4.6 Article

Extracellular vesicles from human plasma and serum are carriers of extravesicular cargo-Implications for biomarker discovery

期刊

PLOS ONE
卷 15, 期 8, 页码 -

出版社

PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0236439

关键词

-

资金

  1. Academy of Finland [287089, 315227]
  2. Magnus Ehrnrooth Foundation
  3. Medicinska Understodsforeningen Liv och Halsa rf
  4. National Research, Development and Innovation Office NKFIH, Hungary [PD 121326, NVKP_16-1-2016-0007]
  5. Janos Bolyai Research Fellowship
  6. Ministry for Innovation and Technology [UNKP-19-3]
  7. Academy of Finland (AKA) [315227, 315227, 287089] Funding Source: Academy of Finland (AKA)

向作者/读者索取更多资源

Extracellular vesicles (EVs) in human blood are a potential source of biomarkers. To which extent anticoagulation affects their concentration, cellular origin and protein composition is largely unexplored. To study this, blood from 23 healthy subjects was collected in acid citrate dextrose (ACD), citrate or EDTA, or without anticoagulation to obtain serum. EVs were isolated by ultracentrifugation or by size-exclusion chromatography (SEC) for fluorescence-SEC. EVs were analyzed by micro flow cytometry, NTA, TEM, Western blot, and protein mass spectrometry. The plasma EV concentration was unaffected by anticoagulants, but serum contained more platelet EVs. The protein composition of plasma EVs differed between anticoagulants, and between plasma and serum. Comparison to other studies further revealed that the shared EV protein composition resembles the protein corona of synthetic nanoparticles incubated in plasma or serum. In conclusion, we have validated a higher concentration of platelet EVs in serum than plasma by contemporary EV methods. Anticoagulation should be carefully described (i) to enable study comparison, (ii) to utilize available sample cohorts, and (iii) when preparing/selecting biobank samples. Further, the similarity of the EV protein corona and that of nanoparticles implicates that EVs carry both intravesicular and extravesicular cargo, which will expand their applicability for biomarker discovery.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.6
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Oncology

Exploration of Extracellular Vesicle miRNAs, Targeted mRNAs and Pathways in Prostate Cancer: Relation to Disease Status and Progression

Maija Puhka, Lisse Thierens, Daniel Nicorici, Tarja Forsman, Tuomas Mirtti, Taija af Haellstroem, Elina Serkkola, Antti Rannikko

Summary: Prostate cancer lacks non-invasive specific biomarkers for aggressive disease. This study focuses on urinary extracellular vesicles (uEV) as potential biomarkers. The results show that uEV carry a comprehensive presentation of differentially expressed miRNAs, target mRNAs, and pathogenesis pathways associated with prostate cancer status and progression.

CANCERS (2022)

Article Cardiac & Cardiovascular Systems

Plasma proteome of brain-dead organ donors predicts heart transplant outcome

Jan Lukac, Kishor Dhaygude, Mayank Saraswat, Sakari Joenvaara, Simo O. Syrjala, Emil J. Holmstrom, Rainer Krebs, Risto Renkonen, Antti Nykanen, Karl B. Lemstrom

Summary: The study investigated systemic changes in donor plasma proteome related to brain death and their impact on heart transplant outcomes. It found specific protein alterations in brain-dead donors compared to healthy controls, with implications for predicting transplant outcomes and improving donor evaluation. Analysis revealed upregulation of coagulation and glucose metabolism pathways in donors, and downregulation of complement activation and nitric oxide production pathways, among others. Notably, certain proteins were associated with post-transplant complications such as acute rejections and mortality, highlighting the potential clinical significance of these plasma proteome changes.

JOURNAL OF HEART AND LUNG TRANSPLANTATION (2022)

Article Multidisciplinary Sciences

Quantitative glycoproteomics of human milk and association with atopic disease

Matilda Holm, Mayank Saraswat, Sakari Joenvaara, Antti Seppo, R. John M. Looney, Tiialotta Tohmola, Jutta Renkonen, Risto Renkonen, Kirsi Jarvinen

Summary: The prevalence of allergic diseases and asthma is increasing worldwide, and lifestyle behaviors and environmental factors have been implicated as reasons. This study compared the N-glycoprotein profiles of breast milk samples from urban/suburban mothers in Rochester and traditional farmers in the Old Order Mennonite community in Upstate New York. The results showed significant differences in the glycosylation of milk proteins between the two populations, and certain glycopeptides were associated with the development of atopic disease. This study suggests that the differential glycosylation of milk proteins could be linked to the risk of atopic disease.

PLOS ONE (2022)

Article Chemistry, Multidisciplinary

TMT-Based Multiplexed Quantitation of N-Glycopeptides Reveals Glycoproteome Remodeling Induced by Oncogenic Mutations

Mayank Saraswat, Kiran Kumar Mangalaparthi, Kishore Garapati, Akhilesh Pandey

Summary: This study presents a workflow that combines TMT-labeled glycopeptide enrichment with size-exclusion chromatography for in-depth and quantitative analysis of the glycoproteome. The workflow was applied to study the cellular glycoproteome of PIK3CA mutant cells and discovered site-specific glycosylation changes in important receptors.

ACS OMEGA (2022)

Article Cell Biology

Reproducibility of extracellular vesicle research

Rienk Nieuwland, Pia R. M. Siljander, Juan M. Falcon-Perez, Kenneth W. Witwer

Summary: Cells release membrane-delimited particles called extracellular vesicles (EVs) into the environment, and these EVs have become a hot topic due to their importance in health and disease. However, studying EVs is challenging due to their heterogeneity and complex composition. Efforts are currently underway to improve the reproducibility of EV measurement results and support the credibility of EV research.

EUROPEAN JOURNAL OF CELL BIOLOGY (2022)

Article Biochemical Research Methods

Proteomic alterations in extracellular vesicles induced by oncogenic PIK3CA mutations

Mayank Saraswat, Kishore Garapati, Jinyong Kim, Rohit Budhraja, Akhilesh Pandey

Summary: This study investigated the impact of PIK3CA gene mutations on extracellular vesicles (EVs). Proteomic analysis of EVs revealed changes in protein composition associated with PIK3CA activating mutations, particularly in cell adhesion molecules and markers of tumor invasion and progression.

PROTEOMICS (2022)

Article Cell Biology

A quick pipeline for the isolation of 3D cell culture-derived extracellular vesicles

Heikki Kyykallio, Alessandra V. S. Faria, Rosabella Hartmann, Janne Capra, Kirsi Rilla, Pia R-M Siljander

Summary: This research developed two methods using nanofibrillar cellulose as a 3D cell culture matrix to isolate extracellular vesicles from cancer spheroids. Both methods were easy to set up, quick to perform, and provided high yields of extracellular vesicles.

JOURNAL OF EXTRACELLULAR VESICLES (2022)

Article Cell Biology

OxLDL sensitizes platelets for increased formation of extracellular vesicles capable of finetuning macrophage gene expression

Katariina Maaninka, Maarit Neuvonen, Erja Kerkela, Kati Hyvarinen, Mari Palviainen, Masood Kamali-Moghaddam, Antonio Federico, Dario Greco, Saara Laitinen, Katariina Oorni, Pia R. M. Siljander

Summary: Platelet extracellular vesicles (PEVs) generated upon platelet activation, particularly in the presence of oxLDL, contribute to the pathogenesis of atherosclerosis by promoting inflammation and macrophage dysfunction. The combination of thrombin, collagen, and oxLDL induces the formation of PEVs that contain inflammatory proteins and alter macrophage gene expression. Scavenger receptor CD36 plays a significant role in oxLDL-induced PEV formation, while HDL has a slight suppressive effect. Pathways related to cell cycle, gene expression regulation, and immune system signaling are affected in macrophages treated with oxLDL-induced PEVs.

EUROPEAN JOURNAL OF CELL BIOLOGY (2023)

Article Cell Biology

RAB23 regulates musculoskeletal development and patterning

Md. Rakibul Hasan, Anna Koskenranta, Kirsi Alakurtti, Maarit Takatalo, David P. P. Rice

Summary: RAB23 plays a crucial role in musculoskeletal development by regulating the formation of the patella bone and maintenance of tendon progenitors. Its loss results in abnormal formation of the patella and knee joint. RAB23 is required for the specification of Sox9 and scleraxis double-positive chondroprogenitors during patella formation and establishment of the patellofemoral joint. Furthermore, RAB23 is involved in TGF beta superfamily signaling, which is important for patella initiation and progenitor differentiation.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2023)

Article Multidisciplinary Sciences

Genome-wide mRNA profiling in urinary extracellular vesicles reveals stress gene signature for diabetic kidney disease

Om Prakash Dwivedi, Karina Barreiro, Annemari Karajamaki, Erkka Valo, Anil K. Giri, Rashmi B. Prasad, Rishi Das Roy, Lena M. Thorn, Antti Rannikko, Harry Holthoefer, Kim M. Gooding, Steven Sourbron, Denis Delic, Maria F. Gomez, Per-Henrik Groop, Tiinamaija Tuomi, Carol Forsblom, Leif Groop, Maija Puhka

Summary: By genome-wide sequencing of 200 urinary extracellular vesicle (uEV) mRNA samples from clinical studies, we identified potential candidate biomarkers and mechanisms for studying diabetic kidney disease (DKD) in Type 1 diabetes (T1D), which were validated in both Type 1 and 2 diabetes. The sequencing results revealed over 10,000 mRNAs with similarity to the kidney transcriptome. Thirteen upregulated genes predominantly expressed in proximal tubules, correlated with hyperglycemia and involved in cellular/oxidative stress homeostasis were found in T1D DKD groups. We constructed a transcriptional stress score based on six of these genes (GPX3, NOX4, MSRB, MSRA, HRSP12, and CRYAB), which reflected long-term decline of kidney function and could identify individuals with early decline even in normoalbuminuric patients.

ISCIENCE (2023)

Article Genetics & Heredity

Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles-From Pre-Analytical Obstacles to Biomarker Research

Karina Barreiro, Om Prakash Dwivedi, Antti Rannikko, Harry Holthoefer, Tiinamaija Tuomi, Per-Henrik Groop, Maija Puhka

Summary: Urinary extracellular vesicles (uEV) contain non-invasive RNA biomarkers for genitourinary tract diseases. This study aimed to assess the effects of preanalytical variables on uEV isolates and discover stable reference mRNAs. The researchers analyzed various sequencing datasets and found that urine storage temperature and isolation workflow affected kidney-RNAs, while ultracentrifugation captured DKD-linked miRNAs. They also identified 11 stable mRNAs across the datasets. These findings highlight the importance of considering preanalytical choices in uEV biomarker studies.
Article Genetics & Heredity

Transcriptomic Landscape of Circulating Extracellular Vesicles in Heart Transplant Ischemia-Reperfusion

Seojeong Joo, Kishor Dhaygude, Sofie Westerberg, Rainer Krebs, Maija Puhka, Emil Holmstrom, Simo Syrjala, Antti I. Nykanen, Karl Lemstrom

Summary: In this study, the transcriptome of plasma extracellular vesicles (EVs) was analyzed before and after transplant reperfusion in heart transplant recipients. The expression of 1317 protein-coding genes in plasma EVs was found to change after reperfusion. Upregulated genes in plasma EVs were related to metabolism and immune activation, while downregulated genes were related to cell survival and extracellular matrix organization. Furthermore, correlations were observed between EV transcriptome and graft ischemia-reperfusion injury, primary graft dysfunction, and acute rejection after heart transplantation. The study revealed that certain plasma EV genes were associated with cardiomyocyte injury and primary graft dysfunction, suggesting their potential as sensitive indicators of reperfusion injury.
Article Medical Informatics

Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study

Seul Kee Byeon, Anil K. Madugundu, Kishore Garapati, Madan Gopal Ramarajan, Mayank Saraswat, Praveen M. Kumar, Travis Hughes, Rameen Shah, Mrinal M. Patnaik, Nicholas Chia, Susan Ashrafzadeh-Kian, Joseph D. Yao, Bobbi S. Pritt, Roberto Cattaneo, Mohamed E. Salama, Roman M. Zenka, Benjamin R. Kipp, Stefan K. G. Grebe, Ravinder J. Singh, Amir A. Sadighi Akha, Alicia Algeciras-Schimnich, Surendra Dasari, Janet E. Olson, Jesse R. Walsh, A. J. Venkatakrishnan, Garrett Jenkinson, John C. O'Horo, Andrew D. Badley, Akhilesh Pandey

Summary: In this retrospective cohort study, biomarkers that reliably predict severe and clinical outcomes of COVID-19 were discovered by analyzing samples from 455 participants. The study found that multiomic molecular signatures in plasma collected before hospital admission could be used to predict disease severity, demonstrating the potential of machine learning approaches in identifying novel clinical signatures.

LANCET DIGITAL HEALTH (2022)

暂无数据