acetonitrile extraction with C18 filtration. Bovine serum and myoglobin served as supporting cushions and the internal standard during sample preparation, respectively. Furthermore, we evaluated the LOD, lower limit of quantification, linearity, accuracy, and precision. Good correlation compared with turbidimetric immunoassay (TIA) and peptide-MRM was observed using 30 clinical sera. Individual APOC-III O-glycoforms were identified by top-down proteomics and simultaneously quantified using the protein-MRM method. The sum abundance of APOC-III proteoforms was significantly correlated with TIA and peptide-MRM. Our protein-MRM method provides an affordable and rapid quantification of potential disease-specific proteoforms. Precise quantification of each proteoform allows investigators to identify novel biological roles potentially related to cardiovascular disease or novel biomarkers. We expect our protein-oriented method to be more clinically useful than antibody-based immunoassays and peptide-oriented MRM analysis, especially for quantification of a biomarker proteoform with certain post-translational modifications.
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Affiliation(s)
- Hyojin Kim
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Dong Huey Cheon
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Won Suk Yang
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Je-Hyun Baek
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
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Decoene I, Herpelinck T, Geris L, Luyten FP, Papantoniou I. Engineering bone-forming callus organoid implants in a xenogeneic-free differentiation medium. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.892190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The field of tissue engineering aspires to provide clinically relevant solutions for patients through the integration of developmental engineering principles with a bottom-up manufacturing approach. However, the manufacturing of cell-based advanced therapy medicinal products is hampered by protocol complexity, lack of non-invasive critical quality controls, and dependency on animal-derived components for tissue differentiation. We investigate a serum-free, chemically defined, xeno- and lipid-free chondrogenic differentiation medium to generate bone-forming callus organoids. Our results show an increase in microtissue homogeneity during prolonged differentiation and the high quality of in vivo bone-forming organoids. The low protein content of the culture medium potentially allows for the monitoring of relevant secreted biomarkers as (critical) quality attributes. Together, we envisage that this xeno- and lipid-free chondrogenic medium is compatible with industrial scale-up and automation while facilitating the implementation of non-invasive imaging and the use of quality control parameters based on secreted biomarkers.
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11
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Li W, Li M, Zhang X, Yue S, Xu Y, Jian W, Qin Y, Lin L, Liu W. Improved profiling of low molecular weight serum proteome for gastric carcinoma by data-independent acquisition. Anal Bioanal Chem 2022; 414:6403-6417. [PMID: 35773495 DOI: 10.1007/s00216-022-04196-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Low molecular weight proteins (LMWPs) in the bloodstream participate in various biological processes and are closely associated with disease status, whereas identification of serous LMWPs remains a great technical challenge due to the wide dynamic range of protein components. In this study, we constructed an integrated LMWP library by combining the LMWPs obtained by three enrichment methods (50% ACN, 20% ACN + 20 mM ABC, and 30 kDa) and their fractions identified by the data-dependent acquisition method. With this newly constructed library, we comprehensively profiled LMWPs in serum using data-independent acquisition and reliably achieved quantitative results for 75% serous LMWPs. When applying this strategy to quantify LMWPs in human serum samples, we could identify 405 proteins on average per sample, of which 136 proteins were with a MW less than 30 kDa and 293 proteins were with a MW less than 65 kDa. Of note, pre- and post-operative gastric carcinoma (GC) patients showed differentially expressed serous LWMPs, which was also different from the pattern of LWMP expression in healthy controls. In conclusion, our results showed that LMWPs could efficiently distinguish GC patients from healthy controls as well as between pre- and post-operative statuses, and more importantly, our newly developed LMWP profiling platform could be used to discover candidate LMWP biomarkers for disease diagnosis and status monitoring.
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Affiliation(s)
- Weifeng Li
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Mengna Li
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Xiaoli Zhang
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Siqin Yue
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Yun Xu
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Wenjing Jian
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Yin Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
| | - Lin Lin
- Sustech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Wenlan Liu
- The Central Laboratory, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
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Abstract
There are probably no biological samples that did more to spur interest in proteomics than serum and plasma. The belief was that comparing the proteomes of these samples obtained from healthy and disease-affected individuals would lead to biomarkers that could be used to diagnose conditions such as cancer. While the continuing development of mass spectrometers with greater sensitivity and resolution has been invaluable, the invention of strategic strategies to separate circulatory proteins has been just as critical. Novel and creative separation techniques were required because serum and plasma probably have the greatest dynamic range of protein concentration of any biological sample. The concentrations of circulating proteins can range over twelve orders of magnitude, making it a challenge to identify low-abundance proteins where the bulk of the useful biomarkers are believed to exist. The major goals of this article are to (i) provide an historical perspective on the rapid development of serum and plasma proteomics; (ii) describe various separation techniques that have made obtaining an in-depth view of the proteome of these biological samples possible; and (iii) describe applications where serum and plasma proteomics have been employed to discover potential biomarkers for pathological conditions.
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