1
|
He X, Chen X, Yang C, Wang W, Sun H, Wang J, Fu J, Dong H. Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformatics. PeerJ 2024; 12:e16951. [PMID: 38436027 PMCID: PMC10909369 DOI: 10.7717/peerj.16951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024] Open
Abstract
Background Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer. Methods In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR). Results In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics. Conclusion Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.
Collapse
Affiliation(s)
- Xionghui He
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Xiang Chen
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Changcheng Yang
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Wei Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Hening Sun
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Junjie Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Jincheng Fu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Huaying Dong
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| |
Collapse
|
2
|
Burnap SA, Ortega-Prieto AM, Jimenez-Guardeño JM, Ali H, Takov K, Fish M, Shankar-Hari M, Giacca M, Malim MH, Mayr M. Cross-Linking Mass Spectrometry Uncovers Interactions Between High-Density Lipoproteins and the SARS-CoV-2 Spike Glycoprotein. Mol Cell Proteomics 2023; 22:100600. [PMID: 37343697 PMCID: PMC10279469 DOI: 10.1016/j.mcpro.2023.100600] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
High-density lipoprotein (HDL) levels are reduced in patients with coronavirus disease 2019 (COVID-19), and the extent of this reduction is associated with poor clinical outcomes. While lipoproteins are known to play a key role during the life cycle of the hepatitis C virus, their influence on coronavirus (CoV) infections is poorly understood. In this study, we utilize cross-linking mass spectrometry (XL-MS) to determine circulating protein interactors of the severe acute respiratory syndrome (SARS)-CoV-2 spike glycoprotein. XL-MS of plasma isolated from patients with COVID-19 uncovered HDL protein interaction networks, dominated by acute-phase serum amyloid proteins, whereby serum amyloid A2 was shown to bind to apolipoprotein (Apo) D. XL-MS on isolated HDL confirmed ApoD to interact with SARS-CoV-2 spike but not SARS-CoV-1 spike. Other direct interactions of SARS-CoV-2 spike upon HDL included ApoA1 and ApoC3. The interaction between ApoD and spike was further validated in cells using immunoprecipitation-MS, which uncovered a novel interaction between both ApoD and spike with membrane-associated progesterone receptor component 1. Mechanistically, XL-MS coupled with data-driven structural modeling determined that ApoD may interact within the receptor-binding domain of the spike. However, ApoD overexpression in multiple cell-based assays had no effect upon viral replication or infectivity. Thus, SARS-CoV-2 spike can bind to apolipoproteins on HDL, but these interactions do not appear to alter infectivity.
Collapse
Affiliation(s)
- Sean A Burnap
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK; The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK; King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Hashim Ali
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK; Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Kaloyan Takov
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK
| | - Matthew Fish
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK; Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Manu Shankar-Hari
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, UK; Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Mauro Giacca
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Manuel Mayr
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
| |
Collapse
|
3
|
The Neuroprotective Lipocalin Apolipoprotein D Stably Interacts with Specific Subtypes of Detergent-Resistant Membrane Domains in a Basigin-Independent Manner. Mol Neurobiol 2022; 59:4015-4029. [PMID: 35460054 PMCID: PMC9167181 DOI: 10.1007/s12035-022-02829-z] [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: 11/26/2021] [Accepted: 04/02/2022] [Indexed: 11/25/2022]
Abstract
Accumulated evidence points to the lipocalin apolipoprotein D (ApoD), one of the few genes consistently upregulated upon brain ageing and neurodegeneration, as an endogenous controller of the redox state of cellular and extracellular lipid structures. This biochemical function has downstream consequences as apparently varied as control of glycocalyx and myelin compaction, cell viability upon oxidative stress or modulation of signalling pathways. In spite of this knowledge, it is still unclear if ApoD function requires canonical receptor-mediated transductions systems. This work aims to examine ApoD-cell membrane interaction and its dependence on a proposed ApoD receptor, Basigin. Whole and fractionated membrane preparations from the brain, primary astrocytes, glial and neuronal cell lines, reveal ApoD as a very specific component of particular subtypes of detergent-resistant microdomains (DRMs). ApoD interacts in vitro with neuronal membranes and is stably associated with astrocytic membranes. ApoD associates with DRMs with specific buoyancy properties that co-fractionate with plasma or late-endosome-lysosome markers. A mass spectrometry analysis reveals that these Triton X-114 DRMs contain both plasma membrane and endosomal-lysosomal compartment lipid raft proteins. ApoD-DRM association is maintained under metabolic and acute oxidative stress conditions. However, ApoD-membrane interaction, its internalization and its lipid-antioxidant function do not require the presence of Basigin. This work supports a stable association of ApoD with membranes, independent of Basigin, and provides the basis to fully understand ApoD antioxidant neuroprotective mechanism as a mechanism taking place in specific membrane subdomains.
Collapse
|
4
|
Li N, Hou R, Liu C, Yang T, Qiao C, Wei J. Integration of transcriptome and proteome profiles in placenta accreta reveals trophoblast over-migration as the underlying pathogenesis. Clin Proteomics 2021; 18:31. [PMID: 34963445 PMCID: PMC8903580 DOI: 10.1186/s12014-021-09336-8] [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: 04/22/2021] [Accepted: 12/09/2021] [Indexed: 12/03/2022] Open
Abstract
Background Placenta accreta (PA) is a major cause of maternal morbidity and mortality in modern obstetrics, few studies have explored the underlying molecular mechanisms. Methods In our study, transcriptome and proteome profiling were performed in placental tissues from ten participants including five cases each in the PA and control groups to clarify the pathogenesis of PA. Results We identified differential expression of 37,743 transcripts and 160 proteins between the PA and control groups with an overlap rate of 0.09%. The 33 most-significant transcripts and proteins were found and further screened and analyzed. Adhesion-related signature, chemotaxis related signatures and immune related signature were found in the PA group and played a certain role. Sum up two points, three significant indicators, methyl-CpG-binding domain protein 2 (MeCP2), podocin (PODN), and apolipoprotein D (ApoD), which participate in “negative regulation of cell migration”, were downregulated at the mRNA and protein levels in PA group. Furthermore, transwell migration and invasion assay of HTR-8/SVneo cell indicated the all of them impaired the migration and invasion of trophoblast. Conclusion A poor correlation was observed between the transcriptome and proteome data and MeCP2, PODN, and ApoD decreased in transcriptome and proteome profiling, resulting in increased migration of trophoblasts in the PA group, which clarify the mechanism of PA and might be the biomarkers or therapy targets in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09336-8.
Collapse
Affiliation(s)
- Na Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province; Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Benxi, China
| | - Rui Hou
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province; Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Benxi, China
| | - Caixia Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province; Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Benxi, China
| | - Tian Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Chong Qiao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China. .,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province; Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Benxi, China.
| | - Jun Wei
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China. .,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province; Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Benxi, China.
| |
Collapse
|
5
|
Sanchez D, Ganfornina MD. The Lipocalin Apolipoprotein D Functional Portrait: A Systematic Review. Front Physiol 2021; 12:738991. [PMID: 34690812 PMCID: PMC8530192 DOI: 10.3389/fphys.2021.738991] [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: 07/09/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022] Open
Abstract
Apolipoprotein D is a chordate gene early originated in the Lipocalin protein family. Among other features, regulation of its expression in a wide variety of disease conditions in humans, as apparently unrelated as neurodegeneration or breast cancer, have called for attention on this gene. Also, its presence in different tissues, from blood to brain, and different subcellular locations, from HDL lipoparticles to the interior of lysosomes or the surface of extracellular vesicles, poses an interesting challenge in deciphering its physiological function: Is ApoD a moonlighting protein, serving different roles in different cellular compartments, tissues, or organisms? Or does it have a unique biochemical mechanism of action that accounts for such apparently diverse roles in different physiological situations? To answer these questions, we have performed a systematic review of all primary publications where ApoD properties have been investigated in chordates. We conclude that ApoD ligand binding in the Lipocalin pocket, combined with an antioxidant activity performed at the rim of the pocket are properties sufficient to explain ApoD association with different lipid-based structures, where its physiological function is better described as lipid-management than by long-range lipid-transport. Controlling the redox state of these lipid structures in particular subcellular locations or extracellular structures, ApoD is able to modulate an enormous array of apparently diverse processes in the organism, both in health and disease. The new picture emerging from these data should help to put the physiological role of ApoD in new contexts and to inspire well-focused future research.
Collapse
Affiliation(s)
- Diego Sanchez
- Instituto de Biologia y Genetica Molecular, Unidad de Excelencia, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas, Valladolid, Spain
| | - Maria D Ganfornina
- Instituto de Biologia y Genetica Molecular, Unidad de Excelencia, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas, Valladolid, Spain
| |
Collapse
|
6
|
Rassart E, Desmarais F, Najyb O, Bergeron KF, Mounier C. Apolipoprotein D. Gene 2020; 756:144874. [PMID: 32554047 DOI: 10.1016/j.gene.2020.144874] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022]
Abstract
ApoD is a 25 to 30 kDa glycosylated protein, member of the lipocalin superfamily. As a transporter of several small hydrophobic molecules, its known biological functions are mostly associated to lipid metabolism and neuroprotection. ApoD is a multi-ligand, multi-function protein that is involved lipid trafficking, food intake, inflammation, antioxidative response and development and in different types of cancers. An important aspect of ApoD's role in lipid metabolism appears to involve the transport of arachidonic acid, and the modulation of eicosanoid production and delivery in metabolic tissues. ApoD expression in metabolic tissues has been associated positively and negatively with insulin sensitivity and glucose homeostasis in a tissue dependent manner. ApoD levels rise considerably in association with aging and neuropathologies such as Alzheimer's disease, stroke, meningoencephalitis, moto-neuron disease, multiple sclerosis, schizophrenia and Parkinson's disease. ApoD is also modulated in several animal models of nervous system injury/pathology.
Collapse
Affiliation(s)
- Eric Rassart
- Laboratoire de Biologie Moléculaire, Département des Sciences Biologiques, Case Postale 8888, Succursale Centre-ville, Montréal, QC H3C 3P8, Canada.
| | - Frederik Desmarais
- Laboratoire de Biologie Moléculaire, Département des Sciences Biologiques, Case Postale 8888, Succursale Centre-ville, Montréal, QC H3C 3P8, Canada; Laboratoire du Métabolisme Moléculaire des Lipides, Université du Québec à Montréal, Département des Sciences Biologiques, Case Postale 8888, Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Ouafa Najyb
- Laboratoire de Biologie Moléculaire, Département des Sciences Biologiques, Case Postale 8888, Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Karl-F Bergeron
- Laboratoire du Métabolisme Moléculaire des Lipides, Université du Québec à Montréal, Département des Sciences Biologiques, Case Postale 8888, Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Catherine Mounier
- Laboratoire du Métabolisme Moléculaire des Lipides, Université du Québec à Montréal, Département des Sciences Biologiques, Case Postale 8888, Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| |
Collapse
|
7
|
Rivas-Urbina A, Rull A, Ordóñez-Llanos J, Sánchez-Quesada JL. Electronegative LDL: An Active Player in Atherogenesis or a By- Product of Atherosclerosis? Curr Med Chem 2019; 26:1665-1679. [PMID: 29600751 DOI: 10.2174/0929867325666180330093953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 11/12/2017] [Accepted: 12/11/2017] [Indexed: 12/16/2022]
Abstract
Low-density lipoproteins (LDLs) are the major plasma carriers of cholesterol. However, LDL particles must undergo various molecular modifications to promote the development of atherosclerotic lesions. Modified LDL can be generated by different mechanisms, but as a common trait, show an increased electronegative charge of the LDL particle. A subfraction of LDL with increased electronegative charge (LDL(-)), which can be isolated from blood, exhibits several pro-atherogenic characteristics. LDL(-) is heterogeneous, due to its multiple origins but is strongly related to the development of atherosclerosis. Nevertheless, the implication of LDL(-) in a broad array of pathologic conditions is complex and in some cases anti-atherogenic LDL(-) properties have been reported. In fact, several molecular modifications generating LDL(-) have been widely studied, but it remains unknown as to whether these different mechanisms are specific or common to different pathological disorders. In this review, we attempt to address these issues examining the most recent findings on the biology of LDL(-) and discussing the relationship between this LDL subfraction and the development of different diseases with increased cardiovascular risk. Finally, the review highlights the importance of minor apolipoproteins associated with LDL(-) which would play a crucial role in the different properties displayed by these modified LDL particles.
Collapse
Affiliation(s)
- Andrea Rivas-Urbina
- Cardiovascular Biochemistry Group, Research Institute of the Hospital de Sant Pau (IIB Sant Pau), Barcelona, Spain.,Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Cerdanyola, Spain
| | - Anna Rull
- Cardiovascular Biochemistry Group, Research Institute of the Hospital de Sant Pau (IIB Sant Pau), Barcelona, Spain.,Hospital Universitari Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
| | - Jordi Ordóñez-Llanos
- Cardiovascular Biochemistry Group, Research Institute of the Hospital de Sant Pau (IIB Sant Pau), Barcelona, Spain.,Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Cerdanyola, Spain
| | - José Luis Sánchez-Quesada
- Cardiovascular Biochemistry Group, Research Institute of the Hospital de Sant Pau (IIB Sant Pau), Barcelona, Spain.,CIBERDEM. Institute of Health Carlos III, Madrid 28029, Spain
| |
Collapse
|
8
|
Panić‐Janković T, Mitulović G. Human chorionic gonadotrophin pharmaceutical formulations of urinary origin display high levels of contaminant proteins-A label-free quantitation proteomics study. Electrophoresis 2019; 40:1622-1629. [PMID: 30883802 PMCID: PMC6593423 DOI: 10.1002/elps.201900087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 12/17/2022]
Abstract
To determine whether there is a measurable protein background in different formulations of urinary and recombinant human chorionic gonadotropin (hCG). Primary outcome measures: identification of contaminant proteins in urinary-derived formulations of hCG; secondary outcome measures: quantitative values of contaminant proteins in different batches of urinary -derived hCG formulations. It was found that urinary-derived batches have high presence of contaminant proteins beside the active substance. The relative amount of contaminant proteins and hCG differs strongly between different batches.
Collapse
Affiliation(s)
- Tanja Panić‐Janković
- Clinical Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - Goran Mitulović
- Clinical Department of Laboratory MedicineMedical University of ViennaViennaAustria
- Proteomic Core FacilityMedical University of ViennaViennaAustria
| |
Collapse
|
9
|
Su J, Miao LF, Ye XH, Cui MS, He XF. Development of prognostic signature and nomogram for patients with breast cancer. Medicine (Baltimore) 2019; 98:e14617. [PMID: 30882627 PMCID: PMC6426514 DOI: 10.1097/md.0000000000014617] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To identify prognostic signature that could predict the survival of patients with breast cancer (BC).Breast cancer samples and normal breast tissues in the TCGA-BRCA and GSE7390 were included. Differentially expressed genes (DEGs) were identified using the "limma" method. Overall survival (OS) associated with DEGs were obtained using univariate and multivariable Cox proportional-hazards regression analysis, and the corresponding prognostic signature and nomogram were constructed. Calibration analysis and decision curve analysis (DCA) were performed.In all, 742 DEGs were identified, 19 of which were independently correlated with the OS of BC patients. The OS of patients in the 19-gene signature low-risk group was significantly better than that in high-risk group (hazard ratio [HR] 0.3506, 95% confidence interval [CI] 0.2488-0.4939), and the 19-gene based signature was demonstrated to be an independent prognostic factor in patient with BC in the TCGA-BRCA cohort (HR 1.501, 95% CI 1.374-1.640) and validation cohort GSE7392 ((HR 0.3557, 95% CI 0.2155-0.5871, P < .0001)). The primary and internally validated C-indexes for the 19-gene signature-based nomogram were 0.817 and 8.013, respectively. The results of calibration analysis and DCA analysis confirmed the robustness and the clinical usability of the nomogram.We constructed a prognostic signature and nomogram for patient with BC, which showed good application prospect.
Collapse
Affiliation(s)
- Jiao Su
- Department of Biological Chemistry, Changzhi Medical College, Shanxi
| | - Li-Feng Miao
- Department of galactophore, Affiliated Heping Hospital, Changzhi Medical College, Shanxi, Changzhi
| | - Xiang-Hua Ye
- Department of Radiotherapy, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou
| | - Meng-Shen Cui
- Department of galactophore, Affiliated Heping Hospital, Changzhi Medical College, Shanxi, Changzhi
| | - Xiao-Feng He
- Department of Science and Education, Affiliated Heping Hospital, Changzhi Medical College, Shanxi, Changzhi, China
| |
Collapse
|
10
|
Ronci M, Leporini L, Felaco P, Sirolli V, Pieroni L, Greco V, Aceto A, Urbani A, Bonomini M. Proteomic Characterization of a New asymmetric Cellulose Triacetate Membrane for Hemodialysis. Proteomics Clin Appl 2018; 12:e1700140. [PMID: 29808585 DOI: 10.1002/prca.201700140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 04/27/2018] [Indexed: 12/24/2022]
Abstract
PURPOSE The artificial membrane inside the haemodialyzer is the main determinant of the quality and success of haemodialysis therapy. The performances of haemodialysis membranes are highly influenced by the interactions with plasma proteins, which in turn are related to the physical and chemical characteristics of the membrane material. The present cross-over study is aimed to analyse the haemodialysis performance of a newly developed asymmetric cellulose triacetate membrane (ATA) in comparison to the conventional parent symmetric polymer (CTA). EXPERIMENTAL DESIGN In four chronic non diabetic haemodialysis patients, the protein constituents of the adsorbed material from the filters after the haemodialysis session, and the proteins recovered in the ultrafiltrate during the session, are identified using a bottom-up shotgun proteomics approach. RESULTS The ATA membrane shows a lower protein adsorption rate and a lower mass distribution pattern of the proteinaceous material. CONCLUSIONS AND CLINICAL RELEVANCE By highlighting the differences between the two haemodialysis filters in terms of adsorbed proteins and flow through, it is demonstrated the higher biocompatibility of the novel ATA membrane, that fulfils the indications for the development of more performant membranes and may represent a step forward for the treatment of patients on chronic haemodialysis.
Collapse
Affiliation(s)
- Maurizio Ronci
- Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti 66100, Italy.,IRCCS-Santa Lucia Foundation, Rome 00144, Italy
| | - Lidia Leporini
- Department of Pharmacy, University "G. D'Annunzio" of Chieti-Pescara, Chieti 66100, Italy
| | - Paolo Felaco
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti 66100, Italy
| | - Vittorio Sirolli
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti 66100, Italy
| | | | | | - Antonio Aceto
- Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti 66100, Italy
| | - Andrea Urbani
- IRCCS-Santa Lucia Foundation, Rome 00144, Italy.,Institute of Biochemistry and Clinical Biochemistry, School of Medicine, Catholic University, Rome 00144, Italy
| | - Mario Bonomini
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti 66100, Italy
| |
Collapse
|
11
|
Lai C, Cheng H, Lin C, Huang S, Chen T, Chung C, Chang C, Wang H, Chuu C. Activation of liver X receptor suppresses angiogenesis
via
induction of ApoD. FASEB J 2017; 31:5568-5576. [DOI: 10.1096/fj.201700374r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 01/25/2023]
Affiliation(s)
- Chih‐Jen Lai
- Institute of Cellular and System MedicineNational Health Research Institutes Miaoli Taiwan
- Institute of BiotechnologyNational Tsing Hua University Hsinchu Taiwan
| | - Hsu‐Chen Cheng
- Department of Life SciencesNational Chung Hsing University Taichung Taiwan
| | - Ching‐Yu Lin
- Institute of Cellular and System MedicineNational Health Research Institutes Miaoli Taiwan
| | - Shih‐Han Huang
- Institute of Cellular and System MedicineNational Health Research Institutes Miaoli Taiwan
- Department of Life SciencesNational Central University Taoyuan Taiwan
| | - Ting‐Huan Chen
- Institute of Cellular and System MedicineNational Health Research Institutes Miaoli Taiwan
- Institute of BiotechnologyNational Tsing Hua University Hsinchu Taiwan
| | - Chi‐Jung Chung
- Department of Health Risk ManagementChina Medical University Taichung Taiwan
| | - Chung‐Ho Chang
- Institute of Cellular and System MedicineNational Health Research Institutes Miaoli Taiwan
- Department of Internal MedicineChanghua Christian Hospital Changhua Taiwan
| | - Horng‐Dar Wang
- Institute of BiotechnologyNational Tsing Hua University Hsinchu Taiwan
| | - Chih‐Pin Chuu
- Institute of Cellular and System MedicineNational Health Research Institutes Miaoli Taiwan
- Biotechnology CenterNational Chung Hsing University Taichung Taiwan
- Graduate Institute of Basic Medical ScienceChina Medical University Taichung Taiwan
- Graduate Program for AgingChina Medical University Taichung Taiwan
| |
Collapse
|
12
|
Antioxidative activity of high-density lipoprotein (HDL): Mechanistic insights into potential clinical benefit. BBA CLINICAL 2017; 8:66-77. [PMID: 28936395 PMCID: PMC5597817 DOI: 10.1016/j.bbacli.2017.07.002] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/29/2022]
Abstract
Uptake of low-density lipoprotein (LDL) particles by macrophages represents a key step in the development of atherosclerotic plaques, leading to the foam cell formation. Chemical modification of LDL is however necessary to induce this process. Proatherogenic LDL modifications include aggregation, enzymatic digestion and oxidation. LDL oxidation by one-electron (free radicals) and two-electron oxidants dramatically increases LDL affinity to macrophage scavenger receptors, leading to rapid LDL uptake and fatty streak formation. Circulating high-density lipoprotein (HDL) particles, primarily small, dense, protein-rich HDL3, provide potent protection of LDL from oxidative damage by free radicals, resulting in the inhibition of the generation of pro-inflammatory oxidized lipids. HDL-mediated inactivation of lipid hydroperoxides involves their initial transfer from LDL to HDL and subsequent reduction to inactive hydroxides by redox-active Met residues of apolipoprotein A-I. Several HDL-associated enzymes are present at elevated concentrations in HDL3 relative to large, light HDL2 and can be involved in the inactivation of short-chain oxidized phospholipids. Therefore, HDL represents a multimolecular complex capable of acquiring and inactivating proatherogenic lipids. Antioxidative function of HDL can be impaired in several metabolic and inflammatory diseases. Structural and compositional anomalies in the HDL proteome and lipidome underlie such functional deficiency. Concomitant normalization of the metabolism, circulating levels, composition and biological activities of HDL particles, primarily those of small, dense HDL3, can constitute future therapeutic target.
Collapse
|
13
|
Emamzadeh FN. Role of Apolipoproteins and α-Synuclein in Parkinson's Disease. J Mol Neurosci 2017; 62:344-355. [PMID: 28695482 PMCID: PMC5541107 DOI: 10.1007/s12031-017-0942-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/12/2017] [Indexed: 12/25/2022]
Abstract
Parkinson's disease (PD) is a progressive brain disorder that interferes with activities of normal life. The main pathological feature of this disease is the loss of more than 80% of dopamine-producing neurons in the substantia nigra (SN). Dopaminergic neuronal cell death occurs when intraneuronal, insoluble, aggregated proteins start to form Lewy bodies (LBs), the most important component of which is a protein called α-synuclein (α-syn). α-Syn structurally contains hexameric repeats of 11 amino acids, which are characteristic of apolipoproteins and thus α-syn can also be considered an apolipoprotein. Moreover, apolipoproteins seem to be involved in the incidence and development of PD. Some apolipoproteins such as ApoD have a neuroprotective role in the brain. In PD, apoD levels increase in glial cells surrounding dopaminergic cells. However, elevated levels of some other apolipoproteins such as ApaA1 and ApoE are reported as a vulnerability factor of PD. At present, when a clinical diagnosis of PD is made, based on symptoms such as shaking, stiff muscles and slow movement, serious damage has already been done to nerve cells of the SN. The diagnosis of PD in its earlier stages, before this irreversible damage, would be of enormous benefit for future treatment strategies designed to slow or halt the progression of PD. This review presents the roles of apolipoproteins and α-syn in PD and how some of them could potentially be used as biomarkers for PD.
Collapse
Affiliation(s)
- Fatemeh Nouri Emamzadeh
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, University of Lancaster, Lancaster, LA1 4AY, UK.
| |
Collapse
|