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Wu H, Xu J, Sun J, Duan J, Xiao J, Ren Q, Zhou P, Yan J, Li Y, Xiong X, Zeng E. APOE as potential biomarkers of moyamoya disease. Front Neurol 2023; 14:1156894. [PMID: 37228412 PMCID: PMC10203507 DOI: 10.3389/fneur.2023.1156894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Objective The mechanisms underpinning Moyamoya disease (MMD) remain unclear, and effective biomarkers remain unknown. The purpose of this study was to identify novel serum biomarkers of MMD. Methods Serum samples were collected from 23 patients with MMD and 30 healthy controls (HCs). Serum proteins were identified using tandem tandem-mass-tag (TMT) labeling combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differentially expressed proteins (DEPs) in the serum samples were identified using the SwissProt database. The DEPs were assessed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, Gene Ontology (GO), and protein-protein interaction (PPI) networks, and hub genes were identified and visualized using Cytoscape software. Microarray datasets GSE157628, GSE189993, and GSE100488 from the Gene Expression Omnibus (GEO) database were collected. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) were identified, and miRNA targets of DEGs were predicted using the miRWalk3.0 database. Serum apolipoprotein E (APOE) levels were compared in 33 MMD patients and 28 Moyamoya syndrome (MMS) patients to investigate the potential of APOE to be as an MMD biomarker. Results We identified 85 DEPs, of which 34 were up- and 51 down-regulated. Bioinformatics analysis showed that some DEPs were significantly enriched in cholesterol metabolism. A total of 1105 DEGs were identified in the GSE157628 dataset (842 up- and 263 down-regulated), whereas 1290 were identified in the GSE189993 dataset (200 up- and 1,090 down-regulated). The APOE only overlaps with the upregulated gene expression in Proteomic Profiling and in GEO databases. Functional enrichment analysis demonstrated that APOE was associated with cholesterol metabolism. Moreover, 149 miRNAs of APOE were predicted in the miRWalk3.0 database, and hsa-miR-718 was the only DE-miRNA overlap identified in MMD samples. Serum APOE levels were significantly higher in patients with MMD than in those without. The performance of APOE as an individual biomarker to diagnose MMD was remarkable. Conclusions We present the first description of the protein profile of patients with MMD. APOE was identified as a potential biomarker for MMD. Cholesterol metabolism was found to potentially be related to MMD, which may provide helpful diagnostic and therapeutic insights for MMD.
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Affiliation(s)
- Haibin Wu
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiang Xu
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiarong Sun
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Duan
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinlin Xiao
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Quan Ren
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Pengfei Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Yan
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Youping Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoxing Xiong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Erming Zeng
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Harkness BM, Hegarty DM, Saugstad JA, Behrens H, Betz J, David LL, Lapidus JA, Chen S, Stutzman R, Chamberlain W, Perez-Blanco M, Galor A, Aicher SA. Experimental design considerations for studies of human tear proteins. Ocul Surf 2023; 28:58-78. [PMID: 36764654 PMCID: PMC10409878 DOI: 10.1016/j.jtos.2023.02.005] [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: 10/04/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
PURPOSE Human tears contain abundant, diverse sets of proteins that may serve as biomarkers of ocular surface health. There is a need for reproducible methods that consider multiple factors influencing the tear proteome, in addition to the variable of interest. Here we examined a workflow for proteomic analysis of tear proteins without the need to pool tear samples from multiple individuals, thus allowing for analyses based on individual factors, and increasing opportunities for protein biomarker discovery. METHODS Tears were collected by Schirmer strip following topical ocular anesthetic application then individually stored at -80 °C prior to processing for proteomics. Tear proteins were extracted from Schirmer strips, digested using suspension trapping spin columns (S-Trap), and labeled with high multiplicity tandem mass tags (TMT). Peptide digests were then extensively fractionated by two-dimensional chromatography and analyzed by mass spectrometry to identify and measure changes in protein abundance in each sample. Analysis of select samples was performed to test protocols and to compare the impact of clinically relevant parameters. To facilitate comparison of separate TMT experiments, common pool samples were included in each TMT instrument run and internal reference scaling (IRS) was performed. RESULTS Differences in subsets of tear proteins were noted for: geographic site of tear collection, contact lens use, and differences in tear fluid volume among individuals. CONCLUSION These findings demonstrate that proteomic analysis of human tear proteins can be performed without the need to pool samples, and that development of analytic workflows must consider factors that may affect outcomes in studies focused on diverse clinical samples.
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Affiliation(s)
- Brooke M Harkness
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Deborah M Hegarty
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Julie A Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Hannah Behrens
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Jason Betz
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
| | - Larry L David
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA; Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Jodi A Lapidus
- Biostatistics and Design Program, Oregon Health & Science University, USA; Oregon Health & Science University-Portland State University School of Public Health, USA
| | - Siting Chen
- Biostatistics and Design Program, Oregon Health & Science University, USA
| | - Richard Stutzman
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Maricarmen Perez-Blanco
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Surgical Services, Miami Veterans Administration Medical Center, Miami, FL, USA
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Surgical Services, Miami Veterans Administration Medical Center, Miami, FL, USA
| | - Sue A Aicher
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA.
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Wu J, Cao L, Wang J, Wang Y, Hao H, Huang L. Characterization of serum protein expression profiles in the early sarcopenia older adults with low grip strength: a cross-sectional study. BMC Musculoskelet Disord 2022; 23:894. [PMID: 36192674 PMCID: PMC9528053 DOI: 10.1186/s12891-022-05844-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Background Sarcopenia refers to the progressive loss of skeletal muscle mass and muscle function, which seriously threatens the quality of life of the older adults. Therefore, early diagnosis is urgently needed. This study aimed to explore the changes of serum protein profiles in sarcopenia patients through a cross-sectional study, and to provide the reference for clinical diagnosis. Methods This study was a cross-sectional study carried out in the Tianjin institute of physical education teaching experiment training center from December 2019 to December 2020. Ten older adults were recruited, including 5 sarcopenia and 5 healthy older adults. After a detailed diagnostic evaluation, blood samples were collected to prepare serum for proteomic analysis using the HPLC System Easy nLC method. The differentially expressed proteins (DEPs) were screened by the limma package of R software (version 4.1.0). Results A total of 114 DEPs were identified between the patients and healthy older adults, including 48 up-regulated proteins and 66 down-regulated proteins. The functional enrichment analysis showed that the 114 DEPs were significantly enriched in 153 GO terms, which mainly involved in low-density lipoprotein particle remodeling, and negative regulation of immune response,etc. The PPI network further suggested that the cholesteryl ester transfer protein and Apolipoprotein A2 could serve as biomarkers to facilitate diagnosis of sarcopenia. Conclusions This study provided a serum proteomic profile of sarcopenia patients, and identified two proteins with diagnostic value, which might help to improve the diagnostic accuracy of sarcopenia. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-022-05844-2.
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Affiliation(s)
- Jingqiong Wu
- TianJin University of Sport, No.16 Donghai Road, West Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China.,Guangxi Medical University, Nanning, 530021, Guangxi, PR China
| | - Longjun Cao
- TianJin University of Sport, No.16 Donghai Road, West Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Jiazhi Wang
- TianJin University of Sport, No.16 Donghai Road, West Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Yizhao Wang
- Tianjin Huanhu Hospital, Tianjin, 300350, PR China
| | - Huimin Hao
- TianJin University of Sport, No.16 Donghai Road, West Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Liping Huang
- TianJin University of Sport, No.16 Donghai Road, West Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China.
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