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Stathopoulou KM, Georgakopoulos S, Tasoulis S, Plagianakos VP. Investigating the overlap of machine learning algorithms in the final results of RNA-seq analysis on gene expression estimation. Health Inf Sci Syst 2024; 12:14. [PMID: 38435719 PMCID: PMC10904690 DOI: 10.1007/s13755-023-00265-4] [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: 06/04/2023] [Accepted: 12/05/2023] [Indexed: 03/05/2024] Open
Abstract
Advances in computer science in combination with the next-generation sequencing have introduced a new era in biology, enabling advanced state-of-the-art analysis of complex biological data. Bioinformatics is evolving as a union field between computer Science and biology, enabling the representation, storage, management, analysis and exploration of many types of data with a plethora of machine learning algorithms and computing tools. In this study, we used machine learning algorithms to detect differentially expressed genes between different types of cancer and showing the existence overlap to final results from RNA-sequencing analysis. The datasets were obtained from the National Center for Biotechnology Information resource. Specifically, dataset GSE68086 which corresponds to PMID:200,068,086. This dataset consists of 171 blood platelet samples collected from patients with six different tumors and healthy individuals. All steps for RNA-sequencing analysis (preprocessing, read alignment, transcriptome reconstruction, expression quantification and differential expression analysis) were followed. Machine Learning- based Random Forest and Gradient Boosting algorithms were applied to predict significant genes. The Rstudio statistical tool was used for the analysis.
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Affiliation(s)
- Kalliopi-Maria Stathopoulou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece
| | | | - Sotiris Tasoulis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece
| | - Vassilis P. Plagianakos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece
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2
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Chen J, Liu S, Ruan Z, Wang K, Xi X, Mao J. Thrombotic events associated with immune checkpoint inhibitors and novel antithrombotic strategies to mitigate bleeding risk. Blood Rev 2024; 67:101220. [PMID: 38876840 DOI: 10.1016/j.blre.2024.101220] [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: 04/26/2024] [Revised: 05/23/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Although immunotherapy is expanding treatment options for cancer patients, the prognosis of advanced cancer remains poor, and these patients must contend with both cancers and cancer-related thrombotic events. In particular, immune checkpoint inhibitors are associated with an increased risk of atherosclerotic thrombotic events. Given the fundamental role of platelets in atherothrombosis, co-administration of antiplatelet agents is always indicated. Platelets are also involved in all steps of cancer progression. Classical antithrombotic drugs can cause inevitable hemorrhagic side effects due to blocking integrin β3 bidirectional signaling, which regulates simultaneously thrombosis and hemostasis. Meanwhile, many promising new targets are emerging with minimal bleeding risk and desirable anti-tumor effects. This review will focus on the issue of thrombosis during immune checkpoint inhibitor treatment and the role of platelet activation in cancer progression as well as explore the mechanisms by which novel antiplatelet therapies may exert both antithrombotic and antitumor effects without excessive bleeding risk.
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Affiliation(s)
- Jiayi Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shuang Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zheng Ruan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Xiaodong Xi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Jianhua Mao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Turizo MJF, Patell R, Zwicker JI. Identifying novel biomarkers using proteomics to predict cancer-associated thrombosis. BLEEDING, THROMBOSIS AND VASCULAR BIOLOGY 2024; 3:120. [PMID: 38828226 PMCID: PMC11143428 DOI: 10.4081/btvb.2024.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/08/2024] [Indexed: 06/05/2024]
Abstract
Comprehensive protein analyses of plasma are made possible by high-throughput proteomic screens, which may help find new therapeutic targets and diagnostic biomarkers. Patients with cancer are frequently affected by venous thromboembolism (VTE). The limited predictive accuracy of current VTE risk assessment tools highlights the need for new, more targeted biomarkers. Although coagulation biomarkers for the diagnosis, prognosis, and treatment of VTE have been investigated, none of them have the necessary clinical validation or diagnostic accuracy. Proteomics holds the potential to uncover new biomarkers and thrombotic pathways that impact the risk of thrombosis. This review explores the fundamental methods used in proteomics and focuses on particular biomarkers found in VTE and cancer-associated thrombosis.
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Affiliation(s)
- Maria J Fernandez Turizo
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Rushad Patell
- Division of Medical Oncology and Hematology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Jeffrey I Zwicker
- Department of Medicine, Hematology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weil Cornell Medical College, New York, NY, United States
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4
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Czaplewska P, Bogucka A, Macur K, Rybicka M, Rychłowski M, Fiołka MJ. Proteomic response of A549 lung cancer cell line to protein-polysaccharide complex Venetin-1 isolated from earthworm coelomic fluid. Front Mol Biosci 2023; 10:1128320. [PMID: 37377864 PMCID: PMC10292018 DOI: 10.3389/fmolb.2023.1128320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Earthworms' celomic fluid has long attracted scientists' interest due to their toxic properties. It has been shown that the elimination of coelomic fluid cytotoxicity to normal human cells was crucial for the generation of the non-toxic Venetin-1 protein-polysaccharide complex, which exhibits selective activity against Candida albicans cells as well as A549 non-small cell lung cancer cells. To find the molecular mechanisms behind the anti-cancer properties of the preparation, this research investigated the proteome response of A549 cells to the presence of Venetin-1. The sequential window acquisition of all theoretical mass spectra (SWATH-MS) methodology was used for the analysis, which allows for a relative quantitative analysis to be carried out without radiolabelling. The results showed that the formulation did not induce significant proteome responses in normal BEAS-2B cells. In the case of the tumour line, 31 proteins were up regulated, and 18 proteins down regulated. Proteins with increased expression in neoplastic cells are mainly associated with the mitochondrion, membrane transport and the endoplasmic reticulum. In the case of altered proteins, Venetin-1 interferes with proteins that stabilise the structures, i.e., keratin, glycolysis/gluconeogenesis and metabolic processes.
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Affiliation(s)
- Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Aleksandra Bogucka
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
- Institute of Biochemistry, Justus Liebig University of Giessen, Giessen, Germany
| | - Katarzyna Macur
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Magda Rybicka
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Michał Rychłowski
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Marta J. Fiołka
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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Ercan H, Resch U, Hsu F, Mitulovic G, Bileck A, Gerner C, Yang JW, Geiger M, Miller I, Zellner M. A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection. Cells 2023; 12:747. [PMID: 36899884 PMCID: PMC10000902 DOI: 10.3390/cells12050747] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques' orthogonality with their different contents of data output to elucidate biological questions.
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Affiliation(s)
- Huriye Ercan
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
- Immunology Outpatient Clinic, 1090 Vienna, Austria
| | - Ulrike Resch
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Felicia Hsu
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Goran Mitulovic
- Proteomics Core Facility, Clinical Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Jae-Won Yang
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Margarethe Geiger
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Ingrid Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Maria Zellner
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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Dong W, Xia Z, Chai Z, Qiu Z, Wang X, Yang Z, Wang J, Zhang T, Zhang Q, Jin J. Proteomic analysis of small extracellular vesicles from the plasma of patients with hepatocellular carcinoma. World J Surg Oncol 2022; 20:387. [PMID: 36471393 PMCID: PMC9724420 DOI: 10.1186/s12957-022-02849-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Liver cancer is one of the most common tumors with the seventh-highest incidence and the third-highest mortality. Many studies have shown that small extracellular vesicles (sEVs) play an important role in liver cancer. Here, we report comprehensive signatures for sEV proteins from plasma obtained from patients with hepatocellular carcinoma (HCC), which might be valuable for the evaluation and diagnosis of HCC. METHODS We extracted sEVs from the plasma of controls and patients with HCC. Differentially expressed proteins in the sEVs were analyzed using label-free quantification and bioinformatic analyses. Western blotting (WB) was used to validate the abovementioned sEV proteins. RESULTS Proteomic analysis was performed for plasma sEVs from 21 patients with HCC and 15 controls. Among the 335 identified proteins in our study, 27 were significantly dysregulated, including 13 upregulated proteins that were involved predominantly in the complement cascade (complement C1Q subcomponent subunit B (C1QB), complement C1Q subcomponent subunit C (C1QC), C4B-binding protein alpha chain (C4BPA), and C4B-binding protein beta chain (C4BPB)) and the coagulation cascade (F13B, fibrinogen alpha chain (FGA), fibrinogen beta chain (FGB), and fibrinogen gamma chain (FGG)). We verified increased levels of the C1QB, C1QC, C4BPA, and C4BPB proteins in the plasma sEVs from patients with HCC in both the discovery cohort and validation cohort. CONCLUSIONS The complement cascade in sEVs was significantly involved in HCC progression. C1QB, C1QC, C4BPA, and C4BPB were highly abundant in the plasma sEVs from patients with HCC and might represent molecular signatures.
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Affiliation(s)
- Wei Dong
- grid.452223.00000 0004 1757 7615Xiangya Hospital, Central South University, Changsha, Hunan 410008 China ,grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Zeyu Xia
- grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Zehua Chai
- grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Zhidong Qiu
- grid.452223.00000 0004 1757 7615Xiangya Hospital, Central South University, Changsha, Hunan 410008 China ,grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Xuehong Wang
- grid.452223.00000 0004 1757 7615Xiangya Hospital, Central South University, Changsha, Hunan 410008 China ,grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Zebin Yang
- grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Junnan Wang
- grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Tingrui Zhang
- grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
| | - Qinqin Zhang
- Department of Thyroid and Breast Surgery, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, 541002 Guangxi China
| | - Junfei Jin
- grid.452223.00000 0004 1757 7615Xiangya Hospital, Central South University, Changsha, Hunan 410008 China ,grid.452806.d0000 0004 1758 1729Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin, 541001 Guangxi China ,grid.452806.d0000 0004 1758 1729Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001 China ,grid.443385.d0000 0004 1798 9548China‒USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, 541001 Guangxi China
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Chen A, Huang R, Wu E, Han R, Wen J, Li Q, Zhang Z, Shen B. The Generation of a Lung Cancer Health Factor Distribution Using Patient Graphs Constructed From Electronic Medical Records: Retrospective Study. J Med Internet Res 2022; 24:e40361. [PMID: 36427233 PMCID: PMC9736747 DOI: 10.2196/40361] [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: 06/21/2022] [Revised: 09/09/2022] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Electronic medical records (EMRs) of patients with lung cancer (LC) capture a variety of health factors. Understanding the distribution of these factors will help identify key factors for risk prediction in preventive screening for LC. OBJECTIVE We aimed to generate an integrated biomedical graph from EMR data and Unified Medical Language System (UMLS) ontology for LC, and to generate an LC health factor distribution from a hospital EMR of approximately 1 million patients. METHODS The data were collected from 2 sets of 1397 patients with and those without LC. A patient-centered health factor graph was plotted with 108,000 standardized data, and a graph database was generated to integrate the graphs of patient health factors and the UMLS ontology. With the patient graph, we calculated the connection delta ratio (CDR) for each of the health factors to measure the relative strength of the factor's relationship to LC. RESULTS The patient graph had 93,000 relations between the 2794 patient nodes and 650 factor nodes. An LC graph with 187 related biomedical concepts and 188 horizontal biomedical relations was plotted and linked to the patient graph. Searching the integrated biomedical graph with any number or category of health factors resulted in graphical representations of relationships between patients and factors, while searches using any patient presented the patient's health factors from the EMR and the LC knowledge graph (KG) from the UMLS in the same graph. Sorting the health factors by CDR in descending order generated a distribution of health factors for LC. The top 70 CDR-ranked factors of disease, symptom, medical history, observation, and laboratory test categories were verified to be concordant with those found in the literature. CONCLUSIONS By collecting standardized data of thousands of patients with and those without LC from the EMR, it was possible to generate a hospital-wide patient-centered health factor graph for graph search and presentation. The patient graph could be integrated with the UMLS KG for LC and thus enable hospitals to bring continuously updated international standard biomedical KGs from the UMLS for clinical use in hospitals. CDR analysis of the graph of patients with LC generated a CDR-sorted distribution of health factors, in which the top CDR-ranked health factors were concordant with the literature. The resulting distribution of LC health factors can be used to help personalize risk evaluation and preventive screening recommendations.
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Affiliation(s)
- Anjun Chen
- Institutes for System Genetics, West China Hospital, Chengdu, China
| | - Ran Huang
- Institutes for System Genetics, West China Hospital, Chengdu, China
| | - Erman Wu
- Institutes for System Genetics, West China Hospital, Chengdu, China
| | | | - Jian Wen
- Guilin Medical University Affiliateted Hospital, Guilin, China
| | - Qinghua Li
- Guilin Medical University, Guilin, China
| | | | - Bairong Shen
- Institutes for System Genetics, West China Hospital, Chengdu, China
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Systematic Analysis and Identification of Molecular Subtypes of TRP-Related Genes and Prognosis Prediction in Lung Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:5388283. [PMID: 36090899 PMCID: PMC9452946 DOI: 10.1155/2022/5388283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022]
Abstract
Background. Transient receptor potential channel (TRP) is a superfamily of nonselective cation channels, which is a member of calcium ion channels with a vital role in different calcium ion signal transduction pathways. TRP channel expression is often changed in the tumor, although the role of TRP proteins in lung cancer is unknown. Methods. Molecular Signatures Database (MsigDB) provided the TRP gene set. Univariate Cox regression analysis was performed on The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) data collection set employing the coxph function of R package survival to find prognosis-related genes. The R package ConsumusClusterPlus was employed for doing the consistency cluster analysis of TCGA-LUAD samples according to the prognosis-related TRP gene. The R-package limma was utilized for investigating the differential expression of TRP subtypes. According to the differentially expressed genes between subtypes, the least absolute shrinkage and selection operator (LASSO) regression was employed to find the major genes and develop the risk model. CIBERPORT algorithm, R package maftools, gene set variation analysis (GSVA), and pRRophetic of R-package were employed for measuring the proportion of immune cells among subtypes, genomic mutation difference, pathway enrichment score, and drug sensitivity analysis. Results. A total of 15 TRP-related genes associated with the prognosis of lung adenocarcinoma were found. According to the expression value of 15 genes, lung adenocarcinoma can be sorted into two subcategories. The prognosis of cluster1 is considerably better in comparison with that of cluster2. There were 123 differentially expressed genes between C1 and C2 subtypes, including 6 up- and 117 downregulated genes. There were major variations in the tumor microenvironment between C1 and C2 subtypes. The proportion of CD8 T cells in the C1 subtype was considerably enhanced in comparison with that in the C2 subtype. We further discovered 123 differentially expressed genes among subtypes, and 8 key genes were obtained at the end. The risk score (RS) model developed by the 8-gene signature had good strength in the TCGA validation set, overall set, and Gene Expression Omnibus (GEO) external dataset. There were major variations in immune checkpoint gene expression, patient sensitivity to immunotherapeutic drugs, immune infiltration, and genomic mutations between high and low groups on the basis of RS. Conclusions. The risk model developed on the basis of TRP-related genes can help in predicting the prognosis of patients suffering from lung adenocarcinoma and guide immunotherapy.
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Moik F, Ay C. Venous and arterial thromboembolism in patients with cancer treated with targeted anti-cancer therapies. Thromb Res 2022; 213 Suppl 1:S58-S65. [DOI: 10.1016/j.thromres.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 10/18/2022]
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10
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Kong Y, Chen H, Chen M, Li Y, Li J, Liu Q, Xiong H, Guo T, Xie Y, Yuan Y, Zhang XL. Abnormal ECA-Binding Membrane Glycans and Galactosylated CAT and P4HB in Lesion Tissues as Potential Biomarkers for Hepatocellular Carcinoma Diagnosis. Front Oncol 2022; 12:855952. [PMID: 35392238 PMCID: PMC8980540 DOI: 10.3389/fonc.2022.855952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/21/2022] [Indexed: 01/22/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common types of cancer. Despite decades of research efforts, the search for novel biomarkers is still urgently needed for the diagnosis of HCC and the improvement of clinical outcomes. Previous studies of HCC clinical biomarkers have usually focused on serum and urine samples (e.g., serum Alpha-fetoprotein (AFP). However, cellular membrane proteins in lesion tissues are less used in HCC diagnosis. The abnormal expression of membrane glycoproteins in tumor lesions are considered as potential targets for tumor diagnosis and tumor therapies. Here, a lectin array has been employed to screen and identify abnormal glycopatterns and cellular membrane glycans in HCC lesion tissues compared with adjacent non-tumor tissues. We found that there was significantly less expression of Erythrina cristagalli (ECA) lectin binding (Galβ1-3/β1-4) glycans on the cellular membrane of HCC lesion tissues compared with those of adjacent non-tumor tissues. Immunohistochemistry analysis further showed that ECA-binding ability on the membrane proteins of HCC tissues progressively decreased in different tumor-node-metastasis (TNM) stages (stage I to stage III) as the malignancy of liver cancer increased. Receiver operating curve (ROC) analysis showed ECA-binding ability yielding a sensitivity of 85% and specificity of 75%, and a combination of ECA and AFP has better clinical diagnostic efficiency, yielding a sensitivity of 90% and specificity of 85%, than ECA or AFP assay alone. ECA pull-down followed by mass spectrometry further showed that there was significantly less expression of ECA binding membrane catalase (CAT) and prolyl 4-hydroxylase beta polypeptide (P4HB) in HCC tissues compared with the adjacent non-tumor tissues. The abnormally increased expression of total CAT and P4HB and decreased expression of galactosylated membrane CAT and P4HB in HCC cell lines were correlated with an HCC metastasis status. Our findings suggest that abnormal declined ECA-binding galatosylated membrane glycans and two galactosylated-CAT and P4HB glycoproteins in lesion tissues are potential biomarkers in the diagnosis and/or metastasis prediction for HCC.
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Affiliation(s)
- Ying Kong
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Hao Chen
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengyu Chen
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Yongshuai Li
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Jiarong Li
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Qi Liu
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Huan Xiong
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Tangxi Guo
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan Xie
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Yufeng Yuan
- Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao-Lian Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Allergy Department of Zhongnan Hospital, State Key Laboratory of Virology, Medical Research Institute Wuhan University School of Medicine, Wuhan, China
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11
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Beck S, Hochreiter B, Schmid JA. Extracellular Vesicles Linking Inflammation, Cancer and Thrombotic Risks. Front Cell Dev Biol 2022; 10:859863. [PMID: 35372327 PMCID: PMC8970602 DOI: 10.3389/fcell.2022.859863] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/21/2022] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) being defined as lipid-bilayer encircled particles are released by almost all known mammalian cell types and represent a heterogenous set of cell fragments that are found in the blood circulation and all other known body fluids. The current nomenclature distinguishes mainly three forms: microvesicles, which are formed by budding from the plasma membrane; exosomes, which are released, when endosomes with intraluminal vesicles fuse with the plasma membrane; and apoptotic bodies representing fragments of apoptotic cells. Their importance for a great variety of biological processes became increasingly evident in the last decade when it was discovered that they contribute to intercellular communication by transferring nucleotides and proteins to recipient cells. In this review, we delineate several aspects of their isolation, purification, and analysis; and discuss some pitfalls that have to be considered therein. Further on, we describe various cellular sources of EVs and explain with different examples, how they link cancer and inflammatory conditions with thrombotic processes. In particular, we elaborate on the roles of EVs in cancer-associated thrombosis and COVID-19, representing two important paradigms, where local pathological processes have systemic effects in the whole organism at least in part via EVs. Finally, we also discuss possible developments of the field in the future and how EVs might be used as biomarkers for diagnosis, and as vehicles for therapeutics.
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Affiliation(s)
- Sarah Beck
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
- Institute of Experimental Biomedicine, University Hospital Würzburg and Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
- *Correspondence: Sarah Beck, ; Johannes A. Schmid,
| | - Bernhard Hochreiter
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Johannes A. Schmid
- Institute of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
- *Correspondence: Sarah Beck, ; Johannes A. Schmid,
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12
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Palacios-Acedo AL, Langiu M, Crescence L, Mège D, Dubois C, Panicot-Dubois L. Platelet and Cancer-Cell Interactions Modulate Cancer-Associated Thrombosis Risk in Different Cancer Types. Cancers (Basel) 2022; 14:730. [PMID: 35159000 PMCID: PMC8833365 DOI: 10.3390/cancers14030730] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
The first cause of death in cancer patients, after tumoral progression itself, is thrombo-embolic disease. This cancer-associated hypercoagulability state is known as Trousseau's syndrome, and the risk for developing thrombotic events differs according to cancer type and stage, as well as within patients. Massive platelet activation by tumor cells is the key mediator of thrombus formation in Trousseau's syndrome. In this literature review, we aimed to compare the interactions between cancer cells and platelets in three different cancer types, with low, medium and high thrombotic risk. We chose oral squamous cell carcinoma for the low-thrombotic-risk, colorectal adenocarcinoma for the medium-thrombotic-risk, and pancreatic carcinoma for the high-thrombotic-risk cancer type. We showcase that understanding these interactions is of the highest importance to find new biomarkers and therapeutic targets for cancer-associated thrombosis.
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Affiliation(s)
- Ana-Luisa Palacios-Acedo
- Aix Marseille University, INSERM 1263 (Institut National de la Santé et de la Recherche), INRAE 1260 (Institut National de la Recherche Agronomique et de l’Environnement), C2VN (Center for CardioVascular and Nutrition Research), 13885 Marseille, France; (A.-L.P.-A.); (M.L.); (L.C.); (D.M.); (L.P.-D.)
| | - Mélanie Langiu
- Aix Marseille University, INSERM 1263 (Institut National de la Santé et de la Recherche), INRAE 1260 (Institut National de la Recherche Agronomique et de l’Environnement), C2VN (Center for CardioVascular and Nutrition Research), 13885 Marseille, France; (A.-L.P.-A.); (M.L.); (L.C.); (D.M.); (L.P.-D.)
| | - Lydie Crescence
- Aix Marseille University, INSERM 1263 (Institut National de la Santé et de la Recherche), INRAE 1260 (Institut National de la Recherche Agronomique et de l’Environnement), C2VN (Center for CardioVascular and Nutrition Research), 13885 Marseille, France; (A.-L.P.-A.); (M.L.); (L.C.); (D.M.); (L.P.-D.)
- Marseille University, PIVMI (Plateforme d’Imagerie Vasculaire et de Microscopie Intravitale), C2VN (Center for CardioVascular and Nutrition Research), 13385 Marseille, France
| | - Diane Mège
- Aix Marseille University, INSERM 1263 (Institut National de la Santé et de la Recherche), INRAE 1260 (Institut National de la Recherche Agronomique et de l’Environnement), C2VN (Center for CardioVascular and Nutrition Research), 13885 Marseille, France; (A.-L.P.-A.); (M.L.); (L.C.); (D.M.); (L.P.-D.)
- Department of Digestive Surgery, La Timone University Hospital, 13005 Marseille, France
| | - Christophe Dubois
- Aix Marseille University, INSERM 1263 (Institut National de la Santé et de la Recherche), INRAE 1260 (Institut National de la Recherche Agronomique et de l’Environnement), C2VN (Center for CardioVascular and Nutrition Research), 13885 Marseille, France; (A.-L.P.-A.); (M.L.); (L.C.); (D.M.); (L.P.-D.)
- Marseille University, PIVMI (Plateforme d’Imagerie Vasculaire et de Microscopie Intravitale), C2VN (Center for CardioVascular and Nutrition Research), 13385 Marseille, France
| | - Laurence Panicot-Dubois
- Aix Marseille University, INSERM 1263 (Institut National de la Santé et de la Recherche), INRAE 1260 (Institut National de la Recherche Agronomique et de l’Environnement), C2VN (Center for CardioVascular and Nutrition Research), 13885 Marseille, France; (A.-L.P.-A.); (M.L.); (L.C.); (D.M.); (L.P.-D.)
- Marseille University, PIVMI (Plateforme d’Imagerie Vasculaire et de Microscopie Intravitale), C2VN (Center for CardioVascular and Nutrition Research), 13385 Marseille, France
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13
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Risk assessment models of cancer-associated thrombosis - Potentials and perspectives. THROMBOSIS UPDATE 2021. [DOI: 10.1016/j.tru.2021.100075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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14
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Ercan H, Schrottmaier WC, Pirabe A, Schmuckenschlager A, Pereyra D, Santol J, Pawelka E, Traugott MT, Schörgenhofer C, Seitz T, Karolyi M, Yang JW, Jilma B, Zoufaly A, Assinger A, Zellner M. Platelet Phenotype Analysis of COVID-19 Patients Reveals Progressive Changes in the Activation of Integrin αIIbβ3, F13A1, the SARS-CoV-2 Target EIF4A1 and Annexin A5. Front Cardiovasc Med 2021; 8:779073. [PMID: 34859078 PMCID: PMC8632253 DOI: 10.3389/fcvm.2021.779073] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 01/08/2023] Open
Abstract
Background: The fatal consequences of an infection with severe acute respiratory syndrome coronavirus 2 are not only caused by severe pneumonia, but also by thrombosis. Platelets are important regulators of thrombosis, but their involvement in the pathogenesis of COVID-19 is largely unknown. The aim of this study was to determine their functional and biochemical profile in patients with COVID-19 in dependence of mortality within 5-days after hospitalization. Methods: The COVID-19-related platelet phenotype was examined by analyzing their basal activation state via integrin αIIbβ3 activation using flow cytometry and the proteome by unbiased two-dimensional differential in-gel fluorescence electrophoresis. In total we monitored 98 surviving and 12 non-surviving COVID-19 patients over 5 days of hospital stay and compared them to healthy controls (n = 12). Results: Over the observation period the level of basal αIIbβ3 activation on platelets from non-surviving COVID-19 patients decreased compared to survivors. In line with this finding, proteomic analysis revealed a decrease in the total amount of integrin αIIb (ITGA2B), a subunit of αIIbβ3, in COVID-19 patients compared to healthy controls; the decline was even more pronounced for the non-survivors. Consumption of the fibrin-stabilizing factor coagulation factor XIIIA (F13A1) was higher in platelets from COVID-19 patients and tended to be higher in non-survivors; plasma concentrations of the latter also differed significantly. Depending on COVID-19 disease status and mortality, increased amounts of annexin A5 (ANXA5), eukaryotic initiation factor 4A-I (EIF4A1), and transaldolase (TALDO1) were found in the platelet proteome and also correlated with the nasopharyngeal viral load. Dysregulation of these proteins may play a role for virus replication. ANXA5 has also been identified as an autoantigen of the antiphospholipid syndrome, which is common in COVID-19 patients. Finally, the levels of two different protein disulfide isomerases, P4HB and PDIA6, which support thrombosis, were increased in the platelets of COVID-19 patients. Conclusion: Platelets from COVID-19 patients showed significant changes in the activation phenotype, in the processing of the final coagulation factor F13A1 and the phospholipid-binding protein ANXA5 compared to healthy subjects. Additionally, these results demonstrate specific alterations in platelets during COVID-19, which are significantly linked to fatal outcome.
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Affiliation(s)
- Huriye Ercan
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Waltraud Cornelia Schrottmaier
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Anita Pirabe
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Anna Schmuckenschlager
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - David Pereyra
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
- Division of Visceral Surgery, Department of General Surgery, General Hospital Vienna, Medical University of Vienna, Vienna, Austria
| | - Jonas Santol
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
- Division of Visceral Surgery, Department of General Surgery, General Hospital Vienna, Medical University of Vienna, Vienna, Austria
| | - Erich Pawelka
- Department of Medicine IV, Clinic Favoriten, Vienna, Austria
| | | | - Christian Schörgenhofer
- Department of Clinical Pharmacology, Medical University of Vienna, General Hospital Vienna, Vienna, Austria
| | - Tamara Seitz
- Department of Medicine IV, Clinic Favoriten, Vienna, Austria
| | - Mario Karolyi
- Department of Medicine IV, Clinic Favoriten, Vienna, Austria
| | - Jae-Won Yang
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Bernd Jilma
- Department of Clinical Pharmacology, Medical University of Vienna, General Hospital Vienna, Vienna, Austria
| | | | - Alice Assinger
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Maria Zellner
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
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