Article
Biochemistry & Molecular Biology
Arnab Datta, Christopher Chen, Yong-Gui Gao, Siu Kwan Sze
Summary: This study identifies blood-based biomarkers for lacunar infarction (LACI), which can be used as a complementary prognostic tool. By analyzing medium-sized extracellular vesicles (MEVs) in the plasma, alterations in proteins related to oxygen-glucose deprivation, endo-lysosomal trafficking, glucose transport, and iron homeostasis were observed. The dataset is provided as a web-based resource for further analysis and validation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Oncology
Risheng He, Yi Xu, Liang Yu, Nanfeng Meng, Hang Wang, Yunfu Cui, Judy Wai Ping Yam
Summary: Hepatocellular carcinoma (HCC) is a major type of liver cancer that causes numerous deaths annually. Despite extensive research, the prognosis of HCC remains unclear. Recent studies have focused on extracellular vesicles (EVs) and their involvement in various diseases, including HCC, by regulating cell signaling pathways. This review summarizes the current literature on the regulation of Wnt signaling by EVs in HCC and explores future research directions.
Article
Oncology
Lin Liu, Masahiro Kawashima, Masahiro Sugimoto, Kazuhiro Sonomura, Fengling Pu, Wei Li, Masashi Takeda, Takayuki Goto, Kosuke Kawaguchi, Taka-Aki Sato, Masakazu Toi
Summary: The study found that the lipid composition of plasma-derived extracellular vesicles can serve as biomarkers for diagnosing breast cancer as well as identifying its progression and subtypes. By analyzing the lipid profiles, a diagnostic model for breast cancer was established, and several lipids were discovered to effectively differentiate the progression and subtypes of breast cancer. Lipid profiling of plasma-derived extracellular vesicles is a non-invasive and promising approach for diagnosing, staging, and subtyping breast cancer.
Review
Biochemistry & Molecular Biology
Lily M. Channon, Victoria M. Tyma, Zhihong Xu, David W. Greening, Jeremy S. Wilson, Chamini J. Perera, Minoti V. Apte
Summary: This review provides an overview of the role of extracellular vesicles (EVs) in the pathobiology of pancreatic cancer, as well as the molecular mechanisms mediated by EVs and their cargo in pancreatic cancer progression. EVs offer stability and act as a form of intercellular communication to regulate the function and phenotype of recipient cells.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Chemistry, Multidisciplinary
Yeongchang Goh, Jongwoo Kim, Hye Sun Park, Taeyoung Jung, Kwan Soo Hong, Sang Hwan Nam, Yung Doug Suh, Kang Taek Lee
Summary: Cell-cell communication is crucial for cellular differentiation, organ function, and immune responses. This study demonstrates the use of dual-colour imaging with upconverting nanoparticles to visualize the intercellular transport of cargo molecules, and shows that extracellular vesicles can be transmitted along with fluorescently labelled proteins.
Article
Cell Biology
Lizandra Jimenez, Bahnisikha Barman, Youn Jae Jung, Lauren Cocozza, Evan Krystofiak, Cherie Saffold, Kasey C. Vickers, John T. Wilson, T. Renee Dawson, Alissa M. Weaver
Summary: Extracellular vesicles can influence gene expression and functional phenotypes in recipient cells through the miRNAs they carry. This study investigated the presence of the miRNA-binding protein Ago2 and other RNA-binding proteins (RBPs) in small extracellular vesicle (SEV) preparations and the factors that can affect their detection, such as growth factors, oncogene signaling, serum, and cell density. The results showed that the presence of RBPs and miRNAs in SEVs can be influenced by the cell culture conditions and cell states, with serum contributing to extracellular miRNA contamination.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Article
Oncology
Jiani Liu, Xinyu Peng, Yang Yang, Yao Zhang, Meng Han, Xiaohui Shi, Jie Zheng, Tong Li, Jinxia Chen, Weihua Lv, Yunjiang Liu, Yixin Qi, Lei Zhang, Qi Liu
Summary: The study found that hsa_circ_0058514 can serve as an early plasma biomarker for breast cancer diagnosis with better diagnostic value than conventional tumor markers. It is also a predictor for the efficacy of neoadjuvant chemotherapy. Additionally, the expression level of hsa_circ_0058514 is associated with clinicopathological characteristics in breast cancer patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Veterinary Sciences
Matias Aguilera-Rojas, Soroush Sharbati, Torsten Stein, Mario Candela Andrade, Barbara Kohn, Ralf Einspanier
Summary: This study investigated the effects of haemolysis on circulating miRNAs in dogs, and found that some miRNAs were significantly sensitive to haemolysis. The study also revealed differences in canine miRNA abundance compared to human miRNA. These findings have important implications for the discovery of circulating biomarkers in dogs, and emphasize the need to carefully consider the impact of haemolysis in serum or plasma-based tests.
BMC VETERINARY RESEARCH
(2022)
Article
Immunology
Emilio Nunez-Borque, Sergio Fernandez-Bravo, Pablo Rodriguez Del Rio, Lucia Palacio-Garcia, Angela Di Giannatale, Virginia Di Paolo, Angela Galardi, Marta Colletti, Luisa Pascucci, Jaime Tome-Amat, Javier Cuesta-Herranz, Maria Dolores Ibanez-Sandin, Jose Julio Laguna, Alberto Benito-Martin, Vanesa Esteban
Summary: This study investigates the involvement of miRNAs in anaphylactic reactions and their potential as biomarkers. The researchers found differential expression profiles of circulating miRNAs in patients with anaphylaxis, particularly miR-375-3p. Functional and molecular experiments demonstrated that miR-375-3p plays a negative role in the stability of the endothelial barrier. These findings provide insights into the molecular mechanisms underlying anaphylactic reactions and suggest the potential of miR-375-3p as a biomarker.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Neurosciences
Rui Chen, Junxia Shi, Hongguang Yang, Minzhe Zhang, Qiutong Chen, Qiqiang He
Summary: The expression profile of extracellular vesicles (EVs)-derived miRNAs (EVs-miRNAs) in schizoaffective disorder (SAD) patients was analyzed through small RNA sequencing. The results showed 32 differentially expressed (DE) miRNAs in SAD patients compared to healthy controls. Weighted gene co-expression network analysis identified a module of 42 miRNAs closely related to SAD, with has-miR-15b-5p, has-miR-301a-3p, has-miR-342-3p, has-miR-219b-5p, and has-miR-145-5p identified as hub miRNAs. Further analysis revealed dysregulation of EVs-miRNAs in SAD patients, suggesting their potential as biomarkers.
MOLECULAR NEUROBIOLOGY
(2023)
Article
Obstetrics & Gynecology
Shay Freger, Mathew Leonardi, Warren (George) Foster
Summary: Endometriosis is a chronic gynaecological disorder characterized by differences in endometrial function compared to normal individuals. Exosomes, small membrane-bound extracellular vesicles, are proposed to play an important role in the transport and protection of signaling molecules involved in the dysregulation of endometrial function in women with endometriosis.
REPRODUCTIVE BIOMEDICINE ONLINE
(2021)
Review
Oncology
Md. Khirul Islam, Misba Khan, Kamlesh Gidwani, Kenneth W. Witwer, Urpo Lamminmaeki, Janne Leivo
Summary: Extracellular vesicles (EVs) have potential as diagnostic, prognostic, and therapeutic agents for cancer. The glycosylation patterns on the EV surface can reveal their cell of origin and be used for targeted delivery. Lectins and other glycan recognizing entities can be powerful tools for discovering and detecting novel cancer biomarkers.
BIOMARKER RESEARCH
(2023)
Article
Immunology
Ramkumar Menon, Christopher Luke Dixon, Samir Cayne, Enkhtuya Radnaa, Carlos Salomon, Samantha Sheller-Miller
Summary: The study compared the proteomic profiles of cord plasma-derived exosomes in patients with spontaneous preterm birth (PTB) or preterm premature rupture of membranes (pPROM) to those who delivered at term, showing both similarities and unique markers in exosomes from different conditions. However, the inflammatory condition represented in exosomes from different conditions was found to be non-specific and not indicative of any specific underlying biological functions. The value of cord plasma exosome proteomic cargo as an indicator of underlying physiology or fetal well-being was deemed limited.
AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Venkatesh Sadananda Rao, Qianyu Gu, Sandra Tzschentke, Kuailu Lin, Nicole Ganig, May-Linn Thepkaysone, Fang Cheng Wong, Heike Polster, Lena Seifert, Adrian M. Seifert, Nathalie Buck, Carina Riediger, Jonas Weisse, Tony Gutschner, Susanne Michen, Achim Temme, Martin Schneider, Franziska Baenke, Juergen Weitz, Christoph Kahlert
Summary: This study reveals the important role of EV-mediated ECM remodeling in colorectal cancer liver microenvironment and identifies EV-associated TIMP1 as a potential therapeutic target and a circulating biomarker for preoperative risk stratification in patients with colorectal liver metastases.
Review
Spectroscopy
Iqbal Jalaludin, David M. Lubman, Jeongkwon Kim
Summary: Exosomes, as small extracellular vesicles, play a crucial role in living organisms for processes like cell proliferation and intercellular communication. They have been extensively studied as biomarkers for various diseases. This review focuses on the enrichment methods, characterization techniques, and recent trends in exosome analysis using mass spectrometry-based approaches for biomarker discovery.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Oncology
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.
Article
Cardiac & Cardiovascular Systems
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
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.
Article
Chemistry, Multidisciplinary
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.
Article
Cell Biology
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
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.
Article
Cell Biology
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
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
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
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.
Article
Genetics & Heredity
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
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
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)